paper-search-mcp

Academic paper search MCP server for Cloudflare Workers, designed for deployment via mcp-deploy.

Searches across multiple platforms with unified ranking via Reciprocal Rank Fusion (RRF):

• Semantic Scholar — CS, social science, interdisciplinary; ML relevance ranking, TLDRs, influential citations, citation graph, paper recommendations

• OpenAlex — 250M+ works; FWCI and citation-percentile quality signals, venue metrics, citation graph, semantic search via GTE-Large embeddings

• CrossRef — 150M+ records; DOI lookups, journal metadata

• arXiv — CS, math, physics preprints

• PubMed — Biomedical literature via NCBI E-utilities

• bioRxiv / medRxiv — Biology and medical preprints

Core platforms (always on): Semantic Scholar, CrossRef, OpenAlex — provide quality scoring signals (FWCI, h-index, venue quality, citations). Optional platforms (configurable via ENABLED_PLATFORMS): arXiv, PubMed, bioRxiv, medRxiv. Default: arxiv.

Tools

Related MCP server: Paper Search MCP

Key features

RRF fusion — search results from all platforms are merged with Reciprocal Rank Fusion (score = Σ 1/(k + rank), k=60) and deduplicated by DOI/arXiv ID with metadata merged from the richest source.

Blended ranking — post-fusion scoring blends query relevance, venue/author quality, recency, and citation impact. Four presets (relevance, balanced, discovery, impact) or custom weight dials per call.

Citation graph traversal — get_citation_graph walks references and citations for multi-hop chaining. Backed by Semantic Scholar, with an automatic OpenAlex fallback (cites: filter / referenced_works) that also makes OpenAlex W… IDs resolvable.

Rate-limit survivability — built for good-citizen behavior on free API tiers:

• Per-domain throttle that serializes concurrent requests into spaced slots; key-aware spacing for Semantic Scholar (1 req/s with an API key, 1 per 3.5s without)

• Exponential backoff with jitter, Retry-After support, and a hard per-call time budget

• 60s domain cooldown after a request exhausts its retries on 429, so one hot-limited platform never stalls every search; other platforms keep answering

• Batched lookups: one S2 POST /paper/batch and one OpenAlex OR-filter call resolve up to 50 papers in rerank_papers instead of a request per paper

• In-memory TTL response cache (24h for paper metadata, 6h for citation graphs and recommendations, 1h for searches); cache hits are served even while a domain is cooling down

Semantic search — OpenAlex semantic search uses GTE-Large embeddings over 217M works to find conceptually related papers even with different vocabulary. Requires OPENALEX_API_KEY.

Date filtering — search_papers supports date_from / date_to (YYYY-MM-DD), mapped to platform-native filters where possible with post-fusion filtering as a safety net.

Deploy

Install mcp-deploy and deploy to Cloudflare Workers:

npm install -g mcp-deploy
mcp-deploy login
mcp-deploy add upascal/paper-search-mcp
mcp-deploy deploy paper-search-mcp

Or use the web UI: mcp-deploy gui

How it works

This repo contains only MCP logic. Auth, deployment, and UI are handled by mcp-deploy (npm install -g mcp-deploy). The repo ships:

• src/ — MCP server code (Cloudflare Workers + Durable Objects)

• mcp-deploy.json — deployment contract (secrets, config, worker settings)

• bench/ — retrieval benchmarks (see below)

All platforms return a normalized Paper interface with consistent fields (title, authors, abstract, doi, url, pdf_url, published_date, citations, etc.). Platform-specific data is stored in the extra field.

Configuration

*OpenAlex keyword search works without a key; semantic search and higher rate limits require one.

Benchmarks

bench/ contains a retrieval evaluation harness over LitSearch (597 queries with ground-truth citations):

npm run bench:download   # fetch queries + resolve ground-truth IDs (cached)
npm run bench:run        # non-agentic: one federated search per query
npm run bench:eval       # compute recall@k / MRR from run output
npm run bench:agentic    # agentic: Claude drives the real MCP over stdio

Runs are resumable and write JSONL + metrics to bench/litsearch/results/. A SEMANTIC_SCHOLAR_API_KEY in .dev.vars speeds up full sweeps dramatically.

Local development

npm install
npx wrangler dev
# Health check: http://localhost:8787/

Testing

npm test

Unit tests are offline; integration tests hit live APIs (only S2 rate limiting is tolerated as a skip). Set .dev.vars with optional API keys for reliable runs:

SEMANTIC_SCHOLAR_API_KEY=...
PUBMED_API_KEY=...
OPENALEX_API_KEY=...
CONTACT_EMAIL=you@example.com

Release

Tag a version to trigger the GitHub Actions release workflow:

git tag v0.4.0
git push --tags

This builds worker.mjs and publishes it alongside mcp-deploy.json as release assets. mcp-deploy fetches these assets to deploy the worker.