--- dataset_info: - config_name: cells features: - name: name dtype: string - name: tissue dtype: string - name: description dtype: string - name: genetic_dependencies dtype: string - name: top_expressed_overall_genes dtype: string - name: top_expressed_cell_specific_genes dtype: string - name: top_expressed_pathways dtype: string - name: top_expressed_genes_depmap dtype: string - name: top_expressed_pathways_old dtype: string - name: top_pathways_from_num_markers dtype: string splits: - name: cells num_bytes: 1366870 num_examples: 161 download_size: 764581 dataset_size: 1366870 - config_name: chebi features: - name: chebi_id dtype: string - name: name dtype: string - name: definition dtype: string - name: formula dtype: string - name: smiles dtype: string - name: synonyms list: string - name: secondary_ids list: string splits: - name: chebi num_bytes: 12759478 num_examples: 55121 download_size: 3959122 dataset_size: 12759478 - config_name: contrastive-perturbqa features: - name: study dtype: string - name: cell_type_A dtype: string - name: cell_type_B dtype: string - name: tissue_A dtype: string - name: tissue_B dtype: string - name: perturbation dtype: string - name: perturbation_type dtype: string - name: concentration dtype: string - name: pathway dtype: string - name: mean_change_A dtype: float64 - name: mean_change_B dtype: float64 - name: pvals_adj_A dtype: float64 - name: pvals_adj_B dtype: float64 - name: cohens_d_A dtype: float64 - name: cohens_d_B dtype: float64 - name: response_A dtype: string - name: response_B dtype: string - name: direction dtype: string - name: cell_file_A dtype: string - name: cell_file_B dtype: string - name: control_file_A dtype: string - name: control_file_B dtype: string splits: - name: train num_bytes: 66612404 num_examples: 114364 - name: val num_bytes: 8325324 num_examples: 14295 - name: test num_bytes: 8327349 num_examples: 14296 download_size: 9231988 dataset_size: 83265077 - config_name: contrastive-tahoe-DMSO-baseline features: - name: study dtype: string - name: cell_type_A dtype: string - name: cell_type_B dtype: string - name: tissue_A dtype: string - name: tissue_B dtype: string - name: perturbation dtype: string - name: perturbation_type dtype: string - name: concentration dtype: string - name: pathway dtype: string - name: mean_change_A dtype: float64 - name: mean_change_B dtype: float64 - name: pvals_adj_A dtype: float64 - name: pvals_adj_B dtype: float64 - name: cohens_d_A dtype: float64 - name: cohens_d_B dtype: float64 - name: response_A dtype: string - name: response_B dtype: string - name: direction dtype: string - name: cell_file_A dtype: string - name: cell_file_B dtype: string - name: control_file_A dtype: string - name: control_file_B dtype: string splits: - name: train num_bytes: 3206375582 num_examples: 5927793 - name: val num_bytes: 400803587 num_examples: 740975 - name: test num_bytes: 400815190 num_examples: 740975 download_size: 422322108 dataset_size: 4007994359 - config_name: contrastive-tahoe-drug features: - name: study dtype: string - name: cell_type_A dtype: string - name: cell_type_B dtype: string - name: tissue_A dtype: string - name: tissue_B dtype: string - name: perturbation dtype: string - name: perturbation_type dtype: string - name: concentration dtype: string - name: pathway dtype: string - name: mean_change_A dtype: float64 - name: mean_change_B dtype: float64 - name: pvals_adj_A dtype: float64 - name: pvals_adj_B dtype: float64 - name: cohens_d_A dtype: float64 - name: cohens_d_B dtype: float64 - name: response_A dtype: string - name: response_B dtype: string - name: direction dtype: string - name: cell_file_A dtype: string - name: cell_file_B dtype: string - name: control_file_A dtype: string - name: control_file_B dtype: string splits: - name: train num_bytes: 11164588361 num_examples: 19745177 - name: val num_bytes: 1395568528 num_examples: 2468148 - name: test num_bytes: 1395539543 num_examples: 2468148 download_size: 1468812083 dataset_size: 13955696432 - config_name: genes features: - name: gene dtype: large_string - name: uniprot_id dtype: large_string - name: protein_name dtype: large_string - name: protein_function dtype: large_string - name: protein_domains list: string - name: protein_interactions list: string - name: pathways list: string - name: go_mf list: string - name: go_bp list: string - name: go_cc list: string - name: subcellular_location dtype: large_string - name: is_essential dtype: bool - name: important_pathways list: string - name: protein_domains_full list: string - name: go_mf_full list: string - name: go_bp_full list: string - name: go_cc_full list: string - name: tissue_specificity dtype: large_string - name: subunit_description dtype: large_string - name: ptm dtype: large_string - name: domain_description