English
Related papers

Related papers: Reconstructing Biological Pathways by Applying Sel…

200 papers

Large Language Models (LLMs) have emerged as transformative tools in the healthcare sector, demonstrating remarkable capabilities in natural language understanding and generation. However, their proficiency in numerical reasoning,…

Artificial Intelligence · Computer Science 2025-01-27 Arjun R. Malghan

Recent advances in Generative Artificial Intelligence, particularly Large Language Models (LLMs), have stimulated growing interest in automating or assisting Business Process Modeling tasks using natural language. Several approaches have…

Software Engineering · Computer Science 2026-04-16 João Bettencourt , Sérgio Guerreiro

Large Language Models (LLMs), particularly those similar to ChatGPT, have significantly influenced the field of Natural Language Processing (NLP). While these models excel in general language tasks, their performance in domain-specific…

Computation and Language · Computer Science 2024-01-02 Omid Rohanian , Mohammadmahdi Nouriborji , David A. Clifton

Background: The potential of large language models (LLMs) to automate and support pharmacoepidemiologic study design is an emerging area of interest, yet their reliability remains insufficiently characterized. General-purpose LLMs often…

Computation and Language · Computer Science 2026-04-21 Xinyao Zhang , Nicole Sonne Heckmann , Manuela Del Castillo Suero , Francesco Paolo Speca , Maurizio Sessa

The biomedical field relies heavily on concept linking in various areas such as literature mining, graph alignment, information retrieval, question-answering, data, and knowledge integration. Although large language models (LLMs) have made…

Computation and Language · Computer Science 2023-07-04 Qinyong Wang , Zhenxiang Gao , Rong Xu

Large language model (LLM)-driven agents are emerging as a powerful new paradigm for solving complex problems. Despite the empirical success of these practices, a theoretical framework to understand and unify their macroscopic dynamics…

Machine Learning · Computer Science 2025-12-12 Zhuo-Yang Song , Qing-Hong Cao , Ming-xing Luo , Hua Xing Zhu

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

Retrieval-Augmented Large Language Models (LLMs), which incorporate the non-parametric knowledge from external knowledge bases into LLMs, have emerged as a promising approach to enhancing response accuracy in several tasks, such as…

Computation and Language · Computer Science 2024-03-29 Soyeong Jeong , Jinheon Baek , Sukmin Cho , Sung Ju Hwang , Jong C. Park

Associative learning--forming links between co-occurring items--is fundamental to human cognition, reshaping internal representations in complex ways. Testing hypotheses on how representational changes occur in biological systems is…

Machine Learning · Computer Science 2025-10-27 Camila Kolling , Vy Ai Vo , Mariya Toneva

Large language models (LLMs) have emerged as transformative tools in medicine, with strong capabilities in language understanding, reasoning, and structured information extraction. Radiation oncology is particularly well suited for LLM…

Scientific research faces high costs and inefficiencies with traditional methods, but the rise of deep learning and large language models (LLMs) offers innovative solutions. This survey reviews transformer-based LLM applications across…

Machine Learning · Computer Science 2025-09-16 Kaiyuan Tian , Linbo Qiao , Baihui Liu , Gongqingjian Jiang , Shanshan Li , Dongsheng Li

Large language models (LLM) hold significant potential for applications in biomedicine, but they struggle with hallucinations and outdated knowledge. While retrieval-augmented generation (RAG) is generally employed to address these issues,…

Computation and Language · Computer Science 2025-09-23 Jiwoong Sohn , Yein Park , Chanwoong Yoon , Sihyeon Park , Hyeon Hwang , Mujeen Sung , Hyunjae Kim , Jaewoo Kang

Large language models (LLMs) are increasingly seen as assistants, copilots, and consultants, capable of supporting a wide range of tasks through natural conversation. However, most systems remain constrained by a linear request-response…

Computation and Language · Computer Science 2026-05-05 Jiaqi Chen , Yanzhe Zhang , Yutong Zhang , Yijia Shao , Diyi Yang

The versatility of large language models (LLMs) has been explored across various sectors, but their application in healthcare poses challenges, particularly in the domain of pharmaceutical contraindications where accurate and reliable…

Artificial Intelligence · Computer Science 2025-08-11 Byeonghun Bang , Jongsuk Yoon , Dong-Jin Chang , Seho Park , Yong Oh Lee

Genes, proteins and other biological entities influence one another via causal molecular networks. Causal relationships in such networks are mediated by complex and diverse mechanisms, through latent variables, and are often specific to…

Machine Learning · Computer Science 2025-03-07 Izzy Newsham , Luka Kovačević , Richard Moulange , Nan Rosemary Ke , Sach Mukherjee

Biomedical literature often uses complex language and inaccessible professional terminologies. That is why simplification plays an important role in improving public health literacy. Applying Natural Language Processing (NLP) models to…

Computation and Language · Computer Science 2024-03-19 Zihao Li , Samuel Belkadi , Nicolo Micheletti , Lifeng Han , Matthew Shardlow , Goran Nenadic

This study investigates uncertainty quantification in large language models (LLMs) for medical applications, emphasizing both technical innovations and philosophical implications. As LLMs become integral to clinical decision-making,…

Artificial Intelligence · Computer Science 2025-04-08 Zahra Atf , Seyed Amir Ahmad Safavi-Naini , Peter R. Lewis , Aref Mahjoubfar , Nariman Naderi , Thomas R. Savage , Ali Soroush

Large language models (LLMs) like ChatGPT can generate and revise text with human-level performance. These models come with clear limitations: they can produce inaccurate information, reinforce existing biases, and be easily misused. Yet,…

Computation and Language · Computer Science 2025-07-04 Dmitry Kobak , Rita González-Márquez , Emőke-Ágnes Horvát , Jan Lause

Tool-augmented large language models (LLMs) leverage tools, often in the form of APIs, to improve their reasoning capabilities on complex tasks. This enables them to act as intelligent agents interacting with the real world. The recently…

Computation and Language · Computer Science 2025-03-24 Sijia Chen , Yibo Wang , Yi-Feng Wu , Qing-Guo Chen , Zhao Xu , Weihua Luo , Kaifu Zhang , Lijun Zhang

Large Language Models (LLMs) process every token through all layers of a transformer stack, causing wasted computation on simple queries and insufficient flexibility for harder ones that need deeper reasoning. Adaptive-depth methods can…

Computation and Language · Computer Science 2026-05-20 Ahmed Heakl , Martin Gubri , Salman Khan , Sangdoo Yun , Seong Joon Oh