% 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"

---

Literature Research Process:
- [ ] Step 1: Define search scope and keywords
- [ ] Step 2: Search arXiv and academic databases
- [ ] Step 3: Screen papers by title/abstract
- [ ] Step 4: Evaluate paper quality (5 dimensions)
- [ ] Step 5: Select top papers and extract citations
- [ ] Step 6: Verify citations programmatically

URL Pattern:
https://arxiv.org/search/?searchtype=all&query=KEYWORDS&abstracts=show&order=-announced_date_first

Example Searches:
- https://arxiv.org/search/?searchtype=all&query=graph+neural+networks&abstracts=show&order=-announced_date_first
- https://arxiv.org/search/?cat:cs.LG+AND+all:transformer&abstracts=show&order=-announced_date_first

You: "Learn writing techniques from this NeurIPS paper: path/to/paper.pdf"
↓
paper-miner analyzes the paper
↓
Extracts patterns → Categorizes into 4 types → Updates knowledge files
↓
Knowledge grows with each paper analyzed

undefined

The paper-miner agent:
1. Extracts paper content (PDF, DOCX, or arXiv link)
2. Analyzes IMRaD structure and writing patterns
3. Identifies venue-specific requirements
4. Updates appropriate knowledge files with new patterns
5. Reports what was added with source attribution

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

undefined

**⚠️ 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 verify a citation through web search:
    → 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: Use WebSearch to find the paper
- [ ] Step 2: Verify paper exists on Google Scholar
- [ ] Step 3: Confirm paper details (title, authors, year, venue)
- [ ] Step 4: Retrieve BibTeX from Google Scholar or DOI
- [ ] Step 5: Verify the claim you're citing actually appears in the paper
- [ ] Step 6: Add verified BibTeX to bibliography
- [ ] Step 7: If ANY step fails → mark as placeholder, inform scientist

WebSearch query examples:
- "Attention is All You Need Vaswani 2017"
- "RLHF language model alignment 2023"
- "sparse autoencoders interpretability Anthropic"
- "transformer architecture NeurIPS"

WebSearch query: "site:scholar.google.com [paper title] [first author]"

Example: "site:scholar.google.com Attention is All You Need Vaswani"

Verification checklist:
- Title: [exact title from Google Scholar]
- Authors: [all authors, in order]
- Year: [publication year]
- Venue: [conference/journal name]
- DOI: [if available]

Verification process:
1. Use WebSearch to access the paper (PDF or HTML)
2. Search for keywords related to your claim
3. Confirm the claim is explicitly stated or clearly implied
4. Note the section/page where claim appears

% Add to your .bib file
@inproceedings{vaswani2017attention,
  title={Attention is All You Need},
  author={Vaswani, Ashish and Shazeer, Noam and ...},
  booktitle={Advances in Neural Information Processing Systems},
  year={2017}
}

% Use in your paper
\cite{vaswani2017attention}

% 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].

Step 1: WebSearch
Query: "Attention is All You Need Vaswani 2017"
Result: Found paper on multiple sources

Step 2: Google Scholar Verification
Query: "site:scholar.google.com Attention is All You Need Vaswani"
Result: ✅ Paper found, 50,000+ citations, NeurIPS 2017

Step 3: Confirm Details
- Title: "Attention is All You Need"
- Authors: Vaswani, Ashish; Shazeer, Noam; Parmar, Niki; ...
- Year: 2017
- Venue: NeurIPS (NIPS)
- DOI: Available

Step 4: Retrieve BibTeX
- Click "Cite" on Google Scholar
- Select BibTeX format
- Copy entry

Step 5: Verify Claim
- Access paper via WebSearch
- Confirm claim appears in paper
- Note section/page

Step 6: Add to Bibliography
- Paste BibTeX to .bib file
- Use \cite{vaswani2017attention} in paper

Step 7: Success
- Citation verified and added
- No placeholder needed

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