Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261001T200638Z-extra-realism-metrics/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores_extra/ye2026_sepsis/pooled/manifest.json

@@ -0,0 +1,156 @@
+{
+ "schema": "paired_ft_extra_metrics.v1",
+ "dataset": "ye2026_sepsis",
+ "design": "pooled",
+ "unit": "pooled",
+ "written_utc": "2026-10-01T18:53:35.232053+00:00",
+ "command": [
+  "tools/extra_metrics.py",
+  "--design",
+  "pooled",
+  "--dataset",
+  "ye2026_sepsis",
+  "--threads",
+  "8",
+  "--fetch-dir",
+  "/tmp/claude-1000/-home-sj-server-1/c8102cb0-e04f-4e04-adda-0728604e4435/scratchpad/fetch"
+ ],
+ "threads": 8,
+ "donors": [
+  "Abd-PS04",
+  "Abd-PS05",
+  "Abd-PS07",
+  "Abd-PS19",
+  "Abd-PS20",
+  "Abd-PS23",
+  "Abd-PS27",
+  "Abd-S102",
+  "Abd-S103",
+  "Abd-S120",
+  "Abd-S123",
+  "Abd-S156",
+  "Abd-S39",
+  "Abd-S42",
+  "Abd-S47",
+  "Abd-S51",
+  "Abd-S54",
+  "Abd-S57",
+  "Abd-S66",
+  "Abd-S79",
+  "Abd-S83",
+  "Abd-S98",
+  "HC01",
+  "HC05",
+  "HC07",
+  "HC09",
+  "HC12",
+  "HC13",
+  "HC16",
+  "IC10",
+  "IC15",
+  "IC16",
+  "IC19",
+  "IC22",
+  "IC23",
+  "PHC01",
+  "PHC02",
+  "PHC03",
+  "PHC05",
+  "PIC01",
+  "PIC02",
+  "PIC04",
+  "PIC05",
+  "Res-PS02",
+  "Res-PS03",
+  "Res-PS12",
+  "Res-PS16",
+  "Res-PS21",
+  "Res-PS22",
+  "Res-PS25",
+  "Res-PS26",
+  "Res-S10",
+  "Res-S125",
+  "Res-S127",
+  "Res-S136",
+  "Res-S139",
+  "Res-S146",
+  "Res-S149",
+  "Res-S150",
+  "Res-S164",
+  "Res-S166",
+  "Res-S174",
+  "Res-S177",
+  "Res-S184",
+  "Res-S19",
+  "Res-S26",
+  "Res-S40",
+  "Res-S77",
+  "Res-S87",
+  "Skin-S140",
+  "Skin-S142",
+  "Skin-S152",
+  "Skin-S38",
+  "Skin-S43",
+  "Skin-S46",
+  "Skin-S52",
+  "Skin-S74",
+  "Uri-S134",
+  "Uri-S147",
+  "Uri-S157",
+  "Uri-S20",
+  "Uri-S93"
+ ],
+ "n_samples": 82,
+ "calls": {
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled": {
+   "arms": [
+    "zs__raw",
+    "zs__cal",
+    "pseudo_full__cal",
+    "real_lora__raw",
+    "zs__pseudo"
+   ],
+   "summary_sha256": "8b3a62e4a2784d93a5986fd3a1d938d4bc660fa482c9fc30d1c7a3bf71610270"
+  }
+ },
+ "reference_sha256": "bac12da8a241652cb75100a1b082b2be56806c9bf2fd20ce6f927f19683ea5b8",
+ "bandwidth_m": 27.935913545117483,
+ "params": {
+  "seed": 20261001,
+  "ks": [
+   3,
+   5,
+   10
+  ],
+  "knn_c2st_k": 5,
+  "rf_trees": 300,
+  "cv_folds": 5,
+  "bw_multiples": [
+   0.5,
+   1.0,
+   2.0
+  ],
+  "bw_max_cells": 4000,
+  "en_pcs": 100,
+  "en_lb_max_queries_all_cells": 20000,
+  "en_all_cells": true
+ },
+ "n_representative_rows": null,
+ "fetched_from_server2": [
+  "/tmp/claude-1000/-home-sj-server-1/c8102cb0-e04f-4e04-adda-0728604e4435/scratchpad/fetch/generated/ye2026_sepsis/pooled/zs__raw.npz",
+  "/tmp/claude-1000/-home-sj-server-1/c8102cb0-e04f-4e04-adda-0728604e4435/scratchpad/fetch/generated/ye2026_sepsis/pooled/zs__cal.npz",
+  "/tmp/claude-1000/-home-sj-server-1/c8102cb0-e04f-4e04-adda-0728604e4435/scratchpad/fetch/generated/ye2026_sepsis/pooled/pseudo_full__cal.npz",
+  "/tmp/claude-1000/-home-sj-server-1/c8102cb0-e04f-4e04-adda-0728604e4435/scratchpad/fetch/generated/ye2026_sepsis/pooled/real_lora__raw.npz",
