Publications

You can also find my articles on my Google Scholar profile.

16 CCF/CAAI-A 7 first-author, 2 co-first, 3 corr. author, 4 other author

10 CCF-B 4 first-author, 1 co-first, 2 corr. author, 3 other author

19 SCI Q1 6 first-author, 6 co-first, 0 corr. author, 7 other author

1118 Total Citations from Google Scholar

First / Co-First Author

Journal Articles

[1] Expanding the RNA Virus Universe by Deep Learning Discovery with Rider

Gaoyang Luo*, Zelin Zang*, et al., Nature Methods (Under Review), Top Journal, Co-first Author

[2] Single Cell Lineage Foundation Model

Zelin Zang, et al., Nature Machine Intelligence (Under Review), Top Journal, First Author

[3] Multi-center multi-omics integration predicts individualized prognosis in medullary thyroid carcinoma

Yan Zhou*, Yingrui Wang*, Xiao Shi*, Jiatong Wang*, Zelin Zang*, Likun Zhang*, Zhiqiang Gui, Xue Cai, Pingping Hu, Jiaxi Wang, Hanqing Liu, Zhihong Wang, Haixia Guan, Xiaohong Wu, Cenkai Shen, Yi He, Mo Li, Hao Zhang, Jianbiao Wang, Yijun Wu, Chuang Chen, Yi Zhu, Yaoting Sun, Zhiyan Liu, Yu Wang, Tiannan Guo, Nature Communications, 2026, SCI Q1, IF=15.7, Co-first Author

[4] MDTree: A Masked Dynamic Autoregressive Model for Phylogenetic Inference

Zelin Zang, Chenrui Duan, Siyuan Li, Jinlin Wu, BingoWing-Kuen Ling, Fuji Yang, Jiebo Luo, Zhen Lei, Stan Z. Li, Transactions on Machine Learning Research (TMLR), 2026, SCI Q1, First Author

[5] DMT-ME: MOE-Enhanced Explanable Deep Manifold Transformation for Complex Data Embedding and Visualization

Zelin Zang, Yuhao Wang, Jinlin Wu, Hong Liu, Yue Shen, Zhen Lei, Stan. Z Li, IEEE Transactions on Pattern Analysis and Machine Intelligence (TPAMI), 2026, CCF-A, IF=20, First Author

[6] The Dawn of Agentic EDA: A Survey of Autonomous Digital Chip Design

Zelin Zang, Yutong Song, Bingo Wing-Kuen Ling, Aoxiao Wang, Fuji Yang, arXiv preprint arXiv:2512.23189, 2025

[7] MuST: Advancing Unified Spatial Transcriptomics Multitask Analysis with Multimodal Structure Transformation

Zelin Zang, Liangyu Li, Yongjie Xu, Chenrui Duan, Yue Shen, Yi Sun, Zhen Lei, Stan Z. Li, Briefings in Bioinformatics, 2025, CCF-B, SCI Q1, AI4SCI, First Author

[8] Complex hierarchical structures analysis in single-cell data with Poincaré deep manifold transformation

Zelin Zang*, Yongjie Xu*, Bozhen Hu, Yue Yuan, Cheng Tan, Jun Xia, Stan Z. Li, Briefings in Bioinformatics, 2025, CCF-B, SCI Q1, AI4SCI, Co-first Author

[9] A review of artificial intelligence based biological-tree construction: Priorities, methods, applications and trends

Zelin Zang, Yongjie Xu, Chenrui Duan, Jinlin Wu, Stan Z. Li, Zhen Lei, Information Fusion, 2025, CCF-A, IF=15.6, First Author

[10] DMTEV: An Explainable Deep Network for Dimension Reduction

Zelin Zang, Shenghui Cheng, Hanchen Xia, Liangyu Li, Yaoting Sun, Yongjie Xu, Lei Shang, Baigui Sun, Stan Z. Li, IEEE Transactions on Visualization and Computer Graphics (TVCG), 2024, CCF-A, First Author

