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- initial_data/clinvar_strict_rebuild_audit/audits/clinvar_label_definition.md +67 -0
- initial_data/clinvar_strict_rebuild_audit/audits/clinvar_relation_risk_audit.tsv +131 -0
- initial_data/clinvar_strict_rebuild_audit/audits/node_inductive_feasibility.md +19 -0
- initial_data/clinvar_strict_rebuild_audit/candidate_graphs/G1_removal_policy.tsv +5 -0
- initial_data/clinvar_strict_rebuild_audit/candidate_graphs/G2_policy_options.tsv +3 -0
- initial_data/clinvar_strict_rebuild_audit/inventory/all_relevant_files.tsv +0 -0
- initial_data/clinvar_strict_rebuild_audit/inventory/archive_contents.tsv +0 -0
- initial_data/clinvar_strict_rebuild_audit/inventory/inventory_summary.txt +3 -0
- initial_data/clinvar_strict_rebuild_audit/manifests/historical_clinvar_asset_recovery.tsv +63 -0
- initial_data/clinvar_strict_rebuild_audit/manifests/node_mapping_manifest.tsv +0 -0
- initial_data/clinvar_strict_rebuild_audit/manifests/relation_catalog.tsv +0 -0
- initial_data/clinvar_strict_rebuild_v1/00_provenance/CLINVAR_STRICT_REBUILD_DECISION.md +53 -0
- initial_data/clinvar_strict_rebuild_v1/00_provenance/CLINVAR_STRICT_REBUILD_FEASIBILITY.tsv +16 -0
- initial_data/clinvar_strict_rebuild_v1/00_provenance/G1_removal_policy.tsv +5 -0
- initial_data/clinvar_strict_rebuild_v1/00_provenance/G2_policy_options.tsv +3 -0
- initial_data/clinvar_strict_rebuild_v1/00_provenance/MASTER_SHA256SUMS.tsv +504 -0
- initial_data/clinvar_strict_rebuild_v1/00_provenance/PHASE1_MISSING_FILES.tsv +13 -0
- initial_data/clinvar_strict_rebuild_v1/00_provenance/POLICY_LOCK.txt +14 -0
- initial_data/clinvar_strict_rebuild_v1/00_provenance/clinvar_label_definition.md +67 -0
- initial_data/clinvar_strict_rebuild_v1/00_provenance/clinvar_relation_risk_audit.tsv +131 -0
- initial_data/clinvar_strict_rebuild_v1/00_provenance/historical_clinvar_asset_recovery.tsv +63 -0
- initial_data/clinvar_strict_rebuild_v1/00_provenance/node_inductive_feasibility.md +19 -0
- initial_data/clinvar_strict_rebuild_v1/00_provenance/node_mapping_manifest.tsv +0 -0
- initial_data/clinvar_strict_rebuild_v1/00_provenance/phase1_audit_sha256.tsv +14 -0
- initial_data/clinvar_strict_rebuild_v1/00_provenance/relation_catalog.tsv +0 -0
- initial_data/clinvar_strict_rebuild_v1/01_raw_manifest/raw_sources.tsv +12 -0
- initial_data/clinvar_strict_rebuild_v1/02_splits/label_policy.yaml +13 -0
- initial_data/clinvar_strict_rebuild_v1/02_splits/label_policy_source_sha256.txt +1 -0
- initial_data/clinvar_strict_rebuild_v1/02_splits/test_effective.tsv +0 -0
- initial_data/clinvar_strict_rebuild_v1/02_splits/test_formal.tsv +0 -0
- initial_data/clinvar_strict_rebuild_v1/02_splits/train.tsv +1 -0
- initial_data/clinvar_strict_rebuild_v1/02_splits/validation.tsv +0 -0
- initial_data/clinvar_strict_rebuild_v1/03_mappings/node_mapping_manifest.tsv +0 -0
- initial_data/clinvar_strict_rebuild_v1/03_mappings/test_cohort_aliases.tsv +0 -0
- initial_data/clinvar_strict_rebuild_v1/04_relation_catalog/clinvar_relation_risk_audit.tsv +131 -0
- initial_data/clinvar_strict_rebuild_v1/04_relation_catalog/relation_catalog.tsv +0 -0
- initial_data/clinvar_strict_rebuild_v1/04_relation_catalog/relations_strict.tsv +13 -0
- initial_data/clinvar_strict_rebuild_v1/05_graph_base/SHA256SUMS +2 -0
- initial_data/clinvar_strict_rebuild_v1/05_graph_base/graph_statistics.json +27 -0
- initial_data/clinvar_strict_rebuild_v1/05_graph_v2_inputs/G1/edge_statistics.tsv +7 -0
- initial_data/clinvar_strict_rebuild_v1/05_graph_v2_inputs/G1/graph_config.json +16 -0
- initial_data/clinvar_strict_rebuild_v1/05_graph_v2_inputs/G1/remap_audit.json +23 -0
- initial_data/clinvar_strict_rebuild_v1/05_graph_v2_inputs/G2a/edge_statistics.tsv +7 -0
- initial_data/clinvar_strict_rebuild_v1/05_graph_v2_inputs/G2a/graph_config.json +16 -0
- initial_data/clinvar_strict_rebuild_v1/05_graph_v2_inputs/G2a/node_mappings/disease.tsv +0 -0
- initial_data/clinvar_strict_rebuild_v1/05_graph_v2_inputs/G2a/node_mappings/pathway.tsv +2836 -0
- initial_data/clinvar_strict_rebuild_v1/05_graph_v2_inputs/G2a/node_mappings/protein.tsv +0 -0
- initial_data/clinvar_strict_rebuild_v1/05_graph_v2_inputs/G2a/node_mappings/ptm.tsv +0 -0
- initial_data/clinvar_strict_rebuild_v1/05_graph_v2_inputs/G2a/relation_mappings/relations.tsv +13 -0
- initial_data/clinvar_strict_rebuild_v1/05_graph_v2_inputs/G2a/remap_audit.json +23 -0
initial_data/clinvar_strict_rebuild_audit/audits/clinvar_label_definition.md
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# ClinVar label definition audit
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Generated from remote project files at 2026-08-31T12:41:12.492905+00:00.
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Evidence taxonomy: VERIFIED_FROM_FILE = observed file content; INFERRED_FROM_CODE = implementation reference; UNKNOWN = not verified.
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## Observed terms
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TEXT
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{"pathogenic": 187896, "benign": 171041, "reference mismatch": 13, "conflicting": 9, "likely pathogenic": 92185, "likely benign": 98938, "uncertain": 12, "out-of-range": 1}
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TEXT
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## Required rules
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| Rule | Status | Evidence |
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|---|---|---|
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| pathogenic + likely pathogenic merged | VERIFIED_FROM_FILE | text/values observed; exact merge/exclusion operation needs code confirmation |
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| benign + likely benign merged | VERIFIED_FROM_FILE | text/values observed; exact merge/exclusion operation needs code confirmation |
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| uncertain significance excluded | VERIFIED_FROM_FILE | text/values observed; exact merge/exclusion operation needs code confirmation |
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| conflicting interpretations excluded | VERIFIED_FROM_FILE | text/values observed; exact merge/exclusion operation needs code confirmation |
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| multiallelic/position mapping | INFERRED_FROM_CODE | matching implementation references found |
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| reference mismatch handling | VERIFIED_FROM_FILE | text/values observed; exact merge/exclusion operation needs code confirmation |
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| out-of-range handling | VERIFIED_FROM_FILE | text/values observed; exact merge/exclusion operation needs code confirmation |
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## Evidence files
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- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/ptm_context_clinvar/augment_l1b_manifest.py; text/path probe; from pathlib import Path import hashlib, pandas as pd ROOT=Path('/root/autodl-tmp/bio/disease_mutation_ptm_gcl'); OUT=ROOT/'work/amplify_generalization/L1B_ptm_context_clinvar_v1'; G=ROOT/'work/amplif
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- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/ptm_context_clinvar/enhance_readme.py; text/path probe; from pathlib import Path import pandas as pd, numpy as np from sklearn.metrics import roc_auc_score, average_precision_score, matthews_corrcoef ROOT=Path('/root/autodl-tmp/bio/disease_mutation_ptm_gcl
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- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/ptm_context_clinvar/finalize_l1b.py; text/path probe; #!/usr/bin/env python3 from pathlib import Path import hashlib, shutil, pandas as pd, numpy as np ROOT=Path('/root/autodl-tmp/bio/disease_mutation_ptm_gcl'); OUT=ROOT/'work/amplify_generalization/L1B_
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- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/ptm_context_clinvar/run_l1b_ptm_context.py; text/path probe; #!/usr/bin/env python3 """Frozen ClinVar PTM-context stratification (Task L1B).""" import os, json, hashlib, shutil, math, textwrap, warnings from pathlib import Path import numpy as np import pandas
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- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/scripts/run_clinvar_gate.py; text/path probe; #!/usr/bin/env python3 """Strict ClinVar AMPLIFY supervised gate (51,896 locked test examples). The source ESM protocol is reused byte-for-byte. All methods start at official P0. Graph inputs are m
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- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_benchmark/clinvar_pathogenicity/reports/benchmark_summary.txt; text/path probe; ClinVar pathogenicity benchmark ================================ Eligible samples: 110791 Pathogenic: 55170 Benign: 55621 Excluded records: 945030 Default split: protein-grouped 70/15/15 Alternative s
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- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_benchmark/clinvar_pathogenicity/reports/class_distribution.tsv; text/path probe; scheme split total pathogenic benign protein train 0 0 0 protein validation 55394 27922 27472 protein test 55397 27248 28149 gene train 0 0 0 gene validation 55394 27922 27472 gene test 55397 27248 28
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- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_benchmark/clinvar_pathogenicity/reports/split_integrity.tsv; text/path probe; check status mutation_split_overlap PASS protein_group_overlap PASS gene_group_overlap PASS binary_labels PASS no_conflicting_labels_in_samples PASS
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- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_benchmark/clinvar_pathogenicity/samples.tsv; text/path probe; mutation_id protein_id gene_symbol reference_aa mutation_position alternate_aa normalized_protein_change clinical_significance_raw label disease_count ptm_count nearest_ptm_distance MUT:A2M:Ala844Val
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- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_benchmark/clinvar_pathogenicity/test.tsv; text/path probe; mutation_id protein_id gene_symbol reference_aa mutation_position alternate_aa normalized_protein_change clinical_significance_raw label disease_count ptm_count nearest_ptm_distance MUT:A2M:Ala844Val
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- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_benchmark/clinvar_pathogenicity/validation.tsv; text/path probe; mutation_id protein_id gene_symbol reference_aa mutation_position alternate_aa normalized_protein_change clinical_significance_raw label disease_count ptm_count nearest_ptm_distance MUT:AACS:Glu564Gln
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- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_processed/labels/disease_labels.tsv; text/path probe; node_id label_type label source DISEASE_NAME:10_conditions disease_name 10 conditions Supplemental_disease_name DISEASE_NAME:10p15_3_microdeletion_syndrome disease_name 10p15.3 microdeletion syndrome
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- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_processed_clean/labels/disease_labels.tsv; text/path probe; node_id label_type label source DISEASE_NAME:10p15_3_microdeletion_syndrome disease_name 10p15.3 microdeletion syndrome Supplemental_disease_name DISEASE_NAME:10q11_22q11_23_deletion_syndrome disease_
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- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_processed_core/labels/disease_labels.tsv; text/path probe; node_id label_type label source DISEASE_NAME:11q_partial_monosomy_syndrome disease_name 11q partial monosomy syndrome Supplemental_disease_name DISEASE_NAME:13q12_3_microdeletion disease_name 13q12.3
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- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_graph_residual_esm2_v2/scripts/evaluate_clinvar_residual_v2.py; text/path probe; #!/usr/bin/env python3 import argparse, hashlib, json, time, warnings from pathlib import Path import numpy as np import pandas as pd import matplotlib matplotlib.use("Agg") import matplotlib.pyplot a
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- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_model_benchmark_v3/scripts/prepare_common_splits.py; text/path probe; #!/usr/bin/env python3 import csv,hashlib,json,os,shutil from pathlib import Path import pandas as pd ROOT=Path('/root/autodl-tmp/bio/disease_mutation_ptm_gcl');OUT=ROOT/'work/model_benchmark_v3/commo
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- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/prott5_two_downstreams/scripts/train_prott5_lora_clinvar.py; text/path probe; #!/usr/bin/env python3 """ProtT5 LoRA ClinVar training under the locked protein-group protocol.""" from __future__ import annotations import argparse import gzip import hashlib import json import mat
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- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/reviewer1_revision/m1_numeric_consistency/all_clinvar_runs.csv; text/path probe; path,experiment_name,backbone,model,split,seed,n_test,auroc,auprc,mcc,timestamp,checkpoint,notes work/amplify_generalization/L1B_ptm_context_clinvar_v1/metrics/graph_coverage_metrics.tsv,metrics,AMPLI
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- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/scripts/build_clinvar_benchmark.py; text/path probe; #!/usr/bin/env python3 """Build leakage-safe ClinVar missense pathogenicity benchmark.""" from __future__ import annotations import argparse,csv,random,shutil,sys from bisect import bisect_left from c
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- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/scripts/evaluate_clinvar_pathogenicity.py; text/path probe; from __future__ import annotations import argparse import json import math import os import platform import random import resource import shutil import sys import time from dataclasses import datacla
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- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/27_clinvar_gate/source_esm_protocol/test.tsv; text/path probe; mutation_id protein_id gene_symbol reference_aa mutation_position alternate_aa normalized_protein_change clinical_significance_raw label disease_count ptm_count nearest_ptm_distance MUT:A2M:Ala844Val
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- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/27_clinvar_gate/source_esm_protocol/train.tsv; text/path probe; mutation_id protein_id gene_symbol reference_aa mutation_position alternate_aa normalized_protein_change clinical_significance_raw label disease_count ptm_count nearest_ptm_distance MUT:AACS:Glu564Gln
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- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/27_clinvar_gate/source_esm_protocol/validation.tsv; text/path probe; mutation_id protein_id gene_symbol reference_aa mutation_position alternate_aa normalized_protein_change clinical_significance_raw label disease_count ptm_count nearest_ptm_distance MUT:AASS:Arg132His
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- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/L1B_ptm_context_clinvar_v1/README_PTMContextClinVar.md; text/path probe; # Task L1B — PTM-context ClinVar Stratified Evaluation ## Scope and interpretation Overall ClinVar performance remains the primary general pathogenicity result. PTM-context results are mechanistic st
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- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/L1B_ptm_context_clinvar_v1/assets/clinvar_prediction_manifest.tsv; text/path probe; method formal_method seed prediction_path prediction_sha256 checkpoint_path checkpoint_sha256 test_rows row_index_sha256 threshold split selection_used_test test_reference_path test_reference_sha256 s
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- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/L1B_ptm_context_clinvar_v1/audit/acceptance_checks.tsv; text/path probe; criterion value formal_predictions_located 1 common_test_universe 1 protein_group_split_confirmed 1 mutation_reference_validation_zero_mismatch 1 ptm_context_definitions_locked_before_scores 1 graph_c
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- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/L1B_ptm_context_clinvar_v1/audit/context_feature_lineage.tsv; text/path probe; feature source pathogenicity_label_derived ptm_distance data_processed_core/nodes_ptm.tsv + edges_protein_ptm.tsv 0 ptm_richness core PTM site counts 0 protein_pathway_count edges_protein_pathway.tsv
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- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/L1B_ptm_context_clinvar_v1/metrics/graph_coverage_metrics.tsv; text/path probe; stratum method seed N pathogenic benign AUROC AUPRC MCC LOW F0 42 18129 9272 8857 0.8712953275040299 0.8751738398133384 0.5753554761599871 LOW F0 3407 18129 9272 8857 0.87094189038313 0.87448417547036
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- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/L1B_ptm_context_clinvar_v1/metrics/overall_frozen_metrics.tsv; text/path probe; method N pathogenic benign AUROC AUPRC MCC F0 51896 25937 25959 0.8885193562036651 0.8903319519456485 0.6106606693839518 F1 51896 25937 25959 0.8915296595834363 0.8943289570249406 0.6166921678448857 F
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- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/L1B_ptm_context_clinvar_v1/metrics/primary_vs_nonlocal_metrics.tsv; text/path probe; stratum method seed N pathogenic benign AUROC AUPRC MCC 0 F0 42 35921 16917 19004 0.8861689867153468 0.8763850101378741 0.6055683963773271 0 F0 3407 35921 16917 19004 0.8858625128117248 0.875944247592
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- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/L1B_ptm_context_clinvar_v1/metrics/ptm_distance_stratified_metrics.tsv; text/path probe; stratum method seed N pathogenic benign AUROC AUPRC MCC B0 F0 42 1112 633 479 0.8660156262883112 0.8951267349116182 0.534611494997289 B0 F0 3407 1112 633 479 0.8677916406943114 0.8968224582681761 0.56
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- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/L1B_ptm_context_clinvar_v1/metrics/ptm_richness_metrics.tsv; text/path probe; stratum method seed N pathogenic benign AUROC AUPRC MCC R0 F0 42 0 0 0 NA NA NA R0 F0 3407 0 0 0 NA NA NA R0 F0 2026 0 0 0 NA NA NA R0 F0 mean 0 0 0 NA NA NA R0 F1 42 0 0 0 NA NA NA R0 F1 3407 0 0 0 N
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- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_relational_hierarchy/FINAL_v1/controls_intrinsic/README_PTMContextClinVar.md; text/path probe; # Task L1B — PTM-context ClinVar Stratified Evaluation ## Scope and interpretation Overall ClinVar performance remains the primary general pathogenicity result. PTM-context results are mechanistic st
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- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_relational_hierarchy/FINAL_v1/controls_intrinsic/clinvar_overall_frozen_metrics.tsv; text/path probe; method N pathogenic benign AUROC AUPRC MCC F0 51896 25937 25959 0.8885193562036651 0.8903319519456485 0.6106606693839518 F1 51896 25937 25959 0.8915296595834363 0.8943289570249406 0.6166921678448857 F
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- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/downstream_core/clinvar_pathogenicity/run_config.json; text/path probe; { "project_dir": "/root/autodl-tmp/bio/disease_mutation_ptm_gcl", "graph_dir": "/root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/graph_core", "pretrain_dir": "/root/autodl-tmp/bio/disease_muta
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- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/downstream_core/clinvar_pathogenicity/training_log.txt; text/path probe; Actual benchmark columns: ["mutation_id", "protein_id", "gene_symbol", "reference_aa", "mutation_position", "alternate_aa", "normalized_protein_change", "clinical_significance_raw", "label", "disease_
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- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/model_benchmark_v3/clinvar/protein_group/excluded_missing_prott5.tsv; text/path probe; split mutation_id protein_id gene_symbol reference_aa mutation_position alternate_aa normalized_protein_change clinical_significance_raw label disease_count ptm_count nearest_ptm_distance train MUT:AC
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- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/model_benchmark_v3/clinvar/protein_group/excluded_missing_ptm_mamba.tsv; text/path probe; split mutation_id protein_id gene_symbol reference_aa mutation_position alternate_aa normalized_protein_change clinical_significance_raw label disease_count ptm_count nearest_ptm_distance train MUT:AC
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| 66 |
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- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/model_benchmark_v3/common/clinvar/gene_group/test.tsv; text/path probe; mutation_id protein_id gene_symbol reference_aa mutation_position alternate_aa normalized_protein_change clinical_significance_raw label disease_count ptm_count nearest_ptm_distance MUT:A2M:Ala844Val
|
| 67 |
+
- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/model_benchmark_v3/common/clinvar/gene_group/train.tsv; text/path probe; mutation_id protein_id gene_symbol reference_aa mutation_position alternate_aa normalized_protein_change clinical_significance_raw label disease_count ptm_count nearest_ptm_distance MUT:AASS:Arg132His
|
initial_data/clinvar_strict_rebuild_audit/audits/clinvar_relation_risk_audit.tsv
ADDED
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@@ -0,0 +1,131 @@
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| 1 |
+
relation_or_path risk_level reason n_test_entities_affected candidate_for_G1_removal candidate_for_G2_removal evidence_source
|
| 2 |
+
10 HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/reviewer1_revision/m4_method_reproducibility/graph_relation_inventory.tsv; relation_catalog.tsv
|
| 3 |
+
11 HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/reviewer1_revision/m4_method_reproducibility/graph_relation_inventory.tsv; relation_catalog.tsv
|
| 4 |
+
6 HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m4_method_reproducibility/graph_relation_inventory.tsv; relation_catalog.tsv
|
| 5 |
+
7 HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m4_method_reproducibility/graph_relation_inventory.tsv; relation_catalog.tsv
|
| 6 |
+
EXPLICIT_CLINVAR_OR_CLASS_LABEL HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/run_clinvar_raw_graph_audit.py; relation_catalog.tsv
|
| 7 |
+
Task38_disease_protein_provenance HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/zero_shot_nonppi/run_n2_u4_nonppi.py; relation_catalog.tsv
|
| 8 |
+
U1_DiseasePermutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_representation_interpretability/zero_shot_disease_similarity/u2_zero_shot_disease_similarity.py; relation_catalog.tsv
|
| 9 |
+
all_model_clinvar_comparison HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 10 |
+
associated_with_mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_processed/edges_disease_mutation.tsv; relation_catalog.tsv
|
| 11 |
+
associated_with_mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_processed_clean/edges_disease_mutation.tsv; relation_catalog.tsv
|
| 12 |
+
associated_with_mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_processed_core/edges_disease_mutation.tsv; relation_catalog.tsv
|
| 13 |
+
associated_with_protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_processed/edges_disease_protein.tsv; relation_catalog.tsv
|
| 14 |
+
associated_with_protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_processed_clean/edges_disease_protein.tsv; relation_catalog.tsv
|
| 15 |
+
associated_with_protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_processed_core/edges_disease_protein.tsv; relation_catalog.tsv
|
| 16 |
+
audit/DISEASE_MUTATION_TARGET_BLIND_PASS.flag HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/disease_mutation_ranking/task43_core.py; relation_catalog.tsv
|
| 17 |
+
bootstrap_iid HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 18 |
+
bootstrap_protein_grouped HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 19 |
+
cached_disease_feature HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/43_disease_mutation_ranking_v1/benchmark/LOCKED_DISEASE_MUTATION_RANKING_v1/S2_mutation_disjoint/target_lineage_manifest.tsv.gz; relation_catalog.tsv
|
| 20 |
+
cached_disease_feature HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/43_disease_mutation_ranking_v1/benchmark/LOCKED_DISEASE_MUTATION_RANKING_v1/S3_protein_disjoint/target_lineage_manifest.tsv.gz; relation_catalog.tsv
|
| 21 |
+
cached_disease_feature HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_other_results_figures_verified_20260809/work/amplify_generalization/43_disease_mutation_ranking_v1/benchmark/LOCKED_DISEASE_MUTATION_RANKING_v1/S2_mutation_disjoint/target_lineage_manifest.tsv.gz; relation_catalog.tsv
|
| 22 |
+
cached_disease_feature HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_other_results_figures_verified_20260809/work/amplify_generalization/43_disease_mutation_ranking_v1/benchmark/LOCKED_DISEASE_MUTATION_RANKING_v1/S3_protein_disjoint/target_lineage_manifest.tsv.gz; relation_catalog.tsv
|
| 23 |
+
classifier_search HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 24 |
+
common_intersection_coverage HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 25 |
+
data_processed/edges_disease_protein.tsv HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/zero_shot_nonppi/run_n2_u4_nonppi.py; relation_catalog.tsv
|
| 26 |
+
data_processed_clean/edges_disease_protein.tsv HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/mechanism_deep/run_mechanism_deep.py; relation_catalog.tsv
|
| 27 |
+
data_processed_core/edges_disease_protein.tsv HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/zero_shot_nonppi/run_n2_u4_nonppi.py; relation_catalog.tsv
|
| 28 |
+
disease-mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/scripts/run_clinvar_gate.py; relation_catalog.tsv
|
| 29 |
+
disease-mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/relation_ablation_results.csv; relation_catalog.tsv
|
| 30 |
+
disease-mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/scripts/m5_finalize_server.py; relation_catalog.tsv
|
| 31 |
+
disease-protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/relation_ablation_results.csv; relation_catalog.tsv
|
| 32 |
+
disease-protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/scripts/m5_finalize_server.py; relation_catalog.tsv
|
| 33 |
+
disease__has_mutation__mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/ppi_partner_ranking_refinement/stage1_analysis_audit.py; relation_catalog.tsv
|
| 34 |
+
disease__has_mutation__mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/scripts/run_step1_data_graph_protocol.py; relation_catalog.tsv
|
| 35 |
+
disease__has_mutation__mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_gcl/relation_mask_forward.py; relation_catalog.tsv
|
| 36 |
+
disease__has_mutation__mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/scripts/build_i1_a1_patch.py; relation_catalog.tsv
|
| 37 |
+
disease__has_mutation__mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/00_protocols/graph_relation_manifest.tsv; relation_catalog.tsv
|
| 38 |
+
disease__has_mutation__mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/U1_zero_shot_ppi_retrieval_v1/audit/core_graph_ppi_leakage.tsv; relation_catalog.tsv
|
| 39 |
+
disease__has_mutation__mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_representation_interpretability/FINAL_verified/U1_zero_shot_ppi/audit/core_graph_ppi_leakage.tsv; relation_catalog.tsv
|
| 40 |
+
disease__has_mutation__mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/graph_core/edge_statistics.tsv; relation_catalog.tsv
|
| 41 |
+
disease__has_mutation__mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/graph_core/relation_mappings/relations.tsv; relation_catalog.tsv
|
| 42 |
+
disease__has_mutation__mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_other_results_figures_verified_20260809/work/amplify_generalization/00_protocols/graph_relation_manifest.tsv; relation_catalog.tsv
|
| 43 |
+
disease__has_mutation__mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 44 |
+
disease__has_mutation__mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/run_clinvar_raw_graph_audit.py; relation_catalog.tsv
|
| 45 |
+
disease__has_mutation__mutation.tsv HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/scripts/downstream_retrieval_visuals.py; relation_catalog.tsv
|
| 46 |
+
disease__has_mutation__mutation.tsv HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/scripts/downstream_soft_relevance_single_figures.py; relation_catalog.tsv
|
| 47 |
+
disease__has_protein__protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/ppi_partner_ranking_refinement/stage1_analysis_audit.py; relation_catalog.tsv
|
| 48 |
+
disease__has_protein__protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/scripts/run_step1_data_graph_protocol.py; relation_catalog.tsv
|
| 49 |
+
disease__has_protein__protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/00_protocols/graph_relation_manifest.tsv; relation_catalog.tsv
|
| 50 |
+
disease__has_protein__protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/U1_zero_shot_ppi_retrieval_v1/audit/core_graph_ppi_leakage.tsv; relation_catalog.tsv
|
| 51 |
+
disease__has_protein__protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_representation_interpretability/FINAL_verified/U1_zero_shot_ppi/audit/core_graph_ppi_leakage.tsv; relation_catalog.tsv
|
| 52 |
+
disease__has_protein__protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/graph_core/edge_statistics.tsv; relation_catalog.tsv
|
| 53 |
+
disease__has_protein__protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/graph_core/relation_mappings/relations.tsv; relation_catalog.tsv
|
| 54 |
+
disease__has_protein__protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_other_results_figures_verified_20260809/work/amplify_generalization/00_protocols/graph_relation_manifest.tsv; relation_catalog.tsv
|
| 55 |
+
disease__has_protein__protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 56 |
+
disease__has_protein__protein.tsv.gz HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/scripts/run_step2_p0_baseline.py; relation_catalog.tsv
|
| 57 |
+
disease_gene_reactome HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/backups/code_before_core_adapt_20260716_023809/build_graph.py; relation_catalog.tsv
|
| 58 |
+
disease_gene_reactome HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_gcl/build_graph.py; relation_catalog.tsv
|
| 59 |
+
disease_mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/disease_mutation_ranking/task43_core.py; relation_catalog.tsv
|
| 60 |
+
disease_mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/ppi_partner_ranking_deep/deep_ablation_v2.py; relation_catalog.tsv
|
| 61 |
+
disease_mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/scripts/build_core_dataset.py; relation_catalog.tsv
|
| 62 |
+
disease_mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/43_disease_mutation_ranking_v1/audit/graph_relation_manifest.tsv; relation_catalog.tsv
|
| 63 |
+
disease_mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_other_results_figures_verified_20260809/work/amplify_generalization/43_disease_mutation_ranking_v1/audit/graph_relation_manifest.tsv; relation_catalog.tsv
|
| 64 |
+
disease_mutation_ptm HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 65 |
+
disease_mutation_ptm_gcl/work/amplify_generalization/28_ppi_gate/source_esm_protocol/protocols/sequence_cluster_disjoint_candidate_pool.tsv.gz HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m6_statistical_evidence/rescue_v3/scripts/reconstruct_m6_v3.py; relation_catalog.tsv
|
| 66 |
+
disease_mutation_ptm_gcl/work/amplify_generalization/33_ppi_selective_graph_residual_v1/bootstrap/paired_grouped_bootstrap.tsv HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m6_statistical_evidence/rescue_v2/scripts/run_m6_rescue_v2.py; relation_catalog.tsv
|
| 67 |
+
disease_mutation_ptm_gcl/work/amplify_generalization/33_ppi_selective_graph_residual_v1/figures/bootstrap_graph_controls_figure_data.tsv HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m6_statistical_evidence/rescue_v2/scripts/run_m6_rescue_v2.py; relation_catalog.tsv
|
| 68 |
+
disease_mutation_ptm_gcl/work/amplify_generalization/43_disease_mutation_ranking_v1/formal/S4_sequence_cluster_disjoint/F3_GraphResidual/seed_42/metrics.tsv HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m6_statistical_evidence/rescue_v2/scripts/run_m6_rescue_v2.py; relation_catalog.tsv
|
| 69 |
+
disease_mutation_ptm_gcl/work/graph_esm2_residual_pretrain_v2/embeddings/node_id_mapping.tsv HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m6_statistical_evidence/rescue_v3/scripts/reconstruct_m6_v3.py; relation_catalog.tsv
|
| 70 |
+
disease_mutation_ptm_gcl/work/graph_esm2_residual_pretrain_v2/embeddings/protein_residual_embeddings.npy HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m6_statistical_evidence/rescue_v3/scripts/reconstruct_m6_v3.py; relation_catalog.tsv
|
| 71 |
+
disease_protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/disease_mutation_ranking/task43_core.py; relation_catalog.tsv
|
| 72 |
+
disease_protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/ppi_partner_ranking_deep/deep_ablation_v2.py; relation_catalog.tsv
|
| 73 |
+
disease_protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/scripts/build_core_dataset.py; relation_catalog.tsv
|
| 74 |
+
disease_protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/43_disease_mutation_ranking_v1/audit/graph_relation_manifest.tsv; relation_catalog.tsv
|
| 75 |
+
disease_protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_other_results_figures_verified_20260809/work/amplify_generalization/43_disease_mutation_ranking_v1/audit/graph_relation_manifest.tsv; relation_catalog.tsv
|
| 76 |
+
disease_protein_counts.tsv HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/disease_conditioned_ppi_audit.py; relation_catalog.tsv
|
| 77 |
+
disease_protein_matched HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/reviewer1_revision/m6_statistical_evidence/rescue_v2/scripts/run_m6_rescue_v2.py; relation_catalog.tsv
|
| 78 |
+
disease_protein_nodes HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/ppi_partner_ranking_refinement/stage1_analysis_audit.py; relation_catalog.tsv
|
| 79 |
+
disease_protein_provenance_audit HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/zero_shot_nonppi/run_n2_u4_nonppi.py; relation_catalog.tsv
|
| 80 |
+
edges/disease__has_protein__protein.tsv.gz HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/ppi_network_completion/task42_core.py; relation_catalog.tsv
|
| 81 |
+
edges/disease__has_protein__protein.tsv.gz HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/zero_shot_ppi_retrieval/task_u1_zero_shot_ppi.py; relation_catalog.tsv
|
| 82 |
+
edges/disease__has_protein__protein.tsv.gz HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_representation_interpretability/zero_shot_disease_similarity/u2_zero_shot_disease_similarity.py; relation_catalog.tsv
|
| 83 |
+
edges_disease_mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/scripts/preprocess_extra_data.py; relation_catalog.tsv
|
| 84 |
+
edges_disease_mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 85 |
+
edges_disease_mutation.tsv HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/scripts/preprocess_extra_data.py; relation_catalog.tsv
|
| 86 |
+
edges_disease_protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/scripts/preprocess_extra_data.py; relation_catalog.tsv
|
| 87 |
+
edges_disease_protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 88 |
+
edges_disease_protein.tsv HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/scripts/preprocess_extra_data.py; relation_catalog.tsv
|
| 89 |
+
edges_mutation_protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 90 |
+
excluded_missing_prott5 HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 91 |
+
excluded_missing_ptm_mamba HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 92 |
+
feasibility/disease_protein_provenance.tsv.gz HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/disease_core_module_prioritization/task41_pipeline.py; relation_catalog.tsv
|
| 93 |
+
graph_core_disease_protein_pairs HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/zero_shot_nonppi/run_n2_u4_nonppi.py; relation_catalog.tsv
|
| 94 |
+
graph_core_serialized_disease_protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/zero_shot_nonppi/run_n2_u4_nonppi.py; relation_catalog.tsv
|
| 95 |
+
has_mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/runs_v3/shuffle_integrity.tsv; relation_catalog.tsv
|
| 96 |
+
has_protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/runs_v3/shuffle_integrity.tsv; relation_catalog.tsv
|
| 97 |
+
model_availability HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 98 |
+
mutation;PTM;pathway (disease used only for candidate metadata) HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/42_ppi_network_completion_v1/audit/ppi_completion_target_blind.tsv; relation_catalog.tsv
|
| 99 |
+
mutation__rev_has_mutation__disease HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_gcl/relation_mask_forward.py; relation_catalog.tsv
|
| 100 |
+
mutation__rev_has_mutation__disease HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/graph_core/relation_mappings/relations.tsv; relation_catalog.tsv
|
| 101 |
+
mutation_disease_count HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/ptm_context_clinvar/run_l1b_ptm_context.py; relation_catalog.tsv
|
| 102 |
+
mutation_disease_count HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_L1B_PTMContextClinVar_verified_20260810/code/run_l1b_ptm_context.py; relation_catalog.tsv
|
| 103 |
+
mutation_disease_count HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_L1B_PTMContextClinVar_verified_20260810_prev2/code/run_l1b_ptm_context.py; relation_catalog.tsv
|
| 104 |
+
mutation_ptm_labels_used HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/zero_shot_mutation_ptm/build_n1_audit.py; relation_catalog.tsv
|
| 105 |
+
physical_ppi HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/43_disease_mutation_ranking_v1/audit/graph_relation_manifest.tsv; relation_catalog.tsv
|
| 106 |
+
physical_ppi HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_other_results_figures_verified_20260809/work/amplify_generalization/43_disease_mutation_ranking_v1/audit/graph_relation_manifest.tsv; relation_catalog.tsv
|
| 107 |
+
positive_pairs/disease_mutation_ptm.tsv HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/backups/code_before_core_adapt_20260716_023809/train_contrastive.py; relation_catalog.tsv
|
| 108 |
+
positive_pairs/disease_mutation_ptm.tsv HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_gcl/export_tasks.py; relation_catalog.tsv
|
| 109 |
+
protein__rev_has_protein__disease HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/graph_core/relation_mappings/relations.tsv; relation_catalog.tsv
|
| 110 |
+
protein_disease_count HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/ptm_context_clinvar/run_l1b_ptm_context.py; relation_catalog.tsv
|
| 111 |
+
protein_disease_count HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_L1B_PTMContextClinVar_verified_20260810/code/run_l1b_ptm_context.py; relation_catalog.tsv
|
| 112 |
+
protein_disease_count HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_L1B_PTMContextClinVar_verified_20260810_prev2/code/run_l1b_ptm_context.py; relation_catalog.tsv
|
| 113 |
+
protein_pathway HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/43_disease_mutation_ranking_v1/audit/graph_relation_manifest.tsv; relation_catalog.tsv
|
| 114 |
+
protein_pathway HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_other_results_figures_verified_20260809/work/amplify_generalization/43_disease_mutation_ranking_v1/audit/graph_relation_manifest.tsv; relation_catalog.tsv
|
| 115 |
+
protein_ptm HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/43_disease_mutation_ranking_v1/audit/graph_relation_manifest.tsv; relation_catalog.tsv
|
| 116 |
+
protein_ptm HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_other_results_figures_verified_20260809/work/amplify_generalization/43_disease_mutation_ranking_v1/audit/graph_relation_manifest.tsv; relation_catalog.tsv
|
| 117 |
+
remove_derived_disease_mutation_path HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/disease_core_module_prioritization/task41_pipeline.py; relation_catalog.tsv
|
| 118 |
+
remove_direct_disease_protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/disease_core_module_prioritization/task41_pipeline.py; relation_catalog.tsv
|
| 119 |
+
test HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 120 |
+
test_metrics HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 121 |
+
test_predictions HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 122 |
+
three_seed_summary HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 123 |
+
train HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 124 |
+
training_history HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 125 |
+
used_for_disease_protein_edges HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/zero_shot_nonppi/run_n2_u4_nonppi.py; relation_catalog.tsv
|
| 126 |
+
validation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 127 |
+
work/amplify_generalization/40_disease_functional_module_discovery_v1 HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/disease_core_module_prioritization/task41_pipeline.py; relation_catalog.tsv
|
| 128 |
+
work/amplify_generalization/41_disease_core_module_prioritization_v1 HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/scripts/m5_v2_finalize.py; relation_catalog.tsv
|
| 129 |
+
ALIAS_EQUIVALENT_TARGET_RELATIONS:10,11,6,7,EXPLICIT_CLINVAR_OR_CLASS_LABEL,Task38_disease_protein_provenance,U1_DiseasePermutation,all_model_clinvar_comparison,associated_with_mutation,associated_with_protein,audit/DISEASE_MUTATION_TARGET_BLIND_PASS.flag,bootstrap_iid,bootstrap_protein_grouped,cached_disease_feature,classifier_search,common_intersection_coverage,data_processed/edges_disease_protein.tsv,data_processed_clean/edges_disease_protein.tsv,data_processed_core/edges_disease_protein.tsv,disease-mutation,disease-protein,disease__has_mutation__mutation,disease__has_mutation__mutation.tsv,disease__has_protein__protein,disease__has_protein__protein.tsv.gz,disease_gene_reactome,disease_mutation,disease_mutation_ptm,disease_mutation_ptm_gcl/work/amplify_generalization/28_ppi_gate/source_esm_protocol/protocols/sequence_cluster_disjoint_candidate_pool.tsv.gz,disease_mutation_ptm_gcl/work/amplify_generalization/33_ppi_selective_graph_residual_v1/bootstrap/paired_grouped_bootstrap.tsv,disease_mutation_ptm_gcl/work/amplify_generalization/33_ppi_selective_graph_residual_v1/figures/bootstrap_graph_controls_figure_data.tsv,disease_mutation_ptm_gcl/work/amplify_generalization/43_disease_mutation_ranking_v1/formal/S4_sequence_cluster_disjoint/F3_GraphResidual/seed_42/metrics.tsv,disease_mutation_ptm_gcl/work/graph_esm2_residual_pretrain_v2/embeddings/node_id_mapping.tsv,disease_mutation_ptm_gcl/work/graph_esm2_residual_pretrain_v2/embeddings/protein_residual_embeddings.npy,disease_protein,disease_protein_counts.tsv,disease_protein_matched,disease_protein_nodes,disease_protein_provenance_audit,edges/disease__has_protein__protein.tsv.gz,edges_disease_mutation,edges_disease_mutation.tsv,edges_disease_protein,edges_disease_protein.tsv,edges_mutation_protein,excluded_missing_prott5,excluded_missing_ptm_mamba,feasibility/disease_protein_provenance.tsv.gz,graph_core_disease_protein_pairs,graph_core_serialized_disease_protein,has_mutation,has_protein,model_availability,mutation;PTM;pathway (disease used only for candidate metadata),mutation__rev_has_mutation__disease,mutation_disease_count,mutation_ptm_labels_used,physical_ppi,positive_pairs/disease_mutation_ptm.tsv,protein__rev_has_protein__disease,protein_disease_count,protein_pathway,protein_ptm,remove_derived_disease_mutation_path,remove_direct_disease_protein,test,test_metrics,test_predictions,three_seed_summary,train,training_history,used_for_disease_protein_edges,validation,work/amplify_generalization/40_disease_functional_module_discovery_v1,work/amplify_generalization/41_disease_core_module_prioritization_v1 HIGH multiple names may encode the same target; confirm from rows before removal 14534 YES YES relation_catalog.tsv; edge overlap scan
|
| 130 |
+
one-hop/two-hop label-proximal candidate paths MEDIUM generic context is not automatically leakage; remove only if semantically target-equivalent 53386 NO_UNTIL_SEMANTICALLY_VERIFIED G2a_ONLY_IF_LABEL_PROXIMAL relation_catalog.tsv; no path deletion executed
|
| 131 |
+
generic biological context (PPI/PTM/pathway/other) LOW not a direct label encoding on current evidence; do not remove solely because a two-hop path exists 3048 NO G2b_ONLY relation_catalog.tsv
|
initial_data/clinvar_strict_rebuild_audit/audits/node_inductive_feasibility.md
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# Node-inductive ClinVar feasibility
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## Conclusion
|
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**SUPPORTED**
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Conclusion from Python implementation evidence; no proposed capability was treated as existing.
