Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261015T131236Z-corpus-five-marker-codetection/diffusion/dataset/server_1/model8/ara/trace/sessions/session_index.yaml

@@ -0,0 +1,25 @@
+sessions:
+- id: 2026-10-13_001
+  date: '2026-10-13'
+  summary: Expanded142 to154slides with corpus/split audit, saved adaptation and disease
+    metrics, and original-paper rare-target observed diagnostics.
+  turn_count: 3
+  events_count: 6
+  claims_touched: []
+  open_threads: 5
+- id: 2026-10-14_001
+  date: '2026-10-14'
+  summary: Redrew Figure1a and inserted exact training-corpus Figure1b in155-slide
+    master.
+  turn_count: 1
+  events_count: 2
+  claims_touched: []
+  open_threads: 1
+- id: 2026-10-15_001
+  date: '2026-10-15'
+  summary: Implemented Figure1 suggestions in156-slide master; all numerical source
+    counts preserved. Verified five-marker co-detection in selected training candidates.
+  turn_count: 2
+  events_count: 2
+  claims_touched: []
+  open_threads: 1

paper-releases/pbisc-diffusion/updates/20261015T131236Z-corpus-five-marker-codetection/diffusion/dataset/server_1/model8/plans/corpus_macrophage_markers_20261015/INDEPENDENT_VERIFICATION.json

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+    {
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+    {
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+    },
+    {
+      "path": "/home/sj_server_1/gblee/datalake/single-cell-RNA-seq-datasets/PBMC-cells/200_A_GSE275067_Immunobiology_of_Aging_Cohort_PBMC_Profiling/86a284b2-abab-403d-bd1a-e5c7378a53fa.h5ad",
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+  ],
+  "historical_row_index_note": "BLOCK metadata retains original H5AD offsets after QC. E2 row_index resets to contiguous CSR row position; source_row_index is the shared identity join. Direct original-H5AD row replay confirms the projected five counts and total for one cell per dataset.",
+  "gene_axis_raw_positions": [
+    291,
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+    13194
+  ],
+  "raw_gene_ids": [
+    "ENSG00000173372",
+    "ENSG00000177575",
+    "ENSG00000129226",
+    "ENSG00000140105",
+    "ENSG00000131981"
+  ],
+  "raw_gene_symbols": [
+    "C1QA",
+    "CD163",
+    "CD68",
+    "WARS",
+    "LGALS3"
+  ],
+  "sources": [
+    {
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+    {
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+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/corpus_macrophage_markers_20261015/check_candidates.py",
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+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/corpus_macrophage_markers_20261015/verify_candidates.py",
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+}

paper-releases/pbisc-diffusion/updates/20261015T131236Z-corpus-five-marker-codetection/diffusion/dataset/server_1/model8/plans/corpus_macrophage_markers_20261015/PROTOCOL.md

@@ -0,0 +1,74 @@
+# C1Q-source candidates: five-marker check (2026-10-15)
+
+User-specified markers: **C1QA, CD163, CD68, WARS1, LGALS3**. The stored
+symbol `WARS` is matched to WARS1 through stable ID `ENSG00000140105`.
+
+## Scope fixed before expression extraction
+
+This is a CPU-only descriptive audit of cells already identified by exact
+source annotation in the registered **training split**. It does not search
+all 33,141,380 training cells or estimate whole-corpus macrophage prevalence.
+
+| Dataset prefix | Original source annotation | Unflagged cells | Flagged cells |
+|---|---|---:|---:|
+| 009 AIFI | C1Q+ CD16 monocyte | 3,058 | 0 |
+| 065 Sound Life | C1Q+ CD16 monocyte | 25,268 | 0 |
+| 200 Immunobiology of Aging | C1Q+ CD16 monocyte | 2,167 | 0 |
+| 006 AIDA | CD16+_Monocyte_C1QAhi | 2,726 | 0 |
+| 006 AIDA | flagged_intermediate_monocyte_C1QAhi | 0 | 903 |
+| Total | | 33,219 | 903 |
+
+Selection uses the exact union of these three labels across retained source
+annotation columns. A cell is counted once. Source annotations are joined by
+equal shard row counts and exact `source_row_index` alignment; training
+membership is joined on `(dataset_id, donor_id, sample_id)` to the registered
+sample index. The mapped broad cell-type label is not used for selection.
+
+## Marker definitions
+
+- Detection means **raw count > 0** (equivalently at least one count).
+- Report every marker separately, the histogram of 0–5 detected markers,
+  all five detected, and C1QA detected plus at least three of the four others.
+- All five measurement-mask entries must be available for each included
+  shard. Unmeasured genes must never be treated as expression zero.
+- The five counts are extracted from the same cell, so co-detection is
+  within-cell rather than an aggregate mixture of different cells.
+- AIDA `flagged_` annotations remain separate throughout summaries.
+
+These definitions measure co-detection, not high expression or a validated
+macrophage identity. Monocytes can express these markers. Zero counts can
+reflect finite sampling even when a gene is measured. Dataset-scoped donor
+IDs are not verified unique people across datasets.
+
+## Storage and resource controls
+
+The metadata pass reads 89 paired metadata shards, covering 20,609,391
+source rows across all splits, and selects only 34,122 training candidates.
+The expression pass reads selected-row spans from local chunked sparse CSR
+arrays. It stores only five marker counts and a 20,097-gene row sum per
+selected cell. It never materializes a full expression matrix.
+
+Before expression extraction, the required chunks were enumerated:
+4.335 GiB compressed and 31.706 GiB decoded across the relevant shards.
+One 1,000,000-entry chunk pair is held at a time (~12 MB decoded). The jobs
+run in bounded user units (MemoryHigh 2 GiB, MemoryMax 3 GiB, no swap,
+OOMPolicy kill, CPU quota 200%, CUDA disabled). The memory guard was active
+and checked before both launches. No training, inference, GPU job, source
+metadata, or original expression artifact was changed.
+
+## Output and reproducibility
+
+- `selected_training_candidates.parquet`: exact selection with source shard,
+  row, label, sample/donor identity, and train membership (private).
+- `candidate_marker_counts.parquet`: those cells with five raw counts and
+  detection flags (private).
+- `summary.csv`: per-dataset and pooled counts, including flagged separation.
+- `sample_support.csv`: sample/donor support (private).
+- `source_label_summary.csv`: exact original label summaries.
+- `extraction_plan.json`: pre-extraction I/O scope and metadata hashes.
+- `expression_source_receipts.json`: hashes of exactly read expression chunks.
+- `RESULT.json`: numerical results, checks, output hashes, and limitations.
+
+This is a complete enumeration of the selected candidate set, not a random
+sample or between-method hypothesis test. No p-values or inferential
+confidence intervals are attached to these descriptive counts.

