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/draw1/manifest.json

@@ -0,0 +1,222 @@
+{
+ "schema": "paired_ft_extra_metrics.v1",
+ "dataset": "imperial_eskd",
+ "design": "fewshot",
+ "unit": "draw1",
+ "written_utc": "2026-10-01T18:09:52.112199+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",
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+  "C21_2504",
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+  "C127_0405",
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+  "C128_2504",
+  "C128_0405",
+  "C128_1105",
+  "C132_2804",
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+  "C140_0402",
+  "C140_0602",
+  "C140_0902",
+  "C140_1103",
+  "C141_2001",
+  "C141_2201",
+  "C141_3001",
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+  "C145_3004",
+  "C145_0701",
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+  "C145_2301",
+  "C146_3004",
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+  "C146_1401",
+  "C146_1601",
+  "C146_1901",
+  "C146_2301",
+  "C146_2701",
+  "C146_2502",
+  "C147_3004",
+  "C147_1401",
+  "C147_1901",
+  "C152_0405",
+  "C161_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",
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+  "C197_2605",
+  "C212_2705",
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+  "C234_2805",
+  "C237_2805",
+  "C238_2905",
+  "C240_2905",
+  "C246_2905",
+  "C251_2905"
+ ],
+ "n_samples": 143,
+ "calls": {
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/fewshot_n5/draw1": {
+   "arms": [
+    "zs_raw",
+    "zs_cal",
+    "lora5",
+    "zs_pseudo"
+   ],
+   "summary_sha256": "7b6126e6269bfa5486d5e3d2a66a7d98ac3faf3cbc42941db859b52f6b8df68e"
+  },
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/fewshot_n5/draw1_scsemi5": {
+   "arms": [
+    "scsemi5"
+   ],
+   "summary_sha256": "c4d05db47013cb5b019e4817f72167ac56d99c028d3dccb7cc04d81f8f6dd716"
+  }
+ },
+ "reference_sha256": "34b4caa3f8a60b46d5faf58f09cdaa5622bcce19e4c45d9902a711fead96375e",
+ "bandwidth_m": 26.023567777096574,
+ "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": 14,
+ "fetched_from_server2": [
+  "/tmp/claude-1000/-home-sj-server-1/c8102cb0-e04f-4e04-adda-0728604e4435/scratchpad/fetch/generated/imperial_eskd/fewshot_n5/draw1/zs__cal.npz",
+  "/tmp/claude-1000/-home-sj-server-1/c8102cb0-e04f-4e04-adda-0728604e4435/scratchpad/fetch/generated/imperial_eskd/fewshot_n5/draw1/lora__raw.npz",
+  "/tmp/claude-1000/-home-sj-server-1/c8102cb0-e04f-4e04-adda-0728604e4435/scratchpad/fetch/generated/imperial_eskd/fewshot_n5/draw1/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": 2296.8,
+ "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/draw1/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,draw1,Real vs real control (held-out real cells),real_R2,R1,raw,21395,21395,0.8427670016358962,0.91946716522552,1.3187816468022124,0.8750175276644852,0.9147464360831971,0.9849964945080626,1.3096891797148866,0.9687609541502247,0.9685440523486796,0.999813040430007,1.28853003038093,0.9990246922230742,0.501061429206294,0.006409508565570394,0.558686926882653,0.008690042591607283,0.502453844356158,0.42594064033652723,0.5789670483757887,5.81467385953327e-05,-8.391490420311953e-07,-2.509358811852991e-06,5.479823074144852e-05,26.023567777096574,78.6
+imperial_eskd,fewshot,draw1,Real vs real control (held-out real cells),real_R2,R1,dm,21395,21395,0.8421126431409208,0.919654124795513,1.3201059437563292,0.8750175276644852,0.9140453376957233,0.9852769338630522,1.3134564150502455,0.9687609541502247,0.9688712315961673,0.999626080860014,1.2930217340500119,0.9990246922230742,0.5013706945898656,0.005136884351282375,0.5629367070964735,0.006395228884484773,0.5026641738724001,0.4249123627015658,0.5804159850432344,4.967886358447915e-05,-3.3705629884916988e-06,-2.9977053621621508e-06,4.33105952338253e-05,26.023567777096574,77.6
