Archive 4 checkpoints (1-4)
Browse files- paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/finalize_cx_20261008T110117.log +86 -0
- paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/finalize_full_20261007T115524.log +115 -0
- paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/run_all_A_20261006T154242.log +56 -0
- paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/run_all_B_20261006T154242.log +42 -0
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/finalize_cx_20261008T110117.log
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{"dataset": "immicro", "comparison": "fewshot", "draw": 0, "gene_mode": "cibersortx", "bayesprism": {"comp_l1": 0.5506126156345467, "comp_l1_by_variant": {"final_cells": 0.5506126156345467, "first_cells": 0.5506126156345467, "final_mrna": 0.63155753806753, "first_mrna": 0.63155753806753}, "mean_fraction": {"final_cells": {"T cell": 0.4298, "B cell": 0.0838, "Monocyte": 0.2848, "NK cell": 0.051, "DC": 0.0254, "Other": 0.1251}, "first_cells": {"T cell": 0.4298, "B cell": 0.0838, "Monocyte": 0.2848, "NK cell": 0.051, "DC": 0.0254, "Other": 0.1251}, "final_mrna": {"T cell": 0.3984, "B cell": 0.0725, "Monocyte": 0.324, "NK cell": 0.0359, "DC": 0.0578, "Other": 0.1115}, "first_mrna": {"T cell": 0.3984, "B cell": 0.0725, "Monocyte": 0.324, "NK cell": 0.0359, "DC": 0.0578, "Other": 0.1115}}}, "lora": {"comp_l1": 0.18149050759378063, "coverage": 0.8003921568627451}, "broadcast": {}}
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{"dataset": "immicro", "comparison": "fewshot", "draw": 1, "gene_mode": "cibersortx", "bayesprism": {"comp_l1": 0.4617486814629545, "comp_l1_by_variant": {"final_cells": 0.4617486814629545, "first_cells": 0.4617486814629545, "final_mrna": 0.6101145215651299, "first_mrna": 0.6101145215651299}, "mean_fraction": {"final_cells": {"T cell": 0.465, "B cell": 0.0859, "Monocyte": 0.2225, "NK cell": 0.0717, "DC": 0.0268, "Other": 0.1281}, "first_cells": {"T cell": 0.465, "B cell": 0.0859, "Monocyte": 0.2225, "NK cell": 0.0717, "DC": 0.0268, "Other": 0.1281}, "final_mrna": {"T cell": 0.3976, "B cell": 0.077, "Monocyte": 0.2644, "NK cell": 0.0508, "DC": 0.062, "Other": 0.1482}, "first_mrna": {"T cell": 0.3976, "B cell": 0.077, "Monocyte": 0.2644, "NK cell": 0.0508, "DC": 0.062, "Other": 0.1482}}}, "lora": {"comp_l1": 0.1566780422080866, "coverage": 0.8619607843137255}, "broadcast": {}}
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{"dataset": "immicro", "comparison": "fewshot", "draw": 2, "gene_mode": "cibersortx", "bayesprism": {"comp_l1": 0.49552826442174286, "comp_l1_by_variant": {"final_cells": 0.49552826442174286, "first_cells": 0.49552826442174286, "final_mrna": 0.6257486040187901, "first_mrna": 0.6257486040187901}, "mean_fraction": {"final_cells": {"T cell": 0.4404, "B cell": 0.1075, "Monocyte": 0.2886, "NK cell": 0.078, "DC": 0.017, "Other": 0.0684}, "first_cells": {"T cell": 0.4404, "B cell": 0.1075, "Monocyte": 0.2886, "NK cell": 0.078, "DC": 0.017, "Other": 0.0684}, "final_mrna": {"T cell": 0.3813, "B cell": 0.0965, "Monocyte": 0.3396, "NK cell": 0.0589, "DC": 0.0403, "Other": 0.0833}, "first_mrna": {"T cell": 0.3813, "B cell": 0.0965, "Monocyte": 0.3396, "NK cell": 0.0589, "DC": 0.0403, "Other": 0.0833}}}, "lora": {"comp_l1": 0.17248763359752534, "coverage": 0.7860784313725491}, "broadcast": {}}
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{"dataset": "immicro", "comparison": "fewshot", "draw": 3, "gene_mode": "cibersortx", "bayesprism": {"comp_l1": 0.3500687319968211, "comp_l1_by_variant": {"final_cells": 0.3500687319968211, "first_cells": 0.3500687319968211, "final_mrna": 0.4609720856629254, "first_mrna": 0.4609720856629254}, "mean_fraction": {"final_cells": {"T cell": 0.5061, "B cell": 0.0907, "Monocyte": 0.2668, "NK cell": 0.0961, "DC": 0.026, "Other": 0.0143}, "first_cells": {"T cell": 0.5061, "B cell": 0.0907, "Monocyte": 0.2668, "NK cell": 0.0961, "DC": 0.026, "Other": 0.0143}, "final_mrna": {"T cell": 0.4578, "B cell": 0.0846, "Monocyte": 0.3093, "NK cell": 0.0682, "DC": 0.0598, "Other": 0.0204}, "first_mrna": {"T cell": 0.4578, "B cell": 0.0846, "Monocyte": 0.3093, "NK cell": 0.0682, "DC": 0.0598, "Other": 0.0204}}}, "lora": {"comp_l1": 0.18654520396343544, "coverage": 0.7829411764705883}, "broadcast": {}}
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{"dataset": "immicro", "comparison": "fewshot", "draw": 4, "gene_mode": "cibersortx", "bayesprism": {"comp_l1": 0.599083099320475, "comp_l1_by_variant": {"final_cells": 0.599083099320475, "first_cells": 0.599083099320475, "final_mrna": 0.7165605084426594, "first_mrna": 0.7165605084426594}, "mean_fraction": {"final_cells": {"T cell": 0.4112, "B cell": 0.0791, "Monocyte": 0.2872, "NK cell": 0.0522, "DC": 0.0217, "Other": 0.1486}, "first_cells": {"T cell": 0.4112, "B cell": 0.0791, "Monocyte": 0.2872, "NK cell": 0.0522, "DC": 0.0217, "Other": 0.1486}, "final_mrna": {"T cell": 0.36, "B cell": 0.071, "Monocyte": 0.3152, "NK cell": 0.0373, "DC": 0.0452, "Other": 0.1714}, "first_mrna": {"T cell": 0.36, "B cell": 0.071, "Monocyte": 0.3152, "NK cell": 0.0373, "DC": 0.0452, "Other": 0.1714}}}, "lora": {"comp_l1": 0.18059655915509124, "coverage": 0.7309803921568627}, "broadcast": {}}
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{"dataset": "immicro", "comparison": "cv", "draw": null, "gene_mode": "cibersortx", "bayesprism": {"comp_l1": 0.5065033643252109, "comp_l1_by_variant": {"final_cells": 0.5065033643252109, "first_cells": 0.5065033643252109, "final_mrna": 0.6252519106334087, "first_mrna": 0.6252519106334087}, "mean_fraction": {"final_cells": {"T cell": 0.4656, "B cell": 0.0984, "Monocyte": 0.2073, "NK cell": 0.0362, "DC": 0.0211, "Other": 0.1715}, "first_cells": {"T cell": 0.4656, "B cell": 0.0984, "Monocyte": 0.2073, "NK cell": 0.0362, "DC": 0.0211, "Other": 0.1715}, "final_mrna": {"T cell": 0.4082, "B cell": 0.0879, "Monocyte": 0.2404, "NK cell": 0.0264, "DC": 0.0479, "Other": 0.1893}, "first_mrna": {"T cell": 0.4082, "B cell": 0.0879, "Monocyte": 0.2404, "NK cell": 0.0264, "DC": 0.0479, "Other": 0.1893}}}, "lora": {"comp_l1": 0.16172890350786212, "coverage": 0.7842990654205607}, "broadcast": {}}
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{"dataset": "ye2026_sepsis", "comparison": "fewshot", "draw": 0, "gene_mode": "cibersortx", "bayesprism": {"comp_l1": 0.594921646565701, "comp_l1_by_variant": {"final_cells": 0.594921646565701, "first_cells": 0.594921646565701, "final_mrna": 0.6285146093050138, "first_mrna": 0.6285146093050138}, "mean_fraction": {"final_cells": {"T cell": 0.3685, "B cell": 0.1149, "Monocyte": 0.1853, "NK cell": 0.1496, "DC": 0.0709, "Other": 0.1109}, "first_cells": {"T cell": 0.3685, "B cell": 0.1149, "Monocyte": 0.1853, "NK cell": 0.1496, "DC": 0.0709, "Other": 0.1109}, "final_mrna": {"T cell": 0.3379, "B cell": 0.1255, "Monocyte": 0.2116, "NK cell": 0.1248, "DC": 0.1471, "Other": 0.0532}, "first_mrna": {"T cell": 0.3379, "B cell": 0.1255, "Monocyte": 0.2116, "NK cell": 0.1248, "DC": 0.1471, "Other": 0.0532}}, "logfc_r_mean_cp10k": 0.07590207961556164, "partial_r_mean_cp10k": 0.008099528439937746, "logfc_r_mean_cp10k_covered_genes": 0.12824472407785847, "deg_top50_sum": 21, "deg_top50_sum_covered_genes": 21, "per_type_logfc_r": {"T cell": -0.0351, "B cell": 0.0344, "Monocyte": 0.2632, "NK cell": 0.0411}}, "lora": {"comp_l1": 0.4723364713369038, "coverage": 0.7058874458874459, "logfc_r_mean_cp10k": 0.4359905652333528, "deg_top50_sum": 7, "partial_r_mean_cp10k": 0.4060106147529024}, "broadcast": {"logfc_r_mean_cp10k": 0.3359901153517466, "logfc_r_mean_cp10k_covered_genes": 0.32424523814709666, "deg_top50_sum": 23}}
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{"dataset": "ye2026_sepsis", "comparison": "fewshot", "draw": 1, "gene_mode": "cibersortx", "bayesprism": {"comp_l1": 0.5458984505842515, "comp_l1_by_variant": {"final_cells": 0.5458984505842515, "first_cells": 0.5458984505842515, "final_mrna": 0.5639663397037358, "first_mrna": 0.5639663397037358}, "mean_fraction": {"final_cells": {"T cell": 0.3869, "B cell": 0.127, "Monocyte": 0.2163, "NK cell": 0.1444, "DC": 0.0356, "Other": 0.0898}, "first_cells": {"T cell": 0.3869, "B cell": 0.127, "Monocyte": 0.2163, "NK cell": 0.1444, "DC": 0.0356, "Other": 0.0898}, "final_mrna": {"T cell": 0.3603, "B cell": 0.1048, "Monocyte": 0.2872, "NK cell": 0.1132, "DC": 0.0734, "Other": 0.061}, "first_mrna": {"T cell": 0.3603, "B cell": 0.1048, "Monocyte": 0.2872, "NK cell": 0.1132, "DC": 0.0734, "Other": 0.061}}, "logfc_r_mean_cp10k": 0.050686071674304126, "partial_r_mean_cp10k": -0.0204134549861548, "logfc_r_mean_cp10k_covered_genes": 0.06479062936380635, "deg_top50_sum": 29, "deg_top50_sum_covered_genes": 29, "per_type_logfc_r": {"T cell": 0.0865, "B cell": -0.1835, "Monocyte": 0.3041, "NK cell": -0.0043}}, "lora": {"comp_l1": 0.4725655492172997, "coverage": 0.6619047619047619, "logfc_r_mean_cp10k": 0.08123703391754132, "deg_top50_sum": 16, "partial_r_mean_cp10k": -0.018935679613692524}, "broadcast": {"logfc_r_mean_cp10k": 0.27941436238089834, "logfc_r_mean_cp10k_covered_genes": 0.2528700926159062, "deg_top50_sum": 20}}
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{"dataset": "ye2026_sepsis", "comparison": "fewshot", "draw": 2, "gene_mode": "cibersortx", "bayesprism": {"comp_l1": 0.5682407267081256, "comp_l1_by_variant": {"final_cells": 0.5682407267081256, "first_cells": 0.5682407267081256, "final_mrna": 0.568766565188311, "first_mrna": 0.568766565188311}, "mean_fraction": {"final_cells": {"T cell": 0.3554, "B cell": 0.1283, "Monocyte": 0.2051, "NK cell": 0.1588, "DC": 0.0374, "Other": 0.1149}, "first_cells": {"T cell": 0.3554, "B cell": 0.1283, "Monocyte": 0.2051, "NK cell": 0.1588, "DC": 0.0374, "Other": 0.1149}, "final_mrna": {"T cell": 0.3466, "B cell": 0.1104, "Monocyte": 0.2715, "NK cell": 0.1301, "DC": 0.0838, "Other": 0.0576}, "first_mrna": {"T cell": 0.3466, "B cell": 0.1104, "Monocyte": 0.2715, "NK cell": 0.1301, "DC": 0.0838, "Other": 0.0576}}, "logfc_r_mean_cp10k": 0.06938666549417015, "partial_r_mean_cp10k": -0.03390934929281273, "logfc_r_mean_cp10k_covered_genes": 0.0954950948817119, "deg_top50_sum": 26, "deg_top50_sum_covered_genes": 26, "per_type_logfc_r": {"T cell": 0.0311, "B cell": -0.1007, "Monocyte": 0.3166, "NK cell": 0.0306}}, "lora": {"comp_l1": 0.4986968896699433, "coverage": 0.7606060606060606, "logfc_r_mean_cp10k": 0.32721881191208096, "deg_top50_sum": 26, "partial_r_mean_cp10k": 0.31447561738686153}, "broadcast": {"logfc_r_mean_cp10k": 0.3386821732452143, "logfc_r_mean_cp10k_covered_genes": 0.31709558933179166, "deg_top50_sum": 18}}
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{"dataset": "ye2026_sepsis", "comparison": "fewshot", "draw": 3, "gene_mode": "cibersortx", "bayesprism": {"comp_l1": 0.6003763342155404, "comp_l1_by_variant": {"final_cells": 0.6003763342155404, "first_cells": 0.6003763342155404, "final_mrna": 0.5956927069312322, "first_mrna": 0.5956927069312322}, "mean_fraction": {"final_cells": {"T cell": 0.426, "B cell": 0.0933, "Monocyte": 0.1617, "NK cell": 0.1723, "DC": 0.0436, "Other": 0.1031}, "first_cells": {"T cell": 0.426, "B cell": 0.0933, "Monocyte": 0.1617, "NK cell": 0.1723, "DC": 0.0436, "Other": 0.1031}, "final_mrna": {"T cell": 0.3633, "B cell": 0.1204, "Monocyte": 0.2045, "NK cell": 0.1299, "DC": 0.1106, "Other": 0.0712}, "first_mrna": {"T cell": 0.3633, "B cell": 0.1204, "Monocyte": 0.2045, "NK cell": 0.1299, "DC": 0.1106, "Other": 0.0712}}, "logfc_r_mean_cp10k": 0.10318048468887185, "partial_r_mean_cp10k": 0.025546390870004418, "logfc_r_mean_cp10k_covered_genes": 0.16823647400051375, "deg_top50_sum": 23, "deg_top50_sum_covered_genes": 23, "per_type_logfc_r": {"T cell": -0.0267, "B cell": 0.088, "Monocyte": 0.2894, "NK cell": 0.062}}, "lora": {"comp_l1": 0.4968788955478774, "coverage": 0.6553246753246753, "logfc_r_mean_cp10k": 0.4108841123350609, "deg_top50_sum": 17, "partial_r_mean_cp10k": 0.3622128751991822}, "broadcast": {"logfc_r_mean_cp10k": 0.3264466405549955, "logfc_r_mean_cp10k_covered_genes": 0.3688405995264496, "deg_top50_sum": 19}}
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{"dataset": "ye2026_sepsis", "comparison": "fewshot", "draw": 4, "gene_mode": "cibersortx", "bayesprism": {"comp_l1": 0.6015123278200128, "comp_l1_by_variant": {"final_cells": 0.6015123278200128, "first_cells": 0.6015123278200128, "final_mrna": 0.5871885532406123, "first_mrna": 0.5871885532406123}, "mean_fraction": {"final_cells": {"T cell": 0.4015, "B cell": 0.1026, "Monocyte": 0.1537, "NK cell": 0.1146, "DC": 0.0517, "Other": 0.1759}, "first_cells": {"T cell": 0.4015, "B cell": 0.1026, "Monocyte": 0.1537, "NK cell": 0.1146, "DC": 0.0517, "Other": 0.1759}, "final_mrna": {"T cell": 0.3823, "B cell": 0.1039, "Monocyte": 0.199, "NK cell": 0.0968, "DC": 0.1334, "Other": 0.0846}, "first_mrna": {"T cell": 0.3823, "B cell": 0.1039, "Monocyte": 0.199, "NK cell": 0.0968, "DC": 0.1334, "Other": 0.0846}}, "logfc_r_mean_cp10k": 0.046581020885791434, "partial_r_mean_cp10k": -0.028764618151420323, "logfc_r_mean_cp10k_covered_genes": 0.07297548835093128, "deg_top50_sum": 28, "deg_top50_sum_covered_genes": 28, "per_type_logfc_r": {"T cell": 0.034, "B cell": -0.1489, "Monocyte": 0.2646, "NK cell": 0.0365}}, "lora": {"comp_l1": 0.39049012270725986, "coverage": 0.687012987012987, "logfc_r_mean_cp10k": 0.49526136963540107, "deg_top50_sum": 16, "partial_r_mean_cp10k": 0.4597246910197378}, "broadcast": {"logfc_r_mean_cp10k": 0.3195942137906433, "logfc_r_mean_cp10k_covered_genes": 0.328250013130998, "deg_top50_sum": 20}}
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{"dataset": "ye2026_sepsis", "comparison": "cv", "draw": null, "gene_mode": "cibersortx", "bayesprism": {"comp_l1": 0.607149641152929, "comp_l1_by_variant": {"final_cells": 0.607149641152929, "first_cells": 0.607149641152929, "final_mrna": 0.6133993055664033, "first_mrna": 0.6133993055664033}, "mean_fraction": {"final_cells": {"T cell": 0.4368, "B cell": 0.1095, "Monocyte": 0.1245, "NK cell": 0.1057, "DC": 0.0794, "Other": 0.1441}, "first_cells": {"T cell": 0.4368, "B cell": 0.1095, "Monocyte": 0.1245, "NK cell": 0.1057, "DC": 0.0794, "Other": 0.1441}, "final_mrna": {"T cell": 0.4004, "B cell": 0.1125, "Monocyte": 0.1573, "NK cell": 0.0838, "DC": 0.1661, "Other": 0.0798}, "first_mrna": {"T cell": 0.4004, "B cell": 0.1125, "Monocyte": 0.1573, "NK cell": 0.0838, "DC": 0.1661, "Other": 0.0798}}, "logfc_r_mean_cp10k": -0.035832909681658, "partial_r_mean_cp10k": -0.0739317360248297, "logfc_r_mean_cp10k_covered_genes": -0.12522813744518627, "deg_top50_sum": 0, "deg_top50_sum_covered_genes": 0, "per_type_logfc_r": {"T cell": -0.067, "B cell": -0.0969, "Monocyte": 0.0328, "NK cell": -0.0121}}, "lora": {"comp_l1": 0.3618246783833512, "coverage": 0.829349593495935, "logfc_r_mean_cp10k": 0.5267612711229187, "deg_top50_sum": 23, "partial_r_mean_cp10k": 0.46874787884206276, "deg_source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled_deg/summary.json"}, "broadcast": {"logfc_r_mean_cp10k": 0.31594581626202867, "logfc_r_mean_cp10k_covered_genes": 0.601490367831679, "deg_top50_sum": 21}}
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| 13 |
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| 14 |
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| 15 |
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| 16 |
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| 17 |
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| 18 |
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| 20 |
