Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261015T141849Z-rare-cell-7k-8k-panels/diffusion/dataset/server_1/model8/plans/rare_gene_context_expansion_20261015/coordination/TASK_CONTRACT.json

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+{
+  "date": "2026-10-15",
+  "user_request": "Subagent-led primary research and concrete expansion of final6k into7k/8k for ILC and disease-specific rare-population coverage.",
+  "ownership": {
+    "research/ilc_dc": "ilc_rare_identity_research",
+    "research/disease": "disease_rare_program_research",
+    "panel_audit_build_and_report": "panel_expansion_audit",
+    "coordination_and_archive": "root"
+  },
+  "deliverables": [
+    "Primary-source evidence ledger with retrieved gene-list provenance",
+    "Exact baseline6k and rare-label ontology audit",
+    "Deterministic nested7000/8000 gene lists and machine-readable positions/ID mapping",
+    "Coverage and missing/unavailable-gene reports",
+    "Budget recommendation tied to coverage, not presumed model performance",
+    "Fair validation protocol separating label absence from generation absence"
+  ],
+  "boundaries": [
+    "No root-led biological literature search; research performed by subagents as requested",
+    "No new model training, inference or GPU jobs for this panel-design task",
+    "No edits to active or frozen model/panel/evaluation artifacts",
+    "No independent validation claim for marker lists derived from the same benchmark papers",
+    "Unmeasured/raw-axis-absent genes are not zero-expression genes",
+    "Do not claim universal rare-cell coverage or that gene addition guarantees generation"
+  ]
+}

paper-releases/pbisc-diffusion/updates/20261015T141849Z-rare-cell-7k-8k-panels/diffusion/dataset/server_1/model8/plans/rare_gene_context_expansion_20261015/coordination/ilc_training_support/ASSET_MANIFEST.json

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+}

paper-releases/pbisc-diffusion/updates/20261015T141849Z-rare-cell-7k-8k-panels/diffusion/dataset/server_1/model8/plans/rare_gene_context_expansion_20261015/coordination/ilc_training_support/REPORT.md

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+# Existing TRAIN ILC: measured and detected support
+
+The fixed source-label/split selection contains **16,439 TRAIN ILC records** from 12 datasets, 2,417 sample keys and 937 corrected dataset-scoped donor identities. The independent all-split replay matches 19,329 source-labelled ILC records exactly. This is an audit of existing source annotations, not new biological adjudication or model output.
+
+The audit reads 48 raw gene loci (47 symbols), including both CRLF2 loci. Measurement masks define the denominator; unavailable genes are never represented as measured zero. TRAC is absent from the canonical 20,097-gene axis. The completed 6k run configuration, manifest, selected gene IDs and position-array hashes were verified unchanged. Final 7k/8k membership was joined from the integrator's frozen panels after extraction; expression did not change membership or ranking.
+
+| Missing from final 6k | Detected / measured TRAIN ILC | Detected corrected donors | Detected datasets | 7k | 8k |
+|---|---:|---:|---:|:---:|:---:|
+| PTGDR2 | 518 / 16,439 (3.151%) | 201 | 11 | Yes | Yes |
+| IL12RB1 | 1,063 / 16,439 (6.466%) | 323 | 12 | No | Yes |
+| CSF2 | 113 / 16,439 (0.687%) | 82 | 12 | Yes | Yes |
+| IL5 | 19 / 16,354 (0.116%) | 10 | 5 | Yes | Yes |
+| IL13 | 46 / 16,354 (0.281%) | 17 | 5 | Yes | Yes |
+| NCR2 | 9 / 16,354 (0.055%) | 8 | 4 | Yes | Yes |
+| IL17A | 0 / 16,354 (0%) | 0 | 0 | Yes | Yes |
+| IL17F | 2 / 16,354 (0.012%) | 2 | 2 | Yes | Yes |
+| IL22 | 1 / 16,354 (0.006%) | 1 | 1 | Yes | Yes |
+| CRLF2, ENSG00000205755 | 57 / 8,954 (0.637%) | 46 | 6 | No | Yes |
+
+Nine of the ten missing-6k loci have at least one positive count in measured source-labelled TRAIN ILC cells. This establishes available native expression evidence, not sufficient training signal, successful generation or improved classification. IL17A is measured but not detected in this subset; that does not establish absent biological function.
+
+Existing 6k identity-associated genes already have support: IL7R 9,318/16,439 (56.68%), KLRB1 7,389 (44.95%), GATA3 4,774 (29.04%), KIT 4,289 (26.09%), RORA 2,375 (14.45%) and RORC 567 (3.45%). Native sampling and cohort concentration matter: canonical raw-count depth has median 2,607, IQR 1,610–3,598 and range 390–28,863. Dataset 304 contributes 7,485/16,439 cells. Its cytokine-context source contributes 1,872/1,880 IL1RL1 detections, 35/46 IL13, 13/19 IL5 and the sole IL22 detection. These are not balanced, unstimulated population frequencies.
+
+Both CRLF2 loci are retained separately: ENSG00000205755 is measured in 8,954 cells outside dataset 304; the already-6k ENSG00000292363 is measured in dataset 304's 7,485 cells and detected in 655. Their mutually different measurement coverage makes symbol-level merging inappropriate for this audit.
+
+Descriptive overlap exposes annotation uncertainty without relabelling: IL7R and KLRB1 are jointly detected in 6,936 cells; CD3D or CD3E in 2,188; NKG7 and GNLY in 1,401. Among IL7R/KLRB1 co-detected cells, 1,381 also have CD3D or CD3E, and 1,106 also have both NKG7 and GNLY. These positive-count patterns are not identity classifiers, and no source labels were changed.
+
+## Verification and bounds
+
+- All 125 selected shards and all 16,439 physical row identities were replayed. E2 row_index is the contiguous CSR position; BLOCK's pre-QC row_index differs for 739 selected cells and was not used for CSR lookup.
+- 29 independently sliced CSR rows, including five crossing chunk boundaries, exactly match cached marker counts and canonical row sums.
+- Original H5AD rows from eight datasets match all 48 gene counts, all 48 measurement states and the projected canonical row sum. Historical original paths for 300b, 301, 302 and 304 are unavailable locally, so original-H5AD replay is incomplete for those four. Their canonical CSR, source metadata, gene axis and direct-row checks passed. No source restore was attempted.
+- Exact metadata, masks, pointers, selected compressed expression chunks and code have hash receipts. Whole original H5AD files were not hashed; replay receipts identify the exact row, gene-axis hash and selected raw sparse-row hash.
+- Raw extraction streamed 12.40 GiB compressed / at most 91.55 GiB cumulative decoded bytes from local NVMe, approximately one 12 MB decoded chunk at a time. Extraction took 189.5 seconds; including grouped summaries took 245.4 seconds. Full-process maximum RSS was 418 MiB; cgroup peak was about 2 GiB including file cache, with zero swap. The unit used MemoryHigh=2G, MemoryMax=3G, MemorySwapMax=0, OOMPolicy=kill, OOMScoreAdjust=500 and CPUQuota=200%, with CUDA disabled.
+
+The 938 original dataset-scoped donor IDs include three 300b condition labels mapping to two subjects; the existing GEO-backed corpus rule yields 937 corrected identities. Cross-dataset person duplication remains unresolved. Donor-aware tables avoid treating 2,417 sample keys or repeated observations as independent people.
+
+## Review entry points
+
+- `RESULT.json`: machine-readable status, limitations and source/output receipts.
+- `marker_support_overall.csv`: all 48 loci, measurement denominators, detection, donor/dataset support and final panel membership.
+- `marker_support_by_dataset.csv`, `marker_support_by_corrected_donor.csv`: complete stratified evidence.
+- `codetection_diagnostics.csv`: descriptive overlap by dataset, with explicit non-classifier interpretation.
+- `verification.json`: all physical checks, direct CSR replays, original H5AD replays and original-source gaps.
+- `extraction_plan.json`, `expression_chunk_receipts.json`: exact selection and consumed-data provenance.
+- `ASSET_MANIFEST.json`: final owned-file hashes for the parent archive workflow.
+
+Archive publication is coordinated by the parent task. This subtask changed only its owned coordination directory and did not train, infer, annotate, edit the baseline or adjust panel ranking.

