Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261008T050202Z-scsemi-imperial-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/scsemi_cv_20261002/fold1/per_donor.csv

@@ -0,0 +1,26 @@
+arm,donor,group,n_generated_cells,n_observed_cells,n_reference_cells,gen_T cell,obs_T cell,gen_B cell,obs_B cell,gen_Monocyte,obs_Monocyte,gen_NK cell,obs_NK cell,gen_DC,obs_DC,gen_Other,obs_Other,comp_l1,comp_l1_obs_loo_null,pb_r,pb_own_rank,pb_top1,precision,coverage,precision_depth_matched,coverage_depth_matched,mono_pct_gen,mono_pct_obs,median_umi_gen,median_umi_obs
+scsemi__raw,C23_2204,covid_positive,1500,3088,150,0.548,0.685880829015544,0.10933333333333334,0.10362694300518134,0.228,0.06703367875647669,0.08466666666666667,0.11269430051813471,0.028,0.025906735751295335,0.002,0.0048575129533678756,0.33753195164075994,0.392897480219601,0.6100159883166134,4,False,0.7933333333333333,0.04,0.54,0.38666666666666666,22.8,6.703367875647668,1304.0,1936.5
+scsemi__raw,C42_1504,covid_positive,1500,2762,150,0.922,0.7320782041998551,0.043333333333333335,0.13613323678493844,0.0,0.020275162925416364,0.019333333333333334,0.0894279507603186,0.002,0.013758146270818247,0.013333333333333334,0.00832729905865315,0.38985566014965006,0.6145434206336013,0.49477886686063766,14,False,0.56,0.09333333333333334,0.8466666666666667,0.09333333333333334,0.0,2.0275162925416366,1303.0,1302.0
+scsemi__raw,C42_2204,covid_positive,1500,4970,150,0.906,0.8511066398390342,0.04933333333333333,0.06317907444668008,0.008666666666666666,0.035211267605633804,0.024,0.035211267605633804,0.008666666666666666,0.012072434607645875,0.0033333333333333335,0.0032193158953722333,0.11001475519785381,0.7066919672354429,0.6640561965323033,1,True,0.7466666666666667,0.10666666666666667,0.68,0.20666666666666667,0.8666666666666666,3.5211267605633805,1302.0,1462.0
+scsemi__raw,C42_2704,covid_positive,1500,8918,150,0.29733333333333334,0.8535546086566494,0.26266666666666666,0.04619869925992375,0.166,0.036891679748822605,0.22466666666666665,0.054047992823503026,0.04466666666666667,0.006391567616057412,0.004666666666666667,0.0029154518950437317,1.1124425506466324,0.7080833154168011,0.6537878475487795,15,False,0.7466666666666667,0.04666666666666667,0.49333333333333335,0.34,16.6,3.6891679748822606,1303.0,1489.0
+scsemi__raw,C104_2204,covid_negative,1500,11388,150,0.7433333333333333,0.29004214963119074,0.04733333333333333,0.03898840885142255,0.128,0.4137688795223042,0.03933333333333333,0.18580962416578856,0.037333333333333336,0.06840533895328416,0.004666666666666667,0.002985598876009835,0.9266343519494205,0.6190820924463764,0.6767117715406867,1,True,0.7133333333333334,0.09333333333333334,0.5933333333333334,0.38666666666666666,12.8,41.37688795223042,1303.0,1965.5
+scsemi__raw,C106_2204,covid_negative,1500,9233,150,0.742,0.6097693057511101,0.04733333333333333,0.036824434095093686,0.12866666666666668,0.19451965774937724,0.04133333333333333,0.10733239467128777,0.034666666666666665,0.047980071482725005,0.006,0.003574136250406152,0.2903309144734467,0.19679092936648,0.6599098562461149,2,False,0.7466666666666667,0.1,0.5933333333333334,0.36666666666666664,12.866666666666667,19.451965774937722,1303.0,1796.0
+scsemi__raw,C123_2404,covid_positive,1500,3758,150,0.366,0.5516232038318254,0.11533333333333333,0.04922831293241086,0.24,0.08541777541245343,0.24333333333333335,0.271953166577967,0.0026666666666666666,0.032730175625332626,0.03266666666666666,0.009047365620010643,0.48861309207025005,0.29521246710176785,0.7370365643996092,3,False,0.8533333333333334,0.08666666666666667,0.56,0.3466666666666667,24.0,8.541777541245343,1302.0,1299.0
