Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261015T141849Z-rare-cell-7k-8k-panels/diffusion/dataset/server_1/model8/ara/staging/observations.yaml

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+observations:
+- id: O01
+  provenance: ai-suggested
+  potential_type: constraint
+  content: Generic marker co-detection should not substitute for original-paper rare-cluster
+    identity.
+  context: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/rare_literature/result.json
+  promoted: false
+- id: O02
+  provenance: user
+  potential_type: claim
+  content: Trunkx4 may improve representative paired LoRA performance relative to
+    current architecture.
+  context: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/trunk4x_lora_sepsis_20261013/README.md
+  promoted: false
+- id: O03
+  provenance: ai-suggested
+  potential_type: heuristic
+  content: The 8k candidate is suitable for broader ILC/DC program coverage, while 7k
+    already covers the resolved disease catalog. Greater feature coverage has not
+    demonstrated better generation; ILC readout and source signal need separate validation.
+  context: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_gene_context_expansion_20261015/REPORT.md
+  bound_to: [N10]
+  promoted: false

paper-releases/pbisc-diffusion/updates/20261015T141849Z-rare-cell-7k-8k-panels/diffusion/dataset/server_1/model8/ara/trace/exploration_tree.yaml

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+tree:
+- id: N01
+  type: decision
+  provenance: user
+  choice: Ground Figure5 targets in each paired cohort original paper.
+  evidence:
+  - /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/rare_literature/result.json
+- id: N02
+  type: experiment
+  provenance: ai-executed
+  result: Observed Ye marker co-detection is present but does not reproduce pulmonary
+    specificity; no author fine labels found in133schemas.
+  evidence:
+  - /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/rare_literature/result.json
+- id: N03
+  type: experiment
+  provenance: ai-executed
+  result: Launched2checkpointparents x5LoRA draws for representative paired Sepsis;
+    firsttrunkdraw completed3000steps and sampling started. Finalcomparison pending.
+  evidence:
+  - /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/trunk4x_lora_sepsis_20261013/PROTOCOL.json
+  - /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/trunk4x_lora_sepsis_20261013/LAUNCH_RECEIPT.json
+- id: N04
+  type: decision
+  provenance: user
+  choice: Pretrain trunkx4 with the exact current-paper f01 6k gene context; prefer
+    server2, fallback server1.
+  evidence:
+  - /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/f01_trunk4x_complete_20261013/PLAN.md
+  - /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/f01_trunk4x_complete_20261013/CONTRACT.json
+- id: N05
+  type: experiment
+  provenance: ai-executed
+  result: 128-stepGPU profile passed, actual genes/positions match f01, full16parttraining
+    launched onserver1 with NAS-backed output.100adaptations scheduled; no outcome
+    superiority claimed.
+  evidence:
+  - /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/f01_trunk4x_complete_20261013/LAUNCH_RECEIPT.json
+  - /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/f01_trunk4x_complete_20261013/PROFILE_GENE_PROOF.json
+  - /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/f01_trunk4x_complete_20261013/MATRIX_VERIFIED.json
+- id: N06
+  type: decision
+  provenance: user
+  timestamp: '2026-10-14'
+  choice: Redraw Figure1a in supplied organic schematic style and add exact33.14M
+    training-corpus main panel.
+  evidence:
+  - /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/figure1_revision_20261014/overview/result.json
+  - /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/figure1_revision_20261014/train_corpus/result.json
+- id: N07
+  type: experiment
+  provenance: ai-executed
+  timestamp: '2026-10-14'
+  result: Metadata-only aggregation across432shards verified33,141,380trainingcells,5232samples,2572corrected
+    donors,Healthy88.4241%;155-page deck rendered and verified. No model training
+    or inference.
+  evidence:
+  - /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/figure1_revision_20261014/train_corpus/VERIFICATION.json
+  - /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/figure1_revision_20261014/qa/VERIFICATION.json
+- id: N08
+  type: decision
+  provenance: user
+  timestamp: '2026-10-15'
+  choice: 'Execute Figure1 review: explicit diffusion mechanism and readable main
+    corpus proportions with complete support details.'
+  evidence:
+  - /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/figure1_focus_20261015/overview/result.json
+  - /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/figure1_focus_20261015/corpus/result.json
+  - /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/figure1_focus_20261015/qa/VERIFICATION.json
+- id: N09
+  type: experiment
+  provenance: ai-executed
+  timestamp: '2026-10-15'
+  result: User-specified C1QA/CD163/CD68/WARS1/LGALS3 co-detection verified in1,319
+    of33,219 unflagged C1Q-source-labelled training candidates;109 additional flagged.
+    Raw count>0, not macrophage identity. Original-source/E2 row replays PASS.
+  evidence:
+  - /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/corpus_macrophage_markers_20261015/RESULT.json
+  - /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/corpus_macrophage_markers_20261015/INDEPENDENT_VERIFICATION.json
+- id: N10
+  type: experiment
+  provenance: ai-executed
+  timestamp: '2026-10-15'
+  result: Subagents assembled 23-primary-paper evidence and exact nested 7000/8000-gene
+    candidates retaining all current 6000 genes. All available disease targets and
+    core/sentinel genes fit 7k; 8k expands ILC/DC programs. Native counts audited in
+    16439 source-labelled train ILC; PTGDR2 positive in 518 cells, IL12RB1 in 1063,
+    IL17A in 0 of 16354 measured cells. Source labels are not biological gold.
+    Existing saved ILC predictions were found under broad Other. No model work launched.
+  evidence:
+  - /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_gene_context_expansion_20261015/REPORT.md
+  - /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_gene_context_expansion_20261015/VERIFIED.json
+  - /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_gene_context_expansion_20261015/DETERMINISM.json
+  - /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_gene_context_expansion_20261015/coordination/ROOT_REVIEW.json
+  - /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_gene_context_expansion_20261015/coordination/ilc_training_support/RESULT.json

