Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/results/ye2026_sepsis/fewshot_draw4/summary.json

@@ -0,0 +1,147 @@
+{
+ "dataset": "ye2026_sepsis",
+ "comparison": "fewshot",
+ "draw": 4,
+ "gene_mode": "score",
+ "stored_scores": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/fewshot_n5/draw4",
+ "lora_arm": "lora5",
+ "n_donors": 77,
+ "contrast": true,
+ "genes_scoring": 5975,
+ "genes_covered_by_Z_all_donors": 5710,
+ "bayesprism": {
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+  "comp_l1_by_variant": {
+   "final_cells": 1.1503124470269723,
+   "first_cells": 0.7707407514452587,
+   "final_mrna": 1.117261442619167,
+   "first_mrna": 0.7573736778194846
+  },
+  "mean_fraction": {
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+    "B cell": 0.0939,
+    "Monocyte": 0.2688,
+    "NK cell": 0.4545,
+    "DC": 0.0128,
+    "Other": 0.1463
+   },
+   "first_cells": {
+    "T cell": 0.2289,
+    "B cell": 0.0825,
+    "Monocyte": 0.2698,
+    "NK cell": 0.2894,
+    "DC": 0.0108,
+    "Other": 0.1187
+   },
+   "final_mrna": {
+    "T cell": 0.0264,
+    "B cell": 0.1014,
+    "Monocyte": 0.3943,
+    "NK cell": 0.3687,
+    "DC": 0.0356,
+    "Other": 0.0735
+   },
+   "first_mrna": {
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+    "B cell": 0.0835,
+    "Monocyte": 0.38,
+    "NK cell": 0.2205,
+    "DC": 0.0276,
+    "Other": 0.0584
+   }
+  },
+  "logfc_r_mean_cp10k": 0.2568730863808132,
+  "partial_r_mean_cp10k": 0.11594592401612624,
+  "logfc_r_mean_cp10k_covered_genes": 0.2684078662410606,
+  "deg_top50_sum": 34,
+  "deg_top50_sum_covered_genes": 34,
+  "per_type_logfc_r": {
+   "T cell": 0.1236,
+   "B cell": 0.1979,
+   "Monocyte": 0.5155,
+   "NK cell": 0.1905
+  }
+ },
+ "observed_mean_fraction": {
+  "T cell": 0.4869,
+  "B cell": 0.1743,
+  "Monocyte": 0.2032,
+  "NK cell": 0.0823,
+  "DC": 0.0055,
+  "Other": 0.0478
+ },
+ "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": 0.26232772053396347,
+  "deg_top50_sum": 20
+ },
+ "other_arms": {
+  "zs_raw": {
+   "comp_l1": 0.5002675627384235,
+   "logfc_r_mean_cp10k": -0.02721553405723006,
+   "deg_top50_sum": 9
+  },
+  "zs_pseudo": {
+   "comp_l1": 0.23791758477651484,
+   "logfc_r_mean_cp10k": 0.4790596969979644,
+   "deg_top50_sum": 21
+  },
+  "zs_cal": {
+   "comp_l1": 0.42094390936735937,
+   "logfc_r_mean_cp10k": 0.0597261589524896,
+   "deg_top50_sum": 8
+  }
+ },
+ "gates": {
+  "observed_composition_equal": true,
+  "broadcast_r_equal": true,
+  "broadcast_deg_equal": true
+ },
+ "n_case": 57,
+ "n_control": 20,
+ "deg_per_type": {
+  "zero_filled": {
+   "bp": {
+    "T cell": 5,
+    "B cell": 4,
+    "Monocyte": 15,
+    "NK cell": 5,
+    "DC": 5
+   },
+   "broadcast": {
+    "T cell": 3,
+    "B cell": 1,
+    "Monocyte": 13,
+    "NK cell": 2,
+    "DC": 1
+   }
+  },
+  "covered": {
+   "bp": {
+    "T cell": 5,
+    "B cell": 4,
+    "Monocyte": 15,
+    "NK cell": 5,
+    "DC": 5
+   },
+   "broadcast": {
+    "T cell": 2,
+    "B cell": 1,
+    "Monocyte": 13,
+    "NK cell": 1,
+    "DC": 1
+   }
+  }
+ },
+ "tool_sha256": "15ed044bbfc39c501c7187ad78586902f2aa0635e7b3a90786b4587cedc2008a",
+ "score_ft_sha256": "ec5f40b4cea6d5062d0138f3b934abb6465e34cbfeac869c8a0906924c033aec",
+ "seconds": 1.8
+}

