PaperPilot

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PaperPilot is a CLI research agent for scholarly literature review across AI, biomedicine, and AI for Science.
It turns one user request into a traceable, evidence-based research workflow and generates bilingual reports (zh/en) in Markdown, HTML, and PDF.

✨ What PaperPilot does

PaperPilot is not a chatbot. It is an interactive scientific workflow:

• Parse natural-language research requests
• Build an explicit search protocol with inclusion/exclusion rules
• Query multi-source literature APIs
• Normalize, deduplicate, and screen papers
• Verify URLs/PDF/code availability
• Synthesize evidence and generate review reports
• Output structured artifacts for reproducibility

Each run creates a dedicated folder under runs/ with full state, logs, and intermediate files.

🚀 Highlights

Core experience

• Natural-language intake with LLM-assisted interpretation
• Interactive shell with:
  • /model to manage LLM profiles
  • /sources to inspect search source/API status
  • /doctor for quick self-checks
• Multi-source retrieval with source registry and diagnostics
• Resume/inspect modes for reproducible research sessions

Retrieval and screening

• Protocol-aware search using plan + diversified keywords
• Canonicalized Paper schema and robust deduplication
• Core/adjacent/excluded paper classification
• PDF + code-link verification (no paywall bypass)
• Optional full-text extraction from downloadable PDFs

Reporting

• Canonical bilingual report model
• Consistent [1][2][3] citation mapping
• Method taxonomy and evidence matrix
• Markdown + HTML + PDF outputs with aligned content
• Final report view keeps up to 100 papers by default, without a hard minimum
• Obsidian Wiki export with paper, method, topic, and claim notes

Quality controls

• Quality gates and reflection workflow
• Evidence ledger linking claims to corpus evidence
• Review checks for citation compliance and source reliability
• Event stream logs for auditability

🗂 Source stack

Default free sources:

• arXiv
• Semantic Scholar
• OpenAlex
• Crossref
• OpenReview
• PubMed / NCBI E-utilities
• Europe PMC
• bioRxiv / medRxiv
• DBLP
• ACL Anthology
• Papers.cool

Optional API-key sources:

• DeepXiv / Agentic Data
• CORE
• Lens.org Scholarly API
• IEEE Xplore
• Springer Nature
• Elsevier / Scopus
• Dimensions

🛠 Installation

python -m pip install paperpilot -i https://pypi.org/simple

Local development:

git clone https://github.com/CHB-learner/PaperPilot.git
cd PaperPilot
python -m pip install -e .

⚙️ LLM + Source Configuration

PaperPilot requires OpenAI-compatible LLM settings for query understanding, planning, synthesis, and report generation.

On first run, it creates an editable configuration template at:

~/.paperpilot/config.json

Minimal default template:

{
  "active": "default",
  "profiles": {
    "default": {
      "api_key": "",
      "base_url": "",
      "model": "gpt-5.2"
    }
  },
  "sources": {
    "core": {"enabled": null, "api_key": "", "base_url": ""},
    "lens": {"enabled": null, "api_key": "", "base_url": ""},
    "ieee": {"enabled": null, "api_key": "", "base_url": ""},
    "springer": {"enabled": null, "api_key": "", "base_url": ""},
    "elsevier": {"enabled": null, "api_key": "", "base_url": ""},
    "dimensions": {"enabled": null, "api_key": "", "base_url": ""},
    "deepxiv": {"enabled": null, "api_key": "", "base_url": ""}
  }
}

Notes:

• Leave optional source API keys empty if unavailable.
• enabled: null means auto-enable once a valid key is provided.
• ~/.paperpilot/config.json is not committed; edit it directly or use CLI commands.

CLI config commands

PaperPilot config set --base-url https://api.deepseek.com --model deepseek-chat
PaperPilot config import ./api.json
PaperPilot config list
PaperPilot config use deepseek
PaperPilot config show
PaperPilot --doctor

PaperPilot sources list
PaperPilot sources config core
PaperPilot sources config deepxiv
PaperPilot sources enable core
PaperPilot sources test core

Inside interactive mode, use /sources and /doctor.

🔑 API source keys references

Source	Access page
CORE	https://core.ac.uk/services/api
Lens.org	https://docs.api.lens.org/
IEEE Xplore	https://developer.ieee.org/getting_started
Springer Nature	https://dev.springernature.com/
Elsevier / Scopus	https://dev.elsevier.com/
Dimensions	https://docs.dimensions.ai/dsl/api.html
DeepXiv / Agentic Data	https://data.rag.ac.cn/api/docs
Papers.cool	https://papers.cool

🧪 Quick Start

Interactive usage:

PaperPilot

Command mode example:

PaperPilot "RNA inverse folding sequence design" \
  --auto-confirm \
  --max-papers 50 \
  --since-year 2021 \
  --github-filter required \
  --sources auto \
  --mode apa \
  --quality balanced

Import local corpus and skip download:

