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Zhang, Zuobai

  1. Neural Bellman-Ford Networks: A General Graph Neural Network Framework for Link Prediction
    2021/06/13 by Zhaocheng Zhu, Zuobai Zhang, Zhu, Zhaocheng +5 · 36 citations
    Computer Science · Physics and Astronomy · #Advanced Graph Neural Networks #Complex Network Analysis Techniques #FOS: Computer and information sciences #Machine Learning (cs.LG) #Topic Modeling
  2. Protein Representation Learning by Geometric Structure Pretraining
    2022/03/11 by Zuobai Zhang, Minghao Xu, Zhang, Zuobai +10 · 18 citations
    Biochemistry, Genetics and Molecular Biology · #Machine Learning in Bioinformatics #Protein Structure and Dynamics #Bioinformatics and Genomic Networks
  3. Proteina: Scaling Flow-based Protein Structure Generative Models
    2025/03/02 by Geffner, Tomas, Didi, Kieran, Zhang, Zuobai +8 · 38 citations
    #FOS: Computer and information sciences #Machine Learning (cs.LG)
  4. PEER: A Comprehensive and Multi-Task Benchmark for Protein Sequence Understanding
    2022/06/05 by Minghao Xu, Xu, Minghao, Zuobai Zhang +13 · 11 citations
    Biochemistry, Genetics and Molecular Biology · #FOS: Computer and information sciences #Genomics and Phylogenetic Studies #Machine Learning (cs.LG) #Machine Learning in Bioinformatics #Protein Structure and Dynamics
  5. Str2Str: A Score-based Framework for Zero-shot Protein Conformation Sampling
    2023/06/05 by Jiarui Lu, Lu, Jiarui, Bozitao Zhong +3 · 7 citations
    Biochemistry, Genetics and Molecular Biology · #Metabolomics and Mass Spectrometry Studies #Protein Structure and Dynamics
  6. Neural-Symbolic Models for Logical Queries on Knowledge Graphs
    2022/05/16 by Zhaocheng Zhu, Mikhail Galkin, Zhu, Zhaocheng +5 · 5 citations
    Computer Science · #Advanced Graph Neural Networks #Artificial Intelligence (cs.AI) #Bayesian Modeling and Causal Inference #FOS: Computer and information sciences #Machine Learning (cs.LG) #Topic Modeling
  7. Effects of Stubbornness on Opinion Dynamics
    2022/08/08 by Wanyue Xu, Xu, Wanyue, Liwang Zhu +7 · 4 citations
    Physics and Astronomy · Social Sciences · #Complex Network Analysis Techniques #FOS: Computer and information sciences #Opinion Dynamics and Social Influence #Social Media and Politics #Social and Information Networks (cs.SI)
  8. Evaluating representation learning on the protein structure universe
    2024/06/19 by Arian R. Jamasb, Jamasb, Arian R., Alex Morehead +19 · 6 citations
    Biochemistry, Genetics and Molecular Biology · #Biomolecules (q-bio.BM) #FOS: Biological sciences #FOS: Computer and information sciences #Genetics, Bioinformatics, and Biomedical Research #Machine Learning (cs.LG) #Machine Learning in Bioinformatics #Protein Structure and Dynamics
  9. TorchDrug: A Powerful and Flexible Machine Learning Platform for Drug Discovery
    2022/02/16 by Zhu, Zhaocheng, Shi, Chence, Zhang, Zuobai +12 · 3 citations
    #FOS: Computer and information sciences #Machine Learning (cs.LG)
  10. Multi-Scale Representation Learning for Protein Fitness Prediction
    2024/12/02 by Zhang, Zuobai, Notin, Pascal, Huang, Yining +5 · 7 citations
    #Biomolecules (q-bio.BM) #FOS: Biological sciences #FOS: Computer and information sciences #Machine Learning (cs.LG)
  11. La-Proteina: Atomistic Protein Generation via Partially Latent Flow Matching
    2025/07/13 by Tomas Geffner, Kieran Didi, Geffner, Tomas +15 · 13 citations
    Engineering · #Innovative Microfluidic and Catalytic Techniques Innovation
  12. FusionRetro: Molecule Representation Fusion via In-Context Learning for Retrosynthetic Planning
