diff --git a/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_reference_coordinates.csv b/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_reference_coordinates.csv
new file mode 100644
index 0000000000000000000000000000000000000000..e344b182ecae7854e43cafe26c523866f260768d
--- /dev/null
+++ b/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_reference_coordinates.csv
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diff --git a/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 b/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
new file mode 100644
index 0000000000000000000000000000000000000000..6fe32e2dc42c974becdc2c80da7d16aa5906836c
--- /dev/null
+++ b/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",
+  "model_genes": 6000,
+  "projection_genes": 2980,
+  "tracked_cells": 4096,
+  "reference_cells": 4362,
+  "observed_frames": 51,
+  "denoiser_calls_per_tracked_batch": 50,
+  "seed": 42,
+  "reference": "Observed real PBMCs from the same conditioning donor; GSE135779. These are not generated cells or independent held-out validation.",
+  "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.",
+  "raw_reference_encoding": {
+    "max_log_value": 8.0,
+    "value_scale": 1.0,
+    "center_values": true,
+    "support_scale": 1.0,
+    "formula": "unit=clip(log1p(observed UMI)/max_log_value,0,1); value=unit/value_scale, then 2*value-1 when centered; support=+support_scale for positive UMI and -support_scale otherwise"
+  },
+  "raw_projection": "PCA2 fitted once on canonically encoded observed value/support states over common measured genes. Generated noisy states are selected and projected without clipping, rescaling or library normalization.",
+  "clean_projection": "Common-gene expression -> expm1(log1p) -> panel sum normalization to 10000 -> log1p -> observed-reference mean/std -> observed-reference PCA30 -> fixed UMAP transform for every generated frame including endpoint.",
+  "pca_components": 30,
+  "umap": {
+    "n_neighbors": 15,
+    "min_dist": 0.25,
+    "metric": "euclidean",
+    "random_state": 42,
+    "transform_seed": 42,
+    "n_jobs": 1
+  },
+  "raw_pca_explained_variance_ratio": [
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+    0.033733855932950974
+  ],
+  "annotation": {
+    "method": "Frozen AIFI scANVI annotation of final generated profiles only",
+    "classifier": "aifi_scanvi_rebuild_20260916_frozen_predict[aifi_scanvi_2980_v1]",
+    "model_sha256": "1e648fba5849b0d0f589eef50b1607d5e3b059aa05e94a0d718e8dfcad477a1b",
+    "versions": {
+      "scvi-tools": "1.4.1",
+      "torch": "2.14.0+cu130",
+      "anndata": "0.12.19"
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+      "model_genes": 2977,
+      "query_genes": 2980,
+      "model_genes_missing_from_query_zero_padded": 0,
+      "query_genes_outside_model_dropped": 3,
+      "rule": "query is subset/reordered to the model's gene list; zero-padding of absent model genes is refused unless --allow-missing-genes"
+    },
+    "readout": {
+      "rule": "One seeded Poisson draw from expm1(endpoint log1p), on the common panel before prediction",
+      "seed": 20260916,
+      "library_scale": 1.0,
+      "raw_observed_counts": false
+    },
+    "code_to_label": [
+      "T cell",
+      "B cell",
+      "Monocyte",
+      "NK cell",
+      "DC",
+      "Other"
+    ],
+    "colors": [
+      "#0072B2",
+      "#D55E00",
+      "#009E73",
+      "#CC79A7",
+      "#E69F00",
+      "#56B4E9"
+    ],
+    "confidence_threshold": 0.0,
+    "confidence_semantics": "L2 probability mass summed for the assigned AIFI L1 label. Other combines labels outside PBMC5, without summing all Other probabilities. final_l2_confidence records the L2 maximum separately.",
+    "other_semantics": "AIFI annotations outside the specified PBMC5 classes map to Other. Threshold 0 does not reject low-confidence assignments.",
+    "temporal_semantics": "Final predicted labels are propagated retrospectively to the same tracked cell IDs; early noisy states are not reclassified.",
+    "counts": {
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+      "B cell": 1008,
+      "Monocyte": 1234,
+      "NK cell": 170,
+      "DC": 85,
+      "Other": 21
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+      "1": 1.0
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+    "source_schema": "pbisc.trajectory.endpoint_annotation.v1"
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+  "state_semantics": "Pre-update actual x_t is paired with that call's clean prediction; final x_0 repeats the previous clean prediction. No extra denoiser call at t=0.",
+  "axis_limits": "Full min/max across all frames and observed reference points with 6.5% padding, fixed throughout.",
+  "repeat_transform_max_abs_difference": 0.0,
+  "raw_repeat_transform_max_abs_difference": 0.0,
+  "duplicate_prediction_max_abs_difference": 0.0,
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+      "dense_values": true,
+      "active_mask": true,
+      "active_logits": true,
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+    "rng_unchanged": true,
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+    "checked_at_utc": "2026-09-17T10:32:13.475853+00:00"
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+    "real_counts_sha256": "208d699a204213dd56e0fb4f40dbf740c331b7cd4ab4998c92cc3280b8de72a9",
+    "real_gene_ids_sha256": "c874339c97a97e46eaaf56b2b62dea0311e60dec0af5ab40deb6ff96d7f65508",
+    "model_columns_sha256": "2c938250300acea1a4e44e0b7a89ce049c1e31595bdad22d0f384b5604f0a8d8",
+    "final_labels_sha256": "954f353e00d436adafefdbcc85d133bed8c0f1eaf3c78aac8b2989ab96d8d0a8",
+    "final_confidence_sha256": "7b283b492b3bf100be3faea6c76e7f420bfcaa4f2a0ee2a32823322c33ae2d79",
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+    "rendering_code_sha256": "ca0ef9baac9468af745c36d8b855ad7f038dff05add89d09b87535a8d59af47c"
+  },
+  "interpretation": [
+    "Gray dots are observed real cells from the conditioning donor; they are not independent validation.",
+    "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."