+scsemi__raw,C123_2904,covid_positive,1500,3252,150,0.47533333333333333,0.49231242312423124,0.11133333333333334,0.07380073800738007,0.07333333333333333,0.19034440344403444,0.29733333333333334,0.22478474784747848,0.016,0.01107011070110701,0.02666666666666667,0.007687576875768758,0.26798031980319803,0.1855780072777172,0.6563113442841032,1,True,0.4866666666666667,0.10666666666666667,0.35333333333333333,0.36,7.333333333333333,19.034440344403443,1302.0,1489.0
+scsemi__raw,C123_0505,covid_positive,1500,2266,150,0.5413333333333333,0.4854368932038835,0.16466666666666666,0.05383936451897617,0.084,0.27184466019417475,0.18333333333333332,0.13901147396293026,0.024,0.025154457193292144,0.0026666666666666666,0.02471315092674316,0.42209120329508676,0.150639778164449,0.739051497143406,4,False,0.5,0.08666666666666667,0.6733333333333333,0.18666666666666668,8.4,27.184466019417474,1303.0,1849.0
+scsemi__raw,C127_2504,covid_positive,1500,2691,150,0.5266666666666666,0.6648086213303604,0.182,0.10999628390932739,0.08066666666666666,0.03121516164994426,0.182,0.18097361575622445,0.02666666666666667,0.00966183574879227,0.002,0.0033444816053511705,0.27897287253809,0.4351675710710127,0.7084605949565586,12,False,0.5266666666666666,0.09333333333333334,0.54,0.14666666666666667,8.066666666666666,3.121516164994426,1303.0,1559.0
+scsemi__raw,C127_0405,covid_positive,1500,9080,150,0.602,0.4183920704845815,0.11733333333333333,0.07444933920704846,0.08533333333333333,0.24295154185022028,0.14333333333333334,0.24295154185022028,0.050666666666666665,0.018502202643171806,0.0013333333333333333,0.0027533039647577094,0.5173127753303964,0.309858574326032,0.634829928642081,3,False,0.7266666666666667,0.16666666666666666,0.5533333333333333,0.16666666666666666,8.533333333333333,24.295154185022028,1301.0,1270.0
+scsemi__raw,C127_1105,covid_positive,1500,5124,150,0.5986666666666667,0.5739656518345043,0.116,0.09543325526932084,0.092,0.14910226385636222,0.13933333333333334,0.1649102263856362,0.052,0.01522248243559719,0.002,0.001366120218579235,0.1653583138173302,0.19222879605811088,0.6305791861524668,6,False,0.7333333333333333,0.13333333333333333,0.5533333333333333,0.26,9.2,14.910226385636221,1301.0,1529.5
+scsemi__raw,C138_3004,covid_negative,1500,1909,150,0.43466666666666665,0.34468308014667365,0.035333333333333335,0.025144054478784705,0.3373333333333333,0.3609219486642221,0.16466666666666666,0.1959140911471975,0.026,0.06862231534834992,0.002,0.004714510214772132,0.2003457307490833,0.6247454835310075,0.6129298345111213,11,False,0.82,0.13333333333333333,0.6533333333333333,0.16666666666666666,33.733333333333334,36.09219486642221,1303.0,1398.0
+scsemi__raw,C138_2301,covid_positive,1500,964,150,0.21533333333333332,0.38278008298755184,0.25266666666666665,0.0508298755186722,0.394,0.12033195020746888,0.12066666666666667,0.3153526970954357,0.011333333333333334,0.03734439834024896,0.006,0.09336099585062241,0.9510096818810511,0.5397215195589845,0.6355151078151919,5,False,0.5933333333333334,0.12,0.32,0.26666666666666666,39.4,12.033195020746888,1303.0,1072.0
+scsemi__raw,C138_3001,covid_positive,1500,731,150,0.6646666666666666,0.12311901504787962,0.122,0.08207934336525308,0.05333333333333334,0.4008207934336525,0.13933333333333334,0.27359781121751026,0.006666666666666667,0.02188782489740082,0.014,0.09849521203830369,1.162936616507068,0.9594417053931343,0.7650826255787521,2,False,0.68,0.19333333333333333,0.58,0.20666666666666667,5.333333333333334,40.08207934336525,1302.0,1223.0
+scsemi__raw,C138_0202,covid_positive,1500,2861,150,0.4266666666666667,0.2153093324012583,0.15933333333333333,0.0740999650471863,0.31333333333333335,0.5159035302341839,0.058666666666666666,0.1422579517651171,0.02266666666666667,0.04194337644180356,0.019333333333333334,0.01048584411045089,0.6108763835488756,0.7931637275964488,0.7451006830682638,9,False,0.9333333333333333,0.19333333333333333,0.78,0.16,31.333333333333336,51.59035302341839,1303.0,1031.0
