{
  "date": "2026-10-02",
  "author": "Pilkwang Kim",
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  "scope": "Original explanatory artwork, an experiment-design schematic and a Private-only plot; no measured optimization landscape or score claim for an unrun alternative.",
  "mobile_variants": "Layout-only adaptations of the same Private scores, verdicts, and composition schematic; intended for a picture source below 620 px.",
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          "text": "Reject that composition; inspect\nwhere the loss occurs.",
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          "text": "Check exposure and convergence;\njustify any change in support.",
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          "text": "BIOHUB / NOTE 9",
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        {
          "text": "Four findings,\nfour different next actions",
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          "text": "Negative graph result",
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          "text": "The measured\ncomposition loses.",
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          "text": "Reject that composition; inspect\nwhere the loss occurs.",
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          "text": "Training insufficient",
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          "text": "The model did not\nlearn enough.",
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        {
          "text": "Check exposure and convergence;\njustify any change in support.",
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          "text": "Execution incomplete",
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          "text": "The run did not\nreach scoring.",
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          "text": "Repair the blocked execution;\nmeasure before judging quality.",
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          "text": "The probe answers\na narrow question.",
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          "text": "Use it to choose the next test;\nkeep its interpretation within scope.",
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    {
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          "text": "BIOHUB CELL TRACKING",
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          "text": "LINEAGE RECONSTRUCTION UNDER SPARSE ANNOTATION",
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          "text": "WORKING NOTE 9 / RETROSPECTIVE",
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          "text": "A Big Plan\nand a Weak Start",
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          "text": "How early choices made changing course harder:\nmodels, experiments and the lessons I learned",
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        {
          "text": "01  MODELS",
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            234.75,
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        },
        {
          "text": "Learn the missing signal",
          "bounds_px": [
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        },
        {
          "text": "Examine targets, support and errors\nbefore judging a model family.",
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          "text": "02  COMPOSITION",
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          "text": "Give new evidence a usable role",
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          "text": "Train and calibrate a compatible\npath to a complete graph.",
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          "text": "03  RESEARCH",
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          "text": "Prepare a runnable question\nand decide from its predictions.",
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        },
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          "text": "PILKWANG KIM / 2 OCTOBER 2026",
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          "text": "SERIES · PART 9",
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      "text_bounds": [
        {
          "text": "BIOHUB CELL TRACKING / NOTE 9",
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        },
        {
          "text": "Two comparisons, two different questions",
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        },
        {
          "text": "A: detector · B: association · C: graph policy · D: new evidence",
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          "text": "1  PLUG-IN COMPARISON",
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        {
          "text": "Keep the incumbent settings",
