mlsanityData to 7 Oct 2026

BioRAG: A RAG-LLM Framework for Biological Question Reasoning

arXiv 2408.01107 ↗First posted 2 Aug 2024cs.CL cs.AI cs.IRcited by 42

On the map: LLM reasoning → Clinical and biomedical applications

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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.

Key facts. Cited by 42 papers in the map (data through 7 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.

Builds on

16 of 31 references.

References · 16

  1. 2020Measuring Massive Multitask Language Understandingcited by 7,768
  2. 2019BioBERT: a pre-trained biomedical language representation model for biomedical text miningcited by 1,935
  3. 2019SciBERT: A Pretrained Language Model for Scientific Textcited by 1,404
  4. 2023LLaVA-Med: Training a Large Language-and-Vision Assistant for Biomedicine in One Daycited by 1,287
  5. 2020Domain-Specific Language Model Pretraining for Biomedical Natural Language Processingcited by 996
  6. 2021Supervision Exists Everywhere: A Data Efficient Contrastive Language-Image Pre-training Paradigmcited by 405
  7. 2024BioMistral: A Collection of Open-Source Pretrained Large Language Models for Medical Domainscited by 299
  8. 2024Nomic Embed: Training a Reproducible Long Context Text Embeddercited by 255
  9. 2023GeneGPT: Augmenting Large Language Models with Domain Tools for Improved Access to Biomedical Informationcited by 115
  10. 2024RA-ISF: Learning to Answer and Understand from Retrieval Augmentation via Iterative Self-Feedbackcited by 46
  11. 2023Empower Large Language Model to Perform Better on Industrial Domain-Specific Question Answeringcited by 41
  12. 2023Prompt-Guided Retrieval Augmentation for Non-Knowledge-Intensive Taskscited by 21
4 more
  1. 2021Theoretically Improving Graph Neural Networks via Anonymous Walk Graph Kernelscited by 19
  2. 2024Enhancing Q&A with Domain-Specific Fine-Tuning and Iterative Reasoning: A Comparative Studycited by 11
  3. 2022Hierarchical Interdisciplinary Topic Detection Model for Research Proposal Classificationcited by 8
  4. 2023Interdisciplinary Fairness in Imbalanced Research Proposal Topic Inference: A Hierarchical Transformer-based Method with Selective Interpolationcited by 8

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Cited by year (2026 to 7 Oct)

Citing papers per year: 2024: 10; 2025: 21; 2026: 11.

42 papers.

