Add GraphResidual dataset card
Browse files
README.md
ADDED
|
@@ -0,0 +1,39 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
---
|
| 2 |
+
license: other
|
| 3 |
+
tags:
|
| 4 |
+
- graph-residual
|
| 5 |
+
- protein
|
| 6 |
+
- mutation
|
| 7 |
+
- ptm
|
| 8 |
+
- biomedical
|
| 9 |
+
private: true
|
| 10 |
+
---
|
| 11 |
+
|
| 12 |
+
# GraphResidual data package
|
| 13 |
+
|
| 14 |
+
Private research dataset package for the GraphResidual repository. The package
|
| 15 |
+
contains the source datasets, derived benchmark tables, processed graph tables,
|
| 16 |
+
and graph artifacts used by the ESM-2 and AMPLIFY-120M experiments.
|
| 17 |
+
|
| 18 |
+
## Layout
|
| 19 |
+
|
| 20 |
+
- `data_raw/`: source data and model assets, including ClinVar, UniProt,
|
| 21 |
+
Reactome, PTMD, PPI/complex resources, and AMPLIFY-120M files.
|
| 22 |
+
- `data_benchmark/`: benchmark splits, candidate sets, and audit tables.
|
| 23 |
+
- `data_processed/`: processed node, edge, and label tables.
|
| 24 |
+
- `data_processed_clean/`: cleaned processed tables.
|
| 25 |
+
- `data_processed_core/`: core processed tables and candidate tables.
|
| 26 |
+
- `work/graph_core/`: compact graph mappings, relations, and graph artifact.
|
| 27 |
+
- `work/graph_full/`: full graph node and relation tables.
|
| 28 |
+
|
| 29 |
+
## Exclusions
|
| 30 |
+
|
| 31 |
+
Images, figures, logs, reports, Python bytecode, and cache directories are not
|
| 32 |
+
included in this dataset package.
|
| 33 |
+
|
| 34 |
+
## Reproducibility
|
| 35 |
+
|
| 36 |
+
Use the public code and usage guide in
|
| 37 |
+
[GraphResidual](https://github.com/zhang-chris0320/GraphResidual) for the
|
| 38 |
+
expected directory layout and model interfaces. Check the original source
|
| 39 |
+
database terms and citation requirements before redistribution or publication.
|