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/pooled/manifest.json

@@ -0,0 +1,231 @@
+{
+ "schema": "paired_ft_extra_metrics.v1",
+ "dataset": "imperial_eskd",
+ "design": "pooled",
+ "unit": "pooled",
+ "written_utc": "2026-10-01T19:34:25.198759+00:00",
+ "command": [
+  "tools/extra_metrics.py",
+  "--design",
+  "pooled",
+  "--dataset",
+  "imperial_eskd",
+  "--threads",
+  "8",
+  "--fetch-dir",
+  "/tmp/claude-1000/-home-sj-server-1/c8102cb0-e04f-4e04-adda-0728604e4435/scratchpad/fetch"
+ ],
+ "threads": 8,
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+ ],
+ "n_samples": 157,
+ "calls": {
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/pooled": {
+   "arms": [
+    "zs__raw",
+    "zs__cal",
+    "pseudo_full__cal",
+    "real_lora__raw",
+    "zs__pseudo"
+   ],
+   "summary_sha256": "b302d03ecf5631785a2d59766f79163d390f89cc94214a1b5f5782fe33ed4848"
+  }
+ },
+ "reference_sha256": "34b4caa3f8a60b46d5faf58f09cdaa5622bcce19e4c45d9902a711fead96375e",
+ "bandwidth_m": 25.605611978636713,
+ "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": null,
+ "fetched_from_server2": [
+  "/tmp/claude-1000/-home-sj-server-1/c8102cb0-e04f-4e04-adda-0728604e4435/scratchpad/fetch/generated/imperial_eskd/pooled/zs__raw.npz",
+  "/tmp/claude-1000/-home-sj-server-1/c8102cb0-e04f-4e04-adda-0728604e4435/scratchpad/fetch/generated/imperial_eskd/pooled/zs__cal.npz",
+  "/tmp/claude-1000/-home-sj-server-1/c8102cb0-e04f-4e04-adda-0728604e4435/scratchpad/fetch/generated/imperial_eskd/pooled/pseudo_full__cal.npz",
+  "/tmp/claude-1000/-home-sj-server-1/c8102cb0-e04f-4e04-adda-0728604e4435/scratchpad/fetch/generated/imperial_eskd/pooled/real_lora__raw.npz",
+  "/tmp/claude-1000/-home-sj-server-1/c8102cb0-e04f-4e04-adda-0728604e4435/scratchpad/fetch/generated/imperial_eskd/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": 2448.6,
+ "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/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
+imperial_eskd,pooled,pooled,Real vs real control (held-out real cells),real_R2,R1,raw,23482,23482,0.8372370326207308,0.9158078528234392,1.2921528546688243,0.8750159698489162,0.9104846265224428,0.9848820373051699,1.2835533600204412,0.9687599806242181,0.9672515117962694,0.9997018993271442,1.2663444340345795,0.9990245807479471,0.504761581853981,0.005153885938834542,0.5567519759696162,0.005704425446713733,0.5033004003066178,0.4326292479345882,0.5739715526786475,3.306619570203617e-05,-5.0570609579914105e-06,-3.0383529483479776e-06,2.4970781795696784e-05,25.605611978636713,74.4
+imperial_eskd,pooled,pooled,Real vs real control (held-out real cells),real_R2,R1,dm,23482,23482,0.8357465292564518,0.9158504386338472,1.2916276296737927,0.8750159698489162,0.9101013542287709,0.9837322204241546,1.2828719870539138,0.9687599806242181,0.9666978962609658,0.9996593135167362,1.267034324163189,0.9990245807479471,0.5028420942633882,0.005344092527437047,0.5496102435938701,0.003952880185005887,0.5057277914998722,0.4352269823694745,0.57622860063027,2.6251926702580697e-05,-7.28861560261862e-06,-3.5331866246046673e-06,1.543012447535741e-05,25.605611978636713,73.5
+imperial_eskd,pooled,pooled,Real vs real control (out-of-sample: R2 vs R3),real_R3,R2,raw,22750,22750,,,,,,,,,,,,,0.4958963748339572,0.0055020771959431,0.5036814104576742,0.006178449190325625,0.498967032967033,0.499956043956044,0.497978021978022,-1.739683675033854e-05,-1.3605249939097064e-05,-4.846557232651705e-06,-3.584864392208731e-05,25.605611978636713,61.5
+imperial_eskd,pooled,pooled,Real vs real control (out-of-sample: R2 vs R3),real_R3,R2,dm,22750,22750,,,,,,,,,,,,,0.49544085013887207,0.004114029149653994,0.49862212293201297,0.00736608904150833,0.4986153846153846,0.4992087912087912,0.498021978021978,-1.7934354957283016e-05,-1.4005321850030228e-05,-5.020169982383749e-06,-3.695984678969699e-05,25.605611978636713,63.1
+imperial_eskd,pooled,pooled,"Zero-shot, real bulk",zs__raw,R1,raw,23482,23482,0.2065837662890725,0.04956988331487948,0.10193623484654912,0.8750159698489162,0.31062090111574825,0.0722681202623286,0.10855123072992079,0.9687599806242181,0.48888510348351927,0.11195809556255855,0.11899753002299633,0.9990245807479471,0.9952415295795397,0.0006862789462009565,0.9976040760781805,0.00031542001053334857,0.9791755387105017,0.9778553785878545,0.9804956988331488,0.16359523514232566,0.24863909849995092,0.11355176554541546,0.525786099187692,25.605611978636713,62.2
+imperial_eskd,pooled,pooled,"Zero-shot, real bulk",zs__raw,R1,dm,23482,23482,0.23907673963035517,0.06766885273826762,0.1207165772364648,0.8750159698489162,0.36470488033387277,0.09488118558896176,0.12954603526105102,0.9687599806242181,0.5657524912699089,0.14704880333872752,0.13846776254152116,0.9990245807479471,0.99439681256094,0.0006088765229967312,0.9964336348510245,0.0004158435693490401,0.9718933651307384,0.969508559747892,0.9742781705135849,0.14728984062982706,0.22939242177626362,0.10479512095139709,0.4814773833574878,25.605611978636713,60.9