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  1. 2024From Generation to Judgment: Opportunities and Challenges of LLM-as-a-judgecited by 480
  2. 2025Large Language Model Agent: A Survey on Methodology, Applications and Challengescited by 194
  3. 2025A Survey on Knowledge-Oriented Retrieval-Augmented Generationcited by 34
  4. 2025NodeRAG: Structuring Graph-based RAG with Heterogeneous Nodescited by 25
  5. 2024C-FedRAG: A Confidential Federated Retrieval-Augmented Generation Systemcited by 19
  6. 2025FinSage: A Multi-aspect RAG System for Financial Filings Question Answeringcited by 18
  7. 2024MCQG-SRefine: Multiple Choice Question Generation and Evaluation with Iterative Self-Critique, Correction, and Comparison Feedbackcited by 14
  8. 2024Investigating Context-Faithfulness in Large Language Models: The Roles of Memory Strength and Evidence Stylecited by 11
  9. 2025HiPerRAG: High-Performance Retrieval Augmented Generation for Scientific Insightscited by 11
  10. 2025Contextualizing biological perturbation experiments through languagecited by 10
  11. 2024No Free Lunch: Retrieval-Augmented Generation Undermines Fairness in LLMs, Even for Vigilant Userscited by 9
  12. 2025CG-RAG: Research Question Answering by Citation Graph Retrieval-Augmented LLMscited by 8
30 more
  1. 2025Modeling Uncertainty Trends for Timely Retrieval in Dynamic RAGcited by 8
  2. 2025BioMARS: A Multi-Agent Robotic System for Autonomous Biological Experimentscited by 6
  3. 2025Large Language Models Meet Text-Attributed Graphs: A Survey of Integration Frameworks and Applicationscited by 5
  4. 2025DoctorRAG: Medical RAG Fusing Knowledge with Patient Analogy through Textual Gradientscited by 4
  5. 2025Understanding Structured Financial Data with LLMs: A Case Study on Fraud Detectioncited by 4
  6. 2024AlzheimerRAG: Multimodal Retrieval Augmented Generation for Clinical Use Cases using PubMed articlescited by 3
  7. 2024scReader: Prompting Large Language Models to Interpret scRNA-seq Datacited by 3
  8. 2025GraPPI: A Retrieve-Divide-Solve GraphRAG Framework for Large-scale Protein-protein Interaction Explorationcited by 3
  9. 2024GeneSUM: Large Language Model-based Gene Summary Extractioncited by 2
  10. 2025Patience is all you need! An agentic system for performing scientific literature reviewcited by 2
  11. 2025A Survey of Large Language Models in Discipline-specific Research: Challenges, Methods and Opportunitiescited by 2
  12. 2025ConfAgents: A Conformal-Guided Multi-Agent Framework for Cost-Efficient Medical Diagnosiscited by 2
  13. 2026AutoSAM: an Agentic Framework for Automating Input File Generation for the SAM Code with Multi-Modal Retrieval-Augmented Generationcited by 2
  14. 2026Knowledge Is Not Static: Order-Aware Hypergraph RAG for Language Modelscited by 2
  15. 2026Leveraging LLM-GNN Integration for Open-World Question Answering over Knowledge Graphscited by 2
  16. 2026Spruce: Scalable Private Outsourced Retrieval Using Compact Embeddingscited by 2
  17. 2024Towards Graph Prompt Learning: A Survey and Beyondcited by 1
  18. 2025Large Language Models Meet Virtual Cell: A Surveycited by 1
  19. 2026SciHorizon-GENE: Benchmarking LLM for Life Sciences Inference from Gene Knowledge to Functional Understandingcited by 1
  20. 2026SC-Arena: A Natural Language Benchmark for Single-Cell Reasoning with Knowledge-Augmented Evaluationcited by 1
  21. 2026CuraView: A Multi-Agent Framework for Medical Hallucination Detection with GraphRAG-Enhanced Knowledge Verificationcited by 1
  22. 2024GuidelineGuard: An Agentic Framework for Medical Note Evaluation with Guideline Adherencecited by 0
  23. 2025Accelerating Causal Network Discovery of Alzheimer Disease Biomarkers via Scientific Literature-based Retrieval Augmented Generationcited by 0
  24. 2025Memory-Driven Self-Improvement for Decision Making with Large Language Modelscited by 0
  25. 2025CareMedEval dataset: Evaluating Critical Appraisal and Reasoning in the Biomedical Fieldcited by 0
  26. 2025Living the Novel: A System for Generating Self-Training Timeline-Aware Conversational Agents from Novelscited by 0
  27. 2026Coordinated Semantic Alignment and Evidence Constraints for Retrieval-Augmented Generation with Large Language Modelscited by 0
  28. 2026Earth Science Foundation Models: From Perception to Reasoning and Discoverycited by 0
  29. 2026HPC-LLM: Practical Domain Adaptation and Retrieval-Augmented Generation for HPC Supportcited by 0
  30. 2026ARIA: A Causal-Aware Framework for Rescuing LLM Reasoning in Trustworthy Materials Discoverycited by 0

Similar, not cited

Close in wording, no citation either way

  1. 2024BioRAGent: A Retrieval-Augmented Generation System for Showcasing Generative Query Expansion and Domain-Specific Search for Scientific Q&A
  2. 2024Improving Medical Reasoning through Retrieval and Self-Reflection with Retrieval-Augmented Large Language Models
  3. 2025RAG-BioQA: A Retrieval-Augmented Generation Framework for Long-Form Biomedical Question Answering
  4. 2026Re-ranking and Late Interaction Drive Retrieval Quality: A Controlled Comparison of RAG Strategies for Scientific Question Answering
  5. 2025BioMol-MQA: A Multi-Modal Question Answering Dataset For LLM Reasoning Over Bio-Molecular Interactions
  6. 2026VecTree-RAG: An Agentic Retrieval-Augmented Generation Framework Combining Vector and Tree Retrieval for Efficiency and Accuracy
  7. 2025MuISQA: Multi-Intent Retrieval-Augmented Generation for Scientific Question Answering
  8. 2025On the Influence of Context Size and Model Choice in Retrieval-Augmented Generation Systems