Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/results/RESULTS.md

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+# BayesPrism with the same paired donors vs LoRA (paired benchmark; gene mode score)
+
+BayesPrism genes: the scorer's ~5.5-6k scoring genes only (sensitivity run; handicaps composition).
+
+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.
+
+## Five-donor draws (mean ± SD over 5 draws)
+
+| 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 |
+|---|---:|---:|---:|---:|---:|---:|---:|---:|---:|---:|---:|---:|
+| ImMicro (5) | 1.364 ± 0.032 | 1.248 ± 0.071 | 0.176 ± 0.012 | – | – | – | – | – | – | – | – | – |
+| 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 |
+| 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 |
+| 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 |
+| 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 |
+
+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).
+
+## 5-fold CV, pooled (BayesPrism reference = each fold's LoRA training + inner-validation pairs)
+
+| 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 |
+|---|---:|---:|---:|---:|---:|---:|---:|---:|---:|---:|---:|---:|---:|---:|---:|
+| ImMicro | 1.390 | 1.247 | 0.162 | 0.217 | – | – | – | – | – | – | – | – | – | – | – |
+| Sepsis | 1.195 | 0.898 | 0.362 | – | 0.273 | 0.268 | 0.527 | – | 0.316 | 0.133 | 0.469 | 33 | 23 | – | 21 |
+| 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 |
+| Imperial | 1.252 | 1.200 | 0.376 | – | 0.643 | 0.648 | 0.819 | – | 0.661 | 0.298 | 0.690 | 98 | 143 | – | 84 |
+| Giroux | 1.013 | 0.550 | 0.258 | – | 0.462 | 0.465 | 0.461 | – | 0.575 | 0.057 | 0.323 | 4 | 5 | – | 5 |

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/results/ye2026_sepsis/fewshot_draw4_full/contrast.csv

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+genes,celltype,statistic,n_genes,r_generated,r_broadcast,partial_r_generated_given_broadcast,r_generated_vs_broadcast
+zero_filled,T cell,mean_cp10k,3259,0.10120148632606482,0.2635493097811775,-0.08834328790808468,0.6340439700921608
+zero_filled,T cell,pseudobulk_log1p_cpm,3259,0.18032159560903022,0.2326120649060939,-0.023140458832602375,0.8292724863891129
+zero_filled,B cell,mean_cp10k,3311,0.14877163756038542,0.2759123555261431,0.012391515724249713,0.5018610378283648
+zero_filled,B cell,pseudobulk_log1p_cpm,3311,0.1795433743974158,0.25121490410279235,0.008253356461035295,0.6917357978031738
+zero_filled,Monocyte,mean_cp10k,3304,0.40855900092247494,0.5497635656505115,0.1438968895210901,0.562363176081191
+zero_filled,Monocyte,pseudobulk_log1p_cpm,3304,0.4406047597102968,0.6130579062755492,-0.09896413618611222,0.7959106535894794
+zero_filled,NK cell,mean_cp10k,3235,0.1875089732632657,0.18915162420474085,0.10356604651658688,0.5381681751542512
+zero_filled,NK cell,pseudobulk_log1p_cpm,3235,0.08694021776438533,0.05607162520288094,0.06878846678257915,0.4682036269729099
+covered,T cell,mean_cp10k,3066,0.10857517282929058,0.17745314378698865,-0.0454202225644086,0.7719709683637838
+covered,T cell,pseudobulk_log1p_cpm,3066,0.18640327330641265,0.20544600224705073,0.007497685895329979,0.8911021934295368
+covered,B cell,mean_cp10k,3118,0.1575471310360663,0.18738897339733646,0.054770804885303274,0.6141730032554396
+covered,B cell,pseudobulk_log1p_cpm,3118,0.1825014618712629,0.2313670560371728,0.015093852280630076,0.7465708873157243
+covered,Monocyte,mean_cp10k,3113,0.44083305937761524,0.5071100430881215,0.16530716829942663,0.6576558428783034
+covered,Monocyte,pseudobulk_log1p_cpm,3113,0.4504726026321867,0.6208809607653824,-0.1650868183068961,0.838964416788295
+covered,NK cell,mean_cp10k,3041,0.1983223727865718,0.08773090000713354,0.18770934359717817,0.6607281877681066
+covered,NK cell,pseudobulk_log1p_cpm,3041,0.08234694081102824,0.01923246441572636,0.08469566751130554,0.5195274074686098

