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/immicro/pooled/manifest.json

@@ -0,0 +1,181 @@
+{
+ "schema": "paired_ft_extra_metrics.v1",
+ "dataset": "immicro",
+ "design": "pooled",
+ "unit": "pooled",
+ "written_utc": "2026-10-01T18:30:41.158500+00:00",
+ "command": [
+  "tools/extra_metrics.py",
+  "--design",
+  "pooled",
+  "--dataset",
+  "immicro",
+  "--threads",
+  "8",
+  "--fetch-dir",
+  "/tmp/claude-1000/-home-sj-server-1/c8102cb0-e04f-4e04-adda-0728604e4435/scratchpad/fetch"
+ ],
+ "threads": 8,
+ "donors": [
+  "HS1",
+  "HS2",
+  "HS3",
+  "HS4",
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+  "HS11",
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+  "HS15",
+  "HS16",
+  "HS17",
+  "HS18",
+  "HS19",
+  "HS20",
+  "HS21",
+  "HS23",
+  "HS24",
+  "HS25",
+  "HS26",
+  "HS27",
+  "HS28",
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+  "HS30",
+  "HS31",
+  "HS32",
+  "HS34",
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+  "HS36",
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+  "HS38",
+  "HS39",
+  "HS40",
+  "HS41",
+  "HS42",
+  "HS43",
+  "HS44",
+  "HS45",
+  "HS46",
+  "HS47",
+  "HS48",
+  "HS49",
+  "HS50",
+  "HS51",
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+  "HS53",
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+  "HS58",
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+  "HS60",
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+  "HS63",
+  "HS64",
+  "HS65",
+  "HS66",
+  "HS67",
+  "HS68",
+  "HS69",
+  "HS70",
+  "HS71",
+  "HS72",
+  "HS73",
+  "HS74",
+  "HS75",
+  "HS76",
+  "HS77",
+  "HS78",
+  "HS79",
+  "HS80",
+  "HS81",
+  "HS82",
+  "HS83",
+  "HS84",
+  "HS85",
+  "HS86",
+  "HS87",
+  "HS88",
+  "HS89",
+  "HS90",
+  "HS91",
+  "HS92",
+  "HS93",
+  "HS94",
+  "HS95",
+  "HS96",
+  "HS97",
+  "HS98",
+  "HS100",
+  "HS101",
+  "HS102",
+  "HS103",
+  "HS104",
+  "HS105",
+  "HS106",
+  "HS107",
+  "HS108",
+  "HS109",
+  "HS110",
+  "HS111"
+ ],
+ "n_samples": 107,
+ "calls": {
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/pooled": {
+   "arms": [
+    "zs__raw",
+    "zs__cal",
+    "pseudo_full__cal",
+    "real_lora__raw",
+    "zs__pseudo"
+   ],
+   "summary_sha256": "6d168fc230f5afe2d0a7395dad811aea615cae1778200694ce740b7cd0765068"
+  }
+ },
+ "reference_sha256": "c5e2547be3ec3b12cb0c0b404a49e14a046ae59d40be70427f98f083a76bce17",
+ "bandwidth_m": 21.691864004615255,
+ "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/immicro/pooled/zs__raw.npz",
+  "/tmp/claude-1000/-home-sj-server-1/c8102cb0-e04f-4e04-adda-0728604e4435/scratchpad/fetch/generated/immicro/pooled/zs__cal.npz",
+  "/tmp/claude-1000/-home-sj-server-1/c8102cb0-e04f-4e04-adda-0728604e4435/scratchpad/fetch/generated/immicro/pooled/pseudo_full__cal.npz",
+  "/tmp/claude-1000/-home-sj-server-1/c8102cb0-e04f-4e04-adda-0728604e4435/scratchpad/fetch/generated/immicro/pooled/real_lora__raw.npz",
+  "/tmp/claude-1000/-home-sj-server-1/c8102cb0-e04f-4e04-adda-0728604e4435/scratchpad/fetch/generated/immicro/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": 1591.2,
+ "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/immicro/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
