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Kangfei Zhao

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NeurIPS Conference 2025 Conference Paper

Model Editing for Vision Transformers

Xinyi Huang
Kangfei Zhao
Long-Kai Huang

Model editing offers a promising paradigm for efficiently and precisely updating knowledge in pre-trained transformers without costly retraining. While extensively studied in language models (LMs), model editing for vision transformers (ViTs) remains underexplored. Existing methods typically adapt LM-based techniques by modifying the multi-layer perceptron (MLP) modules, overlooking the unique characteristics of ViTs. In this work, we show that ViT predictions are more strongly influenced by the multi-head self-attention (MSA) modules than by the MLPs. Building on this observation, we propose a two-stage framework for editing ViTs. First, we identify which attention heads are most responsible for incorrect predictions. Next, we selectively remove the corresponding features to correct the model’s prediction. To further balance error correction with predictive stability on unrelated data, we learn a projection matrix that refines the image representations. Extensive experiments across multiple real-world datasets and model editing benchmarks demonstrate that our method consistently outperforms existing model editing methods for ViTs, achieving superior generalization and locality. Our code is available at https: //github. com/shanghxy/Model-editing-for-vision-transformers.

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JBHI Journal 2024 Journal Article

Equivariant Line Graph Neural Network for Protein-Ligand Binding Affinity Prediction

Yiqiang Yi
Xu Wan
Kangfei Zhao
Le Ou-Yang
Peilin Zhao

Binding affinity prediction of three-dimensional (3D) protein-ligand complexes is critical for drug repositioning and virtual drug screening. Existing approaches usually transform a 3D protein-ligand complex to a two-dimensional (2D) graph, and then use graph neural networks (GNNs) to predict its binding affinity. However, the node and edge features of the 2D graph are extracted based on invariant local coordinate systems of the 3D complex. As a result, these approaches can not fully learn the global information of the complex, such as the physical symmetry and the topological information of bonds. To address these issues, we propose a novel Equivariant Line Graph Network (ELGN) for binding affinity prediction of 3D protein-ligand complexes. The proposed ELGN firstly adds a super node to the 3D complex, and then builds a line graph based on the 3D complex. After that, ELGN uses a new E(3)-equivariant network layer to pass the messages between nodes and edges based on the global coordinate system of the 3D complex. Experimental results on two real datasets demonstrate the effectiveness of ELGN over several state-of-the-art baselines.

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NeurIPS Conference 2020 Conference Paper

Dirichlet Graph Variational Autoencoder

Jia Li
Jianwei Yu
Jiajin Li
Honglei Zhang
Kangfei Zhao
Yu Rong
Hong Cheng
Junzhou Huang

Graph Neural Networks (GNN) and Variational Autoencoders (VAEs) have been widely used in modeling and generating graphs with latent factors. However there is no clear explanation of what these latent factors are and why they perform well. In this work, we present Dirichlet Graph Variational Autoencoder (DGVAE) with graph cluster memberships as latent factors. Our study connects VAEs based graph generation and balanced graph cut, and provides a new way to understand and improve the internal mechanism of VAEs based graph generation. Specifically, we first interpret the reconstruction term of DGVAE as balanced graph cut in a principled way. Furthermore, motivated by the low pass characteristics in balanced graph cut, we propose a new variant of GNN named Heatts to encode the input graph into cluster memberships. Heatts utilizes the Taylor series for fast computation of Heat kernels and has better low pass characteristics than Graph Convolutional Networks (GCN). Through experiments on graph generation and graph clustering, we demonstrate the effectiveness of our proposed framework.

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