Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261004T003810Z-behcet-pair-recovery/diffusion/dataset/server_1/model8/plans/behcet_pair_recovery_20261004/out/_v1_resid_test/SUMMARY.json

@@ -0,0 +1,233 @@
+{
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+  "chosen_on": "ye2026_sepsis: highest sensitivity at <= 1 % wrong calls per sc column",
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+  "seed": 20261004,
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+    "draws": 20
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+ },
+ "behcet_primary_calls": [
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+  {
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+  {
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+  {
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+   "sc_sample": "PBMC_HC_2",
+   "best_bulk": "HC6",
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+  {
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+   "best_bulk": "HC7",
+   "second_bulk": "BDU2",
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+   "margin": 1.1187991636927501,
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+  {
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+   "best_bulk": "HC9",
+   "second_bulk": "BDV5",
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+   "mutual": true,
+   "margin": 0.6949967027077588,
+   "threshold": 1.3144402334737855,
+   "called": false
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+ ],
+ "behcet_onoff_calls": [
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+   "method": "onoff",
+   "sc_sample": "PBMC_BD_1",
+   "best_bulk": "HC4",
+   "second_bulk": "BDV6",
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+   "mutual": true,
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+  {
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+   "sc_sample": "PBMC_BD_2",
+   "best_bulk": "BDV4",
+   "second_bulk": "HC6",
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+   "threshold": 1.4397104875288682,
+   "called": false
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+  {
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+   "sc_sample": "PBMC_BD_3",
+   "best_bulk": "BDV5",
+   "second_bulk": "HC2",
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+   "mutual": true,
+   "margin": 1.3904826887702346,
+   "threshold": 1.4397104875288682,
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+  {
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+   "sc_sample": "PBMC_BD_4",
+   "best_bulk": "HC2",
+   "second_bulk": "BDV2",
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+   "mutual": true,
+   "margin": 0.11944486473893678,
+   "threshold": 1.4397104875288682,
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+  {
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+   "sc_sample": "PBMC_HC_1",
+   "best_bulk": "HC4",
+   "second_bulk": "BDU3",
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+   "margin": 0.12604053671530835,
+   "threshold": 1.4397104875288682,
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+  {
+   "method": "onoff",
+   "sc_sample": "PBMC_HC_2",
+   "best_bulk": "BDU1",
+   "second_bulk": "BDV2",
+   "r_best": 0.6618050926438086,
+   "mutual": true,
+   "margin": 0.40084745881206585,
+   "threshold": 1.4397104875288682,
+   "called": false
+  },
+  {
+   "method": "onoff",
+   "sc_sample": "PBMC_HC_3",
+   "best_bulk": "BDU2",
+   "second_bulk": "BDV1",
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+   "mutual": true,
+   "margin": 1.3383005938892598,
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+  {
+   "method": "onoff",
+   "sc_sample": "PBMC_HC_4",
+   "best_bulk": "HC4",
+   "second_bulk": "HC6",
+   "r_best": 0.49070474805989817,
+   "mutual": false,
+   "margin": 0.48826373619518115,
+   "threshold": 1.4397104875288682,
+   "called": false
+  }
+ ],
+ "inputs": {
+  "bulk": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/strict_qc_v1_20260913/bulk/GSE198533_count/harmonized.h5ad",
+  "sc": {
+   "PBMC_BD_1": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/strict_qc_v1_20260913/singlecell/GSE198616/GSM5953767",
+   "PBMC_BD_2": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/strict_qc_v1_20260913/singlecell/GSE198616/GSM5953768",
+   "PBMC_BD_3": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/strict_qc_v1_20260913/singlecell/GSE198616/GSM5953769",
+   "PBMC_BD_4": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/strict_qc_v1_20260913/singlecell/GSE198616/GSM5953770",
+   "PBMC_HC_1": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/strict_qc_v1_20260913/singlecell/GSE198616/GSM5953771",
+   "PBMC_HC_2": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/strict_qc_v1_20260913/singlecell/GSE198616/GSM5953772",
+   "PBMC_HC_3": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/strict_qc_v1_20260913/singlecell/GSE198616/GSM5953773",
+   "PBMC_HC_4": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/strict_qc_v1_20260913/singlecell/GSE198616/GSM5953774"
+  },
+  "controls": {
+   "ye2026_sepsis": {
+    "bulk": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/ye2026_sepsis_v1_20260927/bulk/GSE279448_htseq_counts/harmonized.h5ad",
+    "pairs": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/pairs.csv"
+   },
+   "liu2021": {
+    "bulk": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/liu2021_v1_20261002/bulk/GSE161918_htseq/harmonized.h5ad",
+    "pairs": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/liu2021/pairs.csv"
+   }
+  }
+ },
+ "code_sha256": "c3d2ea2a52df6f96c7bc4a0d4f6c0989342d7dd546885d4b1ac55c673e6cb999",
+ "ages_used": false
+}