+immicro,pooled,pooled,Real vs real control (held-out real cells),real_R2,R1,raw,16050,16050,0.832834890965732,0.9305295950155763,1.4272481827622014,0.8750233648498914,0.9054205607476635,0.9874766355140187,1.4115389408099688,0.9687646018937646,0.9634267912772586,0.9999376947040498,1.3859065420560748,0.9990251098518792,0.5037100862763366,0.004832934175169548,0.5809284168437806,0.006206010437311157,0.4986292834890966,0.4011214953271028,0.5961370716510903,0.00017786375176598312,3.096665543855792e-05,2.172247022702578e-06,0.00021100265422724362,21.691864004615255,45.3
+immicro,pooled,pooled,Real vs real control (held-out real cells),real_R2,R1,dm,16050,16050,0.829221183800623,0.9284735202492211,1.4060851505711318,0.8750233648498914,0.9051090342679128,0.9873520249221184,1.389619937694704,0.9687646018937646,0.9634890965732087,0.9996884735202493,1.3669096573208723,0.9990251098518792,0.5069457594549742,0.0038438136018735126,0.5767754874273348,0.004051498875042143,0.4984735202492212,0.40822429906542057,0.5887227414330218,0.00016537090090046336,2.8555205985547616e-05,1.5207425512198114e-06,0.00019544684943723079,21.691864004615255,41.7
+immicro,pooled,pooled,Real vs real control (out-of-sample: R2 vs R3),real_R3,R2,raw,16050,16050,,,,,,,,,,,,,0.5048518453819353,0.004273017161051886,0.5065794683669607,0.0039519115010786,0.4967601246105919,0.49383177570093456,0.4996884735202492,-2.2438192525453537e-05,-2.390451746969724e-05,-9.461750874351083e-06,-5.580446086950186e-05,21.691864004615255,37.3
+immicro,pooled,pooled,Real vs real control (out-of-sample: R2 vs R3),real_R3,R2,dm,16050,16050,,,,,,,,,,,,,0.5030166147455868,0.006893624634561338,0.49914185615434625,0.003680173496375167,0.4970404984423676,0.4939563862928349,0.5001246105919003,-2.7443742110777603e-05,-2.718181894456606e-05,-1.0631969257879348e-05,-6.525753031322301e-05,21.691864004615255,39.2
+immicro,pooled,pooled,"Zero-shot, real bulk",zs__raw,R1,raw,16050,16050,0.40049844236760124,0.092398753894081,0.24357217030114228,0.8750233648498914,0.5179439252336449,0.12785046728971963,0.23674766355140187,0.9687646018937646,0.6804361370716511,0.1918380062305296,0.23642367601246103,0.9990251098518792,0.9950887025552936,0.0008520683285463405,0.9982080239904505,0.00027990589996919405,0.9784735202492212,0.9613707165109034,0.9955763239875389,0.09971214735169268,0.09983684270092352,0.04040124125980826,0.23995023131242446,21.691864004615255,35.1
+immicro,pooled,pooled,"Zero-shot, real bulk",zs__raw,R1,dm,16050,16050,0.39532710280373834,0.10012461059190031,0.24220145379023883,0.8750233648498914,0.5026791277258567,0.14018691588785046,0.23379439252336448,0.9687646018937646,0.6597507788161994,0.21750778816199376,0.22603738317757008,0.9990251098518792,0.9950414689298436,0.0009035786684279611,0.9980273580419443,0.0001813504830658669,0.9753271028037384,0.9562616822429907,0.994392523364486,0.09239954200286862,0.09436266419635542,0.03828286730008079,0.22504507349930483,21.691864004615255,33.2
+immicro,pooled,pooled,"Zero-shot, real bulk",zs__raw,R2,raw,16050,16050,,,,,,,,,,,,,0.9963603419997865,0.0004525551176062292,0.9984008889665279,0.0005701985774568899,0.9820560747663551,0.9709034267912773,0.993208722741433,0.10536287811492101,0.10188340466597201,0.04080112359604304,0.24804740637693606,21.691864004615255,32.0
+immicro,pooled,pooled,"Zero-shot, real bulk",zs__raw,R2,dm,16050,16050,,,,,,,,,,,,,0.9960271542395744,0.0005357139450233265,0.9982026863093333,0.00047473560473610115,0.9789719626168224,0.9650467289719626,0.9928971962616823,0.09627523989510639,0.09588866513319072,0.038606097758490776,0.2307700027867879,21.691864004615255,27.4
