Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261003T174003Z-scsemi-readout-sensitivity/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/fewshot_n5/draw4_scsemi5rt/per_donor.csv

@@ -0,0 +1,11 @@
+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
+scsemi5rt,450905_d0,mild,1500,5914,150,0.5493333333333333,0.30943523841731485,0.08133333333333333,0.036185322962461956,0.182,0.4293202570172472,0.18066666666666667,0.12089956036523504,0.005333333333333333,0.009976327358809604,0.0013333333333333333,0.09418329387893135,0.689626423176643,0.5987967413223616,0.6142439837486058,2,False,0.9933333333333333,0.6,0.36,0.2733333333333333,18.2,42.93202570172472,485.0,574.5
+scsemi5rt,450905_d14,mild,1500,7407,150,0.474,0.4422843256379101,0.03333333333333333,0.02929661131362225,0.24533333333333332,0.27420008100445525,0.20866666666666667,0.15782368030241664,0.012,0.02983664101525584,0.02666666666666667,0.06655866072633995,0.17319076549210205,0.33063170582174406,0.5866119832471642,2,False,0.9866666666666667,0.5866666666666667,0.4533333333333333,0.32666666666666666,24.53333333333333,27.420008100445525,484.0,558.0
+scsemi5rt,7085CA_d0,mild,1500,12585,150,0.5433333333333333,0.21660707191100517,0.06466666666666666,0.024791418355184745,0.21933333333333332,0.5874453714739769,0.16266666666666665,0.13198251887167262,0.008666666666666666,0.017719507350019866,0.0013333333333333333,0.021454112038140644,0.7945713150576084,0.8949626862138647,0.5908343372363911,1,True,1.0,0.5333333333333333,0.43333333333333335,0.2866666666666667,21.933333333333334,58.74453714739769,484.0,640.0
+scsemi5rt,7085CA_d7,mild,1500,9515,150,0.528,0.521492380451918,0.03266666666666666,0.0722017866526537,0.20466666666666666,0.10110352075669994,0.21,0.2725170782974251,0.008,0.019863373620599055,0.016666666666666666,0.012821860220704152,0.22783114380802244,0.4348078856615509,0.6210311800755641,1,True,0.9933333333333333,0.7266666666666667,0.54,0.26666666666666666,20.466666666666665,10.110352075669994,484.0,502.0
+scsemi5rt,7085CA_d14,mild,1500,11887,150,0.5406666666666666,0.472533019264743,0.03333333333333333,0.07133843694792631,0.21266666666666667,0.16210986792294102,0.19,0.24270211155043325,0.009333333333333334,0.018591738874400604,0.014,0.032724825439555814,0.23738089229129858,0.3709079832657155,0.6344373645076054,1,True,1.0,0.6533333333333333,0.52,0.29333333333333333,21.266666666666666,16.2109867922941,483.0,536.0
+scsemi5rt,B85D75_d0,severe,1500,11441,150,0.5486666666666666,0.7173324010138974,0.016,0.031203566121842496,0.30133333333333334,0.11441307578008915,0.11133333333333334,0.06039681845992483,0.018,0.016519535005681322,0.004666666666666667,0.06013460361856481,0.4786744748419428,0.4453152798334465,0.6515598070269618,7,False,1.0,0.68,0.5333333333333333,0.12666666666666668,30.133333333333333,11.441307578008916,485.0,347.0
+scsemi5rt,B85D75_d7,severe,1500,12328,150,0.6613333333333333,0.6435756002595717,0.068,0.06448734587929916,0.17,0.13741077222582737,0.07133333333333333,0.04201817001946788,0.005333333333333333,0.027741726151849447,0.024,0.08476638546398442,0.16634955656500108,0.4045481459575713,0.6304440499813153,1,True,1.0,0.7866666666666666,0.46,0.41333333333333333,17.0,13.741077222582737,484.0,363.0
+scsemi5rt,180E1A_d0,severe,1500,7157,150,0.6206666666666667,0.7019700992035769,0.09533333333333334,0.04135811094033813,0.16333333333333333,0.13175911694844208,0.10066666666666667,0.0655302501047925,0.004,0.013273718038284197,0.016,0.04610870476456616,0.24137171067952118,0.4544373307053366,0.615708670268332,7,False,0.9933333333333333,0.6333333333333333,0.44666666666666666,0.24,16.333333333333332,13.175911694844208,483.0,433.0
+scsemi5rt,180E1A_d7,severe,1500,10591,150,0.54,0.7348692285903126,0.03333333333333333,0.04909829100179398,0.21333333333333335,0.09064299877254273,0.18066666666666667,0.08280615617033331,0.011333333333333334,0.010480596733075253,0.021333333333333333,0.03210272873194221,0.4428071633147641,0.5242880319872557,0.6133171145329183,5,False,0.98,0.6933333333333334,0.41333333333333333,0.14666666666666667,21.333333333333336,9.064299877254273,484.0,408.0
+scsemi5rt,180E1A_d14,severe,1500,12511,150,0.6686666666666666,0.680840860043162,0.098,0.05147470226200943,0.122,0.12277196067460634,0.07866666666666666,0.0800095915594277,0.007333333333333333,0.009831348413396212,0.025333333333333333,0.05507153704739829,0.09305059547598118,0.424657551112119,0.6649015689692479,1,True,0.9933333333333333,0.5666666666666667,0.4866666666666667,0.22,12.2,12.277196067460634,483.0,342.0