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{"dataset": "imperial_eskd", "comparison": "fewshot", "draw": 1, "gene_mode": "cibersortx", "bayesprism": {"comp_l1": 0.6541762446688113, "comp_l1_by_variant": {"final_cells": 0.6541762446688113, "first_cells": 0.6541762446688113, "final_mrna": 0.691286377681052, "first_mrna": 0.691286377681052}, "mean_fraction": {"final_cells": {"T cell": 0.3465, "B cell": 0.0616, "Monocyte": 0.3789, "NK cell": 0.1115, "DC": 0.046, "Other": 0.0555}, "first_cells": {"T cell": 0.3465, "B cell": 0.0616, "Monocyte": 0.3789, "NK cell": 0.1115, "DC": 0.046, "Other": 0.0555}, "final_mrna": {"T cell": 0.3377, "B cell": 0.0608, "Monocyte": 0.3639, "NK cell": 0.0931, "DC": 0.0918, "Other": 0.0527}, "first_mrna": {"T cell": 0.3377, "B cell": 0.0608, "Monocyte": 0.3639, "NK cell": 0.0931, "DC": 0.0918, "Other": 0.0527}}, "logfc_r_mean_cp10k": 0.26675079977347094, "partial_r_mean_cp10k": 0.0376822849901401, "logfc_r_mean_cp10k_covered_genes": 0.3351982004659172, "deg_top50_sum": 30, "deg_top50_sum_covered_genes": 30, "per_type_logfc_r": {"T cell": 0.2465, "B cell": 0.0835, "Monocyte": 0.6418, "NK cell": 0.0952}}, "lora": {"comp_l1": 0.5160151799648663, "coverage": 0.7829399392381398, "logfc_r_mean_cp10k": 0.7570901930571807, "deg_top50_sum": 119, "partial_r_mean_cp10k": 0.6045509566158934}, "broadcast": {"logfc_r_mean_cp10k": 0.6611787175621116, "logfc_r_mean_cp10k_covered_genes": 0.6124512133803278, "deg_top50_sum": 86}}
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| 21 |
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{"dataset": "imperial_eskd", "comparison": "fewshot", "draw": 2, "gene_mode": "cibersortx", "bayesprism": {"comp_l1": 0.6855049998932723, "comp_l1_by_variant": {"final_cells": 0.6855049998932723, "first_cells": 0.6855049998932723, "final_mrna": 0.6935421290569926, "first_mrna": 0.6935421290569926}, "mean_fraction": {"final_cells": {"T cell": 0.2637, "B cell": 0.0911, "Monocyte": 0.3414, "NK cell": 0.1934, "DC": 0.0513, "Other": 0.0591}, "first_cells": {"T cell": 0.2637, "B cell": 0.0911, "Monocyte": 0.3414, "NK cell": 0.1934, "DC": 0.0513, "Other": 0.0591}, "final_mrna": {"T cell": 0.2748, "B cell": 0.096, "Monocyte": 0.3317, "NK cell": 0.1436, "DC": 0.0863, "Other": 0.0676}, "first_mrna": {"T cell": 0.2748, "B cell": 0.096, "Monocyte": 0.3317, "NK cell": 0.1436, "DC": 0.0863, "Other": 0.0676}}, "logfc_r_mean_cp10k": 0.277286721740825, "partial_r_mean_cp10k": 0.060739167676012965, "logfc_r_mean_cp10k_covered_genes": 0.3620920993548596, "deg_top50_sum": 28, "deg_top50_sum_covered_genes": 28, "per_type_logfc_r": {"T cell": 0.2126, "B cell": 0.118, "Monocyte": 0.6202, "NK cell": 0.1583}}, "lora": {"comp_l1": 0.5117644876225123, "coverage": 0.6650339110776187, "logfc_r_mean_cp10k": 0.7139546009415169, "deg_top50_sum": 103, "partial_r_mean_cp10k": 0.5764372157359006}, "broadcast": {"logfc_r_mean_cp10k": 0.6433613217171205, "logfc_r_mean_cp10k_covered_genes": 0.5969865485925199, "deg_top50_sum": 65}}
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| 22 |
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{"dataset": "imperial_eskd", "comparison": "fewshot", "draw": 3, "gene_mode": "cibersortx", "bayesprism": {"comp_l1": 0.6212115928563943, "comp_l1_by_variant": {"final_cells": 0.6212115928563943, "first_cells": 0.6212115928563943, "final_mrna": 0.7028502433799985, "first_mrna": 0.7028502433799985}, "mean_fraction": {"final_cells": {"T cell": 0.3485, "B cell": 0.0354, "Monocyte": 0.3249, "NK cell": 0.1924, "DC": 0.0526, "Other": 0.0462}, "first_cells": {"T cell": 0.3485, "B cell": 0.0354, "Monocyte": 0.3249, "NK cell": 0.1924, "DC": 0.0526, "Other": 0.0462}, "final_mrna": {"T cell": 0.3052, "B cell": 0.0429, "Monocyte": 0.3638, "NK cell": 0.1459, "DC": 0.0946, "Other": 0.0476}, "first_mrna": {"T cell": 0.3052, "B cell": 0.0429, "Monocyte": 0.3638, "NK cell": 0.1459, "DC": 0.0946, "Other": 0.0476}}, "logfc_r_mean_cp10k": 0.2875769620209124, "partial_r_mean_cp10k": 0.06329601007176323, "logfc_r_mean_cp10k_covered_genes": 0.3707037183477628, "deg_top50_sum": 26, "deg_top50_sum_covered_genes": 26, "per_type_logfc_r": {"T cell": 0.2226, "B cell": 0.092, "Monocyte": 0.6317, "NK cell": 0.204}}, "lora": {"comp_l1": 0.5275199844470723, "coverage": 0.842680564523568, "logfc_r_mean_cp10k": 0.7455905986374256, "deg_top50_sum": 117, "partial_r_mean_cp10k": 0.6007400715066787}, "broadcast": {"logfc_r_mean_cp10k": 0.6538959233815048, "logfc_r_mean_cp10k_covered_genes": 0.5940125287652693, "deg_top50_sum": 76}}
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| 23 |
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{"dataset": "imperial_eskd", "comparison": "fewshot", "draw": 4, "gene_mode": "cibersortx", "bayesprism": {"comp_l1": 0.6432264870798222, "comp_l1_by_variant": {"final_cells": 0.6432264870798222, "first_cells": 0.6432264870798222, "final_mrna": 0.7155526059071532, "first_mrna": 0.7155526059071532}, "mean_fraction": {"final_cells": {"T cell": 0.3242, "B cell": 0.0651, "Monocyte": 0.3883, "NK cell": 0.1432, "DC": 0.0479, "Other": 0.0313}, "first_cells": {"T cell": 0.3242, "B cell": 0.0651, "Monocyte": 0.3883, "NK cell": 0.1432, "DC": 0.0479, "Other": 0.0313}, "final_mrna": {"T cell": 0.2912, "B cell": 0.074, "Monocyte": 0.4066, "NK cell": 0.1043, "DC": 0.0829, "Other": 0.0411}, "first_mrna": {"T cell": 0.2912, "B cell": 0.074, "Monocyte": 0.4066, "NK cell": 0.1043, "DC": 0.0829, "Other": 0.0411}}, "logfc_r_mean_cp10k": 0.2933124611981251, "partial_r_mean_cp10k": 0.06932961604601938, "logfc_r_mean_cp10k_covered_genes": 0.3762981477946839, "deg_top50_sum": 38, "deg_top50_sum_covered_genes": 38, "per_type_logfc_r": {"T cell": 0.239, "B cell": 0.1295, "Monocyte": 0.6495, "NK cell": 0.1552}}, "lora": {"comp_l1": 0.48142813711177446, "coverage": 0.6369376110747358, "logfc_r_mean_cp10k": 0.7492433446082651, "deg_top50_sum": 113, "partial_r_mean_cp10k": 0.575230848198632}, "broadcast": {"logfc_r_mean_cp10k": 0.6565426449733607, "logfc_r_mean_cp10k_covered_genes": 0.5982397217635673, "deg_top50_sum": 76}}
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| 24 |
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{"dataset": "imperial_eskd", "comparison": "cv", "draw": null, "gene_mode": "cibersortx", "bayesprism": {"comp_l1": 0.5918271288164071, "comp_l1_by_variant": {"final_cells": 0.5918271288164071, "first_cells": 0.5918271288164071, "final_mrna": 0.6633005066634348, "first_mrna": 0.6633005066634348}, "mean_fraction": {"final_cells": {"T cell": 0.3685, "B cell": 0.07, "Monocyte": 0.324, "NK cell": 0.1331, "DC": 0.0376, "Other": 0.0668}, "first_cells": {"T cell": 0.3685, "B cell": 0.07, "Monocyte": 0.324, "NK cell": 0.1331, "DC": 0.0376, "Other": 0.0668}, "final_mrna": {"T cell": 0.3397, "B cell": 0.0751, "Monocyte": 0.3483, "NK cell": 0.0983, "DC": 0.0674, "Other": 0.0712}, "first_mrna": {"T cell": 0.3397, "B cell": 0.0751, "Monocyte": 0.3483, "NK cell": 0.0983, "DC": 0.0674, "Other": 0.0712}}, "logfc_r_mean_cp10k": 0.21113497684457377, "partial_r_mean_cp10k": 0.015667623661280307, "logfc_r_mean_cp10k_covered_genes": 0.3693097049105145, "deg_top50_sum": 1, "deg_top50_sum_covered_genes": 3, "per_type_logfc_r": {"T cell": 0.1634, "B cell": -0.0253, "Monocyte": 0.4332, "NK cell": 0.2733}}, "lora": {"comp_l1": 0.37638560875745664, "coverage": 0.8500127757431224, "logfc_r_mean_cp10k": 0.8187448084273437, "deg_top50_sum": 143, "partial_r_mean_cp10k": 0.6899314750539278}, "broadcast": {"logfc_r_mean_cp10k": 0.6606053132085035, "logfc_r_mean_cp10k_covered_genes": 0.5831498842343769, "deg_top50_sum": 84}}
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| 25 |
+
{"dataset": "giroux2022", "comparison": "fewshot", "draw": 0, "gene_mode": "cibersortx", "bayesprism": {"comp_l1": 0.8513318718371892, "comp_l1_by_variant": {"final_cells": 0.8513318718371892, "first_cells": 0.8513318718371892, "final_mrna": 0.5719201437614763, "first_mrna": 0.5719201437614763}, "mean_fraction": {"final_cells": {"T cell": 0.2944, "B cell": 0.054, "Monocyte": 0.1323, "NK cell": 0.0428, "DC": 0.0018, "Other": 0.4747}, "first_cells": {"T cell": 0.2944, "B cell": 0.054, "Monocyte": 0.1323, "NK cell": 0.0428, "DC": 0.0018, "Other": 0.4747}, "final_mrna": {"T cell": 0.3339, "B cell": 0.0781, "Monocyte": 0.2639, "NK cell": 0.056, "DC": 0.007, "Other": 0.2612}, "first_mrna": {"T cell": 0.3339, "B cell": 0.0781, "Monocyte": 0.2639, "NK cell": 0.056, "DC": 0.007, "Other": 0.2612}}, "logfc_r_mean_cp10k": 0.043169836902222695, "partial_r_mean_cp10k": 0.033616720303144165, "logfc_r_mean_cp10k_covered_genes": 0.11204850205858954, "deg_top50_sum": 0, "deg_top50_sum_covered_genes": 0, "per_type_logfc_r": {"T cell": NaN, "B cell": NaN, "Monocyte": 0.0432, "NK cell": NaN}}, "lora": {"comp_l1": 0.27193277679338645, "coverage": 0.96, "logfc_r_mean_cp10k": 0.243392212681724, "deg_top50_sum": 0, "partial_r_mean_cp10k": 0.15035969319388034}, "broadcast": {"logfc_r_mean_cp10k": 0.4709654147613206, "logfc_r_mean_cp10k_covered_genes": 0.6007393502931081, "deg_top50_sum": 0}}
|
| 26 |
+
{"dataset": "giroux2022", "comparison": "fewshot", "draw": 1, "gene_mode": "cibersortx", "bayesprism": {"comp_l1": 0.5781759971117253, "comp_l1_by_variant": {"final_cells": 0.5781759971117253, "first_cells": 0.5781759971117253, "final_mrna": 0.44474798825029893, "first_mrna": 0.44474798825029893}, "mean_fraction": {"final_cells": {"T cell": 0.4133, "B cell": 0.0285, "Monocyte": 0.179, "NK cell": 0.041, "DC": 0.005, "Other": 0.3333}, "first_cells": {"T cell": 0.4133, "B cell": 0.0285, "Monocyte": 0.179, "NK cell": 0.041, "DC": 0.005, "Other": 0.3333}, "final_mrna": {"T cell": 0.4252, "B cell": 0.0381, "Monocyte": 0.3121, "NK cell": 0.0475, "DC": 0.0163, "Other": 0.1608}, "first_mrna": {"T cell": 0.4252, "B cell": 0.0381, "Monocyte": 0.3121, "NK cell": 0.0475, "DC": 0.0163, "Other": 0.1608}}, "logfc_r_mean_cp10k": NaN, "partial_r_mean_cp10k": NaN, "logfc_r_mean_cp10k_covered_genes": NaN, "deg_top50_sum": 0, "deg_top50_sum_covered_genes": 0, "per_type_logfc_r": {"T cell": NaN, "B cell": NaN, "Monocyte": NaN, "NK cell": NaN}}, "lora": {"comp_l1": 0.22320689222847964, "coverage": 0.9526666666666667, "logfc_r_mean_cp10k": 0.35634959703435354, "deg_top50_sum": 1, "partial_r_mean_cp10k": 0.2523250741286013}, "broadcast": {"logfc_r_mean_cp10k": 0.5012527613870964, "logfc_r_mean_cp10k_covered_genes": NaN, "deg_top50_sum": 0}}
|
| 27 |
+
{"dataset": "giroux2022", "comparison": "fewshot", "draw": 2, "gene_mode": "cibersortx", "bayesprism": {"comp_l1": 0.7362234910018671, "comp_l1_by_variant": {"final_cells": 0.7362234910018671, "first_cells": 0.7362234910018671, "final_mrna": 0.5549823156091591, "first_mrna": 0.5549823156091591}, "mean_fraction": {"final_cells": {"T cell": 0.3282, "B cell": 0.0622, "Monocyte": 0.1744, "NK cell": 0.0325, "DC": 0.0089, "Other": 0.3939}, "first_cells": {"T cell": 0.3282, "B cell": 0.0622, "Monocyte": 0.1744, "NK cell": 0.0325, "DC": 0.0089, "Other": 0.3939}, "final_mrna": {"T cell": 0.3593, "B cell": 0.0877, "Monocyte": 0.2967, "NK cell": 0.0432, "DC": 0.0238, "Other": 0.1894}, "first_mrna": {"T cell": 0.3593, "B cell": 0.0877, "Monocyte": 0.2967, "NK cell": 0.0432, "DC": 0.0238, "Other": 0.1894}}, "logfc_r_mean_cp10k": 0.14207699218896452, "partial_r_mean_cp10k": 0.03670999356082373, "logfc_r_mean_cp10k_covered_genes": 0.28706463437770313, "deg_top50_sum": 0, "deg_top50_sum_covered_genes": 0, "per_type_logfc_r": {"T cell": 0.1421, "B cell": NaN, "Monocyte": NaN, "NK cell": NaN}}, "lora": {"comp_l1": 0.2907494763185344, "coverage": 0.9533333333333334, "logfc_r_mean_cp10k": 0.230513969445487, "deg_top50_sum": 0, "partial_r_mean_cp10k": 0.15040912208962715}, "broadcast": {"logfc_r_mean_cp10k": 0.39643909018360535, "logfc_r_mean_cp10k_covered_genes": 0.3744566448404962, "deg_top50_sum": 0}}
|
| 28 |
+
{"dataset": "giroux2022", "comparison": "fewshot", "draw": 3, "gene_mode": "cibersortx", "bayesprism": {"comp_l1": 0.6273383088965232, "comp_l1_by_variant": {"final_cells": 0.6273383088965232, "first_cells": 0.6273383088965232, "final_mrna": 0.5349181669787998, "first_mrna": 0.5349181669787998}, "mean_fraction": {"final_cells": {"T cell": 0.4205, "B cell": 0.0449, "Monocyte": 0.1614, "NK cell": 0.0285, "DC": 0.0044, "Other": 0.3403}, "first_cells": {"T cell": 0.4205, "B cell": 0.0449, "Monocyte": 0.1614, "NK cell": 0.0285, "DC": 0.0044, "Other": 0.3403}, "final_mrna": {"T cell": 0.4199, "B cell": 0.0634, "Monocyte": 0.2956, "NK cell": 0.0351, "DC": 0.0151, "Other": 0.1709}, "first_mrna": {"T cell": 0.4199, "B cell": 0.0634, "Monocyte": 0.2956, "NK cell": 0.0351, "DC": 0.0151, "Other": 0.1709}}, "logfc_r_mean_cp10k": 0.10122878113268267, "partial_r_mean_cp10k": 0.01560047376617661, "logfc_r_mean_cp10k_covered_genes": 0.20480855492979932, "deg_top50_sum": 0, "deg_top50_sum_covered_genes": 0, "per_type_logfc_r": {"T cell": 0.1402, "B cell": NaN, "Monocyte": 0.0623, "NK cell": NaN}}, "lora": {"comp_l1": 0.2688359990061283, "coverage": 0.9624242424242424, "logfc_r_mean_cp10k": 0.24186295766157903, "deg_top50_sum": 0, "partial_r_mean_cp10k": 0.14697551642627654}, "broadcast": {"logfc_r_mean_cp10k": 0.4657480400911531, "logfc_r_mean_cp10k_covered_genes": 0.4666205977748122, "deg_top50_sum": 0}}
|
| 29 |
+
{"dataset": "giroux2022", "comparison": "fewshot", "draw": 4, "gene_mode": "cibersortx", "bayesprism": {"comp_l1": 0.5538402679700511, "comp_l1_by_variant": {"final_cells": 0.5538402679700511, "first_cells": 0.5538402679700511, "final_mrna": 0.3915609545174028, "first_mrna": 0.3915609545174028}, "mean_fraction": {"final_cells": {"T cell": 0.4197, "B cell": 0.0291, "Monocyte": 0.1543, "NK cell": 0.0698, "DC": 0.0168, "Other": 0.3103}, "first_cells": {"T cell": 0.4197, "B cell": 0.0291, "Monocyte": 0.1543, "NK cell": 0.0698, "DC": 0.0168, "Other": 0.3103}, "final_mrna": {"T cell": 0.436, "B cell": 0.034, "Monocyte": 0.2491, "NK cell": 0.0749, "DC": 0.0467, "Other": 0.1592}, "first_mrna": {"T cell": 0.436, "B cell": 0.034, "Monocyte": 0.2491, "NK cell": 0.0749, "DC": 0.0467, "Other": 0.1592}}, "logfc_r_mean_cp10k": NaN, "partial_r_mean_cp10k": NaN, "logfc_r_mean_cp10k_covered_genes": NaN, "deg_top50_sum": 0, "deg_top50_sum_covered_genes": 0, "per_type_logfc_r": {"T cell": NaN, "B cell": NaN, "Monocyte": NaN, "NK cell": NaN}}, "lora": {"comp_l1": 0.2274734478129418, "coverage": 0.9766666666666667, "logfc_r_mean_cp10k": 0.41085265458568265, "deg_top50_sum": 0, "partial_r_mean_cp10k": 0.24279747694617004}, "broadcast": {"logfc_r_mean_cp10k": 0.6280870820074911, "logfc_r_mean_cp10k_covered_genes": NaN, "deg_top50_sum": 0}}
|
| 30 |
+
{"dataset": "giroux2022", "comparison": "cv", "draw": null, "gene_mode": "cibersortx", "bayesprism": {"comp_l1": 0.5914100321768722, "comp_l1_by_variant": {"final_cells": 0.5914100321768722, "first_cells": 0.5914100321768722, "final_mrna": 0.4536133148837987, "first_mrna": 0.4536133148837987}, "mean_fraction": {"final_cells": {"T cell": 0.4474, "B cell": 0.024, "Monocyte": 0.1585, "NK cell": 0.0474, "DC": 0.0025, "Other": 0.3202}, "first_cells": {"T cell": 0.4474, "B cell": 0.024, "Monocyte": 0.1585, "NK cell": 0.0474, "DC": 0.0025, "Other": 0.3202}, "final_mrna": {"T cell": 0.4645, "B cell": 0.0298, "Monocyte": 0.2756, "NK cell": 0.0547, "DC": 0.0078, "Other": 0.1677}, "first_mrna": {"T cell": 0.4645, "B cell": 0.0298, "Monocyte": 0.2756, "NK cell": 0.0547, "DC": 0.0078, "Other": 0.1677}}}, "lora": {"comp_l1": 0.2580442754044374, "coverage": 0.9280555555555555}, "broadcast": {}}
|
| 31 |
+
# CIBERSORTx with the same paired donors vs LoRA (paired benchmark; gene mode cibersortx)
|
| 32 |
+
|
| 33 |
+
CIBERSORTx in place of BayesPrism ('BP' columns): official Docker Fractions, single-cell reference (<=400 cells per type from the same paired donors) with S-mode batch correction, then HiRes per-sample cell-type expression on the scoring genes (tools/run_cibersortx.sh). One fraction estimate, so 'final' = 'first'. HiRes needs more samples than cell types: splits with <= 8 test samples (Ji and Giroux CV folds) have composition only.