paper-releases/pbisc-diffusion/updates/20261015T131236Z-corpus-five-marker-codetection/diffusion/dataset/server_1/model8/plans/corpus_macrophage_markers_20261015/REPORT.md

@@ -0,0 +1,74 @@
+# Five-marker co-detection in training C1Q-high source candidates
+
+**Result: yes, the training corpus contains cells in which C1QA, CD163,
+CD68, WARS1 and LGALS3 are all detected in the same cell.** Among the
+33,219 previously identified, unflagged C1Q-high source-labelled candidates,
+1,319 cells (3.97%) have all five markers detected. These cells occur in
+580 samples and 204 dataset-scoped donor IDs.
+
+Detection is **raw count > 0**, not a high-expression gate. This establishes
+five-marker co-detection in actual training cells, not definitive macrophage
+identity. The source annotations remain monocyte annotations.
+
+| Dataset | Unflagged C1Q-high candidates | All five detected | C1QA + at least three others |
+|---|---:|---:|---:|
+| AIFI Immune Health Atlas | 3,058 | 140 | 2,483 |
+| Sound Life | 25,268 | 1,048 | 20,389 |
+| Immunobiology of Aging | 2,167 | 124 | 1,573 |
+| AIDA | 2,726 | 7 | 2,458 |
+| **Total** | **33,219** | **1,319 (3.97%)** | **26,903 (80.99%)** |
+
+Additional AIDA source annotations beginning `flagged_` were kept separate:
+109 of 903 cells (12.07%) have all five detected, and 801 have C1QA plus at
+least three other markers. Their all-five-positive cells occur in 86 samples
+and 86 donor IDs. Flagged and unflagged donor/sample sets can overlap; do not
+add those support counts to claim unique people.
+
+| Marker | Detected among 33,219 unflagged candidates | Percent |
+|---|---:|---:|
+| C1QA | 32,958 | 99.21% |
+| CD163 | 1,818 | 5.47% |
+| CD68 | 32,607 | 98.16% |
+| WARS1 (stored symbol WARS) | 28,867 | 86.90% |
+| LGALS3 | 30,962 | 93.21% |
+
+CD163 is the limiting detected marker in this candidate set. All five genes
+are in the final 6,000-gene training panel and are measured in every included
+candidate shard; CD163 non-detection here is not caused by a missing-gene
+measurement mask. Zero counts still do not prove biological absence.
+
+## Verification
+
+- Replayed the exact training membership and original-label union:
+  33,219 unflagged plus 903 flagged cells; no duplicate selected shard rows.
+- Checked physical E2 row positions and source identity for all 34,122 cells
+  across 69 expression-bearing shards.
+- Checked raw gene IDs and WARS1/WARS alias; tied the 6,000-gene panel to the
+  saved training configuration using existing manifest and position hashes.
+- Independently re-read 16 single CSR rows, including a row crossing a
+  compressed-chunk boundary in each of the four datasets; all five counts
+  and complete 20,097-gene row sums matched.
+- Independently read the original H5AD source row for one candidate in each
+  dataset. All five marker counts and canonical-panel total counts exactly
+  matched the analysed training CSR row.
+- The historical BLOCK metadata retains original source offsets in its
+  `row_index` after QC. E2 explicitly resets `row_index` to physical CSR
+  positions. Source annotations were joined by `source_row_index`; the
+  expression extraction correctly used E2 physical positions. This difference
+  was documented and verified, not fixed by altering any source data.
+
+`INDEPENDENT_VERIFICATION.json` is PASS. Expression extraction took about
+79 seconds with 1.2 GiB peak cgroup memory and zero swap. No GPU computation,
+training, generation, or original-data modification was performed.
+
+## Interpretation limits
+
+This was an existence check restricted to the already identified C1Q-high
+source candidates. It is not a full-corpus search and does not count all
+macrophage-like cells in the 33.14M training corpus. A five-marker positive
+cell can still be a monocyte, and a true macrophage-like cell can miss one or
+more markers through sparse sampling. A validated identity claim would need
+an appropriate macrophage reference and alternative myeloid-state checks.
+
+The cell-level and sample-level files contain private source identifiers
+and must remain in the private paper-support archive.