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/fewshot_n5/draw3/manifest.json

@@ -0,0 +1,179 @@
+{
+ "schema": "paired_ft_extra_metrics.v1",
+ "dataset": "immicro",
+ "design": "fewshot",
+ "unit": "draw3",
+ "written_utc": "2026-10-01T17:40:21.395022+00:00",
+ "command": [
+  "tools/extra_metrics.py",
+  "--design",
+  "fewshot",
+  "--dataset",
+  "immicro",
+  "--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": [
+  "HS1",
+  "HS2",
+  "HS3",
+  "HS4",
+  "HS6",
+  "HS7",
+  "HS8",
+  "HS9",
+  "HS10",
+  "HS11",
+  "HS12",
+  "HS13",
+  "HS14",
+  "HS15",
+  "HS16",
+  "HS17",
+  "HS18",
+  "HS19",
+  "HS20",
+  "HS21",
+  "HS23",
+  "HS24",
+  "HS25",
+  "HS26",
+  "HS27",
+  "HS28",
+  "HS29",
+  "HS30",
+  "HS31",
+  "HS32",
+  "HS35",
+  "HS36",
+  "HS37",
+  "HS38",
+  "HS39",
+  "HS40",
+  "HS41",
+  "HS42",
+  "HS43",
+  "HS44",
+  "HS45",
+  "HS46",
+  "HS47",
+  "HS48",
+  "HS49",
+  "HS50",
+  "HS51",
+  "HS52",
+  "HS53",
+  "HS54",
+  "HS55",
+  "HS56",
+  "HS57",
+  "HS58",
+  "HS59",
+  "HS60",
+  "HS61",
+  "HS62",
+  "HS63",
+  "HS64",
+  "HS65",
+  "HS66",
+  "HS67",
+  "HS68",
+  "HS69",
+  "HS70",
+  "HS71",
+  "HS72",
+  "HS73",
+  "HS74",
+  "HS75",
+  "HS76",
+  "HS77",
+  "HS78",
+  "HS79",
+  "HS80",
+  "HS81",
+  "HS82",
+  "HS83",
+  "HS85",
+  "HS86",
+  "HS87",
+  "HS89",
+  "HS90",
+  "HS92",
+  "HS93",
+  "HS94",
+  "HS95",
+  "HS96",
+  "HS97",
+  "HS98",
+  "HS100",
+  "HS101",
+  "HS102",
+  "HS103",
+  "HS104",
+  "HS106",
+  "HS107",
+  "HS108",
+  "HS109",
+  "HS110",
+  "HS111"
+ ],
+ "n_samples": 102,
+ "calls": {
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/fewshot_n5/draw3": {
+   "arms": [
+    "zs_raw",
+    "zs_cal",
+    "lora5",
+    "zs_pseudo"
+   ],
+   "summary_sha256": "08b387df6ae770c029b2086177093e0743e0fdd889d27dff2e3b93944738cff6"
+  },
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/fewshot_n5/draw3_scsemi5": {
+   "arms": [
+    "scsemi5"
+   ],
+   "summary_sha256": "e479f27eb0178e544f28a07609f17f961bd8bdce78eb99bc22da57d76988b4d7"
+  }
+ },
+ "reference_sha256": "c5e2547be3ec3b12cb0c0b404a49e14a046ae59d40be70427f98f083a76bce17",
+ "bandwidth_m": 21.56648532320765,
+ "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": 5,
+ "fetched_from_server2": [
+  "/tmp/claude-1000/-home-sj-server-1/c8102cb0-e04f-4e04-adda-0728604e4435/scratchpad/fetch/generated/immicro/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": 1443.7,
+ "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/immicro/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
+immicro,fewshot,draw3,Real vs real control (held-out real cells),real_R2,R1,raw,15300,15300,0.835359477124183,0.9313071895424837,1.4467538126361656,0.8750245102043823,0.9084967320261438,0.9883006535947713,1.4291372549019608,0.9687653176260699,0.9657516339869281,0.9997385620915032,1.408032679738562,0.9990251917843544,0.5077809816737153,0.007505528036144785,0.5861398500576701,0.004942663175475362,0.4984640522875817,0.395359477124183,0.6015686274509804,0.00020926603413540246,4.23298178602316e-05,4.041495327955502e-06,0.00025563734732358956,21.56648532320765,48.9
