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Recent progress in Large Language Models (LLMs) has drawn attention to their potential for accelerating drug discovery. However, a central problem remains: translating theoretical ideas into robust implementations in the highly specialized…

Machine Learning · Computer Science 2025-03-06 Sizhe Liu , Yizhou Lu , Siyu Chen , Xiyang Hu , Jieyu Zhao , Yingzhou Lu , Yue Zhao

Large language models (LLMs), despite their remarkable progress across various general domains, encounter significant barriers in medicine and healthcare. This field faces unique challenges such as domain-specific terminologies and…

Computation and Language · Computer Science 2024-06-06 Xiangru Tang , Anni Zou , Zhuosheng Zhang , Ziming Li , Yilun Zhao , Xingyao Zhang , Arman Cohan , Mark Gerstein

The substantial data volumes encountered in modern particle physics and other domains of fundamental physics research allow (and require) the use of increasingly complex data analysis tools and workflows. While the use of machine learning…

High Energy Physics - Phenomenology · Physics 2026-02-18 Sascha Diefenbacher , Anna Hallin , Gregor Kasieczka , Michael Krämer , Anne Lauscher , Tim Lukas

Large Language Models (LLMs) are revolutionizing bioinformatics, enabling advanced analysis of DNA, RNA, proteins, and single-cell data. This survey provides a systematic review of recent advancements, focusing on genomic sequence modeling,…

Computation and Language · Computer Science 2026-03-03 Zhenyu Wang , Zikang Wang , Jiyue Jiang , Pengan Chen , Xiangyu Shi , Yu Li

Language is essentially a complex, intricate system of human expressions governed by grammatical rules. It poses a significant challenge to develop capable AI algorithms for comprehending and grasping a language. As a major approach,…

Goal-oriented de novo molecule design, namely generating molecules with specific property or substructure constraints, is a crucial yet challenging task in drug discovery. Existing methods, such as Bayesian optimization and reinforcement…

Computational Engineering, Finance, and Science · Computer Science 2025-02-28 Chuanliu Fan , Ziqiang Cao , Zicheng Ma , Nan Yu , Yimin Peng , Jun Zhang , Yiqin Gao , Guohong Fu

While large language models (LLMs) have demonstrated remarkable versatility across a wide range of general tasks, their effectiveness often diminishes in domain-specific applications due to inherent knowledge gaps. Moreover, their…

Artificial Intelligence · Computer Science 2025-11-21 Hanzhi Yan , Qin Lu , Xianqiao Wang , Xiaoming Zhai , Tianming Liu , He Li

AI agentic programming is an emerging paradigm where large language model (LLM)-based coding agents autonomously plan, execute, and interact with tools such as compilers, debuggers, and version control systems. Unlike conventional code…

Software Engineering · Computer Science 2025-09-16 Huanting Wang , Jingzhi Gong , Huawei Zhang , Jie Xu , Zheng Wang

Large Language Models (LLMs) have achieved remarkable success across a wide array of tasks. Due to the impressive planning and reasoning abilities of LLMs, they have been used as autonomous agents to do many tasks automatically. Recently,…

Computation and Language · Computer Science 2024-04-22 Taicheng Guo , Xiuying Chen , Yaqi Wang , Ruidi Chang , Shichao Pei , Nitesh V. Chawla , Olaf Wiest , Xiangliang Zhang

Large Language Models (LLMs) are transforming artificial intelligence, evolving into task-oriented systems capable of autonomous planning and execution. One of the primary applications of LLMs is conversational AI systems, which must…

Computation and Language · Computer Science 2025-01-22 Elad Levi , Ilan Kadar

Large Language Models (LLMs) show promise in biomedicine but lack true causal understanding, relying instead on correlations. This paper envisions causal LLM agents that integrate multimodal data (text, images, genomics, etc.) and perform…

Artificial Intelligence · Computer Science 2025-05-23 Adib Bazgir , Amir Habibdoust Lafmajani , Yuwen Zhang

With the advancement of web techniques, they have significantly revolutionized various aspects of people's lives. Despite the importance of the web, many tasks performed on it are repetitive and time-consuming, negatively impacting overall…

Artificial Intelligence · Computer Science 2025-08-06 Liangbo Ning , Ziran Liang , Zhuohang Jiang , Haohao Qu , Yujuan Ding , Wenqi Fan , Xiao-yong Wei , Shanru Lin , Hui Liu , Philip S. Yu , Qing Li

Tool learning empowers large language models (LLMs) as agents to use external tools and extend their utility. Existing methods employ one single LLM-based agent to iteratively select and execute tools, thereafter incorporating execution…

Computation and Language · Computer Science 2024-06-25 Zhengliang Shi , Shen Gao , Xiuyi Chen , Yue Feng , Lingyong Yan , Haibo Shi , Dawei Yin , Pengjie Ren , Suzan Verberne , Zhaochun Ren

Large Language Models (LLMs) are rapidly advancing across diverse domains, yet their application in theoretical physics remains inadequate. While current models show competence in mathematical reasoning and code generation, we identify…

Computation and Language · Computer Science 2026-03-13 Sirui Lu , Zhijing Jin , Terry Jingchen Zhang , Pavel Kos , J. Ignacio Cirac , Bernhard Schölkopf

The prediction of protein-protein interactions (PPIs) is crucial for understanding biological functions and diseases. Previous machine learning approaches to PPI prediction mainly focus on direct physical interactions, ignoring the broader…

Biomolecules · Quantitative Biology 2024-07-15 Mingyu Jin , Haochen Xue , Zhenting Wang , Boming Kang , Ruosong Ye , Kaixiong Zhou , Mengnan Du , Yongfeng Zhang

Large language models and autonomous AI agents have evolved rapidly, resulting in a diverse array of evaluation benchmarks, frameworks, and collaboration protocols. Driven by the growing need for standardized evaluation and integration, we…

Artificial Intelligence · Computer Science 2026-03-10 Mohamed Amine Ferrag , Norbert Tihanyi , Merouane Debbah

This article presents a vision for the future of prosthetic devices, leveraging the advancements in large language models (LLMs) and Large Multimodal Models (LMMs) to revolutionize the interaction between humans and assistive technologies.…

Robotics · Computer Science 2024-03-12 Sharmita Dey , Arndt F. Schilling

Recent developments in large language models (LLMs) have unlocked new opportunities for healthcare, from information synthesis to clinical decision support. These new LLMs are not just capable of modeling language, but can also act as…

Human-Computer Interaction · Computer Science 2023-09-21 Nikita Mehandru , Brenda Y. Miao , Eduardo Rodriguez Almaraz , Madhumita Sushil , Atul J. Butte , Ahmed Alaa

Building generalist agents that can handle diverse tasks and evolve themselves across different environments is a long-term goal in the AI community. Large language models (LLMs) are considered a promising foundation to build such agents…