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/giroux2022/fewshot_n5/draw0/en.csv

@@ -0,0 +1,25 @@
+dataset,design,unit,set,cellset,distance,n_samples,n_cells_real,n_cells_gen,n_pcs,lb,ub,dif_mean,en,lb_exact,lb_queries,n_representative_rows,en_reps_at_lb,seconds
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+giroux2022,fewshot,draw0,real_R2,all,l2,11,52637,52643,100,16.2350746087302,18.58185381755008,16.54311583917856,0.1312612747252284,False,"[20000, 20000]",,,18.1
+giroux2022,fewshot,draw0,zs_raw,pc,sq,11,1650,1650,100,454.75476078307184,525.4264690242544,974.4305482471999,7.353378040482926,True,"[1650, 1650]",,,5.4
+giroux2022,fewshot,draw0,zs_raw,pc,l2,11,1650,1650,100,20.874617036010083,22.59222421410357,30.885784709794134,5.828554864853478,True,"[1650, 1650]",,,5.4
+giroux2022,fewshot,draw0,zs_raw,all,sq,11,105280,16500,100,263.42560352426915,328.89281667936115,656.444150622932,6.003288182858815,False,"[20000, 20000]",,,20.7
+giroux2022,fewshot,draw0,zs_raw,all,l2,11,105280,16500,100,15.975770054938181,17.89683477440101,25.350369215822084,4.879897624430497,False,"[20000, 20000]",,,20.7
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+giroux2022,fewshot,draw0,lora5,pc,l2,11,1650,1650,100,21.619550146362975,23.696834104348092,24.590803312871298,1.4303548415163814,True,"[1650, 1650]",,,6.8
+giroux2022,fewshot,draw0,lora5,all,sq,11,105280,16500,100,279.9862875921263,333.80129157482565,403.9441834897735,2.303407725055593,False,"[20000, 20000]",,,22.1
+giroux2022,fewshot,draw0,lora5,all,l2,11,105280,16500,100,16.46092137455397,18.021139686733765,19.880413362693364,2.1916753325129164,False,"[20000, 20000]",,,22.1
+giroux2022,fewshot,draw0,zs_pseudo,pc,sq,11,1650,1650,100,455.5824109979395,593.1076527466149,605.477986060947,1.08994954785783,True,"[1650, 1650]",,,4.3
+giroux2022,fewshot,draw0,zs_pseudo,pc,l2,11,1650,1650,100,20.983997509146857,24.011442469669934,24.296879937884487,1.0942832890231093,True,"[1650, 1650]",,,4.3
+giroux2022,fewshot,draw0,zs_pseudo,all,sq,11,105280,16500,100,276.58560521351933,334.2006948804026,417.82030628155593,2.4513491497561155,False,"[20000, 20000]",,,23.9
+giroux2022,fewshot,draw0,zs_pseudo,all,l2,11,105280,16500,100,16.36067551641662,18.034914976352415,20.187783668032356,2.2858785993268262,False,"[20000, 20000]",,,23.9
+giroux2022,fewshot,draw0,scsemi5,pc,sq,11,1650,1650,100,369.9976139768642,633.4729599383618,670.8268864932985,1.1417738969793225,True,"[1650, 1650]",13.0,0.5233130361155228,5.1
+giroux2022,fewshot,draw0,scsemi5,pc,l2,11,1650,1650,100,18.631223374254237,24.785107358808844,25.55438231147305,1.1250064113322542,True,"[1650, 1650]",13.0,0.5156279385272832,5.1
+giroux2022,fewshot,draw0,scsemi5,all,sq,11,105280,16500,100,262.02770619871785,332.4081500671956,547.064817300365,4.049947619459538,False,"[20000, 20000]",13.0,1.8562259922522883,23.4
+giroux2022,fewshot,draw0,scsemi5,all,l2,11,105280,16500,100,15.903975984589469,17.97810549700058,23.069153205352862,3.4545466798908304,False,"[20000, 20000]",13.0,1.5833338949499638,23.4

paper-releases/pbisc-diffusion/updates/20261001T200638Z-extra-realism-metrics/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores_extra/giroux2022/fewshot_n5/draw0/en_per_sample.csv

@@ -0,0 +1,265 @@
+dataset,design,unit,set,cellset,distance,donor,n_real,n_gen,partner,dif,en_i
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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/giroux2022/fewshot_n5/draw0/manifest.json

@@ -0,0 +1,86 @@
+{
+ "schema": "paired_ft_extra_metrics.v1",