+immicro,fewshot,draw3,Real vs real control (held-out real cells),real_R2,R1,dm,15300,15300,0.8335294117647059,0.928562091503268,1.4314596949891067,0.8750245102043823,0.90640522875817,0.9870588235294118,1.4146143790849672,0.9687653176260699,0.96359477124183,0.9998039215686274,1.3913137254901962,0.9990251917843544,0.5081466957153231,0.008185697094212597,0.5858682771583579,0.007725708822540179,0.4995751633986928,0.4002614379084967,0.5988888888888889,0.00019372965030373113,3.935904920582267e-05,3.448232039016119e-06,0.00023653693154856992,21.56648532320765,51.3
+immicro,fewshot,draw3,Real vs real control (out-of-sample: R2 vs R3),real_R3,R2,raw,15300,15300,,,,,,,,,,,,,0.502377942244436,0.0061601456467235815,0.4948296274936991,0.005895925764376819,0.4976143790849673,0.49483660130718954,0.5003921568627451,-2.460870312737118e-05,-2.6742393218315286e-05,-1.0558735366039684e-05,-6.190983171172615e-05,21.56648532320765,41.5
+immicro,fewshot,draw3,Real vs real control (out-of-sample: R2 vs R3),real_R3,R2,dm,15300,15300,,,,,,,,,,,,,0.5016677239523261,0.007227033187238111,0.49618727839719756,0.004941089816735444,0.4956862745098039,0.4945098039215686,0.49686274509803924,-2.9749409697243934e-05,-3.034625212738895e-05,-1.1877665423654094e-05,-7.197332724828698e-05,21.56648532320765,38.7
+immicro,fewshot,draw3,"Zero-shot, real bulk",zs_raw,R1,raw,15300,15300,0.4031372549019608,0.08980392156862745,0.24581699346405228,0.8750245102043823,0.5196732026143791,0.12359477124183006,0.23728104575163397,0.9687653176260699,0.6762745098039216,0.19248366013071896,0.235640522875817,0.9990251917843544,0.9948891558802169,0.00044888047463046153,0.9981830278952539,0.0001445025215082398,0.9772222222222222,0.9593464052287581,0.9950980392156863,0.09822217705367722,0.09986348347757057,0.040710594128433586,0.23879625465968138,21.56648532320765,34.1
+immicro,fewshot,draw3,"Zero-shot, real bulk",zs_raw,R1,dm,15300,15300,0.37980392156862747,0.09908496732026144,0.2272331154684096,0.8750245102043823,0.4904575163398693,0.13941176470588235,0.22010457516339868,0.9687653176260699,0.6598692810457516,0.214640522875817,0.22142483660130718,0.9990251917843544,0.994702368747063,0.0008464679368546688,0.9981289461318296,9.074633922218732e-05,0.976078431372549,0.9582352941176471,0.993921568627451,0.09096651678536402,0.0942716181607981,0.03849768561407463,0.22373582056023675,21.56648532320765,33.6
+immicro,fewshot,draw3,"Zero-shot, real bulk",zs_raw,R2,raw,15300,15300,,,,,,,,,,,,,0.9966955017301038,0.0013630048912493795,0.9983934704600795,0.00030753523911379165,0.9808169934640523,0.9698692810457517,0.991764705882353,0.10432057713533355,0.10233615535698393,0.04125439936936526,0.24791113186168273,21.56648532320765,33.6
+immicro,fewshot,draw3,"Zero-shot, real bulk",zs_raw,R2,dm,15300,15300,,,,,,,,,,,,,0.9958388440343457,0.0007689393296572824,0.9983077769234056,0.00018768161667766063,0.9776470588235294,0.9639869281045752,0.9913071895424836,0.09510426864497407,0.09601523222732722,0.03888758416500249,0.23000708503730377,21.56648532320765,29.6
+immicro,fewshot,draw3,Zero-shot + calibration,zs_cal,R1,raw,15300,15300,0.7215686274509804,0.3423529411764706,1.1717429193899782,0.8750245102043823,0.815359477124183,0.4218954248366013,1.1700522875816994,0.9687653176260699,0.9095424836601307,0.5311764705882352,1.1613006535947714,0.9990251917843544,0.9642914584134307,0.002439007366630344,0.9858610256738862,0.0009811953885377283,0.8959803921568628,0.8058823529411765,0.986078431372549,0.06500538077821066,0.04480755274061421,0.016244909410963793,0.12605784292978867,21.56648532320765,36.7
