Yixuan Wang (王艺璇)
Yixuan Wang (王艺璇)
PhD candidate @CUHK

About

I am currently a fourth-year PhD candidate at Artificial Intelligencein Healthcare (AIH) group and Machine Intelligence and Social Computing (MISC) Lab of The Chinese University of Hong Kong, supervised by Prof. Yu Li and Prof. Irwin King. Before that, I received the Bachelor’s degree in Mathematics and Applied Mathematics from Harbin Institute of Technology in 2022.

My research interest includes computational challenges in biology and healthcare, especially that related to single-cell data.

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    Selected Publications
  

  
*: equal contribution

  Perturbation Modeling
  

    

      

        
      

      

        

          
          Predicting drug responses of unseen cell types through transfer learning with foundation models
        

        
        

          Yixuan Wang*,
          Xinyuan Liu*,
          Yimin Fan, 
          Binghui Xie, 
          James Cheng, 
          Kam Chung Wong, 
          Peter Cheung,
          Irwin King, and Yu Li

          
        


        

          Nature Computational Science
          
        

        

          [Paper]
        

      

    

  


  Cell State Understanding
    

    

      

        
        
      

      

        

          SCMBench: Benchmarking Domain-specific and Foundation Models for Single-cell Multi-omics Data Integration
        

        

          
        

        

          Yixuan Wang,
          Yimin Fan,
          Xuesong Wang,
          Tingyang Yu,
          Yongshuo Zong, 
          Xinyuan Liu, 
          Gaoyang Zhong, Meitong Liu,
          Qing Li, 
          Kin hei Lee, 
          Khachatur Dallakyan, 
          Zhichao Hu, 
          Yaqian Qi, 
          Junjie Huang,
          Gengjie Jia, 
          Jiao Yuan, 
          Ting-Fung Chan, 
          Xin Gao, 
          Irwin King, and Yu Li
          

          
        

          Nature Communications in Press 
          
        

        
          
          
        
      

    


  

    

      

        
        
      

      

        

          cfDecon: Accurate and Interpretable methylation-based cell type deconvolution for cell-free DNA
        

        

          
        

        

          Yixuan Wang*,
          Jiayi Li*,
          Jingqi Li,
          Shen Yang,
          Yuhan Huang, 
          Xinyuan Liu, 
          Yimin Fan, 
          Irwin King, 
          Yumei Li, and Yu Li

          
        


        

          RECOMB 2025 
          
        

        

          [Paper]
          
        

      

    


    

      

        
      

      

        

          Deep autoencoder for interpretable tissue-adaptive deconvolution and cell-type-specific gene analysis
        

        

        

        

          Yanshuo Chen*,
          Yixuan Wang*,
          Yuelong Chen,
          Yuqi Cheng,
          Yumeng Wei,
          Yunxiang Li,
          Jiuming Wang,
          Yingying Wei,
          Ting-Fung Chan,
          and Yu Li
          
        


        

          Nature Communications
          
        

        

          [Paper]
        

      

    


    

      

        
      

      

        

          scNovel: A Scalable Deep Learning‑based Network for Novel Rare Cell Discovery in Single‑cell Transcriptomics
        

        

        

        

          Chuanyang Zheng*,
          Yixuan Wang*,
          Yuqi Cheng,
          Xuesong Wang,
          Hongxin Wei,
          Irwin King,
          and Yu Li
          
        


        

          Briefings in Bioinformatics
          
        

        

          [Paper]
        

      

    



  Others
    

      

        
      

      

        

          Accurate RNA 3D structure prediction using a language model-based deep learning approach
        

        

          
        

        

          Tao Shen*,
          Zhihang Hu*,
          Siqi Sun*,
          Di Liu*,
          Felix Wong,
          Jiuming Wang,
          Jiayang Chen,          
          Yixuan Wang,
          Liang Hong,
          Jin Xiao,
          Liangzhen Zheng,
          Tejas Krishnamoorthi,
          Irwin King,
          Sheng Wang,
          Peng Yin,
          James J. Collins,
          and Yu Li*
          

          
        


        

          Nature Methods
          
        

        

          [Paper]
          
        

      

    


    
  










  

    

      
      Selected Honors
    

    
    
    
      
  • RECOMB Travel Fellowship (10 each year globally), 2025.
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  • Postgraduate scholarship of CUHK, 2022 ∼ now.
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  • Most 10 of the Outstanding Undergraduate for international influence, 2022.
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  • National Scholarship for performance in the academic year 2019-2020 (Individual), 2020.
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  • International Finalist Winner in Mathematical Contest in Modeling-MCM (Leader), 2020.
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      Research Experience
    

    
    GeneSight Co-founder & CTO

    Genebio.AI Research Intern

    BioMap Intelligent Technology Research Intern

  





      

  




  
  
  
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