# 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](Reference/卒業論文_金子_最終.pdf) — the
   original graduation thesis (Japanese).
2. [Reference/main.tex](Reference/main.tex) / [main_ja.tex](Reference/main_ja.tex)
   (+ their rendered [main.pdf](Reference/main.pdf) / [main_ja.pdf](Reference/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
- [template.tex](template.tex) is the official MDPI template and will become
  the actual manuscript — edit it in place rather than starting a new file.
- **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).
- [Definitions/](Definitions/) holds the official MDPI class/style/bst
  files (`mdpi.cls`, `mdpi.bst`, `journalnames.tex`, logos). Don't edit
  these — they're MDPI-supplied.
- `template.tex` references `\bibliography{references}`. [references.bib](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.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**: as of this writing, no LaTeX toolchain (`pdflatex`,
  `latexmk`, `bibtex`) was found on the Windows PATH or inside WSL on the
  machine this file was written from — `template.tex` couldn't be compiled
  to verify output. Check for one (`which pdflatex`) before relying on
  Claude Code to compile/check the PDF; if missing, install TeX Live
  (`sudo apt install texlive-full` on WSL/Linux, `brew install --cask
  mactex` or the smaller `basictex` on macOS) or compile via Overleaf
  instead.

## 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.