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/imperial_eskd/fewshot_n5/draw3/manifest.json

@@ -0,0 +1,224 @@
+{
+ "schema": "paired_ft_extra_metrics.v1",
+ "dataset": "imperial_eskd",
+ "design": "fewshot",
+ "unit": "draw3",
+ "written_utc": "2026-10-01T19:26:07.588532+00:00",
+ "command": [
+  "tools/extra_metrics.py",
+  "--design",
+  "fewshot",
+  "--dataset",
+  "imperial_eskd",
+  "--draws",
+  "0,1,2,3,4",
+  "--threads",
+  "6",
+  "--fetch-dir",
+  "/tmp/claude-1000/-home-sj-server-1/c8102cb0-e04f-4e04-adda-0728604e4435/scratchpad/fetch"
+ ],
+ "threads": 6,
+ "donors": [
+  "C20_1004",
+  "C20_1404",
+  "C21_1004",
+  "C21_1704",
+  "C21_2504",
+  "C23_2204",
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+  "C123_0505",
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+  "C126_3004",
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+  "C127_1105",
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+  "C128_1105",
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+  "C137_3004",
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+  "C138_0202",
+  "C138_0402",
+  "C140_3004",
+  "C140_2801",
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+  "C140_0402",
+  "C140_0602",
+  "C140_0902",
+  "C140_1103",
+  "C141_2001",
+  "C141_2201",
+  "C141_3001",
+  "C141_0202",
+  "C142_3004",
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+  "C145_1401",
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+  "C145_2301",
+  "C146_3004",
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+  "C146_1401",
+  "C146_1601",
+  "C146_1901",
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+  "C146_2701",
+  "C146_2502",
+  "C147_3004",
+  "C147_1401",
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+  "C152_0405",
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+  "C164_1105",
+  "C167_1205",
+  "C168_1205",
+  "C168_2001",
+  "C168_2301",
+  "C168_3001",
+  "C168_0202",
+  "C168_0403",
+  "C169_1205",
+  "C169_2001",
+  "C169_2301",
+  "C169_0202",
+  "C169_0403",
+  "C170_1205",
+  "C170_2301",
+  "C170_0202",
+  "C170_0402",
+  "C170_0403",
+  "C187_2605",
+  "C187_1201",
+  "C187_1401",
+  "C187_1901",
+  "C187_2301",
+  "C187_2502",
+  "C190_2605",
+  "C190_2901",
+  "C190_0102",
+  "C190_0302",
+  "C190_0502",
+  "C190_0802",
+  "C190_1002",
+  "C190_0903",
+  "C193_2605",
+  "C195_2605",
+  "C197_2605",
+  "C212_2705",
+  "C214_2705",
+  "C234_2805",
+  "C237_2805",
+  "C238_2905",
+  "C246_2905"
+ ],
+ "n_samples": 145,
+ "calls": {
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/fewshot_n5/draw3": {
+   "arms": [
+    "zs_raw",
+    "zs_cal",
+    "lora5",
+    "zs_pseudo"
+   ],
+   "summary_sha256": "ade3bb8d79d0640370adb3298af9c8c047faa24ade8951dc9827454cbb7773ed"
+  },
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/fewshot_n5/draw3_scsemi5": {
+   "arms": [
+    "scsemi5"
+   ],
+   "summary_sha256": "a99e68edf6d778a2304d0a4b586a1b5b9f899451a61b4e024a56243388a90642"
+  }
+ },
+ "reference_sha256": "34b4caa3f8a60b46d5faf58f09cdaa5622bcce19e4c45d9902a711fead96375e",
+ "bandwidth_m": 25.829842899779916,
+ "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": 12,
+ "fetched_from_server2": [
+  "/tmp/claude-1000/-home-sj-server-1/c8102cb0-e04f-4e04-adda-0728604e4435/scratchpad/fetch/generated/imperial_eskd/fewshot_n5/draw3/zs__cal.npz",
+  "/tmp/claude-1000/-home-sj-server-1/c8102cb0-e04f-4e04-adda-0728604e4435/scratchpad/fetch/generated/imperial_eskd/fewshot_n5/draw3/lora__raw.npz",
+  "/tmp/claude-1000/-home-sj-server-1/c8102cb0-e04f-4e04-adda-0728604e4435/scratchpad/fetch/generated/imperial_eskd/fewshot_n5/draw3/scsemi5__raw.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": 2309.4,
+ "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/imperial_eskd/fewshot_n5/draw3/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
+imperial_eskd,fewshot,draw3,Real vs real control (held-out real cells),real_R2,R1,raw,21682,21682,0.8416197767733604,0.9187805552993267,1.3172524059896074,0.8750172956518616,0.916197767733604,0.9851489714970944,1.3090489807213357,0.9687608091591687,0.9691449128309196,0.9997693939673462,1.2893321649294345,0.9990246756210857,0.4994166221059082,0.008860248583849895,0.5615515434369364,0.004799638380831798,0.5053500599575685,0.43091043261691725,0.5797896872982197,4.357956696254828e-05,-3.985764358560573e-06,-2.8828640954436935e-06,3.671093850854401e-05,25.829842899779916,78.8