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| Signal | Evidence |
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| lookup | /root/autodl-tmp/bio/disease_mutation_ptm_gcl/backups/code_before_core_adapt_20260716_023809/train_contrastive.py:45 ure self.embeddings = nn.ModuleDict( {node_type: nn.Embedding(count, hidden_dim) for node_type, count in node_counts.items()} ) self.self_linears = nn.ModuleList( [nn.ModuleDict({nt: nn.Linear(; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_raw/amplify/AMPLIFY_120M/amplify.py:222 module.bias.data.zero_() elif isinstance(module, nn.Embedding): module.weight.data.uniform_(-self.config.embedding_init_range, self.config.embedding_init_range) class AMPLIFY(AMPLIFYPreTrainedModel): """; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_gcl/train_contrastive.py:32 __() self.embeddings = nn.ModuleDict({ node_type: nn.Embedding(count, hidden_dim, sparse=True) for node_type, count in node_counts.items() }) self.relation_projection = nn.ModuleDict({ ; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_gcl/relation_mask_forward.py:115 ture self.embeddings = nn.ModuleDict({ node_type: nn.Embedding(count, hidden_dim) for node_type, count in node_counts.items() }) self.self_linears = nn.ModuleList([ nn.ModuleDict({nt; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_model_benchmark_v3/dmptm_benchmark/models/residual_v2_compat/data.py:7 s: def __init__(self,root): self.root=Path(root);g=self.root/"work/graph_embedding_assets_v1/embeddings";e=self.root/"work/esm2_only_v1/core_embeddings" self.graph={k:np.load(g/f"{k}_embeddings.npy",mmap_mode="r") for k in COUNTS};self.esm=; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_model_benchmark_v3/dmptm_benchmark/models/residual_v2_compat/exporting.py:7 ate_dict"]);model.eval();inputs=Inputs(root);m=pd.read_csv(root/"work/graph_embedding_assets_v1/node_id_mapping.tsv",sep="\t");m.to_csv(out/"embeddings/node_id_mapping.tsv",sep="\t",index=False);modes=[];checks=[] with torch.no_grad(): for ty; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_model_benchmark_v3/dmptm_benchmark/models/residual_v2_compat/training.py:32 "preserve_loss"]+residual_weight*row["residual_loss"] state={"model_state_dict":{k:v.detach().cpu() for k,v in model.state_dict().items()},"relations":relations,"config":{"beta_init":beta_init,"preserve_weight":preserve_weight,"residual_w; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_model_benchmark_v3/scripts/backupclinvar20260721.py:196 r, Representation] = {} status = [] graph_root = ROOT / "work/graph_embedding_assets_v1" try: graph = GraphRepresentation("esm2_original", graph_root) representations[graph.name] = graph status.append({"model"; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_model_benchmark_v3/scripts/diffusiontasks.py:244 dimension=640, ): super().__init__() self.token = nn.Embedding(VOCAB_SIZE, hidden, padding_idx=PAD_ID) self.position = nn.Parameter(torch.randn(1, WINDOW_LENGTH, hidden) * 0.02) self.ptm_type = nn.Embedding; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_model_benchmark_v3/scripts/evaluate_clinvar_all_models.py:202 r, Representation] = {} status = [] graph_root = ROOT / "work/graph_embedding_assets_v1" try: graph = GraphRepresentation("graph_pretrain_core_h64_v1", graph_root) representations[graph.name] = graph status.ap |
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| inductive | /root/autodl-tmp/bio/disease_mutation_ptm_gcl/backups/code_before_core_adapt_20260716_023809/train_contrastive.py:32 __init__( self, node_counts: dict[str, int], edge_index: dict[str, tuple[str, str, torch.Tensor]], hidden_dim: int = 256, layers: int = 2, dropout: float = 0.1, temperature: float = 0; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_gcl/build_graph.py:394 mat_version": 2, "node_counts": node_counts, "edge_index": graph_edges, "core_dir": str(core_dir.resolve()), "leakage_policy": {"forbidden_feature_tokens": list(LEAKAGE_TOKENS)}, }, ; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_gcl/train_contrastive.py:77 ropy(logits, labels) + F.cross_entropy(logits.T, labels)) def parse_neighbors(value: str) -> list[int]: values = [int(x) for x in value.replace(",", " ").split() if x] if not values or any(x <= 0 for x in values): raise ; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_gcl/visual.py:47 n_umap(X): reducer = umap.UMAP( n_components=2, n_neighbors=30, min_dist=0.2, metric="euclidean", random_state=42, ) return reducer.fit_transform(X) def plot_mutation_by_disease(top_k=; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_gcl/relation_mask_forward.py:4 e deliberately keeps the legacy cache-only PPI ranker separate from a message-passing encoder. ``None`` is the backward-compatible path; a mask is applied to edge_index before each graph forward and the context is recomputed. """ from __future_; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_model_benchmark_v3/dmptm_benchmark/downstream/clinvar_evaluator.py:11 ng_path: str | Path, mapping_path: str | Path, name: str = 'esm2_dapt_inductive'): self.name = name self.embedding_path = Path(embedding_path) self.mapping_path = Path(mapping_path) self.array = np.load(self; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_model_benchmark_v3/scripts/diseasetasks.py:191 "ontology subtree leakage gate failed") return frame def sample_neighbor_ids(disease: str, edge_path: Path, limit: int, seed: int): frame = pd.read_csv(edge_path, sep="\t") source, target = edge_columns(frame) direct = f; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_model_benchmark_v3/scripts/evaluate_disease_retrieval.py:203 , "gold_standard": "Disease Ontology top-level branch", "shared_graph_neighbors_used_as_gold": False, "storage_gate": gate, "models": sorted(table["model"].unique().tolist()) if len(table) else [], "elapsed_seconds": time.time() - started; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_model_benchmark_v3/scripts/train_disease_classifier.py:29 tomic_tsv, best_multilabel_threshold, build_labels, build_neighbor_means, disease_predict, make_splits, multilabel_metrics, ) from evaluate_clinvar_all_models import SEEDS, discover_representations, now, storage_ga; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_model_benchmark_v4/scripts/compare_dapt_mutation_ptm.py:12 riginal':V3/'esm2_original/representation_seed_42','esm2_dapt_clinvar_inductive':OUT/'esm2_dapt_clinvar_inductive/representation_seed_42','graph_residual_v2':V3/'graph_residual_v2/representation_seed_42'} SEEDS=[42,3407,2026] METRICS=['mrr |
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| fallback | /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_model_benchmark_v3/scripts/train_residual_v3.py:99 "} if not required.issubset(arrays): raise RuntimeError(f"missing embedding types: {sorted(required - set(arrays))}") return arrays @dataclass class Relation: name: str src_type: str dst_type: str train_src: np.nd; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_model_benchmark_v4/scripts/evaluate_dapt_mutation_ptm.py:282 benchmark_split"] = split excluded["exclusion_reason"] = "missing_dapt_embedding" excluded_parts.append(excluded) named_frames[split] = frame.loc[mask].reset_index(drop=True) train, validation, test = named_frames["t; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/zero_shot_mutation_ptm/build_n1_audit.py:132 _text(OUT/'audit/MUTATION_PTM_TARGET_BLIND_PASS.flag','graph_core has zero direct mutation-PTM target edges; graph_full benchmark edge file is excluded from Z1 lineage.\n') # 3. Freeze representation lineage and determine whether a fair common space exists. def sha; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_L1B_PTMContextClinVar_verified_20260810_prev2/code/finalize_l1b.py:29 ),('protein_group_split_confirmed',1),('mutation_reference_validation_zero_mismatch',1),('ptm_context_definitions_locked_before_scores',1),('graph_coverage_excludes_ClinVar_edges',1),('pathogenicity_label_derived_context',0),('original_threshold_unchanged',1),('retraining',0),('t; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_L1B_PTMContextClinVar_verified_20260810_prev2/code/enhance_readme.py:55 terpretation rule A positive point estimate with an interval crossing zero is only a suggestive context-dependent trend. If all strata are non-positive, the conclusion is a negative mechanism result: Graph-Residual does not gain from PTM/regulatory context on this ClinVar benchma; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_L1B_PTMContextClinVar_verified_20260810/code/finalize_l1b.py:29 ),('protein_group_split_confirmed',1),('mutation_reference_validation_zero_mismatch',1),('ptm_context_definitions_locked_before_scores',1),('graph_coverage_excludes_ClinVar_edges',1),('pathogenicity_label_derived_context',0),('original_threshold_unchanged',1),('retraining',0),('t; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_L1B_PTMContextClinVar_verified_20260810/code/enhance_readme.py:55 terpretation rule A positive point estimate with an interval crossing zero is only a suggestive context-dependent trend. If all strata are non-positive, the conclusion is a negative mechanism result: Graph-Residual does not gain from PTM/regulatory context on this ClinVar benchma; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/disease_conditioned_ppi_train.py:502 ", 0.0) > 0.0 required = [checks["F0_FrozenProbe"]["backbone_grad_zero"], checks["F3_GraphResidual"]["graph_adapter_grad_positive"], checks["F2_LoRAFineTuning"]["lora_grad_positive"], checks["F1_FullFineTuning"]["backbone_grad_positive"]] status = all(required) a; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/finalize_m6_m8_summary.py:26 as a positive C≥2 versus C≤1 contrast with a bootstrap interval above zero. R2 contains no observations at C≥2, so that contrast is not estimable. R4 is positive, but its Holm-adjusted evidence is not decisive. Degree-adjusted and degree-matched outputs are reported separately.\n; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/scripts/step3_graph_adaptation.py:176 def _degree_bin_permutation(self) -> np.ndarray: degree = np.zeros(len(self.graph["protein"]), dtype=np.int64) for name, array in self.train_edges.items(): protein_column = 1 if name == "mutation_on_protein" else 0 |
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| projection | /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_model_benchmark_v4/scripts/evaluate_unified_rankers.py:202 g={'status':'LOCKED','models':['esm2_original_corrected','esm2_dapt','graph_residual_esm2_v2'],'main_features':'[h_mut,h_ptm,abs(h_mut-h_ptm),h_mut*h_ptm]','supplement':'main features plus log-normalized sequence distance','projection_dimension':128,'loss':'pairwise BPR treating ; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/scripts/save_best_residual_checkpoint.py:11 ate_dict(),"scalar") path=root/"work/graph_esm2_fusion_diagnostics_v2/residual_fusion/best_residual_scalar_protein.pt"; torch.save({"model_state_dict":{k:v.detach().cpu() for k,v in model.state_dict().items()},"beta_type":"scalar","threshold":th; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/zero_shot_mutation_ptm/build_n1_audit.py:150 LIFY residue/window assets are incomplete for the benchmark, while Z1 graph mutation/PTM assets are 64-D graph space. No projection/alignment or new training was allowed.','target_graph_leakage':'PASS on graph_core; direct graph_full benchmark edge excluded from Z1'},ensure_ascii; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/graph_residual_ptm_mamba/gr_ptm_mamba/adapter/fusion.py:39 kind: nn.Sequential( nn.Linear(self.graph_dim, projection_dim), nn.LayerNorm(projection_dim), nn.GELU(), nn.Dropout(dropout), nn.Linear(p; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/graph_residual_ptm_mamba/scripts/summarize_results.py:150 oxes = [(0.03, "Frozen\nPTM-Mamba\n768-d", "#8ecae6"), (0.30, "Native graph\n64-d", "#90be6d"), (0.53, "Projection + gate\nresidual <= 0.25", "#f9c74f"), (0.79, "Task head\nclassification/ranking", "#f9844a")] for x, text, color in boxes: ax.add_patch(plt.Rectangle((x, ; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/scripts/step3_graph_adaptation.py:102 be on comparable scales: legacy P0 norms are ~842, # whereas graph projections are ~3, which previously saturated the gate. sequence_unit = F.normalize(sequence, dim=-1) graph_unit = F.normalize(protein_graph, dim=-1) ; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/scripts/run_step4_unsupervised.py:326 e.max()), "residual_norm_mean": float(residual_norm.mean()), "graph_projection_norm_mean": float(graph_norm.mean()), "sequence_norm_mean": float(sequence_norm.mean()), "residual_to_sequence_norm_ratio": float((residual_nor; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/scripts/run_embedding_pipeline_audit.py:183 pe(np.float16), "residual": residual_all.astype(np.float32), "graph_projection": graph_all.astype(np.float32), "gate": gate_all, "pre_normalization": pre_all.astype(np.float32), "graph_input": graph_inputs, } def fuse_from_g; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/scripts/run_supervised_gate_summary.py:234 (diff) comparisons.append({"task":task,"comparison":f"F3_GraphResidual-minus-{baseline}","delta":mcc_from_confusion(scores["F3_GraphResidual"])-mcc_from_confusion(scores[baseline]),"bootstrap_mean":mean,"ci_low":lo,"ci_high":hi,"raw_p_value":pvalue_two_sided(diff),"bootstrap_unit; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/zero_shot_ppi_retrieval/task_u1_zero_shot_ppi.py:795 I label在什么时候被读取？", "U0是什么？", "U1是什么？", "U1训练时是否使用PPI？", "core Graph是否包含PPI？", "是否使用PPI supervised F3 checkpoint？", "是否训练projection？", "是否训练ranker？", "是否训练alignment？", "主similarity是什么？", "为什么固定cosine？", "benchmark来自哪里？", "candidate pools来自哪里？", "U0/U1 protein universe是否一致？", |
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A lookup-table-only representation cannot create a graph residual for a protein absent from graph pretraining. A zero vector fallback is not true node-inductive encoding.
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No training or embedding regeneration was performed.
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initial_data/clinvar_strict_rebuild_audit/candidate_graphs/G1_removal_policy.tsv
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relation remove_or_keep reason affected_edges affected_test_variants affected_test_proteins
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direct ClinVar target relation REMOVE_IF_VERIFIED direct target-label encoding; check exact direction and aliases 608725 53386 3048
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exact reverse of direct target relation REMOVE_IF_VERIFIED reverse target relation is equivalent exposure UNKNOWN 53386 3048
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alias-equivalent target relation REMOVE_IF_VERIFIED same relation under another name; verify from relation/alias tables UNKNOWN 53386 3048
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generic one-hop/two-hop context KEEP_UNLESS_TARGET_EQUIVALENT generic paths are not leakage without explicit semantic equivalence UNKNOWN 0 3048
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initial_data/clinvar_strict_rebuild_audit/candidate_graphs/G2_policy_options.tsv
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condition removed_relation_family test_node_remaining_in_graph graph_embedding_available scientific_interpretation implementation_risk
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G2a label-proximal disease/mutation/variant context YES_IF_NONLABEL_EDGES_OR_EXPLICIT_NODE_TABLE YES tests dependence on disease/mutation context while retaining generic structure medium; freeze relation semantics and node table
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G2b all non-sequence relational context for formal test proteins YES_IF_EXPLICIT_NODE_TABLE; otherwise UNKNOWN PARTIAL tests dependence on test-protein transductive relational context high; isolated nodes may have undefined graph embeddings
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initial_data/clinvar_strict_rebuild_audit/inventory/all_relevant_files.tsv
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generated_utc 2026-08-31T12:25:52.593486+00:00
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relevant_files 11911
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archives_listed 11
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initial_data/clinvar_strict_rebuild_audit/manifests/historical_clinvar_asset_recovery.tsv
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asset status path hash usable_for_exact_reconstruction notes
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exact historical raw graph snapshot PARTIAL /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv b76f3572e9421f5a13f7dee71a7cdd5389754bd954225551df3fc713f11159d2 NO candidate only; time identity/provenance must be verified
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| 3 |
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exact historical raw graph snapshot PARTIAL /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/runs_v2/configs/shufflededges_clinvar.json 025ede18f36f736e4396361e5e4730b8d5618e9f9998067f34e760df9d31f6ca NO candidate only; time identity/provenance must be verified
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+
exact historical raw graph snapshot PARTIAL /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/runs_v3/configs/ShuffledEdges_ClinVar.json 3c553590c3d73ab3cf52198025971116d43ddf3ee08a68716d10203ec281271c NO candidate only; time identity/provenance must be verified
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| 5 |
+
exact historical raw graph snapshot PARTIAL /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/runs_v3/runs/clinvar/shuffled_edges/seed_2026/run_metadata.json 356103e54e2d1edc93164aea414ab9ab942b6207fb43e479c4ca564cc7a1f453 NO candidate only; time identity/provenance must be verified
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| 6 |
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exact historical raw graph snapshot PARTIAL /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/runs_v3/runs/clinvar/shuffled_edges/seed_2026/test_predictions.tsv c653de50a8bfbf95901a5fa2b06e16b30f58ce7568c040ff4890f625ada90ab3 NO candidate only; time identity/provenance must be verified
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| 7 |
+
exact historical node table MISSING NA NA NO no candidate path found
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| 8 |
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exact historical edge table FOUND /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/runs_v2/configs/shufflededges_clinvar.json 025ede18f36f736e4396361e5e4730b8d5618e9f9998067f34e760df9d31f6ca YES candidate only; time identity/provenance must be verified
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| 9 |
+
exact historical edge table FOUND /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/runs_v3/configs/ShuffledEdges_ClinVar.json 3c553590c3d73ab3cf52198025971116d43ddf3ee08a68716d10203ec281271c YES candidate only; time identity/provenance must be verified
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| 10 |
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exact historical edge table FOUND /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/runs_v3/runs/clinvar/shuffled_edges/seed_2026/run_metadata.json 356103e54e2d1edc93164aea414ab9ab942b6207fb43e479c4ca564cc7a1f453 YES candidate only; time identity/provenance must be verified
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| 11 |
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exact historical edge table FOUND /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/runs_v3/runs/clinvar/shuffled_edges/seed_2026/test_predictions.tsv c653de50a8bfbf95901a5fa2b06e16b30f58ce7568c040ff4890f625ada90ab3 YES candidate only; time identity/provenance must be verified
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| 12 |
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exact historical edge table FOUND /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/runs_v3/runs/clinvar/shuffled_edges/seed_2026/validation_history.tsv d9b86fe75df0ad88da4e63fa64b52d6e614308b52c76695af6e776098ef1ed7f YES candidate only; time identity/provenance must be verified
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| 13 |
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relation ordering PARTIAL /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/graph_core/relation_mappings/relations.tsv a354ed64e5eabd83bb510696dd5c734a67b02de4fe6cd6af218d96a05e8c1311 NO candidate only; time identity/provenance must be verified; current-looking graph cannot be assumed historical
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| 14 |
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edge count FOUND /root/autodl-tmp/bio/final_prodisease_v32_clinvar_dataset.metadata.json 2f672e8a73a2a93824a43dd55599e148d66945c39220425b59b81585578e5f4a NO candidate only; time identity/provenance must be verified
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| 15 |
+
edge count FOUND /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/runs_v3/runs/clinvar/additive/seed_2026/run_metadata.json bb0b78dc5be015421c659c4d319731c5b25b798aa2dce0f535b36861d9dac5ff NO candidate only; time identity/provenance must be verified
|
| 16 |
+
edge count FOUND /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/runs_v3/runs/clinvar/additive/seed_3407/run_metadata.json 48c611fdcc752c6a4392c35bbd70fa905c5aa40225906892fc1dbbbb723fcb05 NO candidate only; time identity/provenance must be verified
|
| 17 |
+
edge count FOUND /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/runs_v3/runs/clinvar/additive/seed_42/run_metadata.json c38b142f90164790c09440a0764894e2f5b1afddf982a979e99c36e1750837b4 NO candidate only; time identity/provenance must be verified
|
| 18 |
+
edge count FOUND /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/runs_v3/runs/clinvar/concat/seed_2026/run_metadata.json 906a6b706840cc7c68cd0c114ce5a2974ea4d4b9bf9ec41beced497543655979 NO candidate only; time identity/provenance must be verified
|
| 19 |
+
graph hash FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_L1B_PTMContextClinVar_verified_20260810/SHA256_manifest.tsv 4bd7b834830c5dde49eaa3ca52d03d25c123a36b54742bfd5df93487957026a1 NO candidate only; time identity/provenance must be verified
|
| 20 |
+
graph hash FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_L1B_PTMContextClinVar_verified_20260810_prev2/SHA256_manifest.tsv 2eb4995e4a1c989ff5d18a3809ffade955c02dc58b1c6d89615bd10aa697e0ea NO candidate only; time identity/provenance must be verified
|
| 21 |
+
graph hash FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_raw/amplify/AMPLIFY_120M/AMPLIFY_120M_SHA256.tsv 28c5dc46c7074c6ee10145d8655afcb10b9f0f14962cdb129a9e9864ce86f61f NO candidate only; time identity/provenance must be verified
|
| 22 |
+
graph hash FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_raw/protein_complex_external/complexportal/SHA256_9606_LOCAL.txt eb78081531f21c0ed81948b9ad697519052bb089aefe28887d38a188549d21a2 NO candidate only; time identity/provenance must be verified
|
| 23 |
+
graph hash FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_raw/protein_complex_external/complexportal/SHA256_9606_REMOTE.txt ee88065272dc90ce16bbb0c597b85e3a5a74fa649d8b223555717de833ac6a14 NO candidate only; time identity/provenance must be verified
|
| 24 |
+
checkpoint FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/27_clinvar_gate/formal/C1_ParameterMatchedMLP/seed_2026/best.pt 5c5bd046e3f8d592dfe15cde245712ff1bf45381391038674cc1e528bd026fd6 NO candidate only; time identity/provenance must be verified
|
| 25 |
+
checkpoint FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/27_clinvar_gate/formal/C1_ParameterMatchedMLP/seed_3407/best.pt f65f41fcbf617c60cb9b348605ecab0aec0b174dc9edbb5955e0c81955d0b585 NO candidate only; time identity/provenance must be verified
|
| 26 |
+
checkpoint FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/27_clinvar_gate/formal/C1_ParameterMatchedMLP/seed_42/best.pt 425dea6a4971a6569870c7fb56b716ae05969f9a305693db1b83d320503935a4 NO candidate only; time identity/provenance must be verified
|
| 27 |
+
checkpoint FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/27_clinvar_gate/formal/C2_ShuffledGraph/seed_2026/best.pt 40c73f68b549642a9d4f92ef62d20c98a7e099f803004e2c15369ab93b175671 NO candidate only; time identity/provenance must be verified
|
| 28 |
+
checkpoint FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/27_clinvar_gate/formal/C2_ShuffledGraph/seed_3407/best.pt 2eee51d941609dfa61472a144ac6947c01c0d0039be150e1ee16bb3ac1a382a1 NO candidate only; time identity/provenance must be verified
|
| 29 |
+
graph embedding array FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_graph_residual_esm2_v2/scripts/evaluate_clinvar_residual_v2.py dcf4df2cb71ae5487556659f19db5c8dc311f23d35cee0ad133ae513eef069f5 NO candidate only; time identity/provenance must be verified
|
| 30 |
+
graph embedding array FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/graph_residual_ptm_mamba/configs/clinvar.yaml 86716d807ffb55acde9a5d4899f5b9dbf2d137b5465d0da806388f467deca7d0 NO candidate only; time identity/provenance must be verified
|
| 31 |
+
graph embedding array FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/graph_residual_ptm_mamba/gr_ptm_mamba/clinvar/__init__.py 42f8184e83b5d97b7fb5a2c2996943fd13cc4e93f7673bbd7a00126350a77107 NO candidate only; time identity/provenance must be verified
|
| 32 |
+
graph embedding array FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/graph_residual_ptm_mamba/gr_ptm_mamba/clinvar/model.py 39c2b90853571ffe781fcfcf8aab000b2aa21d20985c1db3c096c7a303c40c6a NO candidate only; time identity/provenance must be verified
|
| 33 |
+
graph embedding array FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/graph_residual_ptm_mamba/scripts/evaluate_clinvar.py eaceb95b12f6982583a3f5125862f5f2d75ca0a5952b92143780b46e4b6659b0 NO candidate only; time identity/provenance must be verified
|
| 34 |
+
training config FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/graph_residual_ptm_mamba/configs/clinvar.yaml 86716d807ffb55acde9a5d4899f5b9dbf2d137b5465d0da806388f467deca7d0 NO candidate only; time identity/provenance must be verified
|
| 35 |
+
training config FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/27_clinvar_gate/acceptance_report.json 7f4ed4b19470cdedfb31fff0d205512a886df4b2e6819a2d192da3be939de8b3 NO candidate only; time identity/provenance must be verified
|
| 36 |
+
training config FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/27_clinvar_gate/formal/C1_ParameterMatchedMLP/seed_2026/run_summary.json 7c93de108975dcd091e4c86e77d185e6e5a577be33b591be8d1ecd729bb0a175 NO candidate only; time identity/provenance must be verified
|
| 37 |
+
training config FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/27_clinvar_gate/formal/C1_ParameterMatchedMLP/seed_3407/run_summary.json 9cacd71f6d432db6abbfbe19b3f1c2be39a620f78fe89ef99210077e358fbe32 NO candidate only; time identity/provenance must be verified
|
| 38 |
+
training config FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/27_clinvar_gate/formal/C1_ParameterMatchedMLP/seed_42/run_summary.json 0459d6fe425686f53518f06655bc2f9c54b3c46f5863ba3e9063a6062a9c3508 NO candidate only; time identity/provenance must be verified
|
| 39 |
+
seed FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/graph_residual_ptm_mamba/configs/clinvar.yaml 86716d807ffb55acde9a5d4899f5b9dbf2d137b5465d0da806388f467deca7d0 NO candidate only; time identity/provenance must be verified
|
| 40 |
+
seed FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/27_clinvar_gate/formal/C1_ParameterMatchedMLP/seed_2026/FORMAL_PASS.flag 7c93de108975dcd091e4c86e77d185e6e5a577be33b591be8d1ecd729bb0a175 NO candidate only; time identity/provenance must be verified
|
| 41 |
+
seed FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/27_clinvar_gate/formal/C1_ParameterMatchedMLP/seed_2026/best.pt 5c5bd046e3f8d592dfe15cde245712ff1bf45381391038674cc1e528bd026fd6 NO candidate only; time identity/provenance must be verified
|
| 42 |
+
seed FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/27_clinvar_gate/formal/C1_ParameterMatchedMLP/seed_2026/history.tsv 97555dab19e2988bbdb3d402c202e280f53cb6bb90b114b2d6c0d4598adae7ff NO candidate only; time identity/provenance must be verified
|
| 43 |
+
seed FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/27_clinvar_gate/formal/C1_ParameterMatchedMLP/seed_2026/metrics.tsv 9f322d0d1003b7fe73319aa0ac024b5fc5d8c7147e31a5dbfed50401e0ecd970 NO candidate only; time identity/provenance must be verified
|
| 44 |
+
split ledger FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_benchmark/clinvar_pathogenicity/reports/split_integrity.tsv 4158970bcc36c03460461d7331deab8520a1a2d59220ca65447cc7039bf4c3b2 NO candidate only; time identity/provenance must be verified
|
| 45 |
+
split ledger FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_benchmark/clinvar_pathogenicity/splits_by_gene.tsv d46ba835256a66b9496c2a842210f718d5ce4610a0e445c309f353b25724b756 NO candidate only; time identity/provenance must be verified
|
| 46 |
+
split ledger FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_benchmark/clinvar_pathogenicity/splits_by_protein.tsv bf8dd1ed0c8d6813f65b6acfbefddede8e40b45b451fb0bf118d701a7d7f04c7 NO candidate only; time identity/provenance must be verified
|
| 47 |
+
split ledger FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/L1B_ptm_context_clinvar_v1/assets/clinvar_test_split_manifest.tsv 4b2f888c24aa759bea0ca76bc6810bf0e802f4c3158aea28c6f2c8890dd10b2d NO candidate only; time identity/provenance must be verified
|
| 48 |
+
split ledger FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_L1B_PTMContextClinVar_verified_20260810/L1B_ptm_context_clinvar_v1/assets/clinvar_test_split_manifest.tsv 4b2f888c24aa759bea0ca76bc6810bf0e802f4c3158aea28c6f2c8890dd10b2d NO candidate only; time identity/provenance must be verified
|
| 49 |
+
exclusion ledger FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/model_benchmark_v6/graph_residual_ptm_mamba/audit/clinvar_leakage_report.tsv 5a119a86b4dfe01851c78fe44469f4dc3ee05aea9c9800652417f5ad1c9f9309 NO candidate only; time identity/provenance must be verified
|
| 50 |
+
exclusion ledger FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_other_results_figures_verified_20260809/work/model_benchmark_v6/graph_residual_ptm_mamba/audit/clinvar_leakage_report.tsv 5a119a86b4dfe01851c78fe44469f4dc3ee05aea9c9800652417f5ad1c9f9309 NO candidate only; time identity/provenance must be verified
|
| 51 |
+
exclusion ledger FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_benchmark/mutation_ptm/reports/leakage_check.tsv 86bd19f19d2a9cd4a9f10f0eb594b49a7428e1aaebb38a270e59f335b0f360f0 NO candidate only; time identity/provenance must be verified
|
| 52 |
+
exclusion ledger FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_gcl/relation_mask_forward.py b61c8994671f0095bd8be005ceabe861355514e765d5c7e35a059387dbd46b21 NO candidate only; time identity/provenance must be verified
|
| 53 |
+
exclusion ledger FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/02_official_baseline/protocols/fixed_validation_mask.tsv.gz 4b366269483830c81b42b26c7599d4236a0d7bcb3856fc8ada590c65c949c4b6 NO candidate only; time identity/provenance must be verified
|
| 54 |
+
leakage audit output FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/L1B_ptm_context_clinvar_v1/audit/acceptance_checks.tsv b1ac44b2bfde335aded461eef6e8926c3d8e2ce2772e0d27cb171bbd9b251c22 NO candidate only; time identity/provenance must be verified
|
| 55 |
+
leakage audit output FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/L1B_ptm_context_clinvar_v1/audit/context_feature_lineage.tsv 9364a38bb104be05b835e4bd738fdd9fe60d9e82564c31a2c4cd90e8b6440ac0 NO candidate only; time identity/provenance must be verified
|
| 56 |
+
leakage audit output FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/L1B_ptm_context_clinvar_v1/audit/data_readiness.tsv e32e18e47543557e583b4342d88e4dd809eb2e0ee6c8f96f36115d232e6bab18 NO candidate only; time identity/provenance must be verified
|
| 57 |
+
leakage audit output FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/L1B_ptm_context_clinvar_v1/audit/mutation_reference_validation.tsv 736143cdc46798efd2d859ec06da1d9f7b784e41a534b5564ebc4517e090b2c7 NO candidate only; time identity/provenance must be verified
|
| 58 |
+
leakage audit output FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/model_benchmark_v6/graph_residual_ptm_mamba/audit/clinvar_leakage_report.tsv 5a119a86b4dfe01851c78fe44469f4dc3ee05aea9c9800652417f5ad1c9f9309 NO candidate only; time identity/provenance must be verified
|
| 59 |
+
provenance manifest FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/ptm_context_clinvar/augment_l1b_manifest.py 24ce4ce3833d3264c92bfd455fc44ef5ca6f8c35445747da9422b44bb5fdb693 NO candidate only; time identity/provenance must be verified
|
| 60 |
+
provenance manifest FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/L1B_ptm_context_clinvar_v1/assets/clinvar_prediction_manifest.tsv 0c95fbf4462c0ec4061b29db0557089ba903643f4bb55f99dd5c056f107486de NO candidate only; time identity/provenance must be verified
|
| 61 |
+
provenance manifest FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/L1B_ptm_context_clinvar_v1/assets/clinvar_test_split_manifest.tsv 4b2f888c24aa759bea0ca76bc6810bf0e802f4c3158aea28c6f2c8890dd10b2d NO candidate only; time identity/provenance must be verified
|
| 62 |
+
provenance manifest FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_L1B_PTMContextClinVar_verified_20260810/L1B_ptm_context_clinvar_v1/assets/clinvar_prediction_manifest.tsv 0c95fbf4462c0ec4061b29db0557089ba903643f4bb55f99dd5c056f107486de NO candidate only; time identity/provenance must be verified
|
| 63 |
+
provenance manifest FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_L1B_PTMContextClinVar_verified_20260810/L1B_ptm_context_clinvar_v1/assets/clinvar_test_split_manifest.tsv 4b2f888c24aa759bea0ca76bc6810bf0e802f4c3158aea28c6f2c8890dd10b2d NO candidate only; time identity/provenance must be verified
|
initial_data/clinvar_strict_rebuild_audit/manifests/node_mapping_manifest.tsv
ADDED
|
The diff for this file is too large to render.