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/results/ye2026_sepsis/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,3259,0.03399276694008989,0.2635493097811775,-0.08794496781001844,0.42096593652323155
+zero_filled,T cell,pseudobulk_log1p_cpm,3259,0.17626164197685,0.2326120649060939,0.060545441123540295,0.5456023959863425
+zero_filled,B cell,mean_cp10k,3311,-0.14885983418507245,0.2759123555261431,-0.16330816905646578,0.029148643008432118
+zero_filled,B cell,pseudobulk_log1p_cpm,3311,-0.06760831964893631,0.25121490410279235,-0.11817923517718197,0.17887538763513686
+zero_filled,Monocyte,mean_cp10k,3304,0.26464964094890203,0.5497635656505115,0.12298621211191,0.3033245435445757
+zero_filled,Monocyte,pseudobulk_log1p_cpm,3304,0.18373450360978447,0.6130579062755492,-0.10101356486552719,0.4179607665695661
+zero_filled,NK cell,mean_cp10k,3235,0.036541509839246276,0.18915162420474085,0.01320845214889289,0.12515610474945107
+zero_filled,NK cell,pseudobulk_log1p_cpm,3235,0.08614321721060476,0.05607162520288094,0.07430801576654567,0.2579275711300384
+covered,T cell,mean_cp10k,3041,0.04278445767730864,0.23279611777993445,-0.1451493695040118,0.6464314112032479
+covered,T cell,pseudobulk_log1p_cpm,3041,0.21194689139526796,0.31683794932308296,-0.006448273398142809,0.683042944058573
+covered,B cell,mean_cp10k,1764,-0.19726359795368276,0.16727112239048889,-0.22221180627869544,0.12083475503636928
+covered,B cell,pseudobulk_log1p_cpm,1764,-0.10653089702853706,0.1501564685943509,-0.16977646574575625,0.34126938097692383
+covered,Monocyte,mean_cp10k,1690,0.38560274332716254,0.6194510810839116,-0.0185134018761894,0.6405088334868442
+covered,Monocyte,pseudobulk_log1p_cpm,1690,0.3232576002742394,0.6685659120876264,-0.24981543744642576,0.6857537728179119
+covered,NK cell,mean_cp10k,1364,0.06077835035293668,0.2934817312696572,-0.03482701020870913,0.31477041725354615
+covered,NK cell,pseudobulk_log1p_cpm,1364,0.16604837303079692,0.22630725266186819,0.06825983689555247,0.4752265633731685

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/results/ye2026_sepsis/fewshot_draw4_cibersortx/per_donor.csv

