Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/results/ji2025_chili/fewshot_draw4_full/summary.json

@@ -0,0 +1,147 @@
+{
+ "dataset": "ji2025_chili",
+ "comparison": "fewshot",
+ "draw": 4,
+ "gene_mode": "full",
+ "stored_scores": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/fewshot_n5/draw4",
+ "lora_arm": "lora5",
+ "n_donors": 24,
+ "contrast": true,
+ "genes_scoring": 5752,
+ "genes_covered_by_Z_all_donors": 5407,
+ "bayesprism": {
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+  "comp_l1_by_variant": {
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+   "first_cells": 1.0782392660957625,
+   "final_mrna": 1.0286173381490102,
+   "first_mrna": 1.1182747575298582
+  },
+  "mean_fraction": {
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+    "B cell": 0.0136,
+    "Monocyte": 0.4361,
+    "NK cell": 0.1295,
+    "DC": 0.0001,
+    "Other": 0.3184
+   },
+   "first_cells": {
+    "T cell": 0.0543,
+    "B cell": 0.021,
+    "Monocyte": 0.3729,
+    "NK cell": 0.1003,
+    "DC": 0.0036,
+    "Other": 0.448
+   },
+   "final_mrna": {
+    "T cell": 0.0744,
+    "B cell": 0.0114,
+    "Monocyte": 0.5472,
+    "NK cell": 0.0978,
+    "DC": 0.0002,
+    "Other": 0.2689
+   },
+   "first_mrna": {
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+    "B cell": 0.0178,
+    "Monocyte": 0.4747,
+    "NK cell": 0.0773,
+    "DC": 0.0072,
+    "Other": 0.3829
+   }
+  },
+  "logfc_r_mean_cp10k": 0.20855067405616556,
+  "partial_r_mean_cp10k": 0.06023029706134373,
+  "logfc_r_mean_cp10k_covered_genes": 0.22223209873735827,
+  "deg_top50_sum": 6,
+  "deg_top50_sum_covered_genes": 6,
+  "per_type_logfc_r": {
+   "T cell": 0.2212,
+   "B cell": 0.0892,
+   "Monocyte": 0.3996,
+   "NK cell": 0.1241
+  }
+ },
+ "observed_mean_fraction": {
+  "T cell": 0.4467,
+  "B cell": 0.0577,
+  "Monocyte": 0.2738,
+  "NK cell": 0.1703,
+  "DC": 0.0137,
+  "Other": 0.0378
+ },
+ "lora": {
+  "comp_l1": 0.6754540168870949,
+  "coverage": 0.6936111111111111,
+  "logfc_r_mean_cp10k": 0.2725492074488929,
+  "deg_top50_sum": 0,
+  "partial_r_mean_cp10k": 0.2467295164617603
+ },
+ "broadcast": {
+  "logfc_r_mean_cp10k": 0.2254541110690231,
+  "logfc_r_mean_cp10k_covered_genes": 0.20567177326138197,
+  "deg_top50_sum": 0
+ },
+ "other_arms": {
+  "zs_raw": {
+   "comp_l1": 0.7317503238566069,
+   "logfc_r_mean_cp10k": 0.05018496145172948,
+   "deg_top50_sum": 0
+  },
+  "zs_pseudo": {
+   "comp_l1": 0.19051591849007043,
+   "logfc_r_mean_cp10k": 0.21609467450510275,
+   "deg_top50_sum": 4
+  },
+  "zs_cal": {
+   "comp_l1": 0.5272117580098429,
+   "logfc_r_mean_cp10k": 0.07003406425395778,
+   "deg_top50_sum": 0
+  }
+ },
+ "gates": {
+  "observed_composition_equal": true,
+  "broadcast_r_equal": true,
+  "broadcast_deg_equal": true
+ },
+ "n_case": 14,
+ "n_control": 10,
+ "deg_per_type": {
+  "zero_filled": {
+   "bp": {
+    "T cell": 3,
+    "B cell": 0,
+    "Monocyte": 2,
+    "NK cell": 1,
+    "DC": 0
+   },
+   "broadcast": {
+    "T cell": 0,
+    "B cell": 0,
+    "Monocyte": 0,
+    "NK cell": 0,
+    "DC": 0
+   }
+  },
+  "covered": {
+   "bp": {
+    "T cell": 3,
+    "B cell": 0,
+    "Monocyte": 2,
+    "NK cell": 1,
+    "DC": 0
+   },
+   "broadcast": {
+    "T cell": 2,
+    "B cell": 0,
+    "Monocyte": 2,
+    "NK cell": 1,
+    "DC": 0
+   }
+  }
+ },
+ "tool_sha256": "15ed044bbfc39c501c7187ad78586902f2aa0635e7b3a90786b4587cedc2008a",
+ "score_ft_sha256": "ec5f40b4cea6d5062d0138f3b934abb6465e34cbfeac869c8a0906924c033aec",
+ "seconds": 2.1
+}

