Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261013T124345Z-trunk4x-lora-sepsis-launch/diffusion/dataset/server_1/model8/plans/trunk4x_lora_sepsis_20261013/LAUNCH_RECEIPT.json

@@ -0,0 +1,34 @@
+{
+  "observed_at": "2026-10-13T12:42:23.207391+00:00",
+  "requested": "Run trunkx4+LoRA representative experiment",
+  "execution_host": "server_2",
+  "gpu_status_snapshot": {
+    "phase": "training",
+    "host": "spark-0110.local",
+    "at": "2026-10-13T12:40:27.398127+00:00",
+    "arm": "panel_matched_1x",
+    "draw": 0,
+    "log": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/trunk4x_lora_sepsis_20261013/runs/panel_matched_1x/draw0/train.log"
+  },
+  "first_training": {
+    "steps": 3000,
+    "train_pairs": 5,
+    "validation_pairs": 0,
+    "test_pairs": 77,
+    "trainable_parameters": 2217824,
+    "base_parameters": 239955168,
+    "wall_seconds": 337.9,
+    "checkpoint_sha256": "d2ef291b0e2d3ad7df40683a79000bb02c77ecc36cdf81331530747766cc6e09"
+  },
+  "gpu_service": "pbisc-trunk4x-sepsis-20261013.service",
+  "collector_service": "pbisc-trunk4x-collect-20261013.service",
+  "requested_draws": 5,
+  "requested_new_adapters": 10,
+  "evaluation_preflight_passed": true,
+  "comparison_complete": false,
+  "new_pretraining": false,
+  "existing_results_reused": [
+    "current_f01",
+    "scsemi"
+  ]
+}

paper-releases/pbisc-diffusion/updates/20261013T124345Z-trunk4x-lora-sepsis-launch/diffusion/dataset/server_1/model8/plans/trunk4x_lora_sepsis_20261013/MATCHED_PARENT_REUSE_AUDIT.json

@@ -0,0 +1,6 @@
+{
+  "candidate_training_records": [],
+  "registry_observation": "2026-10-13T00:45:19Z",
+  "limitation": "Registry is a bounded snapshot; both current run roots and cross-host parent locations inspected separately.",
+  "reason": "Parent checkpoints differ from existing final-panel LoRA; matched old-panel x1 is necessary control."
+}

paper-releases/pbisc-diffusion/updates/20261013T124345Z-trunk4x-lora-sepsis-launch/diffusion/dataset/server_1/model8/plans/trunk4x_lora_sepsis_20261013/PROTOCOL.json

