Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261004T051658Z-behcet-c1q-lora3/diffusion/dataset/server_1/model8/plans/behcet_c1q_lora3_20261004/out/capability.csv

@@ -0,0 +1,9 @@
+arm,monocytes,pooled_rule_A_pct,pooled_rule_B_pct,pooled_rule_C_pct,pooled_rule_D_pct
+zs_raw_s13,19084,2.614755816390694,0.15719974848040244,0.6497589603856634,2.614755816390694
+zs_cal_s13,9555,3.9141810570382,0.32443746729461015,1.0570381998953426,3.9141810570382
+lora3_raw_s13,10722,4.299570975564261,0.2518186905428092,1.2497668345457937,4.299570975564261
+lora3_raw_s04,10769,4.308663757080509,0.35286470424366234,1.337171510818089,4.308663757080509
+zs_raw_s04,19082,2.5521433811969394,0.1467351430667645,0.6288648988575621,2.5521433811969394
+obs,6366,7.084511467169337,2.5290606346214264,4.586867734841345,5.450832547910776
+obs_thin_zs,6366,4.586867734841345,1.5708451146716933,2.591894439208294,4.586867734841345
+obs_thin_lora3,6366,6.880301602262017,2.419101476594408,4.335532516493874,5.419415645617343

paper-releases/pbisc-diffusion/updates/20261004T051658Z-behcet-c1q-lora3/diffusion/dataset/server_1/model8/plans/behcet_c1q_lora3_20261004/out/group_table.csv

