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_draw2_full/summary.json

@@ -0,0 +1,147 @@
+{
+ "dataset": "ye2026_sepsis",
+ "comparison": "fewshot",
+ "draw": 2,
+ "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/draw2",
+ "lora_arm": "lora5",
+ "n_donors": 77,
+ "contrast": true,
+ "genes_scoring": 5975,
+ "genes_covered_by_Z_all_donors": 5367,
+ "bayesprism": {
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+  "comp_l1_by_variant": {
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+   "first_cells": 0.436135409514162,
+   "final_mrna": 0.6868537334974446,
+   "first_mrna": 0.4349919323214119
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+  "mean_fraction": {
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+    "B cell": 0.1916,
+    "Monocyte": 0.2267,
+    "NK cell": 0.2785,
+    "DC": 0.0008,
+    "Other": 0.0564
+   },
+   "first_cells": {
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+    "B cell": 0.0905,
+    "Monocyte": 0.2024,
+    "NK cell": 0.0619,
+    "DC": 0.0103,
+    "Other": 0.0748
+   },
+   "final_mrna": {
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+    "B cell": 0.1536,
+    "Monocyte": 0.337,
+    "NK cell": 0.2539,
+    "DC": 0.0021,
+    "Other": 0.0308
+   },
+   "first_mrna": {
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+    "B cell": 0.0743,
+    "Monocyte": 0.3045,
+    "NK cell": 0.0569,
+    "DC": 0.0265,
+    "Other": 0.0422
+   }
+  },
+  "logfc_r_mean_cp10k": 0.2654125351120938,
+  "partial_r_mean_cp10k": 0.11483895518121781,
+  "logfc_r_mean_cp10k_covered_genes": 0.2826594932185867,
+  "deg_top50_sum": 26,
+  "deg_top50_sum_covered_genes": 26,
+  "per_type_logfc_r": {
+   "T cell": 0.1943,
+   "B cell": 0.228,
+   "Monocyte": 0.5219,
+   "NK cell": 0.1174
+  }
+ },
+ "observed_mean_fraction": {
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+  "B cell": 0.1746,
+  "Monocyte": 0.2119,
+  "NK cell": 0.0818,
+  "DC": 0.0057,
+  "Other": 0.0495
+ },
+ "lora": {
+  "comp_l1": 0.4986968896699433,
+  "coverage": 0.7606060606060606,
+  "logfc_r_mean_cp10k": 0.32721881191208096,
+  "deg_top50_sum": 26,
+  "partial_r_mean_cp10k": 0.31447561738686153
+ },
+ "broadcast": {
+  "logfc_r_mean_cp10k": 0.3386821732452143,
+  "logfc_r_mean_cp10k_covered_genes": 0.26922440985482304,
+  "deg_top50_sum": 18
+ },
+ "other_arms": {
+  "zs_raw": {
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+   "logfc_r_mean_cp10k": 0.005116561986939425,
+   "deg_top50_sum": 10
+  },
+  "zs_pseudo": {
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+   "logfc_r_mean_cp10k": 0.489737657274666,
+   "deg_top50_sum": 23
+  },
+  "zs_cal": {
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+   "logfc_r_mean_cp10k": 0.16980973770431268,
+   "deg_top50_sum": 10
+  }
+ },
+ "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": 4,
+    "B cell": 3,
+    "Monocyte": 14,
+    "NK cell": 1,
+    "DC": 4
+   },
+   "broadcast": {
+    "T cell": 2,
+    "B cell": 2,
+    "Monocyte": 11,
+    "NK cell": 2,
+    "DC": 1
+   }
+  },
+  "covered": {
+   "bp": {
+    "T cell": 4,
+    "B cell": 3,
+    "Monocyte": 14,
+    "NK cell": 1,
+    "DC": 4
+   },
+   "broadcast": {
+    "T cell": 1,
+    "B cell": 2,
+    "Monocyte": 9,
+    "NK cell": 1,
+    "DC": 1
+   }
+  }
+ },
+ "tool_sha256": "15ed044bbfc39c501c7187ad78586902f2aa0635e7b3a90786b4587cedc2008a",
+ "score_ft_sha256": "ec5f40b4cea6d5062d0138f3b934abb6465e34cbfeac869c8a0906924c033aec",
+ "seconds": 4.0
+}

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/results/ye2026_sepsis/fewshot_draw3/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,3267,0.16932863013002375,0.2674058776426976,0.06503762984179706,0.42060548999016856
+zero_filled,T cell,pseudobulk_log1p_cpm,3267,0.0658601429682518,0.2289561663328621,-0.04414665204916164,0.4548128481124568
+zero_filled,B cell,mean_cp10k,3307,0.23778148828015117,0.2947135505142224,0.1347906253360499,0.4077581841725739
+zero_filled,B cell,pseudobulk_log1p_cpm,3307,0.37967810034076604,0.29321258816714024,0.2790626616797598,0.5148327877505069
+zero_filled,Monocyte,mean_cp10k,3299,0.566010013671411,0.5404162642066815,0.37422259827866533,0.5677107506188472
+zero_filled,Monocyte,pseudobulk_log1p_cpm,3299,0.5294479782845603,0.6043259179152038,0.13819405802463428,0.7570617491908822
