2026

[38] Zheng Zheng, Yuzhi Guo, Xiao Hu, Yuwei Miao, Hehuan Ma, Jean Gao and Junzhou Huang, "Heterogeneous Aligned Fusion for Survival Prediction with Missing Modalities", In Proc. of the Conference on Medical Imaging with Deep Learning, MIDL'26, Taipei, July 2026.

[37] Yinhao Wu, Hengrui Zhao, Haiqing Li, Wenliang Zhong, Hehuan Ma, Yuzhi Guo, Dan Nguyen, Daniel X. Yang, Steve B. Jiang and Junzhou Huang, "Guideline-Informed MLLM Reasoning for Pathology-Aware Post-Operative Prostate CTV Segmentation", In Proc. of the Conference on Medical Imaging with Deep Learning, MIDL'26, Taipei, July 2026.

[36] Saiyang Na, Feng Jiang, Qifeng Zhou, Wenliang Zhong, Thao M. Dang, Yuzhi Guo, Hehuan Ma, Chunyuan Li, Weizhi An and Junzhou Huang, "Hyperbolic Gramian Volumes for Multimodal Alignment", In Proc. of IEEE Conference on Computer Vision and Pattern Recognition, CVPR'26, Denver, Colorado, USA, June 2026.

[35] Wenliang Zhong, Rob Barton, Lucas Goncalves, Kushal Kumar, Feng Jiang, Hehuan Ma, Yuzhi Guo, Vidit Bansal, Karim Bouyarmane and Junzhou Huang, "Universal Guideline-Driven Image Clustering via a Hybrid LLM Agent", In Proc. of IEEE Conference on Computer Vision and Pattern Recognition, CVPR'26, Denver, Colorado, USA, June 2026.

[34] Feng Jiang, Amina Mollaysa, Hehuan Ma, Yuzhi Guo, Tommaso Mansi, Junzhou Huang, Mangal Prakash and Rui Liao, "GRAM-DTI: Adaptive Multimodal Representation Learning for Drug-Target Interaction Prediction", In Proc. of the Fourteenth International Conference on Learning Representations, ICLR'26, Rio de Janeiro, Brazil, April 2026.

[33] Jingquan Yan, Yuwei Miao, Lei Yu, Yuzhi Guo, Xue Xiao, Lin Xu and Junzhou Huang, "GenePheno: Interpretable Gene Knockout-Induced Phenotype Abnormality Prediction from Gene Sequences", In Proc. of the 40th Annual AAAI Conference on Artificial Intelligence, AAAI'26, Singapore, January 2026.

[32] Wenliang Zhong, Haiqing Li, Thao M. Dang, Feng Jiang, Hehuan Ma, Yuzhi Guo, Jean Gao and Junzhou Huang, "Learning from Guidelines: Structured Prompt Optimization for Expert Annotation Tasks", In Proc. of the 40th Annual AAAI Conference on Artificial Intelligence, AAAI'26, Singapore, January 2026.

[31] Yuzhi Guo, and Junzhou Huang. "Deep learning for protein secondary structure prediction." Deep Learning in Drug Design (2026): 233-263.

2025

[30] Jitendra Jonnagaddala, Miljana Shulajkovska, Anton Gradisek, Toni Jue, Qifeng Zhou, Yuzhi Guo, Jamil Chayeb, Rujiang Li, Jana Lipkvoa, Jakob Kather and Junzhou Huang, "Multi-modal Analysis of Whole Slide Images in Colorectal Cancer", NPJ Digital Medicine, 8.1 (2025): 719.

[29] Feng Jiang, Mangal Prakash, Hehuan Ma, Jianyuan Deng, Yuzhi Guo, Amina Mollaysa, Tommaso Mansi, Rui Liao and Junzhou Huang, "TRIDENT: Tri-Modal Molecular Representation Learning with Taxonomic Annotations and Local Correspondence", In Proc. of the 39th Annual Conference on Neural Information Processing Systems, NeurIPS'25, San Diego, CA, USA, December 2025.

[28] Wenliang Zhong, Rob Barton, Weizhi An, Feng Jiang, Hehuan Ma, Yuzhi Guo, Abhishek Dan, Shioulin Sam, Karim Bouyarmane and Junzhou Huang, "Zero-Shot Composed Image Retrieval via Dual-Stream Instruction-Aware Distillation", In Proc. of International Conference on Computer Vision, ICCV’25, Honolulu, Hawaii, October 2025.

[27] Haiqing Li, Yuzhi Guo, Feng Jiang, Thao Dang, Hehuan Ma, Qifeng Zhou, Jean Gao and Junzhou Huang, "Text-Guided Multi-Instance Learning for Scoliosis Screening via Gait Video Analysis", In Proc. of the 28th Annual International Conference on Medical Image Computing and Computer Assisted Intervention, MICCAI’25, Daejeon, Korea, September 2025.