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/results/ye2026_sepsis/cv_pooled/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,3258,0.14621812356543457,0.2548893770824626,0.009396667407119726,0.5437354402986021
+zero_filled,T cell,pseudobulk_log1p_cpm,3258,0.11272129943477736,0.2164745523777111,-0.016052751503987103,0.5797048718457152
+zero_filled,B cell,mean_cp10k,3310,0.20192412041721622,0.27458639801653467,0.1034231721855883,0.40408849946126896
+zero_filled,B cell,pseudobulk_log1p_cpm,3310,0.24443124582453798,0.2711145517540278,0.14148035654457908,0.4540361326350766
+zero_filled,Monocyte,mean_cp10k,3289,0.6154197331702096,0.5481103923782986,0.4120372197757791,0.6393254398895536
+zero_filled,Monocyte,pseudobulk_log1p_cpm,3289,0.5756577338220463,0.6203629305570988,0.18410858081644843,0.7832147749564643
+zero_filled,NK cell,mean_cp10k,3240,0.12738359866785692,0.1861970975708186,0.007872785615038819,0.6526582623419278
+zero_filled,NK cell,pseudobulk_log1p_cpm,3240,0.0690757009340606,0.05592238177293225,0.04104972883333741,0.7526521745817394
+covered,T cell,mean_cp10k,3231,0.1380446226630489,0.2099926858859594,0.021782043064419585,0.5743597774658593
+covered,T cell,pseudobulk_log1p_cpm,3231,0.10639046181367146,0.21927740538301124,-0.03293645638114524,0.6021849180059466
+covered,B cell,mean_cp10k,3283,0.2075218654152422,0.23488001158604446,0.11626388491613934,0.45508941876108494
+covered,B cell,pseudobulk_log1p_cpm,3283,0.24635776367972756,0.2835207340863022,0.13129448847034997,0.4791318528999642
+covered,Monocyte,mean_cp10k,3262,0.6133463843504408,0.5146912643436613,0.4192349078702948,0.6789509061839138
+covered,Monocyte,pseudobulk_log1p_cpm,3262,0.5801062569586087,0.6323754584533596,0.1502958544114754,0.809162758425067
+covered,NK cell,mean_cp10k,3213,0.11193201660871518,0.12946584899730643,0.032069843794552036,0.6858066053979707
+covered,NK cell,pseudobulk_log1p_cpm,3213,0.06333499053876042,0.06229677023195237,0.023249003126698923,0.786747785811654

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

@@ -0,0 +1,83 @@
+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,0.781336971361543,0.7139532002268754,0.803145846004802,0.7668954613220468,0.3770081360494281,1.6472314175375068e-05,8.660101843392671e-07,0.14094329234721967,0.00581823124062492,0.010080064390285217,0.17030647825289044,0.8183509932929346,0.899220437783316,0.5608368507983116,0.11292972440818168,0.07375672838928889,0.02147182969352175,0.011858481054274042,2.234905625843266e-06,0.003853918150119288,0.0510260976898094,0.0169396685212997,0.10258763075793724
+Abd-PS05,ped_sepsis,0.9531221939449751,0.8931747883274961,0.9453514955195298,0.882568934691639,0.2455944540727902,0.03944854031311104,1.8651739845127912e-06,0.30387059503177355,0.3239005184405296,0.34232606291281314,0.5060658578856152,0.23946256163256097,0.2979139088278025,0.07019064124783363,0.2711626520103426,0.3040557300699,0.0891103408434431,0.01853302989256082,1.789498773643049e-06,0.008954361640670132,0.10749269771089483,0.055700643516726135,0.021808203350664357
+Abd-PS07,ped_sepsis,1.7606376117118432,1.185230387788701,1.7608132717500495,1.1232586955462747,0.2294900153609831,0.275762250358046,7.241333740853553e-06,0.8626152073732719,0.02186232517991001,0.033239152733422546,0.023329493087557603,0.09744050749222047,0.1020085815011479,0.002304147465437788,0.5889340092322334,0.8575687623322154,0.09331797235023041,0.00215081541874456,0.006741940625541284,0.0002880184331797235,0.013850092318845597,0.0004343214739320945,0.018145161290322582
