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The integration of AI in digital pathology, particularly in whole slide image (WSI) and spatial transcriptomics (ST) analysis, holds immense potential for enhancing our understanding of diseases. Despite challenges such as training pattern…

Quantitative Methods · Quantitative Biology 2024-11-18 Chao-Hui Huang , Sara Lichtarge , Diane Fernandez

Given the great success of large language models (LLMs) across various tasks, in this paper, we introduce LLM-ST, a novel and effective speech translation model constructed upon a pre-trained LLM. By integrating the large language model…

Computation and Language · Computer Science 2023-12-22 Zhichao Huang , Rong Ye , Tom Ko , Qianqian Dong , Shanbo Cheng , Mingxuan Wang , Hang Li

Spatial transcriptomics (ST) enables transcriptome-wide profiling while preserving the spatial context of tissues, offering unprecedented opportunities to study tissue organization and cell-cell interactions in situ. Despite recent…

Computer Vision and Pattern Recognition · Computer Science 2026-01-21 Wei Wang , Quoc-Toan Ly , Chong Yu , Jun Bai

Finetuning large language models (LLMs) has been empirically effective on a variety of downstream tasks. Existing approaches to finetuning an LLM either focus on parameter-efficient finetuning, which only updates a small number of trainable…

Machine Learning · Computer Science 2024-01-17 Zhengxin Zhang , Dan Zhao , Xupeng Miao , Gabriele Oliaro , Qing Li , Yong Jiang , Zhihao Jia

Spatial transcriptomics enables gene expression profiling with spatial context, offering unprecedented insights into the tissue microenvironment. However, most computational models treat genes as isolated numerical features, ignoring the…

Machine Learning · Computer Science 2025-11-17 Jiangkai Long , Yanran Zhu , Chang Tang , Kun Sun , Yuanyuan Liu , Xuesong Yan

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…

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

Although Large Language Models (LLMs) excel in many tasks, their application to Speech-to-Speech Translation (S2ST) is underexplored and hindered by data scarcity. To bridge this gap, we propose PROST-LLM (PROgressive Speech-to-speech…

Computation and Language · Computer Science 2026-01-26 Jing Xu , Jiaqi Wang , Daxin Tan , Xiao Chen

Large Language Models (LLMs) have been emerging as prominent AI models for solving many natural language tasks due to their high performance (e.g., accuracy) and capabilities in generating high-quality responses to the given inputs.…

Neural and Evolutionary Computing · Computer Science 2026-04-22 Rachmad Vidya Wicaksana Putra , Pasindu Wickramasinghe , Muhammad Shafique

Large Language Models (LLMs) are revolutionizing bioinformatics, enabling advanced analysis of DNA, RNA, proteins, and single-cell data. This survey provides a systematic review of recent advancements, focusing on genomic sequence modeling,…

Computation and Language · Computer Science 2026-03-03 Zhenyu Wang , Zikang Wang , Jiyue Jiang , Pengan Chen , Xiangyu Shi , Yu Li

Background: Spatial transcriptomics have emerged as a powerful tool in biomedical research because of its ability to capture both the spatial contexts and abundance of the complete RNA transcript profile in organs of interest. However,…

Genomics · Quantitative Biology 2025-04-18 Shuo Shuo Liu , Shikun Wang , Yuxuan Chen , Anil K. Rustgi , Ming Yuan , Jianhua Hu

Superconducting circuits have demonstrated significant potential in quantum information processing and quantum sensing. Implementing novel control and measurement sequences for superconducting qubits is often a complex and time-consuming…

While Large Language Models (LLMs) dominate tasks like natural language processing and computer vision, harnessing their power for spatial-temporal forecasting remains challenging. The disparity between sequential text and complex…

Machine Learning · Computer Science 2024-05-20 Lei Liu , Shuo Yu , Runze Wang , Zhenxun Ma , Yanming Shen

Large Language Models (LLMs) such as ChatGPT have transformed how we interact with and understand the capabilities of Artificial Intelligence (AI). However, the intersection of LLMs with the burgeoning field of Quantum Machine Learning…

Quantum Physics · Physics 2024-03-15 Yidong Liao , Chris Ferrie

One approach to reducing the massive costs of large language models (LLMs) is the use of quantized or sparse representations for training or deployment. While post-training compression methods are very popular, the question of obtaining…

Machine Learning · Computer Science 2025-06-12 Andrei Panferov , Jiale Chen , Soroush Tabesh , Roberto L. Castro , Mahdi Nikdan , Dan Alistarh

As quantum software frameworks evolve, developers face increasing challenges in maintaining compatibility with rapidly changing APIs. In this work, we present a novel methodology for refactoring Qiskit code using large language models…

Software Engineering · Computer Science 2025-06-18 José Manuel Suárez , Luis Mariano Bibbó , Joaquin Bogado , Alejandro Fernandez

The rapid evolution of large language models (LLMs) holds promise for reforming the methodology of spatio-temporal data mining. However, current works for evaluating the spatio-temporal understanding capability of LLMs are somewhat limited…

Computation and Language · Computer Science 2024-06-28 Wenbin Li , Di Yao , Ruibo Zhao , Wenjie Chen , Zijie Xu , Chengxue Luo , Chang Gong , Quanliang Jing , Haining Tan , Jingping Bi

ChatGPT has drawn considerable attention from both the general public and domain experts with its remarkable text generation capabilities. This has subsequently led to the emergence of diverse applications in the field of biomedicine and…

The emergence of Multimodal Large Language Models (MLLMs) has revolutionized image understanding by bridging textual and visual modalities. However, these models often struggle with capturing fine-grained semantic information, such as the…

Computer Vision and Pattern Recognition · Computer Science 2025-07-16 Jie Yang , Wang Zeng , Sheng Jin , Lumin Xu , Wentao Liu , Chen Qian , Zhen Li , Ruimao Zhang

The understanding of large-scale scientific software poses significant challenges due to its diverse codebase, extensive code length, and target computing architectures. The emergence of generative AI, specifically large language models…

Software Engineering · Computer Science 2024-03-19 Kareem Shaik , Dali Wang , Weijian Zheng , Qinglei Cao , Heng Fan , Peter Schwartz , Yunhe Feng
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