PaperPilot "RNA inverse folding sequence design" \
  --auto-confirm \
  --user-corpus ./papers \
  --user-corpus references.bib \
  --no-download

Inspect/resume workflow:

PaperPilot inspect runs/<task-id>
PaperPilot resume runs/<task-id>

🧭 Workflow

PaperPilot follows this state-machine pipeline:

Intake -> Protocol -> Search -> Corpus -> Screening -> Verification -> Synthesis -> Review -> Report

flowchart LR
  U[User request] --> C[Run context]
  C --> QA[Query understanding]
  QA --> PL[Planning + Protocol]
  PL --> ST[Source Registry search]
  ST --> NB[Corpus normalization]
  NB --> SC[Core/adjacent screening]
  SC --> VF[Verification + PDF + code checks]
  VF --> SY[Literature matrix]
  SY --> QG[Quality gate + reflection]
  QG --> EL[Evidence ledger]
  EL --> RP[Report render (ZH/EN)]

Loading

📁 Run artifacts

runs/<task-id>/ will contain:

• task.json / state.json / events.jsonl / manifest.json
• query_understanding.md / plan.json / protocol.json
• metadata.json / corpus.json / core_papers.json
• adjacent_papers.json / excluded_papers.json / ranked_papers.json
• verification.json / download_log.json / fulltext/ / paper_notes.json
• literature_matrix.json / synthesis.json / quality_gate.json
• evidence_ledger.json / review_agent_findings.json
• report.canonical.json / report.zh.md / report.en.md
• report.zh.html / report.en.html / report.zh.pdf / report.en.pdf
• report_selection.json / shortfall.json when no reportable papers are available
• obsidian_wiki/ with index.md, paper notes, method notes, topic notes, claim notes, and wiki lint metadata
• pdfs/ / source_diagnostics.json / registries.json / prompt_manifest.json

🧠 Obsidian Wiki

Each successful run generates runs/<task-id>/obsidian_wiki/ by default. Open that folder as an Obsidian vault to browse:

• index.md: research entry point and reported-paper overview
• papers/: one note per reported paper with citation label, PDF/code links, method family, and evidence basis
• methods/: method-family notes linked to representative papers
• topics/: query/subtopic notes
• claims/: evidence-map claim notes
• _meta/manifest.json and _meta/wiki_lint.json: provenance, hashes, broken-link checks

Use --no-obsidian-wiki to skip Wiki generation.

🧩 Code filter modes

• any: keep all papers and annotate code availability
• required: keep only papers with detected code repositories in final view
• none: keep only papers without detected public code links

🧪 CLI options (important ones)

--max-papers INT                 maximum papers in final report view; default: 100
--min-report-papers INT          optional minimum report size; default: 0
--since-year INT                 preferred lower year bound
--github-filter any|required|none
--github-search-limit INT
--no-download                    skip PDF downloads
--pdf-limit INT                  maximum PDFs to download
--user-corpus PATH               repeatable local corpus path
--mode quick|apa|systematic
--interaction auto|gated
--quality fast|balanced|strict
--include-adjacent               include adjacent papers in appendices
--sources auto|all|core|biomed|cs|configured
--enable-source SOURCE           enable one source (repeatable)
--disable-source SOURCE          disable one source (repeatable)
--no-obsidian-wiki               skip Obsidian Wiki export

See paperpilot --help for full options and Chinese/English output.

🧱 Development notes

• Keep run outputs and generated artifacts out of source control.
• Keep API keys out of git history.
• Prefer .gitignore over manual cleanup.
• Use semantic tags for releases and keep README + docs aligned.
• Keep .github/workflows/*, RELEASING.md, CHANGELOG.md in sync when publishing.

🧭 Open source checklist

• Ensure ~/.paperpilot/config.json, api.json, and .env with credentials are never committed.
• Add/keep LICENSE and .gitignore.
• Add source code and tags before publishing release assets.
• Publish GitHub Pages from docs/.
• Keep versions in pyproject.toml, literature_agent/__init__.py, and generated manifests aligned.

One-command release

# dry-run checks only
./scripts/release_everywhere.sh --dry-run

# normal release (pushed commit + tag + GH release + PyPI)
export PYPI_TOKEN='pypi-...'
./scripts/release_everywhere.sh

# release without publishing to PyPI
./scripts/release_everywhere.sh --no-pypi

Suggested publish flow (full):

python -m unittest discover -s tests
python -m compileall literature_agent
./publish_pypi.sh --dry-run --version <VERSION>
git add -A
git commit -m "chore: release v<VERSION>"
git tag -a v<VERSION> -m "v<VERSION>"
git push origin main --tags
./publish_pypi.sh --version <VERSION>

For GitHub Pages: enable Pages to deploy from main + /docs, or rely on .github/workflows/gh-pages.yml.

📚 Citation note

If you use PaperPilot in your work, include the repository URL and version used so results are reproducible.