Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/x1_priority_20261015/builds/20261015T120743086141Z/sources/3ecc6baeaba2a0b5/ye2026_sepsis-disease-draw2-score.json

@@ -0,0 +1,143 @@
+{
+  "state": "completed",
+  "signature": "00029367dbb83ea21423fe2e9186859440a22d6b9cb3ea32a985ec837bf57d13",
+  "outputs": [
+    {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw2/score/summary.json",
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+    },
+    {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw2/statistics/status.json",
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+      "sha256": "a8cc04d13bfe9dde4965a8072f939d2861e72e67d137ee4f96d1203b337476f5"
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+    {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw2/statistics/donor_bootstrap_2000.csv",
+      "bytes": 13176,
+      "mtime_ns": 1791823423566087758,
+      "sha256": "cb0ef272106005d5e4196278dc63bd21767c26f13a54fe8190e4a2250835d0a4"
+    },
+    {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw2/extras/ye2026_sepsis/strict/manifest.json",
+      "bytes": 4373,
+      "mtime_ns": 1791823335656426600,
+      "sha256": "d27b3657e1b601c9e5879dde644d94761d41995295adf6daaf7b7d95b4d0d86f"
+    },
+    {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw2/contrast/ye2026_sepsis/strict/manifest.json",
+      "bytes": 18881,
+      "mtime_ns": 1791823423234702234,
+      "sha256": "1e2040dde2f698cf4c5a7a5f994d753b07b8d6f52352a79b43633eaecba1410a"
+    }
+  ],
+  "seconds": 1766.787241901,
+  "at": "2026-10-12T16:46:46.011004+00:00",
+  "execution": {
+    "host": "spark-fa6b",
+    "map_host": null,
+    "map_path": null,
+    "map_sha256": null,
+    "argv": [
+      "/home/sj_server_1/miniforge3/envs/cxg_corpus/bin/python",
+      "-u",
+      "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/tools/score_strict.py",
+      "--support-manifest",
+      "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/protocol/splits/ye2026_sepsis/disease/draw2/support.json",
+      "--out",
+      "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw2",
+      "--action",
+      "all",
+      "--threads",
+      "4",
+      "--arm",
+      "lora=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/ye2026_sepsis/disease/draw2/lora.npz",
+      "--arm",
+      "pairedcal=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/ye2026_sepsis/disease/draw2/pairedcal.npz",
+      "--arm",
+      "scsemi=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/ye2026_sepsis/disease/draw2/scsemi.npz",
+      "--arm",
+      "raw=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/global/ye2026_sepsis/raw.npz",
+      "--arm",
+      "refcal=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/global/ye2026_sepsis/refcal.npz"
+    ],
+    "command": [
+      "systemd-run",
+      "--user",
+      "--wait",
+      "--collect",
+      "--pipe",
+      "--quiet",
+      "--unit=pbisc-strict-ye2026_sepsis-disease-draw2-score-44882-1791821839223163515",
+      "--slice=app.slice",
+      "--working-directory=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012",
+      "--expand-environment=no",
+      "-p",
+      "MemoryMax=32G",
+      "-p",
+      "MemorySwapMax=0",
+      "-p",
+      "OOMPolicy=kill",
+      "-p",
+      "OOMScoreAdjust=500",
+      "-p",
+      "CPUQuota=400%",
+      "/usr/bin/env",
+      "CUDA_VISIBLE_DEVICES=",
+      "PATH=/home/sj_server_1/.local/bin:/home/sj_server_1/miniforge3/bin:/usr/local/bin:/usr/bin:/bin",
+      "PYTHONDONTWRITEBYTECODE=1",
+      "PYTHONUNBUFFERED=1",
+      "OMP_NUM_THREADS=4",
+      "OPENBLAS_NUM_THREADS=4",
+      "MKL_NUM_THREADS=4",
+      "NUMBA_NUM_THREADS=4",
+      "/home/sj_server_1/miniforge3/envs/cxg_corpus/bin/python",
+      "-u",
+      "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/tools/score_strict.py",
+      "--support-manifest",
+      "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/protocol/splits/ye2026_sepsis/disease/draw2/support.json",
+      "--out",
+      "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw2",
+      "--action",
+      "all",
+      "--threads",
+      "4",
+      "--arm",
+      "lora=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/ye2026_sepsis/disease/draw2/lora.npz",
+      "--arm",
+      "pairedcal=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/ye2026_sepsis/disease/draw2/pairedcal.npz",
+      "--arm",
+      "scsemi=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/ye2026_sepsis/disease/draw2/scsemi.npz",
+      "--arm",
+      "raw=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/global/ye2026_sepsis/raw.npz",
+      "--arm",
+      "refcal=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/global/ye2026_sepsis/refcal.npz"
+    ]
+  },
+  "argv": [
+    "/home/sj_server_1/miniforge3/envs/cxg_corpus/bin/python",
+    "-u",
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/tools/score_strict.py",
+    "--support-manifest",
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/protocol/splits/ye2026_sepsis/disease/draw2/support.json",
+    "--out",
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw2",
+    "--action",
+    "all",
+    "--threads",
+    "4",
+    "--arm",
+    "lora=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/ye2026_sepsis/disease/draw2/lora.npz",
+    "--arm",
+    "pairedcal=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/ye2026_sepsis/disease/draw2/pairedcal.npz",
+    "--arm",
+    "scsemi=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/ye2026_sepsis/disease/draw2/scsemi.npz",
+    "--arm",
+    "raw=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/global/ye2026_sepsis/raw.npz",
+    "--arm",
+    "refcal=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/global/ye2026_sepsis/refcal.npz"
+  ],
+  "previous_outputs": null
+}

paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/x1_priority_20261015/builds/20261015T120743086141Z/sources/6979091e266244eb/donor_deg_summary.csv

@@ -0,0 +1,26 @@
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+lora,T cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,5,50,50
+lora,B cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,23
+lora,Monocyte,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,7,50,50
+lora,NK cell,ok,ok,ok,57,20,56,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,4,50,50
+lora,DC,ok,ok,ok,53,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,1,50,50
+pairedcal,T cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,50
+pairedcal,B cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,1,50,50
+pairedcal,Monocyte,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,12,50,50
+pairedcal,NK cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,2,50,50
+pairedcal,DC,ok,ok,ok,53,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,1,50,46
+scsemi,T cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,2,50,50
+scsemi,B cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,1,50,47
+scsemi,Monocyte,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,3,50,50
+scsemi,NK cell,ok,ok,ok,57,20,55,17,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,3,50,50
+scsemi,DC,ok,ok,ok,53,20,56,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,4,50,50
+raw,T cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,5,50,50
+raw,B cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,50
+raw,Monocyte,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,5,50,50
+raw,NK cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,4,50,50
+raw,DC,ok,ok,ok,53,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,0
+refcal,T cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,1,50,50
+refcal,B cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,0
+refcal,Monocyte,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,4,50,50
+refcal,NK cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,1,50,50
+refcal,DC,ok,ok,ok,53,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,33

paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/x1_priority_20261015/builds/20261015T120743086141Z/sources/f63f8311204ce33c/summary.json

@@ -0,0 +1,211 @@
+{
+ "schema": "paired_ft_scores.v1",
+ "dataset": "immicro",
+ "written_utc": "2026-10-15T11:43:18.258499+00:00",
+ "command": [
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+  "--dataset",
+  "immicro",
+  "--out",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/recoveries/x1_priority_completion_20261015/evaluation/units/immicro/healthy/fold4/n10/lora/score",
+  "--donors",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/recoveries/x1_priority_completion_20261015/evaluation/units/immicro/healthy/fold4/n10/lora/test_sample_ids.txt",
+  "--threads",
+  "2",
+  "--arm",
+  "lora=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/immicro/healthy/fold4/n10/lora.npz",
+  "--no-contrast",
+  "--no-deg"
+ ],
+ "arms": [
+  "lora"
+ ],
+ "donors": [
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+  "HS11",
+  "HS20",
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+  "HS70",
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+  "HS103",
+  "HS104"
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+ "n_donors": 21,
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