+scsemi__raw,C138_0402,covid_positive,1500,500,150,0.254,0.344,0.178,0.074,0.074,0.304,0.44,0.202,0.038,0.008,0.016,0.068,0.744,0.5454553852836953,0.7386341310669876,13,False,0.8933333333333333,0.09333333333333334,0.52,0.37333333333333335,7.3999999999999995,30.4,1304.0,1847.5
+scsemi__raw,C141_2001,covid_positive,1500,3028,150,0.6886666666666666,0.3543593130779392,0.032,0.014200792602377808,0.156,0.35402906208718626,0.07,0.10997357992073976,0.020666666666666667,0.04722589167767503,0.03266666666666666,0.1202113606340819,0.7042131219726994,0.6021160983689247,0.7185566453854525,1,True,0.6466666666666666,0.19333333333333333,0.38,0.20666666666666667,15.6,35.402906208718626,1303.0,1203.0
+scsemi__raw,C141_2201,covid_positive,1500,2514,150,0.6906666666666667,0.37748607796340494,0.034,0.07438345266507558,0.14933333333333335,0.31145584725536996,0.07,0.11177406523468576,0.018666666666666668,0.0588703261734288,0.037333333333333336,0.066030230708035,0.6263611774065234,0.452096132835039,0.7135539367791804,2,False,0.5533333333333333,0.26666666666666666,0.30666666666666664,0.18,14.933333333333335,31.145584725536995,1304.0,892.0
+scsemi__raw,C141_3001,covid_positive,1500,1237,150,0.446,0.3556992724333064,0.030666666666666665,0.116410670978173,0.4593333333333333,0.28698464025869036,0.04933333333333333,0.09215844785772029,0.013333333333333334,0.02263540824575586,0.0013333333333333333,0.12611156022635409,0.5252988412826731,0.5379158263401502,0.51691748341497,19,False,0.7133333333333334,0.16666666666666666,0.64,0.18666666666666668,45.93333333333333,28.698464025869036,1303.0,1561.0
+scsemi__raw,C141_0202,covid_positive,1500,1025,150,0.8486666666666667,0.5629268292682926,0.02666666666666667,0.041951219512195125,0.05466666666666667,0.15609756097560976,0.03933333333333333,0.18341463414634146,0.028666666666666667,0.02048780487804878,0.002,0.0351219512195122,0.5878373983739839,0.09812094311791152,0.6122064314672111,15,False,0.5333333333333333,0.21333333333333335,0.5933333333333334,0.17333333333333334,5.466666666666667,15.609756097560975,1304.0,1487.0
+scsemi__raw,C152_0405,covid_negative,1500,4046,150,0.7686666666666667,0.8826000988630747,0.04066666666666666,0.014335145823035097,0.072,0.04572417202174987,0.10133333333333333,0.04745427582797825,0.016666666666666666,0.009886307464162136,0.0006666666666666666,0.0,0.2278668643928159,0.7199148415016544,0.5740774517687914,8,False,0.6133333333333333,0.17333333333333334,0.5066666666666667,0.17333333333333334,7.199999999999999,4.572417202174988,1301.5,1464.5
+scsemi__raw,C238_2905,covid_negative,1500,7843,150,0.636,0.8912405967104424,0.068,0.034298100216753794,0.17,0.03735815376769094,0.09333333333333334,0.023842917251051893,0.023333333333333334,0.010455182965701899,0.009333333333333334,0.002805049088359046,0.5104811934208849,0.7379158786836706,0.5700574512193738,3,False,0.58,0.1,0.7933333333333333,0.30666666666666664,17.0,3.735815376769094,1304.0,1738.0
+scsemi__raw,C240_2905,covid_negative,1500,2346,150,0.5566666666666666,0.5524296675191815,0.08466666666666667,0.03836317135549872,0.14733333333333334,0.20588235294117646,0.18266666666666667,0.18584825234441602,0.025333333333333333,0.014919011082693947,0.0033333333333333335,0.0025575447570332483,0.12346121057118499,0.1302991995646281,0.6894345703496916,2,False,0.8066666666666666,0.24,0.74,0.29333333333333333,14.733333333333334,20.588235294117645,1304.0,1652.5