+imperial_eskd,fewshot,draw1,Real vs real control (out-of-sample: R2 vs R3),real_R3,R2,raw,20906,20906,,,,,,,,,,,,,0.5025808749448755,0.0056520200612888314,0.5077819185283108,0.006156570948837379,0.49842150578781214,0.49583851525877737,0.5010044963168468,-1.746841363964302e-05,-1.3976269470195035e-05,-4.96224774138021e-06,-3.6406930851218267e-05,26.023567777096574,68.0
+imperial_eskd,fewshot,draw1,Real vs real control (out-of-sample: R2 vs R3),real_R3,R2,dm,20906,20906,,,,,,,,,,,,,0.5001436258300872,0.0035743770545071454,0.5028718291342054,0.006224347720809276,0.4986128384195925,0.4988520042093179,0.49837367262986704,-1.8079398137915703e-05,-1.4542512298598709e-05,-5.139131880715908e-06,-3.776104231723032e-05,26.023567777096574,65.1
+imperial_eskd,fewshot,draw1,"Zero-shot, real bulk",zs_raw,R1,raw,21395,21395,0.20322505258237905,0.04959102594064033,0.09992989016125263,0.8750175276644852,0.3002103295162421,0.0724935732647815,0.10566020098153775,0.9687609541502247,0.4784762795045571,0.11577471371815845,0.11895302640803926,0.9990246922230742,0.9953540721626146,0.0007234871174905035,0.997492353975111,0.00023606442556436572,0.9801121757419958,0.978452909558308,0.9817714419256836,0.16397423511239576,0.23901138098236807,0.10719393514688402,0.5101795512416478,26.023567777096574,61.2
+imperial_eskd,fewshot,draw1,"Zero-shot, real bulk",zs_raw,R1,dm,21395,21395,0.22495910259406404,0.07053049777985511,0.11463737633403442,0.8750175276644852,0.32834774480018697,0.09894835241878944,0.12113110539845758,0.9687609541502247,0.5361533068473943,0.153119887824258,0.13843421360130873,0.9990246922230742,0.9938240042608781,0.0005195720822961759,0.9962821960059619,0.00031257198040275484,0.9716989950923113,0.9692918906286515,0.974106099555971,0.1474044827112544,0.220121181147365,0.09878597075174755,0.46631163461036695,26.023567777096574,60.0
+imperial_eskd,fewshot,draw1,"Zero-shot, real bulk",zs_raw,R2,raw,21395,21395,,,,,,,,,,,,,0.9952416954358043,0.0006957950591736606,0.9976232289510323,0.00022336047187800946,0.9803692451507362,0.9828931993456415,0.9778452909558308,0.16927281916286668,0.24057482198893,0.10716406186056715,0.5170117030123638,26.023567777096574,52.4
+imperial_eskd,fewshot,draw1,"Zero-shot, real bulk",zs_raw,R2,dm,21395,21395,,,,,,,,,,,,,0.9942818618687076,0.0006085292785095321,0.9964803462793588,0.00029091866292465797,0.9732180415985043,0.9764430941808834,0.9699929890161253,0.15157865744904264,0.2211152989071159,0.0986071510697577,0.47130110742591624,26.023567777096574,51.4
+imperial_eskd,fewshot,draw1,Zero-shot + calibration,zs_cal,R1,raw,21395,21395,0.5852769338630521,0.3735919607384903,0.5899509231128769,0.8750175276644852,0.7132974994157514,0.4865622809067539,0.6243888759055853,0.9687609541502247,0.8434213601308717,0.633839682168731,0.6512409441458284,0.9990246922230742,0.9590340680730105,0.0024140984701680806,0.9685218675574518,0.0025360656504162422,0.873895770039729,0.8195372750642673,0.9282542650151905,0.03822057098126219,0.021828060662824056,0.00694229814245606,0.06699092978654231,26.023567777096574,57.4
+imperial_eskd,fewshot,draw1,Zero-shot + calibration,zs_cal,R1,dm,21395,21395,0.6411778452909558,0.41271325075952325,0.7328347744800188,0.8750175276644852,0.7502687543818649,0.527412946950222,0.7477634961439589,0.9687609541502247,0.8659032484225286,0.68240243047441,0.7739097920074783,0.9990246922230742,0.9514040728152692,0.0017684988990594383,0.9673234409845504,0.00221857054439888,0.8580743164290722,0.7921944379527928,0.9239541949053517,0.038717809587910934,0.022502060646740096,0.007206481938863085,0.06842635217351412,26.023567777096574,61.3
