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Retrieval-Augmented Generation (RAG) enhances Large Language Models (LLMs) by providing external knowledge for accurate and up-to-date responses. However, this reliance on external sources exposes a security risk, attackers can inject…

Computation and Language · Computer Science 2025-07-25 San Kim , Jonghwi Kim , Yejin Jeon , Gary Geunbae Lee

Aligning terminological resources, including ontologies, controlled vocabularies, taxonomies, and value sets is a critical part of data integration in many domains such as healthcare, chemistry, and biomedical research. Entity mapping is…

While large language models (LLMs) have achieved state-of-the-art performance on a wide range of medical question answering (QA) tasks, they still face challenges with hallucinations and outdated knowledge. Retrieval-augmented generation…

Computation and Language · Computer Science 2024-02-26 Guangzhi Xiong , Qiao Jin , Zhiyong Lu , Aidong Zhang

Natural products are substances produced by organisms in nature and often possess biological activity and structural diversity. Drug development based on natural products has been common for many years. However, the intricate structures of…

Biomolecules · Quantitative Biology 2024-11-21 Koh Sakano , Kairi Furui , Masahito Ohue

Chemical mapping is a widespread technique for structural analysis of nucleic acids in which a molecule's reactivity to different probes is quantified at single-nucleotide resolution and used to constrain structural modeling. This…

Biomolecules · Quantitative Biology 2013-02-01 Pablo Cordero , Wipapat Kladwang , Christopher C. VanLang , Rhiju Das

Purpose: Large Language Models (LLMs) hold significant promise for medical applications. Retrieval Augmented Generation (RAG) emerges as a promising approach for customizing domain knowledge in LLMs. This case study presents the development…

Reducing hallucination of Large Language Models (LLMs) is imperative for use in the sciences, where reliability and reproducibility are crucial. However, LLMs inherently lack long-term memory, making it a nontrivial, ad hoc, and inevitably…

Computation and Language · Computer Science 2024-10-11 Yuan Chiang , Elvis Hsieh , Chia-Hong Chou , Janosh Riebesell

Large language models (LLMs) in biomedicine face a fundamental conflict between static parameter knowledge and the dynamic nature of clinical evidence. Retrieval-Augmented Generation (RAG) addresses this by grounding generation in external…

Other Quantitative Biology · Quantitative Biology 2025-12-19 Jiawei He , Boya Zhang , Hossein Rouhizadeh , Yingjian Chen , Rui Yang , Jin Lu , Xudong Chen , Nan Liu , Douglas Teodoro

Regulatory compliance in the pharmaceutical industry entails navigating through complex and voluminous guidelines, often requiring significant human resources. To address these challenges, our study introduces a chatbot model that utilizes…

Computation and Language · Computer Science 2024-02-07 Jaewoong Kim , Moohong Min

The emergence of Retrieval-augmented generation (RAG) has alleviated the issues of outdated and hallucinatory content in the generation of large language models (LLMs), yet it still reveals numerous limitations. When a general-purpose LLM…

Computation and Language · Computer Science 2024-12-20 Jiayi Wu , Hengyi Cai , Lingyong Yan , Hao Sun , Xiang Li , Shuaiqiang Wang , Dawei Yin , Ming Gao

Retrosynthesis analysis is pivotal yet challenging in drug discovery and organic chemistry. Despite the proliferation of computational tools over the past decade, AI-based systems often fall short in generalizing across diverse reaction…

Machine Learning · Computer Science 2024-08-21 Yifei Yang , Runhan Shi , Zuchao Li , Shu Jiang , Bao-Liang Lu , Yang Yang , Hai Zhao

Retrieval-Augmented Generation (RAG) has been shown to enhance the factual accuracy of Large Language Models (LLMs), but existing methods often suffer from limited reasoning capabilities in effectively using the retrieved evidence,…

Computation and Language · Computer Science 2024-10-03 Shayekh Bin Islam , Md Asib Rahman , K S M Tozammel Hossain , Enamul Hoque , Shafiq Joty , Md Rizwan Parvez

Retrieval-augmented Generation (RAG) has markedly enhanced the capabilities of Large Language Models (LLMs) in tackling knowledge-intensive tasks. The increasing demands of application scenarios have driven the evolution of RAG, leading to…

Computation and Language · Computer Science 2024-08-01 Yunfan Gao , Yun Xiong , Meng Wang , Haofen Wang

Large-scale language models (LLMs) have achieved remarkable success across various language tasks but suffer from hallucinations and temporal misalignment. To mitigate these shortcomings, Retrieval-augmented generation (RAG) has been…

Computation and Language · Computer Science 2024-04-30 Zhongzhen Huang , Kui Xue , Yongqi Fan , Linjie Mu , Ruoyu Liu , Tong Ruan , Shaoting Zhang , Xiaofan Zhang

Safe and trustworthy use of Large Language Models (LLM) in the processing of healthcare documents and scientific papers could substantially help clinicians, scientists and policymakers in overcoming information overload and focusing on the…

Retrieval-Augmented Generation (RAG) enables Large Language Models (LLMs) to extend their existing knowledge by dynamically incorporating external information. However, practical deployment is fundamentally constrained by the LLM's finite…

Information Retrieval · Computer Science 2026-03-24 Jiarui Guo , Yuemeng Xu , Zongwei Lv , Yangyujia Wang , Xiaolin Wang , Kan Liu , Tao Lan , Lin Qu , Tong Yang

Retrieval-Augmented Generation (RAG) enhances Large Language Models (LLMs) by grounding generation in external knowledge, yielding relevance responses that are aligned with factual evidence and evolving corpora. Standard RAG pipelines…

Machine Learning · Computer Science 2026-04-07 Xun Sun , Baiheng Xie , Li Huang , Qiang Gao

Machine learning (ML) holds great promise for clinical applications but is often hindered by limited access to high-quality data due to privacy concerns, high costs, and long timelines associated with clinical trials. While large language…

Computation and Language · Computer Science 2026-03-27 Zerui Xu , Fang Wu , Yingzhou Lu , Yuanyuan Zhang , Yue Zhao

Retrieval-augmented generation (RAG) has become the backbone of grounding Large Language Models (LLMs), improving knowledge updates and reducing hallucinations. Recently, LLM-based retriever models have shown state-of-the-art performance…

Large Language Models frequently generate outputs that appear scientifically reasonable yet violate fundamental principles--a phenomenon we characterize as the "plausibility-validity gap." This challenge proves especially acute in…

Machine Learning · Computer Science 2026-01-07 Malikussaid , Hilal Hudan Nuha , Isman Kurniawan