+ "dataset": "giroux2022",
+ "design": "fewshot",
+ "unit": "draw0",
+ "written_utc": "2026-10-01T15:05:52.129240+00:00",
+ "command": [
+  "tools/extra_metrics.py",
+  "--design",
+  "fewshot",
+  "--dataset",
+  "giroux2022",
+  "--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": [
+  "450905_d0",
+  "450905_d14",
+  "2AD75E_d0",
+  "2AD75E_d7",
+  "2AD75E_d14",
+  "82CCF5_d0",
+  "82CCF5_d7",
+  "82CCF5_d14",
+  "0BF51C_d0",
+  "0BF51C_d7",
+  "0BF51C_d14"
+ ],
+ "n_samples": 11,
+ "calls": {
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/giroux2022/fewshot_n5/draw0": {
+   "arms": [
+    "zs_raw",
+    "zs_cal",
+    "lora5",
+    "zs_pseudo"
+   ],
+   "summary_sha256": "912ba0f2747281fc330dd1ab812705b21a88329969f5ed233d994680878c112f"
+  },
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/giroux2022/fewshot_n5/draw0_scsemi5": {
+   "arms": [
+    "scsemi5"
+   ],
+   "summary_sha256": "597bcb50c2e6e46c9daf99ef66e92f971f3ba11cdd3853df8861666af5b26f75"
+  }
+ },
+ "reference_sha256": "dd0152f7bde41da80e1c71dabf54ee561982f36dc99a336b65fca419880a1593",
+ "bandwidth_m": 33.86304512607047,
+ "params": {
+  "seed": 20261001,
+  "ks": [
+   3,
+   5,
+   10
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+  "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": 13,
+ "fetched_from_server2": [],
+ "code_sha256": {
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/extra_metrics.py": "ca3804cffbaa2fcdbb067a1d62c0ab0f365493837c6ca217f910a5e96fe362f9",
+  "/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": 260.1,
+ "max_abs_diff_k10_pooled": 0.0,
+ "extra_metrics_py_sha256_ran": "ca3804cffbaa2fcdbb067a1d62c0ab0f365493837c6ca217f910a5e96fe362f9",
+ "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/giroux2022/fewshot_n5/draw0/metrics.csv

@@ -0,0 +1,25 @@
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+giroux2022,fewshot,draw0,Real vs real control (out-of-sample: R2 vs R3),real_R3,R2,raw,1650,1650,,,,,,,,,,,,,0.499147842056933,0.027826744363026554,0.5146905417814509,0.020464178000043565,0.516969696969697,0.526060606060606,0.5078787878787879,-0.0001763320847615324,-0.00013817311557651202,-4.6603865511363196e-05,-0.0003611090658494076,33.86304512607047,3.4
+giroux2022,fewshot,draw0,Real vs real control (out-of-sample: R2 vs R3),real_R3,R2,dm,1650,1650,,,,,,,,,,,,,0.4963994490358127,0.01261800021839136,0.5087089072543618,0.020688340040884948,0.5072727272727273,0.5206060606060606,0.49393939393939396,-0.0002579458414722069,-0.00017919995653703502,-5.825237698409147e-05,-0.0004953981749933334,33.86304512607047,3.5
+giroux2022,fewshot,draw0,"Zero-shot, real bulk",zs_raw,R1,raw,1650,1650,0.8824242424242424,0.27515151515151515,1.6759595959595959,0.8752273071416298,0.9381818181818182,0.33575757575757575,1.4473939393939395,0.9688919592358399,0.9872727272727273,0.4478787878787879,1.2558787878787878,0.9990396297778593,0.9560192837465564,0.003284235893615651,0.9961258034894398,0.0020711279881843133,0.9136363636363637,0.8284848484848485,0.9987878787878788,0.13027288299669249,0.10132319443446525,0.03570753293250495,0.2673036103636627,33.86304512607047,3.0
+giroux2022,fewshot,draw0,"Zero-shot, real bulk",zs_raw,R1,dm,1650,1650,0.953939393939394,0.31272727272727274,3.6044444444444443,0.8752273071416298,0.9824242424242424,0.37454545454545457,3.1213333333333333,0.9688919592358399,0.9987878787878788,0.49575757575757573,2.6163636363636362,0.9990396297778593,0.9306593204775023,0.007334204957333544,0.99755463728191,0.0012146993757370468,0.8936363636363637,0.7878787878787878,0.9993939393939394,0.11262193031821438,0.07735821501456819,0.026050835127911842,0.2160309804606944,33.86304512607047,3.0
