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_draw1_cibersortx/summary.json

@@ -0,0 +1,157 @@
+{
+ "dataset": "ye2026_sepsis",
+ "comparison": "fewshot",
+ "draw": 1,
+ "gene_mode": "cibersortx",
+ "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/draw1",
+ "lora_arm": "lora5",
+ "n_donors": 77,
+ "contrast": true,
+ "genes_scoring": 5975,
+ "genes_covered_by_Z_all_donors": 5573,
+ "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
+  }
+ },
+ "observed_mean_fraction": {
+  "T cell": 0.4861,
+  "B cell": 0.1763,
+  "Monocyte": 0.2031,
+  "NK cell": 0.0801,
+  "DC": 0.0054,
+  "Other": 0.0489
+ },
+ "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
+ },
+ "other_arms": {
+  "zs_raw": {
+   "comp_l1": 0.5272653571228263,
+   "logfc_r_mean_cp10k": -0.046618936113183594,
+   "deg_top50_sum": 12
+  },
+  "zs_pseudo": {
+   "comp_l1": 0.2358905430735161,
+   "logfc_r_mean_cp10k": 0.47920669757752815,
+   "deg_top50_sum": 20
+  },
+  "zs_cal": {
+   "comp_l1": 0.5221879948489522,
+   "logfc_r_mean_cp10k": 0.08485199604084404,
+   "deg_top50_sum": 10
+  }
+ },
+ "gates": {
+  "observed_composition_equal": true,
+  "broadcast_r_equal": true,
+  "broadcast_deg_equal": true
+ },
+ "method": "cibersortx",
+ "has_cell_type_expression": true,
+ "n_case": 57,
+ "n_control": 20,
+ "deg_per_type": {
+  "zero_filled": {
+   "bp": {
+    "T cell": 4,
+    "B cell": 9,
+    "Monocyte": 10,
+    "NK cell": 2,
+    "DC": 4
+   },
+   "broadcast": {
+    "T cell": 3,
+    "B cell": 2,
+    "Monocyte": 11,
+    "NK cell": 3,
+    "DC": 1
+   }
+  },
+  "covered": {
+   "bp": {
+    "T cell": 4,
+    "B cell": 9,
+    "Monocyte": 10,
+    "NK cell": 2,
+    "DC": 4
+   },
+   "broadcast": {
+    "T cell": 3,
+    "B cell": 6,
+    "Monocyte": 11,
+    "NK cell": 4,
+    "DC": 5
+   }
+  }
+ },
+ "hires_imputed_genes": {
+  "fewshot1|T cell": 4313,
+  "fewshot1|B cell": 1958,
+  "fewshot1|Monocyte": 2534,
+  "fewshot1|NK cell": 2380,
+  "fewshot1|DC": 993,
+  "fewshot1|Other": 881
+ },
+ "tool_sha256": "b541f68dc286497e8347d487af58ff3550a383d126eeabe347c0726e4fb28799",
+ "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_draw1_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,3259,0.11114444557598013,0.20784062189687463,-0.012971586538986507,0.5843010256819414
+zero_filled,T cell,pseudobulk_log1p_cpm,3259,0.1598573139865615,0.14785190713588403,0.0726797953184643,0.7724373334551752
+zero_filled,B cell,mean_cp10k,3313,0.08811705697678564,0.23984966045152206,-0.0065669716759600375,0.3918393333950665
+zero_filled,B cell,pseudobulk_log1p_cpm,3313,0.20317960484813938,0.2339239474250468,0.09929551605097367,0.514745138486103
+zero_filled,Monocyte,mean_cp10k,3288,0.559847277573494,0.5274763363757402,0.3727513074203916,0.5667244792495083
+zero_filled,Monocyte,pseudobulk_log1p_cpm,3288,0.5433467576179849,0.5904613471818534,0.1616862343963787,0.7826411159630197
+zero_filled,NK cell,mean_cp10k,3237,0.0302031708509091,0.1424908307994565,-0.05449448365339091,0.5323974474937133
+zero_filled,NK cell,pseudobulk_log1p_cpm,3237,0.001592603111663628,0.01673965371875349,-0.016549959596137344,0.7495237526325929
+covered,T cell,mean_cp10k,3064,0.11915549394667609,0.11936377613776858,0.04831547413468182,0.7189035509224384
+covered,T cell,pseudobulk_log1p_cpm,3064,0.16545871364671677,0.12280625418707328,0.11491807243192707,0.8317354283523116
+covered,B cell,mean_cp10k,3119,0.09418826151170773,0.1579625235696957,0.020992429935450682,0.48123780186117887
+covered,B cell,pseudobulk_log1p_cpm,3119,0.20715700711562152,0.22637762837633102,0.10113158296518471,0.5523585046433374
+covered,Monocyte,mean_cp10k,3099,0.5986328731782002,0.4831251758721347,0.42341047907760215,0.6682101815556285
+covered,Monocyte,pseudobulk_log1p_cpm,3099,0.5564400848572806,0.6022308539222041,0.13356086215213625,0.8235293251969882
+covered,NK cell,mean_cp10k,3042,0.03348232388729415,0.046607389829290295,0.0037990218823515643,0.6570077223233247
+covered,NK cell,pseudobulk_log1p_cpm,3042,0.002806492693077693,-0.008096140411188358,0.015804349402097247,0.8067607184855666

