Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261013T072655Z-enriched-140-slide-master/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/figure_enrichment_20261013/trajectory_source_methods.json

@@ -0,0 +1,969 @@
+{
+  "schema_version": "pbisc.diffusion_trajectory_annotated_real_reference.v2",
+  "status": "completed",
+  "title": "PBISC-Diffusion ctx2048 E12 EMA",
+  "checkpoint_label": "PBISC-Diffusion ctx2048 E12 EMA",
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+  "reference_units": "Observed integer UMI counts; no donor identifier is published.",
+  "reference_role": "Only observed reference cells fit every mean, standard deviation, PCA component and UMAP. Tracked generated cells use transform only.",
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+    "temporal_semantics": "Final predicted labels are propagated retrospectively to the same tracked cell IDs; early noisy states are not reclassified.",
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+    "Colored cells are generated; PBMC5+Other names are transferred final predictions, not experimentally observed cell identities.",
+    "Time is computational denoising, not biological time or differentiation.",
+    "Early predictions may lie outside the real reference distribution; UMAP placement does not validate identity or function.",
+    "The first clean-expression panel is already a prediction, not Gaussian noise.",
+    "Distances use high-dimensional state or expression PCA; UMAP distances are not biological effect sizes."
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+      "sha256": "859a8a9ce86c8a09d1313f2f98b4d4f3bf0f5dadf3501dcb38be5fe5aefad467",
+      "bytes": 3021357,
+      "role": "bit-identical stored coordinate cross-check"
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+  "interactive_coordinate_descriptors": {
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+    "volcano_statistics_roundtrip": "float64 bit-identical",
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+    "compute": "server_2 CPU"
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+}

paper-releases/pbisc-diffusion/updates/20261013T072655Z-enriched-140-slide-master/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/figure_order_fixed_20261013/README.md

@@ -0,0 +1,58 @@
+# Figure 순서를 실제 PPTX/PDF에 반영한 131장 덱
+
+> 현재 작업 덱은 [140장 확장본](../figure_enrichment_20261013/README.md)이다. 이 문서는 보존된 131장 재배치 버전의 기록이다.
+
+사용자가 지정한 Figure 구분을 슬라이드 순서, 목차, 구분 페이지, 계획표, 우측 panel label에 모두 반영했다. 이전 131장 덱과 원본 76장 파일은 보존했다.
+
+| 섹션 | 현재 페이지 | 내용 |
+|---|---|---|
+| Introduction | 1–4 | 현재 목차와 Figure 구성 |
+| Figure 1 | 5–9 | 전체 실험 개요와 corpus 통계만 |
+| Figure 2 | 10–14 | SLE pseudobulk architecture/gene-context ablation만 |
+| Figure 3 | 15–23 | 건강인 paired mismatch → full FT → rank → paired 수 → exact-five |
+| Figure 4 | 24–29 | 질환 paired disease-integrity 비교 |
+| Figure 5 | 30–31 | Paired rare-population 정성 패널 계획; 정량 자료는 S10 |
+| Figure 6 | 32–34 | Bulk-only에서 기존 논문 결과 재현 계획 |
+| Supplementary | 35–36 | 보충자료 안내 |
+| Supp S01 | 37–42 | 기존 상세 결과 및 대조군 |
+| Supp S02 | 43–48 | 기존 상세 결과 및 대조군 |
+| Supp S03 | 49–63 | 기존 상세 결과 및 대조군 |
+| Supp S04 | 64–68 | 기존 상세 결과 및 대조군 |
+| Supp S05 | 69–73 | 기존 상세 결과 및 대조군 |
+| Supp S06 | 74–80 | 기존 상세 결과 및 대조군 |
+| Supp S07 | 81–90 | 기존 상세 결과 및 대조군 |
+| Supp S08 | 91–99 | 기존 상세 결과 및 대조군 |
+| Supp S09 | 100–105 | 기존 상세 결과 및 대조군 |
+| Supp S10 | 106–111 | 기존 상세 결과 및 대조군 |
+| Supp S11 | 112–116 | 기존 상세 결과 및 대조군 |
+| Supp S12 | 117–121 | 기존 상세 결과 및 대조군 |
+| Supp S13 | 122–122 | 기존 상세 결과 및 대조군 |
+| Supp S14 | 123–123 | 기존 상세 결과 및 대조군 |
+| Historical archive | 124–129 | 과거 scorer와 탐색 기록; 현재 결론과 분리 |
+| Discussion | 130–131 | 확장 가능성과 전망 |
+
+## 실제 수정
+
+- Figure 1 끝의 architecture/gene ablation을 Figure 2로 이동했다.
+- 이전 Figure 2의 mismatch·adaptation·rank·paired 수와 이전 Figure 3의 건강인 비교를 하나의 Figure 3 흐름으로 통합했다.
+- Figure 3의 full FT 그림은 저장된 ImMicro pooled 결과만 추출했다. Sepsis가 섞인 원본 full-FT 그림은 보충자료에 그대로 유지했다.
+- Eight old planning-card images were replaced with editable tables reflecting the current scope. No old Figure 2=fine-tuning or Figure 3=healthy-only-comparison divider remains.
+- SLE가 들어 있던 이전 Figure 4 자료는 S02로 이동했다. 여러 cohort가 섞인 full/rank 상세 그림도 보충자료로 두었다.
+- Figure 5의 정성 증거와 Figure 6의 실제 재현 결과는 아직 완료되지 않았으므로 계획으로 표시한다. 기존 rare 정량 결과를 완성된 정성 패널로 바꾸어 부르지 않았다.
+- 131개 source-page ID는 각각 한 번씩 대응한다. 76개 original-slide ID도 모두 유지한다. 과거 순서를 유지한다는 제약은 이번 사용자 지시에 따라 해제했다.
+
+## Figure 3 패널
+
+| 현재 페이지 | 내용 |
+|---|---|
+| 17 | Real bulk–pseudobulk mismatch |
+| 18 | 생성 세포 공간의 영향: 기존 native-depth 진단 |
+| 19 | Healthy raw/calibrated/full FT/LoRA: 동일 pooled scoring |
+| 20 | Full FT와 LoRA r4/r16/r64의 성능·파라미터 비교 |
+| 21 | Historical n training + 7 validation 곡선 |
+| 22 | 추가 validation 없는 genuine five-pair 비교 |
+| 23 | Composition 오차와 donor별 비교 |
+
+[페이지 대응표](page_map.csv) · [검증 결과](qa/VERIFICATION.json)
+
+새 학습·생성·scoring·통계 검정은 실행하지 않았다. 새 건강인 비교 그림의 12개 값은 기존 표와 정확히 일치한다. 기존 PBISC gold/scSemi blue와 Arial 스타일을 유지했다.