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BioReasonCell-ReasoningData / README.md
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--- 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 - name: top_expressed_cell_specific_genes_67 dtype: string - name: top_cell_specific_pathways_ora_67 dtype: string - name: description_long dtype: string splits: - name: cells num_bytes: 3091860 num_examples: 240 download_size: 939509 dataset_size: 3091860 - 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-emeraldbay-DMSO-baseline features: - name: study dtype: string - name: cell_type_A dtype: string - name: cell_type_B dtype: string - name: pathway dtype: string - name: mean_A dtype: float64 - name: mean_B dtype: float64 - name: std_A dtype: float64 - name: std_B dtype: float64 - name: n_A dtype: int64 - name: n_B dtype: int64 - name: mean_diff dtype: float64 - name: t_stat dtype: float64 - name: pvals dtype: float64 - name: pvals_adj dtype: float64 - name: cohens_d dtype: float64 - name: direction dtype: string splits: - name: train num_bytes: 1192155008 num_examples: 6676257 - name: validation num_bytes: 153224997 num_examples: 859209 - name: test num_bytes: 146933414 num_examples: 822505 download_size: 1080508325 dataset_size: 1492313419 - config_name: contrastive-emeraldbay-drug features: - name: study dtype: string - name: cell_type_A dtype: string - name: cell_type_B dtype: string - name: drug dtype: string - name: concentration dtype: string - name: pathway dtype: string - name: mean_A dtype: float64 - name: mean_B dtype: float64 - name: std_A dtype: float64 - name: std_B dtype: float64 - name: n_A dtype: int64 - name: n_B dtype: int64 - name: mean_diff dtype: float64 - name: t_stat dtype: float64 - name: pvals dtype: float64 - name: pvals_adj dtype: float64 - name: direction dtype: string splits: - name: train num_bytes: 19386234833 num_examples: 100143855 - name: validation num_bytes: 2491955798 num_examples: 12888135 - name: test num_bytes: 2389303789 num_examples: 12337575 download_size: 14482077733 dataset_size: 24267494420 - config_name: contrastive-kaufman 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: float64 - name: stimulation 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: 330319630 num_examples: 491307 - name: val num_bytes: 43156471 num_examples: 64245 - name: test num_bytes: 43916211 num_examples: 65122 download_size: 58468449 dataset_size: 417392312 - config_name: contrastive-marson 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: float64 - name: stimulation 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: 2095224311 num_examples: 3399351 - name: val num_bytes: 224795946 num_examples: 364660 - name: test num_bytes: 230835722 num_examples: 374487 download_size: 494374857 dataset_size: 2550855979 - 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: 3206218182 num_examples: 5927793 - name: val num_bytes: 400784055 num_examples: 740975 - name: test num_bytes: 400795380 num_examples: 740975 download_size: 844633945 dataset_size: 4007797617 - 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: 11164052673 num_examples: 19745177 - name: val num_bytes: 1395501108 num_examples: 2468148 - name: test num_bytes: 1395473073 num_examples: 2468148 download_size: 2937638395 dataset_size: 13955026854 - config_name: contrastive-xaira-orion features: - name: study dtype: large_string - name: cell_type_A dtype: large_string - name: cell_type_B dtype: large_string - name: tissue_A dtype: large_string - name: tissue_B dtype: large_string - name: perturbation dtype: large_string - name: perturbation_type dtype: large_string - name: concentration dtype: large_string - name: pathway dtype: large_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: large_string - name: response_B dtype: large_string - name: direction dtype: large_string - name: cell_file_A dtype: large_string - name: cell_file_B dtype: large_string - name: control_file_A dtype: large_string - name: control_file_B dtype: large_string splits: - name: train num_bytes: 40648631 num_examples: 62212 - name: val num_bytes: 5081561 num_examples: 7776 - name: test num_bytes: 5081053 num_examples: 7777 download_size: 5017425 dataset_size: 50811245 - config_name: contrastive-xaira-pisces features: - name: study dtype: large_string - name: cell_type_A dtype: large_string - name: cell_type_B dtype: large_string - name: tissue_A dtype: large_string - name: tissue_B dtype: large_string - name: perturbation dtype: large_string - name: perturbation_type dtype: large_string - name: concentration dtype: large_string - name: pathway dtype: large_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: large_string - name: response_B dtype: large_string - name: direction dtype: large_string - name: cell_file_A dtype: large_string - name: cell_file_B dtype: large_string - name: control_file_A dtype: large_string - name: control_file_B dtype: large_string splits: - name: train