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/results/ji2025_chili/fewshot_draw3_cibersortx/summary.json +157 -0
- paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/results/ji2025_chili/fewshot_draw3_full/contrast.csv +17 -0
- paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/results/ji2025_chili/fewshot_draw3_full/per_donor.csv +26 -0
- paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/results/ji2025_chili/fewshot_draw3_full/summary.json +147 -0
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/results/ji2025_chili/fewshot_draw3_cibersortx/summary.json
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| 1 |
+
{
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| 2 |
+
"dataset": "ji2025_chili",
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| 3 |
+
"comparison": "fewshot",
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| 4 |
+
"draw": 3,
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| 5 |
+
"gene_mode": "cibersortx",
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| 6 |
+
"stored_scores": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/fewshot_n5/draw3",
|
| 7 |
+
"lora_arm": "lora5",
|
| 8 |
+
"n_donors": 25,
|
| 9 |
+
"contrast": true,
|
| 10 |
+
"genes_scoring": 5752,
|
| 11 |
+
"genes_covered_by_Z_all_donors": 1373,
|
| 12 |
+
"bayesprism": {
|
| 13 |
+
"comp_l1": 0.7607882960499378,
|
| 14 |
+
"comp_l1_by_variant": {
|
| 15 |
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"final_cells": 0.7607882960499378,
|
| 16 |
+
"first_cells": 0.7607882960499378,
|
| 17 |
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"final_mrna": 0.8501451075273423,
|
| 18 |
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"first_mrna": 0.8501451075273423
|
| 19 |
+
},
|
| 20 |
+
"mean_fraction": {
|
| 21 |
+
"final_cells": {
|
| 22 |
+
"T cell": 0.283,
|
| 23 |
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"B cell": 0.0993,
|
| 24 |
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"Monocyte": 0.1991,
|
| 25 |
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"NK cell": 0.0767,
|
| 26 |
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"DC": 0.0436,
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| 27 |
+
"Other": 0.2982
|
| 28 |
+
},
|
| 29 |
+
"first_cells": {
|
| 30 |
+
"T cell": 0.283,
|
| 31 |
+
"B cell": 0.0993,
|
| 32 |
+
"Monocyte": 0.1991,
|
| 33 |
+
"NK cell": 0.0767,
|
| 34 |
+
"DC": 0.0436,
|
| 35 |
+
"Other": 0.2982
|
| 36 |
+
},
|
| 37 |
+
"final_mrna": {
|
| 38 |
+
"T cell": 0.2421,
|
| 39 |
+
"B cell": 0.0951,
|
| 40 |
+
"Monocyte": 0.2325,
|
| 41 |
+
"NK cell": 0.0536,
|
| 42 |
+
"DC": 0.0803,
|
| 43 |
+
"Other": 0.2964
|
| 44 |
+
},
|
| 45 |
+
"first_mrna": {
|
| 46 |
+
"T cell": 0.2421,
|
| 47 |
+
"B cell": 0.0951,
|
| 48 |
+
"Monocyte": 0.2325,
|
| 49 |
+
"NK cell": 0.0536,
|
| 50 |
+
"DC": 0.0803,
|
| 51 |
+
"Other": 0.2964
|
| 52 |
+
}
|
| 53 |
+
},
|
| 54 |
+
"logfc_r_mean_cp10k": NaN,
|
| 55 |
+
"partial_r_mean_cp10k": NaN,
|
| 56 |
+
"logfc_r_mean_cp10k_covered_genes": NaN,
|
| 57 |
+
"deg_top50_sum": 0,
|
| 58 |
+
"deg_top50_sum_covered_genes": 0,
|
| 59 |
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"per_type_logfc_r": {
|
| 60 |
+
"T cell": NaN,
|
| 61 |
+
"B cell": NaN,
|
| 62 |
+
"Monocyte": NaN,
|
| 63 |
+
"NK cell": NaN
|
| 64 |
+
}
|
| 65 |
+
},
|
| 66 |
+
"observed_mean_fraction": {
|
| 67 |
+
"T cell": 0.464,
|
| 68 |
+
"B cell": 0.0643,
|
| 69 |
+
"Monocyte": 0.2678,
|
| 70 |
+
"NK cell": 0.1577,
|
| 71 |
+
"DC": 0.0113,
|
| 72 |
+
"Other": 0.0348
|
| 73 |
+
},
|
| 74 |
+
"lora": {
|
| 75 |
+
"comp_l1": 0.4487906027467767,
|
| 76 |
+
"coverage": 0.7586666666666667,
|
| 77 |
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"logfc_r_mean_cp10k": 0.4410983924408845,
|
| 78 |
+
"deg_top50_sum": 0,
|
| 79 |
+
"partial_r_mean_cp10k": 0.39982215110012487
|
| 80 |
+
},
|
| 81 |
+
"broadcast": {
|
| 82 |
+
"logfc_r_mean_cp10k": 0.2577780039471977,
|
| 83 |
+
"logfc_r_mean_cp10k_covered_genes": NaN,
|
| 84 |
+
"deg_top50_sum": 0
|
| 85 |
+
},
|
| 86 |
+
"other_arms": {
|
| 87 |
+
"zs_raw": {
|
| 88 |
+
"comp_l1": 0.6998279977951056,
|
| 89 |
+
"logfc_r_mean_cp10k": 0.10707639011920397,
|
| 90 |
+
"deg_top50_sum": 0
|
| 91 |
+
},
|
| 92 |
+
"zs_pseudo": {
|
| 93 |
+
"comp_l1": 0.1694493540051105,
|
| 94 |
+
"logfc_r_mean_cp10k": 0.1391311050440007,
|
| 95 |
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"deg_top50_sum": 0
|
| 96 |
+
},
|
| 97 |
+
"zs_cal": {
|
| 98 |