paper-releases/pbisc-diffusion/updates/20261004T003810Z-behcet-pair-recovery/diffusion/dataset/server_1/model8/plans/behcet_pair_recovery_20261004/out/_v1_resid_test/behcet_calls.csv

@@ -0,0 +1,41 @@
+method,sc_sample,best_bulk,second_bulk,r_best,mutual,margin,threshold,called
+resid_k0,PBMC_BD_1,BDU3,HC2,0.2589300804905917,False,1.651721513838036,0.7393212842494536,False
+resid_k0,PBMC_BD_2,BDV4,BDV2,0.6444054487984058,True,2.1556559066275343,0.7393212842494536,True
+resid_k0,PBMC_BD_3,BDV5,BDV1,0.799918410506915,True,0.49132366674993966,0.7393212842494536,False
+resid_k0,PBMC_BD_4,BDV6,BDV5,0.6268556302115156,True,1.1794514112439891,0.7393212842494536,True
+resid_k0,PBMC_HC_1,HC6,HC5,0.5218556080721793,False,0.11422393267676267,0.7393212842494536,False
+resid_k0,PBMC_HC_2,HC1,BDU1,0.2381384613321125,True,0.08355381265965356,0.7393212842494536,False
+resid_k0,PBMC_HC_3,HC4,BDV3,0.3596814931521641,True,0.09747763129022102,0.7393212842494536,False
+resid_k0,PBMC_HC_4,HC9,HC6,0.536706357516446,True,0.008969153559349685,0.7393212842494536,False
+resid_k1,PBMC_BD_1,BDU3,HC6,0.2955857756961087,True,0.9722459728597672,1.8082082324686677,False
+resid_k1,PBMC_BD_2,BDV4,BDV2,0.6339655431792518,True,1.368982961609363,1.8082082324686677,False
+resid_k1,PBMC_BD_3,BDV5,HC5,0.5538577728887177,True,0.7049844997685966,1.8082082324686677,False
+resid_k1,PBMC_BD_4,BDV6,BDV5,0.6372337384057893,True,1.2009654567190815,1.8082082324686677,False
+resid_k1,PBMC_HC_1,BDV5,BDV6,0.49145318556851036,False,1.2383922780443894,1.8082082324686677,False
+resid_k1,PBMC_HC_2,BDU2,BDV3,0.2760173358191399,False,0.07930878341597469,1.8082082324686677,False
+resid_k1,PBMC_HC_3,HC4,BDV3,0.37557784485209994,True,0.2782695524338725,1.8082082324686677,False
+resid_k1,PBMC_HC_4,HC9,BDU2,0.34851814267790016,True,0.38908535862658655,1.8082082324686677,False
+resid_k2,PBMC_BD_1,BDU3,BDV6,0.21584006042983092,False,0.3173233674783493,1.4773404910375751,False
+resid_k2,PBMC_BD_2,BDV4,BDV2,0.5672191490933115,True,1.4788126850070957,1.4773404910375751,True
+resid_k2,PBMC_BD_3,BDV5,HC5,0.5178903124003389,True,0.990972444289806,1.4773404910375751,False
+resid_k2,PBMC_BD_4,BDV6,HC8,0.5136794366336648,True,1.543620933957427,1.4773404910375751,True
+resid_k2,PBMC_HC_1,BDU3,HC6,0.3138262450504051,True,0.2637318092917116,1.4773404910375751,False
+resid_k2,PBMC_HC_2,HC1,BDU1,0.1850806347132661,False,0.23017387325484373,1.4773404910375751,False