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            120.0,
            353.0,
            640.875,
            387.5
          ]
        },
        {
          "text": "$P_0 = (A_0, B_0, C_0)$",
          "bounds_px": [
            150.0,
            445.0,
            474.7323822021485,
            488.20000000000005
          ]
        },
        {
          "text": "Incumbent training and fitted $\\theta_0$",
          "bounds_px": [
            150.0,
            510.0,
            576.8369598388672,
            543.0
          ]
        },
        {
          "text": "Add D; retain $\\theta_0$",
          "bounds_px": [
            507.0,
            579.0,
            723.9891662597656,
            611.1
          ]
        },
        {
          "text": "$P_D$: $P_0$ with D",
          "bounds_px": [
            150.0,
            654.0,
            413.44978485107424,
            695.2
          ]
        },
        {
          "text": "Same inherited path and settings",
          "bounds_px": [
            150.0,
            719.0,
            592.25,
            747.0
          ]
        },
        {
          "text": "Score both final graphs",
          "bounds_px": [
            290.1875,
            837.0,
            669.8125,
            868.21875
          ]
        },
        {
          "text": "Evidence: D at the inherited $\\theta_0$",
          "bounds_px": [
            120.0,
            935.0,
            584.4755706787109,
            968.4
          ]
        },
        {
          "text": "Retain or reject this plug-in;\nkeep the verdict within that scope.",
          "bounds_px": [
            120.0,
            993.0,
            596.0,
            1056.75
          ]
        },
        {
          "text": "2  COMPATIBLE COMPOSITION",
          "bounds_px": [
            960.0,
            303.0,
            1363.875,
            327.0
          ]
        },
        {
          "text": "Declare the candidate's own path",
          "bounds_px": [
            960.0,
            353.0,
            1561.5,
            387.0
          ]
        },
        {
          "text": "$P_D$ at adapted $\\theta_D$",
          "bounds_px": [
            990.0,
            445.0,
            1305.7099609375,
            488.0
          ]
        },
        {
          "text": "or a separate pipeline $P_1$ at $\\theta_1$",
          "bounds_px": [
            990.0,
            505.0,
            1434.2390411376953,
            542.0
          ]
        },
        {
          "text": "Train and calibrate this path",
          "bounds_px": [
            990.0,
            654.0,
            1468.625,
            687.0
          ]
        },
        {
          "text": "Support, fitting and settings declared first",
          "bounds_px": [
            990.0,
            719.0,
            1527.125,
            745.0
          ]
        },
        {
          "text": "Compare complete final graphs",
          "bounds_px": [
            1065.75,
            837.0,
            1574.25,
            868.21875
          ]
        },
        {
          "text": "Evidence: a compatible, trained path",
          "bounds_px": [
            960.0,
            935.0,
            1516.75,
            964.0
          ]
        },
        {
          "text": "Use the complete incumbent as reference;\njudge the frozen composition.",
          "bounds_px": [
            960.0,
            993.0,
            1546.75,
            1056.75
          ]
        },
        {
          "text": "A conditional loss does not establish family exhaustion",
          "bounds_px": [
            90.0,
            1170.0,
            1116.375,
            1206.75
          ]
        },
        {
          "text": "Adaptation belongs on training-side data; no promise that an alternative will win.",
          "bounds_px": [
            90.0,
            1233.0,
            1164.875,
            1261.0
          ]
        }
      ],
      "out_of_bounds": [],
      "text_intersections": []
    },
    {
      "name": "fig-03-component-and-composition-mobile",
      "dimensions_px": [
        760,
        2070
      ],
      "text_bounds": [
        {
          "text": "BIOHUB / NOTE 9",
          "bounds_px": [
            30.0,
            30.0,
            256.375,
            54.0
          ]
        },
        {
          "text": "Two comparisons,\ntwo different questions",
          "bounds_px": [
            30.0,
            83.0,
            502.875,
            171.375
          ]
        },
        {
          "text": "A: detector · B: association\nC: graph policy · D: new evidence",
          "bounds_px": [
            30.0,
            203.0,
            481.125,
            264.5