|
| 34 |
+
|
| 35 |
+
Same donors, observed truth, contrast and scorer as the benchmark (score_ft.py functions; the recomputed bulk broadcast equals the stored one in every split). BayesPrism reference = the split's paired donors' observed cells (states = gate | AIFI L2); mixture = the test samples' real bulk. Composition L1 in cell units (lower is better): 'final' and 'first' BayesPrism theta. logFC r = case-vs-control per-type logFC (mean CP10K) correlation with observed, mean of T/B/Mono/NK; BayesPrism Z zero-filled on genes it lacks ('covered' = only genes it models, broadcast recomputed there). DEG = top-50 overlap summed over types.
|
| 36 |
+
|
| 37 |
+
## Five-donor draws (mean ± SD over 5 draws)
|
| 38 |
+
|
| 39 |
+
| cohort | L1 BP final | L1 BP first | L1 LoRA-5 | r BP | r BP (covered) | r LoRA-5 | r broadcast | partial r BP | partial r LoRA-5 | DEG BP | DEG LoRA-5 | DEG broadcast |
|
| 40 |
+
|---|---:|---:|---:|---:|---:|---:|---:|---:|---:|---:|---:|---:|
|
| 41 |
+
| ImMicro (5) | 0.491 ± 0.095 | 0.491 ± 0.095 | 0.176 ± 0.012 | – | – | – | – | – | – | – | – | – |
|
| 42 |
+
| Sepsis (5) | 0.582 ± 0.024 | 0.582 ± 0.024 | 0.466 ± 0.044 | 0.069 ± 0.023 | 0.106 ± 0.043 | 0.350 ± 0.162 | 0.320 ± 0.024 | -0.010 ± 0.026 | 0.305 ± 0.189 | 25.4 ± 3.4 | 16.4 ± 6.7 | 20.0 ± 1.9 |
|
| 43 |
+
| Ji ChILI (5) | 0.827 ± 0.145 | 0.827 ± 0.145 | 0.513 ± 0.115 | 0.158 ± 0.054 | 0.263 ± 0.071 | 0.333 ± 0.077 | 0.234 ± 0.026 | 0.005 ± 0.046 | 0.300 ± 0.076 | 0.0 ± 0.0 | 0.2 ± 0.4 | 1.0 ± 2.2 |
|
| 44 |
+
| Imperial (5) | 0.646 ± 0.026 | 0.646 ± 0.026 | 0.503 ± 0.022 | 0.283 ± 0.011 | 0.363 ± 0.016 | 0.749 ± 0.024 | 0.656 ± 0.009 | 0.061 ± 0.014 | 0.603 ± 0.033 | 30.8 ± 4.6 | 113.6 ± 6.3 | 74.8 ± 7.7 |
|
| 45 |
+
| Giroux (5) | 0.669 ± 0.124 | 0.669 ± 0.124 | 0.256 ± 0.030 | 0.095 ± 0.050 | 0.201 ± 0.088 | 0.297 ± 0.082 | 0.492 ± 0.085 | 0.029 ± 0.011 | 0.189 ± 0.054 | 0.0 ± 0.0 | 0.2 ± 0.4 | 0.0 ± 0.0 |
|
| 46 |
+
|
| 47 |
+
Draws where LoRA-5 beats CIBERSORTx: composition 24/25 (vs CIBERSORTx's better theta), logFC r 17/17, partial r 17/17, top-50 DEG 7/20 (ties 9).
|
| 48 |
+
|
| 49 |
+
## 5-fold CV, pooled (CIBERSORTx reference = each fold's LoRA training + inner-validation pairs)
|
| 50 |
+
|
| 51 |
+
| cohort | L1 BP final | L1 BP first | L1 LoRA | L1 scSemi | r BP | r BP (covered) | r LoRA | r scSemi | r broadcast | partial r BP | partial r LoRA | DEG BP | DEG LoRA | DEG scSemi | DEG broadcast |
|
| 52 |
+
|---|---:|---:|---:|---:|---:|---:|---:|---:|---:|---:|---:|---:|---:|---:|---:|
|
| 53 |
+
| ImMicro | 0.507 | 0.507 | 0.162 | 0.217 | – | – | – | – | – | – | – | – | – | – | – |
|
| 54 |
+
| Sepsis | 0.607 | 0.607 | 0.362 | 0.502 | -0.036 | -0.125 | 0.527 | 0.435 | 0.316 | -0.074 | 0.469 | 0 | 23 | 6 | 21 |
|
| 55 |
+
| Ji ChILI | 0.914 | 0.914 | 0.504 | 0.575 | – | – | – | 0.273 | – | – | – | – | – | 0 | – |
|
| 56 |
+
| Imperial | 0.592 | 0.592 | 0.376 | – | 0.211 | 0.369 | 0.819 | – | 0.661 | 0.016 | 0.690 | 1 | 143 | – | 84 |
|
| 57 |
+
| Giroux | 0.591 | 0.591 | 0.258 | 0.243 | – | – | – | 0.537 | – | – | – | – | – | 0 | – |
|
| 58 |
+
{"dataset": "giroux2022", "comparison": "cv", "draw": null, "gene_mode": "full", "bayesprism": {"comp_l1": 1.8027760246078957, "comp_l1_by_variant": {"final_cells": 1.8027760246078957, "first_cells": 0.8778647964495544, "final_mrna": 1.6349594535077872, "first_mrna": 0.6061262872441106}, "mean_fraction": {"final_cells": {"T cell": 0.0, "B cell": 0.0035, "Monocyte": 0.0474, "NK cell": 0.0032, "DC": 0.0, "Other": 0.9459}, "first_cells": {"T cell": 0.476, "B cell": 0.0036, "Monocyte": 0.0804, "NK cell": 0.003, "DC": 0.0005, "Other": 0.4365}, "final_mrna": {"T cell": 0.0, "B cell": 0.0083, "Monocyte": 0.1352, "NK cell": 0.0067, "DC": 0.0, "Other": 0.8498}, "first_mrna": {"T cell": 0.5505, "B cell": 0.0054, "Monocyte": 0.1615, "NK cell": 0.0041, "DC": 0.0017, "Other": 0.2767}}, "logfc_r_mean_cp10k": 0.40594570910829286, "partial_r_mean_cp10k": 0.02157078325029122, "logfc_r_mean_cp10k_covered_genes": 0.40810658821060636, "deg_top50_sum": 3, "deg_top50_sum_covered_genes": 3, "per_type_logfc_r": {"T cell": 0.4601, "B cell": 0.2477, "Monocyte": 0.697, "NK cell": 0.219}}, "lora": {"comp_l1": 0.2580442754044374, "coverage": 0.9280555555555555, "logfc_r_mean_cp10k": 0.46094848304079133, "deg_top50_sum": 5, "partial_r_mean_cp10k": 0.3230347269696575}, "broadcast": {"logfc_r_mean_cp10k": 0.5752659929360795, "logfc_r_mean_cp10k_covered_genes": 0.5750505878963892, "deg_top50_sum": 5}}
|
| 59 |
+
# BayesPrism with the same paired donors vs LoRA (paired benchmark; gene mode full)
|
| 60 |
+
|
| 61 |
+
BayesPrism genes: its recommended set (canonical protein-coding minus chrX/Y/M and RPS/RPL/MRPS/MRPL, measured by the sc assay; 15-19k genes).
|
| 62 |
+
|
| 63 |
+
Same donors, observed truth, contrast and scorer as the benchmark (score_ft.py functions; the recomputed bulk broadcast equals the stored one in every split). BayesPrism reference = the split's paired donors' observed cells (states = gate | AIFI L2); mixture = the test samples' real bulk. Composition L1 in cell units (lower is better): 'final' and 'first' BayesPrism theta. logFC r = case-vs-control per-type logFC (mean CP10K) correlation with observed, mean of T/B/Mono/NK; BayesPrism Z zero-filled on genes it lacks ('covered' = only genes it models, broadcast recomputed there). DEG = top-50 overlap summed over types.
|
| 64 |
+
|
| 65 |
+
## Five-donor draws (mean ± SD over 5 draws)
|
| 66 |
+
|
| 67 |
+
| cohort | L1 BP final | L1 BP first | L1 LoRA-5 | r BP | r BP (covered) | r LoRA-5 | r broadcast | partial r BP | partial r LoRA-5 | DEG BP | DEG LoRA-5 | DEG broadcast |
|
| 68 |
+
|---|---:|---:|---:|---:|---:|---:|---:|---:|---:|---:|---:|---:|
|
| 69 |
+
| ImMicro (5) | 0.594 ± 0.088 | 0.550 ± 0.164 | 0.176 ± 0.012 | – | – | – | – | – | – | – | – | – |
|
| 70 |
+
| Sepsis (5) | 0.643 ± 0.118 | 0.543 ± 0.218 | 0.466 ± 0.044 | 0.241 ± 0.035 | 0.258 ± 0.036 | 0.350 ± 0.162 | 0.320 ± 0.024 | 0.095 ± 0.035 | 0.305 ± 0.189 | 27.0 ± 2.0 | 16.4 ± 6.7 | 20.0 ± 1.9 |
|
| 71 |
+
| Ji ChILI (5) | 0.943 ± 0.117 | 0.952 ± 0.161 | 0.513 ± 0.115 | 0.193 ± 0.013 | 0.212 ± 0.013 | 0.333 ± 0.077 | 0.234 ± 0.026 | 0.032 ± 0.020 | 0.300 ± 0.076 | 2.0 ± 2.4 | 0.2 ± 0.4 | 1.0 ± 2.2 |
|
| 72 |
+
| Imperial (5) | 0.962 ± 0.086 | 0.845 ± 0.063 | 0.503 ± 0.022 | 0.598 ± 0.033 | 0.614 ± 0.034 | 0.749 ± 0.024 | 0.656 ± 0.009 | 0.187 ± 0.039 | 0.603 ± 0.033 | 72.4 ± 10.1 | 113.6 ± 6.3 | 74.8 ± 7.7 |
|
| 73 |
+
| Giroux (5) | 1.807 ± 0.047 | 1.455 ± 0.361 | 0.256 ± 0.030 | 0.371 ± 0.060 | 0.374 ± 0.060 | 0.297 ± 0.082 | 0.492 ± 0.085 | 0.117 ± 0.060 | 0.189 ± 0.054 | 0.2 ± 0.4 | 0.2 ± 0.4 | 0.0 ± 0.0 |
|
| 74 |
+
|
| 75 |
+
Draws where LoRA-5 beats BayesPrism: composition 22/25 (vs BayesPrism's better theta), logFC r 15/20, partial r 18/20, top-50 DEG 6/20 (ties 6).
