README.md

metadata

license: other
tags:
  - graph-residual
  - protein
  - mutation
  - ptm
  - biomedical

GraphResidual data package

Public research dataset package for the GraphResidual repository. It contains source datasets, derived benchmark tables, processed graph tables, and graph artifacts used by the ESM-2 and AMPLIFY-120M experiments.

Layout

• data_raw/: source data and model assets used by the released experiments.
• data_benchmark/: benchmark splits, candidate sets, and audit tables.
• data_processed/: processed node, edge, and label tables.
• data_processed_clean/: cleaned processed tables.
• data_processed_core/: core processed tables and candidate tables.
• work/graph_core/: compact graph mappings, relations, and graph artifacts.
• work/graph_full/: full graph node and relation tables.
• initial_data/root/: additional server-side source resources, including ClinVar, Reactome, UniProt, PTM, GTEx, and final ClinVar tables.
• initial_data/brca_tcga_pan_can_atlas_2018/: BRCA TCGA PanCanAtlas 2018 molecular and clinical source tables.
• initial_data/clinvar_strict_rebuild_v1/: strict ClinVar graph nodes, edges, mappings, splits, graph inputs, and removal ledgers.
• initial_data/clinvar_strict_rebuild_audit/: source manifests and audit tables for the strict ClinVar rebuild.
• initial_data/inductive_graph_residual_extension/: inductive split data, graph mappings, feature inventories, and related data contracts.
• initial_data/data_raw_download/, data_raw_partial/, and data_raw_scp/: retained raw-download copies and transfer artifacts.

Exclusions

Images, figures, logs, Python bytecode, cache directories, code snapshots, model checkpoints, embeddings, predictions, and experiment-only output tables are not included in this data package.

Reproducibility and provenance

Use the public code and usage guide in GraphResidual for the expected directory layout and model interfaces. The uploaded data are public; check the original source database terms, licenses, and citation requirements before redistribution or publication.