@@ -0,0 +1,550 @@
+{
+  "schema": "pbisc.trunk-lora.representative.v1",
+  "cohort": "ye2026_sepsis",
+  "primary_comparison": "legacy_panel_1x_vs_legacy_panel_trunk4x",
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+        "Abd-S66",
+        "Res-S150",
+        "Skin-S74",
+        "Res-S77"
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+        "Abd-PS05",
+        "Abd-PS07",
+        "Abd-PS19",
+        "Abd-PS20",
+        "Abd-PS23",
+        "Abd-PS27",
+        "Abd-S102",
+        "Abd-S103",
+        "Abd-S120",
+        "Abd-S123",
+        "Abd-S156",
+        "Abd-S39",
+        "Abd-S42",
+        "Abd-S47",
+        "Abd-S51",
+        "Abd-S54",
+        "Abd-S57",
+        "Abd-S79",
+        "Abd-S83",
+        "Abd-S98",
+        "HC01",
+        "HC05",
+        "HC09",
+        "HC12",
+        "HC13",
+        "HC16",
+        "IC10",
+        "IC15",
+        "IC16",
+        "IC19",
+        "IC22",
+        "IC23",
+        "PHC01",
+        "PHC02",
+        "PHC03",
+        "PHC05",
+        "PIC01",
+        "PIC02",
+        "PIC04",
+        "PIC05",
+        "Res-PS02",
+        "Res-PS03",
+        "Res-PS12",
+        "Res-PS16",
+        "Res-PS21",
+        "Res-PS22",
+        "Res-PS25",
+        "Res-PS26",
+        "Res-S10",
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+        "Res-S127",
+        "Res-S136",
+        "Res-S139",
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+        "Res-S149",
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+        "Res-S166",
+        "Res-S174",
+        "Res-S177",
+        "Res-S184",
+        "Res-S19",
+        "Res-S26",
+        "Res-S40",
+        "Res-S87",
+        "Skin-S140",
+        "Skin-S142",
+        "Skin-S152",
+        "Skin-S38",
+        "Skin-S43",
+        "Skin-S46",
+        "Skin-S52",
+        "Uri-S134",
+        "Uri-S147",
+        "Uri-S157",
+        "Uri-S20",
+        "Uri-S93"
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+    },
+    {
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+        "Abd-S42",
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+        "HC07",
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+        "IC10",
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+        "IC16",
+        "IC19",
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+        "PIC04",
+        "PIC05",
+        "Res-PS02",
+        "Res-PS03",
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+        "Res-S177",
+        "Res-S184",
+        "Res-S19",
+        "Res-S26",
+        "Res-S40",
+        "Res-S77",
+        "Res-S87",
+        "Skin-S140",
+        "Skin-S142",
+        "Skin-S152",
+        "Skin-S38",
+        "Skin-S43",
+        "Skin-S46",
+        "Skin-S52",
+        "Skin-S74",
+        "Uri-S157",
+        "Uri-S20",
+        "Uri-S93"
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+    },
+    {
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+        "Res-S177",
+        "Skin-S74",
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+        "Abd-PS05",
+        "Abd-PS07",
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+        "Abd-PS20",
+        "Abd-PS23",
+        "Abd-PS27",
+        "Abd-S102",
+        "Abd-S103",
+        "Abd-S120",
+        "Abd-S123",
+        "Abd-S156",
+        "Abd-S39",
+        "Abd-S42",
+        "Abd-S47",
+        "Abd-S51",
+        "Abd-S54",
+        "Abd-S57",
+        "Abd-S66",
+        "Abd-S79",
+        "Abd-S83",
+        "Abd-S98",
+        "HC01",
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+        "HC07",
+        "HC09",
+        "HC12",
+        "HC13",
+        "HC16",
+        "IC10",
+        "IC15",
+        "IC16",
+        "IC19",
+        "IC22",
+        "IC23",
+        "PHC01",
+        "PHC02",
+        "PHC03",
+        "PHC05",
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+        "PIC04",
+        "PIC05",
+        "Res-PS02",
+        "Res-PS03",
+        "Res-PS12",
+        "Res-PS16",
+        "Res-PS21",
+        "Res-PS22",
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+        "Res-PS26",
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+        "Res-S149",
+        "Res-S150",
+        "Res-S164",
+        "Res-S166",
+        "Res-S174",
+        "Res-S184",
+        "Res-S19",
+        "Res-S26",
+        "Res-S40",
+        "Res-S87",
+        "Skin-S140",
+        "Skin-S142",
+        "Skin-S152",
+        "Skin-S38",
+        "Skin-S43",
+        "Skin-S46",
+        "Skin-S52",
+        "Uri-S134",
+        "Uri-S147",
+        "Uri-S157",
+        "Uri-S20",
+        "Uri-S93"
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+    },
+    {
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+        "Skin-S142",
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+        "Skin-S140",
+        "Skin-S152",
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+        "Skin-S46",
+        "Skin-S52",
+        "Skin-S74",
+        "Uri-S134",
+        "Uri-S147",
+        "Uri-S157",
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+    },
+    {
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+        "Res-PS22",
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+        "Skin-S140",
+        "Skin-S152",
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+        "Skin-S74",
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+    }
+  ],
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+    "data/draw1/ye2026_sepsis/folds.csv": "da730548950f084c76ab4325f98efa51966ee2f874f9df2ced9ebe649fc28308",
+    "data/draw3/ye2026_sepsis/train_donors.txt": "191f6856bc6168d6fab8afd4b2ab1ec61db06e3a7b13b1649035b23acd155251",
+    "data/draw3/ye2026_sepsis/support.json": "4f329b51b107925621b89dfc62b41f65baebefd6bc7625b10c3848194121296b",
+    "data/draw3/ye2026_sepsis/PREPARATION.json": "afdca0fb4040f562a640ca4be91a874d18334d9c77c8550a844c68acf84c0840",
+    "data/draw3/ye2026_sepsis/test_raw.npz": "3278dc672b740fbb8ac68faf9fd17229672a8dd5a8d3902bf282a949b7edb1ef",
+    "data/draw3/ye2026_sepsis/cells_panel6k.npz": "0cbff9e7c85db5525f6e69310d0c9a1c29219e8209a0eeed3781ec40b300403f",
+    "data/draw3/ye2026_sepsis/folds.csv": "da730548950f084c76ab4325f98efa51966ee2f874f9df2ced9ebe649fc28308",
+    "data/draw0/ye2026_sepsis/train_donors.txt": "55ca4d1c767db17aba3a9f9e84d60841f66dc7cb0a16fb73ddd33e22237c1d78",
+    "data/draw0/ye2026_sepsis/support.json": "06dd3dede455dd0c86f2fa337830d03d7bb9e60c33475805818a85f9217c13fc",
+    "data/draw0/ye2026_sepsis/PREPARATION.json": "6f3c9d98af7f66815aba0432c17a51d304859ac45dc6617843374f9d693dea76",
+    "data/draw0/ye2026_sepsis/test_raw.npz": "ae163d5eb1531842e2acea7db21a0a500f7642767566cdc639be42951543bba9",
+    "data/draw0/ye2026_sepsis/cells_panel6k.npz": "e3743901ccbbe0baed4f69cc49dee2f8c1d9af0be6a4d624242ef60d39bfacb3",
+    "data/draw0/ye2026_sepsis/folds.csv": "da730548950f084c76ab4325f98efa51966ee2f874f9df2ced9ebe649fc28308"
+  },
+  "code": {
+    "tools/ft_sdd_frozen.py": "9333b296acfb58e52ebe10e30c3334250bf2ce8c3dbfd446d65726f6b8da4abb",
+    "tools/runtime.py": "67ea571aa077aa1d17131a9d5ade3eadc8c310620d8a358be81d3f69e065a7aa",
+    "tools/prepare.py": "e024b2d84c400ba728be6f97fc4c42c5f6d855deaebbe2d5cc48d96acdf13beb",
+    "tools/sample_one_frozen.py": "e1054d2e753361b33c44789eeae888234b700f4e3cafbba123948cd5c203dc04",
+    "tools/gpu_campaign.py": "2345abe387d490b09a76e0d6e0fd73a75b51501d78650ba14ee429a1e132b4c4"
+  }
+}