|
| 76 |
+
|
| 77 |
+
## 5-fold CV, pooled (BayesPrism reference = each fold's LoRA training + inner-validation pairs)
|
| 78 |
+
|
| 79 |
+
| cohort | L1 BP final | L1 BP first | L1 LoRA | L1 scSemi | r BP | r BP (covered) | r LoRA | r scSemi | r broadcast | partial r BP | partial r LoRA | DEG BP | DEG LoRA | DEG scSemi | DEG broadcast |
|
| 80 |
+
|---|---:|---:|---:|---:|---:|---:|---:|---:|---:|---:|---:|---:|---:|---:|---:|
|
| 81 |
+
| ImMicro | 0.575 | 0.909 | 0.162 | 0.217 | – | – | – | – | – | – | – | – | – | – | – |
|
| 82 |
+
| Sepsis | 0.603 | 0.475 | 0.362 | 0.502 | 0.255 | 0.253 | 0.527 | 0.435 | 0.316 | 0.095 | 0.469 | 37 | 23 | 6 | 21 |
|
| 83 |
+
| Ji ChILI | 0.883 | 1.055 | 0.504 | 0.575 | 0.186 | 0.204 | 0.479 | 0.273 | 0.240 | 0.020 | 0.452 | 4 | 15 | 0 | 4 |
|
| 84 |
+
| Imperial | 0.887 | 1.022 | 0.376 | – | 0.568 | 0.584 | 0.819 | – | 0.661 | 0.112 | 0.690 | 91 | 143 | – | 84 |
|
| 85 |
+
| Giroux | 1.803 | 0.878 | 0.258 | 0.243 | 0.406 | 0.408 | 0.461 | 0.537 | 0.575 | 0.022 | 0.323 | 3 | 5 | 0 | 5 |
|
| 86 |
+
2026-10-08T11:02:46 finalize_cx done; failed=0
|
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/finalize_full_20261007T115524.log
ADDED
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| 1 |
+
{"dataset": "immicro", "comparison": "fewshot", "draw": 0, "gene_mode": "full", "bayesprism": {"comp_l1": 0.7007916840315994, "comp_l1_by_variant": {"final_cells": 0.7007916840315994, "first_cells": 0.7095725570550513, "final_mrna": 0.815240548471243, "first_mrna": 0.814890521008765}, "mean_fraction": {"final_cells": {"T cell": 0.3148, "B cell": 0.0786, "Monocyte": 0.2782, "NK cell": 0.2102, "DC": 0.0, "Other": 0.1182}, "first_cells": {"T cell": 0.312, "B cell": 0.0665, "Monocyte": 0.269, "NK cell": 0.1823, "DC": 0.0052, "Other": 0.1649}, "final_mrna": {"T cell": 0.2632, "B cell": 0.0675, "Monocyte": 0.3893, "NK cell": 0.1734, "DC": 0.0, "Other": 0.1067}, "first_mrna": {"T cell": 0.2585, "B cell": 0.0567, "Monocyte": 0.3738, "NK cell": 0.1494, "DC": 0.014, "Other": 0.1476}}}, "lora": {"comp_l1": 0.18149050759378063, "coverage": 0.8003921568627451}, "broadcast": {}}
|
| 2 |
+
{"dataset": "immicro", "comparison": "fewshot", "draw": 1, "gene_mode": "full", "bayesprism": {"comp_l1": 0.5867840853021318, "comp_l1_by_variant": {"final_cells": 0.5867840853021318, "first_cells": 0.5568722574151432, "final_mrna": 0.7188819104413758, "first_mrna": 0.7036569529162466}, "mean_fraction": {"final_cells": {"T cell": 0.3706, "B cell": 0.0941, "Monocyte": 0.2505, "NK cell": 0.2702, "DC": 0.0002, "Other": 0.0145}, "first_cells": {"T cell": 0.3718, "B cell": 0.0865, "Monocyte": 0.2369, "NK cell": 0.1995, "DC": 0.0144, "Other": 0.091}, "final_mrna": {"T cell": 0.3066, "B cell": 0.0845, "Monocyte": 0.3642, "NK cell": 0.2272, "DC": 0.0004, "Other": 0.0171}, "first_mrna": {"T cell": 0.2944, "B cell": 0.0742, "Monocyte": 0.3303, "NK cell": 0.1612, "DC": 0.0374, "Other": 0.1025}}}, "lora": {"comp_l1": 0.1566780422080866, "coverage": 0.8619607843137255}, "broadcast": {}}
|
| 3 |
+
{"dataset": "immicro", "comparison": "fewshot", "draw": 2, "gene_mode": "full", "bayesprism": {"comp_l1": 0.4799919108625404, "comp_l1_by_variant": {"final_cells": 0.4799919108625404, "first_cells": 0.42350657413858, "final_mrna": 0.6284356141851742, "first_mrna": 0.602894578776955}, "mean_fraction": {"final_cells": {"T cell": 0.423, "B cell": 0.1159, "Monocyte": 0.2833, "NK cell": 0.1592, "DC": 0.0, "Other": 0.0187}, "first_cells": {"T cell": 0.4593, "B cell": 0.0995, "Monocyte": 0.2756, "NK cell": 0.0867, "DC": 0.0118, "Other": 0.067}, "final_mrna": {"T cell": 0.3503, "B cell": 0.1028, "Monocyte": 0.3859, "NK cell": 0.1384, "DC": 0.0, "Other": 0.0225}, "first_mrna": {"T cell": 0.3678, "B cell": 0.0854, "Monocyte": 0.3636, "NK cell": 0.0735, "DC": 0.0316, "Other": 0.078}}}, "lora": {"comp_l1": 0.17248763359752534, "coverage": 0.7860784313725491}, "broadcast": {}}
|
| 4 |
+
{"dataset": "immicro", "comparison": "fewshot", "draw": 3, "gene_mode": "full", "bayesprism": {"comp_l1": 0.5433864890686753, "comp_l1_by_variant": {"final_cells": 0.5433864890686753, "first_cells": 0.34901299827821086, "final_mrna": 0.6913389573074368, "first_mrna": 0.5235544271932386}, "mean_fraction": {"final_cells": {"T cell": 0.3967, "B cell": 0.0895, "Monocyte": 0.2811, "NK cell": 0.2309, "DC": 0.0, "Other": 0.0017}, "first_cells": {"T cell": 0.4806, "B cell": 0.0875, "Monocyte": 0.27, "NK cell": 0.1408, "DC": 0.0097, "Other": 0.0113}, "final_mrna": {"T cell": 0.3236, "B cell": 0.0866, "Monocyte": 0.3946, "NK cell": 0.1928, "DC": 0.0001, "Other": 0.0023}, "first_mrna": {"T cell": 0.3852, "B cell": 0.0833, "Monocyte": 0.3741, "NK cell": 0.1161, "DC": 0.0254, "Other": 0.0158}}}, "lora": {"comp_l1": 0.18654520396343544, "coverage": 0.7829411764705883}, "broadcast": {}}
|
| 5 |
+
{"dataset": "immicro", "comparison": "fewshot", "draw": 4, "gene_mode": "full", "bayesprism": {"comp_l1": 0.6570417646897321, "comp_l1_by_variant": {"final_cells": 0.6570417646897321, "first_cells": 0.7111605997430848, "final_mrna": 0.7718138036880455, "first_mrna": 0.8154949515224682}, "mean_fraction": {"final_cells": {"T cell": 0.335, "B cell": 0.1144, "Monocyte": 0.3084, "NK cell": 0.2239, "DC": 0.0, "Other": 0.0182}, "first_cells": {"T cell": 0.3037, "B cell": 0.0992, "Monocyte": 0.291, "NK cell": 0.2107, "DC": 0.0042, "Other": 0.0913}, "final_mrna": {"T cell": 0.278, "B cell": 0.1055, "Monocyte": 0.4119, "NK cell": 0.1839, "DC": 0.0, "Other": 0.0207}, "first_mrna": {"T cell": 0.2468, "B cell": 0.0897, "Monocyte": 0.3819, "NK cell": 0.1699, "DC": 0.01, "Other": 0.1016}}}, "lora": {"comp_l1": 0.18059655915509124, "coverage": 0.7309803921568627}, "broadcast": {}}
|
| 6 |
+
{"dataset": "immicro", "comparison": "cv", "draw": null, "gene_mode": "full", "bayesprism": {"comp_l1": 0.5745628784374615, "comp_l1_by_variant": {"final_cells": 0.5745628784374615, "first_cells": 0.9085350102150449, "final_mrna": 0.7109207210458764, "first_mrna": 1.036502570274581}, "mean_fraction": {"final_cells": {"T cell": 0.378, "B cell": 0.0976, "Monocyte": 0.2791, "NK cell": 0.2356, "DC": 0.0, "Other": 0.0097}, "first_cells": {"T cell": 0.2209, "B cell": 0.067, "Monocyte": 0.2511, "NK cell": 0.1093, "DC": 0.0068, "Other": 0.3449}, "final_mrna": {"T cell": 0.312, "B cell": 0.0861, "Monocyte": 0.3927, "NK cell": 0.1985, "DC": 0.0, "Other": 0.0107}, "first_mrna": {"T cell": 0.1683, "B cell": 0.0542, "Monocyte": 0.3241, "NK cell": 0.0849, "DC": 0.0159, "Other": 0.3526}}}, "lora": {"comp_l1": 0.16172890350786212, "coverage": 0.7842990654205607}, "broadcast": {}}
|
| 7 |
+
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|
| 8 |
+
{"dataset": "ye2026_sepsis", "comparison": "fewshot", "draw": 1, "gene_mode": "full", "bayesprism": {"comp_l1": 0.7545625036164484, "comp_l1_by_variant": {"final_cells": 0.7545625036164484, "first_cells": 0.40696664594222093, "final_mrna": 0.8008746707816097, "first_mrna": 0.46071574366111445}, "mean_fraction": {"final_cells": {"T cell": 0.2035, "B cell": 0.2066, "Monocyte": 0.2591, "NK cell": 0.2976, "DC": 0.0004, "Other": 0.0327}, "first_cells": {"T cell": 0.534, "B cell": 0.1111, "Monocyte": 0.23, "NK cell": 0.098, "DC": 0.0014, "Other": 0.0255}, "final_mrna": {"T cell": 0.1751, "B cell": 0.1605, "Monocyte": 0.3868, "NK cell": 0.2517, "DC": 0.0009, "Other": 0.0249}, "first_mrna": {"T cell": 0.4493, "B cell": 0.0886, "Monocyte": 0.3533, "NK cell": 0.0857, "DC": 0.0033, "Other": 0.0199}}, "logfc_r_mean_cp10k": 0.1973279877442922, "partial_r_mean_cp10k": 0.07467956638801354, "logfc_r_mean_cp10k_covered_genes": 0.21136473813096954, "deg_top50_sum": 30, "deg_top50_sum_covered_genes": 30, "per_type_logfc_r": {"T cell": 0.1111, "B cell": 0.0881, "Monocyte": 0.5598, "NK cell": 0.0302}}, "lora": {"comp_l1": 0.4725655492172997, "coverage": 0.6619047619047619, "logfc_r_mean_cp10k": 0.08123703391754132, "deg_top50_sum": 16, "partial_r_mean_cp10k": -0.018935679613692524}, "broadcast": {"logfc_r_mean_cp10k": 0.27941436238089834, "logfc_r_mean_cp10k_covered_genes": 0.20176471635222232, "deg_top50_sum": 20}}
|
| 9 |
+
{"dataset": "ye2026_sepsis", "comparison": "fewshot", "draw": 2, "gene_mode": "full", "bayesprism": {"comp_l1": 0.673874617567153, "comp_l1_by_variant": {"final_cells": 0.673874617567153, "first_cells": 0.436135409514162, "final_mrna": 0.6868537334974446, "first_mrna": 0.4349919323214119}, "mean_fraction": {"final_cells": {"T cell": 0.246, "B cell": 0.1916, "Monocyte": 0.2267, "NK cell": 0.2785, "DC": 0.0008, "Other": 0.0564}, "first_cells": {"T cell": 0.5601, "B cell": 0.0905, "Monocyte": 0.2024, "NK cell": 0.0619, "DC": 0.0103, "Other": 0.0748}, "final_mrna": {"T cell": 0.2226, "B cell": 0.1536, "Monocyte": 0.337, "NK cell": 0.2539, "DC": 0.0021, "Other": 0.0308}, "first_mrna": {"T cell": 0.4956, "B cell": 0.0743, "Monocyte": 0.3045, "NK cell": 0.0569, "DC": 0.0265, "Other": 0.0422}}, "logfc_r_mean_cp10k": 0.2654125351120938, "partial_r_mean_cp10k": 0.11483895518121781, "logfc_r_mean_cp10k_covered_genes": 0.2826594932185867, "deg_top50_sum": 26, "deg_top50_sum_covered_genes": 26, "per_type_logfc_r": {"T cell": 0.1943, "B cell": 0.228, "Monocyte": 0.5219, "NK cell": 0.1174}}, "lora": {"comp_l1": 0.4986968896699433, "coverage": 0.7606060606060606, "logfc_r_mean_cp10k": 0.32721881191208096, "deg_top50_sum": 26, "partial_r_mean_cp10k": 0.31447561738686153}, "broadcast": {"logfc_r_mean_cp10k": 0.3386821732452143, "logfc_r_mean_cp10k_covered_genes": 0.26922440985482304, "deg_top50_sum": 18}}
|
| 10 |
+
{"dataset": "ye2026_sepsis", "comparison": "fewshot", "draw": 3, "gene_mode": "full", "bayesprism": {"comp_l1": 0.6584478375412718, "comp_l1_by_variant": {"final_cells": 0.6584478375412718, "first_cells": 0.49935002903888365, "final_mrna": 0.6238518076835088, "first_mrna": 0.43200791406540134}, "mean_fraction": {"final_cells": {"T cell": 0.3726, "B cell": 0.0949, "Monocyte": 0.1972, "NK cell": 0.2895, "DC": 0.0014, "Other": 0.0443}, "first_cells": {"T cell": 0.5334, "B cell": 0.0777, "Monocyte": 0.1775, "NK cell": 0.1657, "DC": 0.0009, "Other": 0.0448}, "final_mrna": {"T cell": 0.2987, "B cell": 0.1231, "Monocyte": 0.3028, "NK cell": 0.2396, "DC": 0.0041, "Other": 0.0317}, "first_mrna": {"T cell": 0.4317, "B cell": 0.1053, "Monocyte": 0.2833, "NK cell": 0.1434, "DC": 0.0026, "Other": 0.0337}}, "logfc_r_mean_cp10k": 0.2748463496313776, "partial_r_mean_cp10k": 0.12531483062765006, "logfc_r_mean_cp10k_covered_genes": 0.29289624841134965, "deg_top50_sum": 25, "deg_top50_sum_covered_genes": 25, "per_type_logfc_r": {"T cell": 0.231, "B cell": 0.215, "Monocyte": 0.5253, "NK cell": 0.128}}, "lora": {"comp_l1": 0.4968788955478774, "coverage": 0.6553246753246753, "logfc_r_mean_cp10k": 0.4108841123350609, "deg_top50_sum": 17, "partial_r_mean_cp10k": 0.3622128751991822}, "broadcast": {"logfc_r_mean_cp10k": 0.3264466405549955, "logfc_r_mean_cp10k_covered_genes": 0.25480636308287835, "deg_top50_sum": 19}}
|
| 11 |
+
{"dataset": "ye2026_sepsis", "comparison": "fewshot", "draw": 4, "gene_mode": "full", "bayesprism": {"comp_l1": 0.44194685595873645, "comp_l1_by_variant": {"final_cells": 0.44194685595873645, "first_cells": 0.9281637213458136, "final_mrna": 0.45859472265308704, "first_mrna": 0.6878184432362746}, "mean_fraction": {"final_cells": {"T cell": 0.4119, "B cell": 0.1625, "Monocyte": 0.1873, "NK cell": 0.1395, "DC": 0.0153, "Other": 0.0834}, "first_cells": {"T cell": 0.3263, "B cell": 0.065, "Monocyte": 0.1086, "NK cell": 0.0314, "DC": 0.0063, "Other": 0.4624}, "final_mrna": {"T cell": 0.3619, "B cell": 0.154, "Monocyte": 0.2746, "NK cell": 0.1276, "DC": 0.0417, "Other": 0.0402}, "first_mrna": {"T cell": 0.3601, "B cell": 0.0787, "Monocyte": 0.2108, "NK cell": 0.0378, "DC": 0.0232, "Other": 0.2894}}, "logfc_r_mean_cp10k": 0.21151027451804771, "partial_r_mean_cp10k": 0.0428777909634605, "logfc_r_mean_cp10k_covered_genes": 0.226319434007386, "deg_top50_sum": 28, "deg_top50_sum_covered_genes": 28, "per_type_logfc_r": {"T cell": 0.1012, "B cell": 0.1488, "Monocyte": 0.4086, "NK cell": 0.1875}}, "lora": {"comp_l1": 0.39049012270725986, "coverage": 0.687012987012987, "logfc_r_mean_cp10k": 0.49526136963540107, "deg_top50_sum": 16, "partial_r_mean_cp10k": 0.4597246910197378}, "broadcast": {"logfc_r_mean_cp10k": 0.3195942137906433, "logfc_r_mean_cp10k_covered_genes": 0.23992076506989504, "deg_top50_sum": 20}}
|
| 12 |
+
{"dataset": "ye2026_sepsis", "comparison": "cv", "draw": null, "gene_mode": "full", "bayesprism": {"comp_l1": 0.6029270442284831, "comp_l1_by_variant": {"final_cells": 0.6029270442284831, "first_cells": 0.4750523423944086, "final_mrna": 0.649204630549072, "first_mrna": 0.45424984326877027}, "mean_fraction": {"final_cells": {"T cell": 0.3123, "B cell": 0.1357, "Monocyte": 0.2537, "NK cell": 0.2517, "DC": 0.0064, "Other": 0.0401}, "first_cells": {"T cell": 0.6081, "B cell": 0.0653, "Monocyte": 0.2181, "NK cell": 0.0623, "DC": 0.0041, "Other": 0.0421}, "final_mrna": {"T cell": 0.2639, "B cell": 0.1304, "Monocyte": 0.3495, "NK cell": 0.2163, "DC": 0.015, "Other": 0.0248}, "first_mrna": {"T cell": 0.5244, "B cell": 0.0659, "Monocyte": 0.3155, "NK cell": 0.0569, "DC": 0.0102, "Other": 0.0271}}, "logfc_r_mean_cp10k": 0.2554670801971232, "partial_r_mean_cp10k": 0.09471562043764327, "logfc_r_mean_cp10k_covered_genes": 0.2533386702661269, "deg_top50_sum": 37, "deg_top50_sum_covered_genes": 38, "per_type_logfc_r": {"T cell": 0.1232, "B cell": 0.1825, "Monocyte": 0.5804, "NK cell": 0.1358}}, "lora": {"comp_l1": 0.3618246783833512, "coverage": 0.829349593495935, "logfc_r_mean_cp10k": 0.5267612711229187, "deg_top50_sum": 23, "partial_r_mean_cp10k": 0.46874787884206276, "deg_source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled_deg/summary.json"}, "broadcast": {"logfc_r_mean_cp10k": 0.31594581626202867, "logfc_r_mean_cp10k_covered_genes": 0.2531577574908379, "deg_top50_sum": 21}}
|
| 13 |
+