paper-releases/pbisc-diffusion/updates/20261015T141849Z-rare-cell-7k-8k-panels/diffusion/dataset/server_1/model8/ara/trace/pm_reasoning_log.yaml

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+entries:
+- date: '2026-10-13'
+  provenance: ai-executed
+  note: Recorded source/audit actions without promoting universal superiority or rare-population
+    identity claims. No existing paper-specific ARA found; parent artifact covers
+    broader models and was left unchanged.
+- date: '2026-10-13'
+  provenance: ai-executed
+  note: Checkpointpanels differ; addmatchedold-panelx1control rather than falselyattributeallgainstowidth.
+    Keep superiority hypothesis staged until all prespecified draws finish.
+- date: '2026-10-13'
+  provenance: ai-executed
+  note: Architecture comparison now fixes all6000genes and source stream. Resourcehost
+    follows observedserver2busy→server1fallback. Profile success does not establish
+    E16performance; all scientific claims remain pending.
+- date: '2026-10-14'
+  provenance: ai-executed
+  note: Recorded requested figure changes and metadata arithmetic. No model-performance
+    or rare-population claim promoted; prior trace preserved.
+- date: '2026-10-15'
+  provenance: ai-executed
+  note: Visual revision only; no new efficacy claim. Saved counts preserved, small-category
+    groups auditable and full detail retained.
+- date: '2026-10-15'
+  provenance: ai-executed
+  note: Recorded raw co-detection as descriptive evidence only. Did not promote confirmed
+    macrophage identity or extrapolate candidate subset to full-corpus prevalence.
+    Source metadata and figure labels unchanged.
+- date: '2026-10-15'
+  provenance: ai-executed
+  note: Recorded panel construction and native training-count audit as completed facts.
+    Kept the 8k performance rationale staged. Did not promote classifier calls into
+    biological ILC recovery, endpoint-informed panels into blind validation, or
+    source-labelled counts into expert-confirmed identity. Active models unchanged.

paper-releases/pbisc-diffusion/updates/20261015T141849Z-rare-cell-7k-8k-panels/diffusion/dataset/server_1/model8/ara/trace/sessions/2026-10-15_001.yaml

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+id: 2026-10-15_001
+date: '2026-10-15'
+summary: Implemented Figure1 suggestions in156-slide master; all numerical source
+  counts preserved.
+ai_actions:
+- provenance: ai-executed
+  action: Made diffusion mechanism explicit, enlarged corpus legend, retained full
+    training detail as support and exported2-page preview.
+- provenance: ai-executed
+  action: Verified156PPTX/PDFpages and source counts without new model work or metadata
+    rescan.
+events:
+- N08
+claims_touched: []
+open_threads:
+- Existing Figure2–6 work remains outside this Figure1 task.
+additional_turns:
+- task: five-marker training-cell existence check
+  provenance: ai-executed
+  events:
+  - N09
+  ai_actions:
+  - Extracted exactly five measured genes from34,122 selected training rows with bounded
+    CPU streaming.
+  - Verified physical-row identity,16 directCSR replays and4 originalH5AD source replays.
+  summary: Verified1,319 unflagged all-five-positive cells; candidate-only scope and
+    monocyte source labels retained.
+  claims_touched: []
+- task: rare-cell gene-context research and candidate construction
+  provenance: ai-executed
+  events: [N10]
+  ai_actions:
+  - Delegated primary literature and panel integration to separate agents as requested.
+  - Constructed and independently checked nested 7k and 8k panels, without active config changes.
+  - Audited 48 native loci in source-labelled training ILC with bounded CPU streaming.
+  summary: Candidate features and validation protocol ready; generation improvement untested.
+  claims_touched: []