+imperial_eskd,fewshot,draw3,Real vs real control (held-out real cells),real_R2,R1,dm,21682,21682,0.8424499584909141,0.9220090397564801,1.3159456384712358,0.8750172956518616,0.9139839498201273,0.9850567290840329,1.3062355871229592,0.9687608091591687,0.9692832764505119,0.9997232727608154,1.2884881468499216,0.9990246756210857,0.49963145884047283,0.00765226362686719,0.5585726284552676,0.00334145830483688,0.5045429388432802,0.43026473572548657,0.5788211419610737,3.490823391816278e-05,-6.253350409490821e-06,-3.2624443742079734e-06,2.5392439134463984e-05,25.829842899779916,77.7
+imperial_eskd,fewshot,draw3,Real vs real control (out-of-sample: R2 vs R3),real_R3,R2,raw,20950,20950,,,,,,,,,,,,,0.494903720074504,0.005952035671639213,0.5013619254845894,0.005324128326595687,0.49949880668257757,0.49914081145584727,0.49985680190930787,-1.7985256946739803e-05,-1.4141307294046612e-05,-4.816707208643578e-06,-3.694327144942999e-05,25.829842899779916,70.7
+imperial_eskd,fewshot,draw3,Real vs real control (out-of-sample: R2 vs R3),real_R3,R2,dm,20950,20950,,,,,,,,,,,,,0.49857290628328615,0.004048004959088969,0.5024697626466015,0.007292337232798598,0.4973508353221957,0.49637231503579954,0.4983293556085919,-1.7902641724742985e-05,-1.4166972541529432e-05,-4.855263849634639e-06,-3.6924878115907056e-05,25.829842899779916,66.7
+imperial_eskd,fewshot,draw3,"Zero-shot, real bulk",zs_raw,R1,raw,21682,21682,0.24338160686283553,0.050825569596900655,0.12085293484610889,0.8750172956518616,0.33493220182639977,0.07268702149248224,0.11914030071026657,0.9687608091591687,0.5133290286873905,0.11700950096854534,0.13103034775389724,0.9990246756210857,0.9950413985165664,0.0004950230352417356,0.9972950816598252,0.0001939679305706786,0.9791070934415644,0.977446730006457,0.9807674568766719,0.16028983937889618,0.23807768393880713,0.10761377730286026,0.5059813006205636,25.829842899779916,61.4
+imperial_eskd,fewshot,draw3,"Zero-shot, real bulk",zs_raw,R1,dm,21682,21682,0.26298311963840976,0.0707499308181902,0.13290594348614826,0.8750172956518616,0.3884328014020847,0.09888386680195554,0.1415183101189927,0.9687608091591687,0.5791901116133198,0.1565353749654091,0.1506226362881653,0.9990246756210857,0.9938430326259902,0.0010094555920756726,0.9960683083201097,0.0002924652900885112,0.9720505488423578,0.9696061248962273,0.9744949727884882,0.143786510694432,0.21912116731671438,0.0991409478135663,0.4620486258247127,25.829842899779916,61.3
+imperial_eskd,fewshot,draw3,"Zero-shot, real bulk",zs_raw,R2,raw,21682,21682,,,,,,,,,,,,,0.9952519415130002,0.0007393247226078158,0.9974584781792469,0.00033765491933354435,0.9809750023060603,0.9839498201272945,0.9780001844848262,0.16496255257080616,0.23913889702676194,0.10738464189273977,0.5114860914903079,25.829842899779916,55.2
+imperial_eskd,fewshot,draw3,"Zero-shot, real bulk",zs_raw,R2,dm,21682,21682,,,,,,,,,,,,,0.9939153315181303,0.0006581711523933102,0.9962923350574228,0.00040516748960133734,0.9740337607231805,0.9777234572456416,0.9703440642007195,0.1475417114906522,0.21974940276382482,0.09881394352246109,0.4661050577769381,25.829842899779916,54.5
+imperial_eskd,fewshot,draw3,Zero-shot + calibration,zs_cal,R1,raw,21682,21682,0.5889216861913108,0.36523383451711094,0.5891522922239646,0.8750172956518616,0.7114196107370169,0.4758324877778803,0.6163638040771147,0.9687608091591687,0.8423115948713218,0.6254035605571442,0.6463748731666821,0.9990246756210857,0.961474110378262,0.0020395566644727963,0.9703020381435137,0.0012675808662601902,0.87727146942164,0.8216954155520708,0.9328475232912093,0.04395696869783927,0.024953053032358286,0.007915941378457525,0.07682596310865508,25.829842899779916,58.6
+imperial_eskd,fewshot,draw3,Zero-shot + calibration,zs_cal,R1,dm,21682,21682,0.6452356793653722,0.40448298127479015,0.7494849798604064,0.8750172956518616,0.7558804538326722,0.5160501798727055,0.7676136887740983,0.9687608091591687,0.8669864403652799,0.6774744027303754,0.7928281523844664,0.9990246756210857,0.9524264093572589,0.0033386579206635975,0.9695317404838377,0.0014793851599884558,0.8656950465824186,0.7976662669495433,0.9337238262152938,0.04486197641281703,0.02599703049712665,0.008310508818278217,0.0791695157282219,25.829842899779916,59.8