+immicro,fewshot,draw3,Zero-shot + calibration,zs_cal,R1,dm,15300,15300,0.8075163398692811,0.5515686274509803,2.118649237472767,0.8750245102043823,0.8801960784313726,0.6549673202614379,2.1132287581699347,0.9687653176260699,0.9438562091503268,0.7743137254901961,2.094888888888889,0.9990251917843544,0.9307098338245974,0.004738397704311549,0.9756933017215601,0.001983499852285647,0.8254901960784313,0.6736601307189543,0.9773202614379085,0.045834052081169585,0.027752352066468866,0.009504493353256205,0.08309089750089466,21.56648532320765,36.3
+immicro,fewshot,draw3,Zero-shot + calibration,zs_cal,R2,raw,15300,15300,,,,,,,,,,,,,0.9730396535520527,0.002671413654584829,0.98589583066342,0.0010009096808545378,0.9085294117647059,0.84,0.9770588235294118,0.06404969222953877,0.04478269145750291,0.01638270250176288,0.12521508618880456,21.56648532320765,34.1
+immicro,fewshot,draw3,Zero-shot + calibration,zs_cal,R2,dm,15300,15300,,,,,,,,,,,,,0.9372974283395274,0.0062628183581052155,0.9759548143876288,0.0018635329794646337,0.8352287581699347,0.6969281045751634,0.9735294117647059,0.04439930219538518,0.027529531952164454,0.009519523179615907,0.08144835732716554,21.56648532320765,33.1
+immicro,fewshot,draw3,"LoRA, 5 donors",lora5,R1,raw,15300,15300,0.8226143790849674,0.5581045751633987,1.65239651416122,0.8750245102043823,0.9002614379084968,0.6618300653594771,1.6715947712418302,0.9687653176260699,0.9599346405228758,0.7829411764705883,1.6814509803921571,0.9990251917843544,0.9299222307659448,0.0025244015360714306,0.9656032722457175,0.002958628281033932,0.8212745098039216,0.67,0.9725490196078431,0.04227434054568385,0.0260489718447674,0.008962604116048878,0.07728591650650013,21.56648532320765,40.7
+immicro,fewshot,draw3,"LoRA, 5 donors",lora5,R1,dm,15300,15300,0.8996732026143791,0.8223529411764706,3.174161220043573,0.8750245102043823,0.9455555555555556,0.9071895424836601,3.1556209150326797,0.9687653176260699,0.9788235294117648,0.967843137254902,3.1283071895424834,0.9990251917843544,0.8629338609081978,0.0023510843002341342,0.9457959865863558,0.0023705835917267807,0.7136928104575163,0.45666666666666667,0.970718954248366,0.024893148802059117,0.013186178110157432,0.004253673435894889,0.04233300034811144,21.56648532320765,39.3
+immicro,fewshot,draw3,"LoRA, 5 donors",lora5,R2,raw,15300,15300,,,,,,,,,,,,,0.9399304647785041,0.0018913044464565377,0.9614945747362125,0.001531723636137007,0.8364052287581699,0.7210457516339869,0.951764705882353,0.04070789269583197,0.025848781946493204,0.009061754356918694,0.07561842899924387,21.56648532320765,35.5
+immicro,fewshot,draw3,"LoRA, 5 donors",lora5,R2,dm,15300,15300,,,,,,,,,,,,,0.8684947562903158,0.0012632950266160312,0.9404675552138068,0.0027665121761119246,0.7224183006535948,0.4873856209150327,0.9574509803921568,0.023214133711812135,0.01294193788616016,0.004285461266318791,0.040441532864291085,21.56648532320765,35.6
+immicro,fewshot,draw3,"Zero-shot, sc pseudobulk input (reference)",zs_pseudo,R1,raw,15300,15300,0.7966666666666666,0.35934640522875816,1.7091503267973858,0.8750245102043823,0.8725490196078431,0.43137254901960786,1.6901176470588237,0.9687653176260699,0.9399346405228758,0.5333333333333333,1.6831372549019608,0.9990251917843544,0.9577018027254475,0.002452593910710783,0.9889187171600666,0.0007519419924739895,0.888921568627451,0.7879084967320261,0.9899346405228758,0.07388200133111544,0.04476493544746396,0.01563574365439102,0.13428268043297042,21.56648532320765,40.3
