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Large language models (LLMs) such as ChatGPT have gained considerable interest across diverse research communities. Their notable ability for text completion and generation has inaugurated a novel paradigm for language-interfaced problem…

Quantitative Methods · Quantitative Biology 2024-02-22 Hengchuang Yin , Zhonghui Gu , Fanhao Wang , Yiparemu Abuduhaibaier , Yanqiao Zhu , Xinming Tu , Xian-Sheng Hua , Xiao Luo , Yizhou Sun

Predicting enzymatic reactions is crucial for applications in biocatalysis, metabolic engineering, and drug discovery, yet it remains a complex and resource-intensive task. Large Language Models (LLMs) have recently demonstrated remarkable…

Artificial Intelligence · Computer Science 2025-05-12 Lorenzo Di Fruscia , Jana Marie Weber

Although Large Language Models (LLMs) demonstrate remarkable ability in processing and generating human-like text, they do have limitations when it comes to comprehending and expressing world knowledge that extends beyond the boundaries of…

Computation and Language · Computer Science 2024-02-20 Fangzhi Xu , Zhiyong Wu , Qiushi Sun , Siyu Ren , Fei Yuan , Shuai Yuan , Qika Lin , Yu Qiao , Jun Liu

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

Active learning (AL) accelerates scientific discovery by prioritizing the most informative experiments, but traditional machine learning (ML) models used in AL suffer from cold-start limitations and domain-specific feature engineering,…

Machine Learning · Computer Science 2025-12-05 Hongchen Wang , Rafael Espinosa Castañeda , Jay R. Werber , Yao Fehlis , Edward Kim , Jason Hattrick-Simpers

Large language models have emerged as a promising approach towards achieving general-purpose AI agents. The thriving open-source LLM community has greatly accelerated the development of agents that support human-machine dialogue interaction…

Computer Vision and Pattern Recognition · Computer Science 2023-11-07 Zhenfei Yin , Jiong Wang , Jianjian Cao , Zhelun Shi , Dingning Liu , Mukai Li , Lu Sheng , Lei Bai , Xiaoshui Huang , Zhiyong Wang , Jing Shao , Wanli Ouyang

This paper presents a comprehensive evaluation of cost-efficient Large Language Models (LLMs) for diverse biomedical tasks spanning both text and image modalities. We evaluated a range of closed-source and open-source LLMs on tasks such as…

Computation and Language · Computer Science 2025-07-21 Israt Jahan , Md Tahmid Rahman Laskar , Chun Peng , Jimmy Huang

ChatGPT has drawn considerable attention from both the general public and domain experts with its remarkable text generation capabilities. This has subsequently led to the emergence of diverse applications in the field of biomedicine and…

With the rapid development of artificial intelligence, large language models (LLMs) have shown promising capabilities in mimicking human-level language comprehension and reasoning. This has sparked significant interest in applying LLMs to…

Computation and Language · Computer Science 2023-11-06 Mingze Yuan , Peng Bao , Jiajia Yuan , Yunhao Shen , Zifan Chen , Yi Xie , Jie Zhao , Yang Chen , Li Zhang , Lin Shen , Bin Dong

Medical Large Language Models (LLMs) have demonstrated impressive performance on a wide variety of medical NLP tasks; however, there still lacks a LLM specifically designed for phenotyping identification and diagnosis in cancer domain.…

Computation and Language · Computer Science 2025-04-02 Mingchen Li , Jiatan Huang , Jeremy Yeung , Anne Blaes , Steven Johnson , Hongfang Liu , Hua Xu , Rui Zhang

Understanding biological processes, drug development, and biotechnological advancements requires a detailed analysis of protein structures and functions, a task that is inherently complex and time-consuming in traditional protein research.…

Artificial Intelligence · Computer Science 2025-04-21 Yijia Xiao , Edward Sun , Yiqiao Jin , Qifan Wang , Wei Wang

Machine translation is indispensable in healthcare for enabling the global dissemination of medical knowledge across languages. However, complex medical terminology poses unique challenges to achieving adequate translation quality and…

Computation and Language · Computer Science 2024-07-29 Bunyamin Keles , Murat Gunay , Serdar I. Caglar

Multimodal artificial intelligence (AI) systems have the potential to enhance clinical decision-making by interpreting various types of medical data. However, the effectiveness of these models across all medical fields is uncertain. Each…

Data science plays a critical role in biomedical research, but it requires professionals with expertise in coding and medical data analysis. Large language models (LLMs) have shown great potential in supporting medical tasks and performing…

Artificial Intelligence · Computer Science 2025-04-10 Zifeng Wang , Benjamin Danek , Ziwei Yang , Zheng Chen , Jimeng Sun

Recently, large language models(LLMs) have played an increasingly important role in solving a wide range of NLP tasks, leveraging their capabilities of natural language understanding and generating. Integration with external tools further…

Computation and Language · Computer Science 2025-05-14 Aiyao He , Sijia Cui , Shuai Xu , Yanna Wang , Bo Xu

While Large Language Models (LLMs) are being quickly adapted to many domains, including healthcare, their strengths and pitfalls remain under-explored. In our study, we examine the effects of prompt engineering to guide Large Language…

Computation and Language · Computer Science 2024-09-04 Daniil Filienko , Yinzhou Wang , Caroline El Jazmi , Serena Xie , Trevor Cohen , Martine De Cock , Weichao Yuwen

Time series data is fundamental to decision-making across many domains including healthcare, finance, power systems, and logistics. However, analyzing this data correctly often requires incorporating unstructured contextual information,…

Machine Learning · Computer Science 2026-03-17 Felix Parker , Nimeesha Chan , Chi Zhang , Kimia Ghobadi

The increasing size and complexity of pre-trained language models have demonstrated superior performance in many applications, but they usually require large training datasets to be adequately trained. Insufficient training sets could…

Computation and Language · Computer Science 2025-02-03 Yaping Chai , Haoran Xie , Joe S. Qin

Modern signal processing (SP) pipelines, whether model-based or data-driven, often constrained by complex and fragmented workflow, rely heavily on expert knowledge and manual engineering, and struggle with adaptability and generalization…

Machine Learning · Computer Science 2025-10-31 Junlong Ke , Qiying Hu , Shenghai Yuan , Yuecong Xu , Jianfei Yang

The proliferation of Large Language Models (LLMs) in medicine has enabled impressive capabilities, yet a critical gap remains in their ability to perform systematic, transparent, and verifiable reasoning, a cornerstone of clinical practice.…

Computation and Language · Computer Science 2025-08-04 Wenxuan Wang , Zizhan Ma , Meidan Ding , Shiyi Zheng , Shengyuan Liu , Jie Liu , Jiaming Ji , Wenting Chen , Xiang Li , Linlin Shen , Yixuan Yuan