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 (introduction.tex, related_work.tex, method.tex, experiment.tex, discussion.tex, conclusion.tex), \input from main.tex right after each \section{...} heading.
  • 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.
• 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).

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.