[11] UDRN: Unified Dimensional Reduction Neural Network for Feature Selection and Feature Projection

Zelin Zang, Yongjie Xu, Linyan Lu, Yulan Geng, Senqiao Yang, Stan Z. Li, Neural Networks, 2023, CCF-B, First Author

[12] Structure-preserving visualization for single-cell RNA-Seq profiles using deep manifold transformation with batch-correction

Yongjie Xu*, Zelin Zang*, Jun Xia, Cheng Tan, Yulan Geng, Stan Z. Li, Communications Biology, 2023, SCI Q1, IF=6.5, Co-first Author

[13] Artificial intelligence defines protein-based classification of thyroid nodules

Yaoting Sun*, Sathiyamoorthy Selvarajan*, Zelin Zang*, Wei Liu, Yi Zhu, Hao Zhang, Wanyuan Chen, Hao Chen, Lu Li, Xue Cai, Huanhuan Gao, Zhicheng Wu, Yongfu Zhao, Lirong Chen, Xiaodong Teng, Sangeeta Mantoo, Tony Kiat-Hon Lim, Bhuvaneswari Hariraman, Serene Yeow, Syed Muhammad Fahmy Alkaff, Sze Sing Lee, Guan Ruan, Qiushi Zhang, Tiansheng Zhu, Yifan Hu, Zhen Dong, Weigang Ge, Qi Xiao, Weibin Wang, Guangzhi Wang, Junhong Xiao, Yi He, Zhihong Wang, Wei Sun, Yuan Qin, Jiang Zhu, Xu Zheng, Linyan Wang, Xi Zheng, Kailun Xu, Yingkuan Shao, Shu Zheng, Kexin Liu, Ruedi Aebersold, Haixia Guan, Xiaohong Wu, Dingcun Luo, Wen Tian, Stan Ziqing Li, Oi Lian Kon, Narayanan Gopalakrishna Iyer, Tiannan Guo, Cell Discovery, 2022, SCI Q1, IF=38, Co-first Author

[14] Deep manifold embedding of attributed graphs

Zelin Zang, Siyuan Li, Di Wu, Jianzhu Guo, Yongjie Xu, Stan Z. Li, Neurocomputing, 2022, CCF-B, First Author

[15] Eleven routine clinical features predict COVID-19 severity uncovered by machine learning of longitudinal measurements

Kai Zhou*, Yaoting Sun*, Lu Li*, Zelin Zang*, Jing Wang, Jun Li, Junbo Liang, Fangfei Zhang, Qiushi Zhang, Weigang Ge, Li Yang, Hao Chen, Lu He, Xiaohong Wu, Mingfeng Pei, Hong Zhu, Junhong Xiao, Jinming Li, Sujie Cao, Han Yu, Dingcun Luo, Cheng Zhang, Yi Zhu, Baofu Chen, Stan Z. Li, Tiannan Guo, Computational and structural biotechnology journal, 2021, SCI Q1, IF=6, Co-first Author

[16] Markov-lipschitz deep learning

Stan Z. Li*, Zelin Zang*, Lirong Wu, arXiv preprint arXiv:2006.08256, 2020, Co-first Author

[17] Hybrid Deep Neural Network Scheduler for Job-Shop Problem Based on Convolution Two-Dimensional Transformation

Zelin Zang, Wanliang Wang, Yuhang Song, Linyan Lu, Weikun Li, Yule Wang, Yanwei Zhao, Computational intelligence and neuroscience, 2019, SCI Q2, First Author

Conference Papers

[18] A Medical Multimodal Diagnostic Framework Integrating Vision-Language Models and Logic Tree Reasoning

Zelin Zang, Wenyi Gu, Siqi Ma, Dan Yang, Yue Shen, Zhu Zhang, Guohui Fan, Wing-Kuen Ling, Fuji Yang, IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), 2026, CCF-B, First Author