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/results/ye2026_sepsis/fewshot_draw1_full/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,0.6005412866388937,0.4928727961980852,0.7042331939180082,0.533078324089659,0.541285128769805,0.2961372629757479,0.0002607972720720809,0.14094329234721967,0.029497239921649494,0.09411706195195917,0.17030647825289044,0.6520792782688261,0.7084353252172714,0.5608368507983116,0.011357267396746138,0.17414399859400884,0.02147182969352175,0.003750731922943197,0.003598225089938274,0.003853918150119288,0.007178219514087385,0.01944459187475026,0.10258763075793724
+Abd-PS05,ped_sepsis,0.5586854901643458,0.35781434677908114,0.7428235545512628,0.4891935324750573,0.9890190641247832,0.40004311287060396,0.03347978261059061,0.30387059503177355,0.38402183473486745,0.5111271389332691,0.5060658578856152,0.1424026768738026,0.15567905633846113,0.07019064124783363,0.03859230194795468,0.2521459815567837,0.0891103408434431,0.0026092502973657263,2.4289796802321988e-06,0.008954361640670132,0.03233082327540554,0.047565611581215195,0.021808203350664357
+Abd-PS07,ped_sepsis,1.043544636711069,0.5611654684178491,1.104348813766244,0.6397692532205598,0.3918970814132104,0.5981817962832405,0.3540736557202037,0.8626152073732719,0.04521503626390269,0.05672830655796402,0.023329493087557603,0.055239486036092,0.05772320213590328,0.002304147465437788,0.2983442674441252,0.5205179396497173,0.09331797235023041,0.0010235758012102456,0.006042501348355416,0.0002880184331797235,0.001995838171429465,0.004914394587856288,0.018145161290322582
+Abd-PS19,ped_sepsis,0.7359478768164499,0.3176841403309386,0.7585826631975914,0.24297015475733452,0.1678336673346693,0.5854080801181272,0.18271256728941473,0.4622995991983968,0.06806841596940225,0.17273479558415183,0.11209919839679358,0.24186370631734158,0.2626052386448276,0.2937124248496994,0.09159531269263264,0.3632000646677605,0.05586172344689379,0.004300166317281058,0.0007069653090626328,0.0156563126252505,0.008764318585215144,0.01804036850478276,0.06037074148296593
+Abd-PS20,ped_sepsis,0.3235757183228994,0.5191473671425689,0.2929628733716959,0.554718062797912,0.1880453838411564,0.5637464057447011,0.24785119991334187,0.30496843261048584,0.4268326820836551,0.6597598903186251,0.5780949766675817,0.0031698866919882855,0.004441213783505425,0.08770244304144935,0.0023411989612870322,0.0879461681291271,0.007823222618720834,0.0013447085155758654,3.015762083837996e-07,0.0005489980785067252,0.0025651180027924667,1.2262791921392788e-06,0.02086192698325556
+Abd-PS23,ped_sepsis,0.47936281613860965,0.5717136314811719,0.3383414215927448,0.4356448411937807,0.5293645857507543,0.5300337701554786,0.15440164933600964,0.2529589231840334,0.2069623460638495,0.3621705164624321,0.3272220932931075,0.16241159907507055,0.18238382640059592,0.32142028312833604,0.021229678557675685,0.19521329964643722,0.013460199582269667,0.0031011414530525173,9.74165776748529e-07,0.002088651659317707,0.07626146469487333,0.10582973398874834,0.08284984915293572
+Abd-PS27,ped_sepsis,0.3136214980190096,0.4060464346395394,0.3059434863714686,0.3553526273579951,0.3661887486298221,0.8156253176698282,0.6742933924828547,0.6126021003500584,0.025682497124296697,0.08754329047486101,0.06078285774901877,0.09688914249512816,0.11578879823107295,0.13196138750397793,0.0068476553388207686,0.07864861787103171,0.010289593720165482,0.002618163899583331,1.3247976922865868e-05,0.0029701920016972526,0.0523372234723431,0.04371265296325671,0.1813938686750822
+Abd-S102,adult_sepsis,1.4600288936988284,1.0166660963768857,1.5692714964837875,1.3125061090138639,1.484429492570788,0.3650523475299966,0.046175862670854814,0.47981497056349875,0.040728002090562425,0.09754756210971034,0.39318755256518084,0.47009902811186177,0.5231160314597195,0.0053616484440706475,0.05515374792608808,0.2280241320567302,0.095878889823381,0.00035017974850980085,5.640302392946176e-07,0.0007359125315391085,0.06861669459298134,0.1051358476727458,0.02502102607232969
+Abd-S103,adult_sepsis,1.0660403220541403,0.476886275768129,1.1303811868982427,0.5897559253896987,0.7333605009020481,0.4828870203270333,0.1553310175314014,0.4813753581661891,0.25876878993631836,0.3371875617339145,0.14782977820227103,0.1257289364436563,0.13687910412957033,0.0024408362517245037,0.04604207546188336,0.25315916214862194,0.04393505253104107,0.0008095874969836264,8.819075920691331e-07,0.00021224663058473945,0.08576359033412508,0.11744227254889969,0.3242067282181895
