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Can Chen

PhD - McGill University
Supervisor
Co-supervisor

Publications

Importance-aware Co-teaching for Offline Model-based Optimization
Ye Yuan
Can Chen
Zixuan Liu
Willie Neiswanger
Offline model-based optimization aims to find a design that maximizes a property of interest using only an offline dataset, with application… (see more)s in robot, protein, and molecule design, among others. A prevalent approach is gradient ascent, where a proxy model is trained on the offline dataset and then used to optimize the design. This method suffers from an out-of-distribution issue, where the proxy is not accurate for unseen designs. To mitigate this issue, we explore using a pseudo-labeler to generate valuable data for fine-tuning the proxy. Specifically, we propose
Importance-aware Co-teaching for Offline Model-based Optimization
Ye Yuan
Can Chen
Zixuan Liu
Willie Neiswanger
Parallel-mentoring for Offline Model-based Optimization
Can Chen
Christopher Beckham
Zixuan Liu
Parallel-mentoring for Offline Model-based Optimization
Can Chen
Christopher Beckham
Zixuan Liu
We study offline model-based optimization to maximize a black-box objective function with a static dataset of designs and scores. These desi… (see more)gns encompass a variety of domains, including materials, robots, DNA sequences, and proteins. A common approach trains a proxy on the static dataset and performs gradient ascent to obtain new designs. However, this often results in poor designs due to the proxy inaccuracies for out-of-distribution designs. Recent studies indicate that (a) gradient ascent with a mean ensemble of proxies generally outperforms simple gradient ascent, and (b) a trained proxy provides weak ranking supervision signals for design selection. Motivated by (a) and (b), we propose
Bidirectional Learning for Offline Model-based Biological Sequence Design
Can Chen
Yingxue Zhang
Structure-aware protein self-supervised learning
Can Chen
Jingbo Zhou
Fan Wang
Dejing Dou
Structure-aware protein self-supervised learning
Can Chen
Jingbo Zhou
Fan Wang
Dejing Dou
Abstract Motivation Protein representation learning methods have shown great potential to many downstream tasks in biological applications. … (see more)A few recent studies have demonstrated that the self-supervised learning is a promising solution to addressing insufficient labels of proteins, which is a major obstacle to effective protein representation learning. However, existing protein representation learning is usually pretrained on protein sequences without considering the important protein structural information. Results In this work, we propose a novel structure-aware protein self-supervised learning method to effectively capture structural information of proteins. In particular, a graph neural network model is pretrained to preserve the protein structural information with self-supervised tasks from a pairwise residue distance perspective and a dihedral angle perspective, respectively. Furthermore, we propose to leverage the available protein language model pretrained on protein sequences to enhance the self-supervised learning. Specifically, we identify the relation between the sequential information in the protein language model and the structural information in the specially designed graph neural network model via a novel pseudo bi-level optimization scheme. We conduct experiments on three downstream tasks: the binary classification into membrane/non-membrane proteins, the location classification into 10 cellular compartments, and the enzyme-catalyzed reaction classification into 384 EC numbers, and these experiments verify the effectiveness of our proposed method. Availability and implementation The Alphafold2 database is available in https://alphafold.ebi.ac.uk/. The PDB files are available in https://www.rcsb.org/. The downstream tasks are available in https://github.com/phermosilla/IEConv\_proteins/tree/master/Datasets. The code of the proposed method is available in https://github.com/GGchen1997/STEPS_Bioinformatics.