[26] Thao Dang, Haiqing Li, Yuzhi Guo, Hehuan Ma, Feng Jiang, Yuwei Miao, Qifeng Zhou, Jean Gao and Junzhou Huang, "HAGE: Hierarchical Alignment Gene-Enhanced Pathology Representation Learning with Spatial Transcriptomics", In Proc. of the 28th Annual International Conference on Medical Image Computing and Computer Assisted Intervention, MICCAI’25, Daejeon, Korea, September 2025.

[25] Bing Song, Kaiwen Wang, Saiyang Na, Jia Yao, Farjana J. Fattah, Alexandra L Martin, Mitchell S. von Itzstein, Donghan M. Yang, Jialiang Liu, Yaming Xue, Chaoying Liang, Yuzhi Guo, Indu Raman, Chengsong Zhu, Jonathan E. Dowell, Jade Homsi, Sawsan Rashdan, Shengjie Yang, Mary E. Gwin, Tuoqi Wu, David Hsiehchen, Yvonne Gloria-McCutchen, Catherine Pei-ju Lu, Prithvi Raj, Xiaochen Bai, Jun Wang, Jose Conejo-Garcia, Yang Xie, Junzhou Huang*, David E. Gerber*, Tao Wang*, "Profiling Antigen Binding Affinity of B Cell Repertoires in Tumors by Deep Learning", Nature Cancer, To Appear.

[24] Saiyang Na, Yuzhi Guo, Feng Jiang, Hehuan Ma, Jean Gao and Junzhou Huang, "Segment Any Cell: A SAM-based Auto-prompting Fine-tuning Framework for Nuclei Segmentation", IEEE Transactions on Neural Networks and Learning Systems, To Appear.

[23] Thao M. Dang, Qifeng Zhou, Yuzhi Guo, Hehuan Ma, Saiyang Na, Thao Bich Dang, Jean Gao, and Junzhou Huang. "Abnormality-aware multimodal learning for WSI classification." Frontiers in Medicine 12 (2025): 1546452.

[22] Qifeng Zhou, Thao M Dang, Yuzhi Guo, Hehuan Ma, Wenliang Zhong, Saiyang Na, Jean Gao and Junzhou Huang, "Contrastive Pretraining for Computational Pathology With Visual Language Models", In Proc. of IEEE International Symposium on Biomedical Imaging, ISBI’25, Houston, Texas, USA, April 2025.

[21] Yuwei Miao, Yuzhi Guo, Hehuan Ma, Jingquan Yan, Feng Jiang, Rui Liao and Junzhou Huang, "GoBERT: Gene Ontology Graph Informed BERT for Universal Gene Function Prediction", In Proc. of the Thirty-Ninth AAAI Conference on Artificial Intelligence, AAAI’25, Philadelphia, Pennsylvania, USA, February 2025.

2024

[20] Feng Jiang, Yuzhi Guo, Hehuan Ma, Saiyang Na, Wenliang Zhong, Yi Han, Tao Wang and Junzhou Huang, "GTE: A Graph Learning Framework for Prediction of T-Cell Receptors and Epitopes Binding Specificity", Briefings in Bioinformatics, 25, no. 4, May, 2024

[19] Weizhi An, Yuzhi Guo, Yatao Bian, Hehuan Ma, Jinyu Yang, Chunyuan Li and Junzhou Huang, "Advancing DNA Language Models through Motif-Oriented Pre-training with MoDNA", Biomedinformatics, Volume 4, Number 2, pp.1556-1571, June 2024.

[18] Hehuan Ma, Feng Jiang, Yuzhi Guo and Junzhou Huang, "Towards Robust Self-training for Molecular Biology Prediction Tasks, Journal of Computational Biology, Volume 31, Issue 3, pp. 213-228, March 2024.

[17]Feng Jiang, Yuzhi Guo, Hehuan Ma, Saiyang Na, Weizhi An, Bing Song, Yi Han, Jean Gao, Tao Wang and Junzhou Huang, "AlphaEpi: Enhancing B Cell Epitope Prediction with AlphaFold 3", In Proc. of the 15th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, ACM BCB'24, Shenzhen, China, November 2024.

[16] Thao M. Dang, Yuzhi Guo, Hehuan Ma, Qifeng Zhou, Saiyang Na, Jean Gao and Junzhou Huang, "MFMF: Multiple Foundation Model Fusion Networks for Whole Slide Image Classification", In Proc. of the 15th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, ACM BCB'24, Shenzhen, China, November 2024.

[15] Qifeng Zhou, Wenliang Zhong, Yuzhi Guo, Michael Xiao, Hehuan Ma and Junzhou Huang, "PathM3: A Multimodal Multi-Task Multiple Instance Learning Framework for Whole Slide Image Classification and Captioning", In Proc. of the 27th Annual International Conference on Medical Image Computing and Computer Assisted Intervention, MICCAI’24, Marrakesh, Morocco, October 2024.