+  "/tmp/claude-1000/-home-sj-server-1/c8102cb0-e04f-4e04-adda-0728604e4435/scratchpad/fetch/generated/ye2026_sepsis/pooled/zs__pseudo.npz"
+ ],
+ "code_sha256": {
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/extra_metrics.py": "4e69c029476c108d843265cbc4a9098eab9c7998cb74ae715ce8251287457fef",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/ft_common.py": "4a6366b0f22208cd58714fc0261b8840c643b9d4569704d560cfd93534cbc747",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py": "ec5f40b4cea6d5062d0138f3b934abb6465e34cbfeac869c8a0906924c033aec",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tools/stage_b_embed.py": "d056cfdf38fb0e5f478756f370174e993b75d0c973c48e02e21749175a4ca2da"
+ },
+ "seconds": 1372.7,
+ "max_abs_diff_k10_pooled": 0.0,
+ "extra_metrics_py_sha256_ran": "4e69c029476c108d843265cbc4a9098eab9c7998cb74ae715ce8251287457fef",
+ "code_sha256_note": "code_sha256 was hashed when the unit finished; extra_metrics_py_sha256_ran is the file the process loaded at start (scores_extra/_code/). v1-v3 differ only in the collector and the per-unit lock; metric code identical (scores_extra/_code/README.md)"
+}

paper-releases/pbisc-diffusion/updates/20261001T200638Z-extra-realism-metrics/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores_extra/ye2026_sepsis/pooled/metrics.csv

@@ -0,0 +1,25 @@
+dataset,design,unit,label,set,real_side,mode,n_real,n_gen,precision_k3,coverage_k3,density_k3,expected_coverage_identical_k3,precision_k5,coverage_k5,density_k5,expected_coverage_identical_k5,precision_k10,coverage_k10,density_k10,expected_coverage_identical_k10,c2st_knn_auc,c2st_knn_auc_sd,c2st_rf_auc,c2st_rf_auc_sd,nn1_acc,nn1_acc_real,nn1_acc_gen,mmd2_bw0.5,mmd2_bw1,mmd2_bw2,mmd2_sum,mmd_bandwidth_m,seconds
+ye2026_sepsis,pooled,pooled,Real vs real control (held-out real cells),real_R2,R1,raw,12300,12300,0.8677235772357723,0.921869918699187,1.3163685636856368,0.8750304884244985,0.9363414634146342,0.9869105691056911,1.307512195121951,0.9687690533285568,0.9804878048780488,0.9996747967479674,1.2890731707317074,0.9990256193628076,0.516801622711349,0.003074079657606663,0.5870507799590191,0.004627534384289754,0.5077642276422765,0.4292682926829268,0.5862601626016261,9.044037879168965e-05,1.3528004798146753e-05,-3.3190731532073414e-06,0.00010064931043662906,27.935913545117483,30.8
+ye2026_sepsis,pooled,pooled,Real vs real control (held-out real cells),real_R2,R1,dm,12300,12300,0.8682113821138211,0.9211382113821138,1.314769647696477,0.8750304884244985,0.9326829268292683,0.9854471544715447,1.3033333333333332,0.9687690533285568,0.9795934959349594,0.9998373983739838,1.2835853658536585,0.9990256193628076,0.5142142078128098,0.002669220794344279,0.5813873190561175,0.0031473781664726635,0.5026422764227643,0.4234959349593496,0.5817886178861789,8.717573012606561e-05,1.3038222914429909e-05,-3.5702007259441615e-06,9.664375231455136e-05,27.935913545117483,28.1
+ye2026_sepsis,pooled,pooled,Real vs real control (out-of-sample: R2 vs R3),real_R3,R2,raw,12300,12300,,,,,,,,,,,,,0.5056783991010642,0.006911061467746967,0.49727049044880695,0.009466027829220682,0.5030081300813009,0.49617886178861786,0.5098373983739838,-6.113976974936319e-05,-3.927775354117813e-05,-1.351023669760032e-05,-0.00011392775998814164,27.935913545117483,28.1