dtype: large_string - name: induction dtype: large_string - name: activity_regulation dtype: large_string - name: intact_partners list: string splits: - name: genes num_bytes: 161303868 num_examples: 20045 download_size: 148390551 dataset_size: 161303868 - config_name: pathway_id_mapping features: - name: msigdb_id dtype: string - name: pi_pathway_names list: string splits: - name: pathway_id_mapping num_bytes: 337116 num_examples: 1704 download_size: 84279 dataset_size: 337116 - config_name: pathway_interactions features: - name: participant_a dtype: string - name: interaction_type dtype: string - name: participant_b dtype: string - name: chebi_names dtype: string - name: ascii_chebi_names dtype: string - name: interaction_type_description dtype: string - name: pathway_names dtype: string - name: mediator_ids dtype: string - name: interaction_data_source dtype: string - name: interaction_pubmed_id dtype: string - name: query_gene dtype: string splits: - name: train num_bytes: 596848476 num_examples: 682786 download_size: 11086613 dataset_size: 596848476 - config_name: pathways features: - name: pathway dtype: string - name: genes list: string - name: brief_description dtype: string splits: - name: pathways num_bytes: 22357584 num_examples: 14921 download_size: 5207121 dataset_size: 22357584 - config_name: reasoning-tahoe-pathway-classification features: - name: drug dtype: string - name: concentration dtype: string - name: cell_line dtype: string - name: cell_file dtype: string - name: control_cell_file dtype: string - name: up_pathways dtype: string - name: down_pathways dtype: string - name: unchanged_pathways dtype: string - name: n_up dtype: int64 - name: n_down dtype: int64 - name: n_unchanged dtype: int64 - name: organ dtype: string - name: depmap_id dtype: string - name: driver_genes dtype: string - name: drug_targets dtype: string - name: moa_broad dtype: string - name: moa_fine dtype: string - name: human_approved dtype: string - name: clinical_trials dtype: string - name: canonical_smiles dtype: string splits: - name: train num_bytes: 521426255 num_examples: 21023 - name: val num_bytes: 64284233 num_examples: 2625 - name: test num_bytes: 66128747 num_examples: 2628 download_size: 236143097 dataset_size: 651839235 - config_name: reasoning_kaufman features: - name: gene_target dtype: large_string - name: protein_target dtype: large_string - name: cell_type dtype: large_string - name: tissue_type dtype: large_string - name: stimulation dtype: large_string - name: pathway_name dtype: large_string - name: pathway_change dtype: large_string - name: pathway_score dtype: float64 - name: experiment dtype: large_string - name: cell_file dtype: large_string splits: - name: train num_bytes: 3887398833 num_examples: 11325863 - name: test num_bytes: 422909306 num_examples: 1231665 download_size: 216634639 dataset_size: 4310308139 - config_name: reasoning_marson features: - name: gene_target dtype: large_string - name: protein_target dtype: large_string - name: cell_type dtype: large_string - name: tissue_type dtype: large_string - name: stimulation dtype: large_string - name: pathway_name dtype: large_string - name: pathway_change dtype: large_string - name: pathway_score dtype: float64 - name: experiment dtype: large_string - name: cell_file dtype: large_string - name: donor_id dtype: large_string splits: - name: train num_bytes: 12259760995 num_examples: 33522035 - name: test num_bytes: 1383435286 num_examples: 3779135 download_size: 665735811 dataset_size: 15007839922 - config_name: reasoning_nadig_replogle_new features: - name: gene_target dtype: string - name: protein_target dtype: string - name: cell_type dtype: string - name: tissue_type dtype: string - name: pathway_name dtype: string - name: pathway_change dtype: string - name: pathway_score dtype: float64 - name: experiment dtype: string - name: cell_file dtype: string - name: is_essential dtype: bool - name: is_offtarget dtype: bool splits: - name: train num_bytes: 282609909 num_examples: 1122402 - name: test num_bytes: 371542221 num_examples: 1473942 download_size: 28084042 dataset_size: 654152130 - config_name: reasoning_norman features: - name: gene_target list: string - name: protein_target list: string - name: cell_type dtype: string - name: tissue_type dtype: string - name: stimulation dtype: string - name: pathway_name dtype: string - name: pathway_change dtype: string - name: pathway_score dtype: float64 - name: experiment dtype: string - name: cell_file dtype: string splits: - name: train num_bytes: 485539527 num_examples: 1630264 - name: test num_bytes: 8271934 num_examples: 28108 download_size: 25487556 dataset_size: 493811461 - config_name: reasoning_papalexi2021 features: - name: gene_target dtype: string - name: protein_target dtype: string - name: