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Large Language Models (LLMs) have garnered significant attention due to their remarkable ability to process information across various languages. Despite their capabilities, they exhibit inconsistencies in handling identical queries in…

Computation and Language · Computer Science 2024-06-24 Yue Huang , Chenrui Fan , Yuan Li , Siyuan Wu , Tianyi Zhou , Xiangliang Zhang , Lichao Sun

Large language models (LLMs) and emerging agentic frameworks are beginning to transform single-cell biology by enabling natural-language reasoning, generative annotation, and multimodal data integration. However, progress remains fragmented…

Computation and Language · Computer Science 2025-11-25 Sajib Acharjee Dip , Adrika Zafor , Bikash Kumar Paul , Uddip Acharjee Shuvo , Muhit Islam Emon , Xuan Wang , Liqing Zhang

Large language models (LLMs), such as ChatGPT, have received substantial attention due to their capabilities for understanding and generating human language. While there has been a burgeoning trend in research focusing on the employment of…

Despite the inherent limitations of existing Large Language Models in directly reading and interpreting single-cell omics data, they demonstrate significant potential and flexibility as the Foundation Model. This research focuses on how to…

Genomics · Quantitative Biology 2024-02-21 Cong Li , Meng Xiao , Pengfei Wang , Guihai Feng , Xin Li , Yuanchun Zhou

Background: The surge in single-cell omics data exposes limitations in traditional, manually defined analysis workflows. AI agents offer a paradigm shift, enabling adaptive planning, executable code generation, traceable decisions, and…

Genomics · Quantitative Biology 2026-03-17 Yang Liu , Lu Zhou , Xiawei Du , Ruikun He , Xuguang Zhang , Rongbo Shen , Yixue Li

As Large Language Models (LLMs) rapidly evolve, their influence in science is becoming increasingly prominent. The emerging capabilities of LLMs in task generalization and free-form dialogue can significantly advance fields like chemistry…

Computation and Language · Computer Science 2024-02-21 Yin Fang , Kangwei Liu , Ningyu Zhang , Xinle Deng , Penghui Yang , Zhuo Chen , Xiangru Tang , Mark Gerstein , Xiaohui Fan , Huajun Chen

Adapting large language models (LLMs) to new languages typically involves continual pre-training (CT) followed by supervised fine-tuning (SFT). However, this CT-then-SFT approach struggles with limited data in the context of low-resource…

Computation and Language · Computer Science 2025-02-10 Mingxu Tao , Chen Zhang , Quzhe Huang , Tianyao Ma , Songfang Huang , Dongyan Zhao , Yansong Feng

Large language models (LLMs) have revolutionized the state-of-the-art of many different natural language processing tasks. Although serving LLMs is computationally and memory demanding, the rise of Small Language Models (SLMs) offers new…

Computation and Language · Computer Science 2025-08-11 Pol G. Recasens , Yue Zhu , Chen Wang , Eun Kyung Lee , Olivier Tardieu , Alaa Youssef , Jordi Torres , Josep Ll. Berral

In recent years, large language models (LLMs) have demonstrated remarkable potential across various medical applications. Building on this foundation, multimodal large language models (MLLMs) integrate LLMs with visual models to process…

Computation and Language · Computer Science 2025-03-11 Xiaoyi Liang , Mouxiao Bian , Moxin Chen , Lihao Liu , Junjun He , Jie Xu , Lin Li

Large language models (LLMs) are becoming increasingly better at a wide range of Natural Language Processing tasks (NLP), such as text generation and understanding. Recently, these models have extended their capabilities to coding tasks,…

Machine Learning · Computer Science 2024-10-23 Nishat Raihan , Mohammed Latif Siddiq , Joanna C. S. Santos , Marcos Zampieri

Large Language Models (LLMs) have drawn widespread attention and research due to their astounding performance in text generation and reasoning tasks. Derivative products, like ChatGPT, have been extensively deployed and highly sought after.…

Software Engineering · Computer Science 2024-12-11 Zibin Zheng , Kaiwen Ning , Qingyuan Zhong , Jiachi Chen , Wenqing Chen , Lianghong Guo , Weicheng Wang , Yanlin Wang

Artificial intelligence (AI) methods have become critical in scientific applications to help accelerate scientific discovery. Large language models (LLMs) are being considered as a promising approach to address some of the challenging…

Large language models (LLMs) are increasingly applied in scientific research, offering new capabilities for knowledge discovery and reasoning. In single-cell biology, however, evaluation practices for both general and specialized LLMs…

Artificial Intelligence · Computer Science 2026-02-27 Jiahao Zhao , Feng Jiang , Shaowei Qin , Zhonghui Zhang , Junhao Liu , Guibing Guo , Hamid Alinejad-Rokny , Min Yang

Large Language Models (LLMs), including the LLaMA model, have exhibited their efficacy across various general-domain natural language processing (NLP) tasks. However, their performance in high-performance computing (HPC) domain tasks has…

Distributed, Parallel, and Cluster Computing · Computer Science 2023-11-23 Xianzhong Ding , Le Chen , Murali Emani , Chunhua Liao , Pei-Hung Lin , Tristan Vanderbruggen , Zhen Xie , Alberto E. Cerpa , Wan Du

As large language models (LLMs) advance, the ultimate vision for their role in science is emerging: we could build an AI collaborator to effectively assist human beings throughout the entire scientific research process. We refer to this…

Single-cell analysis is currently one of the most high-resolution techniques to study biology. The large complex datasets that have been generated have spurred numerous developments in computational biology, in particular the use of…

Genomics · Quantitative Biology 2023-04-27 Ionut Sebastian Mihai , Sarang Chafle , Johan Henriksson

The rapid advancement of artificial intelligence, particularly with the development of Large Language Models (LLMs) built on the transformer architecture, has redefined the capabilities of natural language processing. These models now…

Computation and Language · Computer Science 2025-02-11 Andrea Matarazzo , Riccardo Torlone

Large language models (LLMs) have been widely adopted due to their remarkable performance across various applications, driving the accelerated development of a large number of diverse models. However, these individual LLMs show limitations…

Computation and Language · Computer Science 2025-06-13 Kaushal Kumar Maurya , KV Aditya Srivatsa , Ekaterina Kochmar

There is enormous enthusiasm and concerns in using large language models (LLMs) in healthcare, yet current assumptions are all based on general-purpose LLMs such as ChatGPT. This study develops a clinical generative LLM, GatorTronGPT, using…

The transformers have achieved significant accomplishments in the natural language processing as its outstanding parallel processing capabilities and highly flexible attention mechanism. In addition, increasing studies based on transformers…

Computation and Language · Computer Science 2024-07-19 Wei Lan , Guohang He , Mingyang Liu , Qingfeng Chen , Junyue Cao , Wei Peng