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Yijie Zhang

9 accepted papers

2026

h-MINT: Modeling Pocket-Ligand Binding with Hierarchical Molecular Interaction Network

ICLR 2026poster

Accurate molecular representations are critical for drug discovery, and a central challenge lies in capturing the chemical environment of molecular fragments, as key interactions, such as H-bond and π stacking—occur only under specific local conditions. Most existing approaches represent molecules a…

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2025

dyAb: Flow Matching for Flexible Antibody Design with AlphaFold-driven Pre-binding Antigen

AAAI 2025technical

The development of therapeutic antibodies heavily relies on accurate predictions of how antigens will interact with antibodies. Existing computational methods in antibody design often overlook crucial conformational changes that antigens undergo during the binding process, significantly impacting th…

2024

KW-Design: Pushing the Limit of Protein Design via Knowledge Refinement

ICLR 2024poster

Recent studies have shown competitive performance in protein inverse folding, while most of them disregard the importance of predictive confidence, fail to cover the vast protein space, and do not incorporate common protein knowledge. Given the great success of pretrained models on diverse protein-r…

2024

RDesign: Hierarchical Data-efficient Representation Learning for Tertiary Structure-based RNA Design

ICLR 2024poster

While artificial intelligence has made remarkable strides in revealing the relationship between biological macromolecules' primary sequence and tertiary structure, designing RNA sequences based on specified tertiary structures remains challenging. Though existing approaches in protein design have th…

2024

Realigning Confidence with Temporal Saliency Information for Point-Level Weakly-Supervised Temporal Action Localization

CVPR 2024poster

Point-level weakly-supervised temporal action localization (P-TAL) aims to localize action instances in untrimmed videos through the use of single-point annotations in each instance. Existing methods predict the class activation sequences without any boundary information and the unreliable sequences…

2024

Recursive PAC-Bayes: A Frequentist Approach to Sequential Prior Updates with No Information Loss

NeurIPS 2024spotlight

PAC-Bayesian analysis is a frequentist framework for incorporating prior knowledge into learning. It was inspired by Bayesian learning, which allows sequential data processing and naturally turns posteriors from one processing step into priors for the next. However, despite two and a half decades of…

2023

ProteinInvBench: Benchmarking Protein Inverse Folding on Diverse Tasks, Models, and Metrics

NeurIPS 2023poster

Protein inverse folding has attracted increasing attention in recent years. However, we observe that current methods are usually limited to the CATH dataset and the recovery metric. The lack of a unified framework for ensembling and comparing different methods hinders the comprehensive investigation…