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2025

Learning With Noisy Labels Over Imbalanced SubpopulationsMingcai Chen, Yu Zhao 0009, Bing He, Zongbo Han, JunZhou Huang, Bingzhe Wu, Jianhua Yao 0001. tnn, 36(4):6544-6555, April 2025. [doi]

Evaluation of T Cell Receptor Construction Methods from scRNA-Seq DataRuonan Tian, Zhejian Yu, Ziwei Xue, Jiaxin Wu, Lize Wu, Shuo Cai, Bing Gao, Bing He, Yu Zhao 0009, Jianhua Yao 0001, Linrong Lu, Wanlu Liu. gpb, 22(6), 2025. [doi]

Annotation-guided Protein Design with Multi-Level Domain AlignmentChaohao Yuan, Songyou Li, Geyan Ye, Yikun Zhang, Long-Kai Huang, Wenbing Huang 0001, Wei Liu 0005, Jianhua Yao 0001, Yu Rong 0001. kdd 2025: 1855-1866 [doi]

Atomas: Hierarchical Adaptive Alignment on Molecule-Text for Unified Molecule Understanding and GenerationYikun Zhang, Geyan Ye, Chaohao Yuan, Bo Han 0003, Long-Kai Huang, Jianhua Yao 0001, Wei Liu 0005, Yu Rong 0001. iclr 2025: [doi]

2024

Reply to: Deeper evaluation of a single-cell foundation modelFan Yang 0081, Fang Wang, Longkai Huang, Linjing Liu, JunZhou Huang, Jianhua Yao 0001. natmi, 6(12):1447-1450, 2024. [doi]

Deep Spatio-Temporal Network for Low-SNR Cryo-EM Movie Frame EnhancementXiaoya Chong, Howard Leung, Qing Li 0001, Jianhua Yao 0001, Niyun Zhou. tcbb, 21(5):1299-1310, September - October 2024. [doi]

Current opinions on large cellular modelsMinsheng Hao, Lei Wei, Fan Yang 0081, Jianhua Yao 0001, Christina V. Theodoris, Bo Wang 0044, Xin Li, Ge Yang 0002, Xuegong Zhang. quanbio, 12(4):433-443, 2024. [doi]

DePLM: Denoising Protein Language Models for Property OptimizationZeyuan Wang, Keyan Ding, Ming Qin, Xiaotong Li, Xiang Zhuang, Yu Zhao 0009, Jianhua Yao 0001, Qiang Zhang 0026, Huajun Chen. nips 2024: [doi]

Knowledge-aware Reinforced Language Models for Protein Directed EvolutionYuhao Wang, Qiang Zhang, Ming Qin, Xiang Zhuang, Xiaotong Li, Zhichen Gong, Zeyuan Wang, Yu Zhao 0009, Jianhua Yao 0001, Keyan Ding, Huajun Chen. icml 2024: [doi]

A Label Disambiguation-Based Multimodal Massive Multiple Instance Learning Approach for Immune Repertoire ClassificationFan Xu, Yu Zhao, Bingzhe Wu, Yueshan Huang, Qin Ren, Yang Xiao, Bing He, Jie Zheng, Jianhua Yao 0001. AAAI 2024: 16138-16146 [doi]

Relaxing Continuous Constraints of Equivariant Graph Neural Networks for Broad Physical Dynamics LearningZinan Zheng, Yang Liu 0165, Jia Li 0009, Jianhua Yao 0001, Yu Rong. kdd 2024: 4548-4558 [doi]

2023

A Noisy-Label-Learning Formulation for Immune Repertoire Classification and Disease-Associated Immune Receptor Sequence IdentificationMingcai Chen, Yu Zhao, Zhonghuang Wang, Bing He, Jianhua Yao 0001. IJCAI 2023: 4739-4747 [doi]

An Unsupervised Multispectral Image Registration Network for Skin DiseasesSonghui Diao, Wenxue Zhou, Chenchen Qin, Jun Liao, JunZhou Huang, Wenming Yang, Jianhua Yao 0001. miccai 2023: 720-729 [doi]

scMHNN: a novel hypergraph neural network for integrative analysis of single-cell epigenomic, transcriptomic and proteomic dataWei Li, Bin Xiang, Fan Yang, Yu Rong, Yanbin Yin, Jianhua Yao 0001, Han Zhang. bib, 24(6), September 2023. [doi]

Human-Machine Interactive Tissue Prototype Learning for Label-Efficient Histopathology Image SegmentationWentao Pan, Jiangpeng Yan, Hanbo Chen, Jiawei Yang, Zhe Xu, Xiu Li 0001, Jianhua Yao 0001. ipmi 2023: 679-691 [doi]

3D Shuffle-Mixer: An Efficient Context-Aware Vision Learner of Transformer-MLP Paradigm for Dense Prediction in Medical VolumeJianye Pang, Cheng Jiang 0001, Yihao Chen, Jianbo Chang, Ming Feng, Renzhi Wang, Jianhua Yao 0001. tmi, 42(5):1241-1253, May 2023. [doi]

IIB-MIL: Integrated Instance-Level and Bag-Level Multiple Instances Learning with Label Disambiguation for Pathological Image AnalysisQin Ren, Yu Zhao, Bing He, Bingzhe Wu, Sijie Mai, Fan Xu, Yueshan Huang, Yonghong He, JunZhou Huang, Jianhua Yao 0001. miccai 2023: 560-569 [doi]