+zero_filled,NK cell,mean_cp10k,3251,0.1811444887617812,0.2032508698563803,0.07644682067921246,0.5953413087167432
+zero_filled,NK cell,pseudobulk_log1p_cpm,3251,0.09591220200978877,0.06220697008500626,0.07491406207301345,0.7583673111087653
+covered,T cell,mean_cp10k,3245,0.1790175533863587,0.215017354872985,0.0828972387448637,0.508327298432758
+covered,T cell,pseudobulk_log1p_cpm,3245,0.06560908421007311,0.2253344489170946,-0.050646762535276,0.4829181674676205
+covered,B cell,mean_cp10k,3285,0.2514941808646512,0.24019159458823666,0.1588644429549389,0.4859002026396226
+covered,B cell,pseudobulk_log1p_cpm,3285,0.38515081106866833,0.29384551469186393,0.2800019772083062,0.5500996699265436
+covered,Monocyte,mean_cp10k,3277,0.581899925025556,0.5062591455259293,0.3854967122038604,0.650880096174029
+covered,Monocyte,pseudobulk_log1p_cpm,3277,0.5320929130453854,0.6140569521200003,0.09855446176490341,0.7886329266633504
+covered,NK cell,mean_cp10k,3229,0.19225680156968292,0.13315544179371483,0.13998038895888015,0.7067411287068334
+covered,NK cell,pseudobulk_log1p_cpm,3229,0.09825384789221463,0.052393884107161365,0.09502947107808415,0.8079126241966595

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/results/ye2026_sepsis/fewshot_draw3/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,0.6841610419941506,0.6809069281944763,0.7294071271998583,0.7226206541278374,0.5624055790053222,2.2869205693454305e-05,1.184337253152552e-06,0.14094329234721967,0.017890333655126486,0.020137820432099215,0.17030647825289044,0.7117215596739389,0.7348357181636088,0.5608368507983116,0.21104058491513264,0.18955348332529978,0.02147182969352175,0.0017838570028686892,1.925151662918861e-06,0.003853918150119288,0.05754079554723989,0.055469868590076035,0.10258763075793724
+Abd-PS05,ped_sepsis,1.0714375875866264,1.0702237478698478,0.8929981321018,0.886899289486618,1.0313090699017908,0.0011780000299928999,2.014366786912671e-06,0.30387059503177355,0.2789007866888153,0.2831684684868551,0.5060658578856152,0.1972814780372491,0.1938081677607685,0.07019064124783363,0.4180008408925667,0.3821571429895589,0.0891103408434431,0.0037001539043269444,1.5379111036879022e-06,0.008954361640670132,0.1009387404470492,0.14086266848492698,0.021808203350664357
+Abd-PS07,ped_sepsis,1.7286982870176069,1.2180891002124286,1.7273559627372763,1.153013795451905,0.4015207373271889,0.2661194604507362,4.433519199114758e-06,0.8626152073732719,0.020857705005744707,0.040414514494098615,0.023329493087557603,0.06390491729547619,0.06779299532421075,0.002304147465437788,0.6407617526264062,0.8750932465937198,0.09331797235023041,0.00017163625436472557,6.723578482062661e-05,0.0002880184331797235,0.008184528367271848,0.016627574283951167,0.018145161290322582
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+Abd-PS20,ped_sepsis,1.0318390241364794,0.566178706231555,0.7013100323227655,0.3529479093272032,0.1984620733827432,0.3150316921548417,0.04761646572859611,0.30496843261048584,0.3835407623079774,0.41131486241405635,0.5780949766675817,0.00992296756776679,0.00849627650730389,0.08770244304144935,0.2798500467791146,0.5237427346869605,0.007823222618720834,0.0015482674895345595,2.454033567473314e-06,0.0005489980785067252,0.010106263700764902,0.008827206629515654,0.02086192698325556
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+Abd-PS27,ped_sepsis,1.0097269918844214,0.5365276270472025,0.971506048053979,0.5344809394616867,0.548883278526219,0.41332179292020266,0.17636313248691757,0.6126021003500584,0.027979711585065205,0.04602041056498352,0.06078285774901877,0.11488467541985929,0.11946754587396635,0.13196138750397793,0.27816122038172414,0.5151530896623762,0.010289593720165482,0.0033623788637397877,3.1616361530164685e-06,0.0029701920016972526,0.1622902208294089,0.14299265977560346,0.1813938686750822
+Abd-S102,adult_sepsis,1.6792308273066765,1.6665314202316666,1.6654193217582995,1.6470743904902077,0.8616467619848612,4.471942485576858e-05,1.4737479090949746e-06,0.47981497056349875,0.04018872022403218,0.03412080770151105,0.39318755256518084,0.46931821851881284,0.5020061971992253,0.0053616484440706475,0.3496869877867627,0.28170774473346144,0.095878889823381,0.0002392858954973879,7.405574602920863e-07,0.0007359125315391085,0.140522068150039,0.1821630360604328,0.02502102607232969