See raw diff
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|
initial_data/clinvar_strict_rebuild_audit/manifests/relation_catalog.tsv
ADDED
|
The diff for this file is too large to render.
See raw diff
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|
|
initial_data/clinvar_strict_rebuild_v1/00_provenance/CLINVAR_STRICT_REBUILD_DECISION.md
ADDED
|
@@ -0,0 +1,53 @@
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|
| 1 |
+
# ClinVar Strict Rebuild Decision
|
| 2 |
+
|
| 3 |
+
Generated: 2026-08-31T12:41:12.492905+00:00
|
| 4 |
+
|
| 5 |
+
## Executive decision
|
| 6 |
+
|
| 7 |
+
- Old ClinVar results as transductive supporting evidence: **YES**.
|
| 8 |
+
- Exact reconstruction of historical graph: **PARTIAL**.
|
| 9 |
+
- New fully archived strict graph: **YES**.
|
| 10 |
+
- G1 implementable: **YES**.
|
| 11 |
+
- G2a implementable: **YES**.
|
| 12 |
+
- G2b implementable: **YES**.
|
| 13 |
+
- True node-inductive test: **SUPPORTED**.
|
| 14 |
+
- Original formal split needs to change: **NO** unless actual split cannot be recovered; no resampling/re-selection was performed.
|
| 15 |
+
- Immediate retraining: **NO — FEASIBILITY AUDIT ONLY**.
|
| 16 |
+
|
| 17 |
+
## Recommended next step
|
| 18 |
+
|
| 19 |
+
**A. Proceed with G1 + G2 strict rebuild**
|
| 20 |
+
|
| 21 |
+
formal split, test IDs, relation catalog and raw graph sources are sufficiently identifiable for a separately archived strict rebuild.
|
| 22 |
+
|
| 23 |
+
## Evidence boundaries
|
| 24 |
+
|
| 25 |
+
- Asset-based audit; reports were not treated as substitutes for row-level data/code evidence.
|
| 26 |
+
- Generic one-hop/two-hop context was not automatically called leakage.
|
| 27 |
+
- No formal split changed, model trained, embedding regenerated or formal result modified.
|
| 28 |
+
- Current-looking graph paths were not promoted to exact historical snapshots without explicit snapshot/hash/provenance.
|
| 29 |
+
|
| 30 |
+
## Key counts
|
| 31 |
+
|
| 32 |
+
- Formal test N: [53386]
|
| 33 |
+
- Effective test N: [51896]
|
| 34 |
+
- Test proteins recovered: [3048]
|
| 35 |
+
- Test variants recovered: [53386]
|
| 36 |
+
- Relation catalog entries: [7166]
|
| 37 |
+
- Alias-map rows: [600000]
|
| 38 |
+
|
| 39 |
+
## Artifact index
|
| 40 |
+
|
| 41 |
+
- inventory/all_relevant_files.tsv
|
| 42 |
+
- manifests/clinvar_split_manifest.tsv
|
| 43 |
+
- audits/clinvar_label_definition.md
|
| 44 |
+
- manifests/node_mapping_manifest.tsv
|
| 45 |
+
- manifests/variant_alias_map.tsv
|
| 46 |
+
- manifests/relation_catalog.tsv
|
| 47 |
+
- audits/clinvar_relation_risk_audit.tsv
|
| 48 |
+
- candidate_graphs/G1_removal_policy.tsv
|
| 49 |
+
- candidate_graphs/G2_policy_options.tsv
|
| 50 |
+
- audits/node_inductive_feasibility.md
|
| 51 |
+
- manifests/historical_clinvar_asset_recovery.tsv
|
| 52 |
+
- reports/proposed_provenance_spec.md
|
| 53 |
+
- reports/CLINVAR_STRICT_REBUILD_FEASIBILITY.tsv
|
initial_data/clinvar_strict_rebuild_v1/00_provenance/CLINVAR_STRICT_REBUILD_FEASIBILITY.tsv
ADDED
|
@@ -0,0 +1,16 @@
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|
|
| 1 |
+
ITEM STATUS EVIDENCE BLOCKER NEXT_ACTION
|
| 2 |
+
formal split recovered FOUND clinvar_split_manifest.tsv; selected test count=53386 none freeze selected split after manual review
|
| 3 |
+
effective cohort recovered FOUND clinvar_split_manifest.tsv/source scan; effective_n=51896 none verify explicit representation-validity rule
|
| 4 |
+
test protein IDs recovered FOUND selected split rows; unique values=3048 none freeze test protein IDs
|
| 5 |
+
variant aliases recovered PASS variant_alias_map.tsv; rows=600000 none verify canonicalization and duplicates
|
| 6 |
+
node mapping recovered PASS node_mapping_manifest.tsv; verified=17567;unknown=0 none resolve every requested mapping pair
|
| 7 |
+
relation catalog recovered PASS relation_catalog.tsv; relations=7166 none review relation dictionary and reverse pairs
|
| 8 |
+
historical exact graph snapshot recovered PARTIAL historical asset recovery manifest no time-stamped exact raw snapshot do not call current graph historical
|
| 9 |
+
historical audit outputs recovered FOUND historical asset recovery manifest none preserve audit outputs with hashes
|
| 10 |
+
G1 constructible YES G1_removal_policy.tsv; relation catalog; test IDs none construct immutable G1 after sign-off
|
| 11 |
+
G2a constructible YES G2_policy_options.tsv; risk audit none freeze G2a removal ledger
|
| 12 |
+
G2b constructible YES G2_policy_options.tsv; node-inductive audit none decide node table/fallback policy
|
| 13 |
+
true node-inductive constructible SUPPORTED node_inductive_feasibility.md none implement/verify only in authorized phase
|
| 14 |
+
new frozen graph constructible YES raw assets, split, mappings, relations, provenance none build only after blockers clear
|
| 15 |
+
full provenance possible YES proposed_provenance_spec.md none use spec as gate
|
| 16 |
+
retraining required NO scope: feasibility audit only training out of scope no training
|
initial_data/clinvar_strict_rebuild_v1/00_provenance/G1_removal_policy.tsv
ADDED
|
@@ -0,0 +1,5 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
relation remove_or_keep reason affected_edges affected_test_variants affected_test_proteins
|
| 2 |
+
direct ClinVar target relation REMOVE_IF_VERIFIED direct target-label encoding; check exact direction and aliases 608725 53386 3048
|
| 3 |
+
exact reverse of direct target relation REMOVE_IF_VERIFIED reverse target relation is equivalent exposure UNKNOWN 53386 3048
|
| 4 |
+
alias-equivalent target relation REMOVE_IF_VERIFIED same relation under another name; verify from relation/alias tables UNKNOWN 53386 3048
|
| 5 |
+
generic one-hop/two-hop context KEEP_UNLESS_TARGET_EQUIVALENT generic paths are not leakage without explicit semantic equivalence UNKNOWN 0 3048
|
initial_data/clinvar_strict_rebuild_v1/00_provenance/G2_policy_options.tsv
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
condition removed_relation_family test_node_remaining_in_graph graph_embedding_available scientific_interpretation implementation_risk
|
| 2 |
+
G2a label-proximal disease/mutation/variant context YES_IF_NONLABEL_EDGES_OR_EXPLICIT_NODE_TABLE YES tests dependence on disease/mutation context while retaining generic structure medium; freeze relation semantics and node table
|
| 3 |
+
G2b all non-sequence relational context for formal test proteins YES_IF_EXPLICIT_NODE_TABLE; otherwise UNKNOWN PARTIAL tests dependence on test-protein transductive relational context high; isolated nodes may have undefined graph embeddings
|
initial_data/clinvar_strict_rebuild_v1/00_provenance/MASTER_SHA256SUMS.tsv
ADDED
|
@@ -0,0 +1,504 @@
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|
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|
|
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|
|
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|
|
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|
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|
|
|
|
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|
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|
|
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|
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|
|
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|
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|
|
|
|
|
|
|
|
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|
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|
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|
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|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
path sha256 size_bytes
|
| 2 |
+
00_provenance/CLINVAR_STRICT_REBUILD_DECISION.md f4740f786519d916ccc6adfb974c4982d19e03054202411b2ce8adb2e5756c94 1939
|
| 3 |
+
00_provenance/CLINVAR_STRICT_REBUILD_FEASIBILITY.tsv 19cfbd6cff42ea1ae1049fe42552aba6a94a7536d8031e3f1dce3800b15dbca8 1770
|
| 4 |
+
00_provenance/G1_removal_policy.tsv 18149f149471755d4e296a9229140721bdee7c2b877c99067bbc971628e65f3c 638
|
| 5 |
+
00_provenance/G2_policy_options.tsv 7f6f08d5026c736fbee111db7e25305c323badc33b578b2f3a6c6f65004fff2e 608
|
| 6 |
+
00_provenance/PHASE1_MISSING_FILES.tsv d71dc9123c215b0d7532e562da8cd3ff60dfd991530b235fe77473195a9de7c5 426
|
| 7 |
+
00_provenance/POLICY_LOCK.txt e7011562482ac8875caf698a5b534b7241707dc530758f79af7eb31bcda5da9c 881
|
| 8 |
+
00_provenance/clinvar_label_definition.md bcdf12bdb3c31efcab41b63dbd001ae1d8a8f347d8c341ea6f5fa798a5e3eff5 14802
|
| 9 |
+
00_provenance/clinvar_relation_risk_audit.tsv 3ea2e3724f3a6a43df7557eba5079ee5e6e47791a3677677b071d7957a1f3969 36770
|
| 10 |
+
00_provenance/clinvar_split_manifest.tsv 1d44179216a223f67fb7eacf6be37ac0108e7d12f9f503b9c0c0bdabf3af6103 10844062
|
| 11 |
+
00_provenance/historical_clinvar_asset_recovery.tsv 59b80e7135dd84769452fee0e52c2308d089db7099ec1bfd79f2bd2926a364c0 16922
|
| 12 |
+
00_provenance/node_inductive_feasibility.md fd4d42a4fdf5d159606cd66417bc20965c271dd0480d264d70a0c61e6e45e164 14299
|
| 13 |
+
00_provenance/node_mapping_manifest.tsv c2be651ef9e79f1d9e3b8e14a3207e4559147e2caad6d353316454029481c419 4740337
|
| 14 |
+
00_provenance/phase1_audit_sha256.tsv ba31ac7a83e9c8dd6fbbdf45ecd1de2664a08c811b698e6139e8ee23f6ef6765 1233
|
| 15 |
+
00_provenance/relation_catalog.tsv cce7637b263ba7d5c7fbd4ee1eda79c3faee910a8a2a6cc61828837dc9050e89 1530027
|
| 16 |
+
00_provenance/variant_alias_map.tsv 461556f388345455d82c03bc9aa54462c9b54ddcfdda13b00226d6bc42afbc3e 92924269
|
| 17 |
+
01_raw_manifest/esm2_only_v1/core_embeddings/_SUCCESS 4040484dddfe35a4620629ab46aac77eafa4a68b790c9162472a7cc42f9a783b 89
|
| 18 |
+
01_raw_manifest/esm2_only_v1/core_embeddings/cache_sha256.txt b760c1e26365e2db372c45a42486a2128e1166a83cd3e46f6343b3372ca48f76 1113
|
| 19 |
+
01_raw_manifest/esm2_only_v1/core_embeddings/extraction_report.json 35120895bb8adffa10d7332ff6fdc17654b40548fa71acab4d8b615c91e72abe 1172
|
| 20 |
+
01_raw_manifest/esm2_only_v1/core_embeddings/integrity_report.tsv 8410194cbb3005e6e7ba7019a90e2a4409563a7071d17b09e7ce073c1e19fe23 536
|
| 21 |
+
01_raw_manifest/esm2_only_v1/core_embeddings/invalid_sequence_rows.tsv.gz 2ae2e77ed545414ad4c92b6470a3d8923340dca81a9cf3d0fc2b5397b5a5550d 429026
|
| 22 |
+
01_raw_manifest/esm2_only_v1/core_embeddings/mutation_esm2_embeddings.npy 090e9480e598c392ee1ac2223e1f99734939ad5475eb923c5d5d4e9e70293e70 1351451008
|
| 23 |
+
01_raw_manifest/esm2_only_v1/core_embeddings/mutation_mapping.tsv.gz d3cc0659c19c4571c81b5f112f6c1c9e931eddffc6fa436c879110a2523b333c 11197358
|
| 24 |
+
01_raw_manifest/esm2_only_v1/core_embeddings/mutation_sequence_valid_mask.npy 132a6e697c49dc4e7aa9f87fc492b3be0ff7bb19bfc3d88d03ff37f38e1d990a 1055949
|
| 25 |
+
01_raw_manifest/esm2_only_v1/core_embeddings/protein_esm2_embeddings.npy c0d0c8120fdadb72b5fd8c2eb675d5b5e66063160ca4f83a53af336daf67c139 18215808
|
| 26 |
+
01_raw_manifest/esm2_only_v1/core_embeddings/protein_mapping.tsv.gz 1f10b64bfa624452b10102c23de770e9d75982444c0d71982ab3f0ea750df248 107595
|
| 27 |
+
01_raw_manifest/esm2_only_v1/core_embeddings/protein_sequence_valid_mask.npy 6b5a3b2d300bbbf91e71a398b77354324dadbfb93af1570a6434b0850ca87af0 14359
|
| 28 |
+
01_raw_manifest/esm2_only_v1/core_embeddings/ptm_esm2_embeddings.npy 57e4ef32dc5e4c810fb126002d8d7f70bb031bcbc33c727682ceae2625270728 212848768
|
| 29 |
+
01_raw_manifest/esm2_only_v1/core_embeddings/ptm_mapping.tsv.gz 1bd1a44891c9af0237d9c58d7b5f83f201f74e3bd0b8faae9ea2f8b14ec9dbf8 1658171
|
| 30 |
+
01_raw_manifest/esm2_only_v1/core_embeddings/ptm_sequence_valid_mask.npy 37d104a7a83d0a844a253032bf0056be40df6b802faa7bccdfa152d3d5050988 166416
|
| 31 |
+
01_raw_manifest/raw_sources.tsv 3f25a97df8197e60e1c99e67c47b7395b0994fe153041858c66ff1995fa75551 1933
|
| 32 |
+
02_splits/label_policy.yaml 9c5de5b97aed6e5a75d6e8d84f9f66a6a265d7fd82d0e491f93d15e27201a6f1 1061
|
| 33 |
+
02_splits/label_policy_source_sha256.txt 5caf08214d036ac4189681b0dc5246c303a6978149a946b6910a44923c523f83 65
|
| 34 |
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18_logs/v2_train_G2a_seed_42.log 128f4cddb7ba2d7e0ec1297e0a1102339b808a0993053b0e80e285ab54665092 14358
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18_logs/v2_train_G2b_seed_2026.log bc2ff98e7f2cebc5ec84f38699d687ec802c9e1a676f144c2665e2cf92f8e86c 14327
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18_logs/v2_train_G2b_seed_3407.log 59b9c947c4bc0b3c9bdd998d29b3e1ede0f25ea3ea42b52944b97dec0f0507dd 14323
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18_logs/v2_train_G2b_seed_42.log 7a9cf7c7e80a9d3a1c52f9a73ef32a86008b7665c9974269519c40d540fff9d8 14326
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18_logs/v2_train_G3_seed_2026.log 8dd58d0f10f3bc59724f8013b2a4e316e3cc62ec3816cfa7309c27a1a415992e 14328
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18_logs/v2_train_G3_seed_3407.log 79bee1703974fc996ef437ece85570dc4bee66215cbb04f7fd351622b3e9386f 14323
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18_logs/v2_train_G3_seed_42.log ab1ef0bac30c5bcfec3f65a40d3441fffaba85907e0329e734100b2c91b328d6 14337
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reports/CLINVAR_REVIEWER_RESPONSE_TABLE.tsv 35af77d4707c99477cf1e8ab0f1707b5259c62bccbae244cf7b51e9325f74099 2163
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reports/CLINVAR_STRICT_REBUILD_FINAL_REPORT.md 1e18cffaed6c5e542118fb9a1f8fe1f921fa91b2782de7f3c1045c018e85f14f 10899
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reports/CLINVAR_STRICT_SENSITIVITY_INTERPRETATION.md 9aa636081e19b1d055c7202e1450c6521c0ffc9f9d45e28fbb4b42ffdfd91971 406
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reports/G1_GRAPH_AUDIT.md ab59324d925c4384bdbafc519494b69524c894183d15ed327525015687e02fb5 329
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reports/G2A_GRAPH_AUDIT.md 12547816fd35a65cf5755f7808d20495411e5fd9c0474e122943aa84096d5641 342
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reports/G2B_GRAPH_AUDIT.md b388aebf5d152a5e4b09c3d14d987948ed1de9211406f4423934ce81c7ba9f01 368
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reports/G3_NODE_INDUCTIVE_AUDIT.md 1fe639606a1f69c300899f0adbbe67402fdb6c0a02ab68bc8e1afcc88cfcd93e 466
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reports/G3_PRETRAIN_AUDIT.tsv c018e032412480f1ae6aa234dccc106f20f93daba7819a6e2f6cc0cbf10bdcdc 1119
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reports/NUMERICAL_VALIDITY_AUDIT.tsv 58ceb17e39b4682c5db4ba6e2e7c66398281ecd805f40e52b3075fbc90c631f1 51277
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reports/PHASE3C_FINAL_REPORT.md 3877b3075c9536fbd63bb194c2d92ded084d590a63116e9e330b8f892c04d07c 3498
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reports/PHASE3C_INPUT_CHAIN_AUDIT.md 6e4decf818a37f3a66988652d1ac2e335995771f6b8aefcf8841429468bbd5b1 3718
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reports/PHASE3D_SAFETY_GATE_FINAL.md 8b6d80d722c5d5bb1c021ae851dacf08582ac93cdef1495f1cc187166cab9403 6468
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reports/PHASE3_ORIGINAL_RUNNER_AUDIT.md a12b71ac3e7ae89683fc9637494e49fa738be806e846ed819adc6401f3de3f86 5366
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reports/RELATION_SCHEMA_RECOVERY.md c3d4e6d825162f56b97f602582e46c76026c699f7aa3cb3b57c6a02a97e506f4 3002
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reports/SAFETY_GATE_IMPLEMENTATION_AUDIT.md 8b0cecbf54c178ceb88bdcf719f5d97f7d37787dfc1cb31ff941feb9ff0ae2b6 2678
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reports/SAFETY_GATE_RUN_MATRIX.tsv a77a61d47ad7d78fc89f9528128aeef6bdf1e1f2ddac12465d969858351176bc 5355
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reports/SAFETY_GATE_SELECTION_AUDIT.tsv 1b8f2dbcf01de41d3a3812d1e3f486d25ece98416fc5e9e9e6b882198438af44 485
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reports/STATIC_SHAPE_TEST.md e8b565949326a10fc154c33e39c53d74ec8d80d5c29f2006daa871478d09cb82 616
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reports/STRICT_ESM_INPUT_COVERAGE.tsv 9003d582e8554653aa2e2bf8cbf4533fef4e22bfa0e688e05b6c7ea9151cb4c6 692
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reports/STRICT_GRAPH_ADAPTER_VALIDATION.tsv 81f924c23835309712ff76afeda5348807f2d616072fce33062ca683656966ae 328
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reports/STRICT_GRAPH_V2_ADAPTER_VALIDATION_CORRECTED.tsv c65e07659cef66feb23c8a285d54ba5bf5c0e1b8efbb5425f653002f14b4174f 333
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initial_data/clinvar_strict_rebuild_v1/00_provenance/PHASE1_MISSING_FILES.tsv
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file status
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clinvar_split_manifest.tsv FOUND
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clinvar_label_definition.md FOUND
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node_mapping_manifest.tsv FOUND
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variant_alias_map.tsv FOUND
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relation_catalog.tsv FOUND
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clinvar_relation_risk_audit.tsv FOUND
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G1_removal_policy.tsv FOUND
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G2_policy_options.tsv FOUND
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node_inductive_feasibility.md FOUND
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historical_clinvar_asset_recovery.tsv FOUND
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CLINVAR_STRICT_REBUILD_FEASIBILITY.tsv FOUND
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CLINVAR_STRICT_REBUILD_DECISION.md FOUND
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initial_data/clinvar_strict_rebuild_v1/00_provenance/POLICY_LOCK.txt
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POLICY_LOCK
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2026-08-31T21:39:02+0800
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project_git_commit UNAVAILABLE
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G1_policy.yaml 4f72d398fc361566a540264e51f59308fc1106daf73443fcf1c394f5e07a475e
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G2a_policy.yaml 51d22fe4edac8513d882256c5032571b7fcb88b9119e10e30a0e56d058c06abb
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G2b_policy.yaml 6a8dca601c5e26b9ede2c5a5b787142f77a42dd6a68873a514e0e84427ea1ba6
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G3_policy.yaml 43553661d080374a38142f714bb3f6973bc89a2238f5ade67dcb2c4bf8f00fe4
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02_splits/test_formal.tsv 9b1fa7a00c9a1110486340ab1f41bf7f53650a85941d28658a94e878b7f55bf3
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02_splits/test_effective.tsv 80756f06a21b0b49c3ce8b9879f07c89bcd98951d4c8603d7ff313fc803a05b7
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02_splits/train.tsv dd6d9609ceb98e52c85702e354681d2fb5a0cba0b357cb01a80fbb502f90c0b6
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02_splits/validation.tsv 16549d1b5c5ac93ff8b97e43f4525c33421a08379db27cf8fb3b0a2c9e0d52e1
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02_splits/label_policy.yaml 9c5de5b97aed6e5a75d6e8d84f9f66a6a265d7fd82d0e491f93d15e27201a6f1
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POLICY_MUTATION_AFTER_LOCK FORBIDDEN
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initial_data/clinvar_strict_rebuild_v1/00_provenance/clinvar_label_definition.md
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# ClinVar label definition audit
|
| 2 |
+
|
| 3 |
+
Generated from remote project files at 2026-08-31T12:41:12.492905+00:00.
|
| 4 |
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|
| 5 |
+
Evidence taxonomy: VERIFIED_FROM_FILE = observed file content; INFERRED_FROM_CODE = implementation reference; UNKNOWN = not verified.
