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

claude mcp add exa -- npx -y mcp-remote "https://mcp.exa.ai/mcp"

{
  "mcpServers": {
    "exa": {
      "type": "http",
      "url": "https://mcp.exa.ai/mcp"
    }
  }
}

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

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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

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:

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"

---

Paper Writing Progress:
- [ ] Step 1: Define the one-sentence contribution (with scientist)
- [ ] Step 2: Draft Figure 1 → get feedback → revise
- [ ] Step 3: Draft abstract → get feedback → revise
- [ ] Step 4: Draft introduction → get feedback → revise
- [ ] Step 5: Draft methods → get feedback → revise
- [ ] Step 6: Draft experiments → get feedback → revise
- [ ] Step 7: Draft related work → get feedback → revise
- [ ] Step 8: Draft limitations → get feedback → revise
- [ ] Step 9: Complete paper checklist (required)
- [ ] Step 10: Final review cycle and submission

1. What you achieved: "We introduce...", "We prove...", "We demonstrate..."
2. Why this is hard and important
3. How you do it (with specialist keywords for discoverability)
4. What evidence you have
5. Your most remarkable number/result

Template Setup Checklist:
- [ ] Step 1: Copy entire template directory to new project
- [ ] Step 2: Verify template compiles as-is (before any changes)
- [ ] Step 3: Read the template's example content to understand structure
- [ ] Step 4: Replace example content section by section
- [ ] Step 5: Keep template comments/examples as reference until done
- [ ] Step 6: Clean up template artifacts only at the end

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**⚠️ IMPORTANT**: Copy the ENTIRE directory, not just `main.tex`. Templates include:
- Style files (`.sty`) - required for compilation
- Bibliography styles (`.bst`) - required for references
- Example content - useful as reference
- Makefiles - for easy compilation

**Step 2: Verify Template Compiles First**

Before making ANY changes, compile the template as-is:

```bash

If the unmodified template doesn't compile, fix that first. Common issues:
- Missing TeX packages → install via `tlmgr install <package>`
- Wrong TeX distribution → use TeX Live (recommended)

**Step 3: Keep Template Content as Reference**

Don't immediately delete all example content. Instead:

```latex
% KEEP template examples commented out as you write
% This shows you the expected format

% Template example (keep for reference):
% \begin{figure}[t]
%   \centering
%   \includegraphics[width=0.8\linewidth]{example-image}
%   \caption{Template shows caption style}
% \end{figure}

% Your actual figure:
\begin{figure}[t]
  \centering
  \includegraphics[width=0.8\linewidth]{your-figure.pdf}
  \caption{Your caption following the same style.}
\end{figure}

Replacement Order:
1. Title and authors (anonymize for submission)
2. Abstract
3. Introduction
4. Methods
5. Experiments
6. Related Work
7. Conclusion
8. References (your .bib file)
9. Appendix

% Common template macros to use:
\newcommand{\method}{YourMethodName}  % Consistent method naming
\newcommand{\eg}{e.g.,\xspace}        % Proper abbreviations
\newcommand{\ie}{i.e.,\xspace}
\newcommand{\etal}{\textit{et al.}\xspace}

% BEFORE SUBMISSION - remove these:
% - Commented-out template examples
% - Unused packages
% - Template's example figures/tables
% - Lorem ipsum or placeholder text

% KEEP these:
% - All style files (.sty)
% - Bibliography style (.bst)
% - Required packages from template
% - Any custom macros you're using

Format Conversion Checklist:
- [ ] Step 1: Identify source and target template differences
- [ ] Step 2: Create new project with target template
- [ ] Step 3: Copy content sections (not preamble)
- [ ] Step 4: Adjust page limits and content
- [ ] Step 5: Update conference-specific requirements
- [ ] Step 6: Verify compilation and formatting

undefined

**Step 3: Adjusting for Page Limits**

When cutting pages (e.g., NeurIPS 9 → AAAI 7):
- Move detailed proofs to appendix
- Condense related work (cite surveys instead of individual papers)
- Combine similar experiments into unified tables
- Use smaller figure sizes with subfigures
- Tighten writing: eliminate redundancy, use active voice

When expanding (e.g., ICML 8 → ICLR 9):
- Add ablation studies reviewers requested
- Expand limitations discussion
- Include additional baselines
- Add qualitative examples

**Step 4: Conference-Specific Adjustments**

| Target Venue | Required Additions |
|--------------|-------------------|
| **ICML** | Broader Impact Statement (after conclusion) |
| **ICLR** | LLM usage disclosure, reciprocal reviewing agreement |
| **ACL/EMNLP** | Limitations section (mandatory), Ethics Statement |
| **AAAI** | Strict adherence to style file (no modifications) |
| **NeurIPS** | Paper checklist (appendix), lay summary if accepted |

**Step 5: Update References**

```latex
% Remove self-citations that reveal identity (for blind review)
% Update any "under review" citations to published versions
% Add new relevant work published since last submission

IF you cannot programmatically fetch a citation:
    → Mark it as [CITATION NEEDED] or [PLACEHOLDER - VERIFY]
    → Tell the scientist explicitly
    → NEVER invent a plausible-sounding reference

Citation Verification (MANDATORY for every citation):
- [ ] Step 1: Search using Exa MCP or Semantic Scholar API
- [ ] Step 2: Verify paper exists in 2+ sources (Semantic Scholar + arXiv/CrossRef)
- [ ] Step 3: Retrieve BibTeX via DOI (programmatically, not from memory)
- [ ] Step 4: Verify the claim you're citing actually appears in the paper
- [ ] Step 5: Add verified BibTeX to bibliography
- [ ] Step 6: If ANY step fails → mark as placeholder, inform scientist

Search: "RLHF language model alignment 2023"
Search: "sparse autoencoders interpretability"
Search: "attention mechanism transformers Vaswani"

from semanticscholar import SemanticScholar

sch = SemanticScholar()
results = sch.search_paper("attention mechanism transformers", limit=5)
for paper in results:
    print(f"{paper.title} - {paper.paperId}")
    print(f"  DOI: {paper.externalIds.get('DOI', 'N/A')}")

import requests

def doi_to_bibtex(doi: str) -> str:
    """Get verified BibTeX from DOI via CrossRef."""
    response = requests.get(
        f"https://doi.org/{doi}",
        headers={"Accept": "application/x-bibtex"}
    )
    response.raise_for_status()
    return response.text

**Step 4: Verify Claims**

Before citing for a specific claim, access the paper and confirm the attributed claim actually appears.

**Step 5: Handle Failures Explicitly**

If you cannot verify a citation at ANY step:

```latex
% Option 1: Explicit placeholder
\cite{PLACEHOLDER_smith2023_verify}  % TODO: Could not verify - scientist must confirm

% Option 2: Note in text
... as shown in prior work [CITATION NEEDED - could not verify Smith et al. 2023].

\usepackage{booktabs}
\begin{tabular}{lcc}
\toprule
Method & Accuracy ↑ & Latency ↓ \\
\midrule
Baseline & 85.2 & 45ms \\
\textbf{Ours} & \textbf{92.1} & 38ms \\
\bottomrule
\end{tabular}