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"comp_l1": 0.4913179216867248,
|
| 99 |
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"logfc_r_mean_cp10k": 0.23160934103995254,
|
| 100 |
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"deg_top50_sum": 0
|
| 101 |
+
}
|
| 102 |
+
},
|
| 103 |
+
"gates": {
|
| 104 |
+
"observed_composition_equal": true,
|
| 105 |
+
"broadcast_r_equal": true,
|
| 106 |
+
"broadcast_deg_equal": true
|
| 107 |
+
},
|
| 108 |
+
"method": "cibersortx",
|
| 109 |
+
"has_cell_type_expression": true,
|
| 110 |
+
"n_case": 15,
|
| 111 |
+
"n_control": 10,
|
| 112 |
+
"deg_per_type": {
|
| 113 |
+
"zero_filled": {
|
| 114 |
+
"bp": {
|
| 115 |
+
"T cell": 0,
|
| 116 |
+
"B cell": 0,
|
| 117 |
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"Monocyte": 0,
|
| 118 |
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"NK cell": 0,
|
| 119 |
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"DC": 0
|
| 120 |
+
},
|
| 121 |
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"broadcast": {
|
| 122 |
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"T cell": 0,
|
| 123 |
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"B cell": 0,
|
| 124 |
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"Monocyte": 0,
|
| 125 |
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"NK cell": 0,
|
| 126 |
+
"DC": 0
|
| 127 |
+
}
|
| 128 |
+
},
|
| 129 |
+
"covered": {
|
| 130 |
+
"bp": {
|
| 131 |
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"T cell": null,
|
| 132 |
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"B cell": null,
|
| 133 |
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"Monocyte": null,
|
| 134 |
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"NK cell": null,
|
| 135 |
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"DC": 0
|
| 136 |
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},
|
| 137 |
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"broadcast": {
|
| 138 |
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"T cell": null,
|
| 139 |
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"B cell": null,
|
| 140 |
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"Monocyte": null,
|
| 141 |
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"NK cell": null,
|
| 142 |
+
"DC": 0
|
| 143 |
+
}
|
| 144 |
+
}
|
| 145 |
+
},
|
| 146 |
+
"hires_imputed_genes": {
|
| 147 |
+
"fewshot3|T cell": 0,
|
| 148 |
+
"fewshot3|B cell": 0,
|
| 149 |
+
"fewshot3|Monocyte": 0,
|
| 150 |
+
"fewshot3|NK cell": 0,
|
| 151 |
+
"fewshot3|DC": 1373,
|
| 152 |
+
"fewshot3|Other": 0
|
| 153 |
+
},
|
| 154 |
+
"tool_sha256": "b541f68dc286497e8347d487af58ff3550a383d126eeabe347c0726e4fb28799",
|
| 155 |
+
"score_ft_sha256": "ec5f40b4cea6d5062d0138f3b934abb6465e34cbfeac869c8a0906924c033aec",
|
| 156 |
+
"seconds": 1.3
|
| 157 |
+
}
|
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/results/ji2025_chili/fewshot_draw3_full/contrast.csv
ADDED
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@@ -0,0 +1,17 @@
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| 1 |
+
genes,celltype,statistic,n_genes,r_generated,r_broadcast,partial_r_generated_given_broadcast,r_generated_vs_broadcast
|
| 2 |
+
zero_filled,T cell,mean_cp10k,3028,0.17367656307341195,0.2368920077117674,0.001687464455986757,0.7284049501527485
|
| 3 |
+
zero_filled,T cell,pseudobulk_log1p_cpm,3028,0.30168824601701155,0.30559676102300276,0.06350750564495945,0.9016274337014029
|
| 4 |
+
zero_filled,B cell,mean_cp10k,3238,0.10150404799049051,0.16221245678147309,-0.005212228293971392,0.6498466020757766
|
| 5 |
+
zero_filled,B cell,pseudobulk_log1p_cpm,3238,0.09620073361252061,0.047548729682353,0.11163025203621477,0.870961536412301
|
| 6 |
+
zero_filled,Monocyte,mean_cp10k,3132,0.41881239186724156,0.4012426962403039,0.17323884275237722,0.8141571557411685
|
| 7 |
+
zero_filled,Monocyte,pseudobulk_log1p_cpm,3132,0.3399682068948549,0.36057989165867327,0.0007652197552999822,0.9421740442479085
|
| 8 |
+
zero_filled,NK cell,mean_cp10k,3064,0.10952880390219698,0.23076485505524633,-0.07148913369245714,0.6921829907306697
|
| 9 |
+
zero_filled,NK cell,pseudobulk_log1p_cpm,3064,0.07585295666218068,0.11924462462412533,-0.07897932097639816,0.90949217491766
|
| 10 |
+
covered,T cell,mean_cp10k,2841,0.2011120436645301,0.15107115360674153,0.14372831075317602,0.8736535624508605
|
| 11 |
+
covered,T cell,pseudobulk_log1p_cpm,2841,0.32534980389350404,0.29646996354793964,0.14360614467752983,0.9414765926376564