|
| 6 |
+
|
| 7 |
+
## Observed terms
|
| 8 |
+
|
| 9 |
+
TEXT
|
| 10 |
+
{"pathogenic": 187896, "benign": 171041, "reference mismatch": 13, "conflicting": 9, "likely pathogenic": 92185, "likely benign": 98938, "uncertain": 12, "out-of-range": 1}
|
| 11 |
+
TEXT
|
| 12 |
+
|
| 13 |
+
## Required rules
|
| 14 |
+
|
| 15 |
+
| Rule | Status | Evidence |
|
| 16 |
+
|---|---|---|
|
| 17 |
+
| pathogenic + likely pathogenic merged | VERIFIED_FROM_FILE | text/values observed; exact merge/exclusion operation needs code confirmation |
|
| 18 |
+
| benign + likely benign merged | VERIFIED_FROM_FILE | text/values observed; exact merge/exclusion operation needs code confirmation |
|
| 19 |
+
| uncertain significance excluded | VERIFIED_FROM_FILE | text/values observed; exact merge/exclusion operation needs code confirmation |
|
| 20 |
+
| conflicting interpretations excluded | VERIFIED_FROM_FILE | text/values observed; exact merge/exclusion operation needs code confirmation |
|
| 21 |
+
| multiallelic/position mapping | INFERRED_FROM_CODE | matching implementation references found |
|
| 22 |
+
| reference mismatch handling | VERIFIED_FROM_FILE | text/values observed; exact merge/exclusion operation needs code confirmation |
|
| 23 |
+
| out-of-range handling | VERIFIED_FROM_FILE | text/values observed; exact merge/exclusion operation needs code confirmation |
|
| 24 |
+
|
| 25 |
+
|
| 26 |
+
## Evidence files
|
| 27 |
+
|
| 28 |
+
- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/ptm_context_clinvar/augment_l1b_manifest.py; text/path probe; from pathlib import Path import hashlib, pandas as pd ROOT=Path('/root/autodl-tmp/bio/disease_mutation_ptm_gcl'); OUT=ROOT/'work/amplify_generalization/L1B_ptm_context_clinvar_v1'; G=ROOT/'work/amplif
|
| 29 |
+
- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/ptm_context_clinvar/enhance_readme.py; text/path probe; from pathlib import Path import pandas as pd, numpy as np from sklearn.metrics import roc_auc_score, average_precision_score, matthews_corrcoef ROOT=Path('/root/autodl-tmp/bio/disease_mutation_ptm_gcl
|
| 30 |
+
- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/ptm_context_clinvar/finalize_l1b.py; text/path probe; #!/usr/bin/env python3 from pathlib import Path import hashlib, shutil, pandas as pd, numpy as np ROOT=Path('/root/autodl-tmp/bio/disease_mutation_ptm_gcl'); OUT=ROOT/'work/amplify_generalization/L1B_
|
| 31 |
+
- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/ptm_context_clinvar/run_l1b_ptm_context.py; text/path probe; #!/usr/bin/env python3 """Frozen ClinVar PTM-context stratification (Task L1B).""" import os, json, hashlib, shutil, math, textwrap, warnings from pathlib import Path import numpy as np import pandas
|
| 32 |
+
- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/scripts/run_clinvar_gate.py; text/path probe; #!/usr/bin/env python3 """Strict ClinVar AMPLIFY supervised gate (51,896 locked test examples). The source ESM protocol is reused byte-for-byte. All methods start at official P0. Graph inputs are m
|
| 33 |
+
- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_benchmark/clinvar_pathogenicity/reports/benchmark_summary.txt; text/path probe; ClinVar pathogenicity benchmark ================================ Eligible samples: 110791 Pathogenic: 55170 Benign: 55621 Excluded records: 945030 Default split: protein-grouped 70/15/15 Alternative s
|
| 34 |
+
- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_benchmark/clinvar_pathogenicity/reports/class_distribution.tsv; text/path probe; scheme split total pathogenic benign protein train 0 0 0 protein validation 55394 27922 27472 protein test 55397 27248 28149 gene train 0 0 0 gene validation 55394 27922 27472 gene test 55397 27248 28
|
| 35 |
+
- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_benchmark/clinvar_pathogenicity/reports/split_integrity.tsv; text/path probe; check status mutation_split_overlap PASS protein_group_overlap PASS gene_group_overlap PASS binary_labels PASS no_conflicting_labels_in_samples PASS
|
| 36 |
+
- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_benchmark/clinvar_pathogenicity/samples.tsv; text/path probe; mutation_id protein_id gene_symbol reference_aa mutation_position alternate_aa normalized_protein_change clinical_significance_raw label disease_count ptm_count nearest_ptm_distance MUT:A2M:Ala844Val
|
| 37 |
+
- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_benchmark/clinvar_pathogenicity/test.tsv; text/path probe; mutation_id protein_id gene_symbol reference_aa mutation_position alternate_aa normalized_protein_change clinical_significance_raw label disease_count ptm_count nearest_ptm_distance MUT:A2M:Ala844Val
|
| 38 |
+
- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_benchmark/clinvar_pathogenicity/validation.tsv; text/path probe; mutation_id protein_id gene_symbol reference_aa mutation_position alternate_aa normalized_protein_change clinical_significance_raw label disease_count ptm_count nearest_ptm_distance MUT:AACS:Glu564Gln
|
| 39 |
+
- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_processed/labels/disease_labels.tsv; text/path probe; node_id label_type label source DISEASE_NAME:10_conditions disease_name 10 conditions Supplemental_disease_name DISEASE_NAME:10p15_3_microdeletion_syndrome disease_name 10p15.3 microdeletion syndrome
|
| 40 |
+
- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_processed_clean/labels/disease_labels.tsv; text/path probe; node_id label_type label source DISEASE_NAME:10p15_3_microdeletion_syndrome disease_name 10p15.3 microdeletion syndrome Supplemental_disease_name DISEASE_NAME:10q11_22q11_23_deletion_syndrome disease_
|
| 41 |
+
- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_processed_core/labels/disease_labels.tsv; text/path probe; node_id label_type label source DISEASE_NAME:11q_partial_monosomy_syndrome disease_name 11q partial monosomy syndrome Supplemental_disease_name DISEASE_NAME:13q12_3_microdeletion disease_name 13q12.3
|
| 42 |
+
- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_graph_residual_esm2_v2/scripts/evaluate_clinvar_residual_v2.py; text/path probe; #!/usr/bin/env python3 import argparse, hashlib, json, time, warnings from pathlib import Path import numpy as np import pandas as pd import matplotlib matplotlib.use("Agg") import matplotlib.pyplot a
|
| 43 |
+
- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_model_benchmark_v3/scripts/prepare_common_splits.py; text/path probe; #!/usr/bin/env python3 import csv,hashlib,json,os,shutil from pathlib import Path import pandas as pd ROOT=Path('/root/autodl-tmp/bio/disease_mutation_ptm_gcl');OUT=ROOT/'work/model_benchmark_v3/commo
|
| 44 |
+
- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/prott5_two_downstreams/scripts/train_prott5_lora_clinvar.py; text/path probe; #!/usr/bin/env python3 """ProtT5 LoRA ClinVar training under the locked protein-group protocol.""" from __future__ import annotations import argparse import gzip import hashlib import json import mat
|
| 45 |
+
- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/reviewer1_revision/m1_numeric_consistency/all_clinvar_runs.csv; text/path probe; path,experiment_name,backbone,model,split,seed,n_test,auroc,auprc,mcc,timestamp,checkpoint,notes work/amplify_generalization/L1B_ptm_context_clinvar_v1/metrics/graph_coverage_metrics.tsv,metrics,AMPLI
|
| 46 |
+
- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/scripts/build_clinvar_benchmark.py; text/path probe; #!/usr/bin/env python3 """Build leakage-safe ClinVar missense pathogenicity benchmark.""" from __future__ import annotations import argparse,csv,random,shutil,sys from bisect import bisect_left from c
|
| 47 |
+
- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/scripts/evaluate_clinvar_pathogenicity.py; text/path probe; from __future__ import annotations import argparse import json import math import os import platform import random import resource import shutil import sys import time from dataclasses import datacla
|
| 48 |
+
- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/27_clinvar_gate/source_esm_protocol/test.tsv; text/path probe; mutation_id protein_id gene_symbol reference_aa mutation_position alternate_aa normalized_protein_change clinical_significance_raw label disease_count ptm_count nearest_ptm_distance MUT:A2M:Ala844Val
|
| 49 |
+
- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/27_clinvar_gate/source_esm_protocol/train.tsv; text/path probe; mutation_id protein_id gene_symbol reference_aa mutation_position alternate_aa normalized_protein_change clinical_significance_raw label disease_count ptm_count nearest_ptm_distance MUT:AACS:Glu564Gln
|
| 50 |
+
- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/27_clinvar_gate/source_esm_protocol/validation.tsv; text/path probe; mutation_id protein_id gene_symbol reference_aa mutation_position alternate_aa normalized_protein_change clinical_significance_raw label disease_count ptm_count nearest_ptm_distance MUT:AASS:Arg132His
|
| 51 |
+
- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/L1B_ptm_context_clinvar_v1/README_PTMContextClinVar.md; text/path probe; # Task L1B — PTM-context ClinVar Stratified Evaluation ## Scope and interpretation Overall ClinVar performance remains the primary general pathogenicity result. PTM-context results are mechanistic st
|
| 52 |
+
- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/L1B_ptm_context_clinvar_v1/assets/clinvar_prediction_manifest.tsv; text/path probe; method formal_method seed prediction_path prediction_sha256 checkpoint_path checkpoint_sha256 test_rows row_index_sha256 threshold split selection_used_test test_reference_path test_reference_sha256 s
|
| 53 |
+
- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/L1B_ptm_context_clinvar_v1/audit/acceptance_checks.tsv; text/path probe; criterion value formal_predictions_located 1 common_test_universe 1 protein_group_split_confirmed 1 mutation_reference_validation_zero_mismatch 1 ptm_context_definitions_locked_before_scores 1 graph_c
|
| 54 |
+
- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/L1B_ptm_context_clinvar_v1/audit/context_feature_lineage.tsv; text/path probe; feature source pathogenicity_label_derived ptm_distance data_processed_core/nodes_ptm.tsv + edges_protein_ptm.tsv 0 ptm_richness core PTM site counts 0 protein_pathway_count edges_protein_pathway.tsv
|
| 55 |
+
- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/L1B_ptm_context_clinvar_v1/metrics/graph_coverage_metrics.tsv; text/path probe; stratum method seed N pathogenic benign AUROC AUPRC MCC LOW F0 42 18129 9272 8857 0.8712953275040299 0.8751738398133384 0.5753554761599871 LOW F0 3407 18129 9272 8857 0.87094189038313 0.87448417547036
|
| 56 |
+
- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/L1B_ptm_context_clinvar_v1/metrics/overall_frozen_metrics.tsv; text/path probe; method N pathogenic benign AUROC AUPRC MCC F0 51896 25937 25959 0.8885193562036651 0.8903319519456485 0.6106606693839518 F1 51896 25937 25959 0.8915296595834363 0.8943289570249406 0.6166921678448857 F
|
| 57 |
+
- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/L1B_ptm_context_clinvar_v1/metrics/primary_vs_nonlocal_metrics.tsv; text/path probe; stratum method seed N pathogenic benign AUROC AUPRC MCC 0 F0 42 35921 16917 19004 0.8861689867153468 0.8763850101378741 0.6055683963773271 0 F0 3407 35921 16917 19004 0.8858625128117248 0.875944247592
|
| 58 |
+
- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/L1B_ptm_context_clinvar_v1/metrics/ptm_distance_stratified_metrics.tsv; text/path probe; stratum method seed N pathogenic benign AUROC AUPRC MCC B0 F0 42 1112 633 479 0.8660156262883112 0.8951267349116182 0.534611494997289 B0 F0 3407 1112 633 479 0.8677916406943114 0.8968224582681761 0.56
|
| 59 |
+
- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/L1B_ptm_context_clinvar_v1/metrics/ptm_richness_metrics.tsv; text/path probe; stratum method seed N pathogenic benign AUROC AUPRC MCC R0 F0 42 0 0 0 NA NA NA R0 F0 3407 0 0 0 NA NA NA R0 F0 2026 0 0 0 NA NA NA R0 F0 mean 0 0 0 NA NA NA R0 F1 42 0 0 0 NA NA NA R0 F1 3407 0 0 0 N
|
| 60 |
+
- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_relational_hierarchy/FINAL_v1/controls_intrinsic/README_PTMContextClinVar.md; text/path probe; # Task L1B — PTM-context ClinVar Stratified Evaluation ## Scope and interpretation Overall ClinVar performance remains the primary general pathogenicity result. PTM-context results are mechanistic st
|
| 61 |
+
- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_relational_hierarchy/FINAL_v1/controls_intrinsic/clinvar_overall_frozen_metrics.tsv; text/path probe; method N pathogenic benign AUROC AUPRC MCC F0 51896 25937 25959 0.8885193562036651 0.8903319519456485 0.6106606693839518 F1 51896 25937 25959 0.8915296595834363 0.8943289570249406 0.6166921678448857 F
|
| 62 |
+
- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/downstream_core/clinvar_pathogenicity/run_config.json; text/path probe; { "project_dir": "/root/autodl-tmp/bio/disease_mutation_ptm_gcl", "graph_dir": "/root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/graph_core", "pretrain_dir": "/root/autodl-tmp/bio/disease_muta
|
| 63 |
+
- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/downstream_core/clinvar_pathogenicity/training_log.txt; text/path probe; Actual benchmark columns: ["mutation_id", "protein_id", "gene_symbol", "reference_aa", "mutation_position", "alternate_aa", "normalized_protein_change", "clinical_significance_raw", "label", "disease_
|
| 64 |
+
- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/model_benchmark_v3/clinvar/protein_group/excluded_missing_prott5.tsv; text/path probe; split mutation_id protein_id gene_symbol reference_aa mutation_position alternate_aa normalized_protein_change clinical_significance_raw label disease_count ptm_count nearest_ptm_distance train MUT:AC
|
| 65 |
+
- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/model_benchmark_v3/clinvar/protein_group/excluded_missing_ptm_mamba.tsv; text/path probe; split mutation_id protein_id gene_symbol reference_aa mutation_position alternate_aa normalized_protein_change clinical_significance_raw label disease_count ptm_count nearest_ptm_distance train MUT:AC
|
| 66 |
+
- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/model_benchmark_v3/common/clinvar/gene_group/test.tsv; text/path probe; mutation_id protein_id gene_symbol reference_aa mutation_position alternate_aa normalized_protein_change clinical_significance_raw label disease_count ptm_count nearest_ptm_distance MUT:A2M:Ala844Val
|
| 67 |
+
- /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/model_benchmark_v3/common/clinvar/gene_group/train.tsv; text/path probe; mutation_id protein_id gene_symbol reference_aa mutation_position alternate_aa normalized_protein_change clinical_significance_raw label disease_count ptm_count nearest_ptm_distance MUT:AASS:Arg132His
|
initial_data/clinvar_strict_rebuild_v1/00_provenance/clinvar_relation_risk_audit.tsv
ADDED
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@@ -0,0 +1,131 @@
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| 1 |
+
relation_or_path risk_level reason n_test_entities_affected candidate_for_G1_removal candidate_for_G2_removal evidence_source
|
| 2 |
+
10 HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/reviewer1_revision/m4_method_reproducibility/graph_relation_inventory.tsv; relation_catalog.tsv
|
| 3 |
+
11 HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/reviewer1_revision/m4_method_reproducibility/graph_relation_inventory.tsv; relation_catalog.tsv
|
| 4 |
+
6 HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m4_method_reproducibility/graph_relation_inventory.tsv; relation_catalog.tsv
|
| 5 |
+
7 HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m4_method_reproducibility/graph_relation_inventory.tsv; relation_catalog.tsv
|
| 6 |
+
EXPLICIT_CLINVAR_OR_CLASS_LABEL HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/run_clinvar_raw_graph_audit.py; relation_catalog.tsv
|
| 7 |
+
Task38_disease_protein_provenance HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/zero_shot_nonppi/run_n2_u4_nonppi.py; relation_catalog.tsv
|
| 8 |
+
U1_DiseasePermutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_representation_interpretability/zero_shot_disease_similarity/u2_zero_shot_disease_similarity.py; relation_catalog.tsv
|
| 9 |
+
all_model_clinvar_comparison HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 10 |
+
associated_with_mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_processed/edges_disease_mutation.tsv; relation_catalog.tsv
|
| 11 |
+
associated_with_mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_processed_clean/edges_disease_mutation.tsv; relation_catalog.tsv
|
| 12 |
+
associated_with_mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_processed_core/edges_disease_mutation.tsv; relation_catalog.tsv
|
| 13 |
+
associated_with_protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_processed/edges_disease_protein.tsv; relation_catalog.tsv
|
| 14 |
+
associated_with_protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_processed_clean/edges_disease_protein.tsv; relation_catalog.tsv
|
| 15 |
+
associated_with_protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_processed_core/edges_disease_protein.tsv; relation_catalog.tsv
|
| 16 |
+
audit/DISEASE_MUTATION_TARGET_BLIND_PASS.flag HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/disease_mutation_ranking/task43_core.py; relation_catalog.tsv
|
| 17 |
+
bootstrap_iid HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 18 |
+
bootstrap_protein_grouped HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 19 |
+
cached_disease_feature HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/43_disease_mutation_ranking_v1/benchmark/LOCKED_DISEASE_MUTATION_RANKING_v1/S2_mutation_disjoint/target_lineage_manifest.tsv.gz; relation_catalog.tsv
|
| 20 |
+
cached_disease_feature HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/43_disease_mutation_ranking_v1/benchmark/LOCKED_DISEASE_MUTATION_RANKING_v1/S3_protein_disjoint/target_lineage_manifest.tsv.gz; relation_catalog.tsv
|
| 21 |
+
cached_disease_feature HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_other_results_figures_verified_20260809/work/amplify_generalization/43_disease_mutation_ranking_v1/benchmark/LOCKED_DISEASE_MUTATION_RANKING_v1/S2_mutation_disjoint/target_lineage_manifest.tsv.gz; relation_catalog.tsv
|
| 22 |
+
cached_disease_feature HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_other_results_figures_verified_20260809/work/amplify_generalization/43_disease_mutation_ranking_v1/benchmark/LOCKED_DISEASE_MUTATION_RANKING_v1/S3_protein_disjoint/target_lineage_manifest.tsv.gz; relation_catalog.tsv
|
| 23 |
+
classifier_search HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 24 |
+
common_intersection_coverage HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 25 |
+
data_processed/edges_disease_protein.tsv HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/zero_shot_nonppi/run_n2_u4_nonppi.py; relation_catalog.tsv
|
| 26 |
+
data_processed_clean/edges_disease_protein.tsv HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/mechanism_deep/run_mechanism_deep.py; relation_catalog.tsv
|
| 27 |
+
data_processed_core/edges_disease_protein.tsv HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/zero_shot_nonppi/run_n2_u4_nonppi.py; relation_catalog.tsv
|
| 28 |
+
disease-mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/scripts/run_clinvar_gate.py; relation_catalog.tsv
|
| 29 |
+
disease-mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/relation_ablation_results.csv; relation_catalog.tsv
|
| 30 |
+
disease-mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/scripts/m5_finalize_server.py; relation_catalog.tsv
|
| 31 |
+
disease-protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/relation_ablation_results.csv; relation_catalog.tsv
|
| 32 |
+
disease-protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/scripts/m5_finalize_server.py; relation_catalog.tsv
|
| 33 |
+
disease__has_mutation__mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/ppi_partner_ranking_refinement/stage1_analysis_audit.py; relation_catalog.tsv
|
| 34 |
+
disease__has_mutation__mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/scripts/run_step1_data_graph_protocol.py; relation_catalog.tsv
|
| 35 |
+
disease__has_mutation__mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_gcl/relation_mask_forward.py; relation_catalog.tsv
|
| 36 |
+
disease__has_mutation__mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/scripts/build_i1_a1_patch.py; relation_catalog.tsv
|
| 37 |
+
disease__has_mutation__mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/00_protocols/graph_relation_manifest.tsv; relation_catalog.tsv
|
| 38 |
+
disease__has_mutation__mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/U1_zero_shot_ppi_retrieval_v1/audit/core_graph_ppi_leakage.tsv; relation_catalog.tsv
|
| 39 |
+
disease__has_mutation__mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_representation_interpretability/FINAL_verified/U1_zero_shot_ppi/audit/core_graph_ppi_leakage.tsv; relation_catalog.tsv
|
| 40 |
+
disease__has_mutation__mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/graph_core/edge_statistics.tsv; relation_catalog.tsv
|
| 41 |
+
disease__has_mutation__mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/graph_core/relation_mappings/relations.tsv; relation_catalog.tsv
|
| 42 |
+
disease__has_mutation__mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_other_results_figures_verified_20260809/work/amplify_generalization/00_protocols/graph_relation_manifest.tsv; relation_catalog.tsv
|
| 43 |
+
disease__has_mutation__mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 44 |
+
disease__has_mutation__mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/run_clinvar_raw_graph_audit.py; relation_catalog.tsv
|
| 45 |
+
disease__has_mutation__mutation.tsv HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/scripts/downstream_retrieval_visuals.py; relation_catalog.tsv
|
| 46 |
+
disease__has_mutation__mutation.tsv HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/scripts/downstream_soft_relevance_single_figures.py; relation_catalog.tsv
|
| 47 |
+
disease__has_protein__protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/ppi_partner_ranking_refinement/stage1_analysis_audit.py; relation_catalog.tsv
|
| 48 |
+
disease__has_protein__protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/scripts/run_step1_data_graph_protocol.py; relation_catalog.tsv
|
| 49 |
+
disease__has_protein__protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/00_protocols/graph_relation_manifest.tsv; relation_catalog.tsv
|
| 50 |
+
disease__has_protein__protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/U1_zero_shot_ppi_retrieval_v1/audit/core_graph_ppi_leakage.tsv; relation_catalog.tsv
|
| 51 |
+
disease__has_protein__protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_representation_interpretability/FINAL_verified/U1_zero_shot_ppi/audit/core_graph_ppi_leakage.tsv; relation_catalog.tsv
|
| 52 |
+
disease__has_protein__protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/graph_core/edge_statistics.tsv; relation_catalog.tsv
|
| 53 |
+
disease__has_protein__protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/graph_core/relation_mappings/relations.tsv; relation_catalog.tsv
|
| 54 |
+
disease__has_protein__protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_other_results_figures_verified_20260809/work/amplify_generalization/00_protocols/graph_relation_manifest.tsv; relation_catalog.tsv
|
| 55 |
+
disease__has_protein__protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 56 |
+
disease__has_protein__protein.tsv.gz HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/scripts/run_step2_p0_baseline.py; relation_catalog.tsv
|
| 57 |
+
disease_gene_reactome HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/backups/code_before_core_adapt_20260716_023809/build_graph.py; relation_catalog.tsv
|
| 58 |
+
disease_gene_reactome HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_gcl/build_graph.py; relation_catalog.tsv
|
| 59 |
+
disease_mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/disease_mutation_ranking/task43_core.py; relation_catalog.tsv
|
| 60 |
+
disease_mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/ppi_partner_ranking_deep/deep_ablation_v2.py; relation_catalog.tsv
|
| 61 |
+
disease_mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/scripts/build_core_dataset.py; relation_catalog.tsv
|
| 62 |
+
disease_mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/43_disease_mutation_ranking_v1/audit/graph_relation_manifest.tsv; relation_catalog.tsv
|
| 63 |
+
disease_mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_other_results_figures_verified_20260809/work/amplify_generalization/43_disease_mutation_ranking_v1/audit/graph_relation_manifest.tsv; relation_catalog.tsv
|
| 64 |
+
disease_mutation_ptm HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 65 |
+
disease_mutation_ptm_gcl/work/amplify_generalization/28_ppi_gate/source_esm_protocol/protocols/sequence_cluster_disjoint_candidate_pool.tsv.gz HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m6_statistical_evidence/rescue_v3/scripts/reconstruct_m6_v3.py; relation_catalog.tsv
|
| 66 |
+
disease_mutation_ptm_gcl/work/amplify_generalization/33_ppi_selective_graph_residual_v1/bootstrap/paired_grouped_bootstrap.tsv HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m6_statistical_evidence/rescue_v2/scripts/run_m6_rescue_v2.py; relation_catalog.tsv
|
| 67 |
+
disease_mutation_ptm_gcl/work/amplify_generalization/33_ppi_selective_graph_residual_v1/figures/bootstrap_graph_controls_figure_data.tsv HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m6_statistical_evidence/rescue_v2/scripts/run_m6_rescue_v2.py; relation_catalog.tsv
|
| 68 |
+
disease_mutation_ptm_gcl/work/amplify_generalization/43_disease_mutation_ranking_v1/formal/S4_sequence_cluster_disjoint/F3_GraphResidual/seed_42/metrics.tsv HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m6_statistical_evidence/rescue_v2/scripts/run_m6_rescue_v2.py; relation_catalog.tsv
|
| 69 |
+
disease_mutation_ptm_gcl/work/graph_esm2_residual_pretrain_v2/embeddings/node_id_mapping.tsv HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m6_statistical_evidence/rescue_v3/scripts/reconstruct_m6_v3.py; relation_catalog.tsv
|
| 70 |
+
disease_mutation_ptm_gcl/work/graph_esm2_residual_pretrain_v2/embeddings/protein_residual_embeddings.npy HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m6_statistical_evidence/rescue_v3/scripts/reconstruct_m6_v3.py; relation_catalog.tsv
|
| 71 |
+
disease_protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/disease_mutation_ranking/task43_core.py; relation_catalog.tsv
|
| 72 |
+
disease_protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/ppi_partner_ranking_deep/deep_ablation_v2.py; relation_catalog.tsv
|
| 73 |
+
disease_protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/scripts/build_core_dataset.py; relation_catalog.tsv
|
| 74 |
+
disease_protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/43_disease_mutation_ranking_v1/audit/graph_relation_manifest.tsv; relation_catalog.tsv
|
| 75 |
+
disease_protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_other_results_figures_verified_20260809/work/amplify_generalization/43_disease_mutation_ranking_v1/audit/graph_relation_manifest.tsv; relation_catalog.tsv
|
| 76 |
+
disease_protein_counts.tsv HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/disease_conditioned_ppi_audit.py; relation_catalog.tsv
|
| 77 |
+
disease_protein_matched HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/reviewer1_revision/m6_statistical_evidence/rescue_v2/scripts/run_m6_rescue_v2.py; relation_catalog.tsv
|
| 78 |
+
disease_protein_nodes HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/ppi_partner_ranking_refinement/stage1_analysis_audit.py; relation_catalog.tsv
|
| 79 |
+
disease_protein_provenance_audit HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/zero_shot_nonppi/run_n2_u4_nonppi.py; relation_catalog.tsv
|
| 80 |
+
edges/disease__has_protein__protein.tsv.gz HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/ppi_network_completion/task42_core.py; relation_catalog.tsv
|
| 81 |
+
edges/disease__has_protein__protein.tsv.gz HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/zero_shot_ppi_retrieval/task_u1_zero_shot_ppi.py; relation_catalog.tsv
|
| 82 |
+
edges/disease__has_protein__protein.tsv.gz HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_representation_interpretability/zero_shot_disease_similarity/u2_zero_shot_disease_similarity.py; relation_catalog.tsv
|
| 83 |
+
edges_disease_mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/scripts/preprocess_extra_data.py; relation_catalog.tsv
|
| 84 |
+
edges_disease_mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 85 |
+
edges_disease_mutation.tsv HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/scripts/preprocess_extra_data.py; relation_catalog.tsv
|
| 86 |
+
edges_disease_protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/scripts/preprocess_extra_data.py; relation_catalog.tsv
|
| 87 |
+
edges_disease_protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 88 |
+
edges_disease_protein.tsv HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/scripts/preprocess_extra_data.py; relation_catalog.tsv
|
| 89 |
+
edges_mutation_protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 90 |
+
excluded_missing_prott5 HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 91 |
+
excluded_missing_ptm_mamba HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 92 |
+
feasibility/disease_protein_provenance.tsv.gz HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/disease_core_module_prioritization/task41_pipeline.py; relation_catalog.tsv
|
| 93 |
+
graph_core_disease_protein_pairs HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/zero_shot_nonppi/run_n2_u4_nonppi.py; relation_catalog.tsv
|
| 94 |
+
graph_core_serialized_disease_protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/zero_shot_nonppi/run_n2_u4_nonppi.py; relation_catalog.tsv
|
| 95 |
+
has_mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/runs_v3/shuffle_integrity.tsv; relation_catalog.tsv
|
| 96 |
+
has_protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/runs_v3/shuffle_integrity.tsv; relation_catalog.tsv
|
| 97 |
+
model_availability HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 98 |
+
mutation;PTM;pathway (disease used only for candidate metadata) HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/42_ppi_network_completion_v1/audit/ppi_completion_target_blind.tsv; relation_catalog.tsv
|
| 99 |
+
mutation__rev_has_mutation__disease HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_gcl/relation_mask_forward.py; relation_catalog.tsv
|
| 100 |
+
mutation__rev_has_mutation__disease HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/graph_core/relation_mappings/relations.tsv; relation_catalog.tsv
|
| 101 |
+
mutation_disease_count HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/ptm_context_clinvar/run_l1b_ptm_context.py; relation_catalog.tsv
|
| 102 |
+
mutation_disease_count HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_L1B_PTMContextClinVar_verified_20260810/code/run_l1b_ptm_context.py; relation_catalog.tsv
|
| 103 |
+
mutation_disease_count HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_L1B_PTMContextClinVar_verified_20260810_prev2/code/run_l1b_ptm_context.py; relation_catalog.tsv
|
| 104 |
+
mutation_ptm_labels_used HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/zero_shot_mutation_ptm/build_n1_audit.py; relation_catalog.tsv
|
| 105 |
+
physical_ppi HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/43_disease_mutation_ranking_v1/audit/graph_relation_manifest.tsv; relation_catalog.tsv
|
| 106 |
+
physical_ppi HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_other_results_figures_verified_20260809/work/amplify_generalization/43_disease_mutation_ranking_v1/audit/graph_relation_manifest.tsv; relation_catalog.tsv
|
| 107 |
+
positive_pairs/disease_mutation_ptm.tsv HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/backups/code_before_core_adapt_20260716_023809/train_contrastive.py; relation_catalog.tsv
|
| 108 |
+
positive_pairs/disease_mutation_ptm.tsv HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_gcl/export_tasks.py; relation_catalog.tsv
|
| 109 |
+
protein__rev_has_protein__disease HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/graph_core/relation_mappings/relations.tsv; relation_catalog.tsv
|
| 110 |
+
protein_disease_count HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/ptm_context_clinvar/run_l1b_ptm_context.py; relation_catalog.tsv
|
| 111 |
+
protein_disease_count HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_L1B_PTMContextClinVar_verified_20260810/code/run_l1b_ptm_context.py; relation_catalog.tsv
|
| 112 |
+
protein_disease_count HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_L1B_PTMContextClinVar_verified_20260810_prev2/code/run_l1b_ptm_context.py; relation_catalog.tsv
|
| 113 |
+
protein_pathway HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/43_disease_mutation_ranking_v1/audit/graph_relation_manifest.tsv; relation_catalog.tsv
|
| 114 |
+
protein_pathway HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_other_results_figures_verified_20260809/work/amplify_generalization/43_disease_mutation_ranking_v1/audit/graph_relation_manifest.tsv; relation_catalog.tsv
|
| 115 |
+
protein_ptm HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/43_disease_mutation_ranking_v1/audit/graph_relation_manifest.tsv; relation_catalog.tsv
|
| 116 |
+
protein_ptm HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_other_results_figures_verified_20260809/work/amplify_generalization/43_disease_mutation_ranking_v1/audit/graph_relation_manifest.tsv; relation_catalog.tsv
|
| 117 |
+
remove_derived_disease_mutation_path HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/disease_core_module_prioritization/task41_pipeline.py; relation_catalog.tsv
|
| 118 |
+
remove_direct_disease_protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/disease_core_module_prioritization/task41_pipeline.py; relation_catalog.tsv
|
| 119 |
+
test HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 120 |
+
test_metrics HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 121 |
+
test_predictions HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 122 |
+
three_seed_summary HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 123 |
+
train HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 124 |
+
training_history HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 125 |
+
used_for_disease_protein_edges HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/zero_shot_nonppi/run_n2_u4_nonppi.py; relation_catalog.tsv
|
| 126 |
+
validation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 127 |
+
work/amplify_generalization/40_disease_functional_module_discovery_v1 HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/disease_core_module_prioritization/task41_pipeline.py; relation_catalog.tsv
|
| 128 |
+
work/amplify_generalization/41_disease_core_module_prioritization_v1 HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/scripts/m5_v2_finalize.py; relation_catalog.tsv
|
| 129 |
+
ALIAS_EQUIVALENT_TARGET_RELATIONS:10,11,6,7,EXPLICIT_CLINVAR_OR_CLASS_LABEL,Task38_disease_protein_provenance,U1_DiseasePermutation,all_model_clinvar_comparison,associated_with_mutation,associated_with_protein,audit/DISEASE_MUTATION_TARGET_BLIND_PASS.flag,bootstrap_iid,bootstrap_protein_grouped,cached_disease_feature,classifier_search,common_intersection_coverage,data_processed/edges_disease_protein.tsv,data_processed_clean/edges_disease_protein.tsv,data_processed_core/edges_disease_protein.tsv,disease-mutation,disease-protein,disease__has_mutation__mutation,disease__has_mutation__mutation.tsv,disease__has_protein__protein,disease__has_protein__protein.tsv.gz,disease_gene_reactome,disease_mutation,disease_mutation_ptm,disease_mutation_ptm_gcl/work/amplify_generalization/28_ppi_gate/source_esm_protocol/protocols/sequence_cluster_disjoint_candidate_pool.tsv.gz,disease_mutation_ptm_gcl/work/amplify_generalization/33_ppi_selective_graph_residual_v1/bootstrap/paired_grouped_bootstrap.tsv,disease_mutation_ptm_gcl/work/amplify_generalization/33_ppi_selective_graph_residual_v1/figures/bootstrap_graph_controls_figure_data.tsv,disease_mutation_ptm_gcl/work/amplify_generalization/43_disease_mutation_ranking_v1/formal/S4_sequence_cluster_disjoint/F3_GraphResidual/seed_42/metrics.tsv,disease_mutation_ptm_gcl/work/graph_esm2_residual_pretrain_v2/embeddings/node_id_mapping.tsv,disease_mutation_ptm_gcl/work/graph_esm2_residual_pretrain_v2/embeddings/protein_residual_embeddings.npy,disease_protein,disease_protein_counts.tsv,disease_protein_matched,disease_protein_nodes,disease_protein_provenance_audit,edges/disease__has_protein__protein.tsv.gz,edges_disease_mutation,edges_disease_mutation.tsv,edges_disease_protein,edges_disease_protein.tsv,edges_mutation_protein,excluded_missing_prott5,excluded_missing_ptm_mamba,feasibility/disease_protein_provenance.tsv.gz,graph_core_disease_protein_pairs,graph_core_serialized_disease_protein,has_mutation,has_protein,model_availability,mutation;PTM;pathway (disease used only for candidate metadata),mutation__rev_has_mutation__disease,mutation_disease_count,mutation_ptm_labels_used,physical_ppi,positive_pairs/disease_mutation_ptm.tsv,protein__rev_has_protein__disease,protein_disease_count,protein_pathway,protein_ptm,remove_derived_disease_mutation_path,remove_direct_disease_protein,test,test_metrics,test_predictions,three_seed_summary,train,training_history,used_for_disease_protein_edges,validation,work/amplify_generalization/40_disease_functional_module_discovery_v1,work/amplify_generalization/41_disease_core_module_prioritization_v1 HIGH multiple names may encode the same target; confirm from rows before removal 14534 YES YES relation_catalog.tsv; edge overlap scan
|
| 130 |
+
one-hop/two-hop label-proximal candidate paths MEDIUM generic context is not automatically leakage; remove only if semantically target-equivalent 53386 NO_UNTIL_SEMANTICALLY_VERIFIED G2a_ONLY_IF_LABEL_PROXIMAL relation_catalog.tsv; no path deletion executed
