Archive 4 checkpoints (1-4)

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paper-releases/pbisc-diffusion/updates/20261013T044744Z-figure1to6-131page-classification/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/figure_assignment_20261013/panel_plan.json

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+    "figure": 1,
+    "status": "existing",
+    "panels": [
+      {
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+        "purpose": "전체 pretraining–paired adaptation–bulk-to-cell 실험 개요",
+        "pages": [
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+      {
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+      {
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+        "purpose": "dataset별 corpus 규모와 recipe-size 분포",
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+  },
+  {
+    "figure": 2,
+    "status": "existing_with_axis_labels",
+    "panels": [
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+      {
+        "panel": "b",
+        "purpose": "gene-panel/context ablation: 2k/3k/6k/15k와 biological coverage",
+        "pages": [
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+      },
+      {
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+        "purpose": "common-axis SLE precision/coverage와composition 재평가",
+        "pages": [
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+        "action": "1%-floor architecture와0.1%-floor panel families를 합쳐 직접 ranking하지 않음"
+      }
+    ]
+  },
+  {
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+    "status": "existing_with_claim_and_budget_corrections",
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+          23
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+        "action": "23의native-depth 진단을 FT비교 수치 baseline으로 연결하지 않음"
+      },
+      {
+        "panel": "b",
+        "purpose": "paired full FT improves raw real-bulk reconstruction",
+        "pages": [
+          116
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+        "action": "ImMicro pooled만; raw/cal/fullFT/LoRA 비교. condition-encoder fold0와Sepsis 제외"
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+      },
+      {
+        "panel": "d",
+        "purpose": "training-pair budget ablation",
+        "pages": [
+          49
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+        "action": "n train+7val 명시. strict total-n 주장에는기존그림그대로불가"
+      },
+      {
+        "panel": "e",
+        "purpose": "genuine exact-five paired adaptation vs scSemi",
+        "pages": [
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+        "action": "no extra validation/fixed3000/five supportdraws 명시"
+      },
+      {
+        "panel": "f",
+        "purpose": "cell-type composition error and donor-level wins",
+        "pages": [
+          55
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+        "action": "선택 패널; 공간이부족하면SuppS05"
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+    "status": "main_core_with_reanalysis_and_saved_table_replot",
+    "panels": [
+      {
+        "panel": "a",
+        "purpose": "disease cohorts, patient/sample units, separate5fold/five-donor designs",
+        "pages": [
+          62
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+        "action": "healthy행제외; five donors vs five paired samples구분"
+      },
+      {
+        "panel": "b",
+        "purpose": "LoRA-five disease logFC and partial-r comparisons",
+        "pages": [
+          63
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+        "action": "cohort/endpoint별예외유지; 환자단위추정기통일"
+      },
+      {
+        "panel": "c",
+        "purpose": "five-fold disease signal preservation",
+        "pages": [
+          67
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+      {
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+        "purpose": "DEG agreement for both protocols",
+        "pages": [
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+          67
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+      },
+      {
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+        "purpose": "CAT across list lengths, including five-fold scSemi",
+        "pages": [
+          68
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+        "action": "기존per-cohort cat.csv generated rows로누락된scSemiCV곡선추가"
+      },
+      {
+        "panel": "f",
+        "purpose": "cell-type expression comparison with deconvolution methods",
+        "pages": [
+          71
+        ],
+        "support_pages": [
+          84,
+          85
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+        "action": "공통geneaxis/가용draws명시;NA를0으로표기하지않음"
+      }
+    ]
+  },
+  {
+    "figure": 5,
+    "status": "qualitative_visual_assembly_needed",
+    "panels": [
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+        "purpose": "held-out paired sample: observed/LoRA/scSemi rare-state population views",
+        "pages": [],
+        "support_pages": [
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+          91,
+          92,
+          93
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+        "action": "기존generated/observed cells와frozenlabels로공통reference view 작성"
+      },
+      {
+        "panel": "b",
+        "purpose": "per-cell multi-gene marker/co-detection evidence",
+        "pages": [],
+        "action": "samegenes/depth/readout/cellbudget; 정의에쓴marker-space projection을독립identity증명으로해석하지않음"
+      },
+      {
+        "panel": "c",
+        "purpose": "paired case/control donor small multiples",
+        "pages": [],
+        "action": "observedcriteria로사례선택규칙고정; 실제donor/visit단위유지; cell-to-cell일대일대응아님"
+      },
+      {
+        "panel": "d",
+        "purpose": "successful example plus underproduction/failure example",
+        "pages": [],
+        "support_pages": [
+          95,
+          96
+        ],
+        "action": "예:SepsisMS1-like와cyclingmonocyte; 결과가좋은환자만선택하지않음"
+      }
+    ]
+  },
+  {
+    "figure": 6,
+    "status": "TODO",
+    "panels": [
+      {
+        "panel": "a",
+        "purpose": "paired-adaptation set and bulk-only target design",
+        "pages": [],
+        "support_pages": [
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+          106,
+          107
+        ],
+        "action": "대상논문·cohort·sample/visit·overlap고정"
+      },
+      {
+        "panel": "b",
+        "purpose": "prespecified published finding and reproduction endpoint",
+        "pages": [],
+        "action": "기존논문에서어떤방향/효과크기/세포군을재현할지명시"
+      },
+      {
+        "panel": "c",
+        "purpose": "adapted-PBISC bulk-only reproduction result",
+        "pages": [],
+        "action": "실제결과TODO"
+      },
+      {
+        "panel": "d",
+        "purpose": "independent supporting evidence and sensitivity",
+        "pages": [],
+        "action": "bulk-only sample과donor-held-out을동일시하지않음"
+      }
+    ]
+  }
+]

