Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261012T143729Z-strictpairs-recovery-two-host/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T143729Z-strictpairs-recovery-two-host/snapshot/resume_verification/PROGRESS.md

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+# Implementation ledger — paper_figures_strictpairs_20261012
+
+## State (updated 2026-10-12 12:28 UTC)
+- Implementation and guarded execution are in progress; the full scientific campaign is not complete.
+- Source Model8 Git has no commits and existing staged/untracked research assets. All new output is isolated in this versioned plan root; only opt-in legacy adapters may be changed with byte backups.
+- Canonical manuscript is clean at `fb6380f` as observed on 2026-10-12. Other authorized work changed the Abstract during this task; preserve the latest approved frontmatter when assembling the isolated manuscript.
+
+## Work packages
+1. Strict support selection and opt-in legacy adapters: implemented; 40 support units prepared and tested.
+2. Figure1 concept/corpus: complete with SVG/PDF/PNG and source provenance.
+3. Architecture/panel rescoring: eight arms complete on the shared held-out reference; separate sweep floors retained.
+4. Campaign: ImMicro fold0 n5 LoRA training, LoRA/pairedcal/scSemi generation and two all-ImMicro raw/refcal controls complete. The first full five-arm score is running. Remaining strict units await this integration gate.
+5. Figure3–5 visual/statistical pipeline: implemented; strict final outputs await upstream generation/scoring. Historical rare results are explicitly diagnostic.
+6. Review deck and staged manuscript PDF: produced with pending labels. Final rendering/export integration and archive snapshot preparation are in progress. Canonical manuscript is not modified by this task.
+
+Latest completed verification: 93 focused CPU tests passed (2026-10-12). This does not certify unexecuted full-cohort analyses.
+
+## Interface preflight
+| Producer | Consumer | Binding |
+|---|---|---|
+| Support manifests | LoRA/calibration/scSemi/deconvolution | exact sample IDs, unique donors, no test donor or extra visit access |
+| Rescoring/campaign | Figures/Results | source-bound typed metrics and readiness, no mixing old n+validation with strict-n |
+| Figure1 | Methods/other panels | K_cond=1000; rho=3869.603120208939; N_gen=1500 distinct |
+| Rare metrics | Figure5 | include zeros, patient IDs, mandatory marker availability, descriptive Behcet |
+
+Ruling: use a new versioned workspace within the registered Model8 core because its source Git is unborn and has substantial pre-existing research assets; do not stage/commit those assets or clone a misleading incomplete tree. Manuscript changes will be staged as an isolated copy and reviewed before safe integration.
+
+## Prelaunch review correction
+- Fixed inconsistent Imperial date axis (C137 draw4 now2020-04-30), strict QC-excluded visit validation, complete trainer resume binding, runtime outputSHAverification.
+- Restored oldscSemi wrapper byte-exact; added opt-in strictwrapper.
+- Preserved prelaunch generated support/conditions at backups/preflight_rejected_v1; never used for GPU work.
+- Figure1 produced+visually checked; pretrain P/C8arms rescoredCPU; source tables ready.
+
+## Execution checkpoint — 2026-10-12 13:02 UTC
+- First complete five-arm healthy unit (`immicro/healthy/fold0/n5`) passed generation, scoring, extras and donor bootstrap. This is 1/20 healthy learning-curve units and 1/5 Figure3 folds, not a final pooled claim.
+- Sepsis scSemi all five existing exact-five runs were audited and adopted without new GPU training: same 5 representatives, 77 targets, own-n HVG, equivalent prepared cells, model/shard/output SHA checks, independent shard-level export validation. Embedded legacy metadata remains unchanged. See `reports/deconv_scsemi_reuse_audit.md`.
+- Eight pretraining arms now have common-readout composition scores in addition to P/C. Full NPZ hashes and frozen-annotation concordance were verified; neither 6k nor r16 is described as best on every endpoint.
+- Historical healthy rank/full now uses only real-bulk FT with the same outer-fold train/validation/test IDs; strict size curves contain all five comparator arms. Zero-target-pair baselines are explicit.
+- Disease main statistics use patient-aware contrasts and shared patient bootstrap across draws. Old visit-level sensitivity stays separate. Figure4 historical comparison uses actual real-bulk LoRA and scSemi five-fold sources, including Giroux exclusions.
+- Figure3 has common cell-type-colored UMAP panels, full-cell composition fractions, and separate adaptation/generation times. Figure5 has all-state detection/abundance tables and separate Behcet any-C1Q vs multi-C1Q plots; Behcet calibration uses the same three candidate pairs, not external AIFI.
+- `pbisc-strict-global-controls-20261012.service` is generating disease controls sequentially. `pbisc-strict-full-campaign-20261012.service` is queued behind its controller lock, then runs all 40 units, CPU derivations, gated PDFs/PPTX, and a one-time verified final archive delta. Failures stop for inspection; no OOM/restart loop.
+- Latest full test run: 134 passed. Reviewed primary disease statistics/adoption provenance have no outstanding P1/P2 from the final narrow review. Full disease/rare and healthy multi-fold scientific results remain pending execution.
+- Canonical manuscript remains unchanged by this task. Staging refreshes the latest approved frontmatter. Figure6 has no analysis or experiment launched. No GitHub push/Overleaf sync.
+
+## Manual-reboot recovery and two-host continuation — 2026-10-12T14:40:00.856956+00:00
+- Recovered error request 0fca7335-c7fb-4f21-a1a6-062ed275c9b9 to the approved original chat/PLAN.md. Figure6 stays waiting for user data.
+- Healthy fold1 scSemi regenerated only absent/corrupt targets; all22 targets exported and validated, recovery service exited0. Original12valid shards and all checkpoints retained; HS51 corruption quarantined.
+- Finished strict support-only CSR and bulk-only loaders. Real support arrays and3000 seeded cell draws match for completed fold0/fold1. Historical full-array access is explicitly retained as a limitation; four old receipts remain byte-identical and use source/replay-bound reuse attestations.
+- Native runtime maps keep canonical scientific signatures, record actual host/executable and preserve exclusive guarded GPU launches. Remote22shared sources and151staged files verified by SHA256.
+- Durable two-host controller now assigns12healthy fold2/3/4 units to server2 and28other units to server1. Transfers verify hashes/raw receipts and fail closed; all40 results join centrally before scoring/render/archive final gates. No automatic compute retry.
+- Full CPU regression172passed6dependency skips18subtests; isolation cases covered in two environments. Independent review found no P1/P2 blockers.
+- First remote strict LoRA training completed; local historical outputs verified-skipped and fold1 scoring resumed. Full scientific results remain incomplete.
+- Original1455asset implementation upload finished payload publication and is in independent final verification. Caption +36asset recovery implementation delta queued behind that writer; see recoveries/ARCHIVE_RECOVERY_STATUS.json.
+- Live progress: recoveries/two_host/STATUS.json and CAMPAIGN_STATUS.json. Source-backed recovery proof: recoveries/RESUME_VERIFICATION.json.