+scsemi__raw,C251_2905,covid_negative,1500,2117,150,0.7706666666666667,0.8304204062352385,0.012,0.07510628247520075,0.08333333333333333,0.03306565895134624,0.09533333333333334,0.05054322153991497,0.023333333333333334,0.007085498346717053,0.015333333333333332,0.003778932451582428,0.2457200440875452,0.6346035566565048,0.5963822911286726,5,False,0.6466666666666666,0.04,0.6333333333333333,0.36,8.333333333333332,3.306565895134624,1303.0,2293.0

paper-releases/pbisc-diffusion/updates/20261008T050202Z-scsemi-imperial-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/scsemi_cv_20261002/fold1/summary.json

@@ -0,0 +1,533 @@
+{
+ "schema": "paired_ft_scores.v1",
+ "dataset": "imperial_eskd",
+ "written_utc": "2026-10-08T04:46:46.580052+00:00",
+ "command": [
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py",
+  "--dataset",
+  "imperial_eskd",
+  "--out",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/scsemi_cv_20261002/fold1",
+  "--threads",
+  "8",
+  "--arm",
+  "scsemi__raw=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/imperial_eskd/fold1/scsemi__raw.npz",
+  "--case-groups",
+  "covid_positive",
+  "--control-groups",
+  "covid_negative"
+ ],
+ "arms": [
+  "scsemi__raw"
+ ],
+ "donors": [
+  "C23_2204",
+  "C42_1504",
+  "C42_2204",
+  "C42_2704",
+  "C104_2204",
+  "C106_2204",
+  "C123_2404",
+  "C123_2904",
+  "C123_0505",
+  "C127_2504",
+  "C127_0405",
+  "C127_1105",
+  "C138_3004",
+  "C138_2301",
+  "C138_3001",
+  "C138_0202",
+  "C138_0402",
+  "C141_2001",
+  "C141_2201",
+  "C141_3001",
+  "C141_0202",
+  "C152_0405",
+  "C238_2905",
+  "C240_2905",
+  "C251_2905"
+ ],
+ "n_donors": 25,
+ "reference": {
+  "cache": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/imperial_eskd",
+  "reference_sha256": "34b4caa3f8a60b46d5faf58f09cdaa5622bcce19e4c45d9902a711fead96375e",
+  "features_sha256": "e46e5bb1a24eae045efe75125d20e3accaa8f68a1006eb2f60d24159013d4aa7",
+  "n_r1_cells": 3750,
+  "pca": {
+   "n_components": 50,
+   "explained_variance_ratio_sum": 0.30920127034187317,
+   "n_fit_cells": 3750
+  },
+  "r2_control": {
+   "precision": 0.9962666666666666,
+   "coverage": 1.0,
+   "density": 2.1782399999999997,
+   "n_query": 3750,
+   "depth_matched": {
+    "precision": 0.9957333333333334,
+    "coverage": 0.9997333333333334,
+    "density": 2.15168
+   }
+  },
+  "observed_l1_loo_null_mean": 0.48729138790996585
+ },
+ "contrast_definition": {
+  "enabled": true,
+  "rule": "explicit --case-groups / --control-groups",
+  "group_source": "features groups",
+  "case_groups": [
+   "covid_positive"
+  ],
+  "control_groups": [
+   "covid_negative"
+  ],
+  "n_case_donors": 18,
+  "n_control_donors": 7,
+  "n_donors_in_neither": 0,
+  "case": [
+   true,
+   true,
+   true,
+   true,
+   false,
+   false,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   false,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   false,
+   false,
+   false,
+   false
+  ],
+  "ctrl": [
+   false,
+   false,
+   false,
+   false,
+   true,
+   true,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   true,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   true,
+   true,
+   true,
+   true
+  ],
+  "groups": [
+   "covid_positive",
+   "covid_positive",
+   "covid_positive",
+   "covid_positive",
+   "covid_negative",
+   "covid_negative",
+   "covid_positive",
+   "covid_positive",
+   "covid_positive",
+   "covid_positive",
+   "covid_positive",
+   "covid_positive",
+   "covid_negative",
+   "covid_positive",
+   "covid_positive",
+   "covid_positive",
+   "covid_positive",
+   "covid_positive",
+   "covid_positive",
+   "covid_positive",
+   "covid_positive",
+   "covid_negative",
+   "covid_negative",
+   "covid_negative",
+   "covid_negative"
+  ]
+ },
+ "deg_definition": {
+  "enabled": true,
