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PaperQA2

AI agent that retrieves, reads, and synthesises answers from scientific PDFs with citation-level accuracy.

@ai-supply
Installs47k
⟳ upstream v2026.03.18 · updated 4mo ago
↗ Source repository
← More ResearchResearch leaderboard →How we grade security →Source ↗
! Grade B · 75/100 · ReviewSecurity assessment
✓No compromise signals19capabilities surfaced1known CVE9of 20 OWASP controls clear
External endpoints declaredExternal endpoints declaredExternal endpoints declaredSuspicious code patterns
scanned 16d ago·osv · gitleaks · opengrep · picklescan + heuristics·full breakdown in the Security tab ↓

PaperQA2

PaperQA2 by Future House is an AI agent for question-answering over scientific literature. It autonomously retrieves relevant papers, reads full PDFs, and synthesises grounded answers with precise inline citations — achieving human-level performance on the LitQA2 benchmark that evaluates citation accuracy.

Key Features

  • Agentic RAG loop: retrieval → reading → evidence synthesis → answer generation
  • Exact citation tracking: every claim is traceable to a specific passage and paper
  • LitQA2 benchmark leader — outperforms GPT-4 with retrieval on literature QA
  • Supports local PDFs, DOI resolution, and Semantic Scholar/PubMed search
  • Async Python API; pluggable LLM (OpenAI, Anthropic) and embedding providers

Quick Start

pip install paper-qa
export OPENAI_API_KEY=sk-...
from paperqa import Docs
import asyncio

async def main():
    docs = Docs()
    await docs.aadd("paper1.pdf")
    await docs.aadd("paper2.pdf")
    answer = await docs.aquery("What are the key findings on transformer scaling laws?")
    print(answer.formatted_answer)

asyncio.run(main())
npx ai-supply add paperqa-scientific-literature-qa

Curated mirror of the open-source PaperQA2 (Apache-2.0). Get it from the source.

Rating rank
#1
of 17 in Research
Install rank
#8
of 17 in Research
Security score
75/100 · B
review
Security rank
#9
of 17 in Research
Installs
47k
cat avg 51k
This listing vs category average
Installs
this
cat avg
Security (of 100)
this
cat avg
Adoption trend
See the Research leaderboard →
! Security: Review · 7575/100 · grade Bscanned 16d ago
✓ no compromise signals20 risk-surface · 5/20 OWASP controls flagged

Compromise signals — malicious or tampered code (leaked secrets, backdoors, a dropped executable) — reduce the score, and known dependency CVEs carry a bounded penalty (they warrant review but never QUARANTINE — update the dependency to clear). Other dangerous-by-capability traits are risk surface, expected for some capabilities. Every finding is mapped to its OWASP control below.

What this capability can do · med confidence (static)
⚑ filesystem⚑ network⚑ secrets
egress → astral.sh, img.shields.io, badge.fury.io, paper.wikicrow.ai, arxiv.org, docs.litellm.ai, platform.openai.com, www.semanticscholar.org +27

Findings mapped to the OWASP Top 10 for LLM Applications (2025) and the OWASP Machine Learning Security Top 10. Expand any flagged control for the exact findings — compromise reduces the score; expected/risk-surface do not, except a known CVE, which carries a small bounded penalty (high/critical → Review).