[19] Learning Cell-Aware Hierarchical Multi-Modal Representations for Robust Molecular Modeling

Mengran Li*, Zelin Zang*, Wenbin Xing, Junzhou Chen, Ronghui Zhang, Jiebo Luo, Stan Z. Li, AAAI Conference on Artificial Intelligence (AAAI), 2026, CCF-A, Oral, Co-first Author

[20] Hierarchical Quantized Diffusion Based Tree Generation Method for Hierarchical Representation and Lineage Analysis

Zelin Zang, et al., ICLR 2026 (Under Review), CCF-A, First Author, Scores: 6,6,10

[21] PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation

Chenrui Duan*, Zelin Zang*, Siyuan Li, Yongjie Xu, Stan Z. Li, Neural Information Processing Systems (NeurIPS), 2024, CCF-A, Co-first Author

[22] DiffAug: Enhance Unsupervised Contrastive Learning with Domain-Knowledge-Free Diffusion-based Data Augmentation

Zelin Zang, Hao Luo, Kai Wang, Panpan Zhang, Fan Wang, Stan Li, Yang You, International Conference on Machine Learning (ICML), 2024, CCF-A, First Author

[23] Boosting Novel Category Discovery Over Domains with Soft Contrastive Learning and All in One Classifier

Zelin Zang, Lei Shang, Senqiao Yang, Fei Wang, Baigui Sun, Xuansong Xie, Stan Z. Li, International Conference on Computer Vision (ICCV), 2023, CCF-A, Oral, First Author

[24] DLME: Deep Local-flatness Manifold Embedding

Zelin Zang, Siyuan Li, Di Wu, Ge Wang, Kai Wang, Lei Shang, Baigui Sun, Hao Li, Stan Z. Li, European Conference on Computer Vision (ECCV), 2022, CCF-A, First Author

Corresponding Author

Journal Articles

[25] CellScout: Visual Analytics for Mining Biomarkers in Cell State Discovery

Rui Sheng, Zelin Zang, Jiachen Wang, Yan Luo, Zixin Chen, Yan Zhou, Shaolun Ruan, Huamin Qu, IEEE Transactions on Visualization and Computer Graphics (TVCG), 2026, CCF-A, Corresponding Author

[26] Deep Multimanifold Transformation-Based Multivariate Time Series Fault Detection

Hong Liu, Xiuxiu Qiu, Yiming Shi, Miao Xu, Zelin Zang, Zhen Lei, IEEE Transactions on Neural Networks and Learning Systems (TNNLS), 2025, CCF-B, Corresponding Author

Conference Papers

[27] Doloris: Dual Conditional Diffusion Implicit Bridges with Sparsity Masking Strategy for Unpaired Single-Cell Perturbation Estimation

Changxi Chi, Jun Xia, Yufei Huang, Zhuoli Ouyang, Cheng Tan, Yunfan Liu, Jingbo Zhou, Chang Yu, Liangyu Yuan, Siyuan Li, Zelin Zang, Stan Z. Li, International Conference on Learning Representations (ICLR), 2026, CCF-A, Poster, Corresponding Author

[28] MedLA: A Logic-Driven Multi-Agent Framework for Complex Medical Reasoning with Large Language Models

Siqi Ma, Jiajie Huang, Bolin Yang, Fan Zhang, Jinlin Wu, Yue Shen, Guohui Fan, Zhu Zhang, Zelin Zang, AAAI Conference on Artificial Intelligence (AAAI), 2026, CCF-A, Oral, Corresponding Author

[29] USD: Unsupervised Soft Contrastive Learning for Fault Detection in Multivariate Time Series

Hong Liu, Xiuxiu Qiu, Yiming Shi, Zelin Zang, IEEE ICASSP, 2025, CCF-B, Corresponding Author

Other Publications

Journal Articles

[30] UniSurg: A Video-Native Foundation Model for Universal Understanding of Surgical Videos

