| { |
| "protocol": "split-first-v1", |
| "method": "endpoint_mlp", |
| "data_meta": { |
| "reference_fraction": 0.1, |
| "protocol": "split-first-v1", |
| "dataset": "norman", |
| "name": "norman", |
| "operation": "activation", |
| "control_label": "control", |
| "sep": "_", |
| "split": "perturbation", |
| "seed": 0, |
| "input_scale": "counts", |
| "raw_sha256": "21bd3c00b7f243d998aa9ca616490b45bf1b4ba9934d501190a867ddad982dae", |
| "raw_file": "norman_small.h5ad", |
| "n_cells": 920, |
| "n_control": 120, |
| "n_hvg": 201, |
| "n_pca": 10, |
| "pca_explained_var": 0.5626983046531677, |
| "mmd_gamma": 0.06974897265608301, |
| "fit_cell_ids_sha256": "5ff57f6222cd8d3e4dd6b7fa658c8599cf6eb4b553a607ad9100a7fc240f9f22", |
| "selection": { |
| "max_cells": null, |
| "max_per_group": null, |
| "max_groups": null |
| }, |
| "software": { |
| "scanpy": "1.12.4", |
| "anndata": "0.13.3.post0" |
| } |
| }, |
| "partition": "test", |
| "catalog": "all", |
| "reward": "cosine", |
| "seed": 0, |
| "n_controls": 8, |
| "query_cell_ids": [ |
| "CCTTCCCTCACTATTC", |
| "GTGGGTCAGTTAGCGG", |
| "CAGCTGGTCGAATGCT", |
| "ACAGCCGAGAGGGATA", |
| "GGTATTGCACAACTGT", |
| "ATGGGAGAGTCGAGTG", |
| "CTGCGGAGTCTTGCGG", |
| "GGCCGATGTATCACCA", |
| "CGATTGAGTCTAGGTT", |
| "TCTTTCCGTAGATTAG", |
| "GACGGCTCACCAGCAC", |
| "CAGCATAAGGCTAGCA", |
| "AACTCTTCATGGTAGG", |
| "AGCTCCTGTTCCTCCA", |
| "GCGCAGTAGGATTCGG", |
| "GTCTCGTGTGCATCTA", |
| "GGTGAAGTCAGGTAAA", |
| "CATTATCGTACTTAGC", |
| "TGCGTGGGTCTCATCC", |
| "CTGGTCTGTAGCGTGA", |
| "TCACAAGGTCACAAGG-1", |
| "GGCGACTCATTAGCCA", |
| "GGGAGATAGAAGGACA", |
| "GCGCCAACAGCCACCA", |
| "TACGGTAGTACTTCTT", |
| "CTCGAAAGTAGGCTGA", |
| "CAGCCGATCCTTGACC", |
| "GCTGCTTGTGAAAGAG", |
| "CGCTGGAGTACATGTC", |
| "GGCGACTCAGCTGTTA", |
| "GCGCAACGTTGAGGTG", |
| "CGGTTAAGTCAAAGCG", |
| "AGCAGCCGTTAAAGTG", |
| "TTAACTCCAGGGAGAG", |
| "ATCCGAATCTGCTGTC", |
| "ATCATGGAGGACGAAA", |
| "CTGATAGCACTCAGGC", |
| "AGCGGTCAGCACGCCT", |
| "GCGAGAATCAGGTTCA", |
| "CATTCGCCACCATGTA", |
| "TTCGAAGTCGATAGAA", |
| "AGAATAGCATTCCTGC", |
| "AGCGTCGCACAAGACG", |
| "AGGTCCGAGACTGTAA", |
| "TATTACCAGACACGAC", |
| "AAGGTTCCAGGAATCG", |
| "ATTGGACCAACAACCT", |
| "TGAGCCGGTCTCATCC", |
| "AGAGCGACAGCTGTAT", |
| "GGATTACCAAGTAATG", |
| "AGCGTATTCGCGTTTC", |
| "CGCTTCACAATCGGTT", |
| "GGTATTGAGTGGACGT", |
| "TAGTTGGGTTGGACCC", |
| "GTACTTTTCGTGGGAA", |
| "TTGCGTCGTTCGGCAC", |
| "GTACGTATCAACGCTA", |
| "TCGCGAGCACCTCGGA", |
| "AGCATACTCAGCTCGG", |
| "GCGCAACAGTGGGCTA-1", |