paper-releases/pbisc-diffusion/updates/20261003T174003Z-scsemi-readout-sensitivity/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/fewshot_n5/draw4_scsemi5rt/summary.json

@@ -0,0 +1,753 @@
+{
+ "schema": "paired_ft_scores.v1",
+ "dataset": "giroux2022",
+ "written_utc": "2026-10-03T15:10:23.823243+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",
+  "giroux2022",
+  "--threads",
+  "6",
+  "--donors",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/fewshot_n5/draw4/test_samples.txt",
+  "--case-groups",
+  "severe",
+  "--control-groups",
+  "mild",
+  "--arm",
+  "scsemi5rt=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/giroux2022/fewshot_n5/draw4/scsemi5rt__raw.npz",
+  "--out",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/fewshot_n5/draw4_scsemi5rt",
+  "--exclude-genes",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/sex_linked_genes/sex_linked_genes_exclude.csv",
+  "--reuse-labels",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/giroux2022/fewshot_n5/draw4_scsemi5rt"
+ ],
+ "arms": [
+  "scsemi5rt"
+ ],
+ "donors": [
+  "450905_d0",
+  "450905_d14",
+  "7085CA_d0",
+  "7085CA_d7",
+  "7085CA_d14",
+  "B85D75_d0",
+  "B85D75_d7",
+  "180E1A_d0",
+  "180E1A_d7",
+  "180E1A_d14"
+ ],
+ "n_donors": 10,
+ "reference": {
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+  "reference_sha256": "dd0152f7bde41da80e1c71dabf54ee561982f36dc99a336b65fca419880a1593",
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+ "contrast_definition": {
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+  "ctrl": [
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+   true,
+   true,
+   false,
+   false,
+   false,
+   false,
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+   "mild",
+   "mild",
+   "mild",
+   "mild",
+   "severe",
+   "severe",
+   "severe",
+   "severe",
+   "severe"
+  ]
+ },
+ "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,
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+  "types": [
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+   "B cell",
+   "Monocyte",
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+  "aggregates_source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/giroux2022/deg_reference.npz",
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+ "per_arm": {
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+    "symbol": "PRKX"
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+   {
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+    "symbol": "IL1RAPL2"
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+   {
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+    "symbol": "NUP62CL"
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+    "symbol": "FRMPD3"
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+   {
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+    "symbol": "MID2"
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+   {
+    "gene_id": "ENSG00000197565",
+    "symbol": "COL4A6"
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+   {
+    "gene_id": "ENSG00000072315",
+    "symbol": "TRPC5"
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+   {
+    "gene_id": "ENSG00000187823",
+    "symbol": "RTL4"
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+   {
+    "gene_id": "ENSG00000125675",
+    "symbol": "GRIA3"
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+   {
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+    "symbol": "SH2D1A"
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+   {
+    "gene_id": "ENSG00000056277",
+    "symbol": "ZNF280C"
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+   {
+    "gene_id": "ENSG00000171004",
+    "symbol": "HS6ST2"
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+   {
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+    "symbol": "PLAC1"
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+   {
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+    "symbol": "FHL1"
+   },
+   {
+    "gene_id": "ENSG00000102245",
+    "symbol": "CD40LG"
+   },
+   {
+    "gene_id": "ENSG00000129682",
+    "symbol": "FGF13"
+   },
+   {
+    "gene_id": "ENSG00000155966",
+    "symbol": "AFF2"
+   },
+   {
+    "gene_id": "ENSG00000011677",
+    "symbol": "GABRA3"
+   },
+   {
+    "gene_id": "ENSG00000183837",
+    "symbol": "PNMA3"
+   },
+   {
+    "gene_id": "ENSG00000067646",
+    "symbol": "ZFY"
+   },
+   {
+    "gene_id": "ENSG00000099715",
+    "symbol": "PCDH11Y"
+   },
+   {
+    "gene_id": "ENSG00000114374",
+    "symbol": "USP9Y"
+   },
+   {
+    "gene_id": "ENSG00000067048",
+    "symbol": "DDX3Y"
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+   {
+    "gene_id": "ENSG00000183878",
+    "symbol": "UTY"
+   },
+   {
+    "gene_id": "ENSG00000165246",
+    "symbol": "NLGN4Y"
+   },
+   {
+    "gene_id": "ENSG00000012817",
+    "symbol": "KDM5D"
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+  ],
+  "applies_to": "group contrast (logFC r generated / broadcast / partial: dropped from each type's detected-gene set) and top-50 DEG (observed, generated and broadcast tests: columns dropped before log1p CPM, Welch and BH); all other metrics use every scoring gene"
+ },
+ "labels_reused_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/giroux2022/fewshot_n5/draw4_scsemi5rt"
+}