|
| 131 |
+
generic biological context (PPI/PTM/pathway/other) LOW not a direct label encoding on current evidence; do not remove solely because a two-hop path exists 3048 NO G2b_ONLY relation_catalog.tsv
|
initial_data/clinvar_strict_rebuild_v1/00_provenance/historical_clinvar_asset_recovery.tsv
ADDED
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| 1 |
+
asset status path hash usable_for_exact_reconstruction notes
|
| 2 |
+
exact historical raw graph snapshot PARTIAL /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv b76f3572e9421f5a13f7dee71a7cdd5389754bd954225551df3fc713f11159d2 NO candidate only; time identity/provenance must be verified
|
| 3 |
+
exact historical raw graph snapshot PARTIAL /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/runs_v2/configs/shufflededges_clinvar.json 025ede18f36f736e4396361e5e4730b8d5618e9f9998067f34e760df9d31f6ca NO candidate only; time identity/provenance must be verified
|
| 4 |
+
exact historical raw graph snapshot PARTIAL /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/runs_v3/configs/ShuffledEdges_ClinVar.json 3c553590c3d73ab3cf52198025971116d43ddf3ee08a68716d10203ec281271c NO candidate only; time identity/provenance must be verified
|
| 5 |
+
exact historical raw graph snapshot PARTIAL /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/runs_v3/runs/clinvar/shuffled_edges/seed_2026/run_metadata.json 356103e54e2d1edc93164aea414ab9ab942b6207fb43e479c4ca564cc7a1f453 NO candidate only; time identity/provenance must be verified
|
| 6 |
+
exact historical raw graph snapshot PARTIAL /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/runs_v3/runs/clinvar/shuffled_edges/seed_2026/test_predictions.tsv c653de50a8bfbf95901a5fa2b06e16b30f58ce7568c040ff4890f625ada90ab3 NO candidate only; time identity/provenance must be verified
|
| 7 |
+
exact historical node table MISSING NA NA NO no candidate path found
|
| 8 |
+
exact historical edge table FOUND /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/runs_v2/configs/shufflededges_clinvar.json 025ede18f36f736e4396361e5e4730b8d5618e9f9998067f34e760df9d31f6ca YES candidate only; time identity/provenance must be verified
|
| 9 |
+
exact historical edge table FOUND /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/runs_v3/configs/ShuffledEdges_ClinVar.json 3c553590c3d73ab3cf52198025971116d43ddf3ee08a68716d10203ec281271c YES candidate only; time identity/provenance must be verified
|
| 10 |
+
exact historical edge table FOUND /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/runs_v3/runs/clinvar/shuffled_edges/seed_2026/run_metadata.json 356103e54e2d1edc93164aea414ab9ab942b6207fb43e479c4ca564cc7a1f453 YES candidate only; time identity/provenance must be verified
|
| 11 |
+
exact historical edge table FOUND /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/runs_v3/runs/clinvar/shuffled_edges/seed_2026/test_predictions.tsv c653de50a8bfbf95901a5fa2b06e16b30f58ce7568c040ff4890f625ada90ab3 YES candidate only; time identity/provenance must be verified
|
| 12 |
+
exact historical edge table FOUND /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/runs_v3/runs/clinvar/shuffled_edges/seed_2026/validation_history.tsv d9b86fe75df0ad88da4e63fa64b52d6e614308b52c76695af6e776098ef1ed7f YES candidate only; time identity/provenance must be verified
|
| 13 |
+
relation ordering PARTIAL /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/graph_core/relation_mappings/relations.tsv a354ed64e5eabd83bb510696dd5c734a67b02de4fe6cd6af218d96a05e8c1311 NO candidate only; time identity/provenance must be verified; current-looking graph cannot be assumed historical
|
| 14 |
+
edge count FOUND /root/autodl-tmp/bio/final_prodisease_v32_clinvar_dataset.metadata.json 2f672e8a73a2a93824a43dd55599e148d66945c39220425b59b81585578e5f4a NO candidate only; time identity/provenance must be verified
|
| 15 |
+
edge count FOUND /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/runs_v3/runs/clinvar/additive/seed_2026/run_metadata.json bb0b78dc5be015421c659c4d319731c5b25b798aa2dce0f535b36861d9dac5ff NO candidate only; time identity/provenance must be verified
|
| 16 |
+
edge count FOUND /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/runs_v3/runs/clinvar/additive/seed_3407/run_metadata.json 48c611fdcc752c6a4392c35bbd70fa905c5aa40225906892fc1dbbbb723fcb05 NO candidate only; time identity/provenance must be verified
|
| 17 |
+
edge count FOUND /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/runs_v3/runs/clinvar/additive/seed_42/run_metadata.json c38b142f90164790c09440a0764894e2f5b1afddf982a979e99c36e1750837b4 NO candidate only; time identity/provenance must be verified
|
| 18 |
+
edge count FOUND /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/runs_v3/runs/clinvar/concat/seed_2026/run_metadata.json 906a6b706840cc7c68cd0c114ce5a2974ea4d4b9bf9ec41beced497543655979 NO candidate only; time identity/provenance must be verified
|
| 19 |
+
graph hash FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_L1B_PTMContextClinVar_verified_20260810/SHA256_manifest.tsv 4bd7b834830c5dde49eaa3ca52d03d25c123a36b54742bfd5df93487957026a1 NO candidate only; time identity/provenance must be verified
|
| 20 |
+
graph hash FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_L1B_PTMContextClinVar_verified_20260810_prev2/SHA256_manifest.tsv 2eb4995e4a1c989ff5d18a3809ffade955c02dc58b1c6d89615bd10aa697e0ea NO candidate only; time identity/provenance must be verified
|
| 21 |
+
graph hash FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_raw/amplify/AMPLIFY_120M/AMPLIFY_120M_SHA256.tsv 28c5dc46c7074c6ee10145d8655afcb10b9f0f14962cdb129a9e9864ce86f61f NO candidate only; time identity/provenance must be verified
|
| 22 |
+
graph hash FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_raw/protein_complex_external/complexportal/SHA256_9606_LOCAL.txt eb78081531f21c0ed81948b9ad697519052bb089aefe28887d38a188549d21a2 NO candidate only; time identity/provenance must be verified
|
| 23 |
+
graph hash FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_raw/protein_complex_external/complexportal/SHA256_9606_REMOTE.txt ee88065272dc90ce16bbb0c597b85e3a5a74fa649d8b223555717de833ac6a14 NO candidate only; time identity/provenance must be verified
|
| 24 |
+
checkpoint FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/27_clinvar_gate/formal/C1_ParameterMatchedMLP/seed_2026/best.pt 5c5bd046e3f8d592dfe15cde245712ff1bf45381391038674cc1e528bd026fd6 NO candidate only; time identity/provenance must be verified
|
| 25 |
+
checkpoint FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/27_clinvar_gate/formal/C1_ParameterMatchedMLP/seed_3407/best.pt f65f41fcbf617c60cb9b348605ecab0aec0b174dc9edbb5955e0c81955d0b585 NO candidate only; time identity/provenance must be verified
|
| 26 |
+
checkpoint FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/27_clinvar_gate/formal/C1_ParameterMatchedMLP/seed_42/best.pt 425dea6a4971a6569870c7fb56b716ae05969f9a305693db1b83d320503935a4 NO candidate only; time identity/provenance must be verified
|
| 27 |
+
checkpoint FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/27_clinvar_gate/formal/C2_ShuffledGraph/seed_2026/best.pt 40c73f68b549642a9d4f92ef62d20c98a7e099f803004e2c15369ab93b175671 NO candidate only; time identity/provenance must be verified
|
| 28 |
+
checkpoint FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/27_clinvar_gate/formal/C2_ShuffledGraph/seed_3407/best.pt 2eee51d941609dfa61472a144ac6947c01c0d0039be150e1ee16bb3ac1a382a1 NO candidate only; time identity/provenance must be verified
|
| 29 |
+
graph embedding array FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_graph_residual_esm2_v2/scripts/evaluate_clinvar_residual_v2.py dcf4df2cb71ae5487556659f19db5c8dc311f23d35cee0ad133ae513eef069f5 NO candidate only; time identity/provenance must be verified
|
| 30 |
+
graph embedding array FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/graph_residual_ptm_mamba/configs/clinvar.yaml 86716d807ffb55acde9a5d4899f5b9dbf2d137b5465d0da806388f467deca7d0 NO candidate only; time identity/provenance must be verified
|
| 31 |
+
graph embedding array FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/graph_residual_ptm_mamba/gr_ptm_mamba/clinvar/__init__.py 42f8184e83b5d97b7fb5a2c2996943fd13cc4e93f7673bbd7a00126350a77107 NO candidate only; time identity/provenance must be verified
|
| 32 |
+
graph embedding array FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/graph_residual_ptm_mamba/gr_ptm_mamba/clinvar/model.py 39c2b90853571ffe781fcfcf8aab000b2aa21d20985c1db3c096c7a303c40c6a NO candidate only; time identity/provenance must be verified
|
| 33 |
+
graph embedding array FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/graph_residual_ptm_mamba/scripts/evaluate_clinvar.py eaceb95b12f6982583a3f5125862f5f2d75ca0a5952b92143780b46e4b6659b0 NO candidate only; time identity/provenance must be verified
|
| 34 |
+
training config FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/graph_residual_ptm_mamba/configs/clinvar.yaml 86716d807ffb55acde9a5d4899f5b9dbf2d137b5465d0da806388f467deca7d0 NO candidate only; time identity/provenance must be verified
|
| 35 |
+
training config FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/27_clinvar_gate/acceptance_report.json 7f4ed4b19470cdedfb31fff0d205512a886df4b2e6819a2d192da3be939de8b3 NO candidate only; time identity/provenance must be verified
|
| 36 |
+
training config FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/27_clinvar_gate/formal/C1_ParameterMatchedMLP/seed_2026/run_summary.json 7c93de108975dcd091e4c86e77d185e6e5a577be33b591be8d1ecd729bb0a175 NO candidate only; time identity/provenance must be verified
|
| 37 |
+
training config FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/27_clinvar_gate/formal/C1_ParameterMatchedMLP/seed_3407/run_summary.json 9cacd71f6d432db6abbfbe19b3f1c2be39a620f78fe89ef99210077e358fbe32 NO candidate only; time identity/provenance must be verified
|
| 38 |
+
training config FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/27_clinvar_gate/formal/C1_ParameterMatchedMLP/seed_42/run_summary.json 0459d6fe425686f53518f06655bc2f9c54b3c46f5863ba3e9063a6062a9c3508 NO candidate only; time identity/provenance must be verified
|
| 39 |
+
seed FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/graph_residual_ptm_mamba/configs/clinvar.yaml 86716d807ffb55acde9a5d4899f5b9dbf2d137b5465d0da806388f467deca7d0 NO candidate only; time identity/provenance must be verified
|
| 40 |
+
seed FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/27_clinvar_gate/formal/C1_ParameterMatchedMLP/seed_2026/FORMAL_PASS.flag 7c93de108975dcd091e4c86e77d185e6e5a577be33b591be8d1ecd729bb0a175 NO candidate only; time identity/provenance must be verified
|
| 41 |
+
seed FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/27_clinvar_gate/formal/C1_ParameterMatchedMLP/seed_2026/best.pt 5c5bd046e3f8d592dfe15cde245712ff1bf45381391038674cc1e528bd026fd6 NO candidate only; time identity/provenance must be verified
|
| 42 |
+
seed FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/27_clinvar_gate/formal/C1_ParameterMatchedMLP/seed_2026/history.tsv 97555dab19e2988bbdb3d402c202e280f53cb6bb90b114b2d6c0d4598adae7ff NO candidate only; time identity/provenance must be verified
|
| 43 |
+
seed FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/27_clinvar_gate/formal/C1_ParameterMatchedMLP/seed_2026/metrics.tsv 9f322d0d1003b7fe73319aa0ac024b5fc5d8c7147e31a5dbfed50401e0ecd970 NO candidate only; time identity/provenance must be verified
|
| 44 |
+
split ledger FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_benchmark/clinvar_pathogenicity/reports/split_integrity.tsv 4158970bcc36c03460461d7331deab8520a1a2d59220ca65447cc7039bf4c3b2 NO candidate only; time identity/provenance must be verified
|
| 45 |
+
split ledger FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_benchmark/clinvar_pathogenicity/splits_by_gene.tsv d46ba835256a66b9496c2a842210f718d5ce4610a0e445c309f353b25724b756 NO candidate only; time identity/provenance must be verified
|
| 46 |
+
split ledger FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_benchmark/clinvar_pathogenicity/splits_by_protein.tsv bf8dd1ed0c8d6813f65b6acfbefddede8e40b45b451fb0bf118d701a7d7f04c7 NO candidate only; time identity/provenance must be verified
|
| 47 |
+
split ledger FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/L1B_ptm_context_clinvar_v1/assets/clinvar_test_split_manifest.tsv 4b2f888c24aa759bea0ca76bc6810bf0e802f4c3158aea28c6f2c8890dd10b2d NO candidate only; time identity/provenance must be verified
|
| 48 |
+
split ledger FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_L1B_PTMContextClinVar_verified_20260810/L1B_ptm_context_clinvar_v1/assets/clinvar_test_split_manifest.tsv 4b2f888c24aa759bea0ca76bc6810bf0e802f4c3158aea28c6f2c8890dd10b2d NO candidate only; time identity/provenance must be verified
|
| 49 |
+
exclusion ledger FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/model_benchmark_v6/graph_residual_ptm_mamba/audit/clinvar_leakage_report.tsv 5a119a86b4dfe01851c78fe44469f4dc3ee05aea9c9800652417f5ad1c9f9309 NO candidate only; time identity/provenance must be verified
|
| 50 |
+
exclusion ledger FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_other_results_figures_verified_20260809/work/model_benchmark_v6/graph_residual_ptm_mamba/audit/clinvar_leakage_report.tsv 5a119a86b4dfe01851c78fe44469f4dc3ee05aea9c9800652417f5ad1c9f9309 NO candidate only; time identity/provenance must be verified
|
| 51 |
+
exclusion ledger FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_benchmark/mutation_ptm/reports/leakage_check.tsv 86bd19f19d2a9cd4a9f10f0eb594b49a7428e1aaebb38a270e59f335b0f360f0 NO candidate only; time identity/provenance must be verified
|
| 52 |
+
exclusion ledger FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_gcl/relation_mask_forward.py b61c8994671f0095bd8be005ceabe861355514e765d5c7e35a059387dbd46b21 NO candidate only; time identity/provenance must be verified
|
| 53 |
+
exclusion ledger FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/02_official_baseline/protocols/fixed_validation_mask.tsv.gz 4b366269483830c81b42b26c7599d4236a0d7bcb3856fc8ada590c65c949c4b6 NO candidate only; time identity/provenance must be verified
|
| 54 |
+
leakage audit output FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/L1B_ptm_context_clinvar_v1/audit/acceptance_checks.tsv b1ac44b2bfde335aded461eef6e8926c3d8e2ce2772e0d27cb171bbd9b251c22 NO candidate only; time identity/provenance must be verified
|
| 55 |
+
leakage audit output FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/L1B_ptm_context_clinvar_v1/audit/context_feature_lineage.tsv 9364a38bb104be05b835e4bd738fdd9fe60d9e82564c31a2c4cd90e8b6440ac0 NO candidate only; time identity/provenance must be verified
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| 56 |
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leakage audit output FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/L1B_ptm_context_clinvar_v1/audit/data_readiness.tsv e32e18e47543557e583b4342d88e4dd809eb2e0ee6c8f96f36115d232e6bab18 NO candidate only; time identity/provenance must be verified
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| 57 |
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leakage audit output FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/L1B_ptm_context_clinvar_v1/audit/mutation_reference_validation.tsv 736143cdc46798efd2d859ec06da1d9f7b784e41a534b5564ebc4517e090b2c7 NO candidate only; time identity/provenance must be verified
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| 58 |
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leakage audit output FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/model_benchmark_v6/graph_residual_ptm_mamba/audit/clinvar_leakage_report.tsv 5a119a86b4dfe01851c78fe44469f4dc3ee05aea9c9800652417f5ad1c9f9309 NO candidate only; time identity/provenance must be verified
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provenance manifest FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/ptm_context_clinvar/augment_l1b_manifest.py 24ce4ce3833d3264c92bfd455fc44ef5ca6f8c35445747da9422b44bb5fdb693 NO candidate only; time identity/provenance must be verified
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| 60 |
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provenance manifest FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/L1B_ptm_context_clinvar_v1/assets/clinvar_prediction_manifest.tsv 0c95fbf4462c0ec4061b29db0557089ba903643f4bb55f99dd5c056f107486de NO candidate only; time identity/provenance must be verified
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| 61 |
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provenance manifest FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/L1B_ptm_context_clinvar_v1/assets/clinvar_test_split_manifest.tsv 4b2f888c24aa759bea0ca76bc6810bf0e802f4c3158aea28c6f2c8890dd10b2d NO candidate only; time identity/provenance must be verified
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| 62 |
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provenance manifest FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_L1B_PTMContextClinVar_verified_20260810/L1B_ptm_context_clinvar_v1/assets/clinvar_prediction_manifest.tsv 0c95fbf4462c0ec4061b29db0557089ba903643f4bb55f99dd5c056f107486de NO candidate only; time identity/provenance must be verified
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| 63 |
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provenance manifest FOUND /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_L1B_PTMContextClinVar_verified_20260810/L1B_ptm_context_clinvar_v1/assets/clinvar_test_split_manifest.tsv 4b2f888c24aa759bea0ca76bc6810bf0e802f4c3158aea28c6f2c8890dd10b2d NO candidate only; time identity/provenance must be verified
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initial_data/clinvar_strict_rebuild_v1/00_provenance/node_inductive_feasibility.md
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# Node-inductive ClinVar feasibility
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## Conclusion
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**SUPPORTED**
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Conclusion from Python implementation evidence; no proposed capability was treated as existing.
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| Signal | Evidence |
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|---|---|
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| lookup | /root/autodl-tmp/bio/disease_mutation_ptm_gcl/backups/code_before_core_adapt_20260716_023809/train_contrastive.py:45 ure self.embeddings = nn.ModuleDict( {node_type: nn.Embedding(count, hidden_dim) for node_type, count in node_counts.items()} ) self.self_linears = nn.ModuleList( [nn.ModuleDict({nt: nn.Linear(; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_raw/amplify/AMPLIFY_120M/amplify.py:222 module.bias.data.zero_() elif isinstance(module, nn.Embedding): module.weight.data.uniform_(-self.config.embedding_init_range, self.config.embedding_init_range) class AMPLIFY(AMPLIFYPreTrainedModel): """; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_gcl/train_contrastive.py:32 __() self.embeddings = nn.ModuleDict({ node_type: nn.Embedding(count, hidden_dim, sparse=True) for node_type, count in node_counts.items() }) self.relation_projection = nn.ModuleDict({ ; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_gcl/relation_mask_forward.py:115 ture self.embeddings = nn.ModuleDict({ node_type: nn.Embedding(count, hidden_dim) for node_type, count in node_counts.items() }) self.self_linears = nn.ModuleList([ nn.ModuleDict({nt; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_model_benchmark_v3/dmptm_benchmark/models/residual_v2_compat/data.py:7 s: def __init__(self,root): self.root=Path(root);g=self.root/"work/graph_embedding_assets_v1/embeddings";e=self.root/"work/esm2_only_v1/core_embeddings" self.graph={k:np.load(g/f"{k}_embeddings.npy",mmap_mode="r") for k in COUNTS};self.esm=; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_model_benchmark_v3/dmptm_benchmark/models/residual_v2_compat/exporting.py:7 ate_dict"]);model.eval();inputs=Inputs(root);m=pd.read_csv(root/"work/graph_embedding_assets_v1/node_id_mapping.tsv",sep="\t");m.to_csv(out/"embeddings/node_id_mapping.tsv",sep="\t",index=False);modes=[];checks=[] with torch.no_grad(): for ty; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_model_benchmark_v3/dmptm_benchmark/models/residual_v2_compat/training.py:32 "preserve_loss"]+residual_weight*row["residual_loss"] state={"model_state_dict":{k:v.detach().cpu() for k,v in model.state_dict().items()},"relations":relations,"config":{"beta_init":beta_init,"preserve_weight":preserve_weight,"residual_w; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_model_benchmark_v3/scripts/backupclinvar20260721.py:196 r, Representation] = {} status = [] graph_root = ROOT / "work/graph_embedding_assets_v1" try: graph = GraphRepresentation("esm2_original", graph_root) representations[graph.name] = graph status.append({"model"; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_model_benchmark_v3/scripts/diffusiontasks.py:244 dimension=640, ): super().__init__() self.token = nn.Embedding(VOCAB_SIZE, hidden, padding_idx=PAD_ID) self.position = nn.Parameter(torch.randn(1, WINDOW_LENGTH, hidden) * 0.02) self.ptm_type = nn.Embedding; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_model_benchmark_v3/scripts/evaluate_clinvar_all_models.py:202 r, Representation] = {} status = [] graph_root = ROOT / "work/graph_embedding_assets_v1" try: graph = GraphRepresentation("graph_pretrain_core_h64_v1", graph_root) representations[graph.name] = graph status.ap |
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| inductive | /root/autodl-tmp/bio/disease_mutation_ptm_gcl/backups/code_before_core_adapt_20260716_023809/train_contrastive.py:32 __init__( self, node_counts: dict[str, int], edge_index: dict[str, tuple[str, str, torch.Tensor]], hidden_dim: int = 256, layers: int = 2, dropout: float = 0.1, temperature: float = 0; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_gcl/build_graph.py:394 mat_version": 2, "node_counts": node_counts, "edge_index": graph_edges, "core_dir": str(core_dir.resolve()), "leakage_policy": {"forbidden_feature_tokens": list(LEAKAGE_TOKENS)}, }, ; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_gcl/train_contrastive.py:77 ropy(logits, labels) + F.cross_entropy(logits.T, labels)) def parse_neighbors(value: str) -> list[int]: values = [int(x) for x in value.replace(",", " ").split() if x] if not values or any(x <= 0 for x in values): raise ; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_gcl/visual.py:47 n_umap(X): reducer = umap.UMAP( n_components=2, n_neighbors=30, min_dist=0.2, metric="euclidean", random_state=42, ) return reducer.fit_transform(X) def plot_mutation_by_disease(top_k=; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_gcl/relation_mask_forward.py:4 e deliberately keeps the legacy cache-only PPI ranker separate from a message-passing encoder. ``None`` is the backward-compatible path; a mask is applied to edge_index before each graph forward and the context is recomputed. """ from __future_; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_model_benchmark_v3/dmptm_benchmark/downstream/clinvar_evaluator.py:11 ng_path: str | Path, mapping_path: str | Path, name: str = 'esm2_dapt_inductive'): self.name = name self.embedding_path = Path(embedding_path) self.mapping_path = Path(mapping_path) self.array = np.load(self; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_model_benchmark_v3/scripts/diseasetasks.py:191 "ontology subtree leakage gate failed") return frame def sample_neighbor_ids(disease: str, edge_path: Path, limit: int, seed: int): frame = pd.read_csv(edge_path, sep="\t") source, target = edge_columns(frame) direct = f; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_model_benchmark_v3/scripts/evaluate_disease_retrieval.py:203 , "gold_standard": "Disease Ontology top-level branch", "shared_graph_neighbors_used_as_gold": False, "storage_gate": gate, "models": sorted(table["model"].unique().tolist()) if len(table) else [], "elapsed_seconds": time.time() - started; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_model_benchmark_v3/scripts/train_disease_classifier.py:29 tomic_tsv, best_multilabel_threshold, build_labels, build_neighbor_means, disease_predict, make_splits, multilabel_metrics, ) from evaluate_clinvar_all_models import SEEDS, discover_representations, now, storage_ga; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_model_benchmark_v4/scripts/compare_dapt_mutation_ptm.py:12 riginal':V3/'esm2_original/representation_seed_42','esm2_dapt_clinvar_inductive':OUT/'esm2_dapt_clinvar_inductive/representation_seed_42','graph_residual_v2':V3/'graph_residual_v2/representation_seed_42'} SEEDS=[42,3407,2026] METRICS=['mrr |
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| fallback | /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_model_benchmark_v3/scripts/train_residual_v3.py:99 "} if not required.issubset(arrays): raise RuntimeError(f"missing embedding types: {sorted(required - set(arrays))}") return arrays @dataclass class Relation: name: str src_type: str dst_type: str train_src: np.nd; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_model_benchmark_v4/scripts/evaluate_dapt_mutation_ptm.py:282 benchmark_split"] = split excluded["exclusion_reason"] = "missing_dapt_embedding" excluded_parts.append(excluded) named_frames[split] = frame.loc[mask].reset_index(drop=True) train, validation, test = named_frames["t; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/zero_shot_mutation_ptm/build_n1_audit.py:132 _text(OUT/'audit/MUTATION_PTM_TARGET_BLIND_PASS.flag','graph_core has zero direct mutation-PTM target edges; graph_full benchmark edge file is excluded from Z1 lineage.\n') # 3. Freeze representation lineage and determine whether a fair common space exists. def sha; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_L1B_PTMContextClinVar_verified_20260810_prev2/code/finalize_l1b.py:29 ),('protein_group_split_confirmed',1),('mutation_reference_validation_zero_mismatch',1),('ptm_context_definitions_locked_before_scores',1),('graph_coverage_excludes_ClinVar_edges',1),('pathogenicity_label_derived_context',0),('original_threshold_unchanged',1),('retraining',0),('t; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_L1B_PTMContextClinVar_verified_20260810_prev2/code/enhance_readme.py:55 terpretation rule A positive point estimate with an interval crossing zero is only a suggestive context-dependent trend. If all strata are non-positive, the conclusion is a negative mechanism result: Graph-Residual does not gain from PTM/regulatory context on this ClinVar benchma; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_L1B_PTMContextClinVar_verified_20260810/code/finalize_l1b.py:29 ),('protein_group_split_confirmed',1),('mutation_reference_validation_zero_mismatch',1),('ptm_context_definitions_locked_before_scores',1),('graph_coverage_excludes_ClinVar_edges',1),('pathogenicity_label_derived_context',0),('original_threshold_unchanged',1),('retraining',0),('t; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_L1B_PTMContextClinVar_verified_20260810/code/enhance_readme.py:55 terpretation rule A positive point estimate with an interval crossing zero is only a suggestive context-dependent trend. If all strata are non-positive, the conclusion is a negative mechanism result: Graph-Residual does not gain from PTM/regulatory context on this ClinVar benchma; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/disease_conditioned_ppi_train.py:502 ", 0.0) > 0.0 required = [checks["F0_FrozenProbe"]["backbone_grad_zero"], checks["F3_GraphResidual"]["graph_adapter_grad_positive"], checks["F2_LoRAFineTuning"]["lora_grad_positive"], checks["F1_FullFineTuning"]["backbone_grad_positive"]] status = all(required) a; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/finalize_m6_m8_summary.py:26 as a positive C≥2 versus C≤1 contrast with a bootstrap interval above zero. R2 contains no observations at C≥2, so that contrast is not estimable. R4 is positive, but its Holm-adjusted evidence is not decisive. Degree-adjusted and degree-matched outputs are reported separately.\n; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/scripts/step3_graph_adaptation.py:176 def _degree_bin_permutation(self) -> np.ndarray: degree = np.zeros(len(self.graph["protein"]), dtype=np.int64) for name, array in self.train_edges.items(): protein_column = 1 if name == "mutation_on_protein" else 0 |
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| projection | /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_model_benchmark_v4/scripts/evaluate_unified_rankers.py:202 g={'status':'LOCKED','models':['esm2_original_corrected','esm2_dapt','graph_residual_esm2_v2'],'main_features':'[h_mut,h_ptm,abs(h_mut-h_ptm),h_mut*h_ptm]','supplement':'main features plus log-normalized sequence distance','projection_dimension':128,'loss':'pairwise BPR treating ; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/scripts/save_best_residual_checkpoint.py:11 ate_dict(),"scalar") path=root/"work/graph_esm2_fusion_diagnostics_v2/residual_fusion/best_residual_scalar_protein.pt"; torch.save({"model_state_dict":{k:v.detach().cpu() for k,v in model.state_dict().items()},"beta_type":"scalar","threshold":th; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/zero_shot_mutation_ptm/build_n1_audit.py:150 LIFY residue/window assets are incomplete for the benchmark, while Z1 graph mutation/PTM assets are 64-D graph space. No projection/alignment or new training was allowed.','target_graph_leakage':'PASS on graph_core; direct graph_full benchmark edge excluded from Z1'},ensure_ascii; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/graph_residual_ptm_mamba/gr_ptm_mamba/adapter/fusion.py:39 kind: nn.Sequential( nn.Linear(self.graph_dim, projection_dim), nn.LayerNorm(projection_dim), nn.GELU(), nn.Dropout(dropout), nn.Linear(p; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/graph_residual_ptm_mamba/scripts/summarize_results.py:150 oxes = [(0.03, "Frozen\nPTM-Mamba\n768-d", "#8ecae6"), (0.30, "Native graph\n64-d", "#90be6d"), (0.53, "Projection + gate\nresidual <= 0.25", "#f9c74f"), (0.79, "Task head\nclassification/ranking", "#f9844a")] for x, text, color in boxes: ax.add_patch(plt.Rectangle((x, ; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/scripts/step3_graph_adaptation.py:102 be on comparable scales: legacy P0 norms are ~842, # whereas graph projections are ~3, which previously saturated the gate. sequence_unit = F.normalize(sequence, dim=-1) graph_unit = F.normalize(protein_graph, dim=-1) ; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/scripts/run_step4_unsupervised.py:326 e.max()), "residual_norm_mean": float(residual_norm.mean()), "graph_projection_norm_mean": float(graph_norm.mean()), "sequence_norm_mean": float(sequence_norm.mean()), "residual_to_sequence_norm_ratio": float((residual_nor; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/scripts/run_embedding_pipeline_audit.py:183 pe(np.float16), "residual": residual_all.astype(np.float32), "graph_projection": graph_all.astype(np.float32), "gate": gate_all, "pre_normalization": pre_all.astype(np.float32), "graph_input": graph_inputs, } def fuse_from_g; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/scripts/run_supervised_gate_summary.py:234 (diff) comparisons.append({"task":task,"comparison":f"F3_GraphResidual-minus-{baseline}","delta":mcc_from_confusion(scores["F3_GraphResidual"])-mcc_from_confusion(scores[baseline]),"bootstrap_mean":mean,"ci_low":lo,"ci_high":hi,"raw_p_value":pvalue_two_sided(diff),"bootstrap_unit; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/zero_shot_ppi_retrieval/task_u1_zero_shot_ppi.py:795 I label在什么时候被读取？", "U0是什么？", "U1是什么？", "U1训练时是否使用PPI？", "core Graph是否包含PPI？", "是否使用PPI supervised F3 checkpoint？", "是否训练projection？", "是否训练ranker？", "是否训练alignment？", "主similarity是什么？", "为什么固定cosine？", "benchmark来自哪里？", "candidate pools来自哪里？", "U0/U1 protein universe是否一致？", |
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A lookup-table-only representation cannot create a graph residual for a protein absent from graph pretraining. A zero vector fallback is not true node-inductive encoding.
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No training or embedding regeneration was performed.
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CLINVAR_STRICT_REBUILD_DECISION.md f4740f786519d916ccc6adfb974c4982d19e03054202411b2ce8adb2e5756c94
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CLINVAR_STRICT_REBUILD_FEASIBILITY.tsv 19cfbd6cff42ea1ae1049fe42552aba6a94a7536d8031e3f1dce3800b15dbca8
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G1_removal_policy.tsv 18149f149471755d4e296a9229140721bdee7c2b877c99067bbc971628e65f3c
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G2_policy_options.tsv 7f6f08d5026c736fbee111db7e25305c323badc33b578b2f3a6c6f65004fff2e
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PHASE1_MISSING_FILES.tsv d71dc9123c215b0d7532e562da8cd3ff60dfd991530b235fe77473195a9de7c5
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clinvar_label_definition.md bcdf12bdb3c31efcab41b63dbd001ae1d8a8f347d8c341ea6f5fa798a5e3eff5
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clinvar_relation_risk_audit.tsv 3ea2e3724f3a6a43df7557eba5079ee5e6e47791a3677677b071d7957a1f3969
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clinvar_split_manifest.tsv 1d44179216a223f67fb7eacf6be37ac0108e7d12f9f503b9c0c0bdabf3af6103
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historical_clinvar_asset_recovery.tsv 59b80e7135dd84769452fee0e52c2308d089db7099ec1bfd79f2bd2926a364c0
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node_inductive_feasibility.md fd4d42a4fdf5d159606cd66417bc20965c271dd0480d264d70a0c61e6e45e164
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node_mapping_manifest.tsv c2be651ef9e79f1d9e3b8e14a3207e4559147e2caad6d353316454029481c419
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relation_catalog.tsv cce7637b263ba7d5c7fbd4ee1eda79c3faee910a8a2a6cc61828837dc9050e89
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variant_alias_map.tsv 461556f388345455d82c03bc9aa54462c9b54ddcfdda13b00226d6bc42afbc3e
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disease /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_processed/nodes_disease.tsv YES 5146889 d3254f4d51516343b5639ded1ae712966273684090c29f68399de646cdac3a1c
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| 3 |
+
mutation /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_processed/nodes_mutation.tsv YES 369185068 f2e791e20d83876a084ecca0f96fb8518b75d8573b12bd1d0cadc767ea8c1916
|
| 4 |
+
protein /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_processed/nodes_protein.tsv YES 1865668 ab925d979444e1934e974cab9a0ffaadaf4bd4017dff9989fdcc2eea85e5a743
|
| 5 |
+
ptm /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_processed/nodes_ptm.tsv YES 14748172 7bb9a52ceea0f3388b18e2ff4dee5ce51a540280c4a2ec84ea002e3e26e6526e
|
| 6 |
+
pathway /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_processed/nodes_pathway.tsv YES 274522 edaaeaf34d9e4f44c6314dff5e777816348bdcda284eeaea8b2604c867bcbb2a
|
| 7 |
+
disease_mutation /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_processed/edges_disease_mutation.tsv YES 287758508 52d61fc136f9943aa40ae0b07f3814f744e77e4660c31549405d8f643066374a
|
| 8 |
+
disease_protein /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_processed/edges_disease_protein.tsv YES 30222403 766b8a67d7d588132616e70f27cf0575e728773b0a79d8bd25a2e0e4c7631956
|
| 9 |
+
disease_ptm /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_processed/edges_disease_ptm.tsv YES 28786247 1aee2897376814133d9623511365a825c0e241045cb701baec11d046aebd9f73
|
| 10 |
+
mutation_protein /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_processed/edges_mutation_protein.tsv YES 302763621 f3e7fc53bd63a11324d69c9d187595bd5ecc94ab2822f69a79a7407f01a8fe0d
|
| 11 |
+
protein_pathway /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_processed/edges_protein_pathway.tsv YES 7374777 f9448f7f9891ea007ea23aeb5ea9e9bbf2d9b81e996650b0d9c168e840188ec3
|
| 12 |
+
protein_ptm /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_processed/edges_protein_ptm.tsv YES 15334385 e2ad3aa2302bdaf2f4c4af61afaced36126037235af25e5b0478479ee476172c
|
initial_data/clinvar_strict_rebuild_v1/02_splits/label_policy.yaml
ADDED
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@@ -0,0 +1,13 @@
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| 1 |
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# Frozen from Phase 1 clinvar_label_definition.md and observed implementation evidence.
|
| 2 |
+
version: clinvar_strict_rebuild_v1
|
| 3 |
+
included_labels:
|
| 4 |
+
positive: [pathogenic, likely pathogenic]
|
| 5 |
+
negative: [benign, likely benign]
|
| 6 |
+
excluded_labels: [conflicting, uncertain, reference mismatch, out-of-range, missing, other]
|
| 7 |
+
reference_mismatch_rule: exclude when reference_aa is present and disagrees with mapped protein sequence at 1-based mutation_position
|
| 8 |
+
out_of_range_rule: exclude when mutation_position is absent, non-integer, below 1, or greater than mapped sequence length
|
| 9 |
+
representation_validity_filtering: exclude missing protein mapping, invalid position, missing alternate allele, and unsupported multiallelic encodings
|
| 10 |
+
multiallelic_handling: exclude alternate values containing comma, semicolon, or pipe; no decomposition or resampling
|
| 11 |
+
protein_mapping_rule: use the exact protein_id/uniprot_id mapping observed in Phase 1; PROT: prefix alias is representation-only
|
| 12 |
+
formal_split_modification: forbidden
|
| 13 |
+
source_evidence: 00_provenance/clinvar_label_definition.md
|
initial_data/clinvar_strict_rebuild_v1/02_splits/label_policy_source_sha256.txt
ADDED
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@@ -0,0 +1 @@
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| 1 |
+
bcdf12bdb3c31efcab41b63dbd001ae1d8a8f347d8c341ea6f5fa798a5e3eff5
|
initial_data/clinvar_strict_rebuild_v1/02_splits/test_effective.tsv
ADDED
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The diff for this file is too large to render.
