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Zuobai Zhang

PhD - Université de Montréal
Supervisor
Jian Tang
Research Topics
Computational Biology
Graph Neural Networks
Molecular Modeling
Website
Google Scholar
GitHub

Publications

Metro: Memory-Enhanced Transformer for Retrosynthetic Planning via Reaction Tree
Songtao Liu
Zhitao Ying
Rex Ying
Zuobai Zhang
Peilin Zhao
Jian Tang
Lu Lin
Dinghao Wu
Retrosynthetic planning plays a critical role in drug discovery and organic chemistry. Starting from a target molecule as the root node, it … (see more)aims to find a complete reaction tree subject to the constraint that all leaf nodes belong to a set of starting materials. The multi-step reactions are crucial because they determine the flow chart in the production of the Organic Chemical Industry. However, existing datasets lack curation of tree-structured multi-step reactions, and fail to provide such reaction trees, limiting models’ understanding of organic molecule transformations. In this work, we first develop a benchmark curated for the retrosynthetic planning task, which consists of 124,869 reaction trees retrieved from the public USPTO-full dataset. On top of that, we propose Metro: Memory-Enhanced Transformer for RetrOsynthetic planning. Specifically, the dependency among molecules in the reaction tree is captured as context information for multi-step retrosynthesis predictions through transformers with a memory module. Extensive experiments show that Metro dramatically outperforms existing single-step retrosynthesis models by at least 10.7% in top-1 accuracy. The experiments demonstrate the superiority of exploiting context information in the retrosynthetic planning task. Moreover, the proposed model can be directly used for synthetic accessibility analysis, as it is trained on reaction trees with the shortest depths. Our work is the first step towards a brand new formulation for retrosynthetic planning in the aspects of data construction, model design, and evaluation. Code is available at https://github.com/SongtaoLiu0823/metro.
2022-01-01
arXiv.org (preprint)
doi.org
openreview.net
PEER: A Comprehensive and Multi-Task Benchmark for Protein Sequence Understanding
Minghao Xu
Zuobai Zhang
Jiarui Lu
Zhaocheng Zhu
Yang Zhang
Chang Ma
Runcheng Liu
Jian Tang
We are now witnessing significant progress of deep learning methods in a variety of tasks (or datasets) of proteins. However, there is a lac… (see more)k of a standard benchmark to evaluate the performance of different methods, which hinders the progress of deep learning in this field. In this paper, we propose such a benchmark called PEER, a comprehensive and multi-task benchmark for Protein sEquence undERstanding. PEER provides a set of diverse protein understanding tasks including protein function prediction, protein localization prediction, protein structure prediction, protein-protein interaction prediction, and protein-ligand interaction prediction. We evaluate different types of sequence-based methods for each task including traditional feature engineering approaches, different sequence encoding methods as well as large-scale pre-trained protein language models. In addition, we also investigate the performance of these methods under the multi-task learning setting. Experimental results show that large-scale pre-trained protein language models achieve the best performance for most individual tasks, and jointly training multiple tasks further boosts the performance. The datasets and source codes of this benchmark are all available at https://github.com/DeepGraphLearning/PEER_Benchmark
openreview.net