paper-releases/pbisc-diffusion/updates/20261013T044744Z-figure1to6-131page-classification/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/figure_assignment_20261013/supplementary_groups.json

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+      39,
+      41
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+    "purpose": "모델·conditioning·학습·평가 설계 상세",
+    "scope": "개념/방법 설명",
+    "action": "Figure1/2/3를 보완; 경험적 SLE/paired benchmark와 구분"
+  },
+  {
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+    "pages": [
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+      73,
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+    "scope": "pretraining validation 또는 SLE pseudobulk",
+    "action": "12쪽은 corpus validation loss, 나머지는 SLE development. paired disease Figure4에 넣지 않음"
+  },
+  {
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+      34,
+      35,
+      36,
+      37
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+    "action": "sc-derived depth/masks,10-pair calibration,AIFI/pretraining overlap을 명시. strict-five 결과와 합치지 않음"
+  },
+  {
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+    "pages": [
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+      42,
+      43,
+      46,
+      47
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+    "scope": "프로토콜/observed controls/native-depth 진단",
+    "action": "technical repeat와 follow-up, annotation taxonomy, sequencing depth를 각각 구분"
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+    "scope": "paired cell-level/realism/composition",
+    "action": "질환 신호 자체의 증거와 구분. strict6-unit snapshot과 historical designs를 혼합평균하지 않음"
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+    "action": "LoRA-five/scSemi paired rare-state 증거가 아님. Figure4 핵심 adaptation 비교와 분리"
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+      95,
+      96
+    ],
+    "purpose": "paired rare-state 정량 검증과 case 선택 근거",
+    "scope": "paired disease rare-state quantitative",
+    "action": "Fig5 정성 사례를 뒷받침하되 빈도/상관 heatmap을 population-identity 그림으로 대체하지 않음"
+  },
+  {
+    "group": "S11",
+    "pages": [
+      97,
+      98,
+      99,
+      100,
+      101
+    ],
+    "purpose": "pseudobulk rare screen·unmatched Behcet 한계",
+    "scope": "own-sc pseudobulk 또는 unmatched observed reference",
+    "action": "Fig5의 독립 paired qualitative validation으로 사용하지 않음"
+  },
+  {
+    "group": "S12",
+    "pages": [
+      123,
+      124,
+      125,
+      126,
+      127,
+      131
+    ],
+    "purpose": "pretraining·cross-cohort·scratch 대조",
+    "scope": "paired controls; 일부 fold0/one-seed pilot",
+    "action": "131의 다른 tissue 전이는 전망이며 실제 검증 결과가 아님;127은 rare 정량 대조"
+  },
+  {
+    "group": "S13",
+    "pages": [
+      129
+    ],
+    "purpose": "scSemi output-threshold sensitivity",
+    "scope": "paired comparative readout sensitivity",
+    "action": "본문은 official output. 수정 readout은 별도 sensitivity로 표기"
+  },
+  {
+    "group": "S14",
+    "pages": [
+      106
+    ],
+    "purpose": "bulk-only target cohort 차이",
+    "scope": "historical paired vs bulk-only population metadata",
+    "action": "Fig6 설계용 shift 점검; published finding의 재현 결과가 아님"
+  }
+]