num_bytes: 473793064 num_examples: 612433 - name: val num_bytes: 59219712 num_examples: 76554 - name: test num_bytes: 59225272 num_examples: 76555 download_size: 50222876 dataset_size: 592238048 - 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 - name: pathways_old list: string splits: - name: genes num_bytes: 205800525 num_examples: 20045 download_size: 21838963 dataset_size: 205800525 - 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 - name: genes_old list: string splits: - name: pathways num_bytes: 32168726 num_examples: 14829 download_size: 7363878 dataset_size: 32168726 - 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: 521307863 num_examples: 21023 - name: val num_bytes: 64270045 num_examples: 2625 - name: test num_bytes: 66113137 num_examples: 2628 download_size: 472496410 dataset_size: 651691045 - config_name: reasoning_emeraldbay_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: float32 - name: pvals_adj dtype: float64 - name: experiment dtype: string - name: cell_file 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 - name: perturbation_strength dtype: string - name: abs_magnitude dtype: string splits: - name: test num_bytes: 28659063 num_examples: 69204 - name: train num_bytes: 959278943 num_examples: 2061504 - name: validation num_bytes: 102830155 num_examples: 224421 download_size: 43081560 dataset_size: 1090768161 - config_name: reasoning_emeraldbay_drug_fewshot 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: float32 - name: pvals_adj dtype: float64 - name: experiment dtype: string - name: cell_file 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 - name: perturbation_strength dtype: string - name: abs_magnitude dtype: string splits: - name: test num_bytes: 28659063 num_examples: 69204 - name: train num_bytes: 959278943 num_examples: 2061504 - name: validation num_bytes: 102830155 num_examples: 224421 download_size: 43081794 dataset_size: 1090768161 - 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 - name: is_offtarget dtype: bool - name: effect_pvals_adj dtype: float64 - name: perturbation_expressed dtype: bool - name: perturbation_baseline dtype: float64 - name: effect_reliable dtype: bool - name: drop dtype: bool - name: unique_id dtype: string splits: - name: train num_bytes: 4560959111 num_examples: 10163844 - name: test num_bytes: 496239803 num_examples: 1105217 download_size: 657084403 dataset_size: 5057198914 - config_name: reasoning_kaufman_fewshot 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 - name: is_offtarget dtype: bool - name: effect_pvals_adj dtype: float64 - name: perturbation_expressed dtype: bool - name: perturbation_baseline dtype: float64 - name: effect_reliable dtype: bool - name: drop dtype: bool - name: unique_id dtype: string splits: - name: train num_bytes: 4601006137 num_examples: 10246983 - name: test num_bytes: 459265840 num_examples: 1022078 download_size: 658906349 dataset_size: 5060271977 - 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 - name: is_offtarget dtype: bool - name: effect_pvals_adj dtype: float64 - name: perturbation_expressed dtype: bool - name: perturbation_baseline dtype: float64 - name: effect_reliable dtype: bool - name: drop dtype: bool - name: unique_id dtype: string splits: - name: test num_bytes: 1680450467 num_examples: 3749817 - name: train num_bytes: 14863991920 num_examples: 33207311 download_size: 2163588111 dataset_size: 16544442387 - config_name: reasoning_marson_fewshot 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 - name: is_offtarget dtype: bool - name: effect_pvals_adj dtype: float64 - name: perturbation_expressed dtype: bool - name: perturbation_baseline dtype: float64 - name: effect_reliable dtype: bool - name: drop dtype: bool - name: unique_id dtype: string splits: - name: train num_bytes: 14047361753 num_examples: 31267446 - name: validation num_bytes: 1513328624 num_examples: 3369822 - name: test num_bytes: 1034341965 num_examples: 2319860 download_size: 2144051608 dataset_size: 16595032342 - config_name: reasoning_nadig_replogle_fewshot 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 - name: effect_pvals_adj dtype: float64 - name: perturbation_expressed dtype: bool - name: perturbation_baseline dtype: float64 - name: effect_reliable dtype: bool - name: drop dtype: bool splits: - name: train num_bytes: 700286105 num_examples: 1864433 - name: validation num_bytes: 77955856 num_examples: 207097 - name: test num_bytes: 194229723 num_examples: 520805 download_size: 102669753 dataset_size: 972471684 - 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 - name: effect_pvals_adj dtype: float64 - name: perturbation_expressed dtype: bool - name: perturbation_baseline dtype: float64 - name: effect_reliable dtype: bool - name: drop dtype: bool splits: - name: train num_bytes: 417757929 num_examples: 1119552 - name: test num_bytes: 550937370 num_examples: 1472783 download_size: 102382913 dataset_size: 968695299 - 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 - name: is_offtarget dtype: bool - name: effect_pvals_adj dtype: float64 - name: perturbation_expressed dtype: 'null' - name: perturbation_baseline dtype: float64 - name: effect_reliable dtype: bool - name: drop dtype: bool splits: - name: train num_bytes: 550804089 num_examples: 1630264 - name: test num_bytes: 9329790 num_examples: 28108 download_size: 86376174 dataset_size: 560133879 - config_name: reasoning_norman_singleline 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 - name: is_offtarget dtype: bool - name: effect_pvals_adj dtype: float64 - name: perturbation_expressed dtype: 'null' - name: perturbation_baseline dtype: float64 - name: effect_reliable dtype: bool - name: drop dtype: bool splits: - name: train num_bytes: 552781032 num_examples: 1630264 - name: test num_bytes: 9332442 num_examples: 28108 download_size: 86546894 dataset_size: 562113474 - 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 - name: is_offtarget dtype: bool - name: effect_pvals_adj dtype: float64 - name: perturbation_expressed dtype: bool - name: perturbation_baseline dtype: float64 - name: effect_reliable dtype: bool - name: drop dtype: bool - name: unique_id dtype: string splits: - name: train num_bytes: 56881466 num_examples: 148442 - name: test num_bytes: 4895448 num_examples: 12908 download_size: 8043201 dataset_size: 61776914 - config_name: reasoning_papalexi2021_singleline 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 - name: is_offtarget dtype: bool - name: effect_pvals_adj dtype: float64 - name: perturbation_expressed dtype: bool - name: perturbation_baseline dtype: float64 - name: effect_reliable dtype: bool - name: drop dtype: bool - name: unique_id dtype: string splits: - name: train num_bytes: 57027270 num_examples: 148442 - name: test num_bytes: 4907546 num_examples: 12908 download_size: 8058831 dataset_size: 61934816 - config_name: reasoning_tahoe_drug features: - name: drug dtype: string - name: concentration dtype: float64 - name: cell_type dtype: string - name: pathway_name dtype: string - name: pathway_change dtype: string - name: pathway_score dtype: float64 - name: pvals_adj dtype: float64 - name: tissue_type dtype: string - name: cell_file 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 - name: experiment dtype: string - name: perturbation_strength dtype: string - name: abs_magnitude dtype: string - name: unique_id dtype: string splits: - name: test num_bytes: 901494608 num_examples: 1770328 - name: train num_bytes: 11778104833 num_examples: 22919317 - name: validation num_bytes: 53403373 num_examples: 108012 download_size: 1033207259 dataset_size: 12733002814 - config_name: reasoning_tahoe_drug_fewshot features: - name: drug dtype: string - name: concentration dtype: float64 - name: cell_type dtype: string - name: pathway_name dtype: string - name: pathway_change dtype: string - name: pathway_score dtype: float64 - name: pvals_adj dtype: float64 - name: tissue_type dtype: string - name: cell_file 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 - name: experiment dtype: string - name: perturbation_strength dtype: string - name: abs_magnitude dtype: string - name: unique_id dtype: string splits: - name: test num_bytes: 901494608 num_examples: 1770328 - name: train num_bytes: 11778104833 num_examples: 22919317 - name: validation num_bytes: 53403373 num_examples: 108012 download_size: 1033144639 dataset_size: 12733002814 - config_name: reasoning_tahoe_drug_v2 features: - name: drug dtype: string - name: concentration dtype: float64 - name: cell_type dtype: string - name: pathway_name dtype: string - name: pathway_change dtype: string - name: pathway_score dtype: float64 - name: pvals_adj dtype: float64 - name: tissue_type dtype: string - name: cell_file 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 - name: experiment dtype: string - name: perturbation_strength dtype: string - name: abs_magnitude dtype: string - name: unique_id dtype: string - name: well_split dtype: string - name: pair_split dtype: string - name: split dtype: string splits: - name: train num_bytes: 10165873116 num_examples: 18838476 - name: val num_bytes: 623430251 num_examples: 1167001 - name: test num_bytes: 132867544 num_examples: 247107 download_size: 852576506 dataset_size: 10922170911 - 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 - name: effect_pvals_adj dtype: float64 - name: perturbation_expressed dtype: bool - name: perturbation_baseline dtype: float64 - name: effect_reliable dtype: bool - name: drop dtype: bool - name: unique_id dtype: string splits: - name: train num_bytes: 278416532 num_examples: 676647 - name: validation num_bytes: 60327527 num_examples: 146056 - name: test num_bytes: 780191310 num_examples: 1895658 download_size: 118035958 dataset_size: 1118935369 - config_name: reasoning_xaira_orion_fewshot 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 - name: effect_pvals_adj dtype: float64 - name: perturbation_expressed dtype: bool - name: perturbation_baseline dtype: float64 - name: effect_reliable dtype: bool - name: drop dtype: bool - name: unique_id dtype: string splits: - name: train num_bytes: 818328943 num_examples: 1989325 - name: validation num_bytes: 87567901 num_examples: 213076 - name: test num_bytes: 213079552 num_examples: 515960 download_size: 118334402 dataset_size: 1118976396 - 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 - name: effect_pvals_adj dtype: float64 - name: perturbation_expressed dtype: bool - name: perturbation_baseline dtype: float64 - name: effect_reliable dtype: bool - name: drop dtype: bool - name: is_offtarget dtype: bool - name: unique_id dtype: string splits: - name: train num_bytes: 789785892 num_examples: 1727167 - name: validation num_bytes: 92094790 num_examples: 201761 - name: test num_bytes: 136178627 num_examples: 301803 download_size: 103793698 dataset_size: 1018059309 - config_name: reasoning_xaira_pisces_fewshot 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 - name: effect_pvals_adj dtype: float64 - name: perturbation_expressed dtype: bool - name: perturbation_baseline dtype: float64 - name: effect_reliable dtype: bool - name: drop dtype: bool - name: is_offtarget dtype: bool - name: unique_id dtype: string splits: - name: train num_bytes: 715105130 num_examples: 1564067 - name: validation num_bytes: 76232585 num_examples: 166981 - name: test num_bytes: 226827486 num_examples: 499683 download_size: 103927913 dataset_size: 1018165201 - 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 - name: is_offtarget dtype: bool - name: effect_pvals_adj dtype: float64 - name: perturbation_expressed dtype: bool - name: perturbation_baseline dtype: float64 - name: effect_reliable dtype: bool - name: drop dtype: bool - name: unique_id dtype: string splits: - name: train num_bytes: 363389329 num_examples: 850554 - name: test num_bytes: 41621847 num_examples: 96993 download_size: 44616083 dataset_size: 405011176 - config_name: reasoning_xu2026_perturbfate_singleline 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 - name: is_offtarget dtype: bool - name: effect_pvals_adj dtype: float64 - name: perturbation_expressed dtype: bool - name: perturbation_baseline dtype: float64 - name: effect_reliable dtype: bool - name: drop dtype: bool - name: unique_id dtype: string splits: - name: train num_bytes: 363468327 num_examples: 850554 - name: test num_bytes: 41623265 num_examples: 96993 download_size: 44670854 dataset_size: 405091592 configs: - config_name: cells data_files: - split: cells path: cells/cells-* - config_name: chebi data_files: - split: chebi path: chebi/chebi-* - config_name: contrastive-emeraldbay-DMSO-baseline data_files: - split: train path: contrastive-emeraldbay-DMSO-baseline/train-* - split: validation path: contrastive-emeraldbay-DMSO-baseline/validation-* - split: test path: contrastive-emeraldbay-DMSO-baseline/test-* - config_name: contrastive-emeraldbay-drug data_files: - split: train path: contrastive-emeraldbay-drug/train-* - split: validation path: contrastive-emeraldbay-drug/validation-* - split: test path: contrastive-emeraldbay-drug/test-* - config_name: contrastive-kaufman data_files: - split: train path: contrastive-kaufman/train-* - split: val path: contrastive-kaufman/val-* - split: test path: contrastive-kaufman/test-* - config_name: contrastive-marson data_files: - split: train path: contrastive-marson/train-* - split: val path: contrastive-marson/val-* - split: test path: contrastive-marson/test-* - 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: contrastive-xaira-orion data_files: - split: train path: contrastive-xaira-orion/train-* - split: val path: contrastive-xaira-orion/val-* - split: test path: contrastive-xaira-orion/test-* - config_name: contrastive-xaira-pisces data_files: - split: train path: contrastive-xaira-pisces/train-* - split: val path: contrastive-xaira-pisces/val-* - split: test path: contrastive-xaira-pisces/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_emeraldbay_drug data_files: - split: test path: reasoning_emeraldbay_drug/test-* - split: train path: reasoning_emeraldbay_drug/train-* - split: validation path: reasoning_emeraldbay_drug/validation-* - config_name: reasoning_emeraldbay_drug_fewshot data_files: - split: test path: reasoning_emeraldbay_drug_fewshot/test-* - split: train path: reasoning_emeraldbay_drug_fewshot/train-* - split: validation path: reasoning_emeraldbay_drug_fewshot/validation-* - config_name: reasoning_kaufman data_files: - split: train path: reasoning_kaufman/train-* - split: test path: reasoning_kaufman/test-* - config_name: reasoning_kaufman_fewshot data_files: - split: train path: reasoning_kaufman_fewshot/train-* - split: test path: reasoning_kaufman_fewshot/test-* - config_name: reasoning_marson data_files: - split: test path: reasoning_marson/test-* - split: train