Arrow Research search

Author name cluster

Tingyang Xu

Possible papers associated with this exact author name in Arrow. This page groups case-insensitive exact name matches and is not a full identity disambiguation profile.

29 papers
2 author rows

Possible papers

29

ICML Conference 2025 Conference Paper

IBCircuit: Towards Holistic Circuit Discovery with Information Bottleneck

  • Tian Bian
  • Yifan Niu
  • Chaohao Yuan
  • Chengzhi Piao
  • Bingzhe Wu
  • Long-Kai Huang
  • Yu Rong 0001
  • Tingyang Xu

Circuit discovery has recently attracted attention as a potential research direction to explain the non-trivial behaviors of language models. It aims to find the computational subgraphs, also known as circuits, within the model that are responsible for solving specific tasks. However, most existing studies overlook the holistic nature of these circuits and require designing specific corrupted activations for different tasks, which is inaccurate and inefficient. In this work, we propose an end-to-end approach based on the principle of Information Bottleneck, called IBCircuit, to holistically identify informative circuits. In contrast to traditional causal interventions, IBCircuit is an optimization framework for holistic circuit discovery and can be applied to any given task without tediously corrupted activation design. In both the Indirect Object Identification (IOI) and Greater-Than tasks, IBCircuit identifies more faithful and minimal circuits in terms of critical node components and edge components compared to recent related work.

Details

ICLR Conference 2025 Conference Paper

InversionGNN: A Dual Path Network for Multi-Property Molecular Optimization

  • Yifan Niu
  • Ziqi Gao
  • Tingyang Xu
  • Yang Liu 0165
  • Yatao An Bian
  • Yu Rong 0001
  • Junzhou Huang
  • Jia Li 0009

Exploring chemical space to find novel molecules that simultaneously satisfy multiple properties is crucial in drug discovery. However, existing methods often struggle with trading off multiple properties due to the conflicting or correlated nature of chemical properties. To tackle this issue, we introduce InversionGNN framework, an effective yet sample-efficient dual-path graph neural network (GNN) for multi-objective drug discovery. In the direct prediction path of InversionGNN, we train the model for multi-property prediction to acquire knowledge of the optimal combination of functional groups. Then the learned chemical knowledge helps the inversion generation path to generate molecules with required properties. In order to decode the complex knowledge of multiple properties in the inversion path, we propose a gradient-based Pareto search method to balance conflicting properties and generate Pareto optimal molecules. Additionally, InversionGNN is able to search the full Pareto front approximately in discrete chemical space. Comprehensive experimental evaluations show that InversionGNN is both effective and sample-efficient in various discrete multi-objective settings including drug discovery.

Details

ICML Conference 2025 Conference Paper

Large Language-Geometry Model: When LLM meets Equivariance

  • Zongzhao Li
  • Jiacheng Cen
  • Bing Su 0001
  • Tingyang Xu
  • Yu Rong 0001
  • Deli Zhao
  • Wenbing Huang 0001

Accurately predicting 3D structures and dynamics of physical systems is crucial in scientific applications. Existing approaches that rely on geometric Graph Neural Networks (GNNs) effectively enforce $\mathrm{E}(3)$-equivariance, but they often fail in leveraging extensive broader information. While direct application of Large Language Models (LLMs) can incorporate external knowledge, they lack the capability for spatial reasoning with guaranteed equivariance. In this paper, we propose EquiLLM, a novel framework for representing 3D physical systems that seamlessly integrates $\mathrm{E}(3)$-equivariance with LLM capabilities. Specifically, EquiLLM comprises four key components: geometry-aware prompting, an equivariant encoder, an LLM, and an equivariant adapter. Essentially, the LLM guided by the instructive prompt serves as a sophisticated invariant feature processor, while 3D directional information is exclusively handled by the equivariant encoder and adapter modules. Experimental results demonstrate that EquiLLM delivers significant improvements over previous methods across molecular dynamics simulation, human motion simulation, and antibody design, highlighting its promising generalizability.