+  ],
+  "metric_definitions": {
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+    "reference_pca_distance_median": "Median nearest-observed-cell Euclidean distance in frozen expression PCA.",
+    "support_fraction": "Mean hard support over common measured genes and tracked cells."
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+    "interpolation": "none; exact recorded states are held",
+    "width": 1600,
+    "height": 900,
+    "codec": "H.264",
+    "pixel_format": "yuv420p",
+    "full_decode_verified": true
+  },
+  "display_labels": {
+    "gray": "Ground truth",
+    "point_unit": "cell",
+    "left": "Denoising · PCA",
+    "right": "Expression estimate · UMAP",
+    "input": "Pseudobulk counts encoded as condition vector",
+    "marker_size_and_alpha_equal": true
+  },
+  "assets": {
+    "coordinates.npz": {
+      "bytes": 3021357,
+      "sha256": "859a8a9ce86c8a09d1313f2f98b4d4f3bf0f5dadf3501dcb38be5fe5aefad467"
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+      "sha256": "e36b32603be7e176fc307f2f49e4d1d038ce949cfd8ec1a62518c0022f007cac"
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diff --git a/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_provenance.json b/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_provenance.json
new file mode 100644
index 0000000000000000000000000000000000000000..76a3c87ec702f45b02c812f6635f6dd17541b896
--- /dev/null
+++ b/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_provenance.json
@@ -0,0 +1,91 @@
+{
+  "public_page": "https://www.virtualhumanlab.com/research/pbisc-diffusion/",
+  "external_source_bindings": [
+    {
+      "path": "/home/sj_server_1/virtual-human-lab/research/pbisc-diffusion/assets/interactive-v1/manifest.json",
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+      "bytes": 217501,
+      "role": "website interactive export manifest"
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+      "sha256": "f69fa11064f759446202fe0ad86260e53378a916eb6bbce4718d81cbb5adec60",
+      "bytes": 3412128,
+      "role": "website exact recorded coordinates"
+    },
+    {
+      "path": "/home/sj_server_1/virtual-human-lab/research/pbisc-diffusion/assets/v3/methods.json",
+      "sha256": "1d374c2367201d29c54161cbc424fa96194d3764cf1690102085e96c781eba19",
+      "bytes": 36423,
+      "role": "trajectory/annotation definitions"
+    },
+    {
+      "path": "/home/sj_server_1/virtual-human-lab/research/pbisc-diffusion/assets/v3/coordinates.npz",
+      "sha256": "859a8a9ce86c8a09d1313f2f98b4d4f3bf0f5dadf3501dcb38be5fe5aefad467",
+      "bytes": 3021357,
+      "role": "bit-identical stored coordinate cross-check"
+    }
+  ],
+  "interactive_coordinate_descriptors": {
+    "pca": {
+      "file": "cells.bin",
+      "dtype": "float32",
+      "shape": [
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+        2
+      ],
+      "byte_offset": 0,
+      "length": 417792
+    },
+    "umap": {
+      "file": "cells.bin",
+      "dtype": "float32",
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+        2
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+      "byte_offset": 1671168,
+      "length": 417792
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+    "real_pca": {
+      "file": "cells.bin",
+      "dtype": "float32",
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+        2
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+      "byte_offset": 3342336,
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+    "real_umap": {
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+    "source_single_methods_sha256": "336463884005dacbf15892fdb82c74e33c2e7aa1f90b1561bc8a67ad6ed32471",
+    "source_volcano_methods_sha256": "a781c955539a313a60281dc19f374dca9392af56d3f1a86064d248fef02c4bcf",
+    "source_block_metadata_sha256": "af022b0cc312d51e387c8ad5009ffd9cf966bae5055e58f0a59e00f742ad19c5",
+    "exporter_sha256": "8f92dbfb62b53341c8a9969a97cbcb442bf65adcda0f72eeb52b66eb2ea08f50",
+    "cells_coordinates_roundtrip": "float32 bit-identical",
+    "volcano_statistics_roundtrip": "float64 bit-identical",
+    "single_expression_roundtrip": "float32, maximum error recorded above",
+    "compute": "server_2 CPU"
+  },
+  "live_page_reference_checked": true,
+  "live_asset_bytes_verified": false,
+  "live_asset_limitation": "Direct manifest fetch returned HTTP 403; web open could not retrieve the JSON. Local binary/manifest/stored-coordinate equivalence verified.",
+  "archive_scope": "Archive these small Model8 snapshots; no broad website dependency is required."
+}
diff --git a/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 b/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
new file mode 100644
index 0000000000000000000000000000000000000000..e9721556388d2366539b4a0b343e5def5fd7a866
--- /dev/null
+++ b/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.