+immicro,fewshot,draw3,"Zero-shot, sc pseudobulk input (reference)",zs_pseudo,R1,dm,15300,15300,0.8636601307189542,0.5379084967320261,3.0311764705882354,0.8750245102043823,0.9211111111111111,0.6367320261437909,2.976653594771242,0.9687653176260699,0.9665359477124184,0.7557516339869281,2.8968823529411765,0.9990251917843544,0.9264629843222693,0.007881223003051477,0.982066032295271,0.0009122706501114098,0.8310130718954248,0.6762745098039216,0.9857516339869281,0.05700944653203138,0.030353452854773533,0.009975239571169192,0.09733813895797411,21.56648532320765,39.2
+immicro,fewshot,draw3,"Zero-shot, sc pseudobulk input (reference)",zs_pseudo,R2,raw,15300,15300,,,,,,,,,,,,,0.9661861570336197,0.003072821262647932,0.9886978939724038,0.0008446635168999543,0.9044444444444445,0.8241176470588235,0.9847712418300654,0.07169108165841259,0.044411534065101455,0.0157118718367939,0.13181448756030795,21.56648532320765,35.4
+immicro,fewshot,draw3,"Zero-shot, sc pseudobulk input (reference)",zs_pseudo,R2,dm,15300,15300,,,,,,,,,,,,,0.9342483446537656,0.004858973399849214,0.9820471506685463,0.001290504999520402,0.8429084967320262,0.7039869281045752,0.9818300653594771,0.05483463874111094,0.030058972036525855,0.010014650829136551,0.09490826160677335,21.56648532320765,34.0
+immicro,fewshot,draw3,"scSemiProfiler, 5 donors",scsemi5,R1,raw,15300,15300,0.19901960784313724,0.019477124183006535,0.09010893246187364,0.8750245102043823,0.2906535947712418,0.02516339869281046,0.09158169934640523,0.9687653176260699,0.4730718954248366,0.03418300653594771,0.09500653594771243,0.9990251917843544,0.9985100388739374,0.0005816195781834545,0.9999298987568883,3.920162671902121e-05,0.9948039215686274,0.9901960784313726,0.9994117647058823,0.23929128845173397,0.18477209409356354,0.06802487916674771,0.4920882617120452,21.56648532320765,36.2
+immicro,fewshot,draw3,"scSemiProfiler, 5 donors",scsemi5,R1,dm,15300,15300,0.6362745098039215,0.16405228758169935,0.7156862745098039,0.8750245102043823,0.7313725490196078,0.21509803921568627,0.7211764705882353,0.9687653176260699,0.8269281045751634,0.30300653594771243,0.7053464052287581,0.9990251917843544,0.9874996262121408,0.001182618999945338,0.9992854884873339,0.00019747549110168128,0.9602941176470589,0.9211764705882353,0.9994117647058823,0.13906281852961255,0.09471300500174129,0.03233461408225047,0.2661104376136043,21.56648532320765,40.9
+immicro,fewshot,draw3,"scSemiProfiler, 5 donors",scsemi5,R2,raw,15300,15300,,,,,,,,,,,,,0.9986389636464608,8.169555608748628e-05,0.9999320560468196,3.5475574913664095e-05,0.9960457516339869,0.992875816993464,0.9992156862745099,0.24389956443084854,0.18579399966762367,0.06822402781057701,0.4979175919090492,21.56648532320765,34.1
+immicro,fewshot,draw3,"scSemiProfiler, 5 donors",scsemi5,R2,dm,15300,15300,,,,,,,,,,,,,0.9888349032423427,0.0006369106980323582,0.9993038254517493,0.00017829591174977946,0.9629738562091503,0.9265359477124183,0.9994117647058823,0.13900590079064068,0.09445225682666925,0.03219765231610583,0.26565580993341575,21.56648532320765,37.1

paper-releases/pbisc-diffusion/updates/20261001T200638Z-extra-realism-metrics/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores_extra/immicro/fewshot_n5/draw3/repro.json

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