---
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](https://github.com/zhang-chris0320/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.