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Deep learning-based approaches, particularly those leveraging pre-trained language models (PLMs), have shown promise in automated software vulnerability detection. However, existing methods are predominantly limited to specific programming…

Software Engineering · Computer Science 2025-05-13 Junji Yu , Honglin Shu , Michael Fu , Dong Wang , Chakkrit Tantithamthavorn , Yasutaka Kamei , Junjie Chen

Large Language Models (LLMs) and Multi-Agent LLMs (MALLMs) introduce non-determinism unlike traditional or machine learning software, requiring new approaches to verifying correctness beyond simple output comparisons or statistical accuracy…

Software Engineering · Computer Science 2025-10-22 Felix Dobslaw , Robert Feldt , Juyeon Yoon , Shin Yoo

The increasing complexity of software systems has driven significant advancements in program analysis, as traditional methods unable to meet the demands of modern software development. To address these limitations, deep learning techniques,…

Software Engineering · Computer Science 2025-02-27 Jiayimei Wang , Tao Ni , Wei-Bin Lee , Qingchuan Zhao

Large Language Models (LLMs) represent a class of deep learning models adept at understanding natural language and generating coherent responses to various prompts or queries. These models far exceed the complexity of conventional neural…

Machine Learning · Computer Science 2024-12-05 Minghao Shao , Abdul Basit , Ramesh Karri , Muhammad Shafique

Phenotype-driven gene prioritization is a critical process in the diagnosis of rare genetic disorders for identifying and ranking potential disease-causing genes based on observed physical traits or phenotypes. While traditional approaches…

Quantitative Methods · Quantitative Biology 2024-04-04 Junyoung Kim , Jingye Yang , Kai Wang , Chunhua Weng , Cong Liu

Large Language Models (LLMs) have demonstrated remarkable success in various tasks such as natural language understanding, text summarization, and machine translation. However, their general-purpose nature often limits their effectiveness…

Computation and Language · Computer Science 2025-09-03 Zirui Song , Bin Yan , Yuhan Liu , Miao Fang , Mingzhe Li , Rui Yan , Xiuying Chen

Clinical Decision Support Systems (CDSS) utilize evidence-based knowledge and patient data to offer real-time recommendations, with Large Language Models (LLMs) emerging as a promising tool to generate plain-text explanations for medical…

Computation and Language · Computer Science 2023-10-04 D. Umerenkov , G. Zubkova , A. Nesterov

The remarkable performance of large language models (LLMs) in content generation, coding, and common-sense reasoning has spurred widespread integration into many facets of society. However, integration of LLMs raises valid questions on…

Computation and Language · Computer Science 2025-07-03 Ola Shorinwa , Zhiting Mei , Justin Lidard , Allen Z. Ren , Anirudha Majumdar

Large language models (LLMs) have demonstrated significant capabilities in mathematical reasoning, particularly with text-based mathematical problems. However, current multi-modal large language models (MLLMs), especially those specialized…

Computation and Language · Computer Science 2024-12-03 Zhen Yang , Jinhao Chen , Zhengxiao Du , Wenmeng Yu , Weihan Wang , Wenyi Hong , Zhihuan Jiang , Bin Xu , Jie Tang

The large-scale development of large language models (LLMs) in medical contexts, such as diagnostic assistance and treatment recommendations, necessitates that these models possess accurate medical knowledge and deliver traceable…

Artificial Intelligence · Computer Science 2025-08-12 Qiyuan Li , Haijiang Liu , Caicai Guo , Chao Gao , Deyu Chen , Meng Wang , Feng Gao , Frank van Harmelen , Jinguang Gu

Objective: Large language models (LLMs) are attracting increasing interest in healthcare. This commentary evaluates the potential of LLMs to improve clinical prediction models (CPMs) for diagnostic and prognostic tasks, with a focus on…

Computers and Society · Computer Science 2025-11-07 Yusuf Yildiz , Goran Nenadic , Meghna Jani , David A. Jenkins

Emerging topics in biomedical research are continuously expanding, providing a wealth of information about genes and their function. This rapid proliferation of knowledge presents unprecedented opportunities for scientific discovery and…

Genomics · Quantitative Biology 2024-12-25 Zhijian Chen , Chuan Hu , Min Wu , Qingqing Long , Xuezhi Wang , Yuanchun Zhou , Meng Xiao

Large language models (LLMs) have demonstrated remarkable advancements, primarily due to their capabilities in modeling the hidden relationships within text sequences. This innovation presents a unique opportunity in the field of life…

Genomics · Quantitative Biology 2024-12-25 Cong Li , Qingqing Long , Yuanchun Zhou , Meng Xiao

The rapid development of artificial intelligence has led to marked progress in the field. One interesting direction for research is whether Large Language Models (LLMs) can be integrated with structured knowledge-based systems. This…

Computation and Language · Computer Science 2025-05-02 Wenli Yang , Lilian Some , Michael Bain , Byeong Kang

Recent studies have demonstrated the feasibility of modeling single-cell data as natural languages and the potential of leveraging powerful large language models (LLMs) for understanding cell biology. However, a comprehensive evaluation of…

Quantitative Methods · Quantitative Biology 2025-05-14 Fan Zhang , Tianyu Liu , Zhihong Zhu , Hao Wu , Haixin Wang , Donghao Zhou , Yefeng Zheng , Kun Wang , Xian Wu , Pheng-Ann Heng

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,…

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

The integration of Artificial Intelligence (AI), especially Large Language Models (LLMs), into the clinical diagnosis process offers significant potential to improve the efficiency and accessibility of medical care. While LLMs have shown…

Computation and Language · Computer Science 2024-10-15 Mingyu Derek Ma , Chenchen Ye , Yu Yan , Xiaoxuan Wang , Peipei Ping , Timothy S Chang , Wei Wang

Lexical Semantic Change Detection stands out as one of the few areas where Large Language Models (LLMs) have not been extensively involved. Traditional methods like PPMI, and SGNS remain prevalent in research, alongside newer BERT-based…

Computation and Language · Computer Science 2023-12-12 Ruiyu Wang , Matthew Choi

Modern software systems are subjected to various types of uncertainties arising from context, environment, etc. To this end, self-adaptation techniques have been sought out as potential solutions. Although recent advances in self-adaptation…

Software Engineering · Computer Science 2024-04-16 Raghav Donakanti , Prakhar Jain , Shubham Kulkarni , Karthik Vaidhyanathan