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Large language models (LLMs) have shown growing promise in biomedical research, particularly for knowledge-driven interpretation tasks. However, their ability to reliably reason from gene-level knowledge to functional understanding, a core…

Genomics · Quantitative Biology 2026-05-25 Xiaohan Huang , Meng Xiao , Chuan Qin , Qingqing Long , Jinmiao Chen , Yuanchun Zhou , Hengshu Zhu

This paper explores the intersection of technology and sleep pattern comprehension, presenting a cutting-edge two-stage framework that harnesses the power of Large Language Models (LLMs). The primary objective is to deliver precise sleep…

Machine Learning · Computer Science 2024-05-08 Yonchanok Khaokaew , Kaixin Ji , Thuc Hanh Nguyen , Hiruni Kegalle , Marwah Alaofi , Hao Xue , Flora D. Salim

The development of large language models (LLMs) such as ChatGPT has brought a lot of attention recently. However, their evaluation in the benchmark academic datasets remains under-explored due to the difficulty of evaluating the generative…

Computation and Language · Computer Science 2023-07-07 Md Tahmid Rahman Laskar , M Saiful Bari , Mizanur Rahman , Md Amran Hossen Bhuiyan , Shafiq Joty , Jimmy Xiangji Huang

Large Language Models (LLMs) exhibit a notable performance ceiling on complex, multi-faceted tasks, as they often fail to integrate diverse information or adhere to multiple constraints. We posit that such limitation arises when the demands…

Artificial Intelligence · Computer Science 2025-09-26 HaoYang Shang , Xuan Liu , Zi Liang , Jie Zhang , Haibo Hu , Song Guo

The rise of single-cell sequencing technologies has revolutionized the exploration of drug resistance, revealing the crucial role of cellular heterogeneity in advancing precision medicine. By building computational models from existing…

Genomics · Quantitative Biology 2025-02-05 Yu-An Huang , Xiyue Cao , Zhu-Hong You , Yue-Chao Li , Xuequn Shang , Zhi-An Huang

Large Language Models (LLMs) have reshaped our world with significant advancements in science, engineering, and society through applications ranging from scientific discoveries and medical diagnostics to Chatbots. Despite their ubiquity and…

Artificial Intelligence · Computer Science 2025-08-26 Kushal Raj Bhandari , Pin-Yu Chen , Jianxi Gao

Large language models (LLMs) are powerful artificial intelligence (AI) tools transforming how research is conducted. However, their use in research has been met with skepticism, due to concerns about hallucinations, biases and potential…

Artificial Intelligence · Computer Science 2025-07-08 Ruian Ke , Ruy M. Ribeiro

The paper introduces a framework for the evaluation of the encoding of factual scientific knowledge, designed to streamline the manual evaluation process typically conducted by domain experts. Inferring over and extracting information from…

Computation and Language · Computer Science 2024-10-21 Magdalena Wysocka , Oskar Wysocki , Maxime Delmas , Vincent Mutel , Andre Freitas

Single-cell proteomics (SCP) is transforming our understanding of biological complexity by shifting from bulk proteomics, where signals are averaged over thousands of cells, to the proteome analysis of individual cells. This granular…

Quantitative Methods · Quantitative Biology 2025-04-01 Amanda Momenzadeh , Jesse G. Meyer

Large language models (LLMs) have shown impressive ability for open-domain NLP tasks. However, LLMs are sometimes too footloose for natural language understanding (NLU) tasks which always have restricted output and input format. Their…

Software languages evolve over time for reasons such as feature additions. When grammars evolve, textual instances that originally conformed to them may become outdated. While model-driven engineering provides many techniques for…

Software Engineering · Computer Science 2026-02-13 Weixing Zhang , Bowen Jiang , Yuhong Fu , Anne Koziolek , Regina Hebig , Daniel Strüber

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

Large Language Models (LLMs) have become a milestone in the field of artificial intelligence and natural language processing. However, their large-scale deployment remains constrained by the need for significant computational resources.…

Computation and Language · Computer Science 2025-08-07 Julián Camilo Velandia Gutiérrez

Generative Large Language Models (gLLMs), such as ChatGPT, are increasingly being used in communication research for content analysis. Studies show that gLLMs can outperform both crowd workers and trained coders, such as research…

Artificial Intelligence · Computer Science 2025-10-29 Daria Kravets-Meinke , Hannah Schmid-Petri , Sonja Niemann , Ute Schmid

Large Language Models (LLMs) possess substantial reasoning capabilities and are increasingly applied to optimization tasks, particularly in synergy with evolutionary computation. However, while recent surveys have explored specific aspects…

Neural and Evolutionary Computing · Computer Science 2026-01-08 Yisong Zhang , Ran Cheng , Guoxing Yi , Kay Chen Tan

The parallels between protein sequences and natural language in their sequential structures have inspired the application of large language models (LLMs) to protein understanding. Despite the success of LLMs in NLP, their effectiveness in…

Quantitative Methods · Quantitative Biology 2024-07-09 Yiqing Shen , Zan Chen , Michail Mamalakis , Luhan He , Haiyang Xia , Tianbin Li , Yanzhou Su , Junjun He , Yu Guang Wang

With the promotion of chatgpt to the public, Large language models indeed showcase remarkable common sense, reasoning, and planning skills, frequently providing insightful guidance. These capabilities hold significant promise for their…

Artificial Intelligence · Computer Science 2023-09-14 Siyao Zhang , Daocheng Fu , Zhao Zhang , Bin Yu , Pinlong Cai

Understanding biological processes, drug development, and biotechnological advancements requires a detailed analysis of protein structures and functions, a task that is inherently complex and time-consuming in traditional protein research.…

Artificial Intelligence · Computer Science 2025-04-21 Yijia Xiao , Edward Sun , Yiqiao Jin , Qifan Wang , Wei Wang

Latent representation alignment has become a foundational technique for constructing multimodal large language models (MLLM) by mapping embeddings from different modalities into a shared space, often aligned with the embedding space of…

Machine Learning · Computer Science 2025-03-06 Dong Shu , Bingbing Duan , Kai Guo , Kaixiong Zhou , Jiliang Tang , Mengnan Du

Large Language Model (LLM)-based systems present new opportunities for autonomous health monitoring in sensor-rich industrial environments. This study explores the potential of LLMs to detect and classify faults directly from sensor data,…

Artificial Intelligence · Computer Science 2025-09-30 Xian Yeow Lee , Lasitha Vidyaratne , Ahmed Farahat , Chetan Gupta
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