@@ -0,0 +1,66 @@
+arm,rows,metric,n_bd,n_hc,bd_mean_pct,hc_mean_pct,gap_pp,mw_p
+zs_raw_s13,test,c1q_high_rule_A,6,10,2.1583367449262187,3.098138271517645,-0.9398015265914262,0.02247752247752248
+zs_raw_s13,test,c1q_high_rule_B,6,10,0.11096827206163999,0.19972870085722103,-0.08876042879558102,0.23247961915905757
+zs_raw_s13,test,c1q_high_rule_C,6,10,0.5085057019751333,0.7967087427307371,-0.2882030407556037,0.031218781218781223
+zs_raw_s13,test,c1q_high_rule_D,6,10,2.1583367449262187,3.098138271517645,-0.9398015265914262,0.02247752247752248
+zs_raw_s13,test,monocyte_fraction,6,10,30.186666666666667,20.056,10.130666666666666,0.02247752247752248
+zs_raw_s13,all,c1q_high_rule_A,9,10,2.11981803293684,3.098138271517645,-0.9783202385808046,0.01011233392133346
+zs_raw_s13,all,c1q_high_rule_B,9,10,0.09914488424813779,0.19972870085722103,-0.10058381660908322,0.13023503453970625
+zs_raw_s13,all,c1q_high_rule_C,9,10,0.5071710628182634,0.7967087427307371,-0.28953767991247376,0.012763007532641236
+zs_raw_s13,all,c1q_high_rule_D,9,10,2.11981803293684,3.098138271517645,-0.9783202385808046,0.01011233392133346
+zs_raw_s13,all,monocyte_fraction,9,10,32.5,20.056,12.443999999999999,0.00623303496973378
+zs_cal_s13,test,c1q_high_rule_A,6,10,4.54017217468885,3.4256958893505733,1.114476285338277,0.1805694305694306
+zs_cal_s13,test,c1q_high_rule_B,6,10,0.34788103912348,0.307816748287003,0.04006429083647698,0.7856495874541742
+zs_cal_s13,test,c1q_high_rule_C,6,10,1.2722542509892867,0.8922818316454171,0.37997241934386966,0.2197802197802198
+zs_cal_s13,test,c1q_high_rule_D,6,10,4.54017217468885,3.4256958893505733,1.114476285338277,0.1805694305694306
+zs_cal_s13,test,monocyte_fraction,6,10,13.486666666666666,11.018,2.468666666666665,0.26348651348651353
+zs_cal_s13,all,c1q_high_rule_A,9,10,4.291634490905478,3.4256958893505733,0.8659386015549053,0.23644471557230384
+zs_cal_s13,all,c1q_high_rule_B,9,10,0.3286121127031889,0.307816748287003,0.020795364416185916,0.7746663677213794
+zs_cal_s13,all,c1q_high_rule_C,9,10,1.1915308309221655,0.8922818316454171,0.29924899927674836,0.2056671796173556
+zs_cal_s13,all,c1q_high_rule_D,9,10,4.291634490905478,3.4256958893505733,0.8659386015549053,0.23644471557230384
+zs_cal_s13,all,monocyte_fraction,9,10,15.228888888888886,11.018,4.210888888888885,0.06619257972219345
+lora3_raw_s13,test,c1q_high_rule_A,6,10,4.859228750378392,3.9485935457313555,0.9106352046470367,0.26348651348651353
+lora3_raw_s13,test,c1q_high_rule_B,6,10,0.25416353448912,0.241449368802294,0.012714165686825976,0.8703779032953791
+lora3_raw_s13,test,c1q_high_rule_C,6,10,1.4004479223181452,1.120864498814039,0.27958342350410603,0.26348651348651353
+lora3_raw_s13,test,c1q_high_rule_D,6,10,4.859228750378392,3.9485935457313555,0.9106352046470367,0.26348651348651353
+lora3_raw_s13,test,monocyte_fraction,6,10,15.966666666666665,11.863999999999999,4.102666666666666,0.04195804195804197
+lora3_raw_s13,all,c1q_high_rule_A,9,10,4.768353873873404,3.9485935457313555,0.8197603281420489,0.13091112789629078
+lora3_raw_s13,all,c1q_high_rule_B,9,10,0.4191202185181144,0.241449368802294,0.17767084971582037,0.306584044004804
+lora3_raw_s13,all,c1q_high_rule_C,9,10,1.5337043527255467,1.120864498814039,0.41283985391150774,0.09416637543787974
+lora3_raw_s13,all,c1q_high_rule_D,9,10,4.768353873873404,3.9485935457313555,0.8197603281420489,0.13091112789629078
+lora3_raw_s13,all,monocyte_fraction,9,10,16.546666666666667,11.863999999999999,4.682666666666665,0.01011233392133346
+lora3_raw_s04,test,c1q_high_rule_A,6,10,5.2750592287064935,3.55366247827943,1.7213967504270635,0.02247752247752248
+lora3_raw_s04,test,c1q_high_rule_B,6,10,0.3722319033847383,0.35227109606455903,0.019960807320179314,1.0
+lora3_raw_s04,test,c1q_high_rule_C,6,10,1.5545744091570335,1.188600074415685,0.36597433474134833,0.3676323676323677
+lora3_raw_s04,test,c1q_high_rule_D,6,10,5.2750592287064935,3.55366247827943,1.7213967504270635,0.02247752247752248
+lora3_raw_s04,test,monocyte_fraction,6,10,16.040000000000003,11.914,4.126000000000002,0.03917382222370137
+lora3_raw_s04,all,c1q_high_rule_A,9,10,5.089161080380587,3.55366247827943,1.5354986021011576,0.016010990810517163
+lora3_raw_s04,all,c1q_high_rule_B,9,10,0.4455314589700866,0.35227109606455903,0.09326036290552764,0.7750513736700824
+lora3_raw_s04,all,c1q_high_rule_C,9,10,1.5730629489788812,1.188600074415685,0.38446287456319617,0.2703441406547801
+lora3_raw_s04,all,c1q_high_rule_D,9,10,5.089161080380587,3.55366247827943,1.5354986021011576,0.016010990810517163
+lora3_raw_s04,all,monocyte_fraction,9,10,16.6,11.914,4.686000000000002,0.008950586032810934
+zs_raw_s04,test,c1q_high_rule_A,6,10,2.22611526081981,2.8575604376177632,-0.6314451767979533,0.07267732267732269
+zs_raw_s04,test,c1q_high_rule_B,6,10,0.12812021282642833,0.146329097460807,-0.01820888463437867,0.6202940153491607
+zs_raw_s04,test,c1q_high_rule_C,6,10,0.47548495154854664,0.8237119708028681,-0.3482270192543214,0.015984015984015984
+zs_raw_s04,test,c1q_high_rule_D,6,10,2.22611526081981,2.8575604376177632,-0.6314451767979533,0.07267732267732269
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+zs_raw_s04,all,c1q_high_rule_A,9,10,2.126700830012279,2.8575604376177632,-0.7308596076054843,0.030486156935263357
+zs_raw_s04,all,c1q_high_rule_B,9,10,0.10500066622084114,0.146329097460807,-0.04132843123996585,0.43077837697278887
+zs_raw_s04,all,c1q_high_rule_C,9,10,0.4346403584955378,0.8237119708028681,-0.38907161230733023,0.0048487627216789375
+zs_raw_s04,all,c1q_high_rule_D,9,10,2.126700830012279,2.8575604376177632,-0.7308596076054843,0.030486156935263357
+zs_raw_s04,all,monocyte_fraction,9,10,32.50222222222223,20.023999999999997,12.478222222222229,0.00623303496973378
+obs,observed,c1q_high_rule_A,4,4,8.157227537984548,6.833102241576405,1.3241252964081434,0.4857142857142857
+obs,observed,c1q_high_rule_B,4,4,3.029535456022078,2.4456667729132326,0.5838686831088454,0.6857142857142857
+obs,observed,c1q_high_rule_C,4,4,5.431177714654443,4.384459521285133,1.0467181933693102,0.4857142857142857
+obs,observed,c1q_high_rule_D,4,4,6.3212287861446255,5.124211510971602,1.1970172751730235,0.4857142857142857
+obs,observed,monocyte_fraction,4,4,16.674509355178884,13.038897430373867,3.6356119248050183,0.34285714285714286
+obs_thin_zs,observed,c1q_high_rule_A,4,4,5.5272323382678605,4.17756458393819,1.3496677543296705,0.4857142857142857
+obs_thin_zs,observed,c1q_high_rule_B,4,4,2.0190564976998946,1.5231213667557075,0.49593513094418723,0.6857142857142857
+obs_thin_zs,observed,c1q_high_rule_C,4,4,3.130315737915245,2.49013468157716,0.640181056338085,0.6857142857142857
+obs_thin_zs,observed,c1q_high_rule_D,4,4,5.5272323382678605,4.17756458393819,1.3496677543296705,0.4857142857142857
+obs_thin_zs,observed,monocyte_fraction,4,4,16.674509355178884,13.038897430373867,3.6356119248050183,0.34285714285714286
+obs_thin_lora3,observed,c1q_high_rule_A,4,4,7.964010680166572,6.703678440547491,1.2603322396190817,0.4857142857142857
+obs_thin_lora3,observed,c1q_high_rule_B,4,4,2.883235909340543,2.407381933709557,0.4758539756309854,0.6857142857142857
+obs_thin_lora3,observed,c1q_high_rule_C,4,4,5.145956492996743,4.0812599211230225,1.0646965718737202,0.4857142857142857
+obs_thin_lora3,observed,c1q_high_rule_D,4,4,6.244606182993715,5.134259241250175,1.110346941743541,0.4857142857142857
+obs_thin_lora3,observed,monocyte_fraction,4,4,16.674509355178884,13.038897430373867,3.6356119248050183,0.34285714285714286