OWASP Top 10 for LLM Applications
⚠LLM03Supply Chaincritical
Vulnerable/compromised dependencies, models or archives in the artifact.
•Vulnerable dependencies — 101 known vulnerabilities in: aiohttp@3.13.3, cryptography@46.0.5, docling@2.80.0, docling-core@2.70.1, idna@3.11, litellm@1.82.4, lxml@6.0.2, pillow@12.1.1 (CWE-1395)known CVE · -25 pts
⚠LLM05Improper Output Handlingmedium
Code that pipes model/user output into shell, eval, SQL or paths unsafely.
•Suspicious code patterns — pickle deserialization · Future-House-paper-qa-d7675d7/README.md (CWE-502)risk surface
•Suspicious code patterns — dynamic code execution · Future-House-paper-qa-d7675d7/packages/paper-qa-docling/tests/test_paperqa_docling.py (CWE-95)risk surface
•Suspicious code patterns — dynamic code execution; pickle deserialization · Future-House-paper-qa-d7675d7/tests/test_paperqa.py (CWE-95)risk surface
⚠LLM06Excessive Agencymedium
Over-broad tool/permission surface or unrestricted egress.
•External endpoints declared — 2 distinct host(s) · Future-House-paper-qa-d7675d7/.github/renovate.json5risk surface
•External endpoints declared — 1 distinct host(s) · Future-House-paper-qa-d7675d7/.github/workflows/build.ymlrisk surface
•External endpoints declared — 4 distinct host(s) · Future-House-paper-qa-d7675d7/.gitignorerisk surface
•Broad capability surface — 4 high-impact capability categories referenced — verify least-privilege · Future-House-paper-qa-d7675d7/README.md (CWE-272)risk surface
•External endpoints declared — 24 distinct host(s) · Future-House-paper-qa-d7675d7/README.mdrisk surface
•External endpoints declared — 8 distinct host(s) · Future-House-paper-qa-d7675d7/packages/paper-qa-nemotron/README.mdrisk surface
•External endpoints declared — 7 distinct host(s) · Future-House-paper-qa-d7675d7/packages/paper-qa-nemotron/src/paperqa_nemotron/api.pyrisk surface
•External endpoints declared — 3 distinct host(s) · Future-House-paper-qa-d7675d7/packages/paper-qa-pymupdf/README.mdrisk surface
•External endpoints declared — 6 distinct host(s) · Future-House-paper-qa-d7675d7/pyproject.tomlrisk surface
•External endpoints declared — 5 distinct host(s) · Future-House-paper-qa-d7675d7/src/paperqa/settings.pyrisk surface
•Broad capability surface — 3 high-impact capability categories referenced — verify least-privilege · Future-House-paper-qa-d7675d7/src/paperqa/types.py (CWE-272)risk surface
•External endpoints declared — 32 distinct host(s) · Future-House-paper-qa-d7675d7/tests/cassettes/test_docs_lifecycle.yamlrisk surface
•External endpoints declared — 10 distinct host(s) · Future-House-paper-qa-d7675d7/tests/cassettes/test_get_reasoning[deepseek-reasoner].yamlrisk surface
•External endpoints declared — 29 distinct host(s) · Future-House-paper-qa-d7675d7/tests/stub_data/bates.txtrisk surface
•External endpoints declared — 28 distinct host(s) · Future-House-paper-qa-d7675d7/tests/stub_data/flag_day.htmlrisk surface
•External endpoints declared — 11 distinct host(s) · Future-House-paper-qa-d7675d7/tests/test_paperqa.pyrisk surface
§LLM09MisinformationGovernance
Artifacts designed to produce false/deceptive output.
Detectable only by runtime behavioral evaluation; addressed via responsible-use attestation.
◷LLM10Unbounded ConsumptionRuntime-enforced
Unbounded loops/recursion causing DoS or runaway cost.
Enforced at runtime by the gateway (rate limits + spend caps + size caps); static check flags unbounded loops.
✓LLM01Prompt InjectionPassed
✓LLM02Sensitive Information DisclosurePassed
✓LLM04Data and Model PoisoningPassed
Backdoors/poisoning in training data or serialized models.
Behavioral poisoning needs model execution; static check covers unsafe serialization + dataset skew only.
✓LLM07System Prompt LeakagePassed
✓LLM08Vector and Embedding WeaknessesPassed
PII or plaintext source leakage in embedding/vector exports.
Embedding inversion/poisoning is largely runtime; static check covers PII in vector exports.
OWASP Machine Learning Security Top 10
⚠ML06AI Supply Chaincritical
Compromised PyPI/npm packages, typosquats, unsafe serialized models.
•Vulnerable dependencies — 101 known vulnerabilities in: aiohttp@3.13.3, cryptography@46.0.5, docling@2.80.0, docling-core@2.70.1, idna@3.11, litellm@1.82.4, lxml@6.0.2, pillow@12.1.1 (CWE-1395)known CVE · -25 pts
⚠ML09Output Integritymedium
Middleware tampering with model outputs in transit.
Gateway enforces TLS + response integrity; static check flags output-rewriting code.
•Suspicious code patterns — pickle deserialization · Future-House-paper-qa-d7675d7/README.md (CWE-502)risk surface