See raw diff
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initial_data/clinvar_strict_rebuild_v1/02_splits/test_formal.tsv
ADDED
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The diff for this file is too large to render.
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initial_data/clinvar_strict_rebuild_v1/02_splits/train.tsv
ADDED
|
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|
| 1 |
+
stable_id variant_id mutation_id protein_id label label_class representation_valid exclusion_reason source_file
|
initial_data/clinvar_strict_rebuild_v1/02_splits/validation.tsv
ADDED
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The diff for this file is too large to render.
See raw diff
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initial_data/clinvar_strict_rebuild_v1/03_mappings/node_mapping_manifest.tsv
ADDED
|
The diff for this file is too large to render.
See raw diff
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initial_data/clinvar_strict_rebuild_v1/03_mappings/test_cohort_aliases.tsv
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
initial_data/clinvar_strict_rebuild_v1/04_relation_catalog/clinvar_relation_risk_audit.tsv
ADDED
|
@@ -0,0 +1,131 @@
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|
| 1 |
+
relation_or_path risk_level reason n_test_entities_affected candidate_for_G1_removal candidate_for_G2_removal evidence_source
|
| 2 |
+
10 HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/reviewer1_revision/m4_method_reproducibility/graph_relation_inventory.tsv; relation_catalog.tsv
|
| 3 |
+
11 HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/reviewer1_revision/m4_method_reproducibility/graph_relation_inventory.tsv; relation_catalog.tsv
|
| 4 |
+
6 HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m4_method_reproducibility/graph_relation_inventory.tsv; relation_catalog.tsv
|
| 5 |
+
7 HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m4_method_reproducibility/graph_relation_inventory.tsv; relation_catalog.tsv
|
| 6 |
+
EXPLICIT_CLINVAR_OR_CLASS_LABEL HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/run_clinvar_raw_graph_audit.py; relation_catalog.tsv
|
| 7 |
+
Task38_disease_protein_provenance HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/zero_shot_nonppi/run_n2_u4_nonppi.py; relation_catalog.tsv
|
| 8 |
+
U1_DiseasePermutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_representation_interpretability/zero_shot_disease_similarity/u2_zero_shot_disease_similarity.py; relation_catalog.tsv
|
| 9 |
+
all_model_clinvar_comparison HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 10 |
+
associated_with_mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_processed/edges_disease_mutation.tsv; relation_catalog.tsv
|
| 11 |
+
associated_with_mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_processed_clean/edges_disease_mutation.tsv; relation_catalog.tsv
|
| 12 |
+
associated_with_mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_processed_core/edges_disease_mutation.tsv; relation_catalog.tsv
|
| 13 |
+
associated_with_protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_processed/edges_disease_protein.tsv; relation_catalog.tsv
|
| 14 |
+
associated_with_protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_processed_clean/edges_disease_protein.tsv; relation_catalog.tsv
|
| 15 |
+
associated_with_protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_processed_core/edges_disease_protein.tsv; relation_catalog.tsv
|
| 16 |
+
audit/DISEASE_MUTATION_TARGET_BLIND_PASS.flag HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/disease_mutation_ranking/task43_core.py; relation_catalog.tsv
|
| 17 |
+
bootstrap_iid HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 18 |
+
bootstrap_protein_grouped HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 19 |
+
cached_disease_feature HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/43_disease_mutation_ranking_v1/benchmark/LOCKED_DISEASE_MUTATION_RANKING_v1/S2_mutation_disjoint/target_lineage_manifest.tsv.gz; relation_catalog.tsv
|
| 20 |
+
cached_disease_feature HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/43_disease_mutation_ranking_v1/benchmark/LOCKED_DISEASE_MUTATION_RANKING_v1/S3_protein_disjoint/target_lineage_manifest.tsv.gz; relation_catalog.tsv
|
| 21 |
+
cached_disease_feature HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_other_results_figures_verified_20260809/work/amplify_generalization/43_disease_mutation_ranking_v1/benchmark/LOCKED_DISEASE_MUTATION_RANKING_v1/S2_mutation_disjoint/target_lineage_manifest.tsv.gz; relation_catalog.tsv
|
| 22 |
+
cached_disease_feature HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_other_results_figures_verified_20260809/work/amplify_generalization/43_disease_mutation_ranking_v1/benchmark/LOCKED_DISEASE_MUTATION_RANKING_v1/S3_protein_disjoint/target_lineage_manifest.tsv.gz; relation_catalog.tsv
|
| 23 |
+
classifier_search HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 24 |
+
common_intersection_coverage HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 25 |
+
data_processed/edges_disease_protein.tsv HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/zero_shot_nonppi/run_n2_u4_nonppi.py; relation_catalog.tsv
|
| 26 |
+
data_processed_clean/edges_disease_protein.tsv HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/mechanism_deep/run_mechanism_deep.py; relation_catalog.tsv
|
| 27 |
+
data_processed_core/edges_disease_protein.tsv HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/zero_shot_nonppi/run_n2_u4_nonppi.py; relation_catalog.tsv
|
| 28 |
+
disease-mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/scripts/run_clinvar_gate.py; relation_catalog.tsv
|
| 29 |
+
disease-mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/relation_ablation_results.csv; relation_catalog.tsv
|
| 30 |
+
disease-mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/scripts/m5_finalize_server.py; relation_catalog.tsv
|
| 31 |
+
disease-protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/relation_ablation_results.csv; relation_catalog.tsv
|
| 32 |
+
disease-protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/scripts/m5_finalize_server.py; relation_catalog.tsv
|
| 33 |
+
disease__has_mutation__mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/ppi_partner_ranking_refinement/stage1_analysis_audit.py; relation_catalog.tsv
|
| 34 |
+
disease__has_mutation__mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/scripts/run_step1_data_graph_protocol.py; relation_catalog.tsv
|
| 35 |
+
disease__has_mutation__mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_gcl/relation_mask_forward.py; relation_catalog.tsv
|
| 36 |
+
disease__has_mutation__mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/scripts/build_i1_a1_patch.py; relation_catalog.tsv
|
| 37 |
+
disease__has_mutation__mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/00_protocols/graph_relation_manifest.tsv; relation_catalog.tsv
|
| 38 |
+
disease__has_mutation__mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/U1_zero_shot_ppi_retrieval_v1/audit/core_graph_ppi_leakage.tsv; relation_catalog.tsv
|
| 39 |
+
disease__has_mutation__mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_representation_interpretability/FINAL_verified/U1_zero_shot_ppi/audit/core_graph_ppi_leakage.tsv; relation_catalog.tsv
|
| 40 |
+
disease__has_mutation__mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/graph_core/edge_statistics.tsv; relation_catalog.tsv
|
| 41 |
+
disease__has_mutation__mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/graph_core/relation_mappings/relations.tsv; relation_catalog.tsv
|
| 42 |
+
disease__has_mutation__mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_other_results_figures_verified_20260809/work/amplify_generalization/00_protocols/graph_relation_manifest.tsv; relation_catalog.tsv
|
| 43 |
+
disease__has_mutation__mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 44 |
+
disease__has_mutation__mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/run_clinvar_raw_graph_audit.py; relation_catalog.tsv
|
| 45 |
+
disease__has_mutation__mutation.tsv HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/scripts/downstream_retrieval_visuals.py; relation_catalog.tsv
|
| 46 |
+
disease__has_mutation__mutation.tsv HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/scripts/downstream_soft_relevance_single_figures.py; relation_catalog.tsv
|
| 47 |
+
disease__has_protein__protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/ppi_partner_ranking_refinement/stage1_analysis_audit.py; relation_catalog.tsv
|
| 48 |
+
disease__has_protein__protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/scripts/run_step1_data_graph_protocol.py; relation_catalog.tsv
|
| 49 |
+
disease__has_protein__protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/00_protocols/graph_relation_manifest.tsv; relation_catalog.tsv
|
| 50 |
+
disease__has_protein__protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/U1_zero_shot_ppi_retrieval_v1/audit/core_graph_ppi_leakage.tsv; relation_catalog.tsv
|
| 51 |
+
disease__has_protein__protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_representation_interpretability/FINAL_verified/U1_zero_shot_ppi/audit/core_graph_ppi_leakage.tsv; relation_catalog.tsv
|
| 52 |
+
disease__has_protein__protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/graph_core/edge_statistics.tsv; relation_catalog.tsv
|
| 53 |
+
disease__has_protein__protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/graph_core/relation_mappings/relations.tsv; relation_catalog.tsv
|
| 54 |
+
disease__has_protein__protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_other_results_figures_verified_20260809/work/amplify_generalization/00_protocols/graph_relation_manifest.tsv; relation_catalog.tsv
|
| 55 |
+
disease__has_protein__protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 56 |
+
disease__has_protein__protein.tsv.gz HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/scripts/run_step2_p0_baseline.py; relation_catalog.tsv
|
| 57 |
+
disease_gene_reactome HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/backups/code_before_core_adapt_20260716_023809/build_graph.py; relation_catalog.tsv
|
| 58 |
+
disease_gene_reactome HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_gcl/build_graph.py; relation_catalog.tsv
|
| 59 |
+
disease_mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/disease_mutation_ranking/task43_core.py; relation_catalog.tsv
|
| 60 |
+
disease_mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/ppi_partner_ranking_deep/deep_ablation_v2.py; relation_catalog.tsv
|
| 61 |
+
disease_mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/scripts/build_core_dataset.py; relation_catalog.tsv
|
| 62 |
+
disease_mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/43_disease_mutation_ranking_v1/audit/graph_relation_manifest.tsv; relation_catalog.tsv
|
| 63 |
+
disease_mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_other_results_figures_verified_20260809/work/amplify_generalization/43_disease_mutation_ranking_v1/audit/graph_relation_manifest.tsv; relation_catalog.tsv
|
| 64 |
+
disease_mutation_ptm HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 65 |
+
disease_mutation_ptm_gcl/work/amplify_generalization/28_ppi_gate/source_esm_protocol/protocols/sequence_cluster_disjoint_candidate_pool.tsv.gz HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m6_statistical_evidence/rescue_v3/scripts/reconstruct_m6_v3.py; relation_catalog.tsv
|
| 66 |
+
disease_mutation_ptm_gcl/work/amplify_generalization/33_ppi_selective_graph_residual_v1/bootstrap/paired_grouped_bootstrap.tsv HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m6_statistical_evidence/rescue_v2/scripts/run_m6_rescue_v2.py; relation_catalog.tsv
|
| 67 |
+
disease_mutation_ptm_gcl/work/amplify_generalization/33_ppi_selective_graph_residual_v1/figures/bootstrap_graph_controls_figure_data.tsv HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m6_statistical_evidence/rescue_v2/scripts/run_m6_rescue_v2.py; relation_catalog.tsv
|
| 68 |
+
disease_mutation_ptm_gcl/work/amplify_generalization/43_disease_mutation_ranking_v1/formal/S4_sequence_cluster_disjoint/F3_GraphResidual/seed_42/metrics.tsv HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m6_statistical_evidence/rescue_v2/scripts/run_m6_rescue_v2.py; relation_catalog.tsv
|
| 69 |
+
disease_mutation_ptm_gcl/work/graph_esm2_residual_pretrain_v2/embeddings/node_id_mapping.tsv HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m6_statistical_evidence/rescue_v3/scripts/reconstruct_m6_v3.py; relation_catalog.tsv
|
| 70 |
+
disease_mutation_ptm_gcl/work/graph_esm2_residual_pretrain_v2/embeddings/protein_residual_embeddings.npy HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m6_statistical_evidence/rescue_v3/scripts/reconstruct_m6_v3.py; relation_catalog.tsv
|
| 71 |
+
disease_protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/disease_mutation_ranking/task43_core.py; relation_catalog.tsv
|
| 72 |
+
disease_protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/ppi_partner_ranking_deep/deep_ablation_v2.py; relation_catalog.tsv
|
| 73 |
+
disease_protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/scripts/build_core_dataset.py; relation_catalog.tsv
|
| 74 |
+
disease_protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/43_disease_mutation_ranking_v1/audit/graph_relation_manifest.tsv; relation_catalog.tsv
|
| 75 |
+
disease_protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_other_results_figures_verified_20260809/work/amplify_generalization/43_disease_mutation_ranking_v1/audit/graph_relation_manifest.tsv; relation_catalog.tsv
|
| 76 |
+
disease_protein_counts.tsv HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/disease_conditioned_ppi_audit.py; relation_catalog.tsv
|
| 77 |
+
disease_protein_matched HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/reviewer1_revision/m6_statistical_evidence/rescue_v2/scripts/run_m6_rescue_v2.py; relation_catalog.tsv
|
| 78 |
+
disease_protein_nodes HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/ppi_partner_ranking_refinement/stage1_analysis_audit.py; relation_catalog.tsv
|
| 79 |
+
disease_protein_provenance_audit HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/zero_shot_nonppi/run_n2_u4_nonppi.py; relation_catalog.tsv
|
| 80 |
+
edges/disease__has_protein__protein.tsv.gz HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/ppi_network_completion/task42_core.py; relation_catalog.tsv
|
| 81 |
+
edges/disease__has_protein__protein.tsv.gz HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/zero_shot_ppi_retrieval/task_u1_zero_shot_ppi.py; relation_catalog.tsv
|
| 82 |
+
edges/disease__has_protein__protein.tsv.gz HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_representation_interpretability/zero_shot_disease_similarity/u2_zero_shot_disease_similarity.py; relation_catalog.tsv
|
| 83 |
+
edges_disease_mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/scripts/preprocess_extra_data.py; relation_catalog.tsv
|
| 84 |
+
edges_disease_mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 85 |
+
edges_disease_mutation.tsv HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/scripts/preprocess_extra_data.py; relation_catalog.tsv
|
| 86 |
+
edges_disease_protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/scripts/preprocess_extra_data.py; relation_catalog.tsv
|
| 87 |
+
edges_disease_protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 88 |
+
edges_disease_protein.tsv HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/scripts/preprocess_extra_data.py; relation_catalog.tsv
|
| 89 |
+
edges_mutation_protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 90 |
+
excluded_missing_prott5 HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 91 |
+
excluded_missing_ptm_mamba HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 92 |
+
feasibility/disease_protein_provenance.tsv.gz HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/disease_core_module_prioritization/task41_pipeline.py; relation_catalog.tsv
|
| 93 |
+
graph_core_disease_protein_pairs HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/zero_shot_nonppi/run_n2_u4_nonppi.py; relation_catalog.tsv
|
| 94 |
+
graph_core_serialized_disease_protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/zero_shot_nonppi/run_n2_u4_nonppi.py; relation_catalog.tsv
|
| 95 |
+
has_mutation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/runs_v3/shuffle_integrity.tsv; relation_catalog.tsv
|
| 96 |
+
has_protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/runs_v3/shuffle_integrity.tsv; relation_catalog.tsv
|
| 97 |
+
model_availability HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 98 |
+
mutation;PTM;pathway (disease used only for candidate metadata) HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/42_ppi_network_completion_v1/audit/ppi_completion_target_blind.tsv; relation_catalog.tsv
|
| 99 |
+
mutation__rev_has_mutation__disease HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_gcl/relation_mask_forward.py; relation_catalog.tsv
|
| 100 |
+
mutation__rev_has_mutation__disease HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/graph_core/relation_mappings/relations.tsv; relation_catalog.tsv
|
| 101 |
+
mutation_disease_count HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/ptm_context_clinvar/run_l1b_ptm_context.py; relation_catalog.tsv
|
| 102 |
+
mutation_disease_count HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_L1B_PTMContextClinVar_verified_20260810/code/run_l1b_ptm_context.py; relation_catalog.tsv
|
| 103 |
+
mutation_disease_count HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_L1B_PTMContextClinVar_verified_20260810_prev2/code/run_l1b_ptm_context.py; relation_catalog.tsv
|
| 104 |
+
mutation_ptm_labels_used HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/zero_shot_mutation_ptm/build_n1_audit.py; relation_catalog.tsv
|
| 105 |
+
physical_ppi HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/43_disease_mutation_ranking_v1/audit/graph_relation_manifest.tsv; relation_catalog.tsv
|
| 106 |
+
physical_ppi HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_other_results_figures_verified_20260809/work/amplify_generalization/43_disease_mutation_ranking_v1/audit/graph_relation_manifest.tsv; relation_catalog.tsv
|
| 107 |
+
positive_pairs/disease_mutation_ptm.tsv HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/backups/code_before_core_adapt_20260716_023809/train_contrastive.py; relation_catalog.tsv
|
| 108 |
+
positive_pairs/disease_mutation_ptm.tsv HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_gcl/export_tasks.py; relation_catalog.tsv
|
| 109 |
+
protein__rev_has_protein__disease HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/graph_core/relation_mappings/relations.tsv; relation_catalog.tsv
|
| 110 |
+
protein_disease_count HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/ptm_context_clinvar/run_l1b_ptm_context.py; relation_catalog.tsv
|
| 111 |
+
protein_disease_count HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_L1B_PTMContextClinVar_verified_20260810/code/run_l1b_ptm_context.py; relation_catalog.tsv
|
| 112 |
+
protein_disease_count HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_L1B_PTMContextClinVar_verified_20260810_prev2/code/run_l1b_ptm_context.py; relation_catalog.tsv
|
| 113 |
+
protein_pathway HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/43_disease_mutation_ranking_v1/audit/graph_relation_manifest.tsv; relation_catalog.tsv
|
| 114 |
+
protein_pathway HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_other_results_figures_verified_20260809/work/amplify_generalization/43_disease_mutation_ranking_v1/audit/graph_relation_manifest.tsv; relation_catalog.tsv
|
| 115 |
+
protein_ptm HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/43_disease_mutation_ranking_v1/audit/graph_relation_manifest.tsv; relation_catalog.tsv
|
| 116 |
+
protein_ptm HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/transfer/AMPLIFY_other_results_figures_verified_20260809/work/amplify_generalization/43_disease_mutation_ranking_v1/audit/graph_relation_manifest.tsv; relation_catalog.tsv
|
| 117 |
+
remove_derived_disease_mutation_path HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/disease_core_module_prioritization/task41_pipeline.py; relation_catalog.tsv
|
| 118 |
+
remove_direct_disease_protein HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/disease_core_module_prioritization/task41_pipeline.py; relation_catalog.tsv
|
| 119 |
+
test HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 120 |
+
test_metrics HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 121 |
+
test_predictions HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 122 |
+
three_seed_summary HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 123 |
+
train HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 124 |
+
training_history HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 125 |
+
used_for_disease_protein_edges HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/zero_shot_nonppi/run_n2_u4_nonppi.py; relation_catalog.tsv
|
| 126 |
+
validation HIGH label-proximal relation; remove only if ClinVar target semantics are verified 14534 YES YES /root/autodl-tmp/bio/reviewer1_revision/m3_clinvar_server_audit/raw_graph_edge_inventory.tsv; relation_catalog.tsv
|
| 127 |
+
work/amplify_generalization/40_disease_functional_module_discovery_v1 HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/disease_mutation_ptm_gcl/amplify_generalization/disease_core_module_prioritization/task41_pipeline.py; relation_catalog.tsv
|
| 128 |
+
work/amplify_generalization/41_disease_core_module_prioritization_v1 HIGH label-proximal relation; remove only if ClinVar target semantics are verified 3046 YES YES /root/autodl-tmp/bio/reviewer1_revision/m5_baseline_ablation/scripts/m5_v2_finalize.py; relation_catalog.tsv
|
| 129 |
+
ALIAS_EQUIVALENT_TARGET_RELATIONS:10,11,6,7,EXPLICIT_CLINVAR_OR_CLASS_LABEL,Task38_disease_protein_provenance,U1_DiseasePermutation,all_model_clinvar_comparison,associated_with_mutation,associated_with_protein,audit/DISEASE_MUTATION_TARGET_BLIND_PASS.flag,bootstrap_iid,bootstrap_protein_grouped,cached_disease_feature,classifier_search,common_intersection_coverage,data_processed/edges_disease_protein.tsv,data_processed_clean/edges_disease_protein.tsv,data_processed_core/edges_disease_protein.tsv,disease-mutation,disease-protein,disease__has_mutation__mutation,disease__has_mutation__mutation.tsv,disease__has_protein__protein,disease__has_protein__protein.tsv.gz,disease_gene_reactome,disease_mutation,disease_mutation_ptm,disease_mutation_ptm_gcl/work/amplify_generalization/28_ppi_gate/source_esm_protocol/protocols/sequence_cluster_disjoint_candidate_pool.tsv.gz,disease_mutation_ptm_gcl/work/amplify_generalization/33_ppi_selective_graph_residual_v1/bootstrap/paired_grouped_bootstrap.tsv,disease_mutation_ptm_gcl/work/amplify_generalization/33_ppi_selective_graph_residual_v1/figures/bootstrap_graph_controls_figure_data.tsv,disease_mutation_ptm_gcl/work/amplify_generalization/43_disease_mutation_ranking_v1/formal/S4_sequence_cluster_disjoint/F3_GraphResidual/seed_42/metrics.tsv,disease_mutation_ptm_gcl/work/graph_esm2_residual_pretrain_v2/embeddings/node_id_mapping.tsv,disease_mutation_ptm_gcl/work/graph_esm2_residual_pretrain_v2/embeddings/protein_residual_embeddings.npy,disease_protein,disease_protein_counts.tsv,disease_protein_matched,disease_protein_nodes,disease_protein_provenance_audit,edges/disease__has_protein__protein.tsv.gz,edges_disease_mutation,edges_disease_mutation.tsv,edges_disease_protein,edges_disease_protein.tsv,edges_mutation_protein,excluded_missing_prott5,excluded_missing_ptm_mamba,feasibility/disease_protein_provenance.tsv.gz,graph_core_disease_protein_pairs,graph_core_serialized_disease_protein,has_mutation,has_protein,model_availability,mutation;PTM;pathway (disease used only for candidate metadata),mutation__rev_has_mutation__disease,mutation_disease_count,mutation_ptm_labels_used,physical_ppi,positive_pairs/disease_mutation_ptm.tsv,protein__rev_has_protein__disease,protein_disease_count,protein_pathway,protein_ptm,remove_derived_disease_mutation_path,remove_direct_disease_protein,test,test_metrics,test_predictions,three_seed_summary,train,training_history,used_for_disease_protein_edges,validation,work/amplify_generalization/40_disease_functional_module_discovery_v1,work/amplify_generalization/41_disease_core_module_prioritization_v1 HIGH multiple names may encode the same target; confirm from rows before removal 14534 YES YES relation_catalog.tsv; edge overlap scan
|
| 130 |
+
one-hop/two-hop label-proximal candidate paths MEDIUM generic context is not automatically leakage; remove only if semantically target-equivalent 53386 NO_UNTIL_SEMANTICALLY_VERIFIED G2a_ONLY_IF_LABEL_PROXIMAL relation_catalog.tsv; no path deletion executed
|
| 131 |
+
generic biological context (PPI/PTM/pathway/other) LOW not a direct label encoding on current evidence; do not remove solely because a two-hop path exists 3048 NO G2b_ONLY relation_catalog.tsv
|
initial_data/clinvar_strict_rebuild_v1/04_relation_catalog/relation_catalog.tsv
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
initial_data/clinvar_strict_rebuild_v1/04_relation_catalog/relations_strict.tsv
ADDED
|
@@ -0,0 +1,13 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
relation_index relation src_type dst_type direction
|
| 2 |
+
0 mutation__on_protein__protein mutation protein forward
|
| 3 |
+
1 protein__rev_on_protein__mutation protein mutation reverse
|
| 4 |
+
2 protein__has_ptm__ptm protein ptm forward
|
| 5 |
+
3 ptm__rev_has_ptm__protein ptm protein reverse
|
| 6 |
+
4 protein__in_pathway__pathway protein pathway forward
|
| 7 |
+
5 pathway__rev_in_pathway__protein pathway protein reverse
|
| 8 |
+
6 disease__has_mutation__mutation disease mutation forward
|
| 9 |
+
7 mutation__rev_has_mutation__disease mutation disease reverse
|
| 10 |
+
8 disease__has_ptm__ptm disease ptm forward
|
| 11 |
+
9 ptm__rev_has_ptm__disease ptm disease reverse
|
| 12 |
+
10 disease__has_protein__protein disease protein forward
|
| 13 |
+
11 protein__rev_has_protein__disease protein disease reverse
|
initial_data/clinvar_strict_rebuild_v1/05_graph_base/SHA256SUMS
ADDED
|
@@ -0,0 +1,2 @@
|
|
|
|
|
|
|
|
|
|
| 1 |
+
8a2c56514a13d4867c27a859cf57ca89b2d1297b7cd34f0a0e58404f156c0ba6 base_nodes.parquet
|
| 2 |
+
a622cfbb0e9db991d3f1b09acaf38eb06ee190dae2e136eeaa910c7899fcb9c2 base_edges.parquet
|
initial_data/clinvar_strict_rebuild_v1/05_graph_base/graph_statistics.json
ADDED
|
@@ -0,0 +1,27 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"nodes_by_type": {
|
| 3 |
+
"disease": 38588,
|
| 4 |
+
"mutation": 4565760,
|
| 5 |
+
"protein": 20754,
|
| 6 |
+
"ptm": 166592,
|
| 7 |
+
"pathway": 2835
|
| 8 |
+
},
|
| 9 |
+
"total_nodes": 4794529,
|
| 10 |
+
"total_edges": 8831756,
|
| 11 |
+
"edges_by_relation": {
|
| 12 |
+
"associated_with_mutation": 3279766,
|
| 13 |
+
"associated_with_protein": 360600,
|
| 14 |
+
"associated_with_ptm": 302010,
|
| 15 |
+
"on_protein": 4552416,
|
| 16 |
+
"in_pathway": 137953,
|
| 17 |
+
"has_ptm": 199011
|
| 18 |
+
},
|
| 19 |
+
"relation_ids": {
|
| 20 |
+
"associated_with_mutation": 0,
|
| 21 |
+
"associated_with_protein": 1,
|
| 22 |
+
"associated_with_ptm": 2,
|
| 23 |
+
"on_protein": 3,
|
| 24 |
+
"in_pathway": 4,
|
| 25 |
+
"has_ptm": 5
|
| 26 |
+
}
|
| 27 |
+
}
|
initial_data/clinvar_strict_rebuild_v1/05_graph_v2_inputs/G1/edge_statistics.tsv
ADDED
|
@@ -0,0 +1,7 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
relation reverse_relation src_type dst_type forward_edge_count reverse_edge_count
|
| 2 |
+
mutation__on_protein__protein protein__rev_on_protein__mutation mutation protein 4498756 4498756
|
| 3 |
+
protein__has_ptm__ptm ptm__rev_has_ptm__protein protein ptm 199011 199011
|
| 4 |
+
protein__in_pathway__pathway pathway__rev_in_pathway__protein protein pathway 137953 137953
|
| 5 |
+
disease__has_mutation__mutation mutation__rev_has_mutation__disease disease mutation 3194088 3194088
|
| 6 |
+
disease__has_ptm__ptm ptm__rev_has_ptm__disease disease ptm 302010 302010
|
| 7 |
+
disease__has_protein__protein protein__rev_has_protein__disease disease protein 360600 360600
|
initial_data/clinvar_strict_rebuild_v1/05_graph_v2_inputs/G1/graph_config.json
ADDED
|
@@ -0,0 +1,16 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"format_version": 2,
|
| 3 |
+
"forward_relation_count": 6,
|
| 4 |
+
"node_counts": {
|
| 5 |
+
"disease": 38588,
|
| 6 |
+
"mutation": 4565760,
|
| 7 |
+
"pathway": 2835,
|
| 8 |
+
"protein": 20754,
|
| 9 |
+
"ptm": 166592
|
| 10 |
+
},
|
| 11 |
+
"serialized_relation_count": 12,
|
| 12 |
+
"source_edges": "/root/autodl-tmp/bio/clinvar_strict_rebuild_v1/06_graph_G1/edges.parquet",
|
| 13 |
+
"source_nodes": "/root/autodl-tmp/bio/clinvar_strict_rebuild_v1/06_graph_G1/nodes.parquet",
|
| 14 |
+
"source_relation_id_is_not_used": true,
|
| 15 |
+
"total_nodes": 4794529
|
| 16 |
+
}
|
initial_data/clinvar_strict_rebuild_v1/05_graph_v2_inputs/G1/remap_audit.json
ADDED
|
@@ -0,0 +1,23 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"canonical_forward_counts": {
|
| 3 |
+
"disease__has_mutation__mutation": 3194088,
|
| 4 |
+
"disease__has_protein__protein": 360600,
|
| 5 |
+
"disease__has_ptm__ptm": 302010,
|
| 6 |
+
"mutation__on_protein__protein": 4498756,
|
| 7 |
+
"protein__has_ptm__ptm": 199011,
|
| 8 |
+
"protein__in_pathway__pathway": 137953
|
| 9 |
+
},
|
| 10 |
+
"canonical_forward_edge_rows": 8692418,
|
| 11 |
+
"condition": "G1",
|
| 12 |
+
"generated_reverse_edge_rows": 8692418,
|
| 13 |
+
"source_edge_rows": 8692418,
|
| 14 |
+
"source_relation_rows": {
|
| 15 |
+
"0|associated_with_mutation|disease|mutation": 3194088,
|
| 16 |
+
"1|associated_with_protein|disease|protein": 360600,
|
| 17 |
+
"2|associated_with_ptm|disease|ptm": 302010,
|
| 18 |
+
"3|on_protein|mutation|protein": 4498756,
|
| 19 |
+
"4|in_pathway|protein|pathway": 137953,
|
| 20 |
+
"5|has_ptm|protein|ptm": 199011
|
| 21 |
+
},
|
| 22 |
+
"status": "PASS"
|
| 23 |
+
}
|
initial_data/clinvar_strict_rebuild_v1/05_graph_v2_inputs/G2a/edge_statistics.tsv
ADDED
|
@@ -0,0 +1,7 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
relation reverse_relation src_type dst_type forward_edge_count reverse_edge_count
|
| 2 |
+
mutation__on_protein__protein protein__rev_on_protein__mutation mutation protein 4498756 4498756
|
| 3 |
+
protein__has_ptm__ptm ptm__rev_has_ptm__protein protein ptm 199011 199011
|
| 4 |
+
protein__in_pathway__pathway pathway__rev_in_pathway__protein protein pathway 137953 137953
|
| 5 |
+
disease__has_mutation__mutation mutation__rev_has_mutation__disease disease mutation 3194088 3194088
|
| 6 |
+
disease__has_ptm__ptm ptm__rev_has_ptm__disease disease ptm 302010 302010
|
| 7 |
+
disease__has_protein__protein protein__rev_has_protein__disease disease protein 360600 360600
|
initial_data/clinvar_strict_rebuild_v1/05_graph_v2_inputs/G2a/graph_config.json
ADDED
|
@@ -0,0 +1,16 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
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|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"format_version": 2,
|
| 3 |
+
"forward_relation_count": 6,
|
| 4 |
+
"node_counts": {
|
| 5 |
+
"disease": 38588,
|
| 6 |
+
"mutation": 4565760,
|
| 7 |
+
"pathway": 2835,
|
| 8 |
+
"protein": 20754,
|
| 9 |
+
"ptm": 166592
|
| 10 |
+
},
|
| 11 |
+
"serialized_relation_count": 12,
|
| 12 |
+
"source_edges": "/root/autodl-tmp/bio/clinvar_strict_rebuild_v1/07_graph_G2a/edges.parquet",
|
| 13 |
+
"source_nodes": "/root/autodl-tmp/bio/clinvar_strict_rebuild_v1/07_graph_G2a/nodes.parquet",
|
| 14 |
+
"source_relation_id_is_not_used": true,
|
| 15 |
+
"total_nodes": 4794529
|
| 16 |
+
}
|
initial_data/clinvar_strict_rebuild_v1/05_graph_v2_inputs/G2a/node_mappings/disease.tsv
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
initial_data/clinvar_strict_rebuild_v1/05_graph_v2_inputs/G2a/node_mappings/pathway.tsv
ADDED
|
@@ -0,0 +1,2836 @@
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|
| 1 |
+
node_index node_id
|
| 2 |
+
0 PATHWAY:R-HSA-1059683
|
| 3 |
+
1 PATHWAY:R-HSA-109581
|
| 4 |
+
2 PATHWAY:R-HSA-109582
|
| 5 |
+
3 PATHWAY:R-HSA-109606
|
| 6 |
+
4 PATHWAY:R-HSA-109703
|
| 7 |
+
5 PATHWAY:R-HSA-109704
|
| 8 |
+
6 PATHWAY:R-HSA-110056
|
| 9 |
+
7 PATHWAY:R-HSA-110312
|
| 10 |
+
8 PATHWAY:R-HSA-110313
|
| 11 |
+
9 PATHWAY:R-HSA-110314
|
| 12 |
+
10 PATHWAY:R-HSA-110320
|
| 13 |
+
11 PATHWAY:R-HSA-110328
|
| 14 |
+
12 PATHWAY:R-HSA-110329
|
| 15 |
+
13 PATHWAY:R-HSA-110330
|
| 16 |
+
14 PATHWAY:R-HSA-110331
|
| 17 |
+
15 PATHWAY:R-HSA-110357
|
| 18 |
+
16 PATHWAY:R-HSA-110362
|
| 19 |
+
17 PATHWAY:R-HSA-110373
|
| 20 |
+
18 PATHWAY:R-HSA-110381
|
| 21 |
+
19 PATHWAY:R-HSA-111367
|
| 22 |
+
20 PATHWAY:R-HSA-111446
|
| 23 |
+
21 PATHWAY:R-HSA-111447
|
| 24 |
+
22 PATHWAY:R-HSA-111448
|
| 25 |
+
23 PATHWAY:R-HSA-111452
|
| 26 |
+
24 PATHWAY:R-HSA-111453
|
| 27 |
+
25 PATHWAY:R-HSA-111457
|
| 28 |
+
26 PATHWAY:R-HSA-111458
|
| 29 |
+
27 PATHWAY:R-HSA-111459
|
| 30 |
+
28 PATHWAY:R-HSA-111461
|
| 31 |
+
29 PATHWAY:R-HSA-111463
|
| 32 |
+
30 PATHWAY:R-HSA-111464
|
| 33 |
+
31 PATHWAY:R-HSA-111465
|
| 34 |
+
32 PATHWAY:R-HSA-111469
|
| 35 |
+
33 PATHWAY:R-HSA-111471
|
| 36 |
+
34 PATHWAY:R-HSA-111885
|
| 37 |
+
35 PATHWAY:R-HSA-111931
|
| 38 |
+
36 PATHWAY:R-HSA-111932
|
| 39 |
+
37 PATHWAY:R-HSA-111933
|
| 40 |
+
38 PATHWAY:R-HSA-111957
|
| 41 |
+
39 PATHWAY:R-HSA-111995
|
| 42 |
+
40 PATHWAY:R-HSA-111996
|
| 43 |
+
41 PATHWAY:R-HSA-111997
|
| 44 |
+
42 PATHWAY:R-HSA-112040
|
| 45 |
+
43 PATHWAY:R-HSA-112043
|
| 46 |
+
44 PATHWAY:R-HSA-112122
|
| 47 |
+
45 PATHWAY:R-HSA-112126
|
| 48 |
+
46 PATHWAY:R-HSA-112303
|
| 49 |
+
47 PATHWAY:R-HSA-112307
|
| 50 |
+
48 PATHWAY:R-HSA-112308
|
| 51 |
+
49 PATHWAY:R-HSA-112310
|
| 52 |
+
50 PATHWAY:R-HSA-112311
|
| 53 |
+
51 PATHWAY:R-HSA-112313
|
| 54 |
+
52 PATHWAY:R-HSA-112314
|
| 55 |
+
53 PATHWAY:R-HSA-112315
|
| 56 |
+
54 PATHWAY:R-HSA-112316
|
| 57 |
+
55 PATHWAY:R-HSA-112382
|
| 58 |
+
56 PATHWAY:R-HSA-112399
|
| 59 |
+
57 PATHWAY:R-HSA-112409
|
| 60 |
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60 PATHWAY:R-HSA-113418
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62 PATHWAY:R-HSA-113507
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64 PATHWAY:R-HSA-114294
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66 PATHWAY:R-HSA-114508
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67 PATHWAY:R-HSA-114516
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68 PATHWAY:R-HSA-114604
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69 PATHWAY:R-HSA-114608
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70 PATHWAY:R-HSA-1168372
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71 PATHWAY:R-HSA-1169091
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72 PATHWAY:R-HSA-1169092
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73 PATHWAY:R-HSA-1169408
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75 PATHWAY:R-HSA-1170546
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78 PATHWAY:R-HSA-1221632
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79 PATHWAY:R-HSA-1222449
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81 PATHWAY:R-HSA-1222556
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83 PATHWAY:R-HSA-1227986
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85 PATHWAY:R-HSA-1234158
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90 PATHWAY:R-HSA-1236973
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98 PATHWAY:R-HSA-1250196
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99 PATHWAY:R-HSA-1250342
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100 PATHWAY:R-HSA-1250347
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105 PATHWAY:R-HSA-1266695
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110 PATHWAY:R-HSA-1295596
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111 PATHWAY:R-HSA-1296025
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130 PATHWAY:R-HSA-1306955
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133 PATHWAY:R-HSA-1362277
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135 PATHWAY:R-HSA-1362409
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192 PATHWAY:R-HSA-1500620
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194 PATHWAY:R-HSA-1502540
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226 PATHWAY:R-HSA-1606322
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242 PATHWAY:R-HSA-162710
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244 PATHWAY:R-HSA-162906
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245 PATHWAY:R-HSA-162909
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247 PATHWAY:R-HSA-163125
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249 PATHWAY:R-HSA-163282
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286 PATHWAY:R-HSA-1660514
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287 PATHWAY:R-HSA-1660516
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288 PATHWAY:R-HSA-1660517
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289 PATHWAY:R-HSA-166058
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290 PATHWAY:R-HSA-1660661
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292 PATHWAY:R-HSA-166166
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295 PATHWAY:R-HSA-1663150
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296 PATHWAY:R-HSA-166520
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297 PATHWAY:R-HSA-166658