cell_type dtype: string - name: tissue_type dtype: string - name: pathway_name dtype: string - name: pathway_change dtype: string - name: pathway_score dtype: float64 - name: experiment dtype: string - name: cell_file dtype: string splits: - name: train num_bytes: 34219642 num_examples: 129115 - name: test num_bytes: 4276569 num_examples: 16125 download_size: 2583393 dataset_size: 42768915 - config_name: reasoning_tahoe_drug features: - name: drug dtype: string - name: concentration dtype: float64 - name: cell_type dtype: string - name: tissue_type dtype: string - name: pathway_name dtype: string - name: pathway_change dtype: string - name: pathway_score dtype: float64 - name: experiment dtype: string - name: cell_file dtype: string splits: - name: train num_bytes: 58639339 num_examples: 210060 - name: validation num_bytes: 4912243 num_examples: 17040 - name: test num_bytes: 6407075 num_examples: 22980 download_size: 2290190 dataset_size: 69958657 - config_name: reasoning_xaira_offtarget features: - name: gene_target dtype: string - name: protein_target dtype: string - name: cell_type dtype: string - name: tissue_type dtype: string - name: pathway_name dtype: string - name: pathway_change dtype: string - name: pathway_score dtype: float64 - name: experiment dtype: string - name: cell_file dtype: string - name: is_offtarget dtype: bool splits: - name: train num_bytes: 228090015 num_examples: 713430 - name: test num_bytes: 122696851 num_examples: 383340 download_size: 13305453 dataset_size: 350786866 - config_name: reasoning_xu2026_perturbfate features: - name: gene_target dtype: large_string - name: protein_target dtype: large_string - name: cell_type dtype: large_string - name: tissue_type dtype: large_string - name: stimulation dtype: large_string - name: pathway_name dtype: large_string - name: pathway_change dtype: large_string - name: pathway_score dtype: float64 - name: experiment dtype: large_string - name: cell_file dtype: large_string splits: - name: train num_bytes: 303919726 num_examples: 860928 - name: test num_bytes: 34790207 num_examples: 98176 download_size: 13540400 dataset_size: 338709933 configs: - config_name: cells data_files: - split: cells path: cells/cells-* - config_name: chebi data_files: - split: chebi path: chebi/chebi-* - config_name: contrastive-perturbqa data_files: - split: train path: contrastive-perturbqa/train-* - split: val path: contrastive-perturbqa/val-* - split: test path: contrastive-perturbqa/test-* - config_name: contrastive-tahoe-DMSO-baseline data_files: - split: train path: contrastive-tahoe-DMSO-baseline/train-* - split: val path: contrastive-tahoe-DMSO-baseline/val-* - split: test path: contrastive-tahoe-DMSO-baseline/test-* - config_name: contrastive-tahoe-drug data_files: - split: train path: contrastive-tahoe-drug/train-* - split: val path: contrastive-tahoe-drug/val-* - split: test path: contrastive-tahoe-drug/test-* - config_name: genes data_files: - split: genes path: genes/genes-* - config_name: pathway_id_mapping data_files: - split: pathway_id_mapping path: pathway_id_mapping/pathway_id_mapping-* - config_name: pathway_interactions data_files: - split: train path: pathway_interactions/train-* - config_name: pathways data_files: - split: pathways path: pathways/pathways-* - config_name: reasoning-tahoe-pathway-classification data_files: - split: train path: reasoning-tahoe-pathway-classification/train-* - split: val path: reasoning-tahoe-pathway-classification/val-* - split: test path: reasoning-tahoe-pathway-classification/test-* - config_name: reasoning_kaufman data_files: - split: train path: reasoning_kaufman/train-* - split: test path: reasoning_kaufman/test-* - config_name: reasoning_marson data_files: - split: train path: reasoning_marson/train-* - split: test path: reasoning_marson/test-* - config_name: reasoning_nadig_replogle_new data_files: - split: train path: reasoning_nadig_replogle_new/train-* - split: test path: reasoning_nadig_replogle_new/test-* - config_name: reasoning_norman data_files: - split: train path: reasoning_norman/train-* - split: test path: reasoning_norman/test-* - config_name: reasoning_papalexi2021 data_files: - split: train path: reasoning_papalexi2021/train-* - split: test path: reasoning_papalexi2021/test-* - config_name: reasoning_tahoe_drug data_files: - split: train path: reasoning_tahoe_drug/train-* - split: validation path: reasoning_tahoe_drug/validation-* - split: test path: reasoning_tahoe_drug/test-* - config_name: reasoning_xaira_offtarget data_files: - split: train path: reasoning_xaira_offtarget/train-* - split: test path: reasoning_xaira_offtarget/test-* - config_name: reasoning_xu2026_perturbfate data_files: - split: train path: reasoning_xu2026_perturbfate/train-* - split: test path: reasoning_xu2026_perturbfate/test-* ---