| { |
| "protocol": "split-first-v1", |
| "method": "average_effect", |
| "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": 0.045805169735103846, |
| "lower": 0.01835085591301322, |
| "upper": 0.09486332535743713, |
| "n": 4 |
| }, |
| "effect_pearson": { |
| "mean": 0.41796617954969406, |
| "lower": 0.343549944460392, |
| "upper": 0.5240319073200226, |
| "n": 4 |
| }, |
| "effect_pearson_de20": { |
| "mean": 0.4695480614900589, |
| "lower": 0.35698434710502625, |
| "upper": 0.5821117758750916, |
| "n": 4 |
| }, |
| "mmd2": { |
| "mean": 0.3128944492404965, |
| "lower": 0.14772149867443227, |
| "upper": 0.5196701342561875, |
| "n": 4 |
| }, |
| "sliced_wasserstein": { |
| "mean": 0.6564046470179601, |
| "lower": 0.44746863207869164, |
| "upper": 0.9494201417608875, |
| "n": 4 |
| }, |
| "energy": { |
| "mean": 1.8821896037474284, |
| "lower": 0.8898077392829168, |
| "upper": 3.2377672320782658, |
| "n": 4 |
| }, |
| "variance_ratio": { |
| "mean": 0.6377041935920715, |
| "lower": 0.4268268942832947, |
| "upper": 0.8629074543714523, |
| "n": 4 |
| } |
| }, |
| "inverse": { |
| "exhaustive": { |
| "top1": { |
| "mean": 0.0, |
| "lower": 0.0, |
| "upper": 0.0, |
| "n": 4 |
| }, |
| "top5": { |
| "mean": 0.0, |
| "lower": 0.0, |
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| "n": 4 |
| }, |
| "ndcg10": { |
| "mean": 0.16219955252976553, |
| "lower": 0.0, |
| "upper": 0.32439910505953107, |
| "n": 4 |
| }, |
| "measured_reward": { |
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| "lower": 0.06606397964060307, |
| "upper": 0.5570607036352158, |
| "n": 4 |
| }, |
| "measured_regret": { |
| "mean": 0.2774312375113368, |
| "lower": 0.06014348566532135, |
| "upper": 0.49471898935735226, |
| "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": 0.01614457182586193, |
| "effect_pearson": 0.572132408618927, |
| "effect_pearson_de20": 0.6413403749465942, |
| "mmd2": 0.10228323395799088, |
| "sliced_wasserstein": 0.39334637293394104, |
| "energy": 0.649139745889932, |
| "variance_ratio": 0.5182458758354187 |
| }, |
| { |
| "target": "CNN1", |
| "query_cells": 8, |
| "genes_observed_in_training": false, |
| "mse_expression": 0.02343294769525528, |
| "effect_pearson": 0.32709893584251404, |
| "effect_pearson_de20": 0.3710622191429138, |
| "mmd2": 0.2585471367579829, |
| "sliced_wasserstein": 0.534814924915659, |
| "energy": 1.4261759603003354, |
| "variance_ratio": 0.9777946472167969 |
| }, |
| { |
| "target": "HES7", |
| "query_cells": 8, |
| "genes_observed_in_training": false, |
| "mse_expression": 0.11867345124483109, |
| "effect_pearson": 0.3929029703140259, |
| "effect_pearson_de20": 0.34290647506713867, |
| "mmd2": 0.6067111334222557, |
| "sliced_wasserstein": 1.087621880709297, |
| "energy": 3.8416309893375757, |
| "variance_ratio": 0.33540791273117065 |
| }, |
| { |
| "target": "PTPN12", |
| "query_cells": 8, |
| "genes_observed_in_training": true, |
| "mse_expression": 0.024969708174467087, |
| "effect_pearson": 0.3797304034233093, |
| "effect_pearson_de20": 0.5228831768035889, |
| "mmd2": 0.2840362928237564, |
| "sliced_wasserstein": 0.6098354095129435, |
| "energy": 1.6118117194618713, |
| "variance_ratio": 0.7193683385848999 |
| } |
| ], |
| "inverse": [ |
| { |
| "target": "CEBPE_ZC3HAV1", |
| "search": "exhaustive", |
| "top1": 0.0, |
| "top5": 0.0, |
| "ndcg10": 0.3333333333333333, |
| "rank": 7, |
| "selected": "ATL1", |
| "predicted_reward": 0.43243369460105896, |
| "measured_reward": 0.0968346819281578, |
| "measured_regret": 0.5187731757760048, |
| "selected_gene_overlap": 0.0, |
| "catalog_size": 20, |
| "candidate_cell_evaluations": 160, |
| "seconds": 8.740499652049039e-06, |
| "top_score_ties": 20 |
| }, |
| { |
| "target": "CNN1", |
| "search": "exhaustive", |
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| "ndcg10": 0.31546487678572877, |
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| "selected": "ATL1", |
| "predicted_reward": 0.034374676644802094, |
| "measured_reward": 0.4064628779888153, |
| "measured_regret": 0.0941368043422699, |
| "selected_gene_overlap": 0.0, |
| "catalog_size": 20, |
| "candidate_cell_evaluations": 160, |
| "seconds": 8.740499652049039e-06, |
| "top_score_ties": 20 |
| }, |
| { |
| "target": "HES7", |
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| "candidate_cell_evaluations": 160, |
| "seconds": 8.740499652049039e-06, |
| "top_score_ties": 20 |
| }, |
| { |
| "target": "PTPN12", |
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| "selected": "ATL1", |
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| "measured_reward": 0.7076585292816162, |
| "measured_regret": 0.026150166988372803, |
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| "catalog_size": 20, |
| "candidate_cell_evaluations": 160, |
| "seconds": 8.740499652049039e-06, |
| "top_score_ties": 20 |
| } |
| ] |
| } |
