MDPI "AI in Medicine" manuscript

What this project is

Writing a journal article for MDPI's AI in Medicine journal (short name aimed, ISSN 3042-6707), on predicting no-reflow / slow-flow complications after PCI from IVUS images.

Source material — reference only, not a source of facts

Timeline, oldest first:

1. Reference/卒業論文_金子_最終.pdf — the original graduation thesis (Japanese).
2. Reference/main.tex / main_ja.tex (+ their rendered main.pdf / main_ja.pdf) — a later MIDL 2026 short paper built on the thesis.

The dataset and experiments have since changed. These documents are useful for prose style, structure, and terminology — they are NOT a source of current facts. Never cite numbers, case counts, AUC/results, dataset descriptions, ethics approval numbers, etc. from these files as if they still hold for the new manuscript. Any such detail needed in the new paper must come from current data/results the user provides, not by copying it from these references.

The manuscript itself

• main.tex is the actual manuscript and the file to compile — edit it (and the files it \inputs) in place rather than starting new files. It was copied from Template/template.tex, which is now kept untouched as a pristine copy of the official MDPI template for reference (e.g., to check the original boilerplate/instructions for a macro) — do not edit it going forward, and do not re-derive facts from it, it's just the blank starting point main.tex was copied from. It lives in its own Template/ folder (alongside its rendered template.pdf) to keep it visually distinct from the actual manuscript at the repo root; its \documentclass/ \includegraphics calls use ../Definitions/... to match (still resolves to the same Definitions/ folder).
• The manuscript is split across files rather than written as one block, since it's expected to run 10-15 pages (\input, not \include — \include forces a \clearpage per file, which doesn't suit a short continuously-flowing journal article):
  • sections/ holds the body, one file per section, numbered to match reading order (1_introduction.tex, 2_related_work.tex, 3_method.tex, 4_experiment.tex, 5_discussion.tex, 6_conclusion.tex), \input from main.tex right after each \section{...} heading. There's no 0_abstract.tex — see above.
  • figures/ holds figure images; subfolder per section if it grows large.
  • The Abstract is the one exception — it stays written inline inside main.tex's \abstract{...} call, not split into sections/. mdpi.cls also reuses that same argument verbatim as the PDF's pdfsubject metadata via hyperref, which requires it to be fully expandable; \input is not expandable and breaks that (crashes with TeX capacity exceeded). Confirmed empirically — don't try \input for the abstract again.
• Not yet configured for this journal: the \documentclass line currently reads [journal,article,submit,moreauthors]; before submission this must become [aimed,article,submit,moreauthors] (or the correct article type instead of article, if this isn't a standard Article). (This applies to main.tex; Template/template.tex is left as-is.)
• Definitions/ holds the official MDPI class/style/bst files (mdpi.cls, mdpi.bst, journalnames.tex, logos). Don't edit these — they're MDPI-supplied.
• main.tex references \bibliography{references}. references.bib exists but is only a stub (cite keys babapoor2022, wu2011, nishi2021 carried over from the MIDL paper as a starting point) — real bibliographic data still needs to be filled in and verified, and new citations added as the manuscript grows.
• citations/ holds the PDFs of cited papers (one per reference, named after its .bib cite key, e.g. babapoor2022.pdf). Drop a paper's PDF there and Claude Code can read it directly to fill in or verify that key's entry in references.bib (title, authors, venue, year, DOI, etc.) instead of guessing from the key name alone.
• Math/theorem-like environments should use MDPI's names: Theorem, Lemma, Corollary, Proposition, Characterization, Property, Problem, Example, ExamplesandDefinitions, Hypothesis, Remark, Definition, Notation, Assumption (see comments in Template/template.tex, still accurate for main.tex).

Working environment

This repo is edited from more than one machine (Windows/WSL and macOS have both been used), so don't assume either one — check uname/the shell you're actually in before relying on platform-specific behavior below.