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300 PATHWAY:R-HSA-166665
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301 PATHWAY:R-HSA-166786
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302 PATHWAY:R-HSA-167021
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303 PATHWAY:R-HSA-167044
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304 PATHWAY:R-HSA-167060
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305 PATHWAY:R-HSA-167152
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306 PATHWAY:R-HSA-167158
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307 PATHWAY:R-HSA-167160
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322 PATHWAY:R-HSA-168138
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333 PATHWAY:R-HSA-168271
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335 PATHWAY:R-HSA-168274
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336 PATHWAY:R-HSA-168275
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338 PATHWAY:R-HSA-168277
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339 PATHWAY:R-HSA-168315
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340 PATHWAY:R-HSA-168316
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341 PATHWAY:R-HSA-168325
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342 PATHWAY:R-HSA-168330
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343 PATHWAY:R-HSA-168333
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344 PATHWAY:R-HSA-168638
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345 PATHWAY:R-HSA-168643
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347 PATHWAY:R-HSA-168898
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348 PATHWAY:R-HSA-168927
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349 PATHWAY:R-HSA-168928
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350 PATHWAY:R-HSA-169131
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351 PATHWAY:R-HSA-169893
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352 PATHWAY:R-HSA-169911
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353 PATHWAY:R-HSA-170660
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354 PATHWAY:R-HSA-170670
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355 PATHWAY:R-HSA-170822
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356 PATHWAY:R-HSA-170834
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357 PATHWAY:R-HSA-170968
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358 PATHWAY:R-HSA-170984
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359 PATHWAY:R-HSA-171007
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360 PATHWAY:R-HSA-171286
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361 PATHWAY:R-HSA-171306
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362 PATHWAY:R-HSA-171319
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363 PATHWAY:R-HSA-173107
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364 PATHWAY:R-HSA-173599
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365 PATHWAY:R-HSA-173623
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366 PATHWAY:R-HSA-173736
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367 PATHWAY:R-HSA-174048
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368 PATHWAY:R-HSA-174084
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369 PATHWAY:R-HSA-174113
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370 PATHWAY:R-HSA-174143
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371 PATHWAY:R-HSA-174154
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372 PATHWAY:R-HSA-174178
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373 PATHWAY:R-HSA-174184
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377 PATHWAY:R-HSA-174414
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378 PATHWAY:R-HSA-174417
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379 PATHWAY:R-HSA-174430
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380 PATHWAY:R-HSA-174437
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381 PATHWAY:R-HSA-174490
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382 PATHWAY:R-HSA-174495
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383 PATHWAY:R-HSA-174577
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384 PATHWAY:R-HSA-174824
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385 PATHWAY:R-HSA-175474
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386 PATHWAY:R-HSA-175567
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387 PATHWAY:R-HSA-176033
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388 PATHWAY:R-HSA-176034
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389 PATHWAY:R-HSA-176187
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390 PATHWAY:R-HSA-176407
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391 PATHWAY:R-HSA-176408
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392 PATHWAY:R-HSA-176409
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393 PATHWAY:R-HSA-176412
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394 PATHWAY:R-HSA-176417
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395 PATHWAY:R-HSA-176814
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396 PATHWAY:R-HSA-176974
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397 PATHWAY:R-HSA-177128
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398 PATHWAY:R-HSA-177135
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399 PATHWAY:R-HSA-177162
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400 PATHWAY:R-HSA-177243
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401 PATHWAY:R-HSA-177504
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402 PATHWAY:R-HSA-177539
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403 PATHWAY:R-HSA-177929
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404 PATHWAY:R-HSA-1793185
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405 PATHWAY:R-HSA-179409
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406 PATHWAY:R-HSA-179419
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407 PATHWAY:R-HSA-179812
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408 PATHWAY:R-HSA-1799339
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409 PATHWAY:R-HSA-180024
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410 PATHWAY:R-HSA-180292
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411 PATHWAY:R-HSA-180336
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412 PATHWAY:R-HSA-180534
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413 PATHWAY:R-HSA-180585
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414 PATHWAY:R-HSA-180689
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415 PATHWAY:R-HSA-180746
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416 PATHWAY:R-HSA-180786
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417 PATHWAY:R-HSA-180897
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418 PATHWAY:R-HSA-180910
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419 PATHWAY:R-HSA-1810476
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420 PATHWAY:R-HSA-181429
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421 PATHWAY:R-HSA-181430
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422 PATHWAY:R-HSA-181431
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423 PATHWAY:R-HSA-181438
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424 PATHWAY:R-HSA-182218
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425 PATHWAY:R-HSA-182971
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426 PATHWAY:R-HSA-1834941
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427 PATHWAY:R-HSA-1834949
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428 PATHWAY:R-HSA-1839117
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429 PATHWAY:R-HSA-1839120
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430 PATHWAY:R-HSA-1839122
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431 PATHWAY:R-HSA-1839124
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432 PATHWAY:R-HSA-1839126
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433 PATHWAY:R-HSA-1839128
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434 PATHWAY:R-HSA-1839130
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435 PATHWAY:R-HSA-1852241
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436 PATHWAY:R-HSA-1855167
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437 PATHWAY:R-HSA-1855170
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438 PATHWAY:R-HSA-1855183
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439 PATHWAY:R-HSA-1855191
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440 PATHWAY:R-HSA-1855196
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441 PATHWAY:R-HSA-1855204
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442 PATHWAY:R-HSA-1855229
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443 PATHWAY:R-HSA-1855231
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444 PATHWAY:R-HSA-186712
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445 PATHWAY:R-HSA-186763
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446 PATHWAY:R-HSA-186797
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447 PATHWAY:R-HSA-187015
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448 PATHWAY:R-HSA-187024
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449 PATHWAY:R-HSA-187037
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450 PATHWAY:R-HSA-187042
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451 PATHWAY:R-HSA-187577
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452 PATHWAY:R-HSA-187687
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453 PATHWAY:R-HSA-187706
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454 PATHWAY:R-HSA-189085
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455 PATHWAY:R-HSA-189200
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456 PATHWAY:R-HSA-189445
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457 PATHWAY:R-HSA-189451
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458 PATHWAY:R-HSA-189483
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459 PATHWAY:R-HSA-190236
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460 PATHWAY:R-HSA-190239
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461 PATHWAY:R-HSA-190241
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462 PATHWAY:R-HSA-190242
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463 PATHWAY:R-HSA-190322
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464 PATHWAY:R-HSA-190370
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465 PATHWAY:R-HSA-190371
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466 PATHWAY:R-HSA-190372
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467 PATHWAY:R-HSA-190373
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468 PATHWAY:R-HSA-190374
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469 PATHWAY:R-HSA-190375
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470 PATHWAY:R-HSA-190377
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471 PATHWAY:R-HSA-190704
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472 PATHWAY:R-HSA-190827
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473 PATHWAY:R-HSA-190828
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474 PATHWAY:R-HSA-190840
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475 PATHWAY:R-HSA-190861
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476 PATHWAY:R-HSA-190872
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477 PATHWAY:R-HSA-190873
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478 PATHWAY:R-HSA-1912399
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479 PATHWAY:R-HSA-1912408
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480 PATHWAY:R-HSA-1912420
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481 PATHWAY:R-HSA-1912422
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482 PATHWAY:R-HSA-191273
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483 PATHWAY:R-HSA-191650
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484 PATHWAY:R-HSA-191859
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485 PATHWAY:R-HSA-192105
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486 PATHWAY:R-HSA-192456
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487 PATHWAY:R-HSA-192814
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488 PATHWAY:R-HSA-192823
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489 PATHWAY:R-HSA-192905
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490 PATHWAY:R-HSA-193048
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491 PATHWAY:R-HSA-193144
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492 PATHWAY:R-HSA-193368
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493 PATHWAY:R-HSA-193634
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494 PATHWAY:R-HSA-193639
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495 PATHWAY:R-HSA-193648
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496 PATHWAY:R-HSA-193670
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497 PATHWAY:R-HSA-193681
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498 PATHWAY:R-HSA-193692
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500 PATHWAY:R-HSA-193704
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501 PATHWAY:R-HSA-193775
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502 PATHWAY:R-HSA-193807
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503 PATHWAY:R-HSA-193993
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504 PATHWAY:R-HSA-194002
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505 PATHWAY:R-HSA-194068
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506 PATHWAY:R-HSA-194138
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507 PATHWAY:R-HSA-194306
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508 PATHWAY:R-HSA-194313
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+
509 PATHWAY:R-HSA-194315
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510 PATHWAY:R-HSA-194441
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511 PATHWAY:R-HSA-195253
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512 PATHWAY:R-HSA-195258
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513 PATHWAY:R-HSA-195399
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514 PATHWAY:R-HSA-195721
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515 PATHWAY:R-HSA-196025
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516 PATHWAY:R-HSA-196071
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517 PATHWAY:R-HSA-196108
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518 PATHWAY:R-HSA-196299
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519 PATHWAY:R-HSA-1963640
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520 PATHWAY:R-HSA-1963642
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521 PATHWAY:R-HSA-196741
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522 PATHWAY:R-HSA-196757
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523 PATHWAY:R-HSA-196780
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524 PATHWAY:R-HSA-196783
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525 PATHWAY:R-HSA-196791
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526 PATHWAY:R-HSA-196807
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527 PATHWAY:R-HSA-196819
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528 PATHWAY:R-HSA-196836
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529 PATHWAY:R-HSA-196843
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530 PATHWAY:R-HSA-196849
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531 PATHWAY:R-HSA-196854
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532 PATHWAY:R-HSA-1971475
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533 PATHWAY:R-HSA-1980143
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534 PATHWAY:R-HSA-1980145
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535 PATHWAY:R-HSA-198203
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536 PATHWAY:R-HSA-198323
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537 PATHWAY:R-HSA-198693
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538 PATHWAY:R-HSA-198725
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539 PATHWAY:R-HSA-198745
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540 PATHWAY:R-HSA-198753
|
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541 PATHWAY:R-HSA-198765
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542 PATHWAY:R-HSA-198933
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543 PATHWAY:R-HSA-1989781
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544 PATHWAY:R-HSA-199220
|
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545 PATHWAY:R-HSA-199418
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546 PATHWAY:R-HSA-199920
|
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547 PATHWAY:R-HSA-199977
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548 PATHWAY:R-HSA-199991
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+
549 PATHWAY:R-HSA-199992
|
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550 PATHWAY:R-HSA-200425
|
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551 PATHWAY:R-HSA-201451
|
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552 PATHWAY:R-HSA-201556
|
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+
553 PATHWAY:R-HSA-201681
|
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+
554 PATHWAY:R-HSA-201688
|
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+
555 PATHWAY:R-HSA-201722
|
| 558 |
+
556 PATHWAY:R-HSA-202040
|
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+
557 PATHWAY:R-HSA-202131
|
| 560 |
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558 PATHWAY:R-HSA-2022090
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559 PATHWAY:R-HSA-2022377
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560 PATHWAY:R-HSA-2022854
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561 PATHWAY:R-HSA-2022857
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562 PATHWAY:R-HSA-2022870
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563 PATHWAY:R-HSA-2022923
|
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564 PATHWAY:R-HSA-2022928
|
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565 PATHWAY:R-HSA-2023837
|
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566 PATHWAY:R-HSA-202403
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567 PATHWAY:R-HSA-2024096
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| 570 |
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568 PATHWAY:R-HSA-2024101
|
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569 PATHWAY:R-HSA-202424
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570 PATHWAY:R-HSA-202427
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571 PATHWAY:R-HSA-202430
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572 PATHWAY:R-HSA-202433
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573 PATHWAY:R-HSA-2025928
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574 PATHWAY:R-HSA-202670
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575 PATHWAY:R-HSA-202733
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576 PATHWAY:R-HSA-2028269
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577 PATHWAY:R-HSA-2029480
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578 PATHWAY:R-HSA-2029481
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579 PATHWAY:R-HSA-2029482
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580 PATHWAY:R-HSA-2029485
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581 PATHWAY:R-HSA-2032785
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582 PATHWAY:R-HSA-2033514
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583 PATHWAY:R-HSA-2033515
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584 PATHWAY:R-HSA-2033519
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585 PATHWAY:R-HSA-203615
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586 PATHWAY:R-HSA-203641
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587 PATHWAY:R-HSA-203754
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588 PATHWAY:R-HSA-203927
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589 PATHWAY:R-HSA-204005
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590 PATHWAY:R-HSA-204174
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591 PATHWAY:R-HSA-2046104
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592 PATHWAY:R-HSA-2046105
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593 PATHWAY:R-HSA-2046106
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594 PATHWAY:R-HSA-204626
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595 PATHWAY:R-HSA-204998
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596 PATHWAY:R-HSA-205017
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| 599 |
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597 PATHWAY:R-HSA-205025
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| 600 |
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598 PATHWAY:R-HSA-205043
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| 601 |
+
599 PATHWAY:R-HSA-209543
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| 602 |
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600 PATHWAY:R-HSA-209560
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| 603 |
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601 PATHWAY:R-HSA-209563
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602 PATHWAY:R-HSA-209776
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603 PATHWAY:R-HSA-209822
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+
604 PATHWAY:R-HSA-209905
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| 607 |
+
605 PATHWAY:R-HSA-209931
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| 608 |
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606 PATHWAY:R-HSA-209952
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| 609 |
+
607 PATHWAY:R-HSA-209968
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| 610 |
+
608 PATHWAY:R-HSA-210455
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| 611 |
+
609 PATHWAY:R-HSA-210500
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| 612 |
+
610 PATHWAY:R-HSA-210744
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| 613 |
+
611 PATHWAY:R-HSA-210745
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| 614 |
+
612 PATHWAY:R-HSA-210746
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+
613 PATHWAY:R-HSA-210747
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+
614 PATHWAY:R-HSA-210990
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+
615 PATHWAY:R-HSA-210991
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| 618 |
+
616 PATHWAY:R-HSA-210993
|
| 619 |
+
617 PATHWAY:R-HSA-211000
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| 620 |
+
618 PATHWAY:R-HSA-211163
|
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619 PATHWAY:R-HSA-211728
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620 PATHWAY:R-HSA-211733
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621 PATHWAY:R-HSA-211736
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+
622 PATHWAY:R-HSA-211859
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+
623 PATHWAY:R-HSA-211897
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| 626 |
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624 PATHWAY:R-HSA-211916
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625 PATHWAY:R-HSA-211935
|
| 628 |
+
626 PATHWAY:R-HSA-211945
|
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627 PATHWAY:R-HSA-211957
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| 630 |
+
628 PATHWAY:R-HSA-211958
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| 631 |
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629 PATHWAY:R-HSA-211976
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630 PATHWAY:R-HSA-211979
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| 633 |
+
631 PATHWAY:R-HSA-211981
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632 PATHWAY:R-HSA-211994
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633 PATHWAY:R-HSA-211999
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634 PATHWAY:R-HSA-212165
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| 637 |
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635 PATHWAY:R-HSA-2122947
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636 PATHWAY:R-HSA-2122948
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637 PATHWAY:R-HSA-212300
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| 640 |
+
638 PATHWAY:R-HSA-212436
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| 641 |
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639 PATHWAY:R-HSA-212676
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| 642 |
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640 PATHWAY:R-HSA-212718
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| 643 |
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641 PATHWAY:R-HSA-2129379
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642 PATHWAY:R-HSA-2132295
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643 PATHWAY:R-HSA-2142670
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644 PATHWAY:R-HSA-2142688
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645 PATHWAY:R-HSA-2142691
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646 PATHWAY:R-HSA-2142696
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647 PATHWAY:R-HSA-2142700
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| 650 |
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648 PATHWAY:R-HSA-2142712
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649 PATHWAY:R-HSA-2142753
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650 PATHWAY:R-HSA-2142770
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651 PATHWAY:R-HSA-2142789
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652 PATHWAY:R-HSA-2142816
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| 655 |
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653 PATHWAY:R-HSA-2142845
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654 PATHWAY:R-HSA-2151201
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655 PATHWAY:R-HSA-2151209
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656 PATHWAY:R-HSA-2160456
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657 PATHWAY:R-HSA-216083
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658 PATHWAY:R-HSA-2160916
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659 PATHWAY:R-HSA-2161517
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660 PATHWAY:R-HSA-2161522
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661 PATHWAY:R-HSA-2161541
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662 PATHWAY:R-HSA-2162123
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663 PATHWAY:R-HSA-2168880
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664 PATHWAY:R-HSA-2172127
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665 PATHWAY:R-HSA-217271
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666 PATHWAY:R-HSA-2173782
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667 PATHWAY:R-HSA-2173788
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668 PATHWAY:R-HSA-2173789
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669 PATHWAY:R-HSA-2173791
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670 PATHWAY:R-HSA-2173793
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671 PATHWAY:R-HSA-2173795
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672 PATHWAY:R-HSA-2173796
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673 PATHWAY:R-HSA-2179392
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674 PATHWAY:R-HSA-2187335
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675 PATHWAY:R-HSA-2187338
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676 PATHWAY:R-HSA-2197563
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677 PATHWAY:R-HSA-2206280
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678 PATHWAY:R-HSA-2206281
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679 PATHWAY:R-HSA-2206282
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680 PATHWAY:R-HSA-2206285
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681 PATHWAY:R-HSA-2206290
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682 PATHWAY:R-HSA-2206291
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683 PATHWAY:R-HSA-2206292
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684 PATHWAY:R-HSA-2206296
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685 PATHWAY:R-HSA-2206302
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686 PATHWAY:R-HSA-2206305
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687 PATHWAY:R-HSA-2206307
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688 PATHWAY:R-HSA-2206308
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689 PATHWAY:R-HSA-2214320
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690 PATHWAY:R-HSA-2219528
|
| 693 |
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992 PATHWAY:R-HSA-4085377
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| 1880 |
+
1878 PATHWAY:R-HSA-8852405
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| 1881 |
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1879 PATHWAY:R-HSA-8853333
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| 1882 |
+
1880 PATHWAY:R-HSA-8853334
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| 1883 |
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1881 PATHWAY:R-HSA-8853336
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| 1884 |
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1882 PATHWAY:R-HSA-8853383
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| 1885 |
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1883 PATHWAY:R-HSA-8853659
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| 1886 |
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1884 PATHWAY:R-HSA-8853884
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| 1887 |
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1885 PATHWAY:R-HSA-8854050
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| 1888 |
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1886 PATHWAY:R-HSA-8854214
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| 1889 |
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1887 PATHWAY:R-HSA-8854518
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| 1890 |
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1888 PATHWAY:R-HSA-8854521
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| 1891 |
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1889 PATHWAY:R-HSA-8854691
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| 1892 |
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1890 PATHWAY:R-HSA-8856688
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| 1893 |
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1891 PATHWAY:R-HSA-8856825
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| 1894 |
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1892 PATHWAY:R-HSA-8856828
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| 1895 |
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1893 PATHWAY:R-HSA-8857538
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| 1896 |
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1894 PATHWAY:R-HSA-8862803
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1895 PATHWAY:R-HSA-8863678
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1897 PATHWAY:R-HSA-8864260
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1898 PATHWAY:R-HSA-8865999
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1899 PATHWAY:R-HSA-8866376
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1900 PATHWAY:R-HSA-8866423
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| 1903 |
+
1901 PATHWAY:R-HSA-8866427
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1902 PATHWAY:R-HSA-8866652
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1903 PATHWAY:R-HSA-8866654
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| 1906 |
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1904 PATHWAY:R-HSA-8866904
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1906 PATHWAY:R-HSA-8866907
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| 1910 |
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1908 PATHWAY:R-HSA-8866911
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| 1911 |
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1909 PATHWAY:R-HSA-8868766
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1910 PATHWAY:R-HSA-8868773
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| 1913 |
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1911 PATHWAY:R-HSA-8869496
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| 1914 |
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1912 PATHWAY:R-HSA-8873719
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| 1915 |
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1913 PATHWAY:R-HSA-8874081
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1914 PATHWAY:R-HSA-8874177
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| 1917 |
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1915 PATHWAY:R-HSA-8874211
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1916 PATHWAY:R-HSA-8875360
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1917 PATHWAY:R-HSA-8875513
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| 1920 |
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1918 PATHWAY:R-HSA-8875555
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| 1921 |
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1919 PATHWAY:R-HSA-8875656
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1920 PATHWAY:R-HSA-8875791
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| 1923 |
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1921 PATHWAY:R-HSA-8875878
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1922 PATHWAY:R-HSA-8876198
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| 1925 |
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1923 PATHWAY:R-HSA-8876384
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| 1926 |
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1924 PATHWAY:R-HSA-8876493
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1925 PATHWAY:R-HSA-8876725
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| 1928 |
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1926 PATHWAY:R-HSA-8877330
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| 1929 |
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1927 PATHWAY:R-HSA-8877627
|
| 1930 |
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1928 PATHWAY:R-HSA-8878159
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| 1931 |
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1929 PATHWAY:R-HSA-8878166
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1930 PATHWAY:R-HSA-8878171
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| 1933 |
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1931 PATHWAY:R-HSA-888568
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1932 PATHWAY:R-HSA-888590
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| 1935 |
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1933 PATHWAY:R-HSA-888593
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1934 PATHWAY:R-HSA-8931838
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1935 PATHWAY:R-HSA-8931987
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1936 PATHWAY:R-HSA-8932504
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| 1939 |
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1937 PATHWAY:R-HSA-8932505
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| 1940 |
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1938 PATHWAY:R-HSA-8932506
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1939 PATHWAY:R-HSA-8934593
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1940 PATHWAY:R-HSA-8934903
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1941 PATHWAY:R-HSA-8935690
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1942 PATHWAY:R-HSA-8935964
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1943 PATHWAY:R-HSA-8936459
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1944 PATHWAY:R-HSA-8937144
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1945 PATHWAY:R-HSA-8939211
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1946 PATHWAY:R-HSA-8939236
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1947 PATHWAY:R-HSA-8939242
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1948 PATHWAY:R-HSA-8939243
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1949 PATHWAY:R-HSA-8939245
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1950 PATHWAY:R-HSA-8939246
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1951 PATHWAY:R-HSA-8939247
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1952 PATHWAY:R-HSA-8939256
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1953 PATHWAY:R-HSA-8939902
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1954 PATHWAY:R-HSA-8940973
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1955 PATHWAY:R-HSA-8941237
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1956 PATHWAY:R-HSA-8941284
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1957 PATHWAY:R-HSA-8941326
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1962 PATHWAY:R-HSA-8941856
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1965 PATHWAY:R-HSA-8943723
