Xiaoyang Hou

Xiaoyang Hou

I am Xiaoyang Hou (侯晓阳 in Chinese) I am broadly focused on advanced deep learning techniques for unified biomolecule design methods and foundation models. I am passionate about developing new methods in biology and chemistry, particularly for computational drug design and discovery.

I have always embraced opportunities for collaboration and academic discussion—if my research resonates with you, or if you have questions to explore, please do not hesitate to reach out.

Publications

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GGFlow: A Graph Flow Matching Method with Efficient Optimal Transport. | [Code]
Xiaoyang Hou*, Tian Zhu*, Milong Ren, et al. (* equal contribution)
AIDrugX Workshop, Neural Information Processing Systems (NeurIPS) 2024
Transactions on Machine Learning Research (TMLR) 2025

We propose a discrete flow-matching generative model with efficient optimal transport for graphs, featuring an edge-augmented graph transformer for direct edge communications. We also introduces a novel goal-guided framework to control generation trajectories toward desired properties.

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GTAM: A Molecular Pretraining Model with Geometric Triangle Awareness. | [Code]
Xiaoyang Hou*, Tian Zhu*, Milong Ren*, et al. (* equal contribution)
Bioinformatics 2024
This method integrates innovative molecular encoders for 2D graphs and 3D conformations, accurately capturing geometric edge dependencies in molecular graphs. GTAM further employs two contrastive objectives to transfer edge information between 2D topology and 3D geometry, boosting encoder functionality.

EMNGly: predicting N-linked glycosylation sites using the language models for feature extraction. | [Code]
Xiaoyang Hou, Yu Wang, Dongbo Bu, Yaojun Wang, Shiwei Sun, et al. Bioinformatics, 2023.

DMSS: An Attention-based Deep Learning Model for High-Quality Mass Spectrometry Prediction.,
Yihui Ren, Yu Wang, Wenkai Han, Yikang Huang, Xiaoyang Hou, et al. Data Mining and Analytics, 2023.

Honors and Awards

  • 2025 Outstanding Student from the State Key Laboratory of Processor Chips, ICT
  • 2023, 2024 Outstanding Student Scholarship, ICT
  • 2021 Finalist Award in Mathematical Contest in Modeling (MCM)
  • 2021 Innovation Scholarship, SDU
  • 2020 Scholarship of Academic Excellence, SDU

Educations

  2022.09 - 2025.06, Master, Institute of Computing Technology, Chinese Academy of Sciences.
  2018.09 - 2022.06, Undergraduate, Department of Computer Science and Technology, Shandong University.

Internships