Targeting tumor heterogeneity: multiplex-detection-based multiple instance learning for whole slide image classificationZhikang Wang, Yue Bi, Tong Pan, Xiaoyu Wang, Chris Bain, Richard Bassed, Seiya Imoto, Jianhua Yao 0001, Roger J. Daly, Jiangning Song. bioinformatics, 39(3), March 2023. [doi]

Surformer: An interpretable pattern-perceptive survival transformer for cancer survival prediction from histopathology whole slide imagesZhikang Wang, Qian Gao, Xiaoping Yi, Xinyu Zhang 0017, Yiwen Zhang, Daokun Zhang, Pietro Liò, Chris Bain, Richard Bassed, Shanshan Li, Yuming Guo, Seiya Imoto, Jianhua Yao 0001, Roger J. Daly, Jiangning Song. cmpb, 241:107733, November 2023. [doi]

Deep domain adversarial neural network for the deconvolution of cell type mixtures in tissue proteome profilingFang Wang, Fan Yang, Longkai Huang, Wei Li, Jiangning Song, Robin B. Gasser, Ruedi Aebersold, Guohua Wang, Jianhua Yao 0001. natmi, 5(11):1236-1249, October 2023. [doi]

Multimodal-AIR-BERT: A Multimodal Pre-trained Model for Antigen Specificity Prediction in Adaptive Immune ReceptorsYang Xiao, Yueshan Huang, Yu Zhao 0009, Fan Xu, Qin Ren, Bing He, Jianhua Yao 0001, Xiao Liu. bibm 2023: 69-75 [doi]

iAMPCN: a deep-learning approach for identifying antimicrobial peptides and their functional activitiesJing Xu, Fuyi Li, Chen Li 0021, Xudong Guo, Cornelia Landersdorfer, Hsin-Hui Shen, Anton Y. Peleg, Jian Li, Seiya Imoto, Jianhua Yao 0001, Tatsuya Akutsu, Jiangning Song. bib, 24(4), July 2023. [doi]

SC-AIR-BERT: a pre-trained single-cell model for predicting the antigen-binding specificity of the adaptive immune receptorYu Zhao, Xiaona Su, Weitong Zhang, Sijie Mai, Zhimeng Xu, Chenchen Qin, Rongshan Yu, Bing He, Jianhua Yao 0001. bib, 24(4), July 2023. [doi]

Interpretable artificial intelligence model for accurate identification of medical conditions using immune repertoireYu Zhao, Bing He, Zhimeng Xu, Yidan Zhang, Xuan Zhao, Zhi-an Huang, Fan Yang 0081, Liang Wang, Lei Duan, Jiangning Song, Jianhua Yao 0001. bib, 24(1), January 2023. [doi]

Standardized measurement of mid-surface shift of brain based on deep Hough transformWenxue Zhou, Chenchen Qin, Jianbo Chang, Yixun Liu, Yihao Chen, Ming Feng, Renzhi Wang, Wenming Yang, Jianhua Yao 0001. cmig, 108:102284, September 2023. [doi]

2022

scBERT as a large-scale pretrained deep language model for cell type annotation of single-cell RNA-seq dataFan Yang 0081, Wenchuan Wang, Fang Wang, Yuan Fang, Duyu Tang, JunZhou Huang, Hui Lu 0004, Jianhua Yao 0001. natmi, 4(10):852-866, October 2022. [doi]

Clarion is a multi-label problem transformation method for identifying mRNA subcellular localizationsYue Bi, Fuyi Li, Xudong Guo, Zhikang Wang, Tong Pan, Yuming Guo, Geoffrey I. Webb, Jianhua Yao 0001, Cangzhi Jia, Jiangning Song. bib, 23(6), 2022. [doi]

TreeMoCo: Contrastive Neuron Morphology Representation LearningHanbo Chen, Jiawei Yang, Daniel Maxim Iascone, Lijuan Liu, Lei He 0001, Hanchuan Peng, Jianhua Yao 0001. nips 2022: [doi]

Multimodal Dynamics: Dynamical Fusion for Trustworthy Multimodal ClassificationZongbo Han, Fan Yang, JunZhou Huang, Changqing Zhang, Jianhua Yao 0001. cvpr 2022: 20675-20685 [doi]

UMIX: Improving Importance Weighting for Subpopulation Shift via Uncertainty-Aware MixupZongbo Han, Zhipeng Liang, Fan Yang 0081, Liu Liu, Lanqing Li, Yatao Bian, Peilin Zhao, Bingzhe Wu, Changqing Zhang, Jianhua Yao 0001. nips 2022: [doi]

Integrating Prior Knowledge with Graph Encoder for Gene Regulatory Inference from Single-cell RNA-Seq DataJiawei Li, Fan Yang, Fang Wang, Yu Rong, Peilin Zhao, Shizhan Chen, Jianhua Yao 0001, Jijun Tang, Fei Guo 0001. bibm 2022: 102-107 [doi]

Automatic Brain Midline Surface Delineation on 3D CT Images With Intracranial HemorrhageDaSheng Wu, Haoming Li 0012, Jianbo Chang, Chenchen Qin, Yihao Chen, Yixun Liu, Qinghua Zhang, Bingsheng Huang, Ming Feng, Renzhi Wang, Jianhua Yao 0001. tmi, 41(9):2217-2227, 2022. [doi]

ConCL: Concept Contrastive Learning for Dense Prediction Pre-training in Pathology ImagesJiawei Yang, Hanbo Chen, Yuan Liang, JunZhou Huang, Lei He 0001, Jianhua Yao 0001. eccv 2022: 523-539 [doi]

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