paper-releases/pbisc-diffusion/updates/20261003T174003Z-scsemi-readout-sensitivity/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scsemi/analysis/output_variants_20261003/SUMMARY.md

@@ -0,0 +1,58 @@
+# scSemiProfiler read-out sensitivity (few-pair, 5 donors)
+
+Arms: `scsemi5` official output (values <= 10 zeroed by upstream), `scsemi5nt` same trained models without the output threshold, `scsemi5rt` re-read control with the threshold, `lora5` LoRA-5, `copy` = the representative's own cells (composition only). Mean over scored draws; Giroux disease metrics without sex-linked genes.
+
+Scored draws: {'giroux2022': 5, 'immicro': 5, 'imperial_eskd': 5, 'ji2025_chili': 5, 'ye2026_sepsis': 5}; pending: none
+
+Control (max |rt - official| over draws): comp_l1 0.00493, precision 0.00528, coverage 0.0147, contrast_r 0.0188, deg 6
+
+## comp_l1 (lower = better)
+
+| cohort | lora5 | scsemi5 | scsemi5nt | scsemi5rt | copy |
+|---|---|---|---|---|---|
+| immicro | 0.176 | 0.233 | 0.199 | 0.232 | 0.187 |
+| ye2026_sepsis | 0.466 | 0.612 | 0.591 | 0.611 | 0.580 |
+| ji2025_chili | 0.513 | 0.592 | 0.575 | 0.592 | 0.571 |
+| giroux2022 | 0.256 | 0.270 | 0.273 | 0.269 | 0.256 |
+| imperial_eskd | 0.503 | 0.602 | 0.603 | 0.602 | 0.608 |
+
+## precision (higher = better)
+
+| cohort | lora5 | scsemi5 | scsemi5nt | scsemi5rt | copy |
+|---|---|---|---|---|---|
+| immicro | 0.952 | 0.518 | 0.739 | 0.516 |  |
+| ye2026_sepsis | 0.906 | 0.728 | 0.773 | 0.729 |  |
+| ji2025_chili | 0.978 | 0.840 | 0.921 | 0.841 |  |
+| giroux2022 | 1.000 | 0.992 | 0.998 | 0.993 |  |
+| imperial_eskd | 0.853 | 0.330 | 0.722 | 0.330 |  |
+
+## coverage (higher = better)
+
+| cohort | lora5 | scsemi5 | scsemi5nt | scsemi5rt | copy |
+|---|---|---|---|---|---|
+| immicro | 0.792 | 0.036 | 0.233 | 0.036 |  |
+| ye2026_sepsis | 0.694 | 0.080 | 0.184 | 0.080 |  |
+| ji2025_chili | 0.707 | 0.145 | 0.526 | 0.145 |  |
+| giroux2022 | 0.961 | 0.607 | 0.831 | 0.608 |  |
+| imperial_eskd | 0.737 | 0.059 | 0.416 | 0.060 |  |
+
+## contrast_r (higher = better)
+
+| cohort | lora5 | scsemi5 | scsemi5nt | scsemi5rt | copy |
+|---|---|---|---|---|---|
+| immicro |  |  |  |  |  |
+| ye2026_sepsis | 0.350 | 0.402 | 0.458 | 0.400 |  |
+| ji2025_chili | 0.333 | 0.153 | 0.191 | 0.158 |  |
+| giroux2022 | 0.297 | 0.397 | 0.450 | 0.398 |  |
+| imperial_eskd | 0.749 | 0.562 | 0.660 | 0.563 |  |
+
+## deg (higher = better)
+
+| cohort | lora5 | scsemi5 | scsemi5nt | scsemi5rt | copy |
+|---|---|---|---|---|---|
+| immicro |  |  |  |  |  |
+| ye2026_sepsis | 16.400 | 5.200 | 14.000 | 4.800 |  |
+| ji2025_chili | 0.200 | 0.000 | 0.000 | 0.000 |  |
+| giroux2022 | 0.200 | 0.000 | 0.000 | 0.000 |  |
+| imperial_eskd | 113.600 | 46.800 | 94.600 | 49.800 |  |
+

paper-releases/pbisc-diffusion/updates/20261003T174003Z-scsemi-readout-sensitivity/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scsemi/analysis/output_variants_20261003/per_draw.csv

