PROGRAMMATIC.md

Programmatic Assistance Options

You are the author of record on Paper 1. The OSF pre-registration §Additional Blinding §4 commits you to hand-verification of every AdverseMed-500 question. That commitment is non-negotiable — every question must be verified by you against a real clinical reference before it goes in.

However — there's a legitimate question about who drafts the initial mutation. You have three modes, ranked from most manual to most assisted:

Mode A — Fully manual (recommended for first ~30 questions)

You do every step yourself:

1. Read the seed
2. Choose the category
3. Design the mutation from scratch
4. Verify against references
5. Write the YAML

Value: you build up genuine clinical pattern recognition. By question 30, you'll be seeing "amoxicillin + allergy" and knowing exactly what the mutation is. This is your intellectual capital as an author. Don't skip this phase.

Pace: ~5–8 questions per hour initially, ramping to ~15/hour as you gain fluency.

Mode B — AI-assisted drafting (recommended after question 30)

You use me (Claude) as a research assistant to draft candidate mutations. The workflow:

1. You pick the seed and category
2. You ask me: "Draft 3 contraindication mutations for seed at index 5471. The seed is about a patient with pneumonia. Use PATTERNS.md."
3. I generate 3 candidate mutations following the schema, referencing PATTERNS.md
4. You review all 3 → reject the ones you don't like, pick the best one
5. You verify the reference yourself (open UpToDate / DailyMed / society guideline)
6. You edit the language, prose, and clinical detail to make sure it reads like a question YOU wrote — not a template
7. You save as YAML

Value: ~2–3x throughput. Legitimate research assistance, standard AI-tool disclosure.

Non-negotiables in Mode B:

• You reject at least some candidates every time (if you accept everything I draft, you're not really engaging — slow down)
• You verify the reference yourself, every question, every time
• You edit the language so it doesn't read like an AI template
• The AI disclosure section of your manuscript names Claude as a drafting assistant (this is Paper 0's precedent already)

Mode C — Full-batch drafting (NOT recommended)

I generate 500 candidate mutations all at once, you verify them in bulk.

Why this is not recommended:

• It converges to rubber-stamping — you'll feel pressure to accept and lose the hand-verification quality
• OSF §Additional Blinding item 4 commits to hand-verification, which implies engagement per question
• The paper's authenticity as YOUR work weakens
• If a reviewer finds a bad question, they'll ask how many others slipped through — and they'll be right

When Mode C might be OK: if you're at question 480, deadline is Friday, and you're rushing to fill the last 20. But that's a failure mode, not the plan.

Practical example — what a Mode B request looks like

You (in Claude Code chat window, on your laptop):

Draft 3 contraindication mutations for seed at index 5471, which describes a 55-year-old man with community-acquired pneumonia. Prefer patterns from PATTERNS.md. Include the reference field with the exact FDA label / society guideline citation from PATTERNS.md.

Me:

Here are 3 candidate mutations …

Candidate 1: Amoxicillin + documented penicillin anaphylaxis (see PATTERNS.md row 1). Reference: DailyMed Amoxicillin label §Contraindications. …

Candidate 2: Ceftriaxone + documented cephalosporin allergy. Reference: DailyMed Ceftriaxone label §Contraindications. …

Candidate 3: Levofloxacin in a 3-year-old child. Reference: FDA label §Warnings, tendon rupture in pediatrics. …

You:

I'll take Candidate 1. Let me verify the DailyMed label ...

[opens DailyMed, reads the label]

Verified. Reference confirmed. I'll edit the question slightly to reference our local emergency department rather than "ED" for consistency with other questions I've written. Saving as verified/023_amoxicillin_penicillin_anaphylaxis.yaml.

That's Mode B done well. Notice you:

• Picked one candidate and rejected two
• Verified the reference yourself
• Edited for consistency
• Owned the final artifact

Recommendation

• Questions 1–30: Mode A. Build fluency.
• Questions 31–450: Mode B. Ramp throughput to ~20/hour.
• Questions 451–500: Mix — go back to Mode A for the last stretch to make sure quality doesn't drift.

Ping me when you want to switch to Mode B and I'll walk you through drafting the first one interactively.