|
| 12 |
+
covered,B cell,mean_cp10k,3049,0.11119314342410029,0.10380976813614941,0.048936932802568354,0.7745792219410724
|
| 13 |
+
covered,B cell,pseudobulk_log1p_cpm,3049,0.0983245316961167,0.042802155256279666,0.14367558881474818,0.910512965937809
|
| 14 |
+
covered,Monocyte,mean_cp10k,2956,0.4309723261999962,0.4037585652874838,0.1667340036783503,0.9148398752958221
|
| 15 |
+
covered,Monocyte,pseudobulk_log1p_cpm,2956,0.3473046156143719,0.3528100788805959,0.01928949801315103,0.9724752394041637
|
| 16 |
+
covered,NK cell,mean_cp10k,2881,0.13255577512162253,0.14281976574343883,0.026448210177603928,0.8243878888758237
|
| 17 |
+
covered,NK cell,pseudobulk_log1p_cpm,2881,0.08116166404166775,0.10125594023450743,-0.048466052326043674,0.9500978134560493
|
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/results/ji2025_chili/fewshot_draw3_full/per_donor.csv
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| 1 |
+
donor,group,bp_comp_l1_final_cells,bp_comp_l1_first_cells,bp_comp_l1_final_mrna,bp_comp_l1_first_mrna,lora_comp_l1,bp_first_T cell,bp_final_T cell,obs_T cell,bp_first_B cell,bp_final_B cell,obs_B cell,bp_first_Monocyte,bp_final_Monocyte,obs_Monocyte,bp_first_NK cell,bp_final_NK cell,obs_NK cell,bp_first_DC,bp_final_DC,obs_DC,bp_first_Other,bp_final_Other,obs_Other
|
| 2 |
+
N064_TOL,TOL,0.7958086449759493,0.8034277710043206,0.9817852531209148,0.9719864175874849,0.201727248465439,0.26396076623362014,0.26807018743485905,0.6517213771016813,0.03451651185535841,0.039786328598861664,0.044035228182546036,0.40777720469440165,0.433088274936582,0.1677341873498799,0.16656844582241087,0.13599625114727087,0.07606084867894315,0.005573448098212567,3.773167656114451e-06,0.010008006405124099,0.12160362329599628,0.12305518471477031,0.05044035228182546
|
| 3 |
+
N064_FU1,FU1,0.8819008865535056,0.7650152540266542,1.1381722899571345,1.0401837743010311,0.3749663017814982,0.2740854696266611,0.23501409201652743,0.6396222365314446,0.014173832233437393,0.01059516617741087,0.016527151749302426,0.37263786548493427,0.3940228450247576,0.13865636402661516,0.17753895598616234,0.16598179287920017,0.19167203262502683,0.004237579403129485,1.969912826072666e-06,0.00472204335694355,0.15732629726567549,0.19438413398927795,0.008800171710667526
|
| 4 |
+
N032_AC,AC,1.0381477375001276,0.9231834297354368,1.1946235968439098,1.0615531298489103,0.2348571428571428,0.20104294391349115,0.19262107429761258,0.5891156462585034,0.055947841714011556,0.04162581757490454,0.10979591836734694,0.3014723924324502,0.29384307203683135,0.17551020408163265,0.07904383691661361,0.018376482017033836,0.04707482993197279,0.0060433498449149045,3.4376324940879786e-06,0.025714285714285714,0.3564496351785184,0.4535301164411237,0.0527891156462585
|
| 5 |
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paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/results/ji2025_chili/fewshot_draw3_full/summary.json
ADDED
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| 1 |
+
{
|
| 2 |
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"dataset": "ji2025_chili",
|
| 3 |
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"comparison": "fewshot",
|
| 4 |
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"draw": 3,
|
| 5 |
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"gene_mode": "full",
|
| 6 |
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"stored_scores": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/fewshot_n5/draw3",
|
| 7 |
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"lora_arm": "lora5",
|
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"n_donors": 25,
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| 9 |
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"contrast": true,
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| 10 |
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"genes_scoring": 5752,
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| 11 |
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"genes_covered_by_Z_all_donors": 5401,
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| 13 |
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"final_cells": 0.9013817112818979,
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},
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"final_mrna": {
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"first_mrna": {
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}
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