paper-releases/pbisc-diffusion/updates/20261012T143729Z-strictpairs-recovery-two-host/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T143729Z-strictpairs-recovery-two-host/snapshot/resume_verification/RESUME_VERIFICATION.json

@@ -0,0 +1,31 @@
+{
+  "at": "2026-10-12T14:40:00.856956+00:00",
+  "origin_thread": "01a12f5c-9d68-7910-8863-a1ca499a3a8c",
+  "original_error_request_id": "0fca7335-c7fb-4f21-a1a6-062ed275c9b9",
+  "reason": "user_confirmed_manual_reboot_then_requested_resume",
+  "scientific_campaign_complete": false,
+  "figure6": "waiting_user_data_no_execution",
+  "recovery_scsemi_fold1": {
+    "targets": 22,
+    "export_validated": true,
+    "service_exit": 0
+  },
+  "tests": {
+    "environment": "cxg_corpus",
+    "passed": 172,
+    "dependency_skips": 6,
+    "subtests_passed": 18,
+    "isolation_cross_environment": "b2sc33passed1skip;cxg23passed3skip;allnewtestscoveredacrossboth"
+  },
+  "independent_review": "no P1/P2 blockers found; review did not execute tests",
+  "source_reuse_transitions": 4,
+  "remote_base_input_hashes_matched": 22,
+  "remote_staged_hashes_matched": 151,
+  "partition": {
+    "server_1": 28,
+    "server_2": 12
+  },
+  "controller": "pbisc-strict-two-host-controller-20261012.service",
+  "archive_followup": "pbisc-strict-finish-recovery-archives-20261012.service",
+  "no_github_push_or_overleaf_sync": true
+}

paper-releases/pbisc-diffusion/updates/20261012T143729Z-strictpairs-recovery-two-host/diffusion/metadata/inference_locations.json

@@ -0,0 +1,5 @@
+{
+  "locations": [],
+  "project_id": "pbisc-diffusion",
+  "update_id": "20261012T143729Z-strictpairs-recovery-two-host"
+}

paper-releases/pbisc-diffusion/updates/20261012T143729Z-strictpairs-recovery-two-host/diffusion/metadata/request.json

