Archive 3 checkpoints (1-3)

paper-releases/pbisc-diffusion/updates/20261004T174508Z-sepsis-rare-states/diffusion/metadata/NOTE.md

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+# PBISC-diffusion update 20261004T174508Z-sepsis-rare-states
+
+Rare states on held-out donors of the Ye 2026 sepsis paired cohort (plans/rare_states_screen_20261004, 2026-10-05): pooled cross-fitted arms of paired_finetune_intradataset_20260927 (82 donors, real bulk K=1000; no new generation; benchmark Poisson read-out reproduced cell by cell, labels reused). MS1 (IL1R2+) monocytes gen/obs: zero-shot 0.08, LoRA 5 pairs 0.64, LoRA 58 pairs 0.71 (Spearman 0.57), directions kept; C1Q-high monocytes: zero-shot 0.03, pseudobulk zero-shot 0.06, LoRA 0.50-0.71 with directions kept from 10 pairs; cycling monocytes 0.15-0.31; granulocyte-like <= 0.07. Code, README, tables, per-arm marker extracts, logs.
+
+Payload states are recorded as supplied. Inference locations are pointers, not archived generated outputs.

paper-releases/pbisc-diffusion/updates/20261004T174508Z-sepsis-rare-states/diffusion/metadata/inference_locations.json

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+{
+  "locations": [],
+  "project_id": "pbisc-diffusion",
+  "update_id": "20261004T174508Z-sepsis-rare-states"
+}

paper-releases/pbisc-diffusion/updates/20261004T174508Z-sepsis-rare-states/diffusion/metadata/request.json

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+{
+  "assets": [
+    {
+      "host": "server_1",
+      "kind": "document",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_screen_20261004/README.md",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "log",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_screen_20261004/logs/analyze.err",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "log",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_screen_20261004/logs/analyze.log",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "log",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_screen_20261004/logs/extract_lora_n10__raw.err",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "log",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_screen_20261004/logs/extract_lora_n10__raw.log",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "log",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_screen_20261004/logs/extract_lora_n20__raw.err",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "log",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_screen_20261004/logs/extract_lora_n20__raw.log",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "log",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_screen_20261004/logs/extract_lora_n40__raw.err",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "log",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_screen_20261004/logs/extract_lora_n40__raw.log",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "log",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_screen_20261004/logs/extract_lora_n5__raw.err",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "log",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_screen_20261004/logs/extract_lora_n5__raw.log",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "log",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_screen_20261004/logs/extract_real_lora__raw.err",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "log",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_screen_20261004/logs/extract_real_lora__raw.log",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "log",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_screen_20261004/logs/extract_zs__pseudo.err",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "log",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_screen_20261004/logs/extract_zs__pseudo.log",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "log",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_screen_20261004/logs/extract_zs__raw.err",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "log",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_screen_20261004/logs/extract_zs__raw.log",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "table",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_screen_20261004/out/sepsis_contrasts.csv",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "table",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_screen_20261004/out/sepsis_per_donor.csv",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "table",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_screen_20261004/out/sepsis_summary.csv",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "code",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_screen_20261004/tools/sepsis_states.py",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "table",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_screen_20261004/work/sepsis/lora_n10__raw.npz",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "table",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_screen_20261004/work/sepsis/lora_n20__raw.npz",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "table",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_screen_20261004/work/sepsis/lora_n40__raw.npz",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "table",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_screen_20261004/work/sepsis/lora_n5__raw.npz",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "table",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_screen_20261004/work/sepsis/real_lora__raw.npz",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "table",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_screen_20261004/work/sepsis/zs__pseudo.npz",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "table",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_screen_20261004/work/sepsis/zs__raw.npz",
+      "state": "completed"
+    }
+  ],
+  "inference_locations": [],
+  "project_id": "pbisc-diffusion",
+  "summary": "Rare states on held-out donors of the Ye 2026 sepsis paired cohort (plans/rare_states_screen_20261004, 2026-10-05): pooled cross-fitted arms of paired_finetune_intradataset_20260927 (82 donors, real bulk K=1000; no new generation; benchmark Poisson read-out reproduced cell by cell, labels reused). MS1 (IL1R2+) monocytes gen/obs: zero-shot 0.08, LoRA 5 pairs 0.64, LoRA 58 pairs 0.71 (Spearman 0.57), directions kept; C1Q-high monocytes: zero-shot 0.03, pseudobulk zero-shot 0.06, LoRA 0.50-0.71 with directions kept from 10 pairs; cycling monocytes 0.15-0.31; granulocyte-like <= 0.07. Code, README, tables, per-arm marker extracts, logs."
+}