+immicro,pooled,pooled,Zero-shot + calibration,zs__cal,R1,raw,16050,16050,0.7129595015576324,0.3434890965732087,1.123489096573209,0.8750233648498914,0.8069158878504673,0.4190031152647975,1.1218940809968847,0.9687646018937646,0.9050467289719626,0.527227414330218,1.1153707165109035,0.9990251098518792,0.9667195970536001,0.0022409031713385894,0.985746654244427,0.0007393473409974623,0.8989719626168224,0.8084735202492211,0.9894704049844236,0.061863137787471156,0.042301818323591256,0.015263909707081025,0.11942886581814344,21.691864004615255,32.8
+immicro,pooled,pooled,Zero-shot + calibration,zs__cal,R1,dm,16050,16050,0.8071651090342679,0.5500934579439253,2.0323156801661475,0.8750233648498914,0.8801246105919003,0.651588785046729,2.0327352024922116,0.9687646018937646,0.944423676012461,0.7689719626168224,2.006791277258567,0.9990251098518792,0.9340319872672044,0.0035869003112788483,0.9760725245290708,0.000950733953446749,0.8287850467289719,0.6741433021806854,0.9834267912772585,0.04370887574117949,0.026449438100049738,0.009044807604459804,0.07920312144568903,21.691864004615255,37.6
+immicro,pooled,pooled,Zero-shot + calibration,zs__cal,R2,raw,16050,16050,,,,,,,,,,,,,0.9728081346260227,0.0027778425696276905,0.9860599664211334,0.0016438600086618666,0.9138940809968847,0.8441121495327103,0.9836760124610592,0.06124273084127746,0.042528360080333005,0.015489876562048366,0.11926096748365883,21.691864004615255,30.6
+immicro,pooled,pooled,Zero-shot + calibration,zs__cal,R2,dm,16050,16050,,,,,,,,,,,,,0.9425814093419126,0.003139257055108645,0.9761939033976766,0.0017796218698058214,0.8456386292834891,0.7107165109034268,0.9805607476635514,0.0426844760232612,0.026465300425410954,0.009139305908590245,0.0782890823572624,21.691864004615255,34.0
+immicro,pooled,pooled,sc-only fine-tune (+ calibration),pseudo_full__cal,R1,raw,16050,16050,0.5305295950155763,0.37040498442367603,0.500332294911734,0.8750233648498914,0.6563862928348909,0.4801246105919003,0.5140934579439252,0.9687646018937646,0.8047352024922119,0.6233021806853583,0.5324610591900312,0.9990251098518792,0.949796537300686,0.0024783728098524407,0.9530549004765092,0.0031081342798669996,0.8608722741433021,0.819190031152648,0.9025545171339564,0.04440812474813999,0.03379495987141601,0.012270896169449985,0.09047398078900598,21.691864004615255,30.1
+immicro,pooled,pooled,sc-only fine-tune (+ calibration),pseudo_full__cal,R1,dm,16050,16050,0.7391277258566978,0.6957009345794393,1.3047975077881622,0.8750233648498914,0.8260436137071651,0.8094704049844237,1.3062554517133955,0.9687646018937646,0.9136448598130841,0.9193769470404984,1.3134579439252336,0.9990251098518792,0.8700505041682435,0.005757149320164198,0.9168891994448811,0.0017711552010864693,0.7516510903426791,0.601993769470405,0.9013084112149533,0.021776509287874002,0.015179368874091992,0.00528280638713996,0.042238684549105954,21.691864004615255,34.3
+immicro,pooled,pooled,sc-only fine-tune (+ calibration),pseudo_full__cal,R2,raw,16050,16050,,,,,,,,,,,,,0.9524248211876826,0.001267549728268771,0.9539344435710057,0.0017264519508198353,0.8607476635514019,0.8553894080996884,0.8661059190031153,0.045173487433865844,0.03419436550118227,0.012459006809066864,0.09182685974411497,21.691864004615255,28.1
+immicro,pooled,pooled,sc-only fine-tune (+ calibration),pseudo_full__cal,R2,dm,16050,16050,,,,,,,,,,,,,0.8764005687056609,0.0036054759770790604,0.9173621374016168,0.0059772809888976545,0.759968847352025,0.6446728971962616,0.8752647975077882,0.021727662178915863,0.01528840627646999,0.005339194466208452,0.042355262921594306,21.691864004615255,29.2
