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The 21st century is presenting humankind with unprecedented environmental and medical challenges. The ability to design novel proteins tailored for specific purposes could transform our ability to respond timely to these issues. Recent…

Biomolecules · Quantitative Biology 2022-08-24 Noelia Ferruz , Birte Höcker

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

Molecular property prediction has gained significant attention due to its transformative potential in multiple scientific disciplines. Conventionally, a molecule graph can be represented either as a graph-structured data or a SMILES text.…

Machine Learning · Computer Science 2023-07-17 Chen Qian , Huayi Tang , Zhirui Yang , Hong Liang , Yong Liu

Large language models (LLMs) have been touted to enable increased productivity in many areas of today's work life. Scientific research as an area of work is no exception: the potential of LLM-based tools to assist in the daily work of…

Software Engineering · Computer Science 2024-04-24 Mohamed Nejjar , Luca Zacharias , Fabian Stiehle , Ingo Weber

The integration of Large Language Models (LLMs) into the drug discovery and development field marks a significant paradigm shift, offering novel methodologies for understanding disease mechanisms, facilitating drug discovery, and optimizing…

Quantitative Methods · Quantitative Biology 2024-09-10 Yizhen Zheng , Huan Yee Koh , Maddie Yang , Li Li , Lauren T. May , Geoffrey I. Webb , Shirui Pan , George Church

Since the inception of the Transformer architecture in 2017, Large Language Models (LLMs) such as GPT and BERT have evolved significantly, impacting various industries with their advanced capabilities in language understanding and…

Computation and Language · Computer Science 2024-05-30 Yining Huang , Keke Tang , Meilian Chen , Boyuan Wang

Large language models (LLMs) and transformer-based architectures are increasingly utilized for source code analysis. As software systems grow in complexity, integrating LLMs into code analysis workflows becomes essential for enhancing…

Software Engineering · Computer Science 2025-03-25 Hamed Jelodar , Mohammad Meymani , Roozbeh Razavi-Far

The advent of Large Language Models (LLMs) has brought in a new era of possibilities in the realm of education. This survey paper summarizes the various technologies of LLMs in educational settings from multifaceted perspectives,…

Computation and Language · Computer Science 2024-04-03 Shen Wang , Tianlong Xu , Hang Li , Chaoli Zhang , Joleen Liang , Jiliang Tang , Philip S. Yu , Qingsong Wen

Large Language Models (LLMs) trained on extensive textual corpora have emerged as leading solutions for a broad array of Natural Language Processing (NLP) tasks. Despite their notable performance, these models are prone to certain…

Computation and Language · Computer Science 2023-07-25 Yufei Wang , Wanjun Zhong , Liangyou Li , Fei Mi , Xingshan Zeng , Wenyong Huang , Lifeng Shang , Xin Jiang , Qun Liu

Language modeling studies the probability distributions over strings of texts. It is one of the most fundamental tasks in natural language processing (NLP). It has been widely used in text generation, speech recognition, machine…

Computation and Language · Computer Science 2024-07-18 Chengwei Wei , Yun-Cheng Wang , Bin Wang , C. -C. Jay Kuo

Predicting protein stability changes induced by single-point mutations has been a persistent challenge over the years, attracting immense interest from numerous researchers. The ability to precisely predict protein thermostability is…

Biomolecules · Quantitative Biology 2023-12-08 Yijie Zhang , Zhangyang Gao , Cheng Tan , Stan Z. Li

There is a significant potential for coding skills to transition fully to natural language in the future. In this context, large language models (LLMs) have shown impressive natural language processing abilities to generate sophisticated…

Materials Science · Physics 2024-06-25 Prathamesh Satpute , Saurabh Tiwari , Maneet Gupta , Supriyo Ghosh

Log data provides crucial insights for tasks like monitoring, root cause analysis, and anomaly detection. Due to the vast volume of logs, automated log parsing is essential to transform semi-structured log messages into structured…

Machine Learning · Computer Science 2025-05-16 Viktor Beck , Max Landauer , Markus Wurzenberger , Florian Skopik , Andreas Rauber

Protein language models (PLMs) have advanced computational protein science through large-scale pretraining and scalable architectures. In parallel, reinforcement learning (RL) has broadened exploration and enabled precise multi-objective…

Large Language Models (LLMs) represent an advanced evolution of earlier, simpler language models. They boast enhanced abilities to handle complex language patterns and generate coherent text, images, audios, and videos. Furthermore, they…

Cryptography and Security · Computer Science 2024-03-01 Jun Huang , Jiawei Zhang , Qi Wang , Weihong Han , Yanchun Zhang

The use of large language models (LLMs) for qualitative analysis is gaining attention in various fields, including software engineering, where qualitative methods are essential for understanding human and social factors. This study aimed to…

Software Engineering · Computer Science 2025-03-11 Matheus de Morais Leça , Lucas Valença , Reydne Santos , Ronnie de Souza Santos

Large language models (LLMs) have exhibited exceptional capabilities in natural language understanding and generation, image recognition, and multimodal tasks, charting a course towards AGI and emerging as a central issue in the global…

Computation and Language · Computer Science 2025-11-20 Guoqiang Liang , Jingqian Gong , Mengxuan Li , Gege Lin , Shuo Zhang

This paper presents a detailed case study examining the application of Large Language Models (LLMs) in the construction of test cases within the context of software engineering. LLMs, characterized by their advanced natural language…

Large Language Models (LLMs) have recently gained significant attention due to their remarkable capabilities in performing diverse tasks across various domains. However, a thorough evaluation of these models is crucial before deploying them…

In the past year, MultiModal Large Language Models (MM-LLMs) have undergone substantial advancements, augmenting off-the-shelf LLMs to support MM inputs or outputs via cost-effective training strategies. The resulting models not only…

Computation and Language · Computer Science 2024-05-29 Duzhen Zhang , Yahan Yu , Jiahua Dong , Chenxing Li , Dan Su , Chenhui Chu , Dong Yu