Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/results/giroux2022/fewshot_draw4_cibersortx/contrast.csv

@@ -0,0 +1,17 @@
+genes,celltype,statistic,n_genes,r_generated,r_broadcast,partial_r_generated_given_broadcast,r_generated_vs_broadcast
+zero_filled,T cell,mean_cp10k,2870,,0.7344048019011988,,
+zero_filled,T cell,pseudobulk_log1p_cpm,2870,,0.6900634955326531,,
+zero_filled,B cell,mean_cp10k,3061,,0.565884313340693,,
+zero_filled,B cell,pseudobulk_log1p_cpm,3061,,0.4704332503129004,,
+zero_filled,Monocyte,mean_cp10k,3017,,0.5561945453231222,,
+zero_filled,Monocyte,pseudobulk_log1p_cpm,3017,,0.6573550923248582,,
+zero_filled,NK cell,mean_cp10k,2940,,0.6558646674649503,,
+zero_filled,NK cell,pseudobulk_log1p_cpm,2940,,0.5646910960578172,,
+covered,T cell,mean_cp10k,0,,,,
+covered,T cell,pseudobulk_log1p_cpm,0,,,,
+covered,B cell,mean_cp10k,0,,,,
+covered,B cell,pseudobulk_log1p_cpm,0,,,,
+covered,Monocyte,mean_cp10k,0,,,,
+covered,Monocyte,pseudobulk_log1p_cpm,0,,,,
+covered,NK cell,mean_cp10k,0,,,,
+covered,NK cell,pseudobulk_log1p_cpm,0,,,,

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/results/giroux2022/fewshot_draw4_cibersortx/per_donor.csv

