├── .gitignore ├── LICENSE ├── README.md ├── data ├── data_splits │ ├── gene_level_benchmark │ │ ├── go_folds_splits │ │ │ ├── go_cv_fold1_dict_all.pkl │ │ │ ├── go_cv_fold2_dict_all.pkl │ │ │ ├── go_cv_fold3_dict_all.pkl │ │ │ └── go_holdout_dict_all.pkl │ │ ├── go_generalization_folds_splits │ │ │ ├── go_cv_fold1_dict_all.pkl │ │ │ ├── go_cv_fold2_dict_all.pkl │ │ │ ├── go_cv_fold3_dict_all.pkl │ │ │ ├── go_holdout_dict_all.pkl │ │ │ ├── go_holdout_older_dict_all.pkl │ │ │ ├── intersect_ref_genelist.txt │ │ │ └── run_go_generalization_benchmark.py │ │ └── omim_folds_splits │ │ │ ├── omim_cv_fold1_dict_all.pkl │ │ │ ├── omim_cv_fold2_dict_all.pkl │ │ │ ├── omim_cv_fold3_dict_all.pkl │ │ │ └── omim_holdout_dict_all.pkl │ └── gene_pair_benchmark │ │ ├── ng_nested_cv_splits.pkl │ │ ├── pombe_nested_cv_splits.pkl │ │ ├── sl_nested_cv_splits.pkl │ │ └── tf_nested_cv_splits.pkl ├── embed_meta.csv ├── gmt │ ├── 2020_hsa_ALL_BP_direct.gmt │ ├── 2020_hsa_ALL_BP_propagated.gmt │ ├── GO_BP_EXP_propagated_10_since_240328.gmt │ ├── KEGG_CPDB.gmt │ ├── bto_specific.gmt │ ├── hsa_EXP_ALL_BP_direct.gmt │ ├── hsa_EXP_ALL_BP_propagated.gmt │ ├── hsa_experimental_eval_BP_propagated.gmt │ ├── hsa_low_eval_BP_propagated.gmt │ ├── omim.20231030.direct.gmt │ ├── omim.20231030.prop.gmt │ └── omim_entrez.gmt ├── matched_pairs │ ├── matched_list_bto_doid.txt │ ├── matched_pair_kegg_go.txt │ └── matched_pairs_go_go.txt ├── obo │ ├── doid.obo │ └── go.obo └── slim_sets │ ├── doid_agr_slim.txt │ └── goslim_agr.tsv ├── env.yml ├── results ├── plots │ └── README.md └── tsvs │ ├── cca_pca10.tsv │ ├── gene_set_andes_disease_tissue_btoAUROC_no_overlap.tsv │ ├── gene_set_andes_disease_tissue_btoAUROC_no_overlap_full.tsv │ ├── gene_set_andes_disease_tissue_btoAUROC_overlap.tsv │ ├── gene_set_andes_disease_tissue_btoAUROC_overlap_full.tsv │ ├── gene_set_andes_go_go_rank_no_overlap.tsv │ ├── gene_set_andes_go_go_rank_no_overlap_full.tsv │ ├── gene_set_andes_kegg_go_rank_no_overlap.tsv │ ├── gene_set_andes_kegg_go_rank_no_overlap_full.tsv │ ├── gene_set_andes_kegg_go_rank_overlap.tsv │ ├── gene_set_andes_kegg_go_rank_overlap_full.tsv │ ├── jaccard_genes.tsv │ ├── paired_gene_ng_concat_outerloop_AUC.tsv │ ├── paired_gene_ng_concat_outerloop_avgs.tsv │ ├── paired_gene_ng_concat_outerloop_avgs_full.tsv │ ├── paired_gene_ng_product_outerloop_AUC.tsv │ ├── paired_gene_ng_product_outerloop_avgs.tsv │ ├── paired_gene_ng_product_outerloop_avgs_full.tsv │ ├── paired_gene_ng_sum_outerloop_AUC.tsv │ ├── paired_gene_ng_sum_outerloop_avgs.tsv │ ├── paired_gene_ng_sum_outerloop_avgs_full.tsv │ ├── paired_gene_pombe_ng_concat_outerloop_AUC.tsv │ ├── paired_gene_pombe_ng_concat_outerloop_avgs.tsv │ ├── paired_gene_pombe_ng_concat_outerloop_avgs_full.tsv │ ├── paired_gene_pombe_ng_product_outerloop_AUC.tsv │ ├── paired_gene_pombe_ng_product_outerloop_avgs.tsv │ ├── paired_gene_pombe_ng_product_outerloop_avgs_full.tsv │ ├── paired_gene_pombe_ng_sum_outerloop_AUC.tsv │ ├── paired_gene_pombe_ng_sum_outerloop_avgs.tsv │ ├── paired_gene_pombe_ng_sum_outerloop_avgs_full.tsv │ ├── paired_gene_sl_concat_outerloop_AUC.tsv │ ├── paired_gene_sl_concat_outerloop_avgs.tsv │ ├── paired_gene_sl_concat_outerloop_avgs_full.tsv │ ├── paired_gene_sl_product_outerloop_AUC.tsv │ ├── paired_gene_sl_product_outerloop_avgs.tsv │ ├── paired_gene_sl_product_outerloop_avgs_full.tsv │ ├── paired_gene_sl_sum_outerloop_AUC.tsv │ ├── paired_gene_sl_sum_outerloop_avgs.tsv │ ├── paired_gene_sl_sum_outerloop_avgs_full.tsv │ ├── paired_gene_tf_concat_outerloop_AUC.tsv │ ├── paired_gene_tf_concat_outerloop_avgs.tsv │ ├── paired_gene_tf_concat_outerloop_avgs_full.tsv │ ├── paired_gene_tf_product_outerloop_AUC.tsv │ ├── paired_gene_tf_product_outerloop_avgs.tsv │ ├── paired_gene_tf_product_outerloop_avgs_full.tsv │ ├── paired_gene_tf_sum_outerloop_AUC.tsv │ ├── paired_gene_tf_sum_outerloop_avgs.tsv │ ├── paired_gene_tf_sum_outerloop_avgs_full.tsv │ ├── single_gene_go_AUROC.tsv │ ├── 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