Jinlin Wu, Filip Holm, Chuang Chen, Aoxiao Wang, Yutong Hu, Xiangyu Ye, Zelin Zang, Miao Xu, Lei Zhou, Hongliang Liao, et al., arXiv preprint arXiv:2602.05638, 2026

[31] FGeneBERT: Function-driven pre-trained gene language model for metagenomics

Chenrui Duan, Zelin Zang, Yongjie Xu, Hang He, Siyuan Li, Zihan Liu, Zhen Lei, Ju-Sheng Zheng, Stan Z. Li, Briefings in Bioinformatics, 2025, CCF-B, SCI Q1, AI4SCI

[32] Neural network diffusion

Kai Wang, Dongwen Tang, Boya Zeng, Yida Yin, Zhaopan Xu, Yukun Zhou, Zelin Zang, Trevor Darrell, Zhuang Liu, Yang You, arXiv preprint arXiv:2402.13144, 2024

[33] The heterophilic graph learning handbook: Benchmarks, models, theoretical analysis, applications and challenges

Sitao Luan, Chenqing Hua, Qincheng Lu, Liheng Ma, Lirong Wu, Xinyu Wang, Minkai Xu, Xiao-Wen Chang, Zelin Zang, Doina Precup, Rex Ying, Stan Z. Li, Jian Tang, Guy Wolf, Stefanie Jegelka, arXiv preprint arXiv:2407.09618, 2024

[34] Protein structure and folding pathway prediction based on remote homologs recognition using PAthreader

Kailong Zhao, Yuhao Xia, Fujin Zhang, Zelin Zang, Stan Z. Li, Guijun Zhang, Communications biology, 2023, SCI Q1, IF=6.5

[35] Machine learning for predictive deployment of UAVs with multiple access

Feiyang Guo, Linyan Lu, Zelin Zang, Mohammad Shikh-Bahaei, IEEE Open Journal of the Communications Society, 2023, SCI Q1

[36] Align yourself: Self-supervised pre-training for fine-grained recognition via saliency alignment

Di Wu, Siyuan Li, Zelin Zang, Kai Wang, Lei Shang, Baigui Sun, Hao Li, Stan Z. Li, IEEE Transactions on Neural Networks and Learning Systems (TNNLS), 2023, SCI Q1 CCF-B

[37] Phenotype classification using proteome data in a data-independent acquisition tensor format

Fangfei Zhang, Shaoyang Yu, Lirong Wu, Zelin Zang, Xiao Yi, Jiang Zhu, Cong Lu, Ping Sun, Yaoting Sun, Sathiyamoorthy Selvarajan, Lirong Chen, Xiaodong Teng, Yongfu Zhao, Guangzhi Wang, Junhong Xiao, Shiang Huang, Oi Lian Kon, N. Gopalakrishna Iyer, Stan Z. Li, Zhongzhi Luan, Tiannan Guo, Journal of the American Society for Mass Spectrometry, 2020, SCI Q1

[38] Two-dimensional discrete feature based spatial attention CapsNet For sEMG signal recognition

Guoqi Chen, Wanliang Wang, Zheng Wang, Honghai Liu, Zelin Zang, Weikun Li, Applied Intelligence, 2020, CCF-C SCI Q2

[39] Precise control and prediction of the greenhouse growth environment of Dendrobium candidum

Jin-Ting Ding, Hang-Yao Tu, Ze-Lin Zang, Min Huang, Sheng-Jun Zhou, Computers and electronics in agriculture, 2018, SCI Q1

Zelin Zang

Publications

First / Co-First Author

Journal Articles

[1] Expanding the RNA Virus Universe by Deep Learning Discovery with Rider

[2] Single Cell Lineage Foundation Model

[3] Multi-center multi-omics integration predicts individualized prognosis in medullary thyroid carcinoma

[4] MDTree: A Masked Dynamic Autoregressive Model for Phylogenetic Inference

[5] DMT-ME: MOE-Enhanced Explanable Deep Manifold Transformation for Complex Data Embedding and Visualization