• Windows/WSL: the repo lives on the WSL (Ubuntu) filesystem. When it's accessed from a Windows-side shell (Git Bash/MSYS, PowerShell) via \\wsl.localhost\..., WSL's *:Zone.Identifier marker files (harmless Windows download metadata, no content value) show up with a mangled colon character, which makes git status report spurious deleted/untracked pairs for the same files. These are now covered by .gitignore — don't try to "fix" them again. Prefer running git (and anything touching filenames with unusual characters) from inside actual WSL, e.g. wsl.exe -- bash -lc "cd /home/nlab/MDPI && <command>" from PowerShell, rather than Windows Git Bash. Git Bash accessing the repo over the UNC path may also need a one-time git config --global --add safe.directory '%(prefix)///wsl.localhost/Ubuntu/home/nlab/MDPI' (dubious-ownership check) — already set on the Windows machine this was written from.
• macOS: none of the above applies; the repo should behave like a normal local git checkout.
• LaTeX toolchain: on this WSL machine, TeX Live 2026 is installed at /usr/local/texlive/2026/bin/x86_64-linux/ (a full install — pdflatex, latexmk, bibtex, etc.), with PATH set in ~/.zshrc (the default shell is zsh). That PATH export is only loaded for an interactive shell — a plain bash -lc "..."/zsh -lc "..." from Windows (e.g. via wsl.exe --) won't have it on PATH and which pdflatex will (misleadingly) fail. To compile from outside WSL, use an interactive shell explicitly, e.g. from PowerShell: wsl.exe -- zsh -ic "cd /home/nlab/MDPI && pdflatex -interaction=nonstopmode -output-directory=build main.tex". All generated files (.pdf, .aux, .log, the epstopdf-converted logo, etc.) land in build/ this way, keeping the repo root clean; build/ must exist first (mkdir -p build, already done — it's tracked as an empty folder via build/.gitkeep since its contents are gitignored). Verified working: compiling main.tex this way produces a 6-page build/main.pdf (only harmless "undefined reference"/rerun warnings on the first pass — normal for LaTeX before a second pass resolves cross-references). On a machine without this TeX Live install (e.g. a fresh macOS checkout), install one (brew install --cask mactex or the smaller basictex, or sudo apt install texlive-full on Linux) or compile via Overleaf instead (Overleaf manages its own build output and ignores this convention).
• VS Code (LaTeX Workshop): .vscode/settings.json sets a latexmk recipe that outputs to build/. On Windows, VS Code must have the folder open in WSL (Remote-WSL: "WSL: Reopen Folder in WSL", or code . from a WSL shell) — opening it via the \\wsl.localhost\... UNC path runs LaTeX Workshop on the Windows side, where no TeX is installed, so building fails.

Writing conventions

• Manuscript language is English (MDPI submission requirement), even though some source material (main_ja.tex, the thesis PDF) is Japanese.
• Follow the MIDL paper's terminology (e.g. "attenuated plaque", "polar coordinate transformation", "CNN-LSTM") for consistency unless a term needs to change for the current data/results or a journal audience.
• Never fill a gap with an unstated inference — don't write claims, numbers, or details the user hasn't given. If something needed for the manuscript is unclear or unspecified, ask rather than guess.
• When rendering Japanese source material (the thesis, main_ja.tex) into English, translate faithfully — not a loose paraphrase — while still producing natural, idiomatic English rather than a stiff word-for-word rendering.
• Line wrapping (semantic linefeeds + a soft ~80-char cap): in prose files (sections/*.tex, drafts/ja/*.md), start a new line at each sentence boundary (English ./!/? + space; Japanese 。/．) instead of writing a whole paragraph as one unbroken line. That alone isn't enough — a single sentence can still run well past a readable width — so also keep every line at roughly 80 characters: if a sentence (or an enumerated (1)/(2)/(3) item within one) is longer than that, break it further at a clean clause boundary at or before the ~80-char mark (comma, semicolon, or a coordinating/subordinating conjunction like "and"/"but"/"because"/"which"/"while"/"however"; Japanese ，/、/接続助詞など), continuing flush-left with no extra indent — never break mid-phrase just to hit the column exactly. A single newline is invisible in the rendered output — both LaTeX and Markdown treat it as a space within a paragraph, and only a blank line starts a new paragraph — so this is purely a source-readability/diff convention, not something that changes the PDF. Applies whenever a prose file is newly written or substantively redrafted (including the ja-drafter/en-translator pipeline output); not a mandate to mass-reflow untouched files.

Drafting workflow (subagents)

Sections get written through a fixed pipeline rather than drafted directly in English in one pass. Each stage is a project subagent under .claude/agents/; read a stage's .md file for its full brief before invoking it.

1. Discussion — no subagent; this is an ordinary conversation between the user and the main session to settle what a section should say (outline, argument, which facts/numbers apply).
2. ja-drafter — writes a Japanese prose draft of the section from that outline into drafts/ja/<N>_<name>.md (mirroring sections/ numbering). Only uses facts given to it explicitly; never pulls numbers from Reference/.
3. Review, in parallel, on the Japanese draft:
   • fact-checker — checks every number/statistic against the Notion page (below) and flags anything unsupported or copied from Reference/.
   • content-reviewer — checks logical coherence, clinical plausibility, and terminology consistency with Reference/main.tex. Both are read-only; they report findings rather than editing.
4. en-translator — once review findings are resolved, translates the reviewed drafts/ja/*.md file into faithful, idiomatic English LaTeX and writes it into the matching sections/*.tex file. Never changes a number during translation.

Re-run the review stage (3) after any substantive re-draft, and again on the English output of stage 4 if it's not a purely mechanical translation.

実験に関するデータの参照場所

https://app.notion.com/p/AI-in-Medicine-3df9efa583a0803eba3ed15f51bf1b2a?source=copy_link

##注意点 上記のNotion以外の数字は基本的に信頼しないこと