@@ -0,0 +1,11 @@
+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
+450905_d0,mild,0.31830403896611115,0.31830403896611115,0.36405043444349305,0.36405043444349305,0.2785102017810844,0.2646793222450156,0.2646793222450156,0.30943523841731485,0.0,0.0,0.036185322962461956,0.3997475713655552,0.3997475713655552,0.4293202570172472,0.08223779302744227,0.08223779302744227,0.12089956036523504,0.0,0.0,0.009976327358809604,0.25333531336198695,0.25333531336198695,0.09418329387893135
+450905_d14,mild,0.8747717198403877,0.8747717198403877,0.54143377322642,0.54143377322642,0.3955047927636019,0.2083031365235757,0.2083031365235757,0.4422843256379101,0.012871648347330856,0.012871648347330856,0.02929661131362225,0.15374352270406086,0.15374352270406086,0.27420008100445525,0.09798589624199876,0.09798589624199876,0.15782368030241664,0.023151275536499958,0.023151275536499958,0.02983664101525584,0.5039445206465337,0.5039445206465337,0.06655866072633995
+7085CA_d0,mild,0.26573579156694327,0.26573579156694327,0.23640696603391714,0.23640696603391714,0.3972030194676201,0.18019654604451107,0.18019654604451107,0.21660707191100517,0.03674645571850672,0.03674645571850672,0.024791418355184745,0.49098800155699934,0.49098800155699934,0.5874453714739769,0.14665454085848942,0.14665454085848942,0.13198251887167262,0.05450366444927826,0.05450366444927826,0.017719507350019866,0.09091079137221508,0.09091079137221508,0.021454112038140644
+7085CA_d7,mild,0.7739726518594889,0.7739726518594889,0.5143186823869682,0.5143186823869682,0.2734377299001577,0.33545184668133465,0.33545184668133465,0.521492380451918,0.03640140008734073,0.03640140008734073,0.0722017866526537,0.05076024050850483,0.05076024050850483,0.10110352075669994,0.15771495295177207,0.15771495295177207,0.2725170782974251,0.02379587476709557,0.02379587476709557,0.019863373620599055,0.3958756850039521,0.3958756850039521,0.012821860220704152
+7085CA_d14,mild,0.7136507092819611,0.7136507092819611,0.41509504451119744,0.41509504451119744,0.379083817055046,0.3197480357310544,0.3197480357310544,0.472533019264743,0.035140324976256236,0.035140324976256236,0.07133843694792631,0.08815322720415121,0.08815322720415121,0.16210986792294102,0.15487070454419188,0.15487070454419188,0.24270211155043325,0.012537527463809916,0.012537527463809916,0.018591738874400604,0.3895501800805363,0.3895501800805363,0.032724825439555814
+B85D75_d0,severe,0.3330183528755435,0.3330183528755435,0.275271023691341,0.275271023691341,0.0797620254639746,0.7291052863138852,0.7291052863138852,0.7173324010138974,0.010793410449456156,0.010793410449456156,0.031203566121842496,0.028710873474628563,0.028710873474628563,0.11441307578008915,0.0,0.0,0.06039681845992483,0.01660160935784003,0.01660160935784003,0.016519535005681322,0.2147888204041901,0.2147888204041901,0.06013460361856481
+B85D75_d7,severe,0.2369452283914648,0.2369452283914648,0.1558566823129539,0.1558566823129539,0.1892074410555916,0.7307255985476151,0.7307255985476151,0.6435756002595717,0.06898797766057205,0.06898797766057205,0.06448734587929916,0.07975141671261753,0.07975141671261753,0.13741077222582737,0.00045970333916409763,0.00045970333916409763,0.04201817001946788,0.008486934149630709,0.008486934149630709,0.027741726151849447,0.1115883695904006,0.1115883695904006,0.08476638546398442
+180E1A_d0,severe,0.7547579331685885,0.7547579331685885,0.5401077791647806,0.5401077791647806,0.0663425084998369,0.44352582819100483,0.44352582819100483,0.7019700992035769,0.028318202669719,0.028318202669719,0.04135811094033813,0.09356380818182025,0.09356380818182025,0.13175911694844208,0.0,0.0,0.0655302501047925,0.011104489608595489,0.011104489608595489,0.013273718038284197,0.42348767134886045,0.42348767134886045,0.04610870476456616
+180E1A_d7,severe,0.706134942912926,0.706134942912926,0.43630153207346073,0.43630153207346073,0.1035562269851761,0.4942482641617694,0.4942482641617694,0.7348692285903126,0.028102763586965555,0.028102763586965555,0.04909829100179398,0.05459268426638177,0.05459268426638177,0.09064299877254273,0.031565917218398166,0.031565917218398166,0.08280615617033331,0.0063201705780799085,0.0063201705780799085,0.010480596733075253,0.3851702001884052,0.3851702001884052,0.03210272873194221
+180E1A_d14,severe,0.5611113108370971,0.5611113108370971,0.4367676273294961,0.4367676273294961,0.1121267151573282,0.49141015710874275,0.49141015710874275,0.680840860043162,0.033753768253540414,0.033753768253540414,0.05147470226200943,0.10281300523566966,0.10281300523566966,0.12277196067460634,0.026564528522704082,0.026564528522704082,0.0800095915594277,0.011573100411153182,0.011573100411153182,0.009831348413396212,0.3338854404681899,0.3338854404681899,0.05507153704739829

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/results/giroux2022/fewshot_draw4_cibersortx/summary.json

