Xiangyu Shi

Also published as: 响宇


2025

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Large Language Models in Bioinformatics: A Survey
Zhenyu Wang | Zikang Wang | Jiyue Jiang | Pengan Chen | Xiangyu Shi | Yu Li
Findings of the Association for Computational Linguistics: ACL 2025

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, RNA structure prediction, protein function inference, and single-cell transcriptomics. Meanwhile, we also discuss several key challenges, including data scarcity, computational complexity, and cross-omics integration, and explore future directions such as multimodal learning, hybrid AI models, and clinical applications. By offering a comprehensive perspective, this paper underscores the transformative potential of LLMs in driving innovations in bioinformatics and precision medicine.

2024

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融合确定性因子及区域密度的k-最近邻机器翻译方法(A k-Nearest-Neighbor Machine Translation Method Combining Certainty Factor and Region Density)
Rui Qi (齐睿) | Xiangyu Shi (石响宇) | Zhibo Man (满志博) | Jinan Xu (徐金安) | Yufeng Chen (陈钰枫)
Proceedings of the 23rd Chinese National Conference on Computational Linguistics (Volume 1: Main Conference)

“k-最近邻机器翻译(kNN-MT)是近年来神经机器翻译领域的一个重要研究方向。此类方法可以在不更新机器翻译模型的情况下提高翻译质量,但训练数据中高低频单词的数量不均衡限制了模型效果,且固定的k值无法对处于不同密度分布的数据都产生良好的翻译结果。为此本文提出了一种创新的kNN-MT方法,引入确定性因子(CF)来降低数据不均衡对模型效果的影响,并根据测试点周边数据密度动态选择k值。在多领域德-英翻译数据集上,相比基线实验,本方法在四个领域上翻译效果均有提升,其中三个领域上提升超过1个BLEU,有效提高了神经机器翻译模型的翻译质量。”