| { |
| "protocol": "split-first-v1", |
| "method": "ridge", |
| "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": 16, |
| "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": 25, |
| "step_size": 0.5, |
| "k_nearest": 10, |
| "initialization": "best" |
| }, |
| "summary": { |
| "forward": { |
| "mse_expression": { |
| "mean": 0.03555455547757447, |
| "lower": 0.014391686301678419, |
| "upper": 0.07181215658783913, |
| "n": 4 |
| }, |
| "effect_pearson": { |
| "mean": 0.32233380153775215, |
| "lower": 0.11509735509753227, |
| "upper": 0.5571290850639343, |
| "n": 4 |
| }, |
| "effect_pearson_de20": { |
| "mean": 0.37099098414182663, |
| "lower": 0.1954069286584854, |
| "upper": 0.5816667191684246, |
| "n": 4 |
| }, |
| "mmd2": { |
| "mean": 0.21972475027474922, |
| "lower": 0.13688616642828655, |
| "upper": 0.35960212259946533, |
| "n": 4 |
| }, |
| "sliced_wasserstein": { |
| "mean": 0.5801302338411634, |
| "lower": 0.40585043439550433, |
| "upper": 0.8677208962494902, |
| "n": 4 |
| }, |
| "energy": { |
| "mean": 1.390171869699758, |
| "lower": 0.7763791136594997, |
| "upper": 2.4922222558861318, |
| "n": 4 |
| }, |
| "variance_ratio": { |
| "mean": 0.6042074039578438, |
| "lower": 0.3959890455007553, |
| "upper": 0.8124257624149323, |
| "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": 0.19726620657947197, |
| "lower": 0.0, |
| "upper": 0.39453241315894394, |
| "n": 4 |
| }, |
| "measured_reward": { |
| "mean": 0.45840439200401306, |
| "lower": 0.3573573976755142, |
| "upper": 0.5397148579359055, |
| "n": 4 |
| }, |
| "measured_regret": { |
| "mean": 0.08305719494819641, |
| "lower": 0.0, |
| "upper": 0.16611438989639282, |
| "n": 4 |
| }, |
| "selected_gene_overlap": { |
| "mean": 0.125, |
| "lower": 0.0, |
| "upper": 0.375, |
| "n": 4 |
| } |
| } |
| } |
| }, |
| "forward": [ |
| { |
| "target": "CEBPE_ZC3HAV1", |
| "query_cells": 16, |
| "genes_observed_in_training": false, |
| "mse_expression": 0.02307211421430111, |
| "effect_pearson": 0.6488189101219177, |
| "effect_pearson_de20": 0.6929008960723877, |
| "mmd2": 0.14565765795279972, |
| "sliced_wasserstein": 0.41762946411089474, |
| "energy": 0.8085152747528905, |
| "variance_ratio": 0.48148614168167114 |
| }, |
| { |
| "target": "CNN1", |
| "query_cells": 16, |
| "genes_observed_in_training": false, |
| "mse_expression": 0.016160421073436737, |
| "effect_pearson": 0.3074903190135956, |
| "effect_pearson_de20": 0.400249183177948, |
| "mmd2": 0.17420972409406987, |
| "sliced_wasserstein": 0.4910686929446227, |
| "energy": 0.9544713352161538, |
| "variance_ratio": 0.8797879219055176 |
| }, |
| { |
| "target": "HES7", |
| "query_cells": 16, |
| "genes_observed_in_training": false, |
| "mse_expression": 0.09036273509263992, |
| "effect_pearson": 0.05096636712551117, |
| "effect_pearson_de20": 0.14284966886043549, |
| "mmd2": 0.4309169441483539, |
| "sliced_wasserstein": 1.017751373629022, |
| "energy": 3.053457916263879, |
| "variance_ratio": 0.3104919493198395 |
| }, |
| { |
| "target": "PTPN12", |
| "query_cells": 16, |
| "genes_observed_in_training": true, |
| "mse_expression": 0.012622951529920101, |
| "effect_pearson": 0.28205960988998413, |
| "effect_pearson_de20": 0.24796418845653534, |
| "mmd2": 0.12811467490377337, |
| "sliced_wasserstein": 0.3940714046801139, |
| "energy": 0.744242952566109, |
| "variance_ratio": 0.7450636029243469 |
| } |
| ], |
| "inverse": [ |
| { |
| "target": "CEBPE_ZC3HAV1", |
| "search": "exhaustive", |
| "top1": 0.0, |
| "top5": 1.0, |
| "ndcg10": 0.5, |
| "rank": 3, |
| "selected": "CEBPA_ZC3HAV1", |
| "predicted_reward": 0.8645111322402954, |
| "measured_reward": 0.5618105530738831, |
| "measured_regret": 0.0, |
| "selected_gene_overlap": 0.5, |
| "catalog_size": 20, |
| "candidate_cell_evaluations": 320, |
| "seconds": 0.0002608797494758619, |
| "top_score_ties": 1 |
| }, |
| { |
| "target": "CNN1", |
| "search": "exhaustive", |
| "top1": 0.0, |
| "top5": 0.0, |
| "ndcg10": 0.2890648263178879, |
| "rank": 10, |
| "selected": "KLF1_MAP2K6", |
| "predicted_reward": 0.39002832770347595, |
| "measured_reward": 0.48285406827926636, |
| "measured_regret": 0.0, |
| "selected_gene_overlap": 0.0, |
| "catalog_size": 20, |
| "candidate_cell_evaluations": 320, |
| "seconds": 0.0002608797494758619, |
| "top_score_ties": 1 |
| }, |
| { |
| "target": "HES7", |
| "search": "exhaustive", |
| "top1": 0.0, |
| "top5": 0.0, |
| "ndcg10": 0.0, |
| "rank": 12, |
| "selected": "CEBPA_ZC3HAV1", |
| "predicted_reward": 0.565142810344696, |
| "measured_reward": 0.3155251741409302, |
| "measured_regret": 0.1650046706199646, |
| "selected_gene_overlap": 0.0, |
| "catalog_size": 20, |
| "candidate_cell_evaluations": 320, |
| "seconds": 0.0002608797494758619, |
| "top_score_ties": 1 |
| }, |
| { |
| "target": "PTPN12", |
| "search": "exhaustive", |
| "top1": 0.0, |
| "top5": 0.0, |
| "ndcg10": 0.0, |
| "rank": 12, |
| "selected": "CBL_TGFBR2", |
| "predicted_reward": 0.3994004428386688, |
| "measured_reward": 0.47342777252197266, |
| "measured_regret": 0.16722410917282104, |
| "selected_gene_overlap": 0.0, |
| "catalog_size": 20, |
| "candidate_cell_evaluations": 320, |
| "seconds": 0.0002608797494758619, |
| "top_score_ties": 1 |
| } |
| ], |
| "baseline_fit": { |
| "kind": "ridge", |
| "alpha": 1.0, |
| "seed": 0, |
| "train_cell_count": 504 |
| } |
| } |