+imperial_eskd,pooled,pooled,"Zero-shot, real bulk",zs__raw,R2,raw,23482,23482,,,,,,,,,,,,,0.9951331667126798,0.0005613068658109174,0.9976875843005146,0.0005069344105373098,0.9813474150413083,0.9837748062345626,0.9789200238480539,0.16794333690056445,0.24964935329713844,0.11333794394230434,0.5309306341400073,25.605611978636713,53.7
+imperial_eskd,pooled,pooled,"Zero-shot, real bulk",zs__raw,R2,dm,23482,23482,,,,,,,,,,,,,0.9945219364915392,0.0006179886725154901,0.9967203048447791,0.000559984008191477,0.9742781705135849,0.9768759049484712,0.9716804360786986,0.15059686062844277,0.2298503647230996,0.10445248176440436,0.48489970711594677,25.605611978636713,54.1
+imperial_eskd,pooled,pooled,Zero-shot + calibration,zs__cal,R1,raw,23482,23482,0.5889617579422537,0.37650114981688104,0.6109360361127673,0.8750159698489162,0.7094796013968145,0.48956647645004686,0.6302188910654969,0.9687599806242181,0.8417085427135679,0.6392981858444766,0.6611617409079295,0.9990245807479471,0.9586003591044768,0.0011234339657399453,0.9661919210675501,0.0021587275247544994,0.8740311728132186,0.8159441274167447,0.9321182182096925,0.03465721787805942,0.01994438068396165,0.006370008870482113,0.06097160743250318,25.605611978636713,60.4
+imperial_eskd,pooled,pooled,Zero-shot + calibration,zs__cal,R1,dm,23482,23482,0.6452176134911848,0.4179797291542458,0.7652528177611221,0.8750159698489162,0.7583255259347585,0.5382420577463589,0.7875649433608721,0.9687599806242181,0.8640235073673452,0.6882292820032365,0.8093177753172643,0.9990245807479471,0.9480713282022053,0.002597916356218787,0.9652055748119913,0.001846570262188777,0.8587215739715527,0.7882207648411549,0.9292223831019504,0.03612184880547886,0.021569394794896724,0.0069973081374312684,0.06468855173780685,25.605611978636713,61.3
+imperial_eskd,pooled,pooled,Zero-shot + calibration,zs__cal,R2,raw,23482,23482,,,,,,,,,,,,,0.9613413751202173,0.0022365575990916133,0.9666671425845317,0.0008848546056435184,0.8808874882889022,0.8456264372711013,0.916148539306703,0.03397329557304474,0.01973377383947561,0.006339803602789962,0.06004687301531031,25.605611978636713,51.1
+imperial_eskd,pooled,pooled,Zero-shot + calibration,zs__cal,R2,dm,23482,23482,,,,,,,,,,,,,0.9500785568174311,0.0020824645528005983,0.9655892792341282,0.000676725934364338,0.864385486755813,0.8100672855804446,0.9187036879311813,0.03582200428128346,0.02153892702397453,0.0070194468671189725,0.06438037817237696,25.605611978636713,52.4
+imperial_eskd,pooled,pooled,sc-only fine-tune (+ calibration),pseudo_full__cal,R1,raw,23482,23482,0.4144451068903841,0.3230133719444681,0.317122334838032,0.8750159698489162,0.5342815773784175,0.41849075887914144,0.3267779575845328,0.9687599806242181,0.6912954603526105,0.5551912102887318,0.3366621241802231,0.9990245807479471,0.9030113750646098,0.002211357955831063,0.915568369344566,0.003047858463338957,0.7878587854526872,0.8461374669959969,0.7295801039093774,0.0331202083979909,0.025469863064226494,0.008816902388170345,0.06740697385038774,25.605611978636713,60.2
+imperial_eskd,pooled,pooled,sc-only fine-tune (+ calibration),pseudo_full__cal,R1,dm,23482,23482,0.48024018397070095,0.45102631803083215,0.40473554211736645,0.8750159698489162,0.6053572949493229,0.5933480964142748,0.41844817306873355,0.9687599806242181,0.7564091644663998,0.7710160974363343,0.4337024103568691,0.9990245807479471,0.8337191646227451,0.001890195862087434,0.8778881477639059,0.0025912014923710827,0.7219572438463504,0.7917128012946086,0.6522016863980922,0.016278535263786142,0.011314212780429544,0.003864067259225168,0.031456815303440855,25.605611978636713,60.2
+imperial_eskd,pooled,pooled,sc-only fine-tune (+ calibration),pseudo_full__cal,R2,raw,23482,23482,,,,,,,,,,,,,0.9024390771479031,0.002392527974606715,0.9186013306336107,0.001816982459665985,0.7830465888765863,0.8790988842517673,0.6869942935014053,0.03336167451045463,0.02517453153832494,0.008679168499956758,0.06721537454873633,25.605611978636713,52.7
+imperial_eskd,pooled,pooled,sc-only fine-tune (+ calibration),pseudo_full__cal,R2,dm,23482,23482,,,,,,,,,,,,,0.8373542479402578,0.0050087101126534365,0.8815901171990067,0.0021563856118915307,0.7242994634187888,0.8147091389149136,0.6338897879226641,0.016512738315961395,0.011259520815179336,0.003834720235565081,0.03160697936670581,25.605611978636713,57.3
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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/pooled/repro.json

@@ -0,0 +1,423 @@
+{
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