+ye2026_sepsis,pooled,pooled,Real vs real control (out-of-sample: R2 vs R3),real_R3,R2,dm,12300,12300,,,,,,,,,,,,,0.5031293542203714,0.003951913349245326,0.5015891665014212,0.008859520556147586,0.5016260162601626,0.4948780487804878,0.5083739837398374,-6.272248920557999e-05,-3.9454149749929e-05,-1.3297239933596217e-05,-0.00011547387888910521,27.935913545117483,24.8
+ye2026_sepsis,pooled,pooled,"Zero-shot, real bulk",zs__raw,R1,raw,12300,12300,0.30861788617886177,0.0316260162601626,0.16739837398373983,0.8750304884244985,0.42869918699186993,0.043577235772357725,0.18678048780487805,0.9687690533285568,0.6141463414634146,0.06731707317073171,0.21879674796747967,0.9990256193628076,0.9974525580011898,0.0004948992689147566,0.9991371207614514,0.00024031609689542267,0.9902032520325204,0.9852032520325203,0.9952032520325204,0.15271446917149023,0.18969222967315413,0.07990491859801785,0.4223116174426622,27.935913545117483,21.2
+ye2026_sepsis,pooled,pooled,"Zero-shot, real bulk",zs__raw,R1,dm,12300,12300,0.2784552845528455,0.028943089430894308,0.14934959349593493,0.8750304884244985,0.41292682926829266,0.04178861788617886,0.17078048780487803,0.9687690533285568,0.5923577235772358,0.06455284552845529,0.1862520325203252,0.9990256193628076,0.9973086952210986,0.0010559223583366441,0.9990328177672021,0.0002626280165731167,0.9900813008130082,0.9860975609756097,0.9940650406504065,0.15874141774477965,0.19157697736106416,0.07949175320387636,0.4298101483097202,27.935913545117483,23.6
+ye2026_sepsis,pooled,pooled,"Zero-shot, real bulk",zs__raw,R2,raw,12300,12300,,,,,,,,,,,,,0.9977635501355013,0.0005517276983947411,0.9990830358913346,0.000286812511580095,0.9905691056910569,0.988130081300813,0.9930081300813008,0.15825614752383382,0.19196671403168075,0.08037673814180257,0.43059959969731715,27.935913545117483,18.4
+ye2026_sepsis,pooled,pooled,"Zero-shot, real bulk",zs__raw,R2,dm,12300,12300,,,,,,,,,,,,,0.9977282041113094,0.0007497033868873929,0.9990197137946989,0.00027895492278057487,0.9902032520325204,0.9883739837398374,0.9920325203252033,0.16375707717447419,0.19369056072423596,0.07992352439285333,0.4373711622915635,27.935913545117483,19.7
+ye2026_sepsis,pooled,pooled,Zero-shot + calibration,zs__cal,R1,raw,12300,12300,0.6113821138211382,0.22634146341463415,0.476260162601626,0.8750304884244985,0.7540650406504065,0.3051219512195122,0.5112845528455285,0.9687690533285568,0.9034146341463415,0.4308130081300813,0.548479674796748,0.9990256193628076,0.9809489721726485,0.0014026138221978795,0.986930117654835,0.0015097504903187364,0.9329674796747968,0.8965853658536586,0.969349593495935,0.06297133294323631,0.03431031502246884,0.010372658068921181,0.10765430603462633,27.935913545117483,20.5
+ye2026_sepsis,pooled,pooled,Zero-shot + calibration,zs__cal,R1,dm,12300,12300,0.6643089430894309,0.41252032520325205,0.7589159891598917,0.8750304884244985,0.79,0.5321138211382114,0.791479674796748,0.9687690533285568,0.9110569105691056,0.6827642276422764,0.8407235772357724,0.9990256193628076,0.9557185537709035,0.0021226112200827874,0.9726488531958492,0.0014641228096705006,0.8734959349593496,0.797479674796748,0.9495121951219512,0.04288307166765459,0.024999928706477048,0.008252738724425335,0.07613573909855698,27.935913545117483,24.0