+  "score": "top-50 DEG overlap per cell type (benchmark total_top50_overlap, Welch backend)",
+  "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/bulk2sc-paper/scripts/evaluate_generated_vs_truth.py",
+  "functions": [
+   "welch_bh_deg",
+   "top_deg_genes",
+   "jaccard"
+  ],
+  "reproduces": "utility_studies_final6k_20260925/sle top-50 DEG 81 (1,006 genes) / 84 (2,279 genes) = sum over the six gated types of top50_overlap_count",
+  "top_n": 50,
+  "fdr": 0.05,
+  "n_genes": 5927,
+  "types": [
+   "T cell",
+   "B cell",
+   "Monocyte",
+   "NK cell",
+   "DC"
+  ],
+  "aggregates_source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/imperial_eskd/deg_reference.npz",
+  "aggregates_sha256": "8fada1ace7530b79bfc5c5201b9cb60399ff77d083dd8b53b13cfbe900cda55c",
+  "aggregates_note": null,
+  "types_not_scored_observed": [],
+  "observed": {
+   "T cell": {
+    "n_significant": 283,
+    "n_tested": 5577,
+    "n_case_donors": 18,
+    "n_control_donors": 7,
+    "n_cells": 56777,
+    "top_list_size": 50
+   },
+   "B cell": {
+    "n_significant": 6,
+    "n_tested": 5106,
+    "n_case_donors": 18,
+    "n_control_donors": 7,
+    "n_cells": 5613,
+    "top_list_size": 6
+   },
+   "Monocyte": {
+    "n_significant": 177,
+    "n_tested": 5301,
+    "n_case_donors": 18,
+    "n_control_donors": 7,
+    "n_cells": 18012,
+    "top_list_size": 50
+   },
+   "NK cell": {
+    "n_significant": 61,
+    "n_tested": 5148,
+    "n_case_donors": 18,
+    "n_control_donors": 7,
+    "n_cells": 13189,
+    "top_list_size": 50
+   },
+   "DC": {
+    "n_significant": 51,
+    "n_tested": 4978,
+    "n_case_donors": 18,
+    "n_control_donors": 7,
+    "n_cells": 2764,
+    "top_list_size": 50
+   }
+  },
+  "broadcast": "welch_bh_deg + top_deg_genes on the arm's condition bulk_counts (scoring genes, case|control donors), one list compared with every type's observed list (sle_broadcast.py broadcast_input_bulk); not part of the published benchmark"
+ },
+ "headline": {
+  "scsemi__raw": {
+   "comp_l1": 0.5011018810042601,
+   "comp_l1_obs_loo_null": 0.48729138790996585,
+   "precision": 0.6858666666666666,
+   "coverage": 0.1312,
+   "precision_dm": 0.5770666666666666,
+   "coverage_dm": 0.252,
+   "pb_r_median": 0.6563113442841032,
+   "pb_top1": 0.16,
+   "mono_pct_gen": 15.114666666666668,
+   "mono_pct_obs": 19.484607214054268,
+   "median_umi_gen": 1303.0,
+   "median_umi_obs": 1532.0,
+   "contrast_mean_cp10k_r_gen": 0.6519479959928358,
+   "contrast_pseudobulk_log1p_cpm_r_gen": 0.29526468493638575,
+   "contrast_mean_cp10k_r_broadcast": 0.5366707822030754,
+   "contrast_pseudobulk_log1p_cpm_r_broadcast": 0.5098544537340554,
+   "deg_top50_T": 8,
+   "deg_top50_B": 1,
+   "deg_top50_Mono": 4,
+   "deg_top50_NK": 6,
+   "deg_top50_DC": 1,
+   "deg_top50_sum": 20,
+   "deg_top50_max": 206,
+   "deg_top50_sum_4type": 19,
+   "deg_top50_sum_broadcast": 38,
+   "seconds": 7.0
+  }
+ },
+ "per_arm": {
+  "scsemi__raw": {
+   "arm": "scsemi__raw",
+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/imperial_eskd/fold1/scsemi__raw.npz",
+   "npz_sha256": "9d8043a8277ec693e0a368fb8b38a80c777da5dbd69397ccf5aa995a18fea900",
+   "receipt_verified": true,
+   "generation": {
+    "checkpoint": null,
+    "checkpoint_sha256": null,
+    "input_condition_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/fold1/test_raw.npz",
+    "input_condition_sha256": "e5e19d453e39ba25206139a4321e1812d5c6bca9018e68c8a565476b51a275e5",
+    "seed": 20260927,
+    "steps": null,
+    "support_readout": "upstream (values <= 10 normalized units zeroed by fast_semi)",
+    "weights": null
+   },
+   "condition_for_broadcast": {