@@ -0,0 +1,126 @@
+dataset,draw,arm,comp_l1,precision,coverage,contrast_r,deg
+immicro,0,lora5,0.18149050759378063,0.9518300653594771,0.8003921568627451,,
+immicro,0,scsemi5,0.22879079851017084,0.49549019607843137,0.03601307189542484,,
+immicro,0,scsemi5nt,0.19948413777636048,0.7166013071895425,0.21516339869281045,,
+immicro,0,scsemi5rt,0.2298275485463518,0.49529411764705883,0.03509803921568627,,
+immicro,1,lora5,0.1566780422080866,0.9518954248366013,0.8619607843137255,,
+immicro,1,scsemi5,0.20930672962352972,0.5241176470588236,0.039281045751633985,,
+immicro,1,scsemi5nt,0.17809681738680375,0.7481699346405228,0.2583006535947712,,
+immicro,1,scsemi5rt,0.2100682002971473,0.5237254901960784,0.03895424836601307,,
+immicro,2,lora5,0.17248763359752534,0.9458823529411765,0.7860784313725491,,
+immicro,2,scsemi5,0.23723115835965083,0.5677777777777778,0.03607843137254902,,
+immicro,2,scsemi5nt,0.20610904194068622,0.7876470588235294,0.2311764705882353,,
+immicro,2,scsemi5rt,0.23712666926638357,0.5654901960784313,0.03594771241830065,,
+immicro,3,lora5,0.18654520396343544,0.9599346405228758,0.7829411764705883,,
+immicro,3,scsemi5,0.23596095148495141,0.4730718954248366,0.03418300653594771,,
+immicro,3,scsemi5nt,0.20281711862441731,0.7098039215686275,0.2350326797385621,,
+immicro,3,scsemi5rt,0.23447928352582592,0.4700653594771242,0.03483660130718954,,
+immicro,4,lora5,0.18059655915509124,0.9508496732026144,0.7309803921568627,,
+immicro,4,scsemi5,0.25127124608535867,0.5295424836601307,0.033594771241830065,,
+immicro,4,scsemi5nt,0.2080828679073089,0.7319607843137255,0.22477124183006536,,
+immicro,4,scsemi5rt,0.2509816471329434,0.5277124183006536,0.03405228758169935,,
+ye2026_sepsis,0,lora5,0.4723364713369038,0.9267532467532468,0.7058874458874459,0.4359905652333528,7.0
+ye2026_sepsis,0,scsemi5,0.6759019523396683,0.7842424242424243,0.061731601731601735,0.41261269281974167,0.0
+ye2026_sepsis,0,scsemi5nt,0.6157461882715715,0.8288311688311688,0.1478787878787879,0.4923238423463048,18.0
+ye2026_sepsis,0,scsemi5rt,0.6750557701316852,0.7791341991341991,0.06199134199134199,0.40426124244958805,0.0
+ye2026_sepsis,1,lora5,0.4725655492172997,0.9157575757575758,0.6619047619047619,0.08123703391754133,16.0
+ye2026_sepsis,1,scsemi5,0.5282094402108197,0.7483982683982684,0.0825974025974026,0.330440399769891,2.0
+ye2026_sepsis,1,scsemi5nt,0.5168767022441343,0.7613852813852814,0.1754112554112554,0.3503856028412733,9.0
+ye2026_sepsis,1,scsemi5rt,0.5270932081222044,0.7519480519480519,0.08294372294372294,0.33241041331157345,4.0
+ye2026_sepsis,2,lora5,0.4986968896699433,0.9184415584415584,0.7606060606060606,0.3272188119120809,26.0
+ye2026_sepsis,2,scsemi5,0.5800833931598967,0.782077922077922,0.08493506493506493,0.31019769204333947,6.0
+ye2026_sepsis,2,scsemi5nt,0.5473332086477867,0.7946320346320346,0.1768831168831169,0.3906075644579622,13.0
+ye2026_sepsis,2,scsemi5rt,0.5801384207450136,0.7817316017316017,0.0851948051948052,0.3174183390018127,6.0
+ye2026_sepsis,3,lora5,0.4968788955478774,0.8843290043290043,0.6553246753246753,0.4108841123350609,17.0
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