MedBioRAG: Semantic Search and Retrieval-Augmented Generation with Large Language Models for Medical and Biological QA

Seonok Kim

Home/Archive/arXiv

arXiv · 2512.10996

MedBioRAG: Semantic Search and Retrieval-Augmented Generation with Large Language Models for Medical and Biological QA

Seonok Kim

View original source ↗Read source document ↗Export metadata ↓

Abstract

Recent advancements in retrieval-augmented generation (RAG) have significantly enhanced the ability of large language models (LLMs) to perform complex question-answering (QA) tasks. In this paper, we introduce MedBioRAG, a retrieval-augmented model designed to improve biomedical QA performance through a combination of semantic and lexical search, document retrieval, and supervised fine-tuning. MedBioRAG efficiently retrieves and ranks relevant biomedical documents, enabling precise and context-aware response generation. We evaluate MedBioRAG across text retrieval, close-ended QA, and long-form QA tasks using benchmark datasets such as NFCorpus, TREC-COVID, MedQA, PubMedQA, and BioASQ. Experimental results demonstrate that MedBioRAG outperforms previous state-of-the-art (SoTA) models and the GPT-4o base model in all evaluated tasks. Notably, our approach improves NDCG and MRR scores for document retrieval, while achieving higher accuracy in close-ended QA and ROUGE scores in long-form QA. Our findings highlight the effectiveness of semantic search-based retrieval and LLM fine-tuning in biomedical applications.

Explore related subjects

cs.CL cs.AI

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Seonok Kim. 2025-12-10. MedBioRAG: Semantic Search and Retrieval-Augmented Generation with Large Language Models for Medical and Biological QA. https://arxiv.org/abs/2512.10996

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

DA-Cramming: Enhancing Cost-Effective Language Model Pretraining with Dependency Agreement Integration

Pretraining language models is still a challenge for many researchers due to its substantial computational costs. As such, there is growing interest in developing more affordable pretraining methods. One notable advancement in this area is the Cramming technique (Geiping and Goldstein, 2022), which enables the pretraining of BERT-style language models using just one GPU in a single day. Building on this innovative approach, we introduce the Dependency Agreement Cramming (DA-Cramming), an efficient framework that integrates information about dependency agreements into the pretraining process. Unlike existing methods that leverage similar semantic information during finetuning, our approach represents a pioneering effort focusing on enhancing the foundational language understanding with semantic information during pretraining. We meticulously design a dual-stage pretraining work flow with four dedicated submodels to capture representative dependency agreements at the chunk level, effectively transforming these agreements into embeddings to benefit the pretraining. Extensive empirical results demonstrate that our method significantly outperforms previous methods across various tasks.

cs.CL↗

arXiv2026

BigO(Bench): Can LLMs Generate Code with Controlled Time and Space Complexity?

We introduce BigO(Bench), a novel coding benchmark designed to evaluate the capabilities of generative language models in understanding and generating code with specified time and space complexities. This benchmark addresses the gap in current evaluations that often overlook the ability of models to comprehend and produce code constrained by computational complexity. BigO(Bench) includes tooling to infer the algorithmic complexity of any Python function from profiling measurements, including human- or LLM-generated solutions. BigO(Bench) also includes of set of 3,105 coding problems and 1,190,250 solutions from Code Contests annotated with inferred (synthetic) time and space complexity labels from the complexity framework, as well as corresponding runtime and memory footprint values for a large set of input sizes. We present results from evaluating multiple state-of-the-art language models on this benchmark, highlighting their strengths and weaknesses in handling complexity requirements. In particular, token-space reasoning models are unrivaled in code generation but not in complexity understanding, hinting that they may not generalize well to tasks for which no reward was given at training time.

cs.CL↗

arXiv2026

SafetyFlow: An Agent-Flow System for Automated LLM Safety Benchmarking

The rapid proliferation of large language models (LLMs) has intensified the requirement for reliable safety evaluation to uncover model vulnerabilities. To this end, numerous LLM safety evaluation benchmarks are proposed. However, existing benchmarks generally rely on labor-intensive manual curation, which causes excessive time and resource consumption. They also exhibit significant redundancy and limited difficulty. To alleviate these problems, we introduce SafetyFlow, the first agent-flow system designed to automate the construction of LLM safety benchmarks. SafetyFlow can automatically build a comprehensive safety benchmark in only four days without any human intervention by orchestrating seven specialized agents, significantly reducing time and resource cost. Equipped with versatile tools, the agents of SafetyFlow ensure process and cost controllability while integrating human expertise into the automatic pipeline. The final constructed dataset, SafetyFlowBench, contains 23,446 queries with low redundancy and strong discriminative power. Our contribution includes the first fully automated benchmarking pipeline and a comprehensive safety benchmark. We evaluate the safety of 49 advanced LLMs on our dataset and conduct extensive experiments to validate our efficacy and efficiency.

cs.CL↗