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/results/ye2026_sepsis/fewshot_draw4_full/per_donor.csv

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+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,0.2731191430853676,0.6457734660490467,0.4979820295388916,0.37175606791024224,0.4394619196182785,0.2390248212712493,0.1348805412290685,0.14094329234721967,0.0067893367373110195,0.07425216064784246,0.17030647825289044,0.4229349190117589,0.5406860632279238,0.5608368507983116,4.1699711305169815e-06,0.081475892149614,0.02147182969352175,0.021157208117672292,0.08040942723671089,0.003853918150119288,0.31008954489087803,0.08829591550884039,0.10258763075793724
+Abd-PS05,ped_sepsis,0.3786326323458177,0.9939525078113487,0.4525811693010155,0.7650644008763812,0.3335921432697862,0.20683341766944305,0.1283593505816089,0.30387059503177355,0.2085546236913611,0.5051036005162944,0.5060658578856152,0.0612586060030951,0.09101215664091986,0.07019064124783363,7.811673716980633e-06,0.07626752649001971,0.0891103408434431,0.004561083706045011,0.03478437393148562,0.008954361640670132,0.5187844572563387,0.1644729918396715,0.021808203350664357
+Abd-PS07,ped_sepsis,0.5181018307701599,0.43612483742113806,0.6788926794628124,0.3759279236925118,0.2932304147465438,0.6566141123872449,0.6078634876276816,0.8626152073732719,0.01126816936301565,0.03635401685436844,0.023329493087557603,0.018696627526542997,0.019424524709560784,0.002304147465437788,0.11845575186326687,0.28031005157440486,0.09331797235023041,0.007660527835346218,0.04220195358315132,0.0002880184331797235,0.1873048110245835,0.013845965650832855,0.018145161290322582
+Abd-PS19,ped_sepsis,0.2635474527865097,0.6885255018605438,0.3051157211727423,0.3593660544506825,0.2045357381429525,0.40730133887980546,0.4371701096057198,0.4622995991983968,0.029463508206773212,0.14733643022874918,0.11209919839679358,0.13550882231388242,0.18706818804912156,0.2937124248496994,0.01622621079475445,0.12719303563792128,0.05586172344689379,0.006866627391546569,0.03354015096775944,0.0156563126252505,0.40463349241323787,0.06769208551072872,0.06037074148296593
+Abd-PS20,ped_sepsis,0.22794898617332182,0.5335861116168672,0.22373074242385493,0.4682877889382462,0.4187120505078231,0.5238793190686236,0.40717186556060253,0.30496843261048584,0.40729898968485106,0.5898660368041259,0.5780949766675817,1.6829719274581228e-06,0.00295476662251,0.08770244304144935,3.631659057256601e-06,2.934075158662775e-06,0.007823222618720834,7.228028198927807e-05,1.2294329054086695e-06,0.0005489980785067252,0.06874409633355154,3.1675046974531094e-06,0.02086192698325556
+Abd-PS23,ped_sepsis,0.4642266711773553,0.9748859090393254,0.22981105459243295,0.7379624662831071,0.7620509012145122,0.27676332553585686,0.27112438072515405,0.2529589231840334,0.10151275539315796,0.3036457341547941,0.3272220932931075,0.07314370926680389,0.11482345465042428,0.32142028312833604,3.156824088670721e-06,0.011520051609817181,0.013460199582269667,0.003631780890100576,0.00606098743512039,0.002088651659317707,0.5449452720899921,0.29282539142469,0.08284984915293572
+Abd-PS27,ped_sepsis,0.2860409703695796,0.4429241129705259,0.27400815056511457,0.220330034142778,0.5833175630281814,0.5475919882882742,0.7489731974582459,0.6126021003500584,0.010174451019033193,0.057156855490414764,0.06078285774901877,0.03768830381396889,0.07633783522540957,0.13196138750397793,2.363884741487937e-06,1.9351642626551523e-06,0.010289593720165482,0.0016869678336371902,0.009619580078299616,0.0029701920016972526,0.4028559251603453,0.10791059658336769,0.1813938686750822