@@ -0,0 +1,157 @@
+{
+ "dataset": "giroux2022",
+ "comparison": "fewshot",
+ "draw": 4,
+ "gene_mode": "cibersortx",
+ "stored_scores": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/fewshot_n5/draw4",
+ "lora_arm": "lora5",
+ "n_donors": 10,
+ "contrast": true,
+ "genes_scoring": 5563,
+ "genes_covered_by_Z_all_donors": 0,
+ "bayesprism": {
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+  "comp_l1_by_variant": {
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+   "first_cells": 0.5538402679700511,
+   "final_mrna": 0.3915609545174028,
+   "first_mrna": 0.3915609545174028
+  },
+  "mean_fraction": {
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+    "B cell": 0.0291,
+    "Monocyte": 0.1543,
+    "NK cell": 0.0698,
+    "DC": 0.0168,
+    "Other": 0.3103
+   },
+   "first_cells": {
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+   },
+   "final_mrna": {
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+    "Monocyte": 0.2491,
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+   "first_mrna": {
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+  "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
+  }
+ },
+ "observed_mean_fraction": {
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+  "B cell": 0.0471,
+  "Monocyte": 0.2151,
+  "NK cell": 0.1257,
+  "DC": 0.0174,
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+ "lora": {
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+  "partial_r_mean_cp10k": 0.24279747694617004
+ },
+ "broadcast": {
+  "logfc_r_mean_cp10k": 0.6280870820074911,
+  "logfc_r_mean_cp10k_covered_genes": NaN,
+  "deg_top50_sum": 0
+ },
+ "other_arms": {
+  "zs_raw": {
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+   "logfc_r_mean_cp10k": 0.41539285297915385,
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+   "logfc_r_mean_cp10k": 0.428531626840907,
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+ },
+ "gates": {
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+  "broadcast_r_equal": true,
+  "broadcast_deg_equal": true
+ },
+ "method": "cibersortx",
+ "has_cell_type_expression": true,
+ "n_case": 5,
+ "n_control": 5,
+ "deg_per_type": {
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+  "covered": {
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+   }
+  }
+ },
+ "hires_imputed_genes": {
+  "fewshot4|T cell": 0,
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+  "fewshot4|Monocyte": 0,
+  "fewshot4|NK cell": 0,
+  "fewshot4|DC": 0,
+  "fewshot4|Other": 0
+ },
+ "tool_sha256": "b541f68dc286497e8347d487af58ff3550a383d126eeabe347c0726e4fb28799",
+ "score_ft_sha256": "ec5f40b4cea6d5062d0138f3b934abb6465e34cbfeac869c8a0906924c033aec",
+ "seconds": 1.2
+}

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/results/giroux2022/fewshot_draw4_full/contrast.csv

@@ -0,0 +1,17 @@
+genes,celltype,statistic,n_genes,r_generated,r_broadcast,partial_r_generated_given_broadcast,r_generated_vs_broadcast
+zero_filled,T cell,mean_cp10k,2870,0.5900854688220172,0.7344048019011988,-0.028697107317133024,0.818716276275159
+zero_filled,T cell,pseudobulk_log1p_cpm,2870,0.5602744509541148,0.6900634955326531,-0.10657125078329197,0.8675146807894125
+zero_filled,B cell,mean_cp10k,3061,0.2809393468981127,0.565884313340693,0.05482190072771621,0.424125998636992
+zero_filled,B cell,pseudobulk_log1p_cpm,3061,0.14605382086921948,0.4704332503129004,0.006060620112099499,0.2996204329915334
+zero_filled,Monocyte,mean_cp10k,3017,0.7587520930023333,0.5561945453231222,0.6213541604262337,0.7173049730506031
+zero_filled,Monocyte,pseudobulk_log1p_cpm,3017,0.7404994945528651,0.6573550923248582,0.46854864363800713,0.815960829111925
+zero_filled,NK cell,mean_cp10k,2940,0.21056920979586,0.6558646674649503,0.04870360660881044,0.2670352291026419
+zero_filled,NK cell,pseudobulk_log1p_cpm,2940,0.09461181303680184,0.5646910960578172,0.06929410288807487,0.06649618552219679
+covered,T cell,mean_cp10k,2796,0.5940322384627956,0.7348233332429699,-0.032794522771528486,0.8254865338386845
+covered,T cell,pseudobulk_log1p_cpm,2796,0.5655838742640372,0.690279354663692,-0.11708988727425292,0.8780833861138112
+covered,B cell,mean_cp10k,2982,0.28206549955556,0.5682950563105479,0.05252755931146008,0.42758566670471326
+covered,B cell,pseudobulk_log1p_cpm,2982,0.1474304657897089,0.47412821431497393,0.0035285689344538777,0.30470968186463954
+covered,Monocyte,mean_cp10k,2948,0.7606326695163802,0.5584375310812281,0.6227832406949431,0.7214756456706838
+covered,Monocyte,pseudobulk_log1p_cpm,2948,0.743952813742288,0.6593313642884819,0.4717790623346481,0.8218678865764909
+covered,NK cell,mean_cp10k,2870,0.21163658597561005,0.6556531341074379,0.048831996077086985,0.2686184518579867
+covered,NK cell,pseudobulk_log1p_cpm,2870,0.1004324025147993,0.5651136664960269,0.07650484818045286,0.06627636568198836