+Abd-PS19,ped_sepsis,1.0543304168630645,0.7329605144346285,1.0500143444845977,0.7987971186054044,0.3432024048096192,0.198214775567862,2.7806301875167625e-06,0.4622995991983968,0.01857130091237951,0.062406307360547295,0.11209919839679358,0.3595295316657478,0.3527582171690699,0.2937124248496994,0.3565248738481596,0.4989424029978344,0.05586172344689379,0.01310659164764984,0.0004808137981738769,0.0156563126252505,0.05405292635820126,0.08540947804418707,0.06037074148296593
+Abd-PS20,ped_sepsis,0.8452022568033045,0.5368348780135274,0.7295635365374668,0.4874603535909559,0.3857322719370483,0.4463935777384813,0.017199137494406897,0.30496843261048584,0.3998782325173455,0.5256922511574124,0.5780949766675817,0.0114032907744635,0.01267766060168134,0.08770244304144935,0.1213520967507363,0.4304243510203731,0.007823222618720834,0.014012417825259514,3.025599253052183e-06,0.0005489980785067252,0.006960384393713976,0.01400357412687332,0.02086192698325556
+Abd-PS23,ped_sepsis,0.9665778721833891,0.6098655986615553,0.7855935453188424,0.4768478112401063,0.608717567881179,0.21838161547705776,2.5502566653559675e-06,0.2529589231840334,0.12182848375256453,0.16225870666330605,0.3272220932931075,0.25645840104507694,0.258138136658447,0.32142028312833604,0.17025892821711233,0.26521782046089815,0.013460199582269667,0.01507879444901288,1.6215946816942101e-06,0.002088651659317707,0.21799377705917547,0.3143811643660017,0.08284984915293572
+Abd-PS27,ped_sepsis,0.9528197441532272,0.1764055492109365,0.9750674879940749,0.2876451183492407,0.6182166118595522,0.6157639142091282,0.15566350267186238,0.6126021003500584,0.000827508390033769,0.044276366924560044,0.06078285774901877,0.1489256054276625,0.1477091305971489,0.13196138750397793,0.07623279417391703,0.46446906266401183,0.010289593720165482,0.005103734370659486,5.408427738506466e-06,0.0029701920016972526,0.15314644342859893,0.18787652871467847,0.1813938686750822
+Abd-S102,adult_sepsis,1.7004395186681023,1.6357362399322153,1.700060385780837,1.6433595124951261,0.3606717129240259,0.038029672266030726,9.992108884968765e-07,0.47981497056349875,0.017104730896541142,0.02351645437045611,0.39318755256518084,0.5413001563808502,0.573547843374896,0.0053616484440706475,0.24857243324969322,0.2122744120964878,0.095878889823381,0.009993225788774552,1.2227448229783873e-06,0.0007359125315391085,0.14499978141811018,0.19065906820244855,0.02502102607232969
+Abd-S103,adult_sepsis,1.0020675970633977,0.849733704900463,1.1058588255829025,0.9359426364448722,0.5684134564363792,0.16310507559143286,1.1967127488061143e-06,0.4813753581661891,0.1944357424657735,0.18737904722457369,0.14782977820227103,0.16696238689825688,0.169013287887142,0.0024408362517245037,0.25052812948652664,0.33884713040501974,0.04393505253104107,0.007358507215295879,1.2558494158053607e-06,0.00021224663058473945,0.2176101583427143,0.3047580819211,0.3242067282181895
+Abd-S120,adult_sepsis,0.9096048027681977,0.714794906561243,0.9105996801784606,0.7670250337557524,0.1132934463081446,0.06938185762198405,1.2865110602189084e-06,0.3140238630468615,0.00045449040037832055,0.007755925005591851,0.11049628220646723,0.5982100091285277,0.5903191725447521,0.46446481065191075,0.296624760423925,0.4019205451111781,0.07297250561992046,0.0005122099680838331,9.63153495633213e-07,0.0008646031471554556,0.03481667245710112,2.107673922236304e-06,0.03717793532768459
+Abd-S123,adult_sepsis,0.49691591256932177,0.5333079390109564,0.5376318156711168,0.5535136023748874,0.40709255437371,2.1191554029125245e-05,8.084613178851144e-07,0.16986823305286552,0.004235958579565839,0.010085551914573058,0.08779171297031275,0.4895270451489885,0.5026867368083109,0.5027782187648833,0.32658747813165495,0.30424093268917474,0.10938244165740593,0.0025341793583644637,8.881091655054793e-07,0.0007937767899666614,0.1770941472273973,0.18298508201745792,0.1293856167645658