{"dataset": "ji2025_chili", "comparison": "fewshot", "draw": 0, "gene_mode": "full", "bayesprism": {"comp_l1": 0.897833546244817, "comp_l1_by_variant": {"final_cells": 0.897833546244817, "first_cells": 1.0604240102209128, "final_mrna": 0.967617615291296, "first_mrna": 1.0838623302535204}, "mean_fraction": {"final_cells": {"T cell": 0.1168, "B cell": 0.0691, "Monocyte": 0.4223, "NK cell": 0.1651, "DC": 0.0, "Other": 0.2268}, "first_cells": {"T cell": 0.0411, "B cell": 0.0849, "Monocyte": 0.3865, "NK cell": 0.1589, "DC": 0.0017, "Other": 0.3269}, "final_mrna": {"T cell": 0.0866, "B cell": 0.062, "Monocyte": 0.5081, "NK cell": 0.136, "DC": 0.0, "Other": 0.2073}, "first_mrna": {"T cell": 0.0306, "B cell": 0.0759, "Monocyte": 0.4626, "NK cell": 0.1306, "DC": 0.0027, "Other": 0.2975}}, "logfc_r_mean_cp10k": 0.1861628716144019, "partial_r_mean_cp10k": 0.039991272520911975, "logfc_r_mean_cp10k_covered_genes": 0.2091092566585711, "deg_top50_sum": 0, "deg_top50_sum_covered_genes": 0, "per_type_logfc_r": {"T cell": 0.1547, "B cell": 0.0737, "Monocyte": 0.3979, "NK cell": 0.1183}}, "lora": {"comp_l1": 0.46942970758493824, "coverage": 0.6992, "logfc_r_mean_cp10k": 0.38697985726899736, "deg_top50_sum": 0, "partial_r_mean_cp10k": 0.36588903106531123}, "broadcast": {"logfc_r_mean_cp10k": 0.21311861411338662, "logfc_r_mean_cp10k_covered_genes": 0.20508643810380944, "deg_top50_sum": 0}}
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| 14 |
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| 15 |
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| 16 |
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| 17 |
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| 18 |
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| 19 |
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| 20 |
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|
| 21 |
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|
| 22 |
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{"dataset": "imperial_eskd", "comparison": "fewshot", "draw": 3, "gene_mode": "full", "bayesprism": {"comp_l1": 0.952439303710189, "comp_l1_by_variant": {"final_cells": 0.952439303710189, "first_cells": 0.7721033215822146, "final_mrna": 0.9896097918791011, "first_mrna": 0.8395719977060822}, "mean_fraction": {"final_cells": {"T cell": 0.1546, "B cell": 0.0314, "Monocyte": 0.3397, "NK cell": 0.3999, "DC": 0.0037, "Other": 0.0707}, "first_cells": {"T cell": 0.2373, "B cell": 0.0482, "Monocyte": 0.3242, "NK cell": 0.2801, "DC": 0.0106, "Other": 0.0995}, "final_mrna": {"T cell": 0.1267, "B cell": 0.0361, "Monocyte": 0.4376, "NK cell": 0.3193, "DC": 0.0071, "Other": 0.0732}, "first_mrna": {"T cell": 0.1899, "B cell": 0.0546, "Monocyte": 0.4124, "NK cell": 0.2203, "DC": 0.0197, "Other": 0.1031}}, "logfc_r_mean_cp10k": 0.5854045807968098, "partial_r_mean_cp10k": 0.17783522904041, "logfc_r_mean_cp10k_covered_genes": 0.599454910013415, "deg_top50_sum": 61, "deg_top50_sum_covered_genes": 61, "per_type_logfc_r": {"T cell": 0.5127, "B cell": 0.4339, "Monocyte": 0.7062, "NK cell": 0.6888}}, "lora": {"comp_l1": 0.5275199844470723, "coverage": 0.842680564523568, "logfc_r_mean_cp10k": 0.7455905986374256, "deg_top50_sum": 117, "partial_r_mean_cp10k": 0.6007400715066787}, "broadcast": {"logfc_r_mean_cp10k": 0.6538959233815048, "logfc_r_mean_cp10k_covered_genes": 0.6314051959325884, "deg_top50_sum": 76}}
|
| 23 |
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{"dataset": "imperial_eskd", "comparison": "fewshot", "draw": 4, "gene_mode": "full", "bayesprism": {"comp_l1": 1.0185576195402575, "comp_l1_by_variant": {"final_cells": 1.0185576195402575, "first_cells": 0.877165890125515, "final_mrna": 1.0429716754877905, "first_mrna": 0.9348379138470198}, "mean_fraction": {"final_cells": {"T cell": 0.1003, "B cell": 0.0549, "Monocyte": 0.4304, "NK cell": 0.3817, "DC": 0.0001, "Other": 0.0326}, "first_cells": {"T cell": 0.1731, "B cell": 0.0692, "Monocyte": 0.3986, "NK cell": 0.2692, "DC": 0.0027, "Other": 0.0872}, "final_mrna": {"T cell": 0.0893, "B cell": 0.0588, "Monocyte": 0.5093, "NK cell": 0.3013, "DC": 0.0001, "Other": 0.0412}, "first_mrna": {"T cell": 0.1473, "B cell": 0.0717, "Monocyte": 0.4595, "NK cell": 0.2069, "DC": 0.0047, "Other": 0.1099}}, "logfc_r_mean_cp10k": 0.6282271395994876, "partial_r_mean_cp10k": 0.20003452036960517, "logfc_r_mean_cp10k_covered_genes": 0.6456639661993082, "deg_top50_sum": 82, "deg_top50_sum_covered_genes": 82, "per_type_logfc_r": {"T cell": 0.5729, "B cell": 0.5332, "Monocyte": 0.7243, "NK cell": 0.6825}}, "lora": {"comp_l1": 0.48142813711177446, "coverage": 0.6369376110747358, "logfc_r_mean_cp10k": 0.7492433446082651, "deg_top50_sum": 113, "partial_r_mean_cp10k": 0.575230848198632}, "broadcast": {"logfc_r_mean_cp10k": 0.6565426449733607, "logfc_r_mean_cp10k_covered_genes": 0.6340865519335486, "deg_top50_sum": 76}}
|
| 24 |
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{"dataset": "imperial_eskd", "comparison": "cv", "draw": null, "gene_mode": "full", "bayesprism": {"comp_l1": 0.8870870830413495, "comp_l1_by_variant": {"final_cells": 0.8870870830413495, "first_cells": 1.0215635566013643, "final_mrna": 0.9300862395332192, "first_mrna": 1.0602851494967092}, "mean_fraction": {"final_cells": {"T cell": 0.1721, "B cell": 0.0612, "Monocyte": 0.4002, "NK cell": 0.3518, "DC": 0.0006, "Other": 0.014}, "first_cells": {"T cell": 0.0801, "B cell": 0.0973, "Monocyte": 0.3567, "NK cell": 0.2763, "DC": 0.0018, "Other": 0.1878}, "final_mrna": {"T cell": 0.149, "B cell": 0.0657, "Monocyte": 0.4861, "NK cell": 0.2819, "DC": 0.0012, "Other": 0.0161}, "first_mrna": {"T cell": 0.066, "B cell": 0.0997, "Monocyte": 0.4149, "NK cell": 0.212, "DC": 0.0032, "Other": 0.2041}}, "logfc_r_mean_cp10k": 0.5684615839866303, "partial_r_mean_cp10k": 0.11228628082302743, "logfc_r_mean_cp10k_covered_genes": 0.5843506673991777, "deg_top50_sum": 91, "deg_top50_sum_covered_genes": 91, "per_type_logfc_r": {"T cell": 0.3768, "B cell": 0.5227, "Monocyte": 0.7265, "NK cell": 0.6478}}, "lora": {"comp_l1": 0.37638560875745664, "coverage": 0.8500127757431224, "logfc_r_mean_cp10k": 0.8187448084273437, "deg_top50_sum": 143, "partial_r_mean_cp10k": 0.6899314750539278}, "broadcast": {"logfc_r_mean_cp10k": 0.6606053132085035, "logfc_r_mean_cp10k_covered_genes": 0.6388431994811914, "deg_top50_sum": 84}}
|
| 25 |
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{"dataset": "giroux2022", "comparison": "fewshot", "draw": 0, "gene_mode": "full", "bayesprism": {"comp_l1": 1.823568204154302, "comp_l1_by_variant": {"final_cells": 1.823568204154302, "first_cells": 1.760300271065443, "final_mrna": 1.6664742276631346, "first_mrna": 1.5655893271691574}, "mean_fraction": {"final_cells": {"T cell": 0.0, "B cell": 0.0015, "Monocyte": 0.0358, "NK cell": 0.0, "DC": 0.0, "Other": 0.9627}, "first_cells": {"T cell": 0.0421, "B cell": 0.0021, "Monocyte": 0.0246, "NK cell": 0.0, "DC": 0.0001, "Other": 0.9311}, "final_mrna": {"T cell": 0.0, "B cell": 0.0039, "Monocyte": 0.114, "NK cell": 0.0, "DC": 0.0, "Other": 0.8821}, "first_mrna": {"T cell": 0.0795, "B cell": 0.0052, "Monocyte": 0.081, "NK cell": 0.0001, "DC": 0.0005, "Other": 0.8337}}, "logfc_r_mean_cp10k": 0.32005331944484905, "partial_r_mean_cp10k": 0.041926780978093464, "logfc_r_mean_cp10k_covered_genes": 0.32210509323752057, "deg_top50_sum": 0, "deg_top50_sum_covered_genes": 0, "per_type_logfc_r": {"T cell": 0.445, "B cell": 0.2105, "Monocyte": 0.4517, "NK cell": 0.173}}, "lora": {"comp_l1": 0.27193277679338645, "coverage": 0.96, "logfc_r_mean_cp10k": 0.243392212681724, "deg_top50_sum": 0, "partial_r_mean_cp10k": 0.15035969319388034}, "broadcast": {"logfc_r_mean_cp10k": 0.4709654147613206, "logfc_r_mean_cp10k_covered_genes": 0.4703882003663197, "deg_top50_sum": 0}}
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| 26 |
+
{"dataset": "giroux2022", "comparison": "fewshot", "draw": 1, "gene_mode": "full", "bayesprism": {"comp_l1": 1.7796487879351197, "comp_l1_by_variant": {"final_cells": 1.7796487879351197, "first_cells": 1.7057827896282756, "final_mrna": 1.5946579220285848, "first_mrna": 1.4720716270797947}, "mean_fraction": {"final_cells": {"T cell": 0.0, "B cell": 0.0, "Monocyte": 0.0543, "NK cell": 0.0, "DC": 0.0, "Other": 0.9456}, "first_cells": {"T cell": 0.0536, "B cell": 0.0002, "Monocyte": 0.0376, "NK cell": 0.0, "DC": 0.0, "Other": 0.9087}, "final_mrna": {"T cell": 0.0, "B cell": 0.0001, "Monocyte": 0.1622, "NK cell": 0.0, "DC": 0.0, "Other": 0.8377}, "first_mrna": {"T cell": 0.0972, "B cell": 0.0004, "Monocyte": 0.115, "NK cell": 0.0, "DC": 0.0, "Other": 0.7874}}, "logfc_r_mean_cp10k": 0.322615216302418, "partial_r_mean_cp10k": 0.0674219104283513, "logfc_r_mean_cp10k_covered_genes": 0.324889934518131, "deg_top50_sum": 0, "deg_top50_sum_covered_genes": 0, "per_type_logfc_r": {"T cell": 0.5273, "B cell": 0.136, "Monocyte": 0.4721, "NK cell": 0.155}}, "lora": {"comp_l1": 0.22320689222847964, "coverage": 0.9526666666666667, "logfc_r_mean_cp10k": 0.35634959703435354, "deg_top50_sum": 1, "partial_r_mean_cp10k": 0.2523250741286013}, "broadcast": {"logfc_r_mean_cp10k": 0.5012527613870964, "logfc_r_mean_cp10k_covered_genes": 0.5013392952006742, "deg_top50_sum": 0}}
|
| 27 |
+
{"dataset": "giroux2022", "comparison": "fewshot", "draw": 2, "gene_mode": "full", "bayesprism": {"comp_l1": 1.8513410332082703, "comp_l1_by_variant": {"final_cells": 1.8513410332082703, "first_cells": 1.6162854136223028, "final_mrna": 1.7150234163461275, "first_mrna": 1.312386424804014}, "mean_fraction": {"final_cells": {"T cell": 0.0, "B cell": 0.0024, "Monocyte": 0.033, "NK cell": 0.0001, "DC": 0.0, "Other": 0.9645}, "first_cells": {"T cell": 0.1199, "B cell": 0.0028, "Monocyte": 0.0297, "NK cell": 0.0005, "DC": 0.0001, "Other": 0.847}, "final_mrna": {"T cell": 0.0, "B cell": 0.0065, "Monocyte": 0.0994, "NK cell": 0.0003, "DC": 0.0, "Other": 0.8939}, "first_mrna": {"T cell": 0.2109, "B cell": 0.0066, "Monocyte": 0.0858, "NK cell": 0.001, "DC": 0.0005, "Other": 0.6951}}, "logfc_r_mean_cp10k": 0.3505858518250693, "partial_r_mean_cp10k": 0.12928822148729102, "logfc_r_mean_cp10k_covered_genes": 0.352626835275316, "deg_top50_sum": 1, "deg_top50_sum_covered_genes": 1, "per_type_logfc_r": {"T cell": 0.371, "B cell": 0.28, "Monocyte": 0.6126, "NK cell": 0.1388}}, "lora": {"comp_l1": 0.2907494763185344, "coverage": 0.9533333333333334, "logfc_r_mean_cp10k": 0.230513969445487, "deg_top50_sum": 0, "partial_r_mean_cp10k": 0.15040912208962715}, "broadcast": {"logfc_r_mean_cp10k": 0.39643909018360535, "logfc_r_mean_cp10k_covered_genes": 0.39718518838668054, "deg_top50_sum": 0}}
|
| 28 |
+
{"dataset": "giroux2022", "comparison": "fewshot", "draw": 3, "gene_mode": "full", "bayesprism": {"comp_l1": 1.8433952838578165, "comp_l1_by_variant": {"final_cells": 1.8433952838578165, "first_cells": 1.302936224569384, "final_mrna": 1.709759632389227, "first_mrna": 0.9231549241386623}, "mean_fraction": {"final_cells": {"T cell": 0.0, "B cell": 0.0029, "Monocyte": 0.0323, "NK cell": 0.0003, "DC": 0.0, "Other": 0.9644}, "first_cells": {"T cell": 0.2555, "B cell": 0.0035, "Monocyte": 0.046, "NK cell": 0.0007, "DC": 0.0001, "Other": 0.6942}, "final_mrna": {"T cell": 0.0, "B cell": 0.0079, "Monocyte": 0.1099, "NK cell": 0.0007, "DC": 0.0, "Other": 0.8815}, "first_mrna": {"T cell": 0.3747, "B cell": 0.0072, "Monocyte": 0.1269, "NK cell": 0.0012, "DC": 0.0007, "Other": 0.4893}}, "logfc_r_mean_cp10k": 0.4037329126226964, "partial_r_mean_cp10k": 0.17056815748180337, "logfc_r_mean_cp10k_covered_genes": 0.40616851567557477, "deg_top50_sum": 0, "deg_top50_sum_covered_genes": 0, "per_type_logfc_r": {"T cell": 0.5101, "B cell": 0.3237, "Monocyte": 0.6215, "NK cell": 0.1596}}, "lora": {"comp_l1": 0.2688359990061283, "coverage": 0.9624242424242424, "logfc_r_mean_cp10k": 0.24186295766157903, "deg_top50_sum": 0, "partial_r_mean_cp10k": 0.14697551642627654}, "broadcast": {"logfc_r_mean_cp10k": 0.4657480400911531, "logfc_r_mean_cp10k_covered_genes": 0.46502199547649703, "deg_top50_sum": 0}}
|
| 29 |
+
{"dataset": "giroux2022", "comparison": "fewshot", "draw": 4, "gene_mode": "full", "bayesprism": {"comp_l1": 1.7394178030068272, "comp_l1_by_variant": {"final_cells": 1.7394178030068272, "first_cells": 0.8918817885623647, "final_mrna": 1.5197459592589615, "first_mrna": 0.5507970141863743}, "mean_fraction": {"final_cells": {"T cell": 0.0, "B cell": 0.0019, "Monocyte": 0.072, "NK cell": 0.0057, "DC": 0.0, "Other": 0.9203}, "first_cells": {"T cell": 0.4551, "B cell": 0.0014, "Monocyte": 0.0998, "NK cell": 0.0026, "DC": 0.0003, "Other": 0.4409}, "final_mrna": {"T cell": 0.0, "B cell": 0.0043, "Monocyte": 0.1757, "NK cell": 0.0106, "DC": 0.0, "Other": 0.8094}, "first_mrna": {"T cell": 0.5322, "B cell": 0.0021, "Monocyte": 0.1773, "NK cell": 0.0038, "DC": 0.0009, "Other": 0.2836}}, "logfc_r_mean_cp10k": 0.4600865296295808, "partial_r_mean_cp10k": 0.17404564011140683, "logfc_r_mean_cp10k_covered_genes": 0.46209174837758643, "deg_top50_sum": 0, "deg_top50_sum_covered_genes": 0, "per_type_logfc_r": {"T cell": 0.5901, "B cell": 0.2809, "Monocyte": 0.7588, "NK cell": 0.2106}}, "lora": {"comp_l1": 0.2274734478129418, "coverage": 0.9766666666666667, "logfc_r_mean_cp10k": 0.41085265458568265, "deg_top50_sum": 0, "partial_r_mean_cp10k": 0.24279747694617004}, "broadcast": {"logfc_r_mean_cp10k": 0.6280870820074911, "logfc_r_mean_cp10k_covered_genes": 0.6293022636855459, "deg_top50_sum": 0}}
|
| 30 |
+
{"dataset": "giroux2022", "comparison": "cv", "draw": null, "gene_mode": "full", "bayesprism": {"comp_l1": 1.8027760246078957, "comp_l1_by_variant": {"final_cells": 1.8027760246078957, "first_cells": 0.8778647964495544, "final_mrna": 1.6349594535077872, "first_mrna": 0.6061262872441106}, "mean_fraction": {"final_cells": {"T cell": 0.0, "B cell": 0.0035, "Monocyte": 0.0474, "NK cell": 0.0032, "DC": 0.0, "Other": 0.9459}, "first_cells": {"T cell": 0.476, "B cell": 0.0036, "Monocyte": 0.0804, "NK cell": 0.003, "DC": 0.0005, "Other": 0.4365}, "final_mrna": {"T cell": 0.0, "B cell": 0.0083, "Monocyte": 0.1352, "NK cell": 0.0067, "DC": 0.0, "Other": 0.8498}, "first_mrna": {"T cell": 0.5505, "B cell": 0.0054, "Monocyte": 0.1615, "NK cell": 0.0041, "DC": 0.0017, "Other": 0.2767}}, "logfc_r_mean_cp10k": 0.40594570910829286, "partial_r_mean_cp10k": 0.02157078325029122, "logfc_r_mean_cp10k_covered_genes": 0.40810658821060636, "deg_top50_sum": 3, "deg_top50_sum_covered_genes": 3, "per_type_logfc_r": {"T cell": 0.4601, "B cell": 0.2477, "Monocyte": 0.697, "NK cell": 0.219}}, "lora": {"comp_l1": 0.2580442754044374, "coverage": 0.9280555555555555, "logfc_r_mean_cp10k": 0.46094848304079133, "deg_top50_sum": 5, "partial_r_mean_cp10k": 0.3230347269696575}, "broadcast": {"logfc_r_mean_cp10k": 0.5752659929360795, "logfc_r_mean_cp10k_covered_genes": 0.5750505878963892, "deg_top50_sum": 5}}
|
| 31 |
+
# BayesPrism with the same paired donors vs LoRA (paired benchmark; gene mode full)
|
| 32 |
+
|
| 33 |
+
BayesPrism genes: its recommended set (canonical protein-coding minus chrX/Y/M and RPS/RPL/MRPS/MRPL, measured by the sc assay; 15-19k genes).