| "GGAGCAATCCTATTCA", |
| "GCACTCTTCAAACGGG", |
| "ATTACTCAGGATGTAT", |
| "CGACTTCTCCTTCAAT", |
| "TGAGCCGAGAGTCTGG", |
| "ACGAGCCTCGCATGGC-1", |
| "CCCATACCAGGTCCAC", |
| "CAGAGAGTCGTGGGAA", |
| "CGTTCTGAGATGCCAG-1", |
| "ATAACGCCAGGATCGA", |
| "TTTGCGCTCATTCACT-1", |
| "TTGGAACAGTGAACGC", |
| "CTCTGGTAGATATGCA", |
| "AGGTCCGTCGTCCGTT", |
| "CGTAGCGTCACGAAGG", |
| "CCGTACTTCGAATCCA", |
| "CTTAACTGTCTACCTC", |
| "AACACGTAGGAACTGC", |
| "TACACGATCCATTCTA", |
| "CAAGATCGTACGCACC-1", |
| "CTCGAGGGTGCGATAG", |
| "AAAGATGGTTGTCGCG-1", |
| "CTCCTAGCACAGCGTC", |
| "GATGCTAGTCATGCCG", |
| "TCGCGAGGTGACAAAT", |
| "CTACACCAGCGGCTTC", |
| "GCATACAAGACCACGA", |
| "CGCTATCCAAGCGAGT", |
| "GACGGCTGTCTAGTGT", |
| "GCATACATCGCCTGAG", |
| "ACATGGTGTTCCACGG", |
| "CGAGAAGCAAGCTGGA", |
| "GGGACCTGTACCATCA", |
| "TGGGAAGCAAACAACA", |
| "CCACGGAAGAGACTAT", |
| "ACGAGGACATGCTGGC", |
| "GTGCTTCAGGTGGGTT", |
| "TACAGTGGTAGGCATG", |
| "TCGTAGATCCACTCCA", |
| "TCAGCTCCACGTCTCT", |
| "GCTCCTAGTCGCTTCT-1", |
| "GCGAGAACAAATTGCC", |
| "TTGAACGCAGGATTGG", |
| "CGCCAAGCACGCCAGT", |
| "CAGCTGGTCAGTTCGA", |
| "GCCAAATAGTGCGTGA", |
| "TGACAACTCGTCGTTC", |
| "CAAGTTGTCGCCTGAG", |
| "GGAATAATCGACCAGC", |
| "TGTGTTTGTAGGAGTC", |
| "ACGAGCCAGCTAGTTC", |
| "ATGAGGGAGCCACCTG", |
| "CACAGGCGTTGCCTCT", |
| "GGAAAGCCACAGATTC", |
| "CGATGGCTCAAAGTAG", |
| "GTCTCGTAGCCAACAG", |
| "AGCATACCACGTTGGC", |
| "CACCACTCATCCAACA", |
| "CAGCAGCCACTGTGTA", |
| "CATTCGCCACGACTCG", |
| "GATCGATTCGCGGATC", |
| "GGGAGATAGACTTGAA", |
| "GTAGTCACAGGCAGTA", |
| "GACGGCTGTCCGAGTC", |
| "CAGCTAAAGCTACCGC", |
| "TGACAACGTCATACTG", |
| "ACTTACTCACCCTATC-1", |
| "TTTGCGCCAGCAGTTT", |
| "CACAGTACATCCGGGT", |
| "TGGCGCACATTTGCTT", |
| "ATGCGATGTGTCAATC", |
| "AGTGTCAAGATGAGAG", |
| "GTATTCTTCAGGCAAG", |
| "GTACTCCTCTGGTATG", |
| "GGTATTGGTTGTCGCG", |
| "CCTCAGTAGAGGTTAT", |
| "ACACCAAGTACCCAAT", |
| "TGGTTAGGTTGTTTGG", |
| "CTTAACTCAATAGAGT", |
| "ATTCTACTCAAGGCTT", |
| "CGGACGTAGTCATGCT", |
| "TCAATCTAGTATTGGA", |
| "GGGCACTGTTACAGAA", |
| "TTATGCTTCAGGCAAG" |
| ], |
| "guidance": { |
| "steps": 0, |
| "step_size": 0.5, |
| "k_nearest": 10, |
| "initialization": "best" |
| }, |
| "summary": { |
| "forward": { |
| "mse_expression": { |
| "mean": 0.047080633928999305, |
| "lower": 0.012973662000149488, |
| "upper": 0.10819452162832022, |
| "n": 4 |
| }, |
| "effect_pearson": { |
| "mean": 0.4912223592400551, |
| "lower": 0.26083599030971527, |
| "upper": 0.7216087281703949, |
| "n": 4 |
| }, |
| "effect_pearson_de20": { |