+    "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/fold1/test_raw.npz",
+    "sha256": "e5e19d453e39ba25206139a4321e1812d5c6bca9018e68c8a565476b51a275e5"
+   },
+   "poisson": {
+    "seed": 20260916,
+    "rule": "whole NPZ, rows in NPZ order",
+    "nnz_whole_npz": 4884727,
+    "median_library_whole_npz_panel": 1303.0,
+    "n_rows_whole_npz": 37500
+   },
+   "annotation": {
+    "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
+    "zero_padded_model_genes": 0,
+    "label_counts": {
+     "T cell": 22005,
+     "Monocyte": 5668,
+     "NK cell": 4870,
+     "B cell": 3663,
+     "DC": 903,
+     "Other": 391
+    },
+    "mean_l2_max_prob": 0.9281072619704406,
+    "predict_seconds": 3.1
+   },
+   "n_donors": 25,
+   "n_generated_cells": 37500,
+   "composition": {
+    "l1_mean": 0.5011018810042601,
+    "l1_median": 0.48861309207025005,
+    "l1_obs_loo_null_mean": 0.48729138790996585,
+    "l1_generated_loo_mean_vs_observed_mean": 0.48257684331110395,
+    "composition_top1": 0.04,
+    "mean_fraction_generated": {
+     "T cell": 0.5868,
+     "B cell": 0.09768,
+     "Monocyte": 0.151147,
+     "NK cell": 0.129867,
+     "DC": 0.02408,
+     "Other": 0.010427
+    },
+    "mean_fraction_observed": {
+     "T cell": 0.537041,
+     "B cell": 0.063876,
+     "Monocyte": 0.194846,
+     "NK cell": 0.14973,
+     "DC": 0.026249,
+     "Other": 0.028259
+    }
+   },
+   "pseudobulk": {
+    "n_genes": 5927,
+    "r_median": 0.6563113442841032,
+    "r_mean": 0.6541591314470808,
+    "top1": 0.16,
+    "n_top1": 4,
+    "own_rank_median": 4.0,
+    "chance_top1": 0.04
+   },
+   "precision_coverage": {
+    "precision": 0.6858666666666666,
+    "coverage": 0.1312,
+    "density": 0.18109333333333333,
+    "n_query": 3750,
+    "n_reference": 3750
+   },
+   "precision_coverage_depth_matched": {
+    "precision": 0.5770666666666666,
+    "coverage": 0.252,
+    "density": 0.18573333333333333,
+    "detected_median_before": {
+     "R1": 372.0,
+     "Q": 128.0
+    },
+    "detected_median_after": {
+     "R1": 128.0,
+     "Q": 128.0
+    }
+   },
+   "monocyte_pct": {
+    "generated_mean_over_donors": 15.114666666666668,
+    "observed_mean_over_donors": 19.484607214054268,
+    "generated_pooled_cells": 15.114666666666668
+   },
+   "median_umi_per_cell_scoring_genes": {
+    "generated_pooled": 1303.0,
+    "observed_pooled": 1532.0,
+    "generated_mean_of_donor_medians": 1302.8599853515625,
+    "observed_mean_of_donor_medians": 1512.36
+   },
+   "contrast": {
+    "mean_cp10k": {
+     "per_type": {
+      "T cell": {
+       "r_generated": 0.6776850920322486,
+       "r_broadcast": 0.46232281433059214,
+       "partial_r_generated_given_broadcast": 0.6073836312958059,
+       "r_generated_vs_broadcast": 0.39625766944708335,
+       "n_genes": 3029
+      },
+      "B cell": {
+       "r_generated": 0.5838966732805938,
+       "r_broadcast": 0.49424427841997415,
+       "partial_r_generated_given_broadcast": 0.5114252687952369,
+       "r_generated_vs_broadcast": 0.33327857417626594,
+       "n_genes": 3213
+      },
+      "Monocyte": {
+       "r_generated": 0.7357718757673274,
+       "r_broadcast": 0.681168905466175,
+       "partial_r_generated_given_broadcast": 0.597040767738387,
+       "r_generated_vs_broadcast": 0.5401025812970133,
+       "n_genes": 2919
+      },
+      "NK cell": {
+       "r_generated": 0.6104383428911735,
+       "r_broadcast": 0.50894713059556,
+       "partial_r_generated_given_broadcast": 0.5020398537531338,
+       "r_generated_vs_broadcast": 0.4347369074105965,
+       "n_genes": 2952
+      }
+     },
+     "mean_r_generated": 0.6519479959928358,
+     "mean_r_broadcast": 0.5366707822030754,
