• Associate Professor, Electrical & Computer Engineering
  • Affiliated Faculty, Computer Science and Engineering
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Yang Shen

Educational Background

  • Ph.D., Systems Engineering, Boston University – 2008
  • B.E., Automation, University of Science and Technology of China – 2002

Research Interests

  • Algorithms for modeling biological molecules, systems, and data.

    • Algorithms:
      • Optimization and machine learning
      • Systems and control
    • Applications:
      • Protein docking and protein & drug design
      • Systems and synthetic biology
      • Omics

Awards & Honors

  • Maximizing Investigators' Research Award (MIRA) for Early Stage Investigators, National Institute of General Medical Sciences, National Institutes of Health, 2017
  • Faculty Early Career Development (CAREER) Award, National Science Foundation, 2020

Selected Publications

  • Y You and Y Shen (2022). "Cross-Modality and Self-Supervised Protein Embedding for Compound-Protein Affinity and Contact Prediction", Bioinformatics 38(Supplement_2): ii68-ii74.
  • M Karimi, S Zhu, Y Cao, and Y Shen (2020). "De Novo Protein Design for Novel Folds using Guided Conditional Wasserstein Generative Adversarial Networks", Journal of Chemical Information and Modeling 60(12): 5667-5681.
  • Y Cao and Y Shen (2020). "Bayesian Active Learning for Optimization and Uncertainty Quantification in Protein Docking", Journal of Chemical Theory and Computation 16(8): 5334-5347.
  • Y You, T Chen, Z Wang and Y Shen (2019). "When Does Self-Supervision Help Graph Convolutional Networks?." International Conference on Machine Learning (ICML), pp. 10871-10880.
  • Y Cao, T Chen, Z Wang and Y Shen (2019). "Learning to Optimize in Swarms", Advances in Neural Information Processing Systems (NeurIPS) 32: 15018-15028.
  • M Karimi, D Wu, Z Wang and Y Shen (2019). "DeepAffinity: Interpretable Deep Learning of Compound-Protein Affinity through Unified Recurrent and Convolutional Neural Networks", Bioinformatics 35(18): 3329-3338.
  • M Karimi and Y Shen (2018). "iCFN: An Efficient Exact Algorithm for Multistate Protein Design", Bioinformatics 34(18): i811-i820.
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