•Suspicious code patterns — dynamic code execution · Future-House-paper-qa-d7675d7/packages/paper-qa-docling/tests/test_paperqa_docling.py (CWE-95)risk surface
•Suspicious code patterns — dynamic code execution; pickle deserialization · Future-House-paper-qa-d7675d7/tests/test_paperqa.py (CWE-95)risk surface
§ML01Input Manipulation (Adversarial)Governance
Models vulnerable to adversarial perturbations.
Requires runtime robustness evaluation; addressed via publisher robustness attestation.
§ML03Model InversionGovernance
Training data reconstructable from a model's outputs.
Runtime/evaluation property; addressed via model-card data-provenance + DP attestation.
§ML04Membership InferenceGovernance
Determining whether a record was in the training set.
Runtime/evaluation property; addressed via overfitting disclosure + DP attestation.
§ML08Model SkewingGovernance
Models trained on skewed data producing biased output.
Requires fairness evaluation; addressed via model-card bias/limitations disclosure.
✓ML02Data PoisoningPassed
Poisoned training datasets with triggers or anomalous distributions.
Static check covers trigger phrasing, PII and label skew; full poisoning detection is runtime.
✓ML05Model TheftPassed
Unlicensed re-distribution / license-incompatible derivatives.
Static check verifies license declaration; extraction throttling is runtime.
✓ML07Transfer Learning AttackPassed
Backdoored base models / LoRA adapters propagating to derivatives.
Backdoor detection needs behavioral probing; static check covers unsafe serialization + provenance.
✓ML10Model Poisoning (Weights)Passed
Tampered model weight files; integrity must be verifiable.
Static check enforces safe formats + records a content hash for downstream verification.
Other findings (11) · hygiene / uncategorized
•Unrecognized file type — '.gitattributes' is not on the allowlist · Future-House-paper-qa-d7675d7/.gitattributesrisk surface
•Unrecognized file type — '.json5' is not on the allowlist · Future-House-paper-qa-d7675d7/.github/renovate.json5risk surface
•Unrecognized file type — '.gitignore' is not on the allowlist · Future-House-paper-qa-d7675d7/.gitignorerisk surface
•Unrecognized file type — '.mailmap' is not on the allowlist · Future-House-paper-qa-d7675d7/.mailmaprisk surface
•Unrecognized file type — '.python-version' is not on the allowlist · Future-House-paper-qa-d7675d7/.python-versionrisk surface
•Unrecognized file type — '.cff' is not on the allowlist · Future-House-paper-qa-d7675d7/CITATION.cffrisk surface
•Unrecognized file type — '.?' is not on the allowlist · Future-House-paper-qa-d7675d7/LICENSErisk surface
•Unrecognized file type — '.xlsx' is not on the allowlist · Future-House-paper-qa-d7675d7/tests/stub_data/dummy.xlsxrisk surface
•Archive disguised as another type — content is a zip but extension is .xlsx · Future-House-paper-qa-d7675d7/tests/stub_data/dummy.xlsxrisk surface
•Unrecognized file type — '.docx' is not on the allowlist · Future-House-paper-qa-d7675d7/tests/stub_data/dummy_jap.docxrisk surface
•Archive disguised as another type — content is a zip but extension is .docx · Future-House-paper-qa-d7675d7/tests/stub_data/dummy_jap.docxrisk surface
✔ verified source · pinned Future-House-paper-qa-d7675d7
Check against a policy

The same gate an agent runs before installing (POST /api/v1/trust/paperqa-scientific-literature-qa/check). Click a policy:

Consume PaperQA2 programmatically. Authenticate with an API key or session — see Authorize an agent.

# Agents: CHECK BEFORE YOU INSTALL (no auth) — score, grade, level, capability manifest
curl https://ai-supply.store/api/v1/trust/paperqa-scientific-literature-qa

# Gate against your org policy (returns { pass, violations })
curl -X POST https://ai-supply.store/api/v1/trust/paperqa-scientific-literature-qa/check \
  -H "Content-Type: application/json" \
  -d '{"minGrade":"B","denyPermissions":["shell"],"denyUnknownEgress":true}'

# CLI
npx ai-supply add paperqa-scientific-literature-qa

# REST (install → download)
curl -X POST https://ai-supply.store/api/v1/listings/paperqa-scientific-literature-qa/install \
  -H "Authorization: Bearer $AIM_KEY"

# MCP tool
install_listing({ "slug": "paperqa-scientific-literature-qa" })
OpenAPI spec →
vlatest
! Security: Review · 751mo ago

Curated mirror — latest upstream source. See the repository for tagged releases.

Sign in and install this listing to leave a review.

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