+Abd-S103,adult_sepsis,1.0542727356738155,1.0479291374032655,1.1557760081886703,1.1398587321149378,0.86260978456967,0.05695963208020204,1.4371189442687177e-06,0.4813753581661891,0.17339236655684265,0.1769905075304098,0.14782977820227103,0.13826117735550084,0.14070563246849094,0.0024408362517245037,0.40526793094271524,0.40364589482304364,0.04393505253104107,0.0014610074621953279,3.652189928493639e-07,0.00021224663058473945,0.22465788560254388,0.2786561628401185,0.3242067282181895
+Abd-S120,adult_sepsis,0.8383301126514837,0.7924464238329202,0.8362848670262052,0.8093331546601541,0.7816113897054585,0.021144763984209922,1.36496965906801e-06,0.3140238630468615,0.016931635298256007,0.017593423545466655,0.11049628220646723,0.47735490248740714,0.4594367468184758,0.46446481065191075,0.4563056257008842,0.49213756194566244,0.07297250561992046,2.5650124065796373e-05,7.201900391147063e-07,0.0008646031471554556,0.028237422405176925,0.030830182530697088,0.03717793532768459
+Abd-S123,adult_sepsis,0.6400754592374867,0.6590266588445675,0.4992721994703162,0.4818199556512094,1.485342646981002,1.2730972765494975e-05,1.105710088279584e-06,0.16986823305286552,0.022094244029434128,0.02228804894096447,0.08779171297031275,0.4093874523799327,0.41890449424555765,0.5027782187648833,0.40734721078503355,0.4081041560326517,0.10938244165740593,0.0002241847736122153,5.630626744963106e-07,0.0007937767899666614,0.16093417705922194,0.1507016320080634,0.1293856167645658
+Abd-S156,adult_sepsis,0.8361787199992827,0.8720482127830738,0.8266710202956765,0.8236735169964198,1.088669331810394,1.323203837616452e-05,1.5631410019731374e-06,0.3343803540833809,0.004415068162452147,0.0033470222942112125,0.08209594517418618,0.3713573820050287,0.3903830396824857,0.39406053683609366,0.21357957544028686,0.26335085525153157,0.0910908052541405,1.2027507688876045e-05,8.309877425152193e-07,0.0012849800114220445,0.41062271484616725,0.34291668864302693,0.0970873786407767
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+Abd-S42,adult_sepsis,1.4254382749790855,1.300454571832612,1.4183083574620587,1.2963544574460761,0.1635809349779199,0.0857116356013741,3.0483180816978327e-06,0.5748439165524593,0.010198769815189341,0.014609314541510363,0.09760925841327851,0.2224823204704098,0.2225734066617639,0.17039744175422566,0.6567688728617632,0.7191696382436461,0.05862646566164154,2.0344749551869466e-05,2.3457889692575875e-06,0.0016750418760469012,0.02481805650171153,0.043642246446028606,0.0968478757423481
+Abd-S47,adult_sepsis,1.2605712219263618,0.7677530218051928,1.1170239970346005,0.6690796972260971,0.1031228202233094,0.4878417473058629,0.222519985091891,0.7027976414502571,0.06756057319833507,0.07642974321315366,0.20474219044034625,0.05240526871497291,0.052002326955054044,0.03224187680341237,0.3827822445712642,0.6295942863917676,0.019069125580228326,2.9858177396053895e-05,2.419937250346043e-06,0.0006272738677706687,0.009380308032168903,0.01945123841088326,0.040521891857985194
+Abd-S51,adult_sepsis,0.9783435380632165,0.9058888628254258,0.9821614293594746,0.914968243625493,0.5102908472930323,0.04763500875203966,2.5891538588175327e-06,0.25273124544792425,0.06294158377885824,0.05537258126847388,0.269482884195193,0.4102254954071206,0.41337772966270536,0.3551347414420976,0.4345616162677919,0.4676367196311024,0.03670793882010197,5.814409949733019e-06,4.131834128612272e-06,0.0014566642388929353,0.04463048138423987,0.0636062484497309,0.08448652585579024
+Abd-S54,adult_sepsis,1.1652876786223738,1.1215857501723636,1.1181226194680596,1.0752691095058577,0.4997973906369914,0.021499741797385213,1.951499119123671e-06,0.4854182655410591,0.039605566795123344,0.03944636167870689,0.1364799181376311,0.19539479145350425,0.19585189206581613,0.012918905090816066,0.7099089535114893,0.715335448689493,0.340752110514198,0.00269611545481273,0.0009572207522251962,0.0011511895625479663,0.030894830987685352,0.04840712531463977,0.023279611153747763
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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_draw3/summary.json

@@ -0,0 +1,147 @@
+{
+ "dataset": "ye2026_sepsis",
+ "comparison": "fewshot",
+ "draw": 3,
+ "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/draw3",
+ "lora_arm": "lora5",
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