|
| 34 |
+
|
| 35 |
+
Same donors, observed truth, contrast and scorer as the benchmark (score_ft.py functions; the recomputed bulk broadcast equals the stored one in every split). BayesPrism reference = the split's paired donors' observed cells (states = gate | AIFI L2); mixture = the test samples' real bulk. Composition L1 in cell units (lower is better): 'final' and 'first' BayesPrism theta. logFC r = case-vs-control per-type logFC (mean CP10K) correlation with observed, mean of T/B/Mono/NK; BayesPrism Z zero-filled on genes it lacks ('covered' = only genes it models, broadcast recomputed there). DEG = top-50 overlap summed over types.
|
| 36 |
+
|
| 37 |
+
## Five-donor draws (mean ± SD over 5 draws)
|
| 38 |
+
|
| 39 |
+
| cohort | L1 BP final | L1 BP first | L1 LoRA-5 | r BP | r BP (covered) | r LoRA-5 | r broadcast | partial r BP | partial r LoRA-5 | DEG BP | DEG LoRA-5 | DEG broadcast |
|
| 40 |
+
|---|---:|---:|---:|---:|---:|---:|---:|---:|---:|---:|---:|---:|
|
| 41 |
+
| ImMicro (5) | 0.594 ± 0.088 | 0.550 ± 0.164 | 0.176 ± 0.012 | – | – | – | – | – | – | – | – | – |
|
| 42 |
+
| Sepsis (5) | 0.643 ± 0.118 | 0.543 ± 0.218 | 0.466 ± 0.044 | 0.241 ± 0.035 | 0.258 ± 0.036 | 0.350 ± 0.162 | 0.320 ± 0.024 | 0.095 ± 0.035 | 0.305 ± 0.189 | 27.0 ± 2.0 | 16.4 ± 6.7 | 20.0 ± 1.9 |
|
| 43 |
+
| Ji ChILI (5) | 0.943 ± 0.117 | 0.952 ± 0.161 | 0.513 ± 0.115 | 0.193 ± 0.013 | 0.212 ± 0.013 | 0.333 ± 0.077 | 0.234 ± 0.026 | 0.032 ± 0.020 | 0.300 ± 0.076 | 2.0 ± 2.4 | 0.2 ± 0.4 | 1.0 ± 2.2 |
|
| 44 |
+
| Imperial (5) | 0.962 ± 0.086 | 0.845 ± 0.063 | 0.503 ± 0.022 | 0.598 ± 0.033 | 0.614 ± 0.034 | 0.749 ± 0.024 | 0.656 ± 0.009 | 0.187 ± 0.039 | 0.603 ± 0.033 | 72.4 ± 10.1 | 113.6 ± 6.3 | 74.8 ± 7.7 |
|
| 45 |
+
| Giroux (5) | 1.807 ± 0.047 | 1.455 ± 0.361 | 0.256 ± 0.030 | 0.371 ± 0.060 | 0.374 ± 0.060 | 0.297 ± 0.082 | 0.492 ± 0.085 | 0.117 ± 0.060 | 0.189 ± 0.054 | 0.2 ± 0.4 | 0.2 ± 0.4 | 0.0 ± 0.0 |
|
| 46 |
+
|
| 47 |
+
Draws where LoRA-5 beats BayesPrism: composition 22/25 (vs BayesPrism's better theta), logFC r 15/20, partial r 18/20, top-50 DEG 6/20 (ties 6).
|
| 48 |
+
|
| 49 |
+
## 5-fold CV, pooled (BayesPrism reference = each fold's LoRA training + inner-validation pairs)
|
| 50 |
+
|
| 51 |
+
| cohort | L1 BP final | L1 BP first | L1 LoRA | L1 scSemi | r BP | r BP (covered) | r LoRA | r scSemi | r broadcast | partial r BP | partial r LoRA | DEG BP | DEG LoRA | DEG scSemi | DEG broadcast |
|
| 52 |
+
|---|---:|---:|---:|---:|---:|---:|---:|---:|---:|---:|---:|---:|---:|---:|---:|
|
| 53 |
+
| ImMicro | 0.575 | 0.909 | 0.162 | 0.217 | – | – | – | – | – | – | – | – | – | – | – |
|
| 54 |
+
| Sepsis | 0.603 | 0.475 | 0.362 | – | 0.255 | 0.253 | 0.527 | – | 0.316 | 0.095 | 0.469 | 37 | 23 | – | 21 |
|
| 55 |
+
| Ji ChILI | 0.883 | 1.055 | 0.504 | 0.575 | 0.186 | 0.204 | 0.479 | 0.273 | 0.240 | 0.020 | 0.452 | 4 | 15 | 0 | 4 |
|
| 56 |
+
| Imperial | 0.887 | 1.022 | 0.376 | – | 0.568 | 0.584 | 0.819 | – | 0.661 | 0.112 | 0.690 | 91 | 143 | – | 84 |
|
| 57 |
+
| Giroux | 1.803 | 0.878 | 0.258 | – | 0.406 | 0.408 | 0.461 | – | 0.575 | 0.022 | 0.323 | 3 | 5 | – | 5 |
|
| 58 |
+
{"dataset": "immicro", "comparison": "fewshot", "draw": 0, "gene_mode": "score", "bayesprism": {"comp_l1": 1.3888441252388026, "comp_l1_by_variant": {"final_cells": 1.3888441252388026, "first_cells": 1.3494962860735726, "final_mrna": 1.376235368872937, "first_mrna": 1.3167613791422135}, "mean_fraction": {"final_cells": {"T cell": 0.0121, "B cell": 0.0287, "Monocyte": 0.3432, "NK cell": 0.5975, "DC": 0.0001, "Other": 0.0184}, "first_cells": {"T cell": 0.0261, "B cell": 0.0254, "Monocyte": 0.3404, "NK cell": 0.5061, "DC": 0.0083, "Other": 0.0937}, "final_mrna": {"T cell": 0.014, "B cell": 0.0331, "Monocyte": 0.4973, "NK cell": 0.435, "DC": 0.0002, "Other": 0.0204}, "first_mrna": {"T cell": 0.0283, "B cell": 0.0278, "Monocyte": 0.4706, "NK cell": 0.3508, "DC": 0.024, "Other": 0.0984}}}, "lora": {"comp_l1": 0.18149050759378063, "coverage": 0.8003921568627451}, "broadcast": {}}
|
| 59 |
+
{"dataset": "immicro", "comparison": "fewshot", "draw": 1, "gene_mode": "score", "bayesprism": {"comp_l1": 1.3444054950784279, "comp_l1_by_variant": {"final_cells": 1.3444054950784279, "first_cells": 1.172649629210488, "final_mrna": 1.3187337825164387, "first_mrna": 1.1330058893792956}, "mean_fraction": {"final_cells": {"T cell": 0.0337, "B cell": 0.0354, "Monocyte": 0.2861, "NK cell": 0.6423, "DC": 0.0015, "Other": 0.001}, "first_cells": {"T cell": 0.0934, "B cell": 0.0491, "Monocyte": 0.2866, "NK cell": 0.555, "DC": 0.0113, "Other": 0.0045}, "final_mrna": {"T cell": 0.0375, "B cell": 0.0414, "Monocyte": 0.4416, "NK cell": 0.4734, "DC": 0.0047, "Other": 0.0014}, "first_mrna": {"T cell": 0.0976, "B cell": 0.0542, "Monocyte": 0.4206, "NK cell": 0.3881, "DC": 0.0331, "Other": 0.0063}}}, "lora": {"comp_l1": 0.1566780422080866, "coverage": 0.8619607843137255}, "broadcast": {}}
|
| 60 |
+
{"dataset": "immicro", "comparison": "fewshot", "draw": 2, "gene_mode": "score", "bayesprism": {"comp_l1": 1.3190885985901637, "comp_l1_by_variant": {"final_cells": 1.3190885985901637, "first_cells": 1.1892325981577347, "final_mrna": 1.3034732905042083, "first_mrna": 1.154905187570852}, "mean_fraction": {"final_cells": {"T cell": 0.0326, "B cell": 0.0503, "Monocyte": 0.3447, "NK cell": 0.5696, "DC": 0.0003, "Other": 0.0024}, "first_cells": {"T cell": 0.0945, "B cell": 0.0416, "Monocyte": 0.343, "NK cell": 0.5078, "DC": 0.0109, "Other": 0.0023}, "final_mrna": {"T cell": 0.0354, "B cell": 0.0559, "Monocyte": 0.478, "NK cell": 0.4262, "DC": 0.0009, "Other": 0.0035}, "first_mrna": {"T cell": 0.0978, "B cell": 0.0443, "Monocyte": 0.4581, "NK cell": 0.3653, "DC": 0.0312, "Other": 0.0032}}}, "lora": {"comp_l1": 0.17248763359752534, "coverage": 0.7860784313725491}, "broadcast": {}}
|
| 61 |
+
{"dataset": "immicro", "comparison": "fewshot", "draw": 3, "gene_mode": "score", "bayesprism": {"comp_l1": 1.3672894990068964, "comp_l1_by_variant": {"final_cells": 1.3672894990068964, "first_cells": 1.2567720678051184, "final_mrna": 1.3392388245109828, "first_mrna": 1.2112247064506787}, "mean_fraction": {"final_cells": {"T cell": 0.0217, "B cell": 0.0353, "Monocyte": 0.3157, "NK cell": 0.6248, "DC": 0.0015, "Other": 0.001}, "first_cells": {"T cell": 0.068, "B cell": 0.0347, "Monocyte": 0.3141, "NK cell": 0.5714, "DC": 0.0112, "Other": 0.0006}, "final_mrna": {"T cell": 0.0247, "B cell": 0.0436, "Monocyte": 0.4693, "NK cell": 0.4562, "DC": 0.0043, "Other": 0.0019}, "first_mrna": {"T cell": 0.0737, "B cell": 0.041, "Monocyte": 0.4508, "NK cell": 0.4016, "DC": 0.0318, "Other": 0.0011}}}, "lora": {"comp_l1": 0.18654520396343544, "coverage": 0.7829411764705883}, "broadcast": {}}
|
| 62 |
+
{"dataset": "immicro", "comparison": "fewshot", "draw": 4, "gene_mode": "score", "bayesprism": {"comp_l1": 1.3985049750145204, "comp_l1_by_variant": {"final_cells": 1.3985049750145204, "first_cells": 1.2739600827170083, "final_mrna": 1.3800772011415665, "first_mrna": 1.227949635300596}, "mean_fraction": {"final_cells": {"T cell": 0.0078, "B cell": 0.0349, "Monocyte": 0.3615, "NK cell": 0.5941, "DC": 0.0002, "Other": 0.0015}, "first_cells": {"T cell": 0.067, "B cell": 0.0303, "Monocyte": 0.3517, "NK cell": 0.5412, "DC": 0.006, "Other": 0.0037}, "final_mrna": {"T cell": 0.0091, "B cell": 0.0429, "Monocyte": 0.5041, "NK cell": 0.4411, "DC": 0.0005, "Other": 0.0023}, "first_mrna": {"T cell": 0.0738, "B cell": 0.036, "Monocyte": 0.4781, "NK cell": 0.3901, "DC": 0.0167, "Other": 0.0054}}}, "lora": {"comp_l1": 0.18059655915509124, "coverage": 0.7309803921568627}, "broadcast": {}}
|
| 63 |
+
{"dataset": "immicro", "comparison": "cv", "draw": null, "gene_mode": "score", "bayesprism": {"comp_l1": 1.3896436381034112, "comp_l1_by_variant": {"final_cells": 1.3896436381034112, "first_cells": 1.2471449944879396, "final_mrna": 1.375856848044518, "first_mrna": 1.2099504187025492}, "mean_fraction": {"final_cells": {"T cell": 0.0138, "B cell": 0.0334, "Monocyte": 0.3369, "NK cell": 0.6146, "DC": 0.0002, "Other": 0.0012}, "first_cells": {"T cell": 0.0804, "B cell": 0.0243, "Monocyte": 0.3336, "NK cell": 0.5408, "DC": 0.0085, "Other": 0.0123}, "final_mrna": {"T cell": 0.0155, "B cell": 0.0383, "Monocyte": 0.486, "NK cell": 0.4582, "DC": 0.0005, "Other": 0.0016}, "first_mrna": {"T cell": 0.0855, "B cell": 0.0265, "Monocyte": 0.4621, "NK cell": 0.3859, "DC": 0.0231, "Other": 0.0168}}}, "lora": {"comp_l1": 0.16172890350786212, "coverage": 0.7842990654205607}, "broadcast": {}}
|
| 64 |
+
{"dataset": "ye2026_sepsis", "comparison": "fewshot", "draw": 0, "gene_mode": "score", "bayesprism": {"comp_l1": 1.1392577455707993, "comp_l1_by_variant": {"final_cells": 1.1392577455707993, "first_cells": 0.6220990907002514, "final_mrna": 1.1152808734771347, "first_mrna": 0.6222838313901287}, "mean_fraction": {"final_cells": {"T cell": 0.0278, "B cell": 0.0789, "Monocyte": 0.3165, "NK cell": 0.464, "DC": 0.0025, "Other": 0.1103}, "first_cells": {"T cell": 0.3305, "B cell": 0.0473, "Monocyte": 0.307, "NK cell": 0.1658, "DC": 0.0129, "Other": 0.1365}, "final_mrna": {"T cell": 0.0308, "B cell": 0.0962, "Monocyte": 0.4279, "NK cell": 0.3823, "DC": 0.0069, "Other": 0.0559}, "first_mrna": {"T cell": 0.3265, "B cell": 0.0534, "Monocyte": 0.3939, "NK cell": 0.1277, "DC": 0.032, "Other": 0.0665}}, "logfc_r_mean_cp10k": 0.2773581324391346, "partial_r_mean_cp10k": 0.140270759674815, "logfc_r_mean_cp10k_covered_genes": 0.2895072138637591, "deg_top50_sum": 34, "deg_top50_sum_covered_genes": 34, "per_type_logfc_r": {"T cell": 0.1762, "B cell": 0.2161, "Monocyte": 0.599, "NK cell": 0.1181}}, "lora": {"comp_l1": 0.4723364713369038, "coverage": 0.7058874458874459, "logfc_r_mean_cp10k": 0.4359905652333528, "deg_top50_sum": 7, "partial_r_mean_cp10k": 0.4060106147529024}, "broadcast": {"logfc_r_mean_cp10k": 0.3359901153517466, "logfc_r_mean_cp10k_covered_genes": 0.27827433682632724, "deg_top50_sum": 23}}
|
| 65 |
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| 77 |
+
{"dataset": "imperial_eskd", "comparison": "fewshot", "draw": 1, "gene_mode": "score", "bayesprism": {"comp_l1": 1.2602294000362035, "comp_l1_by_variant": {"final_cells": 1.2602294000362035, "first_cells": 1.1404018882964686, "final_mrna": 1.2599940346426761, "first_mrna": 1.112205833851178}, "mean_fraction": {"final_cells": {"T cell": 0.008, "B cell": 0.0249, "Monocyte": 0.5135, "NK cell": 0.3613, "DC": 0.0002, "Other": 0.0921}, "first_cells": {"T cell": 0.0596, "B cell": 0.0223, "Monocyte": 0.4763, "NK cell": 0.3437, "DC": 0.0092, "Other": 0.089}, "final_mrna": {"T cell": 0.0094, "B cell": 0.0312, "Monocyte": 0.5666, "NK cell": 0.2955, "DC": 0.0006, "Other": 0.0966}, "first_mrna": {"T cell": 0.0681, "B cell": 0.0271, "Monocyte": 0.5168, "NK cell": 0.2748, "DC": 0.0215, "Other": 0.0918}}, "logfc_r_mean_cp10k": 0.6313284983048936, "partial_r_mean_cp10k": 0.27947517509494135, "logfc_r_mean_cp10k_covered_genes": 0.6348115703540999, "deg_top50_sum": 96, "deg_top50_sum_covered_genes": 96, "per_type_logfc_r": {"T cell": 0.684, "B cell": 0.3679, "Monocyte": 0.7474, "NK cell": 0.7259}}, "lora": {"comp_l1": 0.5160151799648663, "coverage": 0.7829399392381398, "logfc_r_mean_cp10k": 0.7570901930571807, "deg_top50_sum": 119, "partial_r_mean_cp10k": 0.6045509566158934}, "broadcast": {"logfc_r_mean_cp10k": 0.6611787175621116, "logfc_r_mean_cp10k_covered_genes": 0.6581559719140895, "deg_top50_sum": 86}}
|
| 78 |
+
{"dataset": "imperial_eskd", "comparison": "fewshot", "draw": 2, "gene_mode": "score", "bayesprism": {"comp_l1": 1.2822045893229197, "comp_l1_by_variant": {"final_cells": 1.2822045893229197, "first_cells": 1.1995334458513318, "final_mrna": 1.2714390668849833, "first_mrna": 1.1631974924575916}, "mean_fraction": {"final_cells": {"T cell": 0.0023, "B cell": 0.0264, "Monocyte": 0.4356, "NK cell": 0.512, "DC": 0.0004, "Other": 0.0233}, "first_cells": {"T cell": 0.0373, "B cell": 0.0261, "Monocyte": 0.4199, "NK cell": 0.467, "DC": 0.0051, "Other": 0.0446}, "final_mrna": {"T cell": 0.0032, "B cell": 0.0341, "Monocyte": 0.5241, "NK cell": 0.4031, "DC": 0.0008, "Other": 0.0347}, "first_mrna": {"T cell": 0.0482, "B cell": 0.0322, "Monocyte": 0.4895, "NK cell": 0.3535, "DC": 0.0108, "Other": 0.0657}}, "logfc_r_mean_cp10k": 0.6399604252827782, "partial_r_mean_cp10k": 0.3255231703400274, "logfc_r_mean_cp10k_covered_genes": 0.64365234598455, "deg_top50_sum": 83, "deg_top50_sum_covered_genes": 83, "per_type_logfc_r": {"T cell": 0.695, "B cell": 0.4238, "Monocyte": 0.7206, "NK cell": 0.7205}}, "lora": {"comp_l1": 0.5117644876225123, "coverage": 0.6650339110776187, "logfc_r_mean_cp10k": 0.7139546009415169, "deg_top50_sum": 103, "partial_r_mean_cp10k": 0.5764372157359006}, "broadcast": {"logfc_r_mean_cp10k": 0.6433613217171205, "logfc_r_mean_cp10k_covered_genes": 0.6404865393732804, "deg_top50_sum": 65}}
|
| 79 |
+