          ]
        },
        {
          "text": "1  PLUG-IN COMPARISON",
          "bounds_px": [
            58.0,
            336.0,
            390.375,
            360.0
          ]
        },
        {
          "text": "Keep incumbent settings",
          "bounds_px": [
            58.0,
            388.0,
            521.375,
            424.75
          ]
        },
        {
          "text": "$P_0 = (A_0, B_0, C_0)$",
          "bounds_px": [
            86.0,
            487.0,
            388.38002014160156,
            527.9000000000001
          ]
        },
        {
          "text": "Incumbent training and fitted $\\theta_0$",
          "bounds_px": [
            86.0,
            548.0,
            512.8369598388672,
            581.0
          ]
        },
        {
          "text": "$P_D$: $P_0$ with D",
          "bounds_px": [
            86.0,
            669.0,
            331.31175994873047,
            708.9000000000001
          ]
        },
        {
          "text": "Add D; retain the inherited $\\theta_0$",
          "bounds_px": [
            86.0,
            730.0,
            465.0057678222656,
            760.5999999999999
          ]
        },
        {
          "text": "Score both final graphs",
          "bounds_px": [
            184.875,
            832.0,
            575.125,
            865.0
          ]
        },
        {
          "text": "Evidence: D at inherited $\\theta_0$",
          "bounds_px": [
            58.0,
            908.0,
            478.2381591796875,
            943.7
          ]
        },
        {
          "text": "Retain or reject this plug-in;\nkeep the verdict within that scope.",
          "bounds_px": [
            58.0,
            959.0,
            518.625,
            1020.5
          ]
        },
        {
          "text": "2 COMPATIBLE COMPOSITION",
          "bounds_px": [
            58.0,
            1110.0,
            454.375,
            1134.0
          ]
        },
        {
          "text": "Declare its own path",
          "bounds_px": [
            58.0,
            1162.0,
            437.0,
            1198.25
          ]
        },
        {
          "text": "$P_D$ at adapted $\\theta_D$",
          "bounds_px": [
            86.0,
            1261.0,
            401.7099609375,
            1304.0
          ]
        },
        {
          "text": "or a separate $P_1$ at $\\theta_1$",
          "bounds_px": [
            86.0,
            1322.0,
            377.2089904785156,
            1355.0
          ]
        },
        {
          "text": "Train and calibrate",
          "bounds_px": [
            86.0,
            1443.0,
            439.625,
            1479.0
          ]
        },
        {
          "text": "Declare support, fitting and settings",
          "bounds_px": [
            86.0,
            1504.0,
            548.25,
            1530.0
          ]
        },
        {
          "text": "Compare complete graphs",
          "bounds_px": [
            159.5625,
            1606.0,
            600.4375,
            1639.0
          ]
        },
        {
          "text": "Evidence: a compatible path",
          "bounds_px": [
            58.0,
            1682.0,
            503.125,
            1713.21875
          ]
        },
        {
          "text": "Use the complete incumbent as reference;\njudge the frozen composition.",
          "bounds_px": [
            58.0,
            1733.0,
            625.5,
            1794.5
          ]
        },
        {
          "text": "A conditional loss does not\nestablish family exhaustion",
          "bounds_px": [
            30.0,
            1910.0,
            500.625,
            1982.5
          ]
        },
        {
          "text": "Training-side adaptation; no promised win.",
          "bounds_px": [
            30.0,
            2010.0,
            581.5,
            2036.0
          ]
        }
      ],
      "out_of_bounds": [],
      "text_intersections": []
    }
  ],
  "outputs": [
    {
      "file": "cover.png",
      "sha256": "a3ef7423b8db3cb1ff08e1db28ab4ee6b1274070311c50e9d515bf65970945e9"
    },
    {
      "file": "fig-01-private-submissions-mobile.png",
      "sha256": "5477ac31e139873014d618d5cb0c5f18accdcbc348c05cc327bbcbc8be97a9cc"
    },
    {
      "file": "fig-01-private-submissions.png",
      "sha256": "7663b97f998c991dfb3bd746b17994da26a308be6bf32154c1691a4757444c5d"
    },
    {
      "file": "fig-02-research-verdicts-mobile.png",
      "sha256": "edceded37e126b647af6e03b33321b0faeaba593abf5cfa8771ad1ffc426ebe5"
    },
    {
      "file": "fig-02-research-verdicts.png",
      "sha256": "29b04b56f94f449a07b39c65174adaf36c5f45e54b7a13e478de681fbadf7827"
    },
    {