+ye2026_sepsis,pooled,pooled,Zero-shot + calibration,zs__cal,R2,raw,12300,12300,,,,,,,,,,,,,0.9836200178465198,0.0021597542854799798,0.9876576277348137,0.0009005178040432227,0.9382520325203252,0.9179674796747967,0.9585365853658536,0.0619857019399776,0.03400471097574598,0.010385355846112887,0.10637576876183646,27.935913545117483,22.0
+ye2026_sepsis,pooled,pooled,Zero-shot + calibration,zs__cal,R2,dm,12300,12300,,,,,,,,,,,,,0.9591313702161413,0.0032070362047280187,0.9741224800052878,0.001687386207581178,0.8804065040650406,0.8217073170731707,0.9391056910569106,0.04300915359733337,0.025099052755862328,0.008275743109162459,0.07638394946235816,27.935913545117483,19.8
+ye2026_sepsis,pooled,pooled,sc-only fine-tune (+ calibration),pseudo_full__cal,R1,raw,12300,12300,0.581869918699187,0.41447154471544717,0.5114092140921409,0.8750304884244985,0.7149593495934959,0.5482113821138211,0.5431056910569105,0.9687690533285568,0.8628455284552845,0.7255284552845529,0.586650406504065,0.9990256193628076,0.9070176317007073,0.0043399476870920614,0.9097615506642871,0.0045317777072537485,0.8097560975609757,0.8108943089430894,0.8086178861788618,0.0202462320143853,0.012350839079910081,0.003962201078311578,0.03655927217260696,27.935913545117483,21.7
+ye2026_sepsis,pooled,pooled,sc-only fine-tune (+ calibration),pseudo_full__cal,R1,dm,12300,12300,0.624390243902439,0.609349593495935,0.8147967479674797,0.8750304884244985,0.7377235772357723,0.7504878048780488,0.8314471544715447,0.9687690533285568,0.8634146341463415,0.8922764227642277,0.8667479674796749,0.9990256193628076,0.8224077434067025,0.005775809835529521,0.8700942725890674,0.0053482531985974534,0.7284146341463414,0.6914634146341463,0.7653658536585366,0.009294971486418668,0.005780900626621621,0.001965512301509875,0.017041384414550165,27.935913545117483,23.6
+ye2026_sepsis,pooled,pooled,sc-only fine-tune (+ calibration),pseudo_full__cal,R2,raw,12300,12300,,,,,,,,,,,,,0.9010066263467513,0.0043009327963149015,0.9104780884394209,0.004212835269936295,0.795,0.841869918699187,0.748130081300813,0.01982361797965493,0.01226610022560104,0.004014106855629862,0.03610382506088583,27.935913545117483,17.9
+ye2026_sepsis,pooled,pooled,sc-only fine-tune (+ calibration),pseudo_full__cal,R2,dm,12300,12300,,,,,,,,,,,,,0.8226767796946263,0.00507069793039804,0.8740619009848635,0.0031710290183623326,0.7258130081300813,0.7223577235772358,0.7292682926829268,0.009475589696458842,0.005860784811862141,0.0019724154146720796,0.017308789922993062,27.935913545117483,21.0
+ye2026_sepsis,pooled,pooled,"LoRA, all training pairs",real_lora__raw,R1,raw,12300,12300,0.6844715447154471,0.5378861788617886,0.7790785907859079,0.8750304884244985,0.8121951219512196,0.6719512195121952,0.8191056910569106,0.9687690533285568,0.9256910569105691,0.829349593495935,0.8678455284552845,0.9990256193628076,0.8896844801374844,0.006453610259675883,0.9084994546896688,0.00585918830163282,0.7901219512195122,0.7317073170731707,0.8485365853658536,0.017226225222205738,0.009389244750626302,0.0028077303976323797,0.02942320037046442,27.935913545117483,25.0