    2022/09/30 by Songtao Liu, Liu, Songtao, Tu, Zhengkai +13 · 3 citations
    Biochemistry, Genetics and Molecular Biology · Computer Science · Materials Science · #Biomolecules (q-bio.BM) #Chemical Physics (physics.chem-ph) #Chemical Synthesis and Analysis #Computational Drug Discovery Methods #FOS: Biological sciences #FOS: Computer and information sciences #FOS: Physical sciences #Machine Learning (cs.LG) #Machine Learning in Materials Science #Quantitative Methods (q-bio.QM)
  13. DiffPack: A Torsional Diffusion Model for Autoregressive Protein Side-Chain Packing
    2023/06/01 by Yangtian Zhan, Zhang, Yangtian, Zuobai Zhang +7 · 3 citations
    Biochemistry, Genetics and Molecular Biology · #Enzyme Production and Characterization #FOS: Biological sciences #FOS: Computer and information sciences #Machine Learning (cs.LG) #Protein Structure and Dynamics #Protein purification and stability #Quantitative Methods (q-bio.QM)
  14. Cell-ontology guided transcriptome foundation model
    2024/08/22 by Xinyu Yuan, Yuan, Xinyu, Zuobai Zhang +11 · 4 citations
    Biochemistry, Genetics and Molecular Biology · #Artificial Intelligence (cs.AI) #Bioinformatics and Genomic Networks #Biomedical Text Mining and Ontologies #FOS: Computer and information sciences #Gene expression and cancer classification #Machine Learning (cs.LG)
  15. A Systematic Study of Joint Representation Learning on Protein Sequences and Structures
    2023/03/11 by Zuobai Zhang, Zhang, Zuobai, Wang, Chuanrui +10 · 2 citations
    Biochemistry, Genetics and Molecular Biology · Materials Science · #FOS: Biological sciences #FOS: Computer and information sciences #Machine Learning (cs.LG) #Machine Learning in Bioinformatics #Machine Learning in Materials Science #Protein Structure and Dynamics #Quantitative Methods (q-bio.QM)
  16. Pre-Training Protein Encoder via Siamese Sequence-Structure Diffusion Trajectory Prediction
    2023/01/28 by Zuobai Zhang, Zhang, Zuobai, Minghao Xu +9 · 1 citation
    Biochemistry, Genetics and Molecular Biology · #FOS: Computer and information sciences #Machine Learning (cs.LG) #Machine Learning in Bioinformatics #Protein Structure and Dynamics #RNA and protein synthesis mechanisms
  17. Structure-Informed Protein Language Model
    2024/02/07 by Zhang, Zuobai, Lu, Jiarui, Chenthamarakshan, Vijil +3 · 1 citation
    #Biomolecules (q-bio.BM) #FOS: Biological sciences #FOS: Computer and information sciences #Machine Learning (cs.LG)
  18. Opinion Dynamics Incorporating Higher-Order Interactions
    2021/02/06 by Zuobai Zhang, Wanyue Xu, Zhang, Zuobai +5 · 1 citation
    Physics and Astronomy · #Complex Network Analysis Techniques #Computers and Society (cs.CY) #FOS: Computer and information sciences #Opinion Dynamics and Social Influence #Quantum many-body systems #Social and Information Networks (cs.SI)
  19. Means of Hitting Times for Random Walks on Graphs: Connections, Computation, and Optimization
    2024/12/15 by Haisong Xia, Wanyue Xu, Xia, Haisong +5 · 2 citations
    Computer Science · Physics and Astronomy · #Complex Network Analysis Techniques #Data Visualization and Analytics #FOS: Computer and information sciences #Graph Theory and Algorithms #Social and Information Networks (cs.SI)
  20. PDB-Struct: A Comprehensive Benchmark for Structure-based Protein Design
    2023/11/30 by Chuanrui Wang, Bozitao Zhong, Wang, Chuanrui +9 · 1 citation
    Biochemistry, Genetics and Molecular Biology · #FOS: Biological sciences #FOS: Computer and information sciences #Machine Learning (cs.LG) #Machine Learning in Bioinformatics #Microbial Metabolic Engineering and Bioproduction #Protein Structure and Dynamics #Quantitative Methods (q-bio.QM)