+giroux2022,fewshot,draw0,"Zero-shot, real bulk",zs_raw,R2,raw,1650,1650,,,,,,,,,,,,,0.9949724517906336,0.002838405228048481,0.9956528925619835,0.0022718677359150927,0.9748484848484849,0.9721212121212122,0.9775757575757575,0.14741234287900412,0.10511427271125728,0.03588247050596327,0.2884090860962247,33.86304512607047,2.6
+giroux2022,fewshot,draw0,"Zero-shot, real bulk",zs_raw,R2,dm,1650,1650,,,,,,,,,,,,,0.9900101010101009,0.0034784143270995944,0.9922589531680442,0.0015256958416001922,0.9666666666666667,0.9527272727272728,0.9806060606060606,0.11344815876342468,0.0772963212357034,0.025899581001612493,0.21664406100074057,33.86304512607047,2.7
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+giroux2022,fewshot,draw0,Zero-shot + calibration,zs_cal,R1,dm,1650,1650,0.92,0.7345454545454545,2.6325252525252525,0.8752273071416298,0.9545454545454546,0.8157575757575758,2.5025454545454546,0.9688919592358399,0.9872727272727273,0.9084848484848485,2.3112121212121215,0.9990396297778593,0.889090909090909,0.014262706105858761,0.9636317722681358,0.008179977047280955,0.7536363636363637,0.5303030303030303,0.9769696969696969,0.04282319287740943,0.02123547026004169,0.006407383060738514,0.07046604619818964,33.86304512607047,3.2
+giroux2022,fewshot,draw0,Zero-shot + calibration,zs_cal,R2,raw,1650,1650,,,,,,,,,,,,,0.9457208448117539,0.007160323026327056,0.9505371900826447,0.00663385105906589,0.8666666666666667,0.8606060606060606,0.8727272727272727,0.04952270202678433,0.025999162355598626,0.007976973868586867,0.08349883825096982,33.86304512607047,2.6
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+giroux2022,fewshot,draw0,"LoRA, 5 donors",lora5,R1,raw,1650,1650,0.9806060606060606,0.8072727272727273,5.830707070707071,0.8752273071416298,0.9933333333333333,0.8933333333333333,5.339878787878788,0.9688919592358399,0.9993939393939394,0.96,4.6371515151515155,0.9990396297778593,0.8288099173553718,0.014157954040691732,0.9716299357208449,0.008457877292575817,0.7124242424242424,0.44242424242424244,0.9824242424242424,0.06182363331713059,0.023331257627527968,0.005791834422826492,0.09094672536748505,33.86304512607047,3.5
+giroux2022,fewshot,draw0,"LoRA, 5 donors",lora5,R1,dm,1650,1650,0.9327272727272727,0.8163636363636364,2.9703030303030302,0.8752273071416298,0.9751515151515151,0.9042424242424243,2.8326060606060603,0.9688919592358399,0.9945454545454545,0.9690909090909091,2.62569696969697,0.9990396297778593,0.8081120293847567,0.014607996827956174,0.9303480257116622,0.008459012767200918,0.7015151515151515,0.45575757575757575,0.9472727272727273,0.023906634411241634,0.009273345911593456,0.002520916929634076,0.035700897252469166,33.86304512607047,3.1
+giroux2022,fewshot,draw0,"LoRA, 5 donors",lora5,R2,raw,1650,1650,,,,,,,,,,,,,0.8936106519742884,0.012994763919809417,0.909473829201102,0.00984150145940583,0.7942424242424242,0.7951515151515152,0.7933333333333333,0.03406817631231318,0.017048360975446153,0.0050845886038672905,0.056201125891626624,33.86304512607047,2.8
+giroux2022,fewshot,draw0,"LoRA, 5 donors",lora5,R2,dm,1650,1650,,,,,,,,,,,,,0.8226446280991736,0.0199934338769242,0.8704187327823693,0.01381430749116878,0.7124242424242424,0.7218181818181818,0.703030303030303,0.014110400278470436,0.007274069319094911,0.0022311191184789525,0.0236155887160443,33.86304512607047,2.8