{"dataset": "imperial_eskd", "comparison": "fewshot", "draw": 3, "gene_mode": "score", "bayesprism": {"comp_l1": 1.2606978017175978, "comp_l1_by_variant": {"final_cells": 1.2606978017175978, "first_cells": 1.173508523665221, "final_mrna": 1.2547269731637012, "first_mrna": 1.1465540987906442}, "mean_fraction": {"final_cells": {"T cell": 0.0065, "B cell": 0.0189, "Monocyte": 0.414, "NK cell": 0.4988, "DC": 0.0013, "Other": 0.0605}, "first_cells": {"T cell": 0.0399, "B cell": 0.0202, "Monocyte": 0.3911, "NK cell": 0.4831, "DC": 0.0119, "Other": 0.0538}, "final_mrna": {"T cell": 0.0072, "B cell": 0.0262, "Monocyte": 0.5327, "NK cell": 0.36, "DC": 0.0027, "Other": 0.0712}, "first_mrna": {"T cell": 0.0422, "B cell": 0.0274, "Monocyte": 0.4992, "NK cell": 0.3433, "DC": 0.0247, "Other": 0.0632}}, "logfc_r_mean_cp10k": 0.6273182344451201, "partial_r_mean_cp10k": 0.28547510203613663, "logfc_r_mean_cp10k_covered_genes": 0.6312081095100865, "deg_top50_sum": 69, "deg_top50_sum_covered_genes": 69, "per_type_logfc_r": {"T cell": 0.665, "B cell": 0.3558, "Monocyte": 0.7391, "NK cell": 0.7494}}, "lora": {"comp_l1": 0.5275199844470723, "coverage": 0.842680564523568, "logfc_r_mean_cp10k": 0.7455905986374256, "deg_top50_sum": 117, "partial_r_mean_cp10k": 0.6007400715066787}, "broadcast": {"logfc_r_mean_cp10k": 0.6538959233815048, "logfc_r_mean_cp10k_covered_genes": 0.6513541840409236, "deg_top50_sum": 76}}
|
| 80 |
+
{"dataset": "imperial_eskd", "comparison": "fewshot", "draw": 4, "gene_mode": "score", "bayesprism": {"comp_l1": 1.2836498121844566, "comp_l1_by_variant": {"final_cells": 1.2836498121844566, "first_cells": 1.1942672475358052, "final_mrna": 1.282521324443105, "first_mrna": 1.1775761658792774}, "mean_fraction": {"final_cells": {"T cell": 0.0057, "B cell": 0.0144, "Monocyte": 0.4795, "NK cell": 0.4734, "DC": 0.0001, "Other": 0.0268}, "first_cells": {"T cell": 0.0423, "B cell": 0.0147, "Monocyte": 0.4488, "NK cell": 0.4489, "DC": 0.0059, "Other": 0.0394}, "final_mrna": {"T cell": 0.0064, "B cell": 0.0213, "Monocyte": 0.5822, "NK cell": 0.3475, "DC": 0.0003, "Other": 0.0423}, "first_mrna": {"T cell": 0.0453, "B cell": 0.021, "Monocyte": 0.5369, "NK cell": 0.3219, "DC": 0.0122, "Other": 0.0627}}, "logfc_r_mean_cp10k": 0.5938215544028191, "partial_r_mean_cp10k": 0.2437258990135912, "logfc_r_mean_cp10k_covered_genes": 0.59799600379165, "deg_top50_sum": 96, "deg_top50_sum_covered_genes": 96, "per_type_logfc_r": {"T cell": 0.5616, "B cell": 0.342, "Monocyte": 0.7435, "NK cell": 0.7282}}, "lora": {"comp_l1": 0.48142813711177446, "coverage": 0.6369376110747358, "logfc_r_mean_cp10k": 0.7492433446082651, "deg_top50_sum": 113, "partial_r_mean_cp10k": 0.575230848198632}, "broadcast": {"logfc_r_mean_cp10k": 0.6565426449733607, "logfc_r_mean_cp10k_covered_genes": 0.6528453910767952, "deg_top50_sum": 76}}
|
| 81 |
+
{"dataset": "imperial_eskd", "comparison": "cv", "draw": null, "gene_mode": "score", "bayesprism": {"comp_l1": 1.2520012986063231, "comp_l1_by_variant": {"final_cells": 1.2520012986063231, "first_cells": 1.199848612879087, "final_mrna": 1.245337181637888, "first_mrna": 1.1789149019549443}, "mean_fraction": {"final_cells": {"T cell": 0.0073, "B cell": 0.0299, "Monocyte": 0.442, "NK cell": 0.5017, "DC": 0.0005, "Other": 0.0187}, "first_cells": {"T cell": 0.0278, "B cell": 0.027, "Monocyte": 0.3923, "NK cell": 0.4995, "DC": 0.0053, "Other": 0.0482}, "final_mrna": {"T cell": 0.0083, "B cell": 0.0386, "Monocyte": 0.5551, "NK cell": 0.3701, "DC": 0.0011, "Other": 0.0268}, "first_mrna": {"T cell": 0.0308, "B cell": 0.0344, "Monocyte": 0.4892, "NK cell": 0.364, "DC": 0.0116, "Other": 0.0699}}, "logfc_r_mean_cp10k": 0.643234589352544, "partial_r_mean_cp10k": 0.2982601573161649, "logfc_r_mean_cp10k_covered_genes": 0.6483916675055967, "deg_top50_sum": 98, "deg_top50_sum_covered_genes": 98, "per_type_logfc_r": {"T cell": 0.7042, "B cell": 0.3865, "Monocyte": 0.749, "NK cell": 0.7332}}, "lora": {"comp_l1": 0.37638560875745664, "coverage": 0.8500127757431224, "logfc_r_mean_cp10k": 0.8187448084273437, "deg_top50_sum": 143, "partial_r_mean_cp10k": 0.6899314750539278}, "broadcast": {"logfc_r_mean_cp10k": 0.6606053132085035, "logfc_r_mean_cp10k_covered_genes": 0.6582477222834011, "deg_top50_sum": 84}}
|
| 82 |
+
{"dataset": "giroux2022", "comparison": "fewshot", "draw": 0, "gene_mode": "score", "bayesprism": {"comp_l1": 1.8027415837285268, "comp_l1_by_variant": {"final_cells": 1.8027415837285268, "first_cells": 1.3172890365195966, "final_mrna": 1.5952789694759482, "first_mrna": 1.0142832141087779}, "mean_fraction": {"final_cells": {"T cell": 0.0001, "B cell": 0.0119, "Monocyte": 0.0285, "NK cell": 0.0072, "DC": 0.0, "Other": 0.9523}, "first_cells": {"T cell": 0.238, "B cell": 0.0097, "Monocyte": 0.032, "NK cell": 0.0102, "DC": 0.0005, "Other": 0.7096}, "final_mrna": {"T cell": 0.0002, "B cell": 0.0301, "Monocyte": 0.1055, "NK cell": 0.0156, "DC": 0.0, "Other": 0.8486}, "first_mrna": {"T cell": 0.2991, "B cell": 0.0213, "Monocyte": 0.0991, "NK cell": 0.0189, "DC": 0.0034, "Other": 0.5581}}, "logfc_r_mean_cp10k": 0.42403489559228, "partial_r_mean_cp10k": 0.08333079676882724, "logfc_r_mean_cp10k_covered_genes": 0.4244868945506697, "deg_top50_sum": 0, "deg_top50_sum_covered_genes": 0, "per_type_logfc_r": {"T cell": 0.4132, "B cell": 0.4211, "Monocyte": 0.5517, "NK cell": 0.3101}}, "lora": {"comp_l1": 0.27193277679338645, "coverage": 0.96, "logfc_r_mean_cp10k": 0.243392212681724, "deg_top50_sum": 0, "partial_r_mean_cp10k": 0.15035969319388034}, "broadcast": {"logfc_r_mean_cp10k": 0.4709654147613206, "logfc_r_mean_cp10k_covered_genes": 0.47465918591696865, "deg_top50_sum": 0}}
|
| 83 |
+
{"dataset": "giroux2022", "comparison": "fewshot", "draw": 1, "gene_mode": "score", "bayesprism": {"comp_l1": 1.7599169676086206, "comp_l1_by_variant": {"final_cells": 1.7599169676086206, "first_cells": 0.7385246862506405, "final_mrna": 1.5255549689756318, "first_mrna": 0.4823111070328001}, "mean_fraction": {"final_cells": {"T cell": 0.0042, "B cell": 0.0053, "Monocyte": 0.0478, "NK cell": 0.007, "DC": 0.0, "Other": 0.9358}, "first_cells": {"T cell": 0.5618, "B cell": 0.0041, "Monocyte": 0.0789, "NK cell": 0.0096, "DC": 0.0007, "Other": 0.3449}, "final_mrna": {"T cell": 0.0066, "B cell": 0.0121, "Monocyte": 0.1655, "NK cell": 0.0123, "DC": 0.0, "Other": 0.8035}, "first_mrna": {"T cell": 0.5526, "B cell": 0.0067, "Monocyte": 0.2001, "NK cell": 0.0134, "DC": 0.0033, "Other": 0.2239}}, "logfc_r_mean_cp10k": 0.4000648137127926, "partial_r_mean_cp10k": 0.09411226085159383, "logfc_r_mean_cp10k_covered_genes": 0.4028078113970014, "deg_top50_sum": 0, "deg_top50_sum_covered_genes": 0, "per_type_logfc_r": {"T cell": 0.4506, "B cell": 0.1739, "Monocyte": 0.5981, "NK cell": 0.3777}}, "lora": {"comp_l1": 0.22320689222847964, "coverage": 0.9526666666666667, "logfc_r_mean_cp10k": 0.35634959703435354, "deg_top50_sum": 1, "partial_r_mean_cp10k": 0.2523250741286013}, "broadcast": {"logfc_r_mean_cp10k": 0.5012527613870964, "logfc_r_mean_cp10k_covered_genes": 0.5013362659252331, "deg_top50_sum": 0}}
|
| 84 |
+
{"dataset": "giroux2022", "comparison": "fewshot", "draw": 2, "gene_mode": "score", "bayesprism": {"comp_l1": 1.6999423714160045, "comp_l1_by_variant": {"final_cells": 1.6999423714160045, "first_cells": 0.8243399278333422, "final_mrna": 1.4183639835960766, "first_mrna": 0.5085881594931704}, "mean_fraction": {"final_cells": {"T cell": 0.0286, "B cell": 0.0317, "Monocyte": 0.0335, "NK cell": 0.0173, "DC": 0.0, "Other": 0.8888}, "first_cells": {"T cell": 0.5013, "B cell": 0.0222, "Monocyte": 0.0584, "NK cell": 0.0235, "DC": 0.0021, "Other": 0.3925}, "final_mrna": {"T cell": 0.0422, "B cell": 0.074, "Monocyte": 0.1047, "NK cell": 0.0354, "DC": 0.0, "Other": 0.7436}, "first_mrna": {"T cell": 0.5155, "B cell": 0.0394, "Monocyte": 0.1399, "NK cell": 0.0363, "DC": 0.01, "Other": 0.2589}}, "logfc_r_mean_cp10k": 0.409140060748368, "partial_r_mean_cp10k": 0.12680783898552012, "logfc_r_mean_cp10k_covered_genes": 0.4096064238113356, "deg_top50_sum": 0, "deg_top50_sum_covered_genes": 0, "per_type_logfc_r": {"T cell": 0.2952, "B cell": 0.4492, "Monocyte": 0.6047, "NK cell": 0.2875}}, "lora": {"comp_l1": 0.2907494763185344, "coverage": 0.9533333333333334, "logfc_r_mean_cp10k": 0.230513969445487, "deg_top50_sum": 0, "partial_r_mean_cp10k": 0.15040912208962715}, "broadcast": {"logfc_r_mean_cp10k": 0.39643909018360535, "logfc_r_mean_cp10k_covered_genes": 0.3992349402913996, "deg_top50_sum": 0}}
|
| 85 |
+
{"dataset": "giroux2022", "comparison": "fewshot", "draw": 3, "gene_mode": "score", "bayesprism": {"comp_l1": 1.607186467641661, "comp_l1_by_variant": {"final_cells": 1.607186467641661, "first_cells": 0.6222394921050891, "final_mrna": 1.3159875062686455, "first_mrna": 0.4005043856076437}, "mean_fraction": {"final_cells": {"T cell": 0.0919, "B cell": 0.0194, "Monocyte": 0.0295, "NK cell": 0.0129, "DC": 0.0, "Other": 0.8463}, "first_cells": {"T cell": 0.6493, "B cell": 0.0165, "Monocyte": 0.0597, "NK cell": 0.0224, "DC": 0.0015, "Other": 0.2506}, "final_mrna": {"T cell": 0.1277, "B cell": 0.0443, "Monocyte": 0.1131, "NK cell": 0.0245, "DC": 0.0, "Other": 0.6904}, "first_mrna": {"T cell": 0.621, "B cell": 0.0274, "Monocyte": 0.1625, "NK cell": 0.0311, "DC": 0.0071, "Other": 0.1509}}, "logfc_r_mean_cp10k": 0.4986149233422867, "partial_r_mean_cp10k": 0.20182387848262553, "logfc_r_mean_cp10k_covered_genes": 0.49903850451226733, "deg_top50_sum": 0, "deg_top50_sum_covered_genes": 0, "per_type_logfc_r": {"T cell": 0.4518, "B cell": 0.5125, "Monocyte": 0.6107, "NK cell": 0.4194}}, "lora": {"comp_l1": 0.2688359990061283, "coverage": 0.9624242424242424, "logfc_r_mean_cp10k": 0.24186295766157903, "deg_top50_sum": 0, "partial_r_mean_cp10k": 0.14697551642627654}, "broadcast": {"logfc_r_mean_cp10k": 0.4657480400911531, "logfc_r_mean_cp10k_covered_genes": 0.467863802750279, "deg_top50_sum": 0}}
|
| 86 |
+
{"dataset": "giroux2022", "comparison": "fewshot", "draw": 4, "gene_mode": "score", "bayesprism": {"comp_l1": 0.7421549655922297, "comp_l1_by_variant": {"final_cells": 0.7421549655922297, "first_cells": 0.5690064517688505, "final_mrna": 0.5021313182781816, "first_mrna": 0.3586912819884033}, "mean_fraction": {"final_cells": {"T cell": 0.4289, "B cell": 0.0261, "Monocyte": 0.1034, "NK cell": 0.033, "DC": 0.0, "Other": 0.4086}, "first_cells": {"T cell": 0.8255, "B cell": 0.0083, "Monocyte": 0.0998, "NK cell": 0.0338, "DC": 0.0029, "Other": 0.0297}, "final_mrna": {"T cell": 0.417, "B cell": 0.0388, "Monocyte": 0.2291, "NK cell": 0.04, "DC": 0.0, "Other": 0.275}, "first_mrna": {"T cell": 0.7101, "B cell": 0.0112, "Monocyte": 0.2113, "NK cell": 0.0388, "DC": 0.0111, "Other": 0.0176}}, "logfc_r_mean_cp10k": 0.5441509891552919, "partial_r_mean_cp10k": 0.2027735798353649, "logfc_r_mean_cp10k_covered_genes": 0.5461575303353852, "deg_top50_sum": 0, "deg_top50_sum_covered_genes": 0, "per_type_logfc_r": {"T cell": 0.5308, "B cell": 0.3848, "Monocyte": 0.7311, "NK cell": 0.53}}, "lora": {"comp_l1": 0.2274734478129418, "coverage": 0.9766666666666667, "logfc_r_mean_cp10k": 0.41085265458568265, "deg_top50_sum": 0, "partial_r_mean_cp10k": 0.24279747694617004}, "broadcast": {"logfc_r_mean_cp10k": 0.6280870820074911, "logfc_r_mean_cp10k_covered_genes": 0.6282955787542766, "deg_top50_sum": 0}}
|
| 87 |
+
{"dataset": "giroux2022", "comparison": "cv", "draw": null, "gene_mode": "score", "bayesprism": {"comp_l1": 1.0130932525218068, "comp_l1_by_variant": {"final_cells": 1.0130932525218068, "first_cells": 0.5495314839645408, "final_mrna": 0.734796598559527, "first_mrna": 0.3561888525958372}, "mean_fraction": {"final_cells": {"T cell": 0.3306, "B cell": 0.0341, "Monocyte": 0.0682, "NK cell": 0.0205, "DC": 0.0001, "Other": 0.5464}, "first_cells": {"T cell": 0.8357, "B cell": 0.0161, "Monocyte": 0.0828, "NK cell": 0.0305, "DC": 0.0033, "Other": 0.0316}, "final_mrna": {"T cell": 0.3476, "B cell": 0.0563, "Monocyte": 0.1873, "NK cell": 0.0284, "DC": 0.0007, "Other": 0.3796}, "first_mrna": {"T cell": 0.7192, "B cell": 0.0223, "Monocyte": 0.1915, "NK cell": 0.0363, "DC": 0.0132, "Other": 0.0175}}, "logfc_r_mean_cp10k": 0.4619774813232209, "partial_r_mean_cp10k": 0.057257053963693766, "logfc_r_mean_cp10k_covered_genes": 0.4653101345055838, "deg_top50_sum": 4, "deg_top50_sum_covered_genes": 4, "per_type_logfc_r": {"T cell": 0.3647, "B cell": 0.3919, "Monocyte": 0.6866, "NK cell": 0.4047}}, "lora": {"comp_l1": 0.2580442754044374, "coverage": 0.9280555555555555, "logfc_r_mean_cp10k": 0.46094848304079133, "deg_top50_sum": 5, "partial_r_mean_cp10k": 0.3230347269696575}, "broadcast": {"logfc_r_mean_cp10k": 0.5752659929360795, "logfc_r_mean_cp10k_covered_genes": 0.5757467455051679, "deg_top50_sum": 5}}
|
| 88 |
+
# BayesPrism with the same paired donors vs LoRA (paired benchmark; gene mode score)
|
| 89 |
+
|
| 90 |
+
BayesPrism genes: the scorer's ~5.5-6k scoring genes only (sensitivity run; handicaps composition).