paper-releases/pbisc-diffusion/updates/20261013T124345Z-trunk4x-lora-sepsis-launch/diffusion/dataset/server_1/model8/plans/trunk4x_lora_sepsis_20261013/README.md

@@ -0,0 +1,31 @@
+# Trunk ×4 + LoRA: representative paired Sepsis comparison
+
+User-authorized2026-10-13. Run on server_2 through its verified ml-run/guard/exclusive lock. Existing server_1 campaign remains untouched.
+
+## Question and controlled comparison
+
+Does the saved trunk×4 model's advantage transfer to **five-pair LoRA disease reconstruction**? Use Ye Sepsis, all five existing support draws, 5 training donors / 0 validation / 77 held-out donors per draw.
+
+The requested trunk×4 checkpoint uses the historical6k gene panel, while the current f01 model uses a different6k panel. Therefore:
+
+1. **Primary width comparison:** old-panel×1 versus old-panel trunk×4. Same genes, corpus,16-part pretraining schedule, context512, LoRA rank16/alpha16, lr0.0005, batch256, warmup200, EMA0.999, fixed3000steps and training seed20260927.
+2. **Current-paper reference:** reuse the current f01×1 LoRA and scSemi generated outputs from the strict campaign, without training/regenerating them.
+3. All four arms are evaluated on the **4258 common panel genes;4243 genes measured in both assays**, with the complete frozen1006-gene annotation query retained. This is a newly defined common-axis comparison; do not compare these scores numerically with full-panel historical headline values.
+
+Ten new adapters total: two checkpoint parents × five draws. No new pretraining. Rank is matched; parameter count is not: trunk×4 has2,217,824 trainable LoRA parameters versus1,296,224 for×1. This is the width+fixed-rank comparison, not a parameter-matched adapter-budget claim.
+
+Support/test IDs exactly reproduce saved runs. Training inputs stream **only five support donors' expression ranges** from saved full-axis counts, project to the old panel, and leave every other cell row empty while preserving original cell indexing/RNG semantics. No held-out sc expression is loaded by the trainer. Observed reference construction is separate CPU evaluation.
+
+## Execution and outputs
+
+- `PROTOCOL.json`: immutable training/sampling contract, input hashes and checkpoint identities.
+- `reuse_candidates.json`: registry query found no trunk×4 LoRA candidate; new work is justified by the changed pretrained parent. Same-panel×1 adaptation is required to separate width from gene-panel changes.
+- Remote `GPU_STATUS.json`, `campaign.log`, `runs/<arm>/drawN/train.log`: live GPU progress.
+- Local `STATUS.json`: result collection and CPU scoring progress. No automatic scientific-operation retries.
+- `reference/READY.json`: common-axis reference with preserved frozen observed labels and refreshed normalization/aggregates.
+- `scores/drawN/summary.json`: four-arm common-axis metrics.
+- `COMPARISON.csv`, `COMPARISON_MEANS.csv`, `DONOR_PAIRED_CI.csv`, `COMPARISON.png/pdf/svg`, `RESULT.json`: produced only after all five draws finish.
+
+Metrics: disease logFC Pearson/partial correlation, donor-pseudobulk top50DEG overlap, composition L1, precision/coverage and donor expression correlation. Shared-donor paired bootstrap carries all appearances across draws for donor-level metrics. Draw scatter is descriptive, not independent biological replication. Primary disease contrast definitions use existing benchmark code; no winner-selected endpoint or extra training runs.
+
+GPU controller service on server_2: `pbisc-trunk4x-sepsis-20261013.service` (executes ml-run). Local collector: `pbisc-trunk4x-collect-20261013.service`. Checkpoints remain on server_2; completed generated arrays and small run receipts are copied to server_1 and hash-verified. A failure stops the workflow and preserves outputs/logs; guard stops are never auto-restarted.