paper-releases/pbisc-diffusion/updates/20261015T141849Z-rare-cell-7k-8k-panels/diffusion/dataset/server_1/model8/plans/rare_gene_context_expansion_20261015/coordination/ilc_training_support/RESULT.json

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+{
+  "status": "verified",
+  "scope": "Existing source-labelled ILC records in exact registered TRAIN split; no new annotation or model inference",
+  "source_ilc_cells": 19329,
+  "train_ilc_cells": 16439,
+  "datasets": 12,
+  "source_sample_keys": 2417,
+  "source_dataset_scoped_donor_ids": 938,
+  "corrected_dataset_scoped_donor_ids": 937,
+  "target_raw_loci": 48,
+  "target_gene_symbols": 47,
+  "missing6k_raw_loci": 10,
+  "missing6k_loci_detected_in_at_least_one_measured_train_ilc": 9,
+  "detection_rule": "Native raw count > 0, with denominator restricted to per-shard measurement_mask = true",
+  "compressed_bytes_read": 13310541599,
+  "decoded_bytes_cumulative_upper_bound": 98304000000,
+  "extraction_seconds_before_grouped_summary": 189.4758267402649,
+  "process_peak_rss_kib_before_grouped_summary": 286200,
+  "independent_direct_csr_rows": 29,
+  "original_h5ad_rows": 8,
+  "original_source_replay_gaps": [
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+      "reason": "Historical original H5AD path is absent locally; canonical CSR replay remains available and verified."
+    },
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+    }
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+  "limitations": [
+    "Source ILC labels are inherited annotations, not independently established ILC biological identity.",
+    "No new classifier, relabelling, model generation, model evaluation, or panel ranking optimization was performed.",
+    "These cells belong to the baseline train source universe; genes outside 6k were not baseline 6k model targets.",
+    "Raw non-detection is finite native-depth sampling and cannot establish absent gene function or absent population.",
+    "Feature unavailable and measured zero are kept separate; the two CRLF2 loci are never merged.",
+    "Native depth varies across assays, donors and cohorts; counts are descriptive, with no downsampling or inferential test.",
+    "Only source-labelled ILC cells are selected, so rates do not estimate full-corpus or independently adjudicated ILC prevalence.",
+    "Donor correction for 300b follows existing corpus GEO rules; cross-dataset person duplication remains unresolved.",
+    "TRAC is absent from the canonical 20,097-gene source axis and was not represented as a measured zero.",
+    "Expression is an audit outcome only, not a basis for modifying 7k/8k membership or evidence priority."
+  ],
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