+Abd-S103,adult_sepsis,0.47570245794688,0.7226848964100301,0.758502401375943,0.5066587542412353,0.5648379496975486,0.20243049293055823,0.2549928824014118,0.4813753581661891,0.10936264822538123,0.2818554895613123,0.14782977820227103,0.037615432924086444,0.07877536513434978,0.0024408362517245037,4.599538546717722e-06,0.05173948276185593,0.04393505253104107,0.0020352313619328303,0.019898805131543386,0.00021224663058473945,0.6485515950194946,0.31273797500952677,0.3242067282181895
+Abd-S120,adult_sepsis,0.22023255604238312,0.6440209335734763,0.296411203332183,0.3828420764255334,0.2528897342786328,0.31291604549807717,0.3186886429935995,0.3140238630468615,0.005282625729605045,0.07278173273120433,0.11049628220646723,0.3098368515812781,0.3920630821059822,0.46446481065191075,0.012772770725139536,0.17118064647033515,0.07297250561992046,3.3043514773982043e-06,0.006885326110709233,0.0008646031471554556,0.3591884021144228,0.03840056958816971,0.03717793532768459
+Abd-S123,adult_sepsis,0.3176527861970265,0.9583860946349705,0.18526649694306807,0.4753340317433359,0.9373426469810022,0.13808906063084544,0.18116962189190539,0.16986823305286552,0.011618313054477638,0.0888298612674283,0.08779171297031275,0.21350134206432697,0.34395182566637,0.5027782187648833,0.027807062295544603,0.1908134550243051,0.10938244165740593,0.0004055578727542526,0.013345963443786853,0.0007937767899666614,0.6085786640820511,0.18188927270620436,0.1293856167645658
+Abd-S156,adult_sepsis,0.48693255170826355,1.440114733198814,0.37326412654104546,0.9968532544561164,0.435827907862174,0.034316489403368775,0.21052366922927862,0.3343803540833809,0.004071017484177699,0.05311057128206725,0.08209594517418618,0.14445268341136294,0.31478769251829825,0.39406053683609366,5.263081761660669e-06,0.0809912314816418,0.0910908052541405,9.801379145276786e-06,3.3180993805557424e-05,0.0012849800114220445,0.8171447452401837,0.3405536544949085,0.0970873786407767
+Abd-S39,adult_sepsis,0.7839540789886623,1.5404855557644832,0.3895884740493171,1.1045621676355482,1.2187530490173228,0.026827177210554026,0.13748287184099692,0.13819622465625728,0.004179814309626713,0.05926079209221292,0.06152412025168958,0.1399271116567734,0.30570869032057385,0.6933115823817292,0.002843699008360258,0.09929591613209864,0.049638778839431366,4.840152181709636e-05,8.090018268956913e-07,0.0013982754602656724,0.8261737962928685,0.3982509206122908,0.05593101841062689
+Abd-S42,adult_sepsis,0.4978137387551296,1.1648246966649762,0.6492143753295908,0.8659124734155201,0.2377091518197046,0.16472595095922646,0.3731059602383336,0.5748439165524593,0.025114960340051826,0.12171532596754307,0.09760925841327851,0.07059735708819716,0.17385923150303095,0.17039744175422566,0.06888780446682011,0.2799654777361364,0.05862646566164154,0.008191402659459638,0.0008498882942486302,0.0016750418760469012,0.6624825244862449,0.050504116260707194,0.0968478757423481
+Abd-S47,adult_sepsis,0.1322316588375438,0.9124550009434015,0.1809450250922533,0.6132790736582129,0.1705156191193073,0.3384815776327072,0.6786371119646692,0.7027976414502571,0.15307201220714342,0.2708580198591181,0.20474219044034625,0.0003687583938226486,0.026858231762171447,0.03224187680341237,0.011089353831948019,0.01724957287186949,0.019069125580228326,0.0002389056046927627,7.300784552125555e-07,0.0006272738677706687,0.496749392329686,0.006396333463716359,0.040521891857985194
+Abd-S51,adult_sepsis,0.32243151328060693,1.1820305103317579,0.3049801408889826,0.7780750647063248,0.5556241806263656,0.06492689914405507,0.18927327921666254,0.25273124544792425,0.1285887472056999,0.32250518166807707,0.269482884195193,0.12308494136427259,0.2726550570984831,0.3551347414420976,0.006440967025410369,0.14490139798752144,0.03670793882010197,0.009606052712843824,0.00033537743941890554,0.0014566642388929353,0.6673523925477184,0.07032970658983709,0.08448652585579024