Details

NeurIPS Conference 2025 Conference Paper

MOF-BFN: Metal-Organic Frameworks Structure Prediction via Bayesian Flow Networks

  • Rui Jiao
  • Hanlin Wu
  • Wenbing Huang
  • Yuxuan Song
  • Yawen Ouyang
  • Yu Rong
  • Tingyang Xu
  • Pengju Wang

Metal-Organic Frameworks (MOFs) have attracted considerable attention due to their unique properties including high surface area and tunable porosity, and promising applications in catalysis, gas storage, and drug delivery. Structure prediction for MOFs is a challenging task, as these frameworks are intrinsically periodic and hierarchically organized, where the entire structure is assembled from building blocks like metal nodes and organic linkers. To address this, we introduce MOF-BFN, a novel generative model for MOF structure prediction based on Bayesian Flow Networks (BFNs). Given the local geometry of building blocks, MOF-BFN jointly predicts the lattice parameters, as well as the positions and orientations of all building blocks within the unit cell. In particular, the positions are modelled in the fractional coordinate system to naturally incorporate the periodicity. Meanwhile, the orientations are modeled as unit quaternions sampled from learned Bingham distributions via the proposed Bingham BFN, enabling effective orientation generation on the 4D unit hypersphere. Experimental results demonstrate that MOF-BFN achieves state-of-the-art performance across multiple tasks, including structure prediction, geometric property evaluation, and de novo generation, offering a promising tool for designing complex MOF materials.

PDF Details

NeurIPS Conference 2025 Conference Paper

Non-stationary Equivariant Graph Neural Networks for Physical Dynamics Simulation

  • Chaohao Yuan
  • Maoji Wen
  • Ercan KURUOGLU
  • Yang Liu
  • Jia Li
  • Tingyang Xu
  • Deli Zhao
  • Hong Cheng

To enhance the generalization ability of graph neural networks (GNNs) in learning and simulation physical dynamics, a series of equivariant GNNs have been developed to incorporate the symmetric inductive bias. However, the existing methods do not take into account the non-stationarity nature of physical dynamics, where the joint distribution changes over time. Moreover, previous approaches for modeling non-stationary time series typically involve normalizing the data, which disrupts the symmetric assumption inherent in physical dynamics. To model the non-stationary physical dynamics while preserving the symmetric inductive bias, we introduce a Non-Stationary Equivariant Graph Neural Network (NS-EGNN) to capture the non-stationarity in physical dynamics while preserving the symmetric property of the model. Specifically, NS-EGNN employs Fourier Transform on segments of physical dynamics to extract time-varying frequency information from the trajectories. It then uses the first and second-order differences to mitigate non-stationarity, followed by pooling for future predictions. Through capturing varying frequency characteristics and alleviate the linear and quadric trend in the raw physical dynamics, NS-EGNN better models the temporal dependencies in the physical dynamics. NS-EGNN has been applied on various types of physical dynamics, including molecular, motion and protein dynamics. In various scenario, NS-EGNN consistently surpasses the performance of existing state-of-the-art algorithms, underscoring its effectiveness. The implementation of NS-EGNN is available at https: //github. com/MaojiWEN/NS-EGNN.

PDF Details

NeurIPS Conference 2025 Conference Paper

Universally Invariant Learning in Equivariant GNNs

  • Jiacheng Cen
  • Anyi Li
  • Ning Lin
  • Tingyang Xu
  • Yu Rong
  • Deli Zhao
  • Zihe Wang
  • Wenbing Huang

Equivariant Graph Neural Networks (GNNs) have demonstrated significant success across various applications. To achieve completeness---that is, the universal approximation property over the space of equivariant functions---the network must effectively capture the intricate multi-body interactions among different nodes. Prior methods attain this via deeper architectures, augmented body orders, or increased degrees of steerable features, often at high computational cost and without polynomial-time solutions. In this work, we present a theoretically grounded framework for constructing complete equivariant GNNs that is both efficient and practical. We prove that a complete equivariant GNN can be achieved through two key components: 1) a complete scalar function, referred to as the canonical form of the geometric graph; and 2) a full-rank steerable basis set. Leveraging this finding, we propose an efficient algorithm for constructing complete equivariant GNNs based on two common models: EGNN and TFN. Empirical results demonstrate that our model demonstrates superior completeness and excellent performance with only a few layers, thereby significantly reducing computational overhead while maintaining strong practical efficacy.

PDF Details

ICLR Conference 2024 Conference Paper

SEGNO: Generalizing Equivariant Graph Neural Networks with Physical Inductive Biases

  • Yang Liu 0165
  • Jiashun Cheng
  • Haihong Zhao
  • Tingyang Xu
  • Peilin Zhao
  • Fugee Tsung
  • Jia Li 0009
  • Yu Rong 0001