      "file": "fig-03-component-and-composition-mobile.png",
      "sha256": "9061502684d4a5c0b08a2f69bfbe9e96d4f76a94d9043c5201463e96ea98fcf8"
    },
    {
      "file": "fig-03-component-and-composition.png",
      "sha256": "ce142e053151a04f494dc16e348a7922cda10eb29fbb784f311325bfea3ab0ed"
    },
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      "file": "cover.svg",
      "sha256": "1d348cc3754ef90dc6cbc2f88208b3dca92800bbce3de82d8a7afa58ec252060"
    },
    {
      "file": "fig-01-private-submissions-mobile.svg",
      "sha256": "d17a8482f6356d087f8141fe2680c99a20318d393ee9545ec4f873358eca92c4"
    },
    {
      "file": "fig-01-private-submissions.svg",
      "sha256": "0f513ac07376e125d0e49433486de134c82bf4bbf835ab526a85fe1e3bd9aceb"
    },
    {
      "file": "fig-02-research-verdicts-mobile.svg",
      "sha256": "43d5e6ded00c492a659ae36f4d86992504de71d440c010ac887cc16c026d4639"
    },
    {
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      "sha256": "6f3cc1dfe9676c7e699b7e22cc5e99fd232e350f5adebdca70c90ee34417fab4"
    },
    {
      "file": "fig-03-component-and-composition-mobile.svg",
      "sha256": "db7ac73fabd21e0e06c85476a9c4fc50c0873b30d66239319c94e6ee2388b1ab"
    },
    {
      "file": "fig-03-component-and-composition.svg",
      "sha256": "660a2d23832917bb53d6fa8ac6c0e4bb3eef88fef4d9c97b1e9ca83c4cd58fd8"
    }
  ],
  "visual_review": {
    "status": "passed",
    "method": "Direct view_image inspection of all three original PNGs and all three 760-pixel-wide previews after the final generation.",
    "findings": "No overlapping labels or clipping. White figures use compact layouts; plot grid, exact scores, statuses and verdict actions remain legible at 760 pixels. Cover matches the earlier dark title-card typography and line art; its small footer/summary text remains secondary to the title.",
    "preview_paths": [
      "_qa/cover-760px.png",
      "_qa/fig-01-private-submissions-760px.png",
      "_qa/fig-02-research-verdicts-760px.png"
    ],
    "font_fix": "Used the explicit Arial bold face for bold labels because the macOS Helvetica Neue TTC resolved to a regular face in the initial Matplotlib output.",
    "limits": "Figure layout and embedded EN/KR page rendering, tables and MathJax verified at 1280×900 and 390×844 on 2026-10-03; scope is presentation, not model-performance validation."
  },
  "mobile_visual_review": {
    "status": "passed",
    "method": "Direct view_image inspection of both full 760-pixel mobile PNGs and their 360-pixel-wide previews after final generation.",
    "findings": "All five exact scores, versions and selection/diagnostic statuses are readable at 360 pixels. The four verdicts are stacked with readable observations and actions; no labels overlap or clip. Narrow page margins and card spacing leave no large empty bands.",
    "preview_paths": [
      "_qa/fig-01-private-submissions-mobile-360px.png",
      "_qa/fig-02-research-verdicts-mobile-360px.png"
    ],
    "desktop_preservation": "Ran the generator with --mobile-only; existing cover and desktop PNG/SVG files were not written.",
    "limits": "Figure layout and embedded EN/KR page rendering, tables and MathJax verified at 1280×900 and 390×844 on 2026-10-03; scope is presentation, not model-performance validation."
  },
  "research_revision_visual_review": "Passed: directly inspected revised cover and both composition PNG layouts at article-scale widths; no text overlaps or excessive unused space found. P0/PD/P1 matches the narrative definitions.",
  "article_order": {
    "figure_1": "fig-03-component-and-composition",
    "figure_2": "fig-02-research-verdicts",
    "appendix_figure_3": "fig-01-private-submissions"
  },
  "writeup_revision": {
    "date": "2026-10-02",
    "scope": "Prose and primary evidence expanded. Existing PNG/SVG assets were not regenerated; prior visual QA applies to those unchanged bytes. Embedded page rendering checked separately.",
    "asset_sha256": {
      "cover.png": "0fa8fb42c24e2fc495249f891ab5c107bcfe81b099eed523a5d52b369048a8ab",
      "cover.svg": "2376d014511a1858f8b985a91adc76a1b219f264224061bb470163ffc6d2277c",
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    }
  },
  "narrative_revision": {
    "date": "2026-10-03",
    "scope": "Cover retitled; desktop/mobile composition schematic uses P0, PD and P1 with defined roles and operating choices. Private and verdict plots unchanged. Text bounds and direct image inspection passed; embedded page rendering checked separately.",
    "asset_sha256": {
      "cover.png": "a3ef7423b8db3cb1ff08e1db28ab4ee6b1274070311c50e9d515bf65970945e9",
      "cover.svg": "1d348cc3754ef90dc6cbc2f88208b3dca92800bbce3de82d8a7afa58ec252060",
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}