[6] The Dawn of Agentic EDA: A Survey of Autonomous Digital Chip Design

[7] MuST: Advancing Unified Spatial Transcriptomics Multitask Analysis with Multimodal Structure Transformation

[8] Complex hierarchical structures analysis in single-cell data with Poincaré deep manifold transformation

[9] A review of artificial intelligence based biological-tree construction: Priorities, methods, applications and trends

[10] DMTEV: An Explainable Deep Network for Dimension Reduction

[11] UDRN: Unified Dimensional Reduction Neural Network for Feature Selection and Feature Projection

[12] Structure-preserving visualization for single-cell RNA-Seq profiles using deep manifold transformation with batch-correction

[13] Artificial intelligence defines protein-based classification of thyroid nodules

[14] Deep manifold embedding of attributed graphs

[15] Eleven routine clinical features predict COVID-19 severity uncovered by machine learning of longitudinal measurements

[16] Markov-lipschitz deep learning

[17] Hybrid Deep Neural Network Scheduler for Job-Shop Problem Based on Convolution Two-Dimensional Transformation

Conference Papers

[18] A Medical Multimodal Diagnostic Framework Integrating Vision-Language Models and Logic Tree Reasoning

[19] Learning Cell-Aware Hierarchical Multi-Modal Representations for Robust Molecular Modeling

[20] Hierarchical Quantized Diffusion Based Tree Generation Method for Hierarchical Representation and Lineage Analysis

[21] PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation

[22] DiffAug: Enhance Unsupervised Contrastive Learning with Domain-Knowledge-Free Diffusion-based Data Augmentation

[23] Boosting Novel Category Discovery Over Domains with Soft Contrastive Learning and All in One Classifier

[24] DLME: Deep Local-flatness Manifold Embedding

Corresponding Author

Journal Articles

[25] CellScout: Visual Analytics for Mining Biomarkers in Cell State Discovery

[26] Deep Multimanifold Transformation-Based Multivariate Time Series Fault Detection

Conference Papers

[27] Doloris: Dual Conditional Diffusion Implicit Bridges with Sparsity Masking Strategy for Unpaired Single-Cell Perturbation Estimation

[28] MedLA: A Logic-Driven Multi-Agent Framework for Complex Medical Reasoning with Large Language Models

[29] USD: Unsupervised Soft Contrastive Learning for Fault Detection in Multivariate Time Series

Other Publications

Journal Articles

[30] UniSurg: A Video-Native Foundation Model for Universal Understanding of Surgical Videos

[31] FGeneBERT: Function-driven pre-trained gene language model for metagenomics

[32] Neural network diffusion

[33] The heterophilic graph learning handbook: Benchmarks, models, theoretical analysis, applications and challenges

[34] Protein structure and folding pathway prediction based on remote homologs recognition using PAthreader

[35] Machine learning for predictive deployment of UAVs with multiple access

[36] Align yourself: Self-supervised pre-training for fine-grained recognition via saliency alignment

[37] Phenotype classification using proteome data in a data-independent acquisition tensor format

[38] Two-dimensional discrete feature based spatial attention CapsNet For sEMG signal recognition

[39] Precise control and prediction of the greenhouse growth environment of Dendrobium candidum

Conference Papers

[40] ReGenHOI: Unifying Reconstruction and Generation for 3D Human–Object Interaction Understanding

[41] CDBridge: A Cross-omics Post-training Bridge Strategy for Context-aware Biological Modeling

[42] Departures: Distributional Transport for Single-Cell Perturbation Prediction with Neural Schrödinger Bridges

[43] Reconstructing 3D Hand-Instrument Interaction from a Single 2D Image in Medical Scenes

[44] DaCapo: Score Distillation as Stacked Bridge for Fast and High-quality 3D Editing

[45] Architecture-Agnostic Masked Image Modeling–From ViT back to CNN

[46] Generalized Clustering and Multi-Manifold Learning with Geometric Structure Preservation