Paper Reference Assistant

Use this skill when the user:

• Asks "does this match the paper?" or similar verification questions
• Mentions a paper name, arXiv ID, or method from literature
• Wants to implement or verify an algorithm from a paper
• Asks about equations, formulas, or methods from scientific papers
• Needs paper context loaded into the conversation

Workflow

1. Find the paper database location

papi path

2. List available papers

papi list

Or search for specific topics:

papi search "surface reconstruction"

2b. Audit generated content (optional)

If summaries/equations/tags look suspicious, run an audit to flag obvious issues:

papi audit
papi audit --limit 10 --seed 0

2c. LLM configuration (optional)

export PAPERPIPE_LLM_MODEL="gemini/gemini-3-flash-preview"
export PAPERPIPE_LLM_TEMPERATURE=0.3

3. For code verification

1. Identify which paper(s) the code references (check comments, function names, README)
2. Read {db}/papers/{name}/equations.md — compare symbol-by-symbol with implementation
3. If ambiguous, check {db}/papers/{name}/source.tex for exact definitions
4. Check {db}/papers/{name}/notes.md for local implementation gotchas (or run papi notes {name})

4. For implementation guidance

1. Read {db}/papers/{name}/summary.md for high-level approach
2. Read {db}/papers/{name}/equations.md for formulas to implement
3. Cross-reference with source.tex if equation details are unclear

5. For cross-paper questions

papi search "query"      # fast text search
papi ask "question"      # PaperQA2 RAG (if installed)

Adding New Papers

papi add 2303.13476                           # name auto-generated
papi add https://arxiv.org/abs/2303.13476     # URLs work too
papi add 2303.13476 --name my-custom-name     # override auto-name
papi add 2303.13476 --update                  # refresh existing paper in-place
papi add 2303.13476 --duplicate               # add a second copy (-2/-3 suffix)
papi add --pdf /path/to/paper.pdf --title "Some Paper" --tags my-project  # local PDF ingest

See Also

Read commands.md in this skill directory for the full command reference.