├── LICENSE.txt ├── README.md ├── examples ├── .DS_Store ├── README.md ├── gene_set.ipynb ├── gene_summary.ipynb ├── kg_analysis.ipynb ├── kg_to_prompt.ipynb ├── results.ipynb ├── sanity_check │ ├── .DS_Store │ ├── README.md │ ├── __init__.py │ ├── config │ │ ├── kg_gnn.yaml │ │ ├── kg_gnn_pathway.yaml │ │ ├── mlp.yaml │ │ └── mlp_pathway.yaml │ ├── data.py │ ├── data │ │ ├── 20240710-replogle_k562_gw.csv │ │ ├── 20240712-nadig_hepg2.csv │ │ ├── 20240712-nadig_jurkat.csv │ │ ├── 20240712-replogle_k562_gw.csv │ │ ├── 20240712-replogle_k562_gw_path.csv │ │ ├── 20240712-replogle_rpe1_essential.csv │ │ ├── 20240717-replogle_k562_gw_path.csv │ │ ├── inference.yaml │ │ ├── k562_clusters.json │ │ └── kg_path.yaml │ ├── environment.yml │ ├── inference.py │ ├── inference.sh │ ├── inference_batch.py │ ├── model │ │ ├── __init__.py │ │ ├── factory.py │ │ ├── gnn.py │ │ ├── gnn_pathway.py │ │ ├── mlp.py │ │ └── mlp_pathway.py │ ├── parser.py │ ├── train.py │ ├── train_sweep_gnn.sh │ ├── train_sweep_mlp.sh │ └── utils.py └── summer │ ├── .DS_Store │ ├── README.md │ ├── inputs │ └── sample.json │ ├── outputs │ └── sample.json │ ├── parsing.py │ ├── prompts │ ├── enrich.py │ ├── llm-no_cot.py │ ├── llm-no_retrieve.py │ ├── retrieve.py │ ├── summarize.py │ └── summer_qa.py │ ├── run_llama70b.py │ └── run_llama8b.py ├── perturbqa ├── .DS_Store ├── __init__.py ├── data.py ├── datasets │ ├── hepg2-de.csv │ ├── hepg2-dir.csv │ ├── jurkat-de.csv │ ├── jurkat-dir.csv │ ├── k562-de.csv │ ├── k562-dir.csv │ ├── k562_gene-gse.json │ ├── k562_gw_mapping_full.json │ ├── k562_pert-gse.json │ ├── k562_set-de.csv │ ├── k562_set-dir.csv │ ├── k562_set-mapping.json │ ├── rpe1-de.csv │ └── rpe1-dir.csv └── eval.py └── pyproject.toml /LICENSE.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Genentech/PerturbQA/HEAD/LICENSE.txt -------------------------------------------------------------------------------- /README.md: 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