Graph Neural Networks (GNNs) with equivariant properties have emerged as powerful tools for modeling complex dynamics of multi-object physical systems. However, their generalization ability is limited by the inadequate consideration of physical inductive biases: (1) Existing studies overlook the continuity of transitions among system states, opting to employ several discrete transformation layers to learn the direct mapping between two adjacent states; (2) Most models only account for first-order velocity information, despite the fact that many physical systems are governed by second-order motion laws. To incorporate these inductive biases, we propose the Second-order Equivariant Graph Neural Ordinary Differential Equation (SEGNO). Specifically, we show how the second-order continuity can be incorporated into GNNs while maintaining the equivariant property. Furthermore, we offer theoretical insights into SEGNO, highlighting that it can learn a unique trajectory between adjacent states, which is crucial for model generalization. Additionally, we prove that the discrepancy between this learned trajectory of SEGNO and the true trajectory is bounded. Extensive experiments on complex dynamical systems including molecular dynamics and motion capture demonstrate that our model yields a significant improvement over the state-of-the-art baselines.

Details

IJCAI Conference 2024 Conference Paper

Towards Geometric Normalization Techniques in SE(3) Equivariant Graph Neural Networks for Physical Dynamics Simulations

  • Ziqiao Meng
  • Liang Zeng
  • Zixing Song
  • Tingyang Xu
  • Peilin Zhao
  • Irwin King

SE(3) equivariance is a fundamental property that is highly desirable to maintain in physical dynamics modeling. This property ensures neural outputs to remain robust when the inputs are translated or rotated. Recently, there have been several proposals for SE(3) equivariant graph neural networks (GNNs) that have shown promising results in simulating particle dynamics. However, existing works have neglected an important issue that current SE(3) equivariant GNNs cannot scale to large particle systems. Although some simple normalization techniques are already in use to stabilize the training dynamics of equivariant graph networks, they actually break the SE(3) equivariance of the architectures. In this work, we first show the numerical instability of training equivariant GNNs on large particle systems and then analyze some existing normalization strategies adopted in modern works. We propose a new normalization layer called GeoNorm, which can satisfy the SE(3) equivariance and simultaneously stabilize the training process. We conduct comprehensive experiments on N-body system simulation tasks with larger particle system sizes. The experimental results demonstrate that GeoNorm successfully preserves the SE(3) equivariance compared to baseline techniques and stabilizes the training dynamics of SE(3) equivariant GNNs on large systems.

PDF Details DOI

AAAI Conference 2023 Conference Paper

DrugOOD: Out-of-Distribution Dataset Curator and Benchmark for AI-Aided Drug Discovery – a Focus on Affinity Prediction Problems with Noise Annotations

  • Yuanfeng Ji
  • Lu Zhang
  • Jiaxiang Wu
  • Bingzhe Wu
  • Lanqing Li
  • Long-Kai Huang
  • Tingyang Xu
  • Yu Rong

AI-aided drug discovery (AIDD) is gaining popularity due to its potential to make the search for new pharmaceuticals faster, less expensive, and more effective. Despite its extensive use in numerous fields (e.g., ADMET prediction, virtual screening), little research has been conducted on the out-of-distribution (OOD) learning problem with noise. We present DrugOOD, a systematic OOD dataset curator and benchmark for AIDD. Particularly, we focus on the drug-target binding affinity prediction problem, which involves both macromolecule (protein target) and small-molecule (drug compound). DrugOOD offers an automated dataset curator with user-friendly customization scripts, rich domain annotations aligned with biochemistry knowledge, realistic noise level annotations, and rigorous benchmarking of SOTA OOD algorithms, as opposed to only providing fixed datasets. Since the molecular data is often modeled as irregular graphs using graph neural network (GNN) backbones, DrugOOD also serves as a valuable testbed for graph OOD learning problems. Extensive empirical studies have revealed a significant performance gap between in-distribution and out-of-distribution experiments, emphasizing the need for the development of more effective schemes that permit OOD generalization under noise for AIDD.

PDF Details DOI

AAAI Conference 2023 Conference Paper

Handling Missing Data via Max-Entropy Regularized Graph Autoencoder

  • Ziqi Gao
  • Yifan Niu
  • Jiashun Cheng
  • Jianheng Tang
  • Lanqing Li
  • Tingyang Xu
  • Peilin Zhao
  • Fugee Tsung

Graph neural networks (GNNs) are popular weapons for modeling relational data. Existing GNNs are not specified for attribute-incomplete graphs, making missing attribute imputation a burning issue. Until recently, many works notice that GNNs are coupled with spectral concentration, which means the spectrum obtained by GNNs concentrates on a local part in spectral domain, e.g., low-frequency due to oversmoothing issue. As a consequence, GNNs may be seriously flawed for reconstructing graph attributes as graph spectral concentration tends to cause a low imputation precision. In this work, we present a regularized graph autoencoder for graph attribute imputation, named MEGAE, which aims at mitigating spectral concentration problem by maximizing the graph spectral entropy. Notably, we first present the method for estimating graph spectral entropy without the eigen-decomposition of Laplacian matrix and provide the theoretical upper error bound. A maximum entropy regularization then acts in the latent space, which directly increases the graph spectral entropy. Extensive experiments show that MEGAE outperforms all the other state-of-the-art imputation methods on a variety of benchmark datasets.