path: reasoning_marson/train-* - config_name: reasoning_marson_fewshot data_files: - split: train path: reasoning_marson_fewshot/train-* - split: validation path: reasoning_marson_fewshot/validation-* - split: test path: reasoning_marson_fewshot/test-* - config_name: reasoning_nadig_replogle_fewshot data_files: - split: train path: reasoning_nadig_replogle_fewshot/train-* - split: validation path: reasoning_nadig_replogle_fewshot/validation-* - split: test path: reasoning_nadig_replogle_fewshot/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_norman_singleline data_files: - split: train path: reasoning_norman_singleline/train-* - split: test path: reasoning_norman_singleline/test-* - config_name: reasoning_papalexi2021 data_files: - split: train path: reasoning_papalexi2021/train-* - split: test path: reasoning_papalexi2021/test-* - config_name: reasoning_papalexi2021_singleline data_files: - split: train path: reasoning_papalexi2021_singleline/train-* - split: test path: reasoning_papalexi2021_singleline/test-* - config_name: reasoning_tahoe_drug data_files: - split: test path: reasoning_tahoe_drug/test-* - split: train path: reasoning_tahoe_drug/train-* - split: validation path: reasoning_tahoe_drug/validation-* - config_name: reasoning_tahoe_drug_fewshot data_files: - split: test path: reasoning_tahoe_drug_fewshot/test-* - split: train path: reasoning_tahoe_drug_fewshot/train-* - split: validation path: reasoning_tahoe_drug_fewshot/validation-* - config_name: reasoning_tahoe_drug_v2 data_files: - split: train path: reasoning_tahoe_drug_v2/train-* - split: val path: reasoning_tahoe_drug_v2/val-* - split: test path: reasoning_tahoe_drug_v2/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_orion_fewshot data_files: - split: train path: reasoning_xaira_orion_fewshot/train-* - split: validation path: reasoning_xaira_orion_fewshot/validation-* - split: test path: reasoning_xaira_orion_fewshot/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_xaira_pisces_fewshot data_files: - split: train path: reasoning_xaira_pisces_fewshot/train-* - split: validation path: reasoning_xaira_pisces_fewshot/validation-* - split: test path: reasoning_xaira_pisces_fewshot/test-* - config_name: reasoning_xu2026_perturbfate data_files: - split: train path: reasoning_xu2026_perturbfate/train-* - split: test path: reasoning_xu2026_perturbfate/test-* - config_name: reasoning_xu2026_perturbfate_singleline data_files: - split: train path: reasoning_xu2026_perturbfate_singleline/train-* - split: test path: reasoning_xu2026_perturbfate_singleline/test-* - config_name: vcc1_eval data_files: - split: test path: vcc1_eval/arc_eval_ds/test.parquet - split: validation path: vcc1_eval/arc_eval_ds/validation.parquet - split: train path: vcc1_eval/arc_eval_ds/train.parquet ---
---
dataset_info:
- config_name: cells
features:
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- name: tissue
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- name: description
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- name: top_expressed_genes_depmap
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- name: top_expressed_pathways_old
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- name: top_pathways_from_num_markers
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- name: top_cell_specific_pathways_ora
dtype: string
- name: description_new
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- name: top_expressed_cell_specific_genes_67
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- name: top_cell_specific_pathways_ora_67
dtype: string
- name: description_long
dtype: string
splits:
- name: cells
num_bytes: 3091860
num_examples: 240
download_size: 939509
dataset_size: 3091860
- config_name: chebi
features:
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- name: name
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- name: definition
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- name: formula
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- name: smiles
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- 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-emeraldbay-DMSO-baseline
features:
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- name: cell_type_A
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- name: cell_type_B
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- name: pathway
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- name: mean_B
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- name: std_B
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- name: n_A
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- name: n_B
dtype: int64
- name: mean_diff
dtype: float64
- name: t_stat
dtype: float64
- name: pvals
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- name: pvals_adj
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- name: cohens_d
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