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Although large language models (LLMs) show promising potential in code translation, they still struggle to generate accurate translations using the commonly adopted direct code-to-code translation approach, which converts an original…

Software Engineering · Computer Science 2026-02-24 Songqiang Chen , Congying Xu , Jingyi Chen , Jialun Cao , Jiarong Wu , Shing-Chi Cheung

Large Language Models (LLMs) have emerged as powerful tools for software development tasks such as code completion, translation, and optimization. However, their ability to generate efficient and correct code, particularly in complex…

Distributed, Parallel, and Cluster Computing · Computer Science 2025-03-19 Bowen Cui , Tejas Ramesh , Oscar Hernandez , Keren Zhou

Objectives: The vast and complex nature of human genomic sequencing data presents challenges for effective analysis. This review aims to investigate the application of Natural Language Processing (NLP) techniques, particularly Large…

Genomics · Quantitative Biology 2025-02-28 Shuyan Cheng , Yishu Wei , Yiliang Zhou , Zihan Xu , Drew N Wright , Jinze Liu , Yifan Peng

Large Language Models (LLMs) have demonstrated surprising performance across various natural language processing tasks. Recently, medical LLMs enhanced with domain-specific knowledge have exhibited excellent capabilities in medical…

Computation and Language · Computer Science 2024-09-24 Jinqiang Wang , Huansheng Ning , Yi Peng , Qikai Wei , Daniel Tesfai , Wenwei Mao , Tao Zhu , Runhe Huang

Recent advances in artificial intelligence, particularly large language models LLMs, have shown promising capabilities in transforming rare disease research. This survey paper explores the integration of LLMs in the analysis of rare…

Computation and Language · Computer Science 2025-05-26 Valentina Carbonari , Pierangelo Veltri , Pietro Hiram Guzzi

Large language models (LLMs) have shown great potential in automating significant aspects of coding by producing natural code from informal natural language (NL) intent. However, given NL is informal, it does not lend easily to checking…

Software Engineering · Computer Science 2024-10-04 Sarah Fakhoury , Aaditya Naik , Georgios Sakkas , Saikat Chakraborty , Shuvendu K. Lahiri

Large Language Models (LLMs) are one of the most promising developments in the field of artificial intelligence, and the software engineering community has readily noticed their potential role in the software development life-cycle.…

Software Engineering · Computer Science 2026-03-16 Greta Dolcetti , Vincenzo Arceri , Eleonora Iotti , Sergio Maffeis , Agostino Cortesi , Enea Zaffanella

In the realm of Business Process Management (BPM), process modeling plays a crucial role in translating complex process dynamics into comprehensible visual representations, facilitating the understanding, analysis, improvement, and…

Software Engineering · Computer Science 2024-07-01 Humam Kourani , Alessandro Berti , Daniel Schuster , Wil M. P. van der Aalst

Recent advancements in large language models (LLMs) have demonstrated extraordinary comprehension capabilities with remarkable breakthroughs on various vision-language tasks. However, the application of LLMs in generating reliable medical…

Artificial Intelligence · Computer Science 2025-02-18 Xueshen Li , Xinlong Hou , Ziyi Huang , Yu Gan

Large Language Models (LLMs) have succeeded remarkably in understanding long-form contents. However, exploring their capability for generating long-form contents, such as reports and articles, has been relatively unexplored and inadequately…

Computation and Language · Computer Science 2024-06-05 Haochen Tan , Zhijiang Guo , Zhan Shi , Lu Xu , Zhili Liu , Yunlong Feng , Xiaoguang Li , Yasheng Wang , Lifeng Shang , Qun Liu , Linqi Song

Large language models (LLMs) require well-crafted prompts for effective use. Prompt engineering, the process of designing prompts, is challenging, particularly for non-experts who are less familiar with AI technologies. While researchers…

Human-Computer Interaction · Computer Science 2024-01-29 Zijie J. Wang , Aishwarya Chakravarthy , David Munechika , Duen Horng Chau

We consider the protein sequence engineering problem, which aims to find protein sequences with high fitness levels, starting from a given wild-type sequence. Directed evolution has been a dominating paradigm in this field which has an…

Machine Learning · Computer Science 2025-01-20 Yinkai Wang , Jiaxing He , Yuanqi Du , Xiaohui Chen , Jianan Canal Li , Li-Ping Liu , Xiaolin Xu , Soha Hassoun

We propose ProtLLM, a versatile cross-modal large language model (LLM) for both protein-centric and protein-language tasks. ProtLLM features a unique dynamic protein mounting mechanism, enabling it to handle complex inputs where the natural…

Biomolecules · Quantitative Biology 2024-03-14 Le Zhuo , Zewen Chi , Minghao Xu , Heyan Huang , Heqi Zheng , Conghui He , Xian-Ling Mao , Wentao Zhang

Large Language Models (LLMs) and pre-trained Language Models (LMs) have achieved impressive success on many software engineering tasks (e.g., code completion and code generation). By leveraging huge existing code corpora (e.g., GitHub),…

Software Engineering · Computer Science 2025-01-16 Xin Yin , Chao Ni , Xiaodan Xu , Xinrui Li , Xiaohu Yang

This study applies Large Language Models (LLMs) to two foundational Electronic Health Record (EHR) data science tasks: structured data querying (using programmatic languages, Python/Pandas) and information extraction from unstructured…

Computation and Language · Computer Science 2026-01-29 Juan Jose Rubio Jan , Jack Wu , Julia Ive

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

Background: Identification of the interactions and regulatory relations between biomolecules play pivotal roles in understanding complex biological systems and the mechanisms underlying diverse biological functions. However, the collection…

Computation and Language · Computer Science 2025-04-24 Gilchan Park , Byung-Jun Yoon , Xihaier Luo , Vanessa López-Marrero , Shinjae Yoo , Shantenu Jha

Considering the significance of proteins, computational protein science has always been a critical scientific field, dedicated to revealing knowledge and developing applications within the protein sequence-structure-function paradigm. In…

Computational Engineering, Finance, and Science · Computer Science 2025-01-28 Wenqi Fan , Yi Zhou , Shijie Wang , Yuyao Yan , Hui Liu , Qian Zhao , Le Song , Qing Li

Recently, Large Language Models (LLMs) have showcased remarkable capabilities in natural language understanding. While demonstrating proficiency in everyday conversations and question-answering situations, these models frequently struggle…

Computation and Language · Computer Science 2023-08-28 Chaoyi Wu , Weixiong Lin , Xiaoman Zhang , Ya Zhang , Yanfeng Wang , Weidi Xie

This paper provides a comprehensive review of the current methods and metrics used to evaluate the performance of Large Language Models (LLMs) in code generation tasks. With the rapid growth in demand for automated software development,…

Software Engineering · Computer Science 2025-03-05 Liguo Chen , Qi Guo , Hongrui Jia , Zhengran Zeng , Xin Wang , Yijiang Xu , Jian Wu , Yidong Wang , Qing Gao , Jindong Wang , Wei Ye , Shikun Zhang