+giroux2022,fewshot,draw0,"Zero-shot, sc pseudobulk input (reference)",zs_pseudo,R1,raw,1650,1650,0.9660606060606061,0.7642424242424243,4.597777777777778,0.8752273071416298,0.9836363636363636,0.8503030303030303,4.346787878787879,0.9688919592358399,0.9957575757575757,0.9357575757575758,3.9046666666666665,0.9990396297778593,0.8628191000918275,0.01221452900049194,0.9728741965105602,0.007123188562692279,0.7342424242424243,0.476969696969697,0.9915151515151515,0.062155790144688416,0.023331188675975945,0.005867236369223372,0.09135421518988773,33.86304512607047,3.2
+giroux2022,fewshot,draw0,"Zero-shot, sc pseudobulk input (reference)",zs_pseudo,R1,dm,1650,1650,0.9406060606060606,0.8109090909090909,2.7626262626262625,0.8752273071416298,0.9690909090909091,0.9030303030303031,2.6281212121212123,0.9688919592358399,0.9921212121212121,0.9618181818181818,2.480121212121212,0.9990396297778593,0.8465840220385674,0.011310354070251591,0.93655463728191,0.005962178133253604,0.7087878787878787,0.4581818181818182,0.9593939393939394,0.03586161083236594,0.016915355079658134,0.0050282708358491135,0.05780523674787319,33.86304512607047,2.9
+giroux2022,fewshot,draw0,"Zero-shot, sc pseudobulk input (reference)",zs_pseudo,R2,raw,1650,1650,,,,,,,,,,,,,0.9342865013774105,0.010434225790728556,0.9422727272727274,0.0066005832850921375,0.8445454545454546,0.8266666666666667,0.8624242424242424,0.04301209623419355,0.01998313897378745,0.0058364799050627525,0.06883171511304376,33.86304512607047,2.9
+giroux2022,fewshot,draw0,"Zero-shot, sc pseudobulk input (reference)",zs_pseudo,R2,dm,1650,1650,,,,,,,,,,,,,0.8717502295684113,0.005807497693192038,0.9007878787878788,0.006111797190660886,0.7621212121212121,0.7424242424242424,0.7818181818181819,0.034223574784046806,0.01735380523719532,0.0052805969801081876,0.05685797700135031,33.86304512607047,3.0
+giroux2022,fewshot,draw0,"scSemiProfiler, 5 donors",scsemi5,R1,raw,1650,1650,0.8945454545454545,0.3690909090909091,1.2315151515151515,0.8752273071416298,0.96,0.47515151515151516,1.2344242424242424,0.9688919592358399,0.9963636363636363,0.6127272727272727,1.2477575757575758,0.9990396297778593,0.9681542699724519,0.0019440663109426266,0.9992231404958677,0.00032898683238195034,0.9084848484848485,0.8175757575757576,0.9993939393939394,0.11921892886130125,0.07119659087321284,0.022779830043082594,0.2131953497775967,33.86304512607047,3.0
+giroux2022,fewshot,draw0,"scSemiProfiler, 5 donors",scsemi5,R1,dm,1650,1650,0.21212121212121213,0.11454545454545455,0.16141414141414143,0.8752273071416298,0.283030303030303,0.16121212121212122,0.17115151515151514,0.9688919592358399,0.3896969696969697,0.2503030303030303,0.17466666666666666,0.9990396297778593,0.9950321395775941,0.002438407758198758,0.9993838383838384,0.0005721404887043033,0.9748484848484849,0.9521212121212121,0.9975757575757576,0.1548094368838513,0.08886312499610982,0.027814186295253007,0.2714867481752141,33.86304512607047,3.0
+giroux2022,fewshot,draw0,"scSemiProfiler, 5 donors",scsemi5,R2,raw,1650,1650,,,,,,,,,,,,,0.9970789715335171,0.0019555359015721563,0.998504132231405,0.0006393008326178625,0.9848484848484849,0.9733333333333334,0.9963636363636363,0.11953193960285691,0.07096859457289217,0.022763474361620295,0.21326400853736938,33.86304512607047,2.8
+giroux2022,fewshot,draw0,"scSemiProfiler, 5 donors",scsemi5,R2,dm,1650,1650,,,,,,,,,,,,,0.9972956841138659,0.0019076789663588982,0.9991919191919191,0.000790295716430423,0.9842424242424243,0.9721212121212122,0.9963636363636363,0.17562946836515314,0.09192063210005652,0.027975659057109192,0.29552575952231885,33.86304512607047,2.8