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Background: Several studies show that large language models (LLMs) struggle with phenotype-driven gene prioritization for rare diseases. These studies typically use Human Phenotype Ontology (HPO) terms to prompt foundation models like GPT…

Computation and Language · Computer Science 2026-02-19 Zhanliang Wang , Da Wu , Quan Nguyen , Kai Wang

Retrieval-Augmented Generation (RAG) represents a major advancement in natural language processing (NLP), combining large language models (LLMs) with information retrieval systems to enhance factual grounding, accuracy, and contextual…

Computation and Language · Computer Science 2025-07-28 Agada Joseph Oche , Ademola Glory Folashade , Tirthankar Ghosal , Arpan Biswas

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…

Computation and Language · Computer Science 2024-08-15 Chengrui Wang , Qingqing Long , Meng Xiao , Xunxin Cai , Chengjun Wu , Zhen Meng , Xuezhi Wang , Yuanchun Zhou

Large Language Models (LLMs) and Knowledge Graphs (KGs) offer a promising approach to robust and explainable Question Answering (QA). While LLMs excel at natural language understanding, they suffer from knowledge gaps and hallucinations.…

Machine Learning · Computer Science 2025-04-15 Jasper Linders , Jakub M. Tomczak

Retrieval-Augmented Generation (RAG) has become a foundational paradigm for equipping large language models (LLMs) with external knowledge, playing a critical role in information retrieval and knowledge-intensive applications. However,…

Computation and Language · Computer Science 2025-06-10 Weihang Su , Qingyao Ai , Jingtao Zhan , Qian Dong , Yiqun Liu

The volume of scientific literature is growing exponentially, leading to underutilized discoveries, duplicated efforts, and limited cross-disciplinary collaboration. Retrieval Augmented Generation (RAG) offers a way to assist scientists by…

As one of the most advanced techniques in AI, Retrieval-Augmented Generation (RAG) can offer reliable and up-to-date external knowledge, providing huge convenience for numerous tasks. Particularly in the era of AI-Generated Content (AIGC),…

Computation and Language · Computer Science 2024-06-18 Wenqi Fan , Yujuan Ding , Liangbo Ning , Shijie Wang , Hengyun Li , Dawei Yin , Tat-Seng Chua , Qing Li

The emergence of Large Language Models (LLMs) has significantly advanced natural language processing, but these models often generate factually incorrect information, known as "hallucination". Initial retrieval-augmented generation (RAG)…

Computation and Language · Computer Science 2024-11-12 Yujia Zhou , Zheng Liu , Zhicheng Dou

Large Language Models (LLMs) showcase impressive capabilities but encounter challenges like hallucination, outdated knowledge, and non-transparent, untraceable reasoning processes. Retrieval-Augmented Generation (RAG) has emerged as a…

Computation and Language · Computer Science 2024-03-28 Yunfan Gao , Yun Xiong , Xinyu Gao , Kangxiang Jia , Jinliu Pan , Yuxi Bi , Yi Dai , Jiawei Sun , Meng Wang , Haofen Wang

Large language models (LLMs) have achieved strong empirical performance in various fields, benefiting from their huge amount of parameters that store knowledge. However, LLMs still suffer from several key issues, such as hallucination…

Computation and Language · Computer Science 2026-05-20 Shangyu Wu , Ying Xiong , Yufei Cui , Haolun Wu , Can Chen , Ye Yuan , Lianming Huang , Xue Liu , Tei-Wei Kuo , Nan Guan , Chun Jason Xue

Retrieval-Augmented Generation (RAG), by incorporating external knowledge with parametric memory of language models, has become the state-of-the-art architecture for open-domain QA tasks. However, common knowledge bases are inherently…

Computation and Language · Computer Science 2023-12-01 Zhebin Zhang , Xinyu Zhang , Yuanhang Ren , Saijiang Shi , Meng Han , Yongkang Wu , Ruofei Lai , Zhao Cao

The utilization of conversational AI systems by leveraging Retrieval Augmented Generation (RAG) techniques to solve customer problems has been on the rise with the rapid progress of Large Language Models (LLMs). However, the absence of a…

Computation and Language · Computer Science 2025-10-10 Md Tahmid Rahman Laskar , Julien Bouvier Tremblay , Xue-Yong Fu , Cheng Chen , Shashi Bhushan TN

Advancements in artificial intelligence for molecular science are necessitating a paradigm shift from purely data-driven predictions to knowledge-guided computational reasoning. Existing molecular models are predominantly proprietary,…

Machine Learning · Computer Science 2026-03-16 Pengfei Liu , Shuang Ge , Jun Tao , Zhixiang Ren

In this article, we evaluate four Large Language Models (LLMs) and their effectiveness at retrieving data within a specialized Retrieval-Augmented Generation (RAG) system, using a comprehensive food composition database. Our method is…

Computation and Language · Computer Science 2026-03-12 Maks Požarnik Vavken , Matevž Ogrinc , Tome Eftimov , Barbara Koroušić Seljak

Retrieval-Augmented Generation (RAG) lifts the factuality of Large Language Models (LLMs) by injecting external knowledge, yet it falls short on problems that demand multi-step inference; conversely, purely reasoning-oriented approaches…

Knowing that the generative capabilities of large language models (LLM) are sometimes hampered by tendencies to hallucinate or create non-factual responses, researchers have increasingly focused on methods to ground generated outputs in…

Information Retrieval · Computer Science 2024-11-20 Sonal Prabhune , Donald J. Berndt

Artificial intelligence (AI) is reshaping modern healthcare by advancing disease diagnosis, treatment decision-making, and biomedical research. Among AI technologies, large language models (LLMs) have become especially impactful, enabling…

Artificial Intelligence · Computer Science 2025-11-18 Zhengda Wang , Daqian Shi , Jingyi Zhao , Xiaolei Diao , Xiongfeng Tang , Yanguo Qin

Phenotype-driven gene prioritization is a critical process in the diagnosis of rare genetic disorders for identifying and ranking potential disease-causing genes based on observed physical traits or phenotypes. While traditional approaches…

Quantitative Methods · Quantitative Biology 2024-04-04 Junyoung Kim , Jingye Yang , Kai Wang , Chunhua Weng , Cong Liu

Large language models (LLMs) have reshaped the research landscape by enabling new approaches to knowledge retrieval and creative ideation. Yet their application in discipline-specific experimental science, particularly in highly…

Machine Learning · Computer Science 2025-08-12 Rachel K. Luu , Jingyu Deng , Mohammed Shahrudin Ibrahim , Nam-Joon Cho , Ming Dao , Subra Suresh , Markus J. Buehler

Large Multi-modal Models (LMMs) have made impressive progress in many vision-language tasks. Nevertheless, the performance of general LMMs in specific domains is still far from satisfactory. This paper proposes FoodLMM, a versatile food…

Computer Vision and Pattern Recognition · Computer Science 2024-04-15 Yuehao Yin , Huiyan Qi , Bin Zhu , Jingjing Chen , Yu-Gang Jiang , Chong-Wah Ngo