+Abd-S156,adult_sepsis,1.147749335324694,1.0315991039945946,0.893803856088446,0.8354260179713614,0.5273359984770607,2.859316479836305e-05,5.183657147273201e-07,0.3343803540833809,7.535085428405612e-06,1.3542735261786945e-06,0.08209594517418618,0.29598327843918826,0.25575265828514115,0.39406053683609366,0.14060781845675172,0.07328277046619933,0.0910908052541405,2.8574183705376003e-06,6.523062949625202e-07,0.0012849800114220445,0.5633699174354628,0.6709620463031236,0.0970873786407767
+Abd-S39,adult_sepsis,0.977377276408388,1.0286304619815296,0.5864659675075742,0.6389514112425194,0.8112340557756543,9.551856116481327e-06,8.958795752489343e-07,0.13819622465625728,9.989596390208347e-06,5.070227858125962e-06,0.06152412025168958,0.3800907483515077,0.4057350667436558,0.6933115823817292,0.16982172216555205,0.15804033729363529,0.049638778839431366,4.681955162513175e-06,5.316946585951605e-07,0.0013982754602656724,0.45006330607527106,0.43621809816061696,0.05593101841062689
+Abd-S42,adult_sepsis,1.3843390526446961,1.18528760699669,1.4119750492740775,1.2000355325541465,0.1889142683112532,0.13538557468905502,2.0256707706332363e-06,0.5748439165524593,0.0033324932706705218,0.018541646247963412,0.09760925841327851,0.2590240181408207,0.26067521071008715,0.17039744175422566,0.5609994156139815,0.660518223028128,0.05862646566164154,0.003319319035456755,0.0001216806535648844,0.0016750418760469012,0.0379391792500153,0.06014121368948575,0.0968478757423481
+Abd-S47,adult_sepsis,1.3087203878032894,0.645930962707097,1.221986557370131,0.5690560989013699,0.1654567808305106,0.4879160337266701,0.0966006792665049,0.7027976414502571,0.12180168160959014,0.16791374095402023,0.20474219044034625,0.06440456016252123,0.07099882801500028,0.03224187680341237,0.30987192357466803,0.6346723682702852,0.019069125580228326,7.722851182088691e-06,1.6112268646306107e-06,0.0006272738677706687,0.015998078075368457,0.02981277226732478,0.040521891857985194
+Abd-S51,adult_sepsis,0.9304043541903309,0.8197738969637182,0.9598998065306702,0.8514196968787264,0.3662083029861617,0.05478909339962377,1.385377991043273e-06,0.25273124544792425,0.09595811345762911,0.08282111239124398,0.269482884195193,0.4837546989821654,0.49791748405741626,0.3551347414420976,0.3179749297618933,0.3579421821195536,0.03670793882010197,0.000530936469347346,0.0026418554192881283,0.0014566642388929353,0.0469922279293411,0.058675980634506957,0.08448652585579024
+Abd-S54,adult_sepsis,1.148088817691588,1.0318947506821614,1.132319342519902,1.0147511840259154,0.5083407521105142,0.06992699415396479,1.2579664586269125e-06,0.4854182655410591,0.036023814183644844,0.04785251686643759,0.1364799181376311,0.22684610164647664,0.22453506178061572,0.012918905090816066,0.6128211349137092,0.6550179856242399,0.340752110514198,0.00896857926872212,0.00579060287514267,0.0011511895625479663,0.04541337583348252,0.0668025748871055,0.023279611153747763
+Abd-S57,adult_sepsis,1.705119213662466,1.5194316001097439,1.7143957271983943,1.5276092054527743,0.7179777482331537,0.09283785026111266,2.7329059560336498e-06,0.8422783570079071,3.681600217338325e-06,9.657940064004331e-07,0.009026660135749773,0.4337726896067681,0.5029305910874838,0.016164019312854244,0.38923229934262643,0.4647869413632337,0.10671051710866979,7.219199885308151e-06,1.245584891742881e-06,0.0012595339724302008,0.08414625998939022,0.032277523264428426,0.024560912462388916
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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/cv_pooled/summary.json

@@ -0,0 +1,193 @@
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