+Abd-S54,adult_sepsis,0.4619158395921444,1.2067228099190694,0.543079710786778,1.0308169251794204,0.4588375543617293,0.19818510912364873,0.2544603457449869,0.4854182655410591,0.05867435681431329,0.16522294063910495,0.1364799181376311,0.07884315754415708,0.14976071343315076,0.012918905090816066,0.10242942329539141,0.3593243022809626,0.340752110514198,0.006142851335415465,0.011669487522091734,0.0011511895625479663,0.5557251018870739,0.05956221037970301,0.023279611153747763
+Abd-S57,adult_sepsis,0.8281035649324898,1.2521313186477716,0.9939351991270076,1.1902219678445622,0.8179777482331538,0.3109108349867503,0.4372490365018217,0.8422783570079071,3.286388415764516e-06,4.198175590260405e-06,0.009026660135749773,0.15492048873142175,0.2692080828909051,0.016164019312854244,0.021035753553274895,0.1318097191221294,0.10671051710866979,0.011091437667921245,0.028974440265325186,0.0012595339724302008,0.5020381986722161,0.13275452304422844,0.024560912462388916
+Abd-S66,adult_sepsis,0.7341673288389184,1.4219545676150083,0.9225381508871229,1.3484453677408523,0.497912576558436,0.12251985090810086,0.17792122652238426,0.49295242889504154,0.05535753931823938,0.1955090581528368,0.23873647118046817,0.17849966438965234,0.34324594232721345,0.03788069468915178,0.029720709807081972,0.24757200502234997,0.18688648376541656,0.00451246532272247,0.0014104439765156053,0.0003775484520513466,0.609389770254203,0.03434132399870004,0.04316637301787063
+Abd-S79,adult_sepsis,0.5515005794401612,1.1451642033475875,0.7351583234560423,1.0596787296328172,0.115916459472899,0.25680705842489465,0.32962244970312715,0.5500994530084535,0.10746246455040175,0.2536526210939479,0.30892590750870214,0.14544990486134363,0.2466142785131273,0.024365987071108902,0.015908196335494538,0.12944268697040343,0.09373446046742914,0.0055541057810667704,0.00158913766291311,0.00012431626056688214,0.46881827004679855,0.039078826056481095,0.022749875683739432
+Abd-S83,adult_sepsis,1.2275759363180971,1.543838669732339,1.3171700187821143,1.5258295915484614,0.7305028184892897,0.09122188568896412,0.09935313243172308,0.3924947656627476,1.4617530801913558e-05,0.02043263729791782,0.16991464003865356,0.2542111923898955,0.441128006236843,0.049927524561120956,0.0005903368214568314,0.13017243701870299,0.3013367692059913,0.0035071466453450305,0.02168357271573862,0.0009663391850539539,0.6504548209235366,0.28723021429907447,0.0853599613464326
+Abd-S98,adult_sepsis,1.3133553144510584,1.4307524264531988,1.418153702814138,1.4356951184880038,1.111329341317365,0.2216374025815853,0.19094731797199513,0.7477045908183633,4.038272237925816e-06,0.00966045394419242,0.10958083832335329,0.2891864648252788,0.4460695588089445,0.019560878243512974,0.031993984339423104,0.22065841569369019,0.11037924151696607,0.00024983862606250436,0.015095332144768298,0.0015968063872255488,0.45692827135541236,0.11756892143640962,0.011177644710578843
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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_full/summary.json

@@ -0,0 +1,147 @@
+{
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+ "n_control": 20,
+ "deg_per_type": {
+  "zero_filled": {
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+    "B cell": 3,
+    "Monocyte": 12,
+    "NK cell": 4,
+    "DC": 5
+   },
+   "broadcast": {
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+    "B cell": 1,
+    "Monocyte": 13,
+    "NK cell": 2,
+    "DC": 1
+   }
+  },
+  "covered": {
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+    "B cell": 3,
+    "Monocyte": 12,
+    "NK cell": 4,
+    "DC": 5
+   },
+   "broadcast": {
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+    "B cell": 1,
+    "Monocyte": 12,
+    "NK cell": 1,
+    "DC": 1
+   }
+  }
+ },
+ "tool_sha256": "15ed044bbfc39c501c7187ad78586902f2aa0635e7b3a90786b4587cedc2008a",
+ "score_ft_sha256": "ec5f40b4cea6d5062d0138f3b934abb6465e34cbfeac869c8a0906924c033aec",
+ "seconds": 4.0
+}