+imperial_eskd,fewshot,draw3,Zero-shot + calibration,zs_cal,R2,raw,21682,21682,,,,,,,,,,,,,0.9650620298872497,0.0018771721746264625,0.9703062665770876,0.001556978535184274,0.8849045291024813,0.8544414721889124,0.9153675860160502,0.04293777419368394,0.024797486583645334,0.007942161885994947,0.07567742266332422,25.829842899779916,53.0
+imperial_eskd,fewshot,draw3,Zero-shot + calibration,zs_cal,R2,dm,21682,21682,,,,,,,,,,,,,0.9543777285597572,0.0014064842396422062,0.970434991555881,0.001442290729937344,0.8701457430126373,0.8229406881284015,0.917350797896873,0.04463132580319906,0.026254369443161618,0.008463221481981309,0.07934891672834199,25.829842899779916,51.3
+imperial_eskd,fewshot,draw3,"LoRA, 5 donors",lora5,R1,raw,21682,21682,0.6569504658241859,0.5576515081634535,0.7564492820465517,0.8750172956518616,0.7700857854441472,0.6940780370814501,0.7759247301909418,0.9687608091591687,0.8801771054330781,0.842680564523568,0.8028917996494789,0.9990246756210857,0.9010672626493037,0.003496517984964728,0.9025089827782387,0.0038752880113191736,0.7830458444792916,0.7182455493035698,0.8478461396550133,0.013577819899686816,0.008413816019667841,0.002688536024697985,0.024680171944052642,25.829842899779916,58.6
+imperial_eskd,fewshot,draw3,"LoRA, 5 donors",lora5,R1,dm,21682,21682,0.7062540356055714,0.6316760446453279,0.9381053408357163,0.8750172956518616,0.8066599022230422,0.7723918457706853,0.9589244534637027,0.9687608091591687,0.9077575869384743,0.9035605571441749,0.9761645604649016,0.9990246756210857,0.8762569039037154,0.004253444104732635,0.9002168833626252,0.003509769613390718,0.7550502721151185,0.6702333733050456,0.8398671709251914,0.012098642727527975,0.007882196845943934,0.0026548556219614383,0.022635695195433347,25.829842899779916,57.4
+imperial_eskd,fewshot,draw3,"LoRA, 5 donors",lora5,R2,raw,21682,21682,,,,,,,,,,,,,0.9059014035946127,0.0025660442405255187,0.9005748612559025,0.0016960664112534584,0.7866202379854257,0.7662116040955631,0.8070288718752883,0.013053445638180006,0.008214366572013354,0.0026436045510593864,0.023911416761252746,25.829842899779916,52.0
+imperial_eskd,fewshot,draw3,"LoRA, 5 donors",lora5,R2,dm,21682,21682,,,,,,,,,,,,,0.8776738842176212,0.0022094796031627353,0.9002510127843097,0.0019480144075417747,0.7582326353657411,0.7026565814961719,0.8138086892353104,0.01192514490608243,0.00785770987676071,0.0026613368008936433,0.022444191583736783,25.829842899779916,51.1
+imperial_eskd,fewshot,draw3,"Zero-shot, sc pseudobulk input (reference)",zs_pseudo,R1,raw,21682,21682,0.5832948989945577,0.421824554930357,0.6262644897457185,0.8750172956518616,0.7040863388986256,0.545706115671986,0.648971497094364,0.9687608091591687,0.8396826860990684,0.7054699750945485,0.6823955354672078,0.9990246756210857,0.9562471257324319,0.001015221468102854,0.9669825925554052,0.0012064942763580912,0.8621206530762845,0.7957291762752514,0.9285121298773176,0.02808367686028801,0.017785544567348266,0.005937239531208283,0.05180646095884456,25.829842899779916,52.5
+imperial_eskd,fewshot,draw3,"Zero-shot, sc pseudobulk input (reference)",zs_pseudo,R1,dm,21682,21682,0.6633151923254312,0.4517110967622913,0.8168834363373613,0.8750172956518616,0.7659809980629093,0.5750392030255511,0.831740614334471,0.9687608091591687,0.8789779540632783,0.73337330504566,0.8596670048888478,0.9990246756210857,0.9473056995204836,0.003012856968969605,0.9677650075333162,0.0017762606161842494,0.8515358361774744,0.7705008763029241,0.9325707960520248,0.030691042614928776,0.01937027088317178,0.006416780243636566,0.05647809374173712,25.829842899779916,60.4
+imperial_eskd,fewshot,draw3,"Zero-shot, sc pseudobulk input (reference)",zs_pseudo,R2,raw,21682,21682,,,,,,,,,,,,,0.9597748891987031,0.0018562837768291117,0.9666801268676215,0.0008690032423882442,0.8704685914583525,0.8301355963472005,0.9108015865695046,0.027392264685930257,0.01763430258183618,0.005934129675354338,0.050960696943120776,25.829842899779916,50.8
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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/imperial_eskd/fewshot_n5/draw3/repro.json

@@ -0,0 +1,411 @@
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