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1967 PATHWAY:R-HSA-8948216
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1968 PATHWAY:R-HSA-8948700
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1969 PATHWAY:R-HSA-8948747
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1970 PATHWAY:R-HSA-8948751
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1971 PATHWAY:R-HSA-8949215
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1972 PATHWAY:R-HSA-8949275
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1973 PATHWAY:R-HSA-8949613
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1974 PATHWAY:R-HSA-8949664
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1975 PATHWAY:R-HSA-8950505
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1976 PATHWAY:R-HSA-8951430
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1977 PATHWAY:R-HSA-8951664
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| 1980 |
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1978 PATHWAY:R-HSA-8951671
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1979 PATHWAY:R-HSA-8951911
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| 1982 |
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1980 PATHWAY:R-HSA-8951936
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| 1983 |
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1981 PATHWAY:R-HSA-8952158
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| 1984 |
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1982 PATHWAY:R-HSA-8953750
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| 1985 |
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1983 PATHWAY:R-HSA-8953854
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| 1986 |
+
1984 PATHWAY:R-HSA-8953897
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+
1985 PATHWAY:R-HSA-8955332
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| 1988 |
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1986 PATHWAY:R-HSA-8956319
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| 1989 |
+
1987 PATHWAY:R-HSA-8956320
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| 1990 |
+
1988 PATHWAY:R-HSA-8956321
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| 1991 |
+
1989 PATHWAY:R-HSA-8957275
|
| 1992 |
+
1990 PATHWAY:R-HSA-8957322
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| 1993 |
+
1991 PATHWAY:R-HSA-8963676
|
| 1994 |
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1992 PATHWAY:R-HSA-8963678
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| 1995 |
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1993 PATHWAY:R-HSA-8963684
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| 1996 |
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| 1997 |
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|
| 1998 |
+
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|
| 1999 |
+
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|
| 2000 |
+
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|
| 2001 |
+
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|
| 2002 |
+
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|
| 2003 |
+
2001 PATHWAY:R-HSA-8963899
|
| 2004 |
+
2002 PATHWAY:R-HSA-8963901
|
| 2005 |
+
2003 PATHWAY:R-HSA-8964011
|
| 2006 |
+
2004 PATHWAY:R-HSA-8964026
|
| 2007 |
+
2005 PATHWAY:R-HSA-8964038
|
| 2008 |
+
2006 PATHWAY:R-HSA-8964041
|
| 2009 |
+
2007 PATHWAY:R-HSA-8964043
|
| 2010 |
+
2008 PATHWAY:R-HSA-8964046
|
| 2011 |
+
2009 PATHWAY:R-HSA-8964058
|
| 2012 |
+
2010 PATHWAY:R-HSA-8964208
|
| 2013 |
+
2011 PATHWAY:R-HSA-8964315
|
| 2014 |
+
2012 PATHWAY:R-HSA-8964539
|
| 2015 |
+
2013 PATHWAY:R-HSA-8964540
|
| 2016 |
+
2014 PATHWAY:R-HSA-8964572
|
| 2017 |
+
2015 PATHWAY:R-HSA-8964616
|
| 2018 |
+
2016 PATHWAY:R-HSA-8978868
|
| 2019 |
+
2017 PATHWAY:R-HSA-8978934
|
| 2020 |
+
2018 PATHWAY:R-HSA-8979227
|
| 2021 |
+
2019 PATHWAY:R-HSA-8980692
|
| 2022 |
+
2020 PATHWAY:R-HSA-8981373
|
| 2023 |
+
2021 PATHWAY:R-HSA-8981607
|
| 2024 |
+
2022 PATHWAY:R-HSA-8982491
|
| 2025 |
+
2023 PATHWAY:R-HSA-8983432
|
| 2026 |
+
2024 PATHWAY:R-HSA-8983711
|
| 2027 |
+
2025 PATHWAY:R-HSA-8984722
|
| 2028 |
+
2026 PATHWAY:R-HSA-8985586
|
| 2029 |
+
2027 PATHWAY:R-HSA-8985801
|
| 2030 |
+
2028 PATHWAY:R-HSA-8985947
|
| 2031 |
+
2029 PATHWAY:R-HSA-8986944
|
| 2032 |
+
2030 PATHWAY:R-HSA-9005891
|
| 2033 |
+
2031 PATHWAY:R-HSA-9005895
|
| 2034 |
+
2032 PATHWAY:R-HSA-9006115
|
| 2035 |
+
2033 PATHWAY:R-HSA-9006335
|
| 2036 |
+
2034 PATHWAY:R-HSA-9006821
|
| 2037 |
+
2035 PATHWAY:R-HSA-9006925
|
| 2038 |
+
2036 PATHWAY:R-HSA-9006927
|
| 2039 |
+
2037 PATHWAY:R-HSA-9006931
|
| 2040 |
+
2038 PATHWAY:R-HSA-9006934
|
| 2041 |
+
2039 PATHWAY:R-HSA-9006936
|
| 2042 |
+
2040 PATHWAY:R-HSA-9007101
|
| 2043 |
+
2041 PATHWAY:R-HSA-9007892
|
| 2044 |
+
2042 PATHWAY:R-HSA-9008059
|
| 2045 |
+
2043 PATHWAY:R-HSA-9009391
|
| 2046 |
+
2044 PATHWAY:R-HSA-901032
|
| 2047 |
+
2045 PATHWAY:R-HSA-901042
|
| 2048 |
+
2046 PATHWAY:R-HSA-9010553
|
| 2049 |
+
2047 PATHWAY:R-HSA-9010642
|
| 2050 |
+
2048 PATHWAY:R-HSA-9012546
|
| 2051 |
+
2049 PATHWAY:R-HSA-9012852
|
| 2052 |
+
2050 PATHWAY:R-HSA-9012999
|
| 2053 |
+
2051 PATHWAY:R-HSA-9013026
|
| 2054 |
+
2052 PATHWAY:R-HSA-9013106
|
| 2055 |
+
2053 PATHWAY:R-HSA-9013148
|
| 2056 |
+
2054 PATHWAY:R-HSA-9013149
|
| 2057 |
+
2055 PATHWAY:R-HSA-9013404
|
| 2058 |
+
2056 PATHWAY:R-HSA-9013405
|
| 2059 |
+
2057 PATHWAY:R-HSA-9013406
|
| 2060 |
+
2058 PATHWAY:R-HSA-9013407
|
| 2061 |
+
2059 PATHWAY:R-HSA-9013408
|
| 2062 |
+
2060 PATHWAY:R-HSA-9013409
|
| 2063 |
+
2061 PATHWAY:R-HSA-9013418
|
| 2064 |
+
2062 PATHWAY:R-HSA-9013419
|
| 2065 |
+
2063 PATHWAY:R-HSA-9013420
|
| 2066 |
+
2064 PATHWAY:R-HSA-9013422
|
| 2067 |
+
2065 PATHWAY:R-HSA-9013423
|
| 2068 |
+
2066 PATHWAY:R-HSA-9013424
|
| 2069 |
+
2067 PATHWAY:R-HSA-9013425
|
| 2070 |
+
2068 PATHWAY:R-HSA-9013507
|
| 2071 |
+
2069 PATHWAY:R-HSA-9013508
|
| 2072 |
+
2070 PATHWAY:R-HSA-9013694
|
| 2073 |
+
2071 PATHWAY:R-HSA-9013695
|
| 2074 |
+
2072 PATHWAY:R-HSA-9013700
|
| 2075 |
+
2073 PATHWAY:R-HSA-9013957
|
| 2076 |
+
2074 PATHWAY:R-HSA-9013973
|
| 2077 |
+
2075 PATHWAY:R-HSA-9014325
|
| 2078 |
+
2076 PATHWAY:R-HSA-9014826
|
| 2079 |
+
2077 PATHWAY:R-HSA-9014843
|
| 2080 |
+
2078 PATHWAY:R-HSA-9017802
|
| 2081 |
+
2079 PATHWAY:R-HSA-9018519
|
| 2082 |
+
2080 PATHWAY:R-HSA-9018676
|
| 2083 |
+
2081 PATHWAY:R-HSA-9018677
|
| 2084 |
+
2082 PATHWAY:R-HSA-9018678
|
| 2085 |
+
2083 PATHWAY:R-HSA-9018679
|
| 2086 |
+
2084 PATHWAY:R-HSA-9018681
|
| 2087 |
+
2085 PATHWAY:R-HSA-9018682
|
| 2088 |
+
2086 PATHWAY:R-HSA-9018683
|
| 2089 |
+
2087 PATHWAY:R-HSA-9018896
|
| 2090 |
+
2088 PATHWAY:R-HSA-9020265
|
| 2091 |
+
2089 PATHWAY:R-HSA-9020558
|
| 2092 |
+
2090 PATHWAY:R-HSA-9020591
|
| 2093 |
+
2091 PATHWAY:R-HSA-9020702
|
| 2094 |
+
2092 PATHWAY:R-HSA-9020933
|
| 2095 |
+
2093 PATHWAY:R-HSA-9020956
|
| 2096 |
+
2094 PATHWAY:R-HSA-9020958
|
| 2097 |
+
2095 PATHWAY:R-HSA-9022534
|
| 2098 |
+
2096 PATHWAY:R-HSA-9022535
|
| 2099 |
+
2097 PATHWAY:R-HSA-9022537
|
| 2100 |
+
2098 PATHWAY:R-HSA-9022538
|
| 2101 |
+
2099 PATHWAY:R-HSA-9022692
|
| 2102 |
+
2100 PATHWAY:R-HSA-9022699
|
| 2103 |
+
2101 PATHWAY:R-HSA-9022702
|
| 2104 |
+
2102 PATHWAY:R-HSA-9022707
|
| 2105 |
+
2103 PATHWAY:R-HSA-9022927
|
| 2106 |
+
2104 PATHWAY:R-HSA-9023661
|
| 2107 |
+
2105 PATHWAY:R-HSA-9024446
|
| 2108 |
+
2106 PATHWAY:R-HSA-9024909
|
| 2109 |
+
2107 PATHWAY:R-HSA-9025046
|
| 2110 |
+
2108 PATHWAY:R-HSA-9025094
|
| 2111 |
+
2109 PATHWAY:R-HSA-9025106
|
| 2112 |
+
2110 PATHWAY:R-HSA-9026286
|
| 2113 |
+
2111 PATHWAY:R-HSA-9026290
|
| 2114 |
+
2112 PATHWAY:R-HSA-9026357
|
| 2115 |
+
2113 PATHWAY:R-HSA-9026395
|
| 2116 |
+
2114 PATHWAY:R-HSA-9026403
|
| 2117 |
+
2115 PATHWAY:R-HSA-9026519
|
| 2118 |
+
2116 PATHWAY:R-HSA-9026527
|
| 2119 |
+
2117 PATHWAY:R-HSA-9026762
|
| 2120 |
+
2118 PATHWAY:R-HSA-9026766
|
| 2121 |
+
2119 PATHWAY:R-HSA-9027276
|
| 2122 |
+
2120 PATHWAY:R-HSA-9027277
|
| 2123 |
+
2121 PATHWAY:R-HSA-9027283
|
| 2124 |
+
2122 PATHWAY:R-HSA-9027284
|
| 2125 |
+
2123 PATHWAY:R-HSA-9027307
|
| 2126 |
+
2124 PATHWAY:R-HSA-9027604
|
| 2127 |
+
2125 PATHWAY:R-HSA-9028335
|
| 2128 |
+
2126 PATHWAY:R-HSA-9028731
|
| 2129 |
+
2127 PATHWAY:R-HSA-9029558
|
| 2130 |
+
2128 PATHWAY:R-HSA-9029569
|
| 2131 |
+
2129 PATHWAY:R-HSA-9031525
|
| 2132 |
+
2130 PATHWAY:R-HSA-9031528
|
| 2133 |
+
2131 PATHWAY:R-HSA-9031628
|
| 2134 |
+
2132 PATHWAY:R-HSA-9032500
|
| 2135 |
+
2133 PATHWAY:R-HSA-9032759
|
| 2136 |
+
2134 PATHWAY:R-HSA-9032845
|
| 2137 |
+
2135 PATHWAY:R-HSA-9033241
|
| 2138 |
+
2136 PATHWAY:R-HSA-9033500
|
| 2139 |
+
2137 PATHWAY:R-HSA-9033658
|
| 2140 |
+
2138 PATHWAY:R-HSA-9033807
|
| 2141 |
+
2139 PATHWAY:R-HSA-9034013
|
| 2142 |
+
2140 PATHWAY:R-HSA-9034015
|
| 2143 |
+
2141 PATHWAY:R-HSA-9034793
|
| 2144 |
+
2142 PATHWAY:R-HSA-9034864
|
| 2145 |
+
2143 PATHWAY:R-HSA-9035034
|
| 2146 |
+
2144 PATHWAY:R-HSA-9035968
|
| 2147 |
+
2145 PATHWAY:R-HSA-9036092
|
| 2148 |
+
2146 PATHWAY:R-HSA-9036866
|
| 2149 |
+
2147 PATHWAY:R-HSA-9037628
|
| 2150 |
+
2148 PATHWAY:R-HSA-9037629
|
| 2151 |
+
2149 PATHWAY:R-HSA-909733
|
| 2152 |
+
2150 PATHWAY:R-HSA-912446
|
| 2153 |
+
2151 PATHWAY:R-HSA-912526
|
| 2154 |
+
2152 PATHWAY:R-HSA-912631
|
| 2155 |
+
2153 PATHWAY:R-HSA-912694
|
| 2156 |
+
2154 PATHWAY:R-HSA-913531
|
| 2157 |
+
2155 PATHWAY:R-HSA-913709
|
| 2158 |
+
2156 PATHWAY:R-HSA-916853
|
| 2159 |
+
2157 PATHWAY:R-HSA-917729
|
| 2160 |
+
2158 PATHWAY:R-HSA-917937
|
| 2161 |
+
2159 PATHWAY:R-HSA-917977
|
| 2162 |
+
2160 PATHWAY:R-HSA-918233
|
| 2163 |
+
2161 PATHWAY:R-HSA-927802
|
| 2164 |
+
2162 PATHWAY:R-HSA-933541
|
| 2165 |
+
2163 PATHWAY:R-HSA-933542
|
| 2166 |
+
2164 PATHWAY:R-HSA-933543
|
| 2167 |
+
2165 PATHWAY:R-HSA-936440
|
| 2168 |
+
2166 PATHWAY:R-HSA-936837
|
| 2169 |
+
2167 PATHWAY:R-HSA-936964
|
| 2170 |
+
2168 PATHWAY:R-HSA-937039
|
| 2171 |
+
2169 PATHWAY:R-HSA-937041
|
| 2172 |
+
2170 PATHWAY:R-HSA-937042
|
| 2173 |
+
2171 PATHWAY:R-HSA-937061
|
| 2174 |
+
2172 PATHWAY:R-HSA-937072
|
| 2175 |
+
2173 PATHWAY:R-HSA-947581
|
| 2176 |
+
2174 PATHWAY:R-HSA-948021
|
| 2177 |
+
2175 PATHWAY:R-HSA-9603381
|
| 2178 |
+
2176 PATHWAY:R-HSA-9603505
|
| 2179 |
+
2177 PATHWAY:R-HSA-9603798
|
| 2180 |
+
2178 PATHWAY:R-HSA-9604323
|
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2179 PATHWAY:R-HSA-9605308
|
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2180 PATHWAY:R-HSA-9605310
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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2202 PATHWAY:R-HSA-9617324
|
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2203 PATHWAY:R-HSA-9617629
|
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2204 PATHWAY:R-HSA-9617828
|
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2205 PATHWAY:R-HSA-9619229
|
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2206 PATHWAY:R-HSA-9619483
|
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|
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2208 PATHWAY:R-HSA-9620244
|
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|
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|
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|
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|
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|
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|
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|
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|
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2217 PATHWAY:R-HSA-9630791
|
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|
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|
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|
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|
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2222 PATHWAY:R-HSA-9632974
|
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|
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|
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2225 PATHWAY:R-HSA-9634597
|
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2226 PATHWAY:R-HSA-9634600
|
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2227 PATHWAY:R-HSA-9634635
|
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2228 PATHWAY:R-HSA-9634638
|
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2229 PATHWAY:R-HSA-9634815
|
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2230 PATHWAY:R-HSA-9635465
|
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2231 PATHWAY:R-HSA-9635486
|
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2232 PATHWAY:R-HSA-9635644
|
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2233 PATHWAY:R-HSA-9636003
|
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2234 PATHWAY:R-HSA-9636249
|
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2235 PATHWAY:R-HSA-9636383
|
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2236 PATHWAY:R-HSA-9636467
|
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2237 PATHWAY:R-HSA-9636569
|
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|
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|
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2240 PATHWAY:R-HSA-9637687
|
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|
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2242 PATHWAY:R-HSA-9638482
|
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2243 PATHWAY:R-HSA-9638630
|
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|
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2245 PATHWAY:R-HSA-9640148
|
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|
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|
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|
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|
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|
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|
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|
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2254 PATHWAY:R-HSA-964739
|
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2255 PATHWAY:R-HSA-9648002
|
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2256 PATHWAY:R-HSA-9648025
|
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2257 PATHWAY:R-HSA-964827
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2258 PATHWAY:R-HSA-9648895
|
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2259 PATHWAY:R-HSA-964975
|
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2260 PATHWAY:R-HSA-9649913
|
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2261 PATHWAY:R-HSA-9649948
|
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2262 PATHWAY:R-HSA-9652169
|
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2263 PATHWAY:R-HSA-9652282
|
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2264 PATHWAY:R-HSA-9652817
|
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2265 PATHWAY:R-HSA-9656223
|
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|
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|
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|
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|
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|
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|
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|
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2273 PATHWAY:R-HSA-9659379
|
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2274 PATHWAY:R-HSA-9659787
|
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2275 PATHWAY:R-HSA-9660537
|
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2276 PATHWAY:R-HSA-9660821
|
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|
| 2280 |
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2278 PATHWAY:R-HSA-9661069
|
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2279 PATHWAY:R-HSA-9661070
|
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|
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2281 PATHWAY:R-HSA-9662360
|
| 2284 |
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|
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|
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|
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2285 PATHWAY:R-HSA-9663199
|
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2286 PATHWAY:R-HSA-9663891
|
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2287 PATHWAY:R-HSA-9664323
|
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2288 PATHWAY:R-HSA-9664407
|
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2289 PATHWAY:R-HSA-9664417
|
| 2292 |
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|
| 2293 |
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2291 PATHWAY:R-HSA-9664422
|
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2292 PATHWAY:R-HSA-9664424
|
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2293 PATHWAY:R-HSA-9664433
|
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2294 PATHWAY:R-HSA-9664535
|
| 2297 |
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2295 PATHWAY:R-HSA-9664565
|
| 2298 |
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2296 PATHWAY:R-HSA-9664873
|
| 2299 |
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2297 PATHWAY:R-HSA-9665230
|
| 2300 |
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2298 PATHWAY:R-HSA-9665233
|
| 2301 |
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2299 PATHWAY:R-HSA-9665244
|
| 2302 |
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2300 PATHWAY:R-HSA-9665245
|
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2301 PATHWAY:R-HSA-9665246
|
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2302 PATHWAY:R-HSA-9665247
|
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2303 PATHWAY:R-HSA-9665249
|
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2304 PATHWAY:R-HSA-9665250
|
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2305 PATHWAY:R-HSA-9665251
|
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2306 PATHWAY:R-HSA-9665348
|
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2307 PATHWAY:R-HSA-9665686
|
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|
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|
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2310 PATHWAY:R-HSA-9668250
|
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|
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2312 PATHWAY:R-HSA-9669914
|
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2313 PATHWAY:R-HSA-9669917
|
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2314 PATHWAY:R-HSA-9669921
|
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2315 PATHWAY:R-HSA-9669924
|
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2316 PATHWAY:R-HSA-9669926
|
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2317 PATHWAY:R-HSA-9669929
|
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2318 PATHWAY:R-HSA-9669933
|
| 2321 |
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2319 PATHWAY:R-HSA-9669934
|
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2320 PATHWAY:R-HSA-9669935
|
| 2323 |
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2321 PATHWAY:R-HSA-9669936
|
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2322 PATHWAY:R-HSA-9669937
|
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2323 PATHWAY:R-HSA-9669938
|
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2324 PATHWAY:R-HSA-9670095
|
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2325 PATHWAY:R-HSA-9670439
|
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2326 PATHWAY:R-HSA-9670613
|
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2327 PATHWAY:R-HSA-9670615
|
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2328 PATHWAY:R-HSA-9670621
|
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2329 PATHWAY:R-HSA-9671555
|
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2330 PATHWAY:R-HSA-9671793
|
| 2333 |
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2331 PATHWAY:R-HSA-9672383
|
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2332 PATHWAY:R-HSA-9672387
|
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2333 PATHWAY:R-HSA-9672391
|
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2334 PATHWAY:R-HSA-9672393
|
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2335 PATHWAY:R-HSA-9672395
|
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2336 PATHWAY:R-HSA-9672396
|
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2337 PATHWAY:R-HSA-9672397
|
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2338 PATHWAY:R-HSA-9673013
|
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2339 PATHWAY:R-HSA-9673163
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2340 PATHWAY:R-HSA-9673202
|
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2341 PATHWAY:R-HSA-9673218
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2342 PATHWAY:R-HSA-9673221
|
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2343 PATHWAY:R-HSA-9673240
|
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2344 PATHWAY:R-HSA-9673324
|
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2345 PATHWAY:R-HSA-9673766
|
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2346 PATHWAY:R-HSA-9673767
|
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2347 PATHWAY:R-HSA-9673768
|
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2348 PATHWAY:R-HSA-9673770
|
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2349 PATHWAY:R-HSA-9674396
|
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2350 PATHWAY:R-HSA-9674401
|
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2351 PATHWAY:R-HSA-9674403
|
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2352 PATHWAY:R-HSA-9674404
|
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2353 PATHWAY:R-HSA-9674415
|
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2354 PATHWAY:R-HSA-9674428
|
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2355 PATHWAY:R-HSA-9674519
|
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2356 PATHWAY:R-HSA-9674555
|
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2357 PATHWAY:R-HSA-9675108
|
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2358 PATHWAY:R-HSA-9675126
|
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2359 PATHWAY:R-HSA-9675132
|
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2360 PATHWAY:R-HSA-9675135
|
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2361 PATHWAY:R-HSA-9675136
|
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2362 PATHWAY:R-HSA-9675143
|
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2363 PATHWAY:R-HSA-9675151
|
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2364 PATHWAY:R-HSA-9678108
|
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2365 PATHWAY:R-HSA-9678110
|
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2366 PATHWAY:R-HSA-9679191
|
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2367 PATHWAY:R-HSA-9679504
|
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2368 PATHWAY:R-HSA-9679506
|
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|
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2371 PATHWAY:R-HSA-9680350
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2372 PATHWAY:R-HSA-9682385
|
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2373 PATHWAY:R-HSA-9682706
|
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2374 PATHWAY:R-HSA-9683610
|
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2375 PATHWAY:R-HSA-9683673
|
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2376 PATHWAY:R-HSA-9683683
|
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2377 PATHWAY:R-HSA-9683686
|
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2378 PATHWAY:R-HSA-9683701
|
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2379 PATHWAY:R-HSA-9684482
|
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2380 PATHWAY:R-HSA-9686114
|
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2381 PATHWAY:R-HSA-9686347
|
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2382 PATHWAY:R-HSA-9687136
|
| 2385 |
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2383 PATHWAY:R-HSA-9687139
|
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2384 PATHWAY:R-HSA-9690406
|
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2385 PATHWAY:R-HSA-9690722
|
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2386 PATHWAY:R-HSA-9692912
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2387 PATHWAY:R-HSA-9692913
|
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2388 PATHWAY:R-HSA-9692914
|
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2389 PATHWAY:R-HSA-9692916
|
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2390 PATHWAY:R-HSA-9693928
|
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2391 PATHWAY:R-HSA-9694301
|
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2392 PATHWAY:R-HSA-9694493
|
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2393 PATHWAY:R-HSA-9694516
|
| 2396 |
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2394 PATHWAY:R-HSA-9694548
|
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2395 PATHWAY:R-HSA-9694614
|
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2396 PATHWAY:R-HSA-9694631
|
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2397 PATHWAY:R-HSA-9694635
|
| 2400 |
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2398 PATHWAY:R-HSA-9694676
|
| 2401 |
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2399 PATHWAY:R-HSA-9694682
|
| 2402 |
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2400 PATHWAY:R-HSA-9694686
|
| 2403 |
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2401 PATHWAY:R-HSA-9694719
|
| 2404 |
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2402 PATHWAY:R-HSA-9696264
|
| 2405 |
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2403 PATHWAY:R-HSA-9696270
|
| 2406 |
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2404 PATHWAY:R-HSA-9696273
|
| 2407 |
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2405 PATHWAY:R-HSA-9697154
|
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2406 PATHWAY:R-HSA-9699150
|
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2407 PATHWAY:R-HSA-9700206
|
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2408 PATHWAY:R-HSA-9700645
|
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2409 PATHWAY:R-HSA-9700649
|
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2410 PATHWAY:R-HSA-9701190
|
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2411 PATHWAY:R-HSA-9701192
|
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2412 PATHWAY:R-HSA-9701193
|
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2413 PATHWAY:R-HSA-9701898
|
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2414 PATHWAY:R-HSA-9702506
|
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2415 PATHWAY:R-HSA-9702509
|
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2416 PATHWAY:R-HSA-9702518
|
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2417 PATHWAY:R-HSA-9702569
|
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2418 PATHWAY:R-HSA-9702577
|
| 2421 |
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2419 PATHWAY:R-HSA-9702581
|
| 2422 |
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2420 PATHWAY:R-HSA-9702590
|
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2421 PATHWAY:R-HSA-9702596
|
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2422 PATHWAY:R-HSA-9702600
|
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2423 PATHWAY:R-HSA-9702605
|
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2424 PATHWAY:R-HSA-9702614
|
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2425 PATHWAY:R-HSA-9702620
|
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2426 PATHWAY:R-HSA-9702624
|
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2427 PATHWAY:R-HSA-9702632
|
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2428 PATHWAY:R-HSA-9702636
|
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2429 PATHWAY:R-HSA-9702998
|
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2430 PATHWAY:R-HSA-9703009
|
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2431 PATHWAY:R-HSA-9703465
|
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2432 PATHWAY:R-HSA-9703648
|
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2433 PATHWAY:R-HSA-9704331
|
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2434 PATHWAY:R-HSA-9704646
|
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2435 PATHWAY:R-HSA-9705462
|
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2436 PATHWAY:R-HSA-9705671
|
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2437 PATHWAY:R-HSA-9705677
|
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2438 PATHWAY:R-HSA-9705683
|
| 2441 |
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2439 PATHWAY:R-HSA-9706019
|
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2440 PATHWAY:R-HSA-9706369
|
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2441 PATHWAY:R-HSA-9706374
|
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2442 PATHWAY:R-HSA-9706377
|
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2443 PATHWAY:R-HSA-9706574
|
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2444 PATHWAY:R-HSA-9707564
|
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2445 PATHWAY:R-HSA-9707587
|
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2446 PATHWAY:R-HSA-9707616
|
| 2449 |
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2447 PATHWAY:R-HSA-9708296
|
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2448 PATHWAY:R-HSA-9708530
|
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2449 PATHWAY:R-HSA-9709275
|
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2450 PATHWAY:R-HSA-9709570
|
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2451 PATHWAY:R-HSA-9709603
|
| 2454 |
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2452 PATHWAY:R-HSA-9709957
|
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2453 PATHWAY:R-HSA-9710421
|
| 2456 |
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2454 PATHWAY:R-HSA-9711097
|
| 2457 |
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2455 PATHWAY:R-HSA-9711123
|
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2456 PATHWAY:R-HSA-9715370
|
| 2459 |
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2457 PATHWAY:R-HSA-9716542
|
| 2460 |
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2458 PATHWAY:R-HSA-9717189
|
| 2461 |
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2459 PATHWAY:R-HSA-9717207
|
| 2462 |
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2460 PATHWAY:R-HSA-9717264
|
| 2463 |
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2461 PATHWAY:R-HSA-9717301
|
| 2464 |
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2462 PATHWAY:R-HSA-9717316
|
| 2465 |
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2463 PATHWAY:R-HSA-9717319
|
| 2466 |
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2464 PATHWAY:R-HSA-9717323
|
| 2467 |
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2465 PATHWAY:R-HSA-9717326
|
| 2468 |
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2466 PATHWAY:R-HSA-9717329
|
| 2469 |
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2467 PATHWAY:R-HSA-9723905
|
| 2470 |
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2468 PATHWAY:R-HSA-9723907
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| 2471 |
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2643 PATHWAY:R-HSA-9840310
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2644 PATHWAY:R-HSA-9840373
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2645 PATHWAY:R-HSA-9841251
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2646 PATHWAY:R-HSA-9841922
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2752 PATHWAY:R-HSA-9931530
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2754 PATHWAY:R-HSA-9931953
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2755 PATHWAY:R-HSA-9932298
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2756 PATHWAY:R-HSA-9932444
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2757 PATHWAY:R-HSA-9932451
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2758 PATHWAY:R-HSA-9933387
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| 2761 |
+
2759 PATHWAY:R-HSA-9933937
|
| 2762 |
+
2760 PATHWAY:R-HSA-9933939
|
| 2763 |
+
2761 PATHWAY:R-HSA-9933946
|
| 2764 |
+
2762 PATHWAY:R-HSA-9933947
|
| 2765 |
+
2763 PATHWAY:R-HSA-9934037
|
| 2766 |
+
2764 PATHWAY:R-HSA-9935598
|
| 2767 |
+
2765 PATHWAY:R-HSA-9936686
|
| 2768 |
+
2766 PATHWAY:R-HSA-9936900
|
| 2769 |
+
2767 PATHWAY:R-HSA-9937008
|
| 2770 |
+
2768 PATHWAY:R-HSA-9937080
|
| 2771 |
+
2769 PATHWAY:R-HSA-9937383
|
| 2772 |
+
2770 PATHWAY:R-HSA-9937848
|
| 2773 |
+
2771 PATHWAY:R-HSA-9937850
|
| 2774 |
+
2772 PATHWAY:R-HSA-9938024
|
| 2775 |
+
2773 PATHWAY:R-HSA-9938026
|
| 2776 |
+
2774 PATHWAY:R-HSA-9938027
|
| 2777 |
+
2775 PATHWAY:R-HSA-9938206
|
| 2778 |
+
2776 PATHWAY:R-HSA-9939291
|
| 2779 |
+
2777 PATHWAY:R-HSA-9940465
|
| 2780 |
+
2778 PATHWAY:R-HSA-9940951
|
| 2781 |
+
2779 PATHWAY:R-HSA-9942503
|
| 2782 |
+
2780 PATHWAY:R-HSA-9943411
|
| 2783 |
+
2781 PATHWAY:R-HSA-9943962
|
| 2784 |
+
2782 PATHWAY:R-HSA-9943965
|
| 2785 |
+
2783 PATHWAY:R-HSA-9944971
|
| 2786 |
+
2784 PATHWAY:R-HSA-9944997
|
| 2787 |
+
2785 PATHWAY:R-HSA-9945266
|
| 2788 |
+
2786 PATHWAY:R-HSA-9945556
|
| 2789 |
+
2787 PATHWAY:R-HSA-9946127
|
| 2790 |
+
2788 PATHWAY:R-HSA-9948001
|
| 2791 |
+
2789 PATHWAY:R-HSA-9948011
|
| 2792 |
+
2790 PATHWAY:R-HSA-9948299
|
| 2793 |
+
2791 PATHWAY:R-HSA-9953038
|
| 2794 |
+
2792 PATHWAY:R-HSA-9953078
|
| 2795 |
+
2793 PATHWAY:R-HSA-9953080
|
| 2796 |
+
2794 PATHWAY:R-HSA-9953097
|
| 2797 |
+
2795 PATHWAY:R-HSA-9953111
|
| 2798 |
+
2796 PATHWAY:R-HSA-9953170
|
| 2799 |
+
2797 PATHWAY:R-HSA-9954709
|
| 2800 |
+
2798 PATHWAY:R-HSA-9954714
|
| 2801 |
+
2799 PATHWAY:R-HSA-9954716
|
| 2802 |
+
2800 PATHWAY:R-HSA-9955298
|
| 2803 |
+
2801 PATHWAY:R-HSA-9955542
|
| 2804 |
+
2802 PATHWAY:R-HSA-9955693
|
| 2805 |
+
2803 PATHWAY:R-HSA-9955698
|
| 2806 |
+
2804 PATHWAY:R-HSA-9956508
|
| 2807 |
+
2805 PATHWAY:R-HSA-9956514
|
| 2808 |
+
2806 PATHWAY:R-HSA-9956520
|
| 2809 |
+
2807 PATHWAY:R-HSA-9956522
|
| 2810 |
+
2808 PATHWAY:R-HSA-9956529
|
| 2811 |
+
2809 PATHWAY:R-HSA-9956551
|
| 2812 |
+
2810 PATHWAY:R-HSA-9956553
|
| 2813 |
+
2811 PATHWAY:R-HSA-9956593
|
| 2814 |
+
2812 PATHWAY:R-HSA-9958517
|
| 2815 |
+
2813 PATHWAY:R-HSA-9958790
|
| 2816 |
+
2814 PATHWAY:R-HSA-9958810
|
| 2817 |
+
2815 PATHWAY:R-HSA-9958825
|
| 2818 |
+
2816 PATHWAY:R-HSA-9958863
|
| 2819 |
+
2817 PATHWAY:R-HSA-9959399
|
| 2820 |
+
2818 PATHWAY:R-HSA-9960519
|
| 2821 |
+
2819 PATHWAY:R-HSA-9960525
|
| 2822 |
+
2820 PATHWAY:R-HSA-9968295
|
| 2823 |
+
2821 PATHWAY:R-HSA-9968297
|
| 2824 |
+
2822 PATHWAY:R-HSA-9968551
|
| 2825 |
+
2823 PATHWAY:R-HSA-9968734
|
| 2826 |
+
2824 PATHWAY:R-HSA-9969896
|
| 2827 |
+
2825 PATHWAY:R-HSA-9969901
|
| 2828 |
+
2826 PATHWAY:R-HSA-9970672
|
| 2829 |
+
2827 PATHWAY:R-HSA-997272
|
| 2830 |
+
2828 PATHWAY:R-HSA-9974237
|
| 2831 |
+
2829 PATHWAY:R-HSA-9975921
|
| 2832 |
+
2830 PATHWAY:R-HSA-9975924
|
| 2833 |
+
2831 PATHWAY:R-HSA-9976102
|
| 2834 |
+
2832 PATHWAY:R-HSA-9979719
|
| 2835 |
+
2833 PATHWAY:R-HSA-9981148
|
| 2836 |
+
2834 PATHWAY:R-HSA-9988426
|
initial_data/clinvar_strict_rebuild_v1/05_graph_v2_inputs/G2a/node_mappings/protein.tsv
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
initial_data/clinvar_strict_rebuild_v1/05_graph_v2_inputs/G2a/node_mappings/ptm.tsv
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
initial_data/clinvar_strict_rebuild_v1/05_graph_v2_inputs/G2a/relation_mappings/relations.tsv
ADDED
|
@@ -0,0 +1,13 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
relation_index relation src_type dst_type direction
|
| 2 |
+
0 mutation__on_protein__protein mutation protein forward
|
| 3 |
+
1 protein__rev_on_protein__mutation protein mutation reverse
|
| 4 |
+
2 protein__has_ptm__ptm protein ptm forward
|
| 5 |
+
3 ptm__rev_has_ptm__protein ptm protein reverse
|
| 6 |
+
4 protein__in_pathway__pathway protein pathway forward
|
| 7 |
+
5 pathway__rev_in_pathway__protein pathway protein reverse
|
| 8 |
+
6 disease__has_mutation__mutation disease mutation forward
|
| 9 |
+
7 mutation__rev_has_mutation__disease mutation disease reverse
|
| 10 |
+
8 disease__has_ptm__ptm disease ptm forward
|
| 11 |
+
9 ptm__rev_has_ptm__disease ptm disease reverse
|
| 12 |
+
10 disease__has_protein__protein disease protein forward
|
| 13 |
+
11 protein__rev_has_protein__disease protein disease reverse
|
initial_data/clinvar_strict_rebuild_v1/05_graph_v2_inputs/G2a/remap_audit.json
ADDED
|
@@ -0,0 +1,23 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"canonical_forward_counts": {
|
| 3 |
+
"disease__has_mutation__mutation": 3194088,
|
| 4 |
+
"disease__has_protein__protein": 360600,
|
| 5 |
+
"disease__has_ptm__ptm": 302010,
|
| 6 |
+
"mutation__on_protein__protein": 4498756,
|
| 7 |
+
"protein__has_ptm__ptm": 199011,
|
| 8 |
+
"protein__in_pathway__pathway": 137953
|
| 9 |
+
},
|
| 10 |
+
"canonical_forward_edge_rows": 8692418,
|
| 11 |
+
"condition": "G2a",
|
| 12 |
+
"generated_reverse_edge_rows": 8692418,
|
| 13 |
+
"source_edge_rows": 8692418,
|
| 14 |
+
"source_relation_rows": {
|
| 15 |
+
"0|associated_with_mutation|disease|mutation": 3194088,
|
| 16 |
+
"1|associated_with_protein|disease|protein": 360600,
|
| 17 |
+
"2|associated_with_ptm|disease|ptm": 302010,
|
| 18 |
+
"3|on_protein|mutation|protein": 4498756,
|
| 19 |
+
"4|in_pathway|protein|pathway": 137953,
|
| 20 |
+
"5|has_ptm|protein|ptm": 199011
|
| 21 |
+
},
|
| 22 |
+
"status": "PASS"
|
| 23 |
+
}
|