--- 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_cell_specific_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 - name: top_cell_specific_pathways_ora dtype: string - name: description_new dtype: string splits: - name: cells num_bytes: 1433613 num_examples: 165 download_size: 763144 dataset_size: 1433613 - 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: string - name: uniprot_id dtype: string - name: protein_name dtype: string - name: protein_function dtype: 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: 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: string - name: subunit_description dtype: string - name: ptm dtype: string - name: domain_description dtype: string - name: induction dtype: string - name: activity_regulation dtype: string - name: intact_partners list: string - name: string_partners list: string splits: - name: genes num_bytes: 164093671 num_examples: 20045 download_size: 19315005 dataset_size: 164093671 - config_name: pathway_id_mapping features: - name: msigdb_id dtype: string - name: pi_pathway_names list: string splits: - name: pathway_id_mapping num_bytes: 331301 num_examples: 1695 download_size: 83797 dataset_size: 331301 - 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: 668570564 num_examples: 817031 download_size: 18471937 dataset_size: 668570564 - 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_type 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: 521552393 num_examples: 21023 - name: val num_bytes: 64299983 num_examples: 2625 - name: test num_bytes: 66144515 num_examples: 2628 download_size: 236212545 dataset_size: 651996891 - config_name: reasoning_kaufman features: - name: gene_target dtype: string - name: protein_target dtype: 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 - name: perturbation_strength dtype: string - name: abs_magnitude dtype: string splits: - name: train num_bytes: 3397635165 num_examples: 10297261 - name: test num_bytes: 369491952 num_examples: 1119711 download_size: 189244010 dataset_size: 3767127117 - config_name: reasoning_marson features: - name: gene_target dtype: string - name: protein_target dtype: 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 - name: donor_id dtype: string - name: perturbation_strength dtype: string - name: abs_magnitude dtype: string splits: - name: train num_bytes: 11622302828 num_examples: 33522035 - name: test num_bytes: 1311629927 num_examples: 3779135 download_size: 661441581 dataset_size: 12933932755 - 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_offtarget dtype: bool - name: unique_id dtype: string - name: perturbation_strength dtype: string - name: abs_magnitude dtype: string splits: - name: train num_bytes: 401859607 num_examples: 1121502 - name: test num_bytes: 528982102 num_examples: 1472783 download_size: 133167125 dataset_size: 930841709 - 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 - name: perturbation_strength dtype: string - name: abs_magnitude dtype: string splits: - name: train num_bytes: 525854685 num_examples: 1630264 - name: test num_bytes: 8868158 num_examples: 28108 download_size: 71446084 dataset_size: 534722843 - 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 - name: perturbation_strength dtype: string - name: abs_magnitude dtype: string splits: - name: train num_bytes: 43305241 num_examples: 148442 - name: test num_bytes: 3726784 num_examples: 12908 download_size: 2523740 dataset_size: 47032025 - 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 - name: perturbation_strength dtype: string - name: abs_magnitude dtype: string splits: - name: train num_bytes: 3799781333 num_examples: 12832228 - name: validation num_bytes: 442878634 num_examples: 1478198 - name: test num_bytes: 341609330 num_examples: 1157511 download_size: 139155027 dataset_size: 4584269297 - config_name: reasoning_xaira_orion 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: float32 - name: pvals_adj dtype: float64 - name: experiment dtype: string - name: cell_file dtype: string - name: is_offtarget dtype: bool - name: perturbation_strength dtype: string - name: abs_magnitude dtype: string splits: - name: train num_bytes: 211831787 num_examples: 676647 - name: validation num_bytes: 45890991 num_examples: 146056 - name: test num_bytes: 593597271 num_examples: 1895658 download_size: 39501546 dataset_size: 851320049 - config_name: reasoning_xaira_pisces 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: float32 - name: pvals_adj dtype: float64 - name: experiment dtype: string - name: cell_file dtype: string - name: perturbation_strength dtype: string - name: abs_magnitude dtype: string splits: - name: train num_bytes: 629780245 num_examples: 1810178 - name: validation num_bytes: 74000851 num_examples: 213130 - name: test num_bytes: 72179928 num_examples: 207423 download_size: 36994831 dataset_size: 775961024 - config_name: reasoning_xu2026_perturbfate features: - name: gene_target dtype: string - name: protein_target dtype: 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 - name: perturbation_strength dtype: string - name: abs_magnitude dtype: string splits: - name: train num_bytes: 291275944 num_examples: 860928 - name: test num_bytes: 33321973 num_examples: 98176 download_size: 13566219 dataset_size: 324597917 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_orion data_files: - split: train path: reasoning_xaira_orion/train-* - split: validation path: reasoning_xaira_orion/validation-* - split: test path: reasoning_xaira_orion/test-* - config_name: reasoning_xaira_pisces data_files: - split: train path: reasoning_xaira_pisces/train-* - split: validation path: reasoning_xaira_pisces/validation-* - split: test path: reasoning_xaira_pisces/test-* - config_name: reasoning_xu2026_perturbfate data_files: - split: train path: reasoning_xu2026_perturbfate/train-* - split: test path: reasoning_xu2026_perturbfate/test-* ---