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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.
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