paper-releases/pbisc-diffusion/updates/20261004T051658Z-behcet-c1q-lora3/diffusion/dataset/server_1/model8/plans/behcet_c1q_lora3_20261004/work/scanvi_labels_zs_raw_s13_f01common/labels.manifest.json

@@ -0,0 +1,168 @@
+{
+  "dataset_id": "GSE198533",
+  "split": "",
+  "input_h5ad": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/behcet_c1q_lora3_20261004/work/zs_raw_s13_poisson.h5ad",
+  "method": "generated_GSE198533_all19_lora3study_zs_raw_s13",
+  "out_parquet": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/behcet_c1q_lora3_20261004/work/scanvi_labels_zs_raw_s13_f01common/labels.parquet",
+  "training_source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/reference/aifi_reference_f01common.h5ad",
+  "target_truth_used_for_fitting": false,
+  "classifier": "aifi_scanvi_rebuild_20260916_frozen_predict[aifi_scanvi_f01common_v1]",
+  "labels": [
+    "T cell",
+    "B cell",
+    "Monocyte",
+    "NK cell",
+    "DC",
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+  ],
+  "l2_labels": [
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+    "CD16 monocyte",
+    "CD56bright NK cell",
+    "CD56dim NK cell",
+    "CD8aa",
+    "DN T cell",
+    "Effector B cell",
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+    "ILC",
+    "Intermediate monocyte",
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+    "Memory B cell",
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+    "Naive B cell",
+    "Naive CD4 T cell",
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+    "Plasma cell",
+    "Platelet",
+    "Progenitor cell",
+    "Proliferating NK cell",
+    "Proliferating T cell",
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+    "cDC2",
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+  ],
+  "n_cells": 95000,
+  "n_genes": 1005,
+  "note": "Evaluation-only annotation with a frozen AIFI scANVI (zero query-training epochs); L1 outside PBMC5 -> Other, never dropped.",
+  "label_source_column": "AIFI_L2 (reference) -> AIFI_L2_TO_L1 -> PBMC5 + Other",
+  "query_train_epochs": 0,
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+  "evaluator_aligned": true,
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+    "library_size_handling": "no rescaling (library_scale=1.0): E[library] = generated library",
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+  "model": {
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+    "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
+    "model_manifest": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/runs/aifi_scanvi_f01common_v1/MODEL_MANIFEST.json",
+    "held_out_summary": {
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+  "label_counts": {
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+      "Plasma cell": 166,
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+  },
+  "confidence": {
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+    "mean_l1_mass": 0.9791163802146912,
+    "frac_l2_max_prob_ge_0.5": 0.9708842105263158
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+  "timings_s": {
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+  "versions": {
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+    "torch": "2.11.0+cu130",
+    "anndata": "0.12.19"
+  },
+  "device": "cpu",
+  "created_at_utc": "2026-10-04T04:29:56.679601+00:00"
+}