+Abd-S120,adult_sepsis,0.6084386384651134,0.25587018791278326,0.7221781442363076,0.33746435389157664,0.3389853017464984,0.4380916857677248,0.09220677788114384,0.3140238630468615,0.01776423727662393,0.06037519415097511,0.11049628220646723,0.463373585272426,0.49619401904884924,0.46446481065191075,0.07683977685544884,0.3454626164555386,0.07297250561992046,3.0121750925045854e-05,5.742727369982275e-07,0.0008646031471554556,0.0039005930768514895,0.005760818190756222,0.03717793532768459
+Abd-S123,adult_sepsis,0.5074261975518072,0.40182238280084503,0.5310336093572476,0.32690697650225997,0.4584528761179023,0.34264169531752203,0.023382314552678907,0.16986823305286552,0.0318579820165056,0.09267739457033525,0.08779171297031275,0.4265126126063832,0.4537331490418407,0.5027782187648833,0.13752017079317186,0.35820985883328704,0.10938244165740593,0.0003511727737550751,1.2740382184313402e-06,0.0007937767899666614,0.06111636649266211,0.0719960089636396,0.1293856167645658
+Abd-S156,adult_sepsis,0.5487728420899094,0.23872384165281635,0.6447878535330399,0.4266969977208738,0.5831342090234152,0.339712331758008,0.06186920225307201,0.3343803540833809,0.015591310641445207,0.08150451978199102,0.08209594517418618,0.38186137691492855,0.43306047826480065,0.39406053683609366,0.051707701359001566,0.22732100192705254,0.0910908052541405,9.957534058836188e-06,1.136188971367392e-06,0.0012849800114220445,0.2111173217925577,0.19624366158411236,0.0970873786407767
+Abd-S39,adult_sepsis,0.7551571613046463,0.7273933424018085,0.44776852109023607,0.3993148569721101,0.2142822962790336,0.3021911989527092,0.02902532932142956,0.13819622465625728,0.024788756316225534,0.08103953566268671,0.06152412025168958,0.367276299703289,0.42630114252081996,0.6933115823817292,0.08052550555361045,0.2401024697463445,0.049638778839431366,0.0004722508732656214,1.0300036794960407e-06,0.0013982754602656724,0.22474598860090014,0.2235304927450398,0.05593101841062689
+Abd-S42,adult_sepsis,0.9742162844416433,0.3186934249945832,1.0444715588799183,0.49342652306000434,0.2182476016445865,0.501997957148752,0.17228696726366127,0.5748439165524593,0.12162461226240719,0.204617883168167,0.09760925841327851,0.19309900196870702,0.22363071136049278,0.17039744175422566,0.17125626409532316,0.3854927135213076,0.05862646566164154,5.329722019818977e-05,3.171000435525351e-07,0.0016750418760469012,0.011968867304612555,0.013971407586327693,0.0968478757423481
+Abd-S47,adult_sepsis,0.5675798975752675,0.1213627710484528,0.5827599745956036,0.1438143994998556,0.1124561535566427,0.671171288735157,0.4576030238490542,0.7027976414502571,0.2554964541870041,0.387421181799177,0.20474219044034625,0.03403819814556678,0.03945873074152542,0.03224187680341237,0.027199926015642483,0.11296322907091823,0.019069125580228326,6.684072791681872e-06,3.817830372767297e-07,0.0006272738677706687,0.012087448843837986,0.0025534527562877875,0.040521891857985194
+Abd-S51,adult_sepsis,0.6016830607657175,0.2814627387325217,0.5980179935586096,0.3051021029956537,0.344021364408837,0.3838450032021366,0.03556647113445896,0.25273124544792425,0.2652147790255821,0.41425798663876817,0.269482884195193,0.2907976885688699,0.3401811692425426,0.3551347414420976,0.04632555043215041,0.19277436675938556,0.03670793882010197,5.8482803032930105e-06,7.773904827719538e-07,0.0014566642388929353,0.013811130490957607,0.01721922883436183,0.08448652585579024
+Abd-S54,adult_sepsis,0.8418341981959405,0.31614609022051327,0.871483344291479,0.5617947689205804,0.5104640573036582,0.437809954508955,0.07028646277310685,0.4854182655410591,0.13078241770061366,0.23307742000676981,0.1364799181376311,0.16984590013862083,0.19127608075514554,0.012918905090816066,0.24585298285563975,0.4867145320787001,0.340752110514198,0.0022972396249998583,0.0002743211850752191,0.0011511895625479663,0.013411505171170953,0.018371183201202495,0.023279611153747763
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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_draw1_full/summary.json

@@ -0,0 +1,147 @@
+{
+ "dataset": "ye2026_sepsis",
+ "comparison": "fewshot",
+ "draw": 1,
+ "gene_mode": "full",
+ "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/draw1",
+ "lora_arm": "lora5",
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