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Bacteriophages, often referred to as the dark matter of the biosphere, play a critical role in regulating microbial ecosystems and in antibiotic alternatives. Thus, accurate interpretation of their genomes holds significant scientific and…

Computation and Language · Computer Science 2026-04-08 Yusen Hou , Weicai Long , Haitao Hu , Houcheng Su , Junning Feng , Yanlin Zhang

Automatic disease diagnosis has become increasingly valuable in clinical practice. The advent of large language models (LLMs) has catalyzed a paradigm shift in artificial intelligence, with growing evidence supporting the efficacy of LLMs…

Multimodal large language models (MLLMs) have made impressive progress in many applications in recent years. However, chemical MLLMs that can handle cross-modal understanding and generation remain underexplored. To fill this gap, we propose…

Machine Learning · Computer Science 2025-08-05 Qian Tan , Dongzhan Zhou , Peng Xia , Wanhao Liu , Wanli Ouyang , Lei Bai , Yuqiang Li , Tianfan Fu

Large Language Models(LLMs)have become effective tools for natural language processing and have been used in many different fields. This essay offers a succinct summary of various LLM subcategories. The survey emphasizes recent developments…

Computation and Language · Computer Science 2023-07-21 Saurabh Pahune , Manoj Chandrasekharan

As large language models (LLMs) are increasingly applied to various NLP tasks, their inherent biases are gradually disclosed. Therefore, measuring biases in LLMs is crucial to mitigate its ethical risks. However, most existing bias…

Computation and Language · Computer Science 2025-08-08 Tian Lan , Xiangdong Su , Xu Liu , Ruirui Wang , Ke Chang , Jiang Li , Guanglai Gao

Large Language models (LLMs) have emerged as powerful tools for addressing challenges across diverse domains. Notably, recent studies have demonstrated that large language models significantly enhance the efficiency of biomolecular analysis…

Computation and Language · Computer Science 2025-03-07 Jiyue Jiang , Zikang Wang , Yuheng Shan , Heyan Chai , Jiayi Li , Zixian Ma , Xinrui Zhang , Yu Li

Developing therapeutics is a lengthy and expensive process that requires the satisfaction of many different criteria, and AI models capable of expediting the process would be invaluable. However, the majority of current AI approaches…

Clinical reasoning in medicine is a hypothesis-driven process where physicians refine diagnoses from limited information through targeted history, physical examination, and diagnostic investigations. In contrast, current medical benchmarks…

Machine Learning · Computer Science 2025-10-14 Christopher Chiu , Silviu Pitis , Mihaela van der Schaar

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

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

In contrast to their remarkable performance on general knowledge QA, the true abilities of Large Language Models (LLMs) in tasks demanding deep, specialized reasoning, such as in protein biology, have yet to be thoroughly investigated.…

Quantitative Methods · Quantitative Biology 2025-12-30 Dingyi Rong , Zijian Chen , Qi Jia , Kaiwei Zhang , Haotian Lu , Guangtao Zhai , Ning Liu

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

Unlocking the potential of Large Language Models (LLMs) in data classification represents a promising frontier in natural language processing. In this work, we evaluate the performance of different LLMs in comparison with state-of-the-art…

Computation and Language · Computer Science 2025-01-16 Arina Kostina , Marios D. Dikaiakos , Dimosthenis Stefanidis , George Pallis

Large language models (LLMs) hold great promise for medical applications and are evolving rapidly, with new models being released at an accelerated pace. However, benchmarking on large-scale real-world data such as electronic health records…

Large language models (LLMs) have shown to be valuable tools for tackling process mining tasks. Existing studies report on their capability to support various data-driven process analyses and even, to some extent, that they are able to…

Databases · Computer Science 2025-05-01 Adrian Rebmann , Fabian David Schmidt , Goran Glavaš , Han van der Aa

Recent advances in large language models (LLMs) have shown impressive ability in biomedical question-answering, but have not been adequately investigated for more specific biomedical applications. This study investigates the performance of…

Computation and Language · Computer Science 2024-03-29 Shan Chen , Yingya Li , Sheng Lu , Hoang Van , Hugo JWL Aerts , Guergana K. Savova , Danielle S. Bitterman

The field of healthcare has increasingly turned its focus towards Large Language Models (LLMs) due to their remarkable performance. However, their performance in actual clinical applications has been underexplored. Traditional evaluations…

Large Language Models (LLMs) hold great promise to revolutionize current clinical systems for their superior capacities on medical text processing tasks and medical licensing exams. Meanwhile, traditional ML models such as SVM and XGBoost…

Computation and Language · Computer Science 2024-11-12 Canyu Chen , Jian Yu , Shan Chen , Che Liu , Zhongwei Wan , Danielle Bitterman , Fei Wang , Kai Shu

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

The biomedical domain has sparked a significant interest in the field of Natural Language Processing (NLP), which has seen substantial advancements with pre-trained language models (PLMs). However, comparing these models has proven…

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