@@ -0,0 +1,78 @@
+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
+Abd-PS04,ped_sepsis,0.40343931172770187,0.40343931172770187,0.48935060099261507,0.48935060099261507,0.4394619196182785,0.053866445198985966,0.053866445198985966,0.14094329234721967,0.06814297660808255,0.06814297660808255,0.17030647825289044,0.5714497484497819,0.5714497484497819,0.5608368507983116,0.0089925226227124,0.0089925226227124,0.02147182969352175,0.07219087325155124,0.07219087325155124,0.003853918150119288,0.22535743386888588,0.22535743386888588,0.10258763075793724
+Abd-PS05,ped_sepsis,1.0337179985287985,1.0337179985287985,0.831681147641761,0.831681147641761,0.3335921432697862,0.12332129631784917,0.12332129631784917,0.30387059503177355,0.23253996189336157,0.23253996189336157,0.5060658578856152,0.09666844423484593,0.09666844423484593,0.07019064124783363,0.02632653628522179,0.02632653628522179,0.0891103408434431,0.020872999076564737,0.020872999076564737,0.008954361640670132,0.5002707621921566,0.5002707621921566,0.021808203350664357
+Abd-PS07,ped_sepsis,0.7417772061388722,0.7417772061388722,0.7710565887870682,0.7710565887870682,0.2932304147465438,0.5150560973913934,0.5150560973913934,0.8626152073732719,0.0,0.0,0.023329493087557603,0.009799791271632679,0.009799791271632679,0.002304147465437788,0.3869660188114837,0.3869660188114837,0.09331797235023041,0.04465251135456084,0.04465251135456084,0.0002880184331797235,0.043525581170929355,0.043525581170929355,0.018145161290322582
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+Abd-PS23,ped_sepsis,0.9971952799528105,0.9971952799528105,0.5806106766146433,0.5806106766146433,0.7620509012145122,0.18635643659584522,0.18635643659584522,0.2529589231840334,0.16534372379502443,0.16534372379502443,0.3272220932931075,0.0668523504797894,0.0668523504797894,0.32142028312833604,0.0,0.0,0.013460199582269667,0.0,0.0,0.002088651659317707,0.581447489129341,0.581447489129341,0.08284984915293572
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+Abd-S103,adult_sepsis,0.7157683624419768,0.7157683624419768,0.4812107210290545,0.4812107210290545,0.5648379496975486,0.2804332823409079,0.2804332823409079,0.4813753581661891,0.03482272533760485,0.03482272533760485,0.14782977820227103,0.05142230820957233,0.05142230820957233,0.0024408362517245037,0.0,0.0,0.04393505253104107,0.023897887048379703,0.023897887048379703,0.00021224663058473945,0.6094237970635352,0.6094237970635352,0.3242067282181895
+Abd-S120,adult_sepsis,0.4399741414456415,0.4399741414456415,0.35748724486856576,0.35748724486856576,0.2528897342786328,0.295010854129098,0.295010854129098,0.3140238630468615,0.06319222185437083,0.06319222185437083,0.11049628220646723,0.31079480919894986,0.31079480919894986,0.46446481065191075,0.12241960671624973,0.12241960671624973,0.07297250561992046,0.049110361184315,0.049110361184315,0.0008646031471554556,0.15947214691701656,0.15947214691701656,0.03717793532768459
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+Abd-S156,adult_sepsis,0.43810291415382613,0.43810291415382613,0.4882508854689147,0.4882508854689147,0.435827907862174,0.195110221163972,0.195110221163972,0.3343803540833809,0.016520491802200034,0.016520491802200034,0.08209594517418618,0.3850042578712636,0.3850042578712636,0.39406053683609366,0.08594121343345254,0.08594121343345254,0.0910908052541405,0.05502667574784625,0.05502667574784625,0.0012849800114220445,0.26239713998126557,0.26239713998126557,0.0970873786407767
+Abd-S39,adult_sepsis,0.706772387513319,0.706772387513319,0.42467760064434035,0.42467760064434035,1.2187530490173228,0.15687639764655087,0.15687639764655087,0.13819622465625728,0.05413519966149164,0.05413519966149164,0.06152412025168958,0.3473143092152676,0.3473143092152676,0.6933115823817292,0.09360735215023754,0.09360735215023754,0.049638778839431366,0.02365956655175242,0.02365956655175242,0.0013982754602656724,0.3244071747746998,0.3244071747746998,0.05593101841062689
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+Abd-S57,adult_sepsis,0.9702022081520606,0.9702022081520606,0.9910021730246241,0.9910021730246241,0.8179777482331538,0.3753096031304049,0.3753096031304049,0.8422783570079071,0.0,0.0,0.009026660135749773,0.18145078936573383,0.18145078936573383,0.016164019312854244,0.09760482704589153,0.09760482704589153,0.10671051710866979,0.05383842301773166,0.05383842301773166,0.0012595339724302008,0.29179635744023813,0.29179635744023813,0.024560912462388916
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paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/results/ye2026_sepsis/fewshot_draw4_cibersortx/summary.json

@@ -0,0 +1,157 @@
+{
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+  "fewshot4|Other": 961
+ },
+ "tool_sha256": "b541f68dc286497e8347d487af58ff3550a383d126eeabe347c0726e4fb28799",
+ "score_ft_sha256": "ec5f40b4cea6d5062d0138f3b934abb6465e34cbfeac869c8a0906924c033aec",
+ "seconds": 1.7
+}