# BioRAG: A RAG-LLM Framework for Biological Question Reasoning

arXiv: https://arxiv.org/abs/2408.01107 · HTML: https://mlsanity.com/paper/2408.01107/

## Key facts

- Cited by 43 papers in the map (data through 14 Oct 2026).
- Placed in Clinical and biomedical applications, one of 17 directions in LLM reasoning.
- Builds on 16 of its 31 references that are in the map.
- First posted on arXiv 2 Aug 2024.

## Placed in

- LLM reasoning / [Clinical and biomedical applications](https://mlsanity.com/lr/clinical-and-biomedical-applications/)
- Retrieval-augmented generation / [Medical and biomedical RAG](https://mlsanity.com/rag/medical-and-biomedical-rag/)

## Builds on (most cited first, 16 of 16)

- [Measuring Massive Multitask Language Understanding](https://mlsanity.com/paper/2009.03300/) (2020)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [SciBERT: A Pretrained Language Model for Scientific Text](https://mlsanity.com/paper/1903.10676/) (2019)
- [LLaVA-Med: Training a Large Language-and-Vision Assistant for Biomedicine in One Day](https://mlsanity.com/paper/2306.00890/) (2023)
- [Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing](https://mlsanity.com/paper/2007.15779/) (2020)
- [Supervision Exists Everywhere: A Data Efficient Contrastive Language-Image Pre-training Paradigm](https://mlsanity.com/paper/2110.05208/) (2021)
- [BioMistral: A Collection of Open-Source Pretrained Large Language Models for Medical Domains](https://mlsanity.com/paper/2402.10373/) (2024)
- [Nomic Embed: Training a Reproducible Long Context Text Embedder](https://mlsanity.com/paper/2402.01613/) (2024)
- [GeneGPT: Augmenting Large Language Models with Domain Tools for Improved Access to Biomedical Information](https://mlsanity.com/paper/2304.09667/) (2023)
- [RA-ISF: Learning to Answer and Understand from Retrieval Augmentation via Iterative Self-Feedback](https://mlsanity.com/paper/2403.06840/) (2024)
- [Empower Large Language Model to Perform Better on Industrial Domain-Specific Question Answering](https://mlsanity.com/paper/2305.11541/) (2023)
- [Prompt-Guided Retrieval Augmentation for Non-Knowledge-Intensive Tasks](https://mlsanity.com/paper/2305.17653/) (2023)
- [Theoretically Improving Graph Neural Networks via Anonymous Walk Graph Kernels](https://mlsanity.com/paper/2104.02995/) (2021)
- [Enhancing Q&A with Domain-Specific Fine-Tuning and Iterative Reasoning: A Comparative Study](https://mlsanity.com/paper/2404.11792/) (2024)
- [Hierarchical Interdisciplinary Topic Detection Model for Research Proposal Classification](https://mlsanity.com/paper/2209.13519/) (2022)
- [Interdisciplinary Fairness in Imbalanced Research Proposal Topic Inference: A Hierarchical Transformer-based Method with Selective Interpolation](https://mlsanity.com/paper/2309.01717/) (2023)