@@ -0,0 +1,235 @@
+{
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+      "state": "completed"
+    },
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+      "state": "completed"
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+      "state": "completed"
+    },
+    {
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+      "state": "completed"
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+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "report",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/archive/20261012T143729Z-strictpairs-recovery-two-host/snapshot/11/REMOTE_SOURCE_VERIFICATION.json",
+      "state": "completed"
+    },
+    {
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+      "kind": "report",
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+      "kind": "report",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/archive/20261012T143729Z-strictpairs-recovery-two-host/snapshot/13/config.json",
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+    {
+      "host": "server_1",
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+    {
+      "host": "server_1",
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+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/archive/20261012T143729Z-strictpairs-recovery-two-host/snapshot/16/ft_sdd.py",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "code",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/archive/20261012T143729Z-strictpairs-recovery-two-host/snapshot/17/prepare_draw_inputs.py",
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+    },
+    {
+      "host": "server_1",
+      "kind": "report",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/archive/20261012T143729Z-strictpairs-recovery-two-host/snapshot/18/immicro-healthy-fold1-n5-train-proof.json",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "report",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/archive/20261012T143729Z-strictpairs-recovery-two-host/snapshot/19/immicro-healthy-fold0-n5-train-proof.json",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "report",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/archive/20261012T143729Z-strictpairs-recovery-two-host/snapshot/20/immicro-healthy-fold1-n5-train.json",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "report",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/archive/20261012T143729Z-strictpairs-recovery-two-host/snapshot/21/immicro-healthy-fold0-n5-scinputs-proof.json",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "report",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/archive/20261012T143729Z-strictpairs-recovery-two-host/snapshot/22/immicro-healthy-fold0-n5-train.json",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "report",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/archive/20261012T143729Z-strictpairs-recovery-two-host/snapshot/23/immicro-healthy-fold1-n5-scinputs-proof.json",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "report",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/archive/20261012T143729Z-strictpairs-recovery-two-host/snapshot/24/immicro-healthy-fold1-n5-scinputs.json",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "report",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/archive/20261012T143729Z-strictpairs-recovery-two-host/snapshot/25/immicro-healthy-fold0-n5-scinputs.json",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "report",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/archive/20261012T143729Z-strictpairs-recovery-two-host/snapshot/26/REPLAY.json",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "report",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/archive/20261012T143729Z-strictpairs-recovery-two-host/snapshot/27/REPLAY.json",
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+    },
+    {
+      "host": "server_1",
+      "kind": "report",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/archive/20261012T143729Z-strictpairs-recovery-two-host/snapshot/28/ISOLATION.json",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "report",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/archive/20261012T143729Z-strictpairs-recovery-two-host/snapshot/29/ISOLATION.json",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "code",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/archive/20261012T143729Z-strictpairs-recovery-two-host/snapshot/30/support_input_isolation.py",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "code",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/archive/20261012T143729Z-strictpairs-recovery-two-host/snapshot/31/ft_sdd.py",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "code",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/archive/20261012T143729Z-strictpairs-recovery-two-host/snapshot/32/prepare_draw_inputs.py",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "report",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/archive/20261012T143729Z-strictpairs-recovery-two-host/SOURCE_MAP.json",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "code",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/archive/20261012T143729Z-strictpairs-recovery-two-host/snapshot/archive_queue/finish_recovery_archives.py",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "report",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/archive/20261012T143729Z-strictpairs-recovery-two-host/snapshot/archive_queue/ARCHIVE_RECOVERY_QUEUE.json",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "report",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/archive/20261012T143729Z-strictpairs-recovery-two-host/snapshot/resume_verification/PROGRESS.md",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "report",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/archive/20261012T143729Z-strictpairs-recovery-two-host/snapshot/resume_verification/RESUME_VERIFICATION.json",
+      "state": "completed"
+    }
+  ],
+  "inference_locations": [],
+  "project_id": "pbisc-diffusion",
+  "summary": "Manual-reboot recovery resumed: prior healthy fold1 scSemi 22-target generation/export independently validated; strict support-only loaders finished and selected-value/3000 draw parity checked for two historical units, whose original receipts and access limitation remain preserved. Added source-attested receipt reuse and native host execution maps, disjoint12 remote/28local durable execution with verified imports and central finalization. Integrated CPU tests172pass6dependency skips18subtests; new isolation tests exercised across two environments; independent review no P1/P2. 22base inputs and151 stagedfiles matched server2SHA. Scientific campaign still running, figures3–5 not final, Figure6waiting user data; no GitHub/Overleaf actions. This delta snapshots stable recovery implementation/evidence only."
+}