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Deep learning has become a powerful tool in computational biology, revolutionising the analysis and interpretation of biological data over time. In our article review, we delve into various aspects of deep learning in computational biology.…

Large language models (LLMs) are transforming cellular biology by enabling the development of "virtual cells"--computational systems that represent, predict, and reason about cellular states and behaviors. This work provides a comprehensive…

Computation and Language · Computer Science 2025-10-10 Krinos Li , Xianglu Xiao , Shenglong Deng , Lucas He , Zijun Zhong , Yuanjie Zou , Zhonghao Zhan , Zheng Hui , Weiye Bao , Guang Yang

Large language models (LLMs) have revolutionized natural language processing by achieving state-of-the-art performance across various tasks. Recently, their effectiveness as embedding models has gained attention, marking a paradigm shift…

Computation and Language · Computer Science 2025-07-28 Chongyang Tao , Tao Shen , Shen Gao , Junshuo Zhang , Zhen Li , Kai Hua , Wenpeng Hu , Zhengwei Tao , Shuai Ma

This survey and application guide to multimodal large language models(MLLMs) explores the rapidly developing field of MLLMs, examining their architectures, applications, and impact on AI and Generative Models. Starting with foundational…

Artificial Intelligence · Computer Science 2025-12-02 Chia Xin Liang , Pu Tian , Caitlyn Heqi Yin , Yao Yua , Wei An-Hou , Li Ming , Xinyuan Song , Tianyang Wang , Ziqian Bi , Ming Liu

Large Language Models (LLMs) have transformed numerous domains by providing advanced capabilities in natural language understanding, generation, and reasoning. Despite their groundbreaking applications across industries such as research,…

Artificial Intelligence · Computer Science 2025-01-22 Aditi Singh , Nirmal Prakashbhai Patel , Abul Ehtesham , Saket Kumar , Tala Talaei Khoei

Current approaches to data discovery match keywords between metadata and queries. This matching requires researchers to know the exact wording that other researchers previously used, creating a challenging process that could lead to missing…

Human-Computer Interaction · Computer Science 2025-10-03 Maura E Halstead , Mark A. Green , Caroline Jay , Richard Kingston , David Topping , Alexander Singleton

Recent breakthroughs in large language models (LLMs) offer unprecedented natural language understanding and generation capabilities. However, existing surveys on LLMs in biomedicine often focus on specific applications or model…

Protein representation learning plays a crucial role in understanding the structure and function of proteins, which are essential biomolecules involved in various biological processes. In recent years, deep learning has emerged as a…

Biomolecules · Quantitative Biology 2024-03-11 Bozhen Hu , Cheng Tan , Lirong Wu , Jiangbin Zheng , Jun Xia , Zhangyang Gao , Zicheng Liu , Fandi Wu , Guijun Zhang , Stan Z. Li

As multiple crises threaten the sustainability of our societies and pose at risk the planetary boundaries, complex challenges require timely, updated, and usable information. Natural-language processing (NLP) tools enhance and expand data…

Computers and Society · Computer Science 2025-02-05 Francesca Larosa , Sergio Hoyas , H. Alberto Conejero , Javier Garcia-Martinez , Francesco Fuso Nerini , Ricardo Vinuesa

In recent years, the development of Large Language Models (LLMs) has made significant breakthroughs in the field of natural language processing and has gradually been applied to the field of humanities and social sciences research. LLMs…

Computers and Society · Computer Science 2025-04-16 Peiran Gu , Fuhao Duan , Wenhao Li , Bochen Xu , Ying Cai , Teng Yao , Chenxun Zhuo , Tianming Liu , Bao Ge

Background: The inception of next generations sequencing technologies have exponentially increased the volume of biological sequence data. Protein sequences, being quoted as the `language of life', has been analyzed for a multitude of…

Quantitative Methods · Quantitative Biology 2020-12-08 Nabil Ibtehaz , S. M. Shakhawat Hossain Sourav , Md. Shamsuzzoha Bayzid , M. Sohel Rahman

Large Language Models (LLMs) are starting to be profiled as one of the most significant disruptions in the Software Testing field. Specifically, they have been successfully applied in software testing tasks such as generating test code, or…

Software Engineering · Computer Science 2025-09-30 Cristian Augusto , Antonia Bertolino , Guglielmo De Angelis , Francesca Lonetti , Jesús Morán

The prediction of amyloidogenicity in peptides and proteins remains a focal point of ongoing bioinformatics. The crucial step in this field is to apply advanced computational methodologies. Many recent approaches to predicting…

Machine Learning · Computer Science 2025-08-19 Zohra Yagoub , Hafida Bouziane

Large Language Models (LLMs) have been employed in financial decision making, enhancing analytical capabilities for investment strategies. Traditional investment strategies often utilize quantitative models, fundamental analysis, and…

General Finance · Quantitative Finance 2025-07-04 Sedigheh Mahdavi , Jiating , Chen , Pradeep Kumar Joshi , Lina Huertas Guativa , Upmanyu Singh

Artificial intelligence (AI) technology has advanced rapidly in recent years, with large language models (LLMs) emerging as a significant breakthrough. LLMs are increasingly making an impact across various industries, with the medical field…

Artificial Intelligence · Computer Science 2025-09-24 Zhiyu Kan , Wensheng Gan , Zhenlian Qi , Philip S. Yu

Recently, the intersection of Large Language Models (LLMs) and Computer Vision (CV) has emerged as a pivotal area of research, driving significant advancements in the field of Artificial Intelligence (AI). As transformers have become the…

Computer Vision and Pattern Recognition · Computer Science 2023-11-29 Raby Hamadi

Recent advances in Natural Language Processing (NLP) have ignited interest in developing effective methods for predicting protein-ligand interactions (PLIs) given their relevance to drug discovery and protein engineering efforts and the…

Quantitative Methods · Quantitative Biology 2024-10-18 James Michels , Ramya Bandarupalli , Amin Ahangar Akbari , Thai Le , Hong Xiao , Jing Li , Erik F. Y. Hom

Language models (LMs) are machine learning models designed to predict linguistic patterns by estimating the probability of word sequences based on large-scale datasets, such as text. LMs have a wide range of applications in natural language…

In recent years, the rapid advancement and impressive capabilities of Large Language Models (LLMs) have been evident across various domains. This paper explores the application, implications, and potential of LLMs in building energy…

Systems and Control · Electrical Eng. & Systems 2023-12-20 Liang Zhang , Zhelun Chen

In the field of Artificial (General) Intelligence (AI), the several recent advancements in Natural language processing (NLP) activities relying on Large Language Models (LLMs) have come to encourage the adoption of LLMs as scientific models…

Computation and Language · Computer Science 2023-10-18 Evelina Leivada , Vittoria Dentella , Elliot Murphy
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