+ye2026_sepsis,pooled,pooled,"LoRA, all training pairs",real_lora__raw,R1,dm,12300,12300,0.7431707317073171,0.7232520325203252,1.210840108401084,0.8750304884244985,0.8427642276422764,0.8463414634146341,1.245089430894309,0.9687690533285568,0.9334959349593496,0.9490243902439024,1.275569105691057,0.9990256193628076,0.8062482318725627,0.005741273546314698,0.8613154702888494,0.008487401974971017,0.7109756097560975,0.6041463414634146,0.8178048780487804,0.008833652190491481,0.004967538159686313,0.0016221823297952742,0.015423372679973069,27.935913545117483,22.5
+ye2026_sepsis,pooled,pooled,"LoRA, all training pairs",real_lora__raw,R2,raw,12300,12300,,,,,,,,,,,,,0.8860724436512658,0.002998163665065374,0.9010247042104567,0.007093597038105434,0.7848373983739837,0.7717886178861788,0.7978861788617886,0.015656371733338725,0.00894123804725222,0.0027803303755022934,0.02737794015609324,27.935913545117483,20.4
+ye2026_sepsis,pooled,pooled,"LoRA, all training pairs",real_lora__raw,R2,dm,12300,12300,,,,,,,,,,,,,0.805462357062595,0.007412054400616472,0.8576275034701567,0.004306926483384638,0.7095528455284553,0.6339024390243903,0.7852032520325203,0.008126875553287616,0.004765270507303354,0.0015752243414379752,0.014467370402028945,27.935913545117483,20.3
+ye2026_sepsis,pooled,pooled,"Zero-shot, sc pseudobulk input (reference)",zs__pseudo,R1,raw,12300,12300,0.630569105691057,0.24902439024390244,0.5166124661246613,0.8750304884244985,0.7729268292682927,0.33463414634146343,0.5555934959349593,0.9687690533285568,0.9152032520325203,0.48,0.6000975609756097,0.9990256193628076,0.9780299424945469,0.0022535114353403854,0.9826320807720272,0.001381859885884806,0.9249593495934959,0.8856910569105692,0.9642276422764228,0.05309057404087231,0.029032007456767595,0.008818988315090648,0.09094156981273055,27.935913545117483,24.3
+ye2026_sepsis,pooled,pooled,"Zero-shot, sc pseudobulk input (reference)",zs__pseudo,R1,dm,12300,12300,0.7261788617886179,0.4653658536585366,0.9507588075880756,0.8750304884244985,0.8360975609756097,0.5891056910569106,0.9774471544715448,0.9687690533285568,0.931869918699187,0.7456910569105691,1.020821138211382,0.9990256193628076,0.9433624661246613,0.00410932033774199,0.9634228138013088,0.0028095688727788034,0.853170731707317,0.7668292682926829,0.9395121951219512,0.033249497529836414,0.019205575112414053,0.0064367201685018305,0.0588917928107523,27.935913545117483,25.6
+ye2026_sepsis,pooled,pooled,"Zero-shot, sc pseudobulk input (reference)",zs__pseudo,R2,raw,12300,12300,,,,,,,,,,,,,0.9803673573930862,0.0020819438450975425,0.9839677771167956,0.0018043576528761639,0.9300813008130081,0.9078861788617886,0.9522764227642276,0.05158062690938198,0.02851827750208935,0.008769533469960011,0.08886843788143134,27.935913545117483,18.6
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paper-releases/pbisc-diffusion/updates/20261001T200638Z-extra-realism-metrics/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores_extra/ye2026_sepsis/pooled/repro.json

@@ -0,0 +1,312 @@
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