I am a lecturer at the School of Big Data and Software Engineering at Chongqing University. Prior to that, I finished my Ph.D. in Computer Science and Technology at Sun Yat-Sen University, supervised by Yuedong Yang.

My research interests lie in deep learning, single-cell omics, spatial transcriptomics and computational biology.

I am currently seeking undergraduates who share our passion in ML & AI for single-cell omics.

Google Scholar / DBLP

• Accurately predicting cell type abundance from spatial histology image through HPCell Yuansong Zeng, et al..
  Currently under peer review. 2025
• SANNO: A Graph-Transformer Enhanced Optimal Transport Tool for Spatial Transcriptomic Annotation Yuansong Zeng, et al..
  Currently under peer review. 2025
• Deciphering Cell Types by Integrating scATAC-seq Data with Genome Sequences Yuansong Zeng, Mai Luo, Ningyuan Shangguan, Peiyu Shi, Junxi Feng, Jin Xu, Ken, Chen, Yutong Lu, Weijiang Yu, Yuedong Yang^†.
  Nature Computational Science 2024 Nature Computational Science |
• Identifying Spatial Domain by Adapting Transcriptomics with Histology through Contrastive Learning Yuansong Zeng, Rui Yin, Mai Luo, Jianing Chen, Zixiang Pan, Yutong Lu, Weijiang Yu, Yuedong Yang^†.
  Briefings Bioinform 2023 BIB |
• Identifying B-cell epitopes using AlphaFold2 predicted structures and pretrained language model Yuansong Zeng, Zhuoyi Wei, Qianmu Yuan, Sheng Chen, Weijiang Yu, Yutong Lu, Jianzhao Gao^†, Yuedong Yang^†.
  Bioinformatics 2023 Bioinformatics |
• Accurately clustering single-cell RNA-seq data by capturing structural relations between cells through graph convolutional network Yuansong Zeng, Xiang Zhou, Jiahua Rao, Yutong Lu^†, Yuedong Yang^†.
  IEEE, International Conference on Bioinformatics and Biomedicine (BIBM) 2020 BIBM | code
• A robust and scalable graph neural network for accurate single-cell classification Yuansong Zeng,Zhuoyi Wei, Zixiang Pan, Yutong Lu, Yuedong Yang^†.
  Briefings Bioinform 2022 BIB |
• Spatial transcriptomics prediction from histology jointly through Transformer and graph neural networks Yuansong Zeng, Zhuoyi Wei, Weijiang Yu, Rui Yin, Yuchen Yuan, Bingling Li, Zhonghui Tang, Yutong Lu, Yuedong Yang^†.
  Briefings Bioinform 2022 BIB |
• A parameter-free deep embedded clustering method for single-cell RNA-seq data Yuansong Zeng, Zhuoyi Wei, Fengqi Zhong, Zixiang Pan, Yutong Lu, Yuedong Yang^†.
  Briefings Bioinform 2022 BIB |
• An efficient file system for hybrid in-memory nvm and block devices Yuansong Zeng, Edwin Hsing-Mean Sha, Qingfeng Zhuge, Xianzhang Chen, Zhulin Ma, Lin Wu.
  IEEE 7th Non-Volatile Memory Systems and Applications Symposium (NVMSA) 2018 NVMSA |
• scAdapt: virtual adversarial domain adaptation network for single cell RNA-seq data classification across platforms and species Xiang Zhou, Hua Chai, Yuansong Zeng, Huiying Zhao, Yuedong Yang^†.
  Briefings Bioinform 2021 BIB |
• SCdenoise: a reference-based scRNA-seq denoising method using semi-supervised learning Fengqi Zhong, Yuansong Zeng, Yubao Liu, Yuedong Yang^†.
  IEEE International Conference on Bioinformatics and Biomedicine (BIBM) 2022 BIBM |
• A Meta-learning based Graph-Hierarchical Clustering Method for Single Cell RNA-Seq Data Zixiang Pan, Yuansong Zeng, Yuefan Lin, Haokun Zhang, Weijiang Yu, Yuedong Yang^†.
  IEEE International Conference on Bioinformatics and Biomedicine (BIBM) 2022 BIBM |
• Efficient wear leveling for inodes of file systems on persistent memories Xianzhang Chen, Edwin Hsing-Mean Sha, Yuansong Zeng, Chaoshu Yang, Weiwen Jiang, Qingfeng Zhuge.
  Design, Automation & Test in Europe Conference & Exhibition (DATE) 2018 DATE |
† denotes corresponding author.