+immicro,pooled,pooled,"LoRA, all training pairs",real_lora__raw,R1,raw,16050,16050,0.7345794392523365,0.5335202492211838,1.079086188992731,0.8750233648498914,0.8340809968847352,0.6479750778816199,1.0976947040498444,0.9687646018937646,0.9241121495327103,0.7842990654205607,1.1239127725856697,0.9990251098518792,0.9360485534884173,0.004166264397877368,0.9537199755437156,0.0028211102453493623,0.8286915887850468,0.7083489096573209,0.9490342679127726,0.040474795496876215,0.026404574215806997,0.008991479082331999,0.07587084879501521,21.691864004615255,32.6
+immicro,pooled,pooled,"LoRA, all training pairs",real_lora__raw,R1,dm,16050,16050,0.8479127725856698,0.8113395638629284,2.3780269989615785,0.8750233648498914,0.9092834890965732,0.8995638629283489,2.3650467289719623,0.9687646018937646,0.9606230529595016,0.9623052959501558,2.3486479750778817,0.9990251098518792,0.8611856154346327,0.005377231354903567,0.9313829058336003,0.0026440081304586254,0.7196884735202492,0.4876635514018692,0.9517133956386293,0.021461792266035173,0.011501785799600484,0.0036082993220154513,0.03657187738765111,21.691864004615255,35.0
+immicro,pooled,pooled,"LoRA, all training pairs",real_lora__raw,R2,raw,16050,16050,,,,,,,,,,,,,0.940942149241564,0.0010604377307306988,0.9508616181908172,0.002481461979112626,0.841619937694704,0.7580685358255451,0.9251713395638629,0.03959663329676871,0.026395113567568407,0.009118143890548547,0.07510989075488567,21.691864004615255,26.2
+immicro,pooled,pooled,"LoRA, all training pairs",real_lora__raw,R2,dm,16050,16050,,,,,,,,,,,,,0.8684694442018227,0.003041370118508875,0.927208441300065,0.004245644392975313,0.7321495327102804,0.5232398753894081,0.9410591900311527,0.020293807255052865,0.011355487917015239,0.003635711040807843,0.03528500621287595,21.691864004615255,29.6
+immicro,pooled,pooled,"Zero-shot, sc pseudobulk input (reference)",zs__pseudo,R1,raw,16050,16050,0.7941433021806854,0.3553271028037383,1.6739771547248183,0.8750233648498914,0.8700934579439252,0.4273520249221184,1.6586791277258566,0.9687646018937646,0.9361993769470405,0.5244236760124611,1.6376635514018691,0.9990251098518792,0.9592865267223726,0.002346925479710278,0.9890999213905145,0.0008390339699465471,0.8942990654205607,0.7949532710280374,0.9936448598130841,0.07253216368755966,0.04345245098351569,0.015072270441638613,0.13105688511271396,21.691864004615255,34.4
+immicro,pooled,pooled,"Zero-shot, sc pseudobulk input (reference)",zs__pseudo,R1,dm,16050,16050,0.8671028037383177,0.5264174454828661,3.0029906542056075,0.8750233648498914,0.918816199376947,0.6269158878504673,2.930915887850467,0.9687646018937646,0.9652959501557632,0.7405607476635514,2.8750155763239875,0.9990251098518792,0.9272365757319901,0.0039630499138866805,0.9826741879446047,0.0009918992031333717,0.8344548286604362,0.6778816199376947,0.9910280373831776,0.05594292684581581,0.029605174504197862,0.00969630470496785,0.09524440605498152,21.691864004615255,38.4
+immicro,pooled,pooled,"Zero-shot, sc pseudobulk input (reference)",zs__pseudo,R2,raw,16050,16050,,,,,,,,,,,,,0.9671174289845789,0.002909426678755657,0.9888199260488543,0.001193997925919803,0.9077570093457944,0.826417445482866,0.9890965732087228,0.07073143877461541,0.043344267915814916,0.015228531107261523,0.12930423779769185,21.691864004615255,32.1
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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/immicro/pooled/repro.json

@@ -0,0 +1,337 @@
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