# PaperQA: Retrieval-Augmented Generative Agent for Scientific Research

arXiv: https://arxiv.org/abs/2312.07559 · HTML: https://mlsanity.com/paper/2312.07559/

## Key facts

- Cited by 149 papers in the map (data through 14 Oct 2026).
- Placed in Agentic RAG, agents and memory, one of 15 directions in Retrieval-augmented generation.
- Builds on 55 of its 78 references that are in the map.
- First posted on arXiv 8 Dec 2023.

## Placed in

- Retrieval-augmented generation / [Agentic RAG, agents and memory](https://mlsanity.com/rag/agentic-rag-agents-and-memory/)
- LLM agents and tool use / [Web, search, and research agents](https://mlsanity.com/agents/web-search-and-research-agents/)

## Builds on (most cited first, 30 of 55)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [Chain-of-Thought Prompting Elicits Reasoning in Large Language Models](https://mlsanity.com/paper/2201.11903/) (2022)
- [Retrieval-Augmented Generation for Knowledge-Intensive NLP Tasks](https://mlsanity.com/paper/2005.11401/) (2020)
- [ReAct: Synergizing Reasoning and Acting in Language Models](https://mlsanity.com/paper/2210.03629/) (2022)
- [Measuring Massive Multitask Language Understanding](https://mlsanity.com/paper/2009.03300/) (2020)
- [PaLM: Scaling Language Modeling with Pathways](https://mlsanity.com/paper/2204.02311/) (2022)
- [Toolformer: Language Models Can Teach Themselves to Use Tools](https://mlsanity.com/paper/2302.04761/) (2023)
- [On the Opportunities and Risks of Foundation Models](https://mlsanity.com/paper/2108.07258/) (2021)
- [Tree of Thoughts: Deliberate Problem Solving with Large Language Models](https://mlsanity.com/paper/2305.10601/) (2023)
- [Self-Instruct: Aligning Language Models with Self-Generated Instructions](https://mlsanity.com/paper/2212.10560/) (2022)
- [Billion-scale similarity search with GPUs](https://mlsanity.com/paper/1702.08734/) (2017)
- [Voyager: An Open-Ended Embodied Agent with Large Language Models](https://mlsanity.com/paper/2305.16291/) (2023)
- [REALM: Retrieval-Augmented Language Model Pre-Training](https://mlsanity.com/paper/2002.08909/) (2020)
- [PaLM-E: An Embodied Multimodal Language Model](https://mlsanity.com/paper/2303.03378/) (2023)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [Large Language Models Encode Clinical Knowledge](https://mlsanity.com/paper/2212.13138/) (2022)
- [Enriching Word Vectors with Subword Information](https://mlsanity.com/paper/1607.04606/) (2016)
- [SciBERT: A Pretrained Language Model for Scientific Text](https://mlsanity.com/paper/1903.10676/) (2019)
- [What Disease does this Patient Have? A Large-scale Open Domain Question Answering Dataset from Medical Exams](https://mlsanity.com/paper/2009.13081/) (2020)
- [Improving language models by retrieving from trillions of tokens](https://mlsanity.com/paper/2112.04426/) (2021)
- [PubMedQA: A Dataset for Biomedical Research Question Answering](https://mlsanity.com/paper/1909.06146/) (2019)
- [Leveraging Passage Retrieval with Generative Models for Open Domain Question Answering](https://mlsanity.com/paper/2007.01282/) (2020)
- [HuggingGPT: Solving AI Tasks with ChatGPT and its Friends in Hugging Face](https://mlsanity.com/paper/2303.17580/) (2023)
- [MoleculeNet: A Benchmark for Molecular Machine Learning](https://mlsanity.com/paper/1703.00564/) (2017)
- [Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing](https://mlsanity.com/paper/2007.15779/) (2020)
- [Large Language Models as Optimizers](https://mlsanity.com/paper/2309.03409/) (2023)
- [REPLUG: Retrieval-Augmented Black-Box Language Models](https://mlsanity.com/paper/2301.12652/) (2023)
- [Galactica: A Large Language Model for Science](https://mlsanity.com/paper/2211.09085/) (2022)