| "mean": 0.564788319170475, |
| "lower": 0.29036472737789154, |
| "upper": 0.8392119109630585, |
| "n": 4 |
| }, |
| "mmd2": { |
| "mean": 0.4294277083339675, |
| "lower": 0.22245881832001374, |
| "upper": 0.773859405438333, |
| "n": 4 |
| }, |
| "sliced_wasserstein": { |
| "mean": 0.8412104467935287, |
| "lower": 0.6323051038878027, |
| "upper": 1.1933313137980632, |
| "n": 4 |
| }, |
| "energy": { |
| "mean": 3.1491717542942532, |
| "lower": 1.977639447815982, |
| "upper": 5.245467270106316, |
| "n": 4 |
| }, |
| "variance_ratio": { |
| "mean": 3.3575813413381426e-16, |
| "lower": 1.2577669906038624e-16, |
| "upper": 5.457395692072423e-16, |
| "n": 4 |
| } |
| }, |
| "inverse": { |
| "exhaustive": { |
| "top1": { |
| "mean": 0.0, |
| "lower": 0.0, |
| "upper": 0.0, |
| "n": 4 |
| }, |
| "top5": { |
| "mean": 0.25, |
| "lower": 0.0, |
| "upper": 0.75, |
| "n": 4 |
| }, |
| "ndcg10": { |
| "mean": 0.2719784352113491, |
| "lower": 0.08905179677700555, |
| "upper": 0.3982649174710401, |
| "n": 4 |
| }, |
| "measured_reward": { |
| "mean": 0.06799789145588875, |
| "lower": -0.07572989165782928, |
| "upper": 0.2051202654838562, |
| "n": 4 |
| }, |
| "measured_regret": { |
| "mean": 0.5209956876933575, |
| "lower": 0.3556627035140991, |
| "upper": 0.7571854740381241, |
| "n": 4 |
| }, |
| "selected_gene_overlap": { |
| "mean": 0.0, |
| "lower": 0.0, |
| "upper": 0.0, |
| "n": 4 |
| } |
| } |
| } |
| }, |
| "forward": [ |
| { |
| "target": "CEBPE_ZC3HAV1", |
| "query_cells": 8, |
| "genes_observed_in_training": false, |
| "mse_expression": 0.022559911012649536, |
| "effect_pearson": 0.3868451714515686, |
| "effect_pearson_de20": 0.32508429884910583, |
| "mmd2": 0.32572190262681056, |
| "sliced_wasserstein": 0.7289019652303823, |
| "energy": 2.3396031175098964, |
| "variance_ratio": 6.14452417135728e-16 |
| }, |
| { |
| "target": "CNN1", |
| "query_cells": 8, |
| "genes_observed_in_training": false, |
| "mse_expression": 0.01333218440413475, |
| "effect_pearson": 0.6667251586914062, |
| "effect_pearson_de20": 0.7680767178535461, |
| "mmd2": 0.18803779021774814, |
| "sliced_wasserstein": 0.6052737950877346, |
| "energy": 1.856984891251344, |
| "variance_ratio": 2.376368932972069e-16 |
| }, |
| { |
| "target": "HES7", |
| "query_cells": 8, |
| "genes_observed_in_training": false, |
| "mse_expression": 0.1398153007030487, |
| "effect_pearson": 0.13482680916786194, |
| "effect_pearson_de20": 0.25564515590667725, |
| "mmd2": 0.9457432406310105, |
