Phase 0: Paradigm Capture

Before writing the manuscript, extract a style spec from 2-3 exemplar reviews in the target journal tier. This anchors the draft to flagship-review style and prevents drift toward the generic "survey paper" register that LLMs default to.

Why this phase exists

LLMs trained on the entire web have absorbed every register of medical writing — vendor white papers, methodological surveys, textbook chapters, narrative reviews, systematic reviews, flagship reviews — and have no built-in preference among them. By default, the register they generate is somewhere between "good survey paper" and "Wikipedia article": numbered chapters, hedging language, neutral catalogue, dense subsections.

Flagship-tier reviews (Nature Reviews / Nat Med / Lancet family / JACC) write differently:

2 heading levels, no number prefixes
1-2 sentence "verdict" closers per axis section
Equations and dataset details in Boxes, not body
Vendor names confined to a single Table
Authorial position taken explicitly when evidence supports it
1.5-2.5 references per paragraph, well-targeted
Often a 4-5 bullet "Key Points" box after the title

Without an exemplar anchor, even careful writing drifts toward the generic register. With one, every paragraph has a benchmark.

Action 1: Select 2-3 exemplar reviews

Selection criteria

Same modality or same problem family as your topic. (For coronary AI, look at recent coronary or cardiovascular AI reviews. For brain tumor segmentation, look at neuroradiology AI reviews.)
Same journal tier as your target. If aiming for Nat Med, read a recent Nat Med review. If aiming for Eur Radiol, read a recent Eur Radiol review.
Last 3 years. Older exemplars may have outdated stylistic conventions.
Recognized authors. Reviews authored by senior figures in the field carry the conventions of their target journals more reliably.

Suggested exemplars by tier

Top tier (Nature Reviews / Nat Med / Lancet family):

Nature Reviews Cardiology — for cardiovascular AI
Nat Med — for AI-in-medicine narrative reviews
Lancet Digital Health — for AI clinical translation

Second tier (specialty journals):

JACC: Cardiovascular Imaging — for cardiac imaging AI
Radiology / Eur Radiol — for general imaging AI
IEEE TMI — for methodological reviews with clinical context

Methodological tier:

Medical Image Analysis — for purely methodological reviews
IEEE JBHI — for AI-in-healthcare methods

Acquiring the PDFs

Most flagship reviews are accessible via:

The user's Zotero library (check first — they likely already have them)
PubMed Central (for open-access)
The journal's website (subscription / institutional access)
arXiv preprint version (sometimes available)

Action 2: Read carefully — not skim

Spend 60-90 minutes per exemplar. Read the full text, including Boxes, Figure captions, and Table footnotes.

Pay attention to:

Heading structure

How many levels deep? (Almost always 2 for top tier.)
Are headings numbered or unnumbered? (Almost always unnumbered for top tier.)
How long are H2 sections? (Typically 800-1500 words.)
How long are H3 sections? (Typically 300-800 words.)
How are deeper subsections handled? (Bold lead-in **Topic.**, not H4.)

Paragraph rhythm

How does a paragraph open? (Topic claim — almost never "In recent years," or "It is worth noting.")
How does evidence flow? (1-3 sentences of specifics with citations, not loose generalities.)
How does a paragraph close? (Either with a transition or with a verdict — not with hedging.)
How many sentences per paragraph? (Usually 4-7.)

Citation density

Count references per paragraph in 5 random paragraphs.
Top tier: usually 1.5-2.5 refs per paragraph.
Lower density suggests overclaiming; higher suggests stacking refs uncritically.

Equation handling

Are display equations in body or Boxes?
If in body, is there a Box at all?
How are metric definitions handled — formula or prose?

Vendor handling

Search for any commercial product name. Does it appear in body text or only in Tables?
How are FDA / regulatory facts cited?

Authorial voice

Find the 3-5 strongest claims in the review. How are they phrased?
Does the author take positions like "X is currently the best approach for Y" or stay neutral throughout?
Where does hedging appear? (Usually only when evidence genuinely supports caution.)

Boxes and Figures

How many Boxes? (1-3 typical.)
What goes in a Box? (Definitions, key trials, controversies.)
How many Figures? (3-5 typical.)
What kinds of Figures? (Overview / taxonomy / workflow / data-driven plot.)

Tables

How many Tables? (2-4 typical — rarely 5+.)
What goes in a Table? (Datasets, methods comparison, commercial products.)
How dense? (10-20 rows is common; 30+ is unusual.)

Key Points box

Is there one? (Yes for most top tier.)
How many bullets? (4-5 typical.)
How long is each bullet? (1-3 sentences.)

Action 3: Write `PARADIGM.md` in the project root

Use this template:

# Paradigm Spec for [Project Name]

## Target journal: [name and tier]

## Exemplars studied
1. [Author Year]. [Title]. [Journal]. [PMID/DOI]. (PDF: <path>)
2. [Author Year]. [Title]. [Journal]. [PMID/DOI]. (PDF: <path>)

## Extracted style spec

### Heading structure
- Max depth: [N] levels
- Numbering: [yes / no]
- Typical H2 length: [N-N] words
- Deeper subsections: [H4 / bold lead-in / other]

### Paragraph rhythm
- Opening: [observed pattern, e.g., "Topic claim sentence, no temporal preamble"]
- Body: [observed pattern, e.g., "2-4 sentences of specifics with citations"]
- Closing: [observed pattern, e.g., "Transition or verdict"]
- Typical length: [N-N] sentences

### Citation density
- Average refs per paragraph: [N]
- Multi-citation cap (max refs in one bracket): [N]

### Equations
- Location: [body / Box / both / none]
- Display style: [LaTeX / inline / prose]

### Vendor handling
- Body: [allowed / disallowed]
- Table: [yes / no]
- Total Tables containing vendor names: [N]

### Authorial voice
- Hedging frequency: [observed examples]
- Strong claims: [N observed across 3 reviews]
- Verdict closers per section: [observed pattern]

### Boxes and Figures
- Box count: [N]
- Box purposes: [list]
- Figure count: [N]
- Figure types: [list]

### Tables
- Count: [N]
- Density: [N-N rows]

### Key Points
- Present: [yes / no]
- Bullet count: [N]
- Bullet length: [N-N sentences]

## Manuscript style targets (binding for Phase 4 writing)

Phase 4 writing should conform to this spec. Specifically:
- Max heading depth: ...
- No numbered headings.
- Box 1 for metrics / formulas.
- Vendor names only in Table N.
- ≥ 3 verdict sentences across the manuscript.
- Citation density 1.5-2.5 refs/paragraph.
- Key Points: 4-5 bullets after title.

## Anti-patterns observed in v2 drafting (to specifically avoid)

(Copy / adapt from this skill's HALLUCINATION_PATTERNS.md to the extent the patterns are domain-relevant.)

Action 4: Re-read PARADIGM.md before each Phase 4 writing session

Phase 4 is multi-day. Drift is the main risk. At the start of each writing session, re-read PARADIGM.md to re-anchor.

Time budget

Exemplar selection: 30 min
Reading 2 exemplars: 2-3 hours
Writing the spec: 30-45 min

Total: 3-4 hours.

This is the highest-ROI 3-4 hours in the entire project. Skipping it almost guarantees survey-paper-register drift, which is then extremely expensive to fix in revision.

PARADIGM.md 7.4 KB History Raw