## Built on by (most cited first, 30 of 43)

- [From Generation to Judgment: Opportunities and Challenges of LLM-as-a-judge](https://mlsanity.com/paper/2411.16594/) (2024)
- [Large Language Model Agent: A Survey on Methodology, Applications and Challenges](https://mlsanity.com/paper/2503.21460/) (2025)
- [A Survey on Knowledge-Oriented Retrieval-Augmented Generation](https://mlsanity.com/paper/2503.10677/) (2025)
- [NodeRAG: Structuring Graph-based RAG with Heterogeneous Nodes](https://mlsanity.com/paper/2504.11544/) (2025)
- [C-FedRAG: A Confidential Federated Retrieval-Augmented Generation System](https://mlsanity.com/paper/2412.13163/) (2024)
- [FinSage: A Multi-aspect RAG System for Financial Filings Question Answering](https://mlsanity.com/paper/2504.14493/) (2025)
- [MCQG-SRefine: Multiple Choice Question Generation and Evaluation with Iterative Self-Critique, Correction, and Comparison Feedback](https://mlsanity.com/paper/2410.13191/) (2024)
- [Investigating Context-Faithfulness in Large Language Models: The Roles of Memory Strength and Evidence Style](https://mlsanity.com/paper/2409.10955/) (2024)
- [HiPerRAG: High-Performance Retrieval Augmented Generation for Scientific Insights](https://mlsanity.com/paper/2505.04846/) (2025)
- [Contextualizing biological perturbation experiments through language](https://mlsanity.com/paper/2502.21290/) (2025)
- [No Free Lunch: Retrieval-Augmented Generation Undermines Fairness in LLMs, Even for Vigilant Users](https://mlsanity.com/paper/2410.07589/) (2024)
- [CG-RAG: Research Question Answering by Citation Graph Retrieval-Augmented LLMs](https://mlsanity.com/paper/2501.15067/) (2025)
- [Modeling Uncertainty Trends for Timely Retrieval in Dynamic RAG](https://mlsanity.com/paper/2511.09980/) (2025)
- [BioMARS: A Multi-Agent Robotic System for Autonomous Biological Experiments](https://mlsanity.com/paper/2507.01485/) (2025)
- [Large Language Models Meet Text-Attributed Graphs: A Survey of Integration Frameworks and Applications](https://mlsanity.com/paper/2510.21131/) (2025)
- [DoctorRAG: Medical RAG Fusing Knowledge with Patient Analogy through Textual Gradients](https://mlsanity.com/paper/2505.19538/) (2025)
- [Understanding Structured Financial Data with LLMs: A Case Study on Fraud Detection](https://mlsanity.com/paper/2512.13040/) (2025)
- [AlzheimerRAG: Multimodal Retrieval Augmented Generation for Clinical Use Cases using PubMed articles](https://mlsanity.com/paper/2412.16701/) (2024)
- [scReader: Prompting Large Language Models to Interpret scRNA-seq Data](https://mlsanity.com/paper/2412.18156/) (2024)
- [GraPPI: A Retrieve-Divide-Solve GraphRAG Framework for Large-scale Protein-protein Interaction Exploration](https://mlsanity.com/paper/2501.16382/) (2025)
- [GeneSUM: Large Language Model-based Gene Summary Extraction](https://mlsanity.com/paper/2412.18154/) (2024)
- [Patience is all you need! An agentic system for performing scientific literature review](https://mlsanity.com/paper/2504.08752/) (2025)
- [A Survey of Large Language Models in Discipline-specific Research: Challenges, Methods and Opportunities](https://mlsanity.com/paper/2507.08425/) (2025)
- [ConfAgents: A Conformal-Guided Multi-Agent Framework for Cost-Efficient Medical Diagnosis](https://mlsanity.com/paper/2508.04915/) (2025)
- [AutoSAM: an Agentic Framework for Automating Input File Generation for the SAM Code with Multi-Modal Retrieval-Augmented Generation](https://mlsanity.com/paper/2603.24736/) (2026)
- [Knowledge Is Not Static: Order-Aware Hypergraph RAG for Language Models](https://mlsanity.com/paper/2604.12185/) (2026)
- [Leveraging LLM-GNN Integration for Open-World Question Answering over Knowledge Graphs](https://mlsanity.com/paper/2604.13979/) (2026)
- [Spruce: Scalable Private Outsourced Retrieval Using Compact Embeddings](https://mlsanity.com/paper/2609.03376/) (2026)
- [Towards Graph Prompt Learning: A Survey and Beyond](https://mlsanity.com/paper/2408.14520/) (2024)
- [Large Language Models Meet Virtual Cell: A Survey](https://mlsanity.com/paper/2510.07706/) (2025)

## Abstract (arXiv)

The question-answering system for Life science research, which is characterized by the rapid pace of discovery, evolving insights, and complex interactions among knowledge entities, presents unique challenges in maintaining a comprehensive knowledge warehouse and accurate information retrieval. To address these issues, we introduce BioRAG, a novel Retrieval-Augmented Generation (RAG) with the Large Language Models (LLMs) framework. Our approach starts with parsing, indexing, and segmenting an extensive collection of 22 million scientific papers as the basic knowledge, followed by training a specialized embedding model tailored to this domain. Additionally, we enhance the vector retrieval process by incorporating a domain-specific knowledge hierarchy, which aids in modeling the intricate interrelationships among each query and context. For queries requiring the most current information, BioRAG deconstructs the question and employs an iterative retrieval process incorporated with the search engine for step-by-step reasoning. Rigorous experiments have demonstrated that our model outperforms fine-tuned LLM, LLM with search engines, and other scientific RAG frameworks across multiple life science question-answering tasks.