## Built on by (most cited first, 30 of 149)

- [Retrieval-Augmented Generation for Large Language Models: A Survey](https://mlsanity.com/paper/2312.10997/) (2023)
- [The WMDP Benchmark: Measuring and Reducing Malicious Use With Unlearning](https://mlsanity.com/paper/2403.03218/) (2024)
- [AgentPoison: Red-teaming LLM Agents via Poisoning Memory or Knowledge Bases](https://mlsanity.com/paper/2407.12784/) (2024)
- [Agent Laboratory: Using LLM Agents as Research Assistants](https://mlsanity.com/paper/2501.04227/) (2025)
- [Benchmarking Retrieval-Augmented Generation for Medicine](https://mlsanity.com/paper/2402.13178/) (2024)
- [AI Agents vs. Agentic AI: A Conceptual Taxonomy, Applications and Challenges](https://mlsanity.com/paper/2505.10468/) (2025)
- [Language agents achieve superhuman synthesis of scientific knowledge](https://mlsanity.com/paper/2409.13740/) (2024)
- [Empowering Biomedical Discovery with AI Agents](https://mlsanity.com/paper/2404.02831/) (2024)
- [A Review of Large Language Models and Autonomous Agents in Chemistry](https://mlsanity.com/paper/2407.01603/) (2024)
- [From Automation to Autonomy: A Survey on Large Language Models in Scientific Discovery](https://mlsanity.com/paper/2505.13259/) (2025)
- [AutoML-Agent: A Multi-Agent LLM Framework for Full-Pipeline AutoML](https://mlsanity.com/paper/2410.02958/) (2024)
- [AgentRxiv: Towards Collaborative Autonomous Research](https://mlsanity.com/paper/2503.18102/) (2025)
- [LLM Agents for Education: Advances and Applications](https://mlsanity.com/paper/2503.11733/) (2025)
- [BioDiscoveryAgent: An AI Agent for Designing Genetic Perturbation Experiments](https://mlsanity.com/paper/2405.17631/) (2024)
- [ScienceBoard: Evaluating Multimodal Autonomous Agents in Realistic Scientific Workflows](https://mlsanity.com/paper/2505.19897/) (2025)
- [A Survey of Agentic Reasoning for Large Language Models: Towards Recursively Self-Improving and Collective Agents](https://mlsanity.com/paper/2601.12538/) (2026)
- [CiteME: Can Language Models Accurately Cite Scientific Claims?](https://mlsanity.com/paper/2407.12861/) (2024)
- [Code as Agent Harness](https://mlsanity.com/paper/2605.18747/) (2026)
- [A Survey on the Optimization of Large Language Model-based Agents](https://mlsanity.com/paper/2503.12434/) (2025)
- [DrugAgent: Automating AI-aided Drug Discovery Programming through LLM Multi-Agent Collaboration](https://mlsanity.com/paper/2411.15692/) (2024)
- [BMRetriever: Tuning Large Language Models as Better Biomedical Text Retrievers](https://mlsanity.com/paper/2404.18443/) (2024)
- [EXP-Bench: Can AI Conduct AI Research Experiments?](https://mlsanity.com/paper/2505.24785/) (2025)
- [Are large language models superhuman chemists?](https://mlsanity.com/paper/2404.01475/) (2024)
- [Position: Multimodal Large Language Models Can Significantly Advance Scientific Reasoning](https://mlsanity.com/paper/2502.02871/) (2025)
- [HM-RAG: Hierarchical Multi-Agent Multimodal Retrieval Augmented Generation](https://mlsanity.com/paper/2504.12330/) (2025)
- [Single-agent or Multi-agent Systems? Why Not Both?](https://mlsanity.com/paper/2505.18286/) (2025)
- [TC-RAG:Turing-Complete RAG's Case study on Medical LLM Systems](https://mlsanity.com/paper/2408.09199/) (2024)
- [Towards Execution-Grounded Automated AI Research](https://mlsanity.com/paper/2601.14525/) (2026)
- [SciSciGPT: Advancing Human-AI Collaboration in the Science of Science](https://mlsanity.com/paper/2504.05559/) (2025)
- [Aviary: training language agents on challenging scientific tasks](https://mlsanity.com/paper/2412.21154/) (2024)

## Abstract (arXiv)

Large Language Models (LLMs) generalize well across language tasks, but suffer from hallucinations and uninterpretability, making it difficult to assess their accuracy without ground-truth. Retrieval-Augmented Generation (RAG) models have been proposed to reduce hallucinations and provide provenance for how an answer was generated. Applying such models to the scientific literature may enable large-scale, systematic processing of scientific knowledge. We present PaperQA, a RAG agent for answering questions over the scientific literature. PaperQA is an agent that performs information retrieval across full-text scientific articles, assesses the relevance of sources and passages, and uses RAG to provide answers. Viewing this agent as a question answering model, we find it exceeds performance of existing LLMs and LLM agents on current science QA benchmarks. To push the field closer to how humans perform research on scientific literature, we also introduce LitQA, a more complex benchmark that requires retrieval and synthesis of information from full-text scientific papers across the literature. Finally, we demonstrate PaperQA's matches expert human researchers on LitQA.