|
| 91 |
+
|
| 92 |
+
Same donors, observed truth, contrast and scorer as the benchmark (score_ft.py functions; the recomputed bulk broadcast equals the stored one in every split). BayesPrism reference = the split's paired donors' observed cells (states = gate | AIFI L2); mixture = the test samples' real bulk. Composition L1 in cell units (lower is better): 'final' and 'first' BayesPrism theta. logFC r = case-vs-control per-type logFC (mean CP10K) correlation with observed, mean of T/B/Mono/NK; BayesPrism Z zero-filled on genes it lacks ('covered' = only genes it models, broadcast recomputed there). DEG = top-50 overlap summed over types.
|
| 93 |
+
|
| 94 |
+
## Five-donor draws (mean ± SD over 5 draws)
|
| 95 |
+
|
| 96 |
+
| cohort | L1 BP final | L1 BP first | L1 LoRA-5 | r BP | r BP (covered) | r LoRA-5 | r broadcast | partial r BP | partial r LoRA-5 | DEG BP | DEG LoRA-5 | DEG broadcast |
|
| 97 |
+
|---|---:|---:|---:|---:|---:|---:|---:|---:|---:|---:|---:|---:|
|
| 98 |
+
| ImMicro (5) | 1.364 ± 0.032 | 1.248 ± 0.071 | 0.176 ± 0.012 | – | – | – | – | – | – | – | – | – |
|
| 99 |
+
| Sepsis (5) | 1.177 ± 0.038 | 0.838 ± 0.158 | 0.466 ± 0.044 | 0.259 ± 0.043 | 0.270 ± 0.045 | 0.350 ± 0.162 | 0.320 ± 0.024 | 0.129 ± 0.035 | 0.305 ± 0.189 | 29.0 ± 6.2 | 16.4 ± 6.7 | 20.0 ± 1.9 |
|
| 100 |
+
| Ji ChILI (5) | 1.085 ± 0.024 | 1.040 ± 0.031 | 0.513 ± 0.115 | 0.207 ± 0.015 | 0.210 ± 0.015 | 0.333 ± 0.077 | 0.234 ± 0.026 | 0.042 ± 0.020 | 0.300 ± 0.076 | 1.6 ± 1.7 | 0.2 ± 0.4 | 1.0 ± 2.2 |
|
| 101 |
+
| Imperial (5) | 1.273 ± 0.012 | 1.183 ± 0.027 | 0.503 ± 0.022 | 0.630 ± 0.024 | 0.634 ± 0.024 | 0.749 ± 0.024 | 0.656 ± 0.009 | 0.292 ± 0.035 | 0.603 ± 0.033 | 84.8 ± 11.5 | 113.6 ± 6.3 | 74.8 ± 7.7 |
|
| 102 |
+
| Giroux (5) | 1.522 ± 0.442 | 0.814 ± 0.298 | 0.256 ± 0.030 | 0.455 ± 0.063 | 0.456 ± 0.063 | 0.297 ± 0.082 | 0.492 ± 0.085 | 0.142 ± 0.058 | 0.189 ± 0.054 | 0.0 ± 0.0 | 0.2 ± 0.4 | 0.0 ± 0.0 |
|
| 103 |
+
|
| 104 |
+
Draws where LoRA-5 beats BayesPrism: composition 25/25 (vs BayesPrism's better theta), logFC r 14/20, partial r 18/20, top-50 DEG 7/20 (ties 6).
|
| 105 |
+
|
| 106 |
+
## 5-fold CV, pooled (BayesPrism reference = each fold's LoRA training + inner-validation pairs)
|
| 107 |
+
|
| 108 |
+
| cohort | L1 BP final | L1 BP first | L1 LoRA | L1 scSemi | r BP | r BP (covered) | r LoRA | r scSemi | r broadcast | partial r BP | partial r LoRA | DEG BP | DEG LoRA | DEG scSemi | DEG broadcast |
|
| 109 |
+
|---|---:|---:|---:|---:|---:|---:|---:|---:|---:|---:|---:|---:|---:|---:|---:|
|
| 110 |
+
| ImMicro | 1.390 | 1.247 | 0.162 | 0.217 | – | – | – | – | – | – | – | – | – | – | – |
|
| 111 |
+
| Sepsis | 1.195 | 0.898 | 0.362 | – | 0.273 | 0.268 | 0.527 | – | 0.316 | 0.133 | 0.469 | 33 | 23 | – | 21 |
|
| 112 |
+
| Ji ChILI | 1.098 | 1.065 | 0.504 | 0.575 | 0.241 | 0.251 | 0.479 | 0.273 | 0.240 | 0.077 | 0.452 | 4 | 15 | 0 | 4 |
|
| 113 |
+
| Imperial | 1.252 | 1.200 | 0.376 | – | 0.643 | 0.648 | 0.819 | – | 0.661 | 0.298 | 0.690 | 98 | 143 | – | 84 |
|
| 114 |
+
| Giroux | 1.013 | 0.550 | 0.258 | – | 0.462 | 0.465 | 0.461 | – | 0.575 | 0.057 | 0.323 | 4 | 5 | – | 5 |
|
| 115 |
+
2026-10-07T11:59:23 finalize done; failed=0
|
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/run_all_A_20261006T154242.log
ADDED
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@@ -0,0 +1,56 @@
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| 1 |
+
2026-10-06T15:42:42 lane A: 4 cores, cohorts imperial_eskd ji2025_chili giroux2022
|
| 2 |
+
2026-10-06T15:42:42 --- imperial_eskd fewshot0 (142 mixture, 15 reference samples, 29 states, 5687 genes)
|
| 3 |
+
2026-10-06T16:08:05 imperial_eskd fewshot0: elapsed min: 25.32
|
| 4 |
+
2026-10-06T16:08:06 --- imperial_eskd fewshot1 (143 mixture, 14 reference samples, 29 states, 5636 genes)
|
| 5 |
+
2026-10-06T16:33:34 imperial_eskd fewshot1: elapsed min: 25.39
|
| 6 |
+
2026-10-06T16:33:36 --- imperial_eskd fewshot2 (142 mixture, 15 reference samples, 29 states, 5598 genes)
|
| 7 |
+
2026-10-06T16:59:02 imperial_eskd fewshot2: elapsed min: 25.37
|
| 8 |
+
2026-10-06T16:59:04 --- imperial_eskd fewshot3 (145 mixture, 12 reference samples, 28 states, 5620 genes)
|
| 9 |
+
2026-10-06T17:25:16 imperial_eskd fewshot3: elapsed min: 26.13
|
| 10 |
+
2026-10-06T17:25:18 --- imperial_eskd fewshot4 (143 mixture, 14 reference samples, 29 states, 5622 genes)
|
| 11 |
+
2026-10-06T17:50:18 imperial_eskd fewshot4: elapsed min: 24.93
|
| 12 |
+
2026-10-06T17:50:18 WARN: build_split imperial_eskd cv0 failed
|
| 13 |
+
2026-10-06T17:50:19 WARN: build_split imperial_eskd cv1 failed
|
| 14 |
+
2026-10-06T17:50:19 WARN: build_split imperial_eskd cv2 failed
|
| 15 |
+
2026-10-06T17:50:19 WARN: build_split imperial_eskd cv3 failed
|
| 16 |
+
2026-10-06T17:50:20 WARN: build_split imperial_eskd cv4 failed
|
| 17 |
+
2026-10-06T17:50:20 --- ji2025_chili fewshot0 (25 mixture, 8 reference samples, 29 states, 5697 genes)
|
| 18 |
+
2026-10-06T17:54:57 ji2025_chili fewshot0: elapsed min: 4.53
|
| 19 |
+
2026-10-06T17:54:58 --- ji2025_chili fewshot1 (26 mixture, 7 reference samples, 28 states, 5652 genes)
|
| 20 |
+
2026-10-06T17:59:23 ji2025_chili fewshot1: elapsed min: 4.34
|
| 21 |
+
2026-10-06T17:59:23 --- ji2025_chili fewshot2 (26 mixture, 7 reference samples, 29 states, 5656 genes)
|
| 22 |
+
2026-10-06T18:03:45 ji2025_chili fewshot2: elapsed min: 4.29
|
| 23 |
+
2026-10-06T18:03:46 --- ji2025_chili fewshot3 (25 mixture, 8 reference samples, 29 states, 5689 genes)
|
| 24 |
+
2026-10-06T18:08:16 ji2025_chili fewshot3: elapsed min: 4.42
|
| 25 |
+
2026-10-06T18:08:17 --- ji2025_chili fewshot4 (24 mixture, 9 reference samples, 29 states, 5694 genes)
|
| 26 |
+
2026-10-06T18:12:45 ji2025_chili fewshot4: elapsed min: 4.38
|
| 27 |
+
2026-10-06T18:12:46 --- ji2025_chili cv0 (7 mixture, 26 reference samples, 29 states, 5732 genes)
|
| 28 |
+
2026-10-06T18:14:20 ji2025_chili cv0: elapsed min: 1.5
|
| 29 |
+
2026-10-06T18:14:21 --- ji2025_chili cv1 (6 mixture, 27 reference samples, 29 states, 5733 genes)
|
| 30 |
+
2026-10-06T18:15:51 ji2025_chili cv1: elapsed min: 1.43
|
| 31 |
+
2026-10-06T18:15:52 --- ji2025_chili cv2 (6 mixture, 27 reference samples, 29 states, 5730 genes)
|
| 32 |
+
2026-10-06T18:17:23 ji2025_chili cv2: elapsed min: 1.43
|
| 33 |
+
2026-10-06T18:17:23 --- ji2025_chili cv3 (8 mixture, 25 reference samples, 29 states, 5728 genes)
|
| 34 |
+
2026-10-06T18:18:56 ji2025_chili cv3: elapsed min: 1.47
|
| 35 |
+
2026-10-06T18:18:56 --- ji2025_chili cv4 (6 mixture, 27 reference samples, 29 states, 5731 genes)
|
| 36 |
+
2026-10-06T18:20:29 ji2025_chili cv4: elapsed min: 1.46
|
| 37 |
+
2026-10-06T18:20:29 --- giroux2022 fewshot0 (11 mixture, 13 reference samples, 29 states, 5400 genes)
|
| 38 |
+
2026-10-06T18:22:41 giroux2022 fewshot0: elapsed min: 2.12
|
| 39 |
+
2026-10-06T18:22:42 --- giroux2022 fewshot1 (10 mixture, 14 reference samples, 29 states, 5400 genes)
|
| 40 |
+
2026-10-06T18:24:45 giroux2022 fewshot1: elapsed min: 1.99
|
| 41 |
+
2026-10-06T18:24:46 --- giroux2022 fewshot2 (12 mixture, 12 reference samples, 29 states, 5389 genes)
|
| 42 |
+
2026-10-06T18:26:55 giroux2022 fewshot2: elapsed min: 2.07
|
| 43 |
+
2026-10-06T18:26:55 --- giroux2022 fewshot3 (11 mixture, 13 reference samples, 29 states, 5394 genes)
|
| 44 |
+
2026-10-06T18:29:00 giroux2022 fewshot3: elapsed min: 2
|
| 45 |
+
2026-10-06T18:29:01 --- giroux2022 fewshot4 (10 mixture, 14 reference samples, 29 states, 5406 genes)
|
| 46 |
+
2026-10-06T18:31:16 giroux2022 fewshot4: elapsed min: 2.18
|
| 47 |
+
2026-10-06T18:31:16 giroux2022 cv0: done already
|
| 48 |
+
2026-10-06T18:31:17 --- giroux2022 cv1 (5 mixture, 19 reference samples, 29 states, 5422 genes)
|
| 49 |
+
2026-10-06T18:32:43 giroux2022 cv1: elapsed min: 1.35
|
| 50 |
+
2026-10-06T18:32:43 --- giroux2022 cv2 (6 mixture, 18 reference samples, 29 states, 5418 genes)
|
| 51 |
+
2026-10-06T18:34:17 giroux2022 cv2: elapsed min: 1.48
|
| 52 |
+
2026-10-06T18:34:17 --- giroux2022 cv3 (6 mixture, 18 reference samples, 29 states, 5425 genes)
|
| 53 |
+
2026-10-06T18:35:44 giroux2022 cv3: elapsed min: 1.37
|
| 54 |
+
2026-10-06T18:35:45 --- giroux2022 cv4 (3 mixture, 21 reference samples, 29 states, 5429 genes)
|
| 55 |
+
2026-10-06T18:36:35 giroux2022 cv4: elapsed min: 0.75
|
| 56 |
+
2026-10-06T18:36:35 lane A finished; failed=5
|
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/run_all_B_20261006T154242.log
ADDED
|
@@ -0,0 +1,42 @@
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|
| 1 |
+
2026-10-06T15:42:42 lane B: 4 cores, cohorts ye2026_sepsis immicro
|
| 2 |
+
2026-10-06T15:42:42 --- ye2026_sepsis fewshot0 (77 mixture, 5 reference samples, 28 states, 5686 genes)
|
| 3 |
+
2026-10-06T15:56:21 ye2026_sepsis fewshot0: elapsed min: 13.58
|
| 4 |
+
2026-10-06T15:56:22 --- ye2026_sepsis fewshot1 (77 mixture, 5 reference samples, 28 states, 5657 genes)
|
| 5 |
+
2026-10-06T16:09:31 ye2026_sepsis fewshot1: elapsed min: 13.07
|
| 6 |
+
2026-10-06T16:09:32 --- ye2026_sepsis fewshot2 (77 mixture, 5 reference samples, 27 states, 5650 genes)
|
| 7 |
+
2026-10-06T16:23:11 ye2026_sepsis fewshot2: elapsed min: 13.58
|
| 8 |
+
2026-10-06T16:23:12 --- ye2026_sepsis fewshot3 (77 mixture, 5 reference samples, 28 states, 5664 genes)
|
| 9 |
+
2026-10-06T16:36:38 ye2026_sepsis fewshot3: elapsed min: 13.34
|
| 10 |
+
2026-10-06T16:36:39 --- ye2026_sepsis fewshot4 (77 mixture, 5 reference samples, 28 states, 5718 genes)
|
| 11 |
+
2026-10-06T16:50:33 ye2026_sepsis fewshot4: elapsed min: 13.82
|
| 12 |
+
2026-10-06T16:50:33 --- ye2026_sepsis cv0 (17 mixture, 65 reference samples, 29 states, 5889 genes)
|
| 13 |
+
2026-10-06T16:54:13 ye2026_sepsis cv0: elapsed min: 3.58
|
| 14 |
+
2026-10-06T16:54:14 --- ye2026_sepsis cv1 (17 mixture, 65 reference samples, 29 states, 5889 genes)
|
| 15 |
+
2026-10-06T16:57:58 ye2026_sepsis cv1: elapsed min: 3.65
|
| 16 |
+
2026-10-06T16:57:58 --- ye2026_sepsis cv2 (16 mixture, 66 reference samples, 29 states, 5883 genes)
|
| 17 |
+
2026-10-06T17:00:54 ye2026_sepsis cv2: elapsed min: 2.86
|
| 18 |
+
2026-10-06T17:00:55 --- ye2026_sepsis cv3 (16 mixture, 66 reference samples, 29 states, 5893 genes)
|
| 19 |
+
2026-10-06T17:03:51 ye2026_sepsis cv3: elapsed min: 2.85
|
| 20 |
+
2026-10-06T17:03:52 --- ye2026_sepsis cv4 (16 mixture, 66 reference samples, 29 states, 5896 genes)
|
| 21 |
+
2026-10-06T17:06:48 ye2026_sepsis cv4: elapsed min: 2.87
|
| 22 |
+
2026-10-06T17:06:48 --- immicro fewshot0 (102 mixture, 5 reference samples, 27 states, 5233 genes)
|
| 23 |
+
2026-10-06T17:23:10 immicro fewshot0: elapsed min: 16.27
|
| 24 |
+
2026-10-06T17:23:11 --- immicro fewshot1 (102 mixture, 5 reference samples, 28 states, 5281 genes)
|
| 25 |
+
2026-10-06T17:39:09 immicro fewshot1: elapsed min: 15.9
|
| 26 |
+
2026-10-06T17:39:11 --- immicro fewshot2 (102 mixture, 5 reference samples, 28 states, 5249 genes)
|
| 27 |
+
2026-10-06T17:55:40 immicro fewshot2: elapsed min: 16.42
|
| 28 |
+
2026-10-06T17:55:41 --- immicro fewshot3 (102 mixture, 5 reference samples, 27 states, 5283 genes)
|
| 29 |
+
2026-10-06T18:11:48 immicro fewshot3: elapsed min: 16.03
|
| 30 |
+
2026-10-06T18:11:49 --- immicro fewshot4 (102 mixture, 5 reference samples, 28 states, 5250 genes)
|
| 31 |
+
2026-10-06T18:28:13 immicro fewshot4: elapsed min: 16.33
|
| 32 |
+
2026-10-06T18:28:14 --- immicro cv0 (22 mixture, 85 reference samples, 29 states, 5462 genes)
|
| 33 |
+
2026-10-06T18:32:24 immicro cv0: elapsed min: 4.11
|
| 34 |
+
2026-10-06T18:32:25 --- immicro cv1 (22 mixture, 85 reference samples, 29 states, 5466 genes)
|
| 35 |
+
2026-10-06T18:36:31 immicro cv1: elapsed min: 4.02
|
| 36 |
+
2026-10-06T18:36:31 --- immicro cv2 (21 mixture, 86 reference samples, 29 states, 5468 genes)
|
| 37 |
+
2026-10-06T18:40:27 immicro cv2: elapsed min: 3.86
|
| 38 |
+
2026-10-06T18:40:28 --- immicro cv3 (21 mixture, 86 reference samples, 29 states, 5467 genes)
|
| 39 |
+
2026-10-06T18:44:18 immicro cv3: elapsed min: 3.76
|
| 40 |
+
2026-10-06T18:44:19 --- immicro cv4 (21 mixture, 86 reference samples, 29 states, 5468 genes)
|
| 41 |
+
2026-10-06T18:48:14 immicro cv4: elapsed min: 3.85
|
| 42 |
+
2026-10-06T18:48:14 lane B finished; failed=0
|