+     "mean_partial_r": 0.5544723803956408
+    },
+    "pseudobulk_log1p_cpm": {
+     "per_type": {
+      "T cell": {
+       "r_generated": 0.3631668405654728,
+       "r_broadcast": 0.5164283353485094,
+       "partial_r_generated_given_broadcast": 0.26543950432324825,
+       "r_generated_vs_broadcast": 0.2807891549778624,
+       "n_genes": 3029
+      },
+      "B cell": {
+       "r_generated": 0.12914715520774103,
+       "r_broadcast": 0.42919551372600845,
+       "partial_r_generated_given_broadcast": 0.0510593931759632,
+       "r_generated_vs_broadcast": 0.19552831282100025,
+       "n_genes": 3213
+      },
+      "Monocyte": {
+       "r_generated": 0.4007917287420853,
+       "r_broadcast": 0.6287245857944659,
+       "partial_r_generated_given_broadcast": 0.19664793114875986,
+       "r_generated_vs_broadcast": 0.4163279191953283,
+       "n_genes": 2919
+      },
+      "NK cell": {
+       "r_generated": 0.2879530152302438,
+       "r_broadcast": 0.46506938006723775,
+       "partial_r_generated_given_broadcast": 0.15900800761262054,
+       "r_generated_vs_broadcast": 0.3338504122941196,
+       "n_genes": 2952
+      }
+     },
+     "mean_r_generated": 0.29526468493638575,
+     "mean_r_broadcast": 0.5098544537340554,
+     "mean_partial_r": 0.16803870906514798
+    }
+   },
+   "deg_top50": {
+    "types_scored": [
+     "T cell",
+     "B cell",
+     "Monocyte",
+     "NK cell",
+     "DC"
+    ],
+    "types_not_scored": {},
+    "per_type": {
+     "T cell": {
+      "deg_scored": true,
+      "top50_overlap": 8,
+      "top50_jaccard": 0.10810810810810811,
+      "obs_top_list_size": 50,
+      "gen_top_list_size": 32,
+      "top50_overlap_broadcast": 10,
+      "top50_jaccard_broadcast": 0.1111111111111111,
+      "n_cells_obs": 56777,
+      "n_cells_gen": 22005
+     },
+     "B cell": {
+      "deg_scored": true,
+      "top50_overlap": 1,
+      "top50_jaccard": 0.01818181818181818,
+      "obs_top_list_size": 6,
+      "gen_top_list_size": 50,
+      "top50_overlap_broadcast": 0,
+      "top50_jaccard_broadcast": 0.0,
+      "n_cells_obs": 5613,
+      "n_cells_gen": 3663
+     },
+     "Monocyte": {
+      "deg_scored": true,
+      "top50_overlap": 4,
+      "top50_jaccard": 0.04819277108433735,
+      "obs_top_list_size": 50,
+      "gen_top_list_size": 37,
+      "top50_overlap_broadcast": 15,
+      "top50_jaccard_broadcast": 0.17647058823529413,
+      "n_cells_obs": 18012,
+      "n_cells_gen": 5668
+     },
+     "NK cell": {
+      "deg_scored": true,
+      "top50_overlap": 6,
+      "top50_jaccard": 0.1016949152542373,
+      "obs_top_list_size": 50,
+      "gen_top_list_size": 15,
+      "top50_overlap_broadcast": 7,
+      "top50_jaccard_broadcast": 0.07526881720430108,
+      "n_cells_obs": 13189,
+      "n_cells_gen": 4870
+     },
+     "DC": {
+      "deg_scored": true,
+      "top50_overlap": 1,
+      "top50_jaccard": 0.018518518518518517,
+      "obs_top_list_size": 50,
+      "gen_top_list_size": 5,
+      "top50_overlap_broadcast": 6,
+      "top50_jaccard_broadcast": 0.06382978723404255,
+      "n_cells_obs": 2764,
+      "n_cells_gen": 903
+     }
+    },
+    "sum": 20,
+    "sum_4type": 19,
+    "max": 206,
+    "mean": 4.0,
+    "sum_broadcast": 38,
+    "sum_broadcast_4type": 32,
+    "broadcast_n_significant": 1531,
+    "seconds": 0.04
+   },
+   "seconds": 7.0
+  }
+ },
+ "code_sha256": {
+  "/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/paired_finetune_intradataset_20260927/tools/ft_common.py": "4a6366b0f22208cd58714fc0261b8840c643b9d4569704d560cfd93534cbc747",