+imperial_eskd,fewshot,draw1,Zero-shot + calibration,zs_cal,R2,raw,21395,21395,,,,,,,,,,,,,0.9615461597946153,0.0023799417928298417,0.9684637840383212,0.0018727370912460417,0.8759523253096518,0.8449637765833139,0.9069408740359897,0.03742909336458006,0.02164220932433958,0.006931518160620653,0.06600282084954029,26.023567777096574,49.6
+imperial_eskd,fewshot,draw1,Zero-shot + calibration,zs_cal,R2,dm,21395,21395,,,,,,,,,,,,,0.9535408090108483,0.002544519303538707,0.9681504061122104,0.0017207572485754311,0.8657630287450339,0.8173872400093479,0.9141388174807198,0.03845358110666197,0.02258420243297876,0.007278065665323741,0.06831584920496447,26.023567777096574,49.7
+imperial_eskd,fewshot,draw1,"LoRA, 5 donors",lora5,R1,raw,21395,21395,0.5990184622575369,0.4925917270390278,0.6203318532367376,0.8750175276644852,0.7144192568357093,0.6229960271091376,0.6289974293059126,0.9687609541502247,0.8449637765833139,0.7829399392381398,0.6529095583080159,0.9990246922230742,0.9070703727028542,0.003276929155746207,0.9102315962219443,0.0039920511227805495,0.7902547324141155,0.7548025239541949,0.825706940874036,0.02345115257154251,0.015452133213774921,0.005001904741339214,0.043905190526656646,26.023567777096574,55.5
+imperial_eskd,fewshot,draw1,"LoRA, 5 donors",lora5,R1,dm,21395,21395,0.6594531432577705,0.5957934096751577,0.8259873802290255,0.8750175276644852,0.7713017060060762,0.7288618836176677,0.8431409207758822,0.9687609541502247,0.8828698293993924,0.8706239775648515,0.8576723533535873,0.9990246922230742,0.8745122800356377,0.006073482650478331,0.902769832900242,0.0029203072217497904,0.7565552699228791,0.6945548025239542,0.8185557373218042,0.016627214117155675,0.010529536455587962,0.0034670408417487586,0.030623791414492396,26.023567777096574,56.6
+imperial_eskd,fewshot,draw1,"LoRA, 5 donors",lora5,R2,raw,21395,21395,,,,,,,,,,,,,0.9098389986018993,0.001296154869651333,0.9083052332349583,0.0020831426540611686,0.7910025706940874,0.7975695255900911,0.7844356157980836,0.022728711869752893,0.01527232735968731,0.00499232919704351,0.042993368426483713,26.023567777096574,53.8
+imperial_eskd,fewshot,draw1,"LoRA, 5 donors",lora5,R2,dm,21395,21395,,,,,,,,,,,,,0.8763479977788993,0.0014534533759039368,0.9021446663572885,0.003286720692359607,0.7608086001402197,0.7299369011451273,0.791680299135312,0.01637727033816333,0.0105855522077829,0.0035240173138668673,0.030486839859813097,26.023567777096574,56.2
+imperial_eskd,fewshot,draw1,"Zero-shot, sc pseudobulk input (reference)",zs_pseudo,R1,raw,21395,21395,0.5836877775181117,0.4230427670016359,0.6220768092233389,0.8750175276644852,0.7070810937134845,0.5418088338396821,0.653517176910493,0.9687609541502247,0.8394952091610189,0.706239775648516,0.6844075718625847,0.9990246922230742,0.9557481520456677,0.002231336481472783,0.9664101452328285,0.0014660324588481478,0.8632624444963777,0.7968684272026174,0.9296564617901378,0.0277456236210728,0.0173542094864072,0.005770965609504852,0.050870798716984855,26.023567777096574,57.1
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+imperial_eskd,fewshot,draw1,"Zero-shot, sc pseudobulk input (reference)",zs_pseudo,R2,raw,21395,21395,,,,,,,,,,,,,0.9595149023959302,0.00047403247034525904,0.965808315866861,0.00030840143603312023,0.8696891797148867,0.8279971956064501,0.9113811638233232,0.027077835823908547,0.017205732242341787,0.005762979673304969,0.0500465477395553,26.023567777096574,48.8
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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/draw1/repro.json

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