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Protein representation learning has primarily benefited from the remarkable development of language models (LMs). Accordingly, pre-trained protein models also suffer from a problem in LMs: a lack of factual knowledge. The recent solution…

Machine Learning · Computer Science 2023-02-16 Hong-Yu Zhou , Yunxiang Fu , Zhicheng Zhang , Cheng Bian , Yizhou Yu

We study how to impose domain-consistent structure on large language models (LLMs) used for scientific reasoning and early-stage drug discovery. We present MedRule-KG, a compact knowledge-graph scaffold paired with a lightweight verifier…

Artificial Intelligence · Computer Science 2025-12-15 Crystal Su

Knowledge graph (KG) reasoning is a task that aims to predict unknown facts based on known factual samples. Reasoning methods can be divided into two categories: rule-based methods and KG-embedding based methods. The former possesses…

Artificial Intelligence · Computer Science 2024-07-08 Fengsong Sun , Jinyu Wang , Zhiqing Wei , Xianchao Zhang

Drug repurposing is often framed as a candidate identification task, but existing approaches provide limited guidance for distinguishing biologically plausible candidates from historically well-connected ones. Here we introduce DrugKLM, a…

Autonomous agents powered by large language models (LLMs) have shown impressive capabilities in tool manipulation for complex task-solving. However, existing paradigms such as ReAct rely on sequential reasoning and execution, failing to…

Artificial Intelligence · Computer Science 2025-10-30 Jiaqi Wu , Qinlao Zhao , Zefeng Chen , Kai Qin , Yifei Zhao , Xueqian Wang , Yuhang Yao

Large language models (LLMs) have shown promise in medical domains, but their ability to handle specialized neurological reasoning requires systematic evaluation. We developed a comprehensive benchmark using 305 questions from Israeli Board…

Information Retrieval · Computer Science 2025-08-21 Moran Sorka , Alon Gorenshtein , Dvir Aran , Shahar Shelly

Accurate interpretation of pediatric dental clinical records and safe antibiotic prescribing remain persistent challenges in dental informatics. Traditional rule-based clinical decision support systems struggle with unstructured dental…

Computation and Language · Computer Science 2025-12-11 Zihan Han , Junyan Ge , Caifeng Li

Accurate diagnosis of Alzheimer's disease (AD) requires handling tabular biomarker data, yet such data are often small and incomplete, where deep learning models frequently fail to outperform classical methods. Pretrained large language…

Computation and Language · Computer Science 2026-03-19 Sophie Kearney , Shu Yang , Zixuan Wen , Weimin Lyu , Bojian Hou , Duy Duong-Tran , Tianlong Chen , Jason H. Moore , Marylyn D. Ritchie , Chao Chen , Li Shen

In recent years, the introduction of knowledge graphs (KGs) has significantly advanced recommender systems by facilitating the discovery of potential associations between items. However, existing methods still face several limitations.…

Information Retrieval · Computer Science 2025-04-18 Ziqiang Cui , Yunpeng Weng , Xing Tang , Fuyuan Lyu , Dugang Liu , Xiuqiang He , Chen Ma

We introduce a novel large language model (LLM)-driven agent framework, which iteratively refines queries and filters contextual evidence by leveraging dynamically evolving knowledge. A defining feature of the system is its decoupling of…

Artificial Intelligence · Computer Science 2025-04-02 Seyoung Song

Large language models (LLMs) show promise for healthcare question answering, but clinical use is limited by weak verification, insufficient evidence grounding, and unreliable confidence signalling. We propose a multi-agent medical QA…

Computation and Language · Computer Science 2026-02-17 Naeimeh Nourmohammadi , Md Meem Hossain , The Anh Han , Safina Showkat Ara , Zia Ush Shamszaman

Explaining Machine Learning (ML) results in a transparent and user-friendly manner remains a challenging task of Explainable Artificial Intelligence (XAI). In this paper, we present a method to enhance the interpretability of ML models by…

Artificial Intelligence · Computer Science 2026-04-20 Thomas Bayer , Alexander Lohr , Sarah Weiß , Bernd Michelberger , Wolfram Höpken

Despite the impressive performance of large language models (LLMs) pretrained on vast knowledge corpora, advancing their knowledge manipulation-the ability to effectively recall, reason, and transfer relevant knowledge-remains challenging.…

Computation and Language · Computer Science 2026-01-13 Qitan Lv , Tianyu Liu , Qiaosheng Zhang , Xingcheng Xu , Chaochao Lu

The development of intelligent agents, particularly those powered by language models (LMs), has shown a critical role in various environments that require intelligent and autonomous decision-making. Environments are not passive testing…

Artificial Intelligence · Computer Science 2025-10-21 Antonin Sulc , Thorsten Hellert

Large language models (LLMs) used in medical applications are known to be prone to exhibiting biased and unfair patterns. Prior to deploying these in clinical decision-making, it is crucial to identify such bias patterns to enable effective…

Artificial Intelligence · Computer Science 2025-12-23 Farzana Islam Adiba , Rahmatollah Beheshti

Advancements in large language models (LLMs) allow them to address diverse questions using human-like interfaces. Still, limitations in their training prevent them from answering accurately in scenarios that could benefit from multiple…

Artificial Intelligence · Computer Science 2025-04-09 Yoshitaka Inoue , Tianci Song , Xinling Wang , Augustin Luna , Tianfan Fu

Generating long and semantic-coherent reports to describe medical images poses great challenges towards bridging visual and linguistic modalities, incorporating medical domain knowledge, and generating realistic and accurate descriptions.…

Computer Vision and Pattern Recognition · Computer Science 2019-03-26 Christy Y. Li , Xiaodan Liang , Zhiting Hu , Eric P. Xing

This paper presents RAG-KG-IL, a novel multi-agent hybrid framework designed to enhance the reasoning capabilities of Large Language Models (LLMs) by integrating Retrieval-Augmented Generation (RAG) and Knowledge Graphs (KGs) with an…

Computation and Language · Computer Science 2025-03-19 Hong Qing Yu , Frank McQuade

Recent advances in Large Language Models (LLMs) have positioned them as a prominent solution for Natural Language Processing tasks. Notably, they can approach these problems in a zero or few-shot manner, thereby eliminating the need for…

Machine Learning · Computer Science 2025-05-07 Gerard Pons , Besim Bilalli , Anna Queralt

Knowledge Graphs (KGs) serve as a critical foundation for AI systems, yet their automated construction inevitably introduces noise, compromising data trustworthiness. Existing triple verification methods, based on graph embeddings or…

Artificial Intelligence · Computer Science 2026-04-07 Xinyan Ma , Xianhao Ou , Weihao Zhang , Shixin Jiang , Runxuan Liu , Dandan Tu , Lei Chen , Ming Liu , Bing Qin