+  "/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",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/bulk2sc-paper/scripts/evaluate_generated_vs_truth.py": "48b12d794782b840838853e93e0fc55fab00532c4b3698f4588e926b985d2881",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/immicro/tools/immicro_common.py": "c5c30e917148cc5e664e91ea30c11bbdff9b6d1f53a3e0a13e16b1917eff37e9",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/predict_scanvi.py": "482ee5dcf4d72b54bc36cbb6dcff62e5030bc7afc46cb5fb01eca73a82ee45a5",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/poisson_readout.py": "8bfa080942fbcdc89ae23b276524a1a83266fb8cbc56b9af279e50f82e6cde38"
+ },
+ "seconds": 8.5
+}

paper-releases/pbisc-diffusion/updates/20261008T050202Z-scsemi-imperial-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/scsemi_cv_20261002/fold2/arms/scsemi__raw/deg_top50_lists.csv

@@ -0,0 +1,56 @@
+celltype,source,rank,gene_id
+Monocyte,observed,1,ENSG00000147138
+Monocyte,observed,2,ENSG00000178175
+Monocyte,observed,3,ENSG00000135636
+Monocyte,generated,1,ENSG00000165949
+Monocyte,generated,2,ENSG00000122026
+all (input bulk),broadcast,1,ENSG00000165949
+all (input bulk),broadcast,2,ENSG00000115155
+all (input bulk),broadcast,3,ENSG00000185745
+all (input bulk),broadcast,4,ENSG00000134321
+all (input bulk),broadcast,5,ENSG00000146122
+all (input bulk),broadcast,6,ENSG00000148773
+all (input bulk),broadcast,7,ENSG00000163666
+all (input bulk),broadcast,8,ENSG00000123610
+all (input bulk),broadcast,9,ENSG00000126262
+all (input bulk),broadcast,10,ENSG00000152766
+all (input bulk),broadcast,11,ENSG00000129538
+all (input bulk),broadcast,12,ENSG00000126787
+all (input bulk),broadcast,13,ENSG00000145386
+all (input bulk),broadcast,14,ENSG00000078053
+all (input bulk),broadcast,15,ENSG00000135114
+all (input bulk),broadcast,16,ENSG00000171848
+all (input bulk),broadcast,17,ENSG00000196141
+all (input bulk),broadcast,18,ENSG00000169385
+all (input bulk),broadcast,19,ENSG00000089685
+all (input bulk),broadcast,20,ENSG00000176890
+all (input bulk),broadcast,21,ENSG00000131747
+all (input bulk),broadcast,22,ENSG00000117399
+all (input bulk),broadcast,23,ENSG00000143476
+all (input bulk),broadcast,24,ENSG00000139734
+all (input bulk),broadcast,25,ENSG00000066279
+all (input bulk),broadcast,26,ENSG00000133216
+all (input bulk),broadcast,27,ENSG00000117724
+all (input bulk),broadcast,28,ENSG00000109805
+all (input bulk),broadcast,29,ENSG00000175063
+all (input bulk),broadcast,30,ENSG00000088325
+all (input bulk),broadcast,31,ENSG00000092853
+all (input bulk),broadcast,32,ENSG00000073737
+all (input bulk),broadcast,33,ENSG00000169679
+all (input bulk),broadcast,34,ENSG00000113088
+all (input bulk),broadcast,35,ENSG00000138669
+all (input bulk),broadcast,36,ENSG00000138160
+all (input bulk),broadcast,37,ENSG00000123485
+all (input bulk),broadcast,38,ENSG00000010030
+all (input bulk),broadcast,39,ENSG00000136689
+all (input bulk),broadcast,40,ENSG00000205413
+all (input bulk),broadcast,41,ENSG00000143344
+all (input bulk),broadcast,42,ENSG00000258227
+all (input bulk),broadcast,43,ENSG00000185304
+all (input bulk),broadcast,44,ENSG00000135636
+all (input bulk),broadcast,45,ENSG00000221955
+all (input bulk),broadcast,46,ENSG00000125148
+all (input bulk),broadcast,47,ENSG00000051341
+all (input bulk),broadcast,48,ENSG00000183486
+all (input bulk),broadcast,49,ENSG00000158373
+all (input bulk),broadcast,50,ENSG00000163563

paper-releases/pbisc-diffusion/updates/20261008T050202Z-scsemi-imperial-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/scsemi_cv_20261002/fold2/arms/scsemi__raw/generated_cells.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:a3df4b858e63aaf515545793e2ba3f27ce534c716512a69185aed2b5a0b93f78
+size 334143