ml-paper-writing

What this skill does

# ML Paper Writing for Top AI Conferences

Expert-level guidance for writing publication-ready papers targeting **NeurIPS, ICML, ICLR, ACL, AAAI, and COLM**. This skill combines writing philosophy from top researchers (Nanda, Farquhar, Karpathy, Lipton, Steinhardt) with practical tools: LaTeX templates, citation verification APIs, and conference checklists.

## Core Philosophy: Collaborative Writing

**Paper writing is collaborative, but Claude should be proactive in delivering drafts.**

The typical workflow starts with a research repository containing code, results, and experimental artifacts. Claude's role is to:

1. **Understand the project** by exploring the repo, results, and existing documentation
2. **Deliver a complete first draft** when confident about the contribution
3. **Search literature** using web search and APIs to find relevant citations
4. **Refine through feedback cycles** when the scientist provides input
5. **Ask for clarification** only when genuinely uncertain about key decisions

**Key Principle**: Be proactive. If the repo and results are clear, deliver a full draft. Don't block waiting for feedback on every section—scientists are busy. Produce something concrete they can react to, then iterate based on their response.

---

## ⚠️ CRITICAL: Never Hallucinate Citations

**This is the most important rule in academic writing with AI assistance.**

### The Problem
AI-generated citations have a **~40% error rate**. Hallucinated references—papers that don't exist, wrong authors, incorrect years, fabricated DOIs—are a serious form of academic misconduct that can result in desk rejection or retraction.

### The Rule
**NEVER generate BibTeX entries from memory. ALWAYS fetch programmatically.**

| Action | ✅ Correct | ❌ Wrong |
|--------|-----------|----------|
| Adding a citation | Search API → verify → fetch BibTeX | Write BibTeX from memory |
| Uncertain about a paper | Mark as `[CITATION NEEDED]` | Guess the reference |
| Can't find exact paper | Note: "placeholder - verify" | Invent similar-sounding paper |

### When You Can't Verify a Citation

If you cannot programmatically verify a citation, you MUST:

```latex
% EXPLICIT PLACEHOLDER - requires human verification
\cite{PLACEHOLDER_author2024_verify_this}  % TODO: Verify this citation exists
```

**Always tell the scientist**: "I've marked [X] citations as placeholders that need verification. I could not confirm these papers exist."

### Recommended: Install Exa MCP for Paper Search

For the best paper search experience, install **Exa MCP** which provides real-time academic search:

**Claude Code:**
```bash
claude mcp add exa -- npx -y mcp-remote "https://mcp.exa.ai/mcp"
```

**Cursor / VS Code** (add to MCP settings):
```json
{
  "mcpServers": {
    "exa": {
      "type": "http",
      "url": "https://mcp.exa.ai/mcp"
    }
  }
}
```

Exa MCP enables searches like:
- "Find papers on RLHF for language models published after 2023"
- "Search for transformer architecture papers by Vaswani"
- "Get recent work on sparse autoencoders for interpretability"

Then verify results with Semantic Scholar API and fetch BibTeX via DOI.

---

## Workflow 0: Starting from a Research Repository

When beginning paper writing, start by understanding the project:

```
Project Understanding:
- [ ] Step 1: Explore the repository structure
- [ ] Step 2: Read README, existing docs, and key results
- [ ] Step 3: Identify the main contribution with the scientist
- [ ] Step 4: Find papers already cited in the codebase
- [ ] Step 5: Search for additional relevant literature
- [ ] Step 6: Outline the paper structure together
- [ ] Step 7: Draft sections iteratively with feedback
```

**Step 1: Explore the Repository**

```bash
# Understand project structure
ls -la
find . -name "*.py" | head -20
find . -name "*.md" -o -name "*.txt" | xargs grep -l -i "result\|conclusion\|finding"
```

Look for:
- `README.md` - Project overview and claims
- `results/`, `outputs/`, `experiments/` - Key findings
- `configs/` - Experimental settings
- Existing `.bib` files or citation references
- Any draft documents or notes

**Step 2: Identify Existing Citations**

Check for papers already referenced in the codebase:

```bash
# Find existing citations
grep -r "arxiv\|doi\|cite" --include="*.md" --include="*.bib" --include="*.py"
find . -name "*.bib"
```

These are high-signal starting points for Related Work—the scientist has already deemed them relevant.

**Step 3: Clarify the Contribution**

Before writing, explicitly confirm with the scientist:

> "Based on my understanding of the repo, the main contribution appears to be [X].
> The key results show [Y]. Is this the framing you want for the paper,
> or should we emphasize different aspects?"

**Never assume the narrative—always verify with the human.**

**Step 4: Search for Additional Literature**

Use web search to find relevant papers:

```
Search queries to try:
- "[main technique] + [application domain]"
- "[baseline method] comparison"
- "[problem name] state-of-the-art"
- Author names from existing citations
```

Then verify and retrieve BibTeX using the citation workflow below.

**Step 5: Deliver a First Draft**

**Be proactive—deliver a complete draft rather than asking permission for each section.**

If the repo provides clear results and the contribution is apparent:
1. Write the full first draft end-to-end
2. Present the complete draft for feedback
3. Iterate based on scientist's response

If genuinely uncertain about framing or major claims:
1. Draft what you can confidently
2. Flag specific uncertainties: "I framed X as the main contribution—let me know if you'd prefer to emphasize Y instead"
3. Continue with the draft rather than blocking

**Questions to include with the draft** (not before):
- "I emphasized X as the main contribution—adjust if needed"
- "I highlighted results A, B, C—let me know if others are more important"
- "Related work section includes [papers]—add any I missed"

---

## When to Use This Skill

Use this skill when:
- **Starting from a research repo** to write a paper
- **Drafting or revising** specific sections
- **Finding and verifying citations** for related work
- **Formatting** for conference submission
- **Resubmitting** to a different venue (format conversion)
- **Iterating** on drafts with scientist feedback

**Always remember**: First drafts are starting points for discussion, not final outputs.

---

## Balancing Proactivity and Collaboration

**Default: Be proactive. Deliver drafts, then iterate.**

| Confidence Level | Action |
|-----------------|--------|
| **High** (clear repo, obvious contribution) | Write full draft, deliver, iterate on feedback |
| **Medium** (some ambiguity) | Write draft with flagged uncertainties, continue |
| **Low** (major unknowns) | Ask 1-2 targeted questions, then draft |

**Draft first, ask with the draft** (not before):

| Section | Draft Autonomously | Flag With Draft |
|---------|-------------------|-----------------|
| Abstract | Yes | "Framed contribution as X—adjust if needed" |
| Introduction | Yes | "Emphasized problem Y—correct if wrong" |
| Methods | Yes | "Included details A, B, C—add missing pieces" |
| Experiments | Yes | "Highlighted results 1, 2, 3—reorder if needed" |
| Related Work | Yes | "Cited papers X, Y, Z—add any I missed" |

**Only block for input when:**
- Target venue is unclear (affects page limits, framing)
- Multiple contradictory framings seem equally valid
- Results seem incomplete or inconsistent
- Explicit request to review before continuing

**Don't block for:**
- Word choice decisions
- Section ordering
- Which specific results to show (make a choice, flag it)
- Citation completeness (draft with what you find, note gaps)

---

## The Narrative Principle

**The single most critical insight**: Your paper is not a collection of experiments—it's a story with one clear contribution supported by evidence.

Every successful ML paper centers on what Neel Nanda calls "