Archive 4 checkpoints (1-4)
Browse files- paper-releases/pbisc-diffusion/updates/20261013T005008Z-reuse-audit-results-deck/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/PROGRESS.md +61 -0
- paper-releases/pbisc-diffusion/updates/20261013T005008Z-reuse-audit-results-deck/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/audit_reuse_20261013/CLEANUP.json +565 -0
- paper-releases/pbisc-diffusion/updates/20261013T005008Z-reuse-audit-results-deck/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/audit_reuse_20261013/CONFIRMED_DUPLICATE_TRAINING.json +1354 -0
- paper-releases/pbisc-diffusion/updates/20261013T005008Z-reuse-audit-results-deck/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/audit_reuse_20261013/FINAL_VERIFICATION.json +16 -0
paper-releases/pbisc-diffusion/updates/20261013T005008Z-reuse-audit-results-deck/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/PROGRESS.md
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| 1 |
+
# Implementation ledger — paper_figures_strictpairs_20261012
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| 2 |
+
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| 3 |
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## State (updated 2026-10-12 12:28 UTC)
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| 4 |
+
- Implementation and guarded execution are in progress; the full scientific campaign is not complete.
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| 5 |
+
- 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.
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| 6 |
+
- 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.
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| 7 |
+
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| 8 |
+
## Work packages
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| 9 |
+
1. Strict support selection and opt-in legacy adapters: implemented; 40 support units prepared and tested.
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| 10 |
+
2. Figure1 concept/corpus: complete with SVG/PDF/PNG and source provenance.
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| 11 |
+
3. Architecture/panel rescoring: eight arms complete on the shared held-out reference; separate sweep floors retained.
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| 12 |
+
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.
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| 13 |
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5. Figure3–5 visual/statistical pipeline: implemented; strict final outputs await upstream generation/scoring. Historical rare results are explicitly diagnostic.
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| 14 |
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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.
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| 15 |
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| 16 |
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Latest completed verification: 93 focused CPU tests passed (2026-10-12). This does not certify unexecuted full-cohort analyses.
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## Interface preflight
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| Producer | Consumer | Binding |
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| 20 |
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|---|---|---|
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| 21 |
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| Support manifests | LoRA/calibration/scSemi/deconvolution | exact sample IDs, unique donors, no test donor or extra visit access |
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| 22 |
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| Rescoring/campaign | Figures/Results | source-bound typed metrics and readiness, no mixing old n+validation with strict-n |
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| Figure1 | Methods/other panels | K_cond=1000; rho=3869.603120208939; N_gen=1500 distinct |
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| 24 |
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| Rare metrics | Figure5 | include zeros, patient IDs, mandatory marker availability, descriptive Behcet |
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| 25 |
+
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| 26 |
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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.
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| 28 |
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## Prelaunch review correction
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- Fixed inconsistent Imperial date axis (C137 draw4 now2020-04-30), strict QC-excluded visit validation, complete trainer resume binding, runtime outputSHAverification.
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| 30 |
+
- Restored oldscSemi wrapper byte-exact; added opt-in strictwrapper.
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| 31 |
+
- Preserved prelaunch generated support/conditions at backups/preflight_rejected_v1; never used for GPU work.
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| 32 |
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- Figure1 produced+visually checked; pretrain P/C8arms rescoredCPU; source tables ready.
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| 33 |
+
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| 34 |
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## Execution checkpoint — 2026-10-12 13:02 UTC
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- 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.
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| 36 |
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- 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`.
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| 37 |
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- 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.
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| 38 |
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- 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.
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| 39 |
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- 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.
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| 40 |
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- 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.
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| 41 |
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- `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.
|
| 42 |
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- 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.
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| 43 |
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- 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.
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| 44 |
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| 45 |
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## Manual-reboot recovery and two-host continuation — 2026-10-12T14:40:00.856956+00:00
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| 46 |
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- Recovered error request 0fca7335-c7fb-4f21-a1a6-062ed275c9b9 to the approved original chat/PLAN.md. Figure6 stays waiting for user data.
|
| 47 |
+
- 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.
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| 48 |
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- 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.
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| 49 |
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- Native runtime maps keep canonical scientific signatures, record actual host/executable and preserve exclusive guarded GPU launches. Remote22shared sources and151staged files verified by SHA256.
|
| 50 |
+
- 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.
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| 51 |
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- Full CPU regression172passed6dependency skips18subtests; isolation cases covered in two environments. Independent review found no P1/P2 blockers.
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| 52 |
+
- First remote strict LoRA training completed; local historical outputs verified-skipped and fold1 scoring resumed. Full scientific results remain incomplete.
|
| 53 |
+
- 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.
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| 54 |
+
- Live progress: recoveries/two_host/STATUS.json and CAMPAIGN_STATUS.json. Source-backed recovery proof: recoveries/RESUME_VERIFICATION.json.
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| 55 |
+
|
| 56 |
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## Existing-result reuse correction — 2026-10-13T00:43:48.209963+00:00
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| 57 |
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- Whole-Model8 metadata inventory and mandatory reuse gate added at root. Native receipt format is not a scientific reason to rerun.
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| 58 |
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- Five tensor-identical Sepsis duplicate trainings identified; historical serialized checkpoints retained solely for existing output provenance, excluded as independent evidence.
|
| 59 |
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- Sepsis deconvolution now adopts all5 verified old outputs and performs only corrected CPUscoring. Other15 disease supports remain new exact-five designs.
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| 60 |
+
- Available-results34slide PDF/PPTX replaces the TODO-heavy8page working layout.45obsolete generatedpreview files deleted after archive readback; see audit_reuse_20261013/CLEANUP.json.
|
| 61 |
+
- Scientific campaign continues; available-results review is not a full strict-campaign completion claim.
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paper-releases/pbisc-diffusion/updates/20261013T005008Z-reuse-audit-results-deck/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/audit_reuse_20261013/CLEANUP.json
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paper-releases/pbisc-diffusion/updates/20261013T005008Z-reuse-audit-results-deck/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/audit_reuse_20261013/FINAL_VERIFICATION.json
ADDED
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@@ -0,0 +1,16 @@
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{
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