| "sliced_wasserstein": 1.3713296141681275, |
| "energy": 6.290885036004745, |
| "variance_ratio": 4.770267212787565e-16 |
| }, |
| { |
| "target": "PTPN12", |
| "query_cells": 8, |
| "genes_observed_in_training": true, |
| "mse_expression": 0.012615139596164227, |
| "effect_pearson": 0.7764922976493835, |
| "effect_pearson_de20": 0.9103471040725708, |
| "mmd2": 0.2582078998603008, |
| "sliced_wasserstein": 0.6593364126878708, |
| "energy": 2.1092139724110273, |
| "variance_ratio": 1.3916504823565614e-17 |
| } |
| ], |
| "inverse": [ |
| { |
| "target": "CEBPE_ZC3HAV1", |
| "search": "exhaustive", |
| "top1": 0.0, |
| "top5": 0.0, |
| "ndcg10": 0.3562071871080222, |
| "rank": 6, |
| "selected": "KLF1_MAP2K6", |
| "predicted_reward": 0.441496878862381, |
| "measured_reward": 0.2507260739803314, |
| "measured_regret": 0.3648817837238312, |
| "selected_gene_overlap": 0.0, |
| "catalog_size": 20, |
| "candidate_cell_evaluations": 160, |
| "seconds": 0.0029098115001033875, |
| "top_score_ties": 1 |
| }, |
| { |
| "target": "CNN1", |
| "search": "exhaustive", |
| "top1": 0.0, |
| "top5": 0.0, |
| "ndcg10": 0.0, |
| "rank": 12, |
| "selected": "CBFA2T3", |
| "predicted_reward": 0.7330882549285889, |
| "measured_reward": 0.01589570939540863, |
| "measured_regret": 0.4847039729356766, |
| "selected_gene_overlap": 0.0, |
| "catalog_size": 20, |
| "candidate_cell_evaluations": 160, |
| "seconds": 0.0029098115001033875, |
| "top_score_ties": 1 |
| }, |
| { |
| "target": "HES7", |
| "search": "exhaustive", |
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| "top5": 1.0, |
| "ndcg10": 0.43067655807339306, |
| "rank": 4, |
| "selected": "KLF1_MAP2K6", |
| "predicted_reward": 0.2321934849023819, |
| "measured_reward": 0.15951445698738098, |
| "measured_regret": 0.34644362330436707, |
| "selected_gene_overlap": 0.0, |
| "catalog_size": 20, |
| "candidate_cell_evaluations": 160, |
| "seconds": 0.0029098115001033875, |
| "top_score_ties": 1 |
| }, |
| { |
| "target": "PTPN12", |
| "search": "exhaustive", |
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| "top5": 0.0, |
| "ndcg10": 0.3010299956639812, |
| "rank": 9, |
| "selected": "CBFA2T3", |
| "predicted_reward": 0.8227013945579529, |
| "measured_reward": -0.15414467453956604, |
| "measured_regret": 0.887953370809555, |
| "selected_gene_overlap": 0.0, |
| "catalog_size": 20, |
| "candidate_cell_evaluations": 160, |
| "seconds": 0.0029098115001033875, |
| "top_score_ties": 1 |
| } |
| ] |
| } |