+resid_k2,PBMC_HC_3,HC4,BDV3,0.3445958320844305,True,0.29966496035452184,1.4773404910375751,False
+resid_k2,PBMC_HC_4,HC9,BDV5,0.3621425110139769,True,0.4866987434645522,1.4773404910375751,False
+resid_k3,PBMC_BD_1,HC7,HC1,0.2611566713185011,True,1.4110225742794253,1.3144402334737855,True
+resid_k3,PBMC_BD_2,BDV4,BDV2,0.586818587068594,True,1.6703591679839322,1.3144402334737855,True
+resid_k3,PBMC_BD_3,BDV5,HC5,0.5034295126363176,True,0.9549963776669632,1.3144402334737855,False
+resid_k3,PBMC_BD_4,BDV6,HC8,0.48397716033689664,True,1.2727787146831786,1.3144402334737855,False
+resid_k3,PBMC_HC_1,BDV5,BDU3,0.2796692915398297,False,0.09434551369735411,1.3144402334737855,False
+resid_k3,PBMC_HC_2,HC6,BDU1,0.1729453842122527,True,0.03389872544927308,1.3144402334737855,False
+resid_k3,PBMC_HC_3,HC7,BDU2,0.24013555239325435,False,1.1187991636927501,1.3144402334737855,False
+resid_k3,PBMC_HC_4,HC9,BDV5,0.32802823299946754,True,0.6949967027077588,1.3144402334737855,False
+onoff,PBMC_BD_1,HC4,BDV6,0.6695854049677601,True,0.21666733298029373,1.4397104875288682,False
+onoff,PBMC_BD_2,BDV4,HC6,0.7993027081256191,True,0.476703925140767,1.4397104875288682,False
+onoff,PBMC_BD_3,BDV5,HC2,0.6583120080796163,True,1.3904826887702346,1.4397104875288682,False
+onoff,PBMC_BD_4,HC2,BDV2,0.5471644929801652,True,0.11944486473893678,1.4397104875288682,False
+onoff,PBMC_HC_1,HC4,BDU3,0.5438423161949414,False,0.12604053671530835,1.4397104875288682,False
+onoff,PBMC_HC_2,BDU1,BDV2,0.6618050926438086,True,0.40084745881206585,1.4397104875288682,False
+onoff,PBMC_HC_3,BDU2,BDV1,0.6432479109969809,True,1.3383005938892598,1.4397104875288682,False
+onoff,PBMC_HC_4,HC4,HC6,0.49070474805989817,False,0.48826373619518115,1.4397104875288682,False

paper-releases/pbisc-diffusion/updates/20261004T003810Z-behcet-pair-recovery/diffusion/dataset/server_1/model8/plans/behcet_pair_recovery_20261004/out/_v1_resid_test/behcet_onoff_scores.csv

@@ -0,0 +1,20 @@
+,PBMC_BD_1,PBMC_BD_2,PBMC_BD_3,PBMC_BD_4,PBMC_HC_1,PBMC_HC_2,PBMC_HC_3,PBMC_HC_4
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paper-releases/pbisc-diffusion/updates/20261004T003810Z-behcet-pair-recovery/diffusion/dataset/server_1/model8/plans/behcet_pair_recovery_20261004/out/_v1_resid_test/behcet_scores_k0.csv

@@ -0,0 +1,20 @@
+,PBMC_BD_1,PBMC_BD_2,PBMC_BD_3,PBMC_BD_4,PBMC_HC_1,PBMC_HC_2,PBMC_HC_3,PBMC_HC_4
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