| --- |
| 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. |
|
|