2023

[14] Wenliang Zhong, Hehuan Ma, Yu Rong, Yatao Bian, Long-Kai Huang, Yuzhi Guo, Peilin Zhao and Junzhou Huang, "CoSSL: A Context-based Semi-Supervised Framework for Molecular Property Prediction", ICML Workshop on Computational Biology, July 2023.

2022

[13] An, Weizhi, Yuzhi Guo, Yatao Bian, Hehuan Ma, Jinyu Yang, Chunyuan Li, and Junzhou Huang. "MoDNA: motif-oriented pre-training for DNA language model." In Proceedings of the 13th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, pp. 1-5. 2022.

[12] Ma, Hehuan, Feng Jiang, Yu Rong, Yuzhi Guo, and Junzhou Huang. "Robust self-training strategy for various molecular biology prediction tasks." In Proceedings of the 13th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, pp. 1-5. 2022.

[11] Yuzhi Guo, Jiaxiang Wu, Hehuan Ma, Sheng Wang, and Junzhou Huang. 2022. "Deep Ensemble Learning with Atrous Spatial Pyramid Networks for Protein Secondary Structure Prediction" Biomolecules 12, no. 6: 774. https://doi.org/10.3390/biom12060774

[10] Yuzhi Guo, Jiaxiang Wu, Hehuan Ma and Junzhou Huang, "Self-supervised Pretraining for Protein Embeddings Using Tertiary Structures", In Proc. of the Thirty-Sixth AAAI Conference on Artificial Intelligence, AAAI'22, Vancouver, Canada, February 2022.

2021

[9] Hehuan Ma, Yu Rong, Boyang Liu, Yuzhi Guo, Chaochao Yan, and Junzhou Huang, "Gradient-Norm Based Attentive Loss for Molecular Property Prediction”, In Proc. of IEEE International Conference on Bioinformatics and Biomedicine, BIBM’21, December 2021.

[8] Yang, Jinyu, Chunyuan Li, Weizhi An, Hehuan Ma, Yuzhi Guo, Yu Rong, Peilin Zhao, and Junzhou Huang. "Exploring Robustness of Unsupervised Domain Adaptation in Semantic Segmentation", In Proc. of International Conference on Computer Vision, ICCV'21, October 2021.

[7] Yuzhi Guo, Jiaxiang Wu, Hehuan Ma, Sheng Wang, and Junzhou Huang. "Comprehensive Study on Enhancing Low-Quality Position-Specific Scoring Matrix with Deep Learning for Accurate Protein Structure Property Prediction: Using Multiple Sequence Alignment Learning." Journal of Computational Biology 28, no. 4 (2021): 346-361.

[6] Yuzhi Guo, Jiaxiang Wu, Hehuan Ma, Sheng Wang, and Junzhou Huang. "EPTool: A New Enhancing PSSM Tool for Protein Secondary Structure Prediction." Journal of Computational Biology 28, no. 4 (2021): 362-364.

2020

[5] Yuzhi Guo, Jiaxiang Wu, Hehuan Ma, Jinyu Yang, Xinliang Zhu, and Junzhou Huang. "WeightAln: Weighted Homologous Alignment for Protein Structure Property Prediction." In 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 72-75. IEEE, 2020.

[4] Yuzhi Guo, Jiaxiang Wu, Hehuan Ma, Sheng Wang, and Junzhou Huang. "Protein Ensemble Learning with Atrous Spatial Pyramid Networks for Secondary Structure Prediction." In 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 17-22. IEEE, 2020.

[3] Yuzhi Guo, Jiaxiang Wu, Hehuan Ma, Sheng Wang, and Junzhou Huang. "Bagging msa learning: Enhancing low-quality pssm with deep learning for accurate protein structure property prediction." In International Conference on Research in Computational Molecular Biology (RECOMB), pp. 88-103. Springer, Cham, 2020.

[2] Ma, Hehuan, Chaochao Yan, Yuzhi Guo, Sheng Wang, Yuhong Wang, Hongmao Sun, and Junzhou Huang. "Improving Molecular Property Prediction on Limited Data with Deep Multi-Label Learning." In 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 2779-2784. IEEE, 2020.

2019

[1] Wang, Sheng, Yuzhi Guo, Yuhong Wang, Hongmao Sun, and Junzhou Huang. "SMILES-BERT: large scale unsupervised pre-training for molecular property prediction." In Proceedings of the 10th ACM international conference on bioinformatics, computational biology and health informatics (BCB), pp. 429-436. 2019.

NIH R01 grant of $3,136,243 for antigen-antibody interaction studies (a main contributor) 2025

Johnson & Johnson award of $200,000 for LLM based toxicity prediction (a main contributor) 2024

 CPRIT grant of $1,199,997 for TCRs and Neoantigens binding prediction (a main contributor) 2023