PDF Details DOI

AAAI Conference 2023 Conference Paper

Human Mobility Modeling during the COVID-19 Pandemic via Deep Graph Diffusion Infomax

  • Yang Liu
  • Yu Rong
  • Zhuoning Guo
  • Nuo Chen
  • Tingyang Xu
  • Fugee Tsung
  • Jia Li

Non-Pharmaceutical Interventions (NPIs), such as social gathering restrictions, have shown effectiveness to slow the transmission of COVID-19 by reducing the contact of people. To support policy-makers, multiple studies have first modelled human mobility via macro indicators (e.g., average daily travel distance) and then study the effectiveness of NPIs. In this work, we focus on mobility modelling and, from a micro perspective, aim to predict locations that will be visited by COVID-19 cases. Since NPIs generally cause economic and societal loss, such a prediction benefits governments when they design and evaluate them. However, in real-world situations, strict privacy data protection regulations result in severe data sparsity problems (i.e., limited case and location information). To address these challenges and jointly model variables including a geometric graph, a set of diffusions and a set of locations, we propose a model named Deep Graph Diffusion Infomax (DGDI). We show the maximization of DGDI can be bounded by two tractable components: a univariate Mutual Information (MI) between geometric graph and diffusion representation, and a univariate MI between diffusion representation and location representation. To facilitate the research of COVID-19 prediction, we present two benchmarks that contain geometric graphs and location histories of COVID-19 cases. Extensive experiments on the two benchmarks show that DGDI significantly outperforms other competing methods.

PDF Details DOI

AAAI Conference 2023 Conference Paper

MDM: Molecular Diffusion Model for 3D Molecule Generation

  • Lei Huang
  • Hengtong Zhang
  • Tingyang Xu
  • Ka-Chun Wong

Molecule generation, especially generating 3D molecular geometries from scratch (i.e., 3D de novo generation), has become a fundamental task in drug design. Existing diffusion based 3D molecule generation methods could suffer from unsatisfactory performances, especially when generating large molecules. At the same time, the generated molecules lack enough diversity. This paper proposes a novel diffusion model to address those two challenges. First, interatomic relations are not included in molecules' 3D point cloud representations. Thus, it is difficult for existing generative models to capture the potential interatomic forces and abundant local constraints. To tackle this challenge, we propose to augment the potential interatomic forces and further involve dual equivariant encoders to encode interatomic forces of different strengths. Second, existing diffusion-based models essentially shift elements in geometry along the gradient of data density. Such a process lacks enough exploration in the intermediate steps of the Langevin dynamics. To address this issue, we introduce a distributional controlling variable in each diffusion/reverse step to enforce thorough explorations and further improve generation diversity. Extensive experiments on multiple benchmarks demonstrate that the proposed model significantly outperforms existing methods for both unconditional and conditional generation tasks. We also conduct case studies to help understand the physicochemical properties of the generated molecules. The codes are available at https://github.com/tencent-ailab/MDM.

PDF Details DOI

TMLR Journal 2023 Journal Article

Noise-robust Graph Learning by Estimating and Leveraging Pairwise Interactions

  • Xuefeng Du
  • Tian Bian
  • Yu Rong
  • Bo Han
  • Tongliang Liu
  • Tingyang Xu
  • Wenbing Huang
  • Yixuan Li

Teaching Graph Neural Networks (GNNs) to accurately classify nodes under severely noisy labels is an important problem in real-world graph learning applications, but is currently underexplored. Although pairwise training methods have demonstrated promise in supervised metric learning and unsupervised contrastive learning, they remain less studied on noisy graphs, where the structural pairwise interactions (PI) between nodes are abundant and thus might benefit label noise learning rather than the pointwise methods. This paper bridges the gap by proposing a pairwise framework for noisy node classification on graphs, which relies on the PI as a primary learning proxy in addition to the pointwise learning from the noisy node class labels. Our proposed framework PI-GNN contributes two novel components: (1) a confidence-aware PI estimation model that adaptively estimates the PI labels, which are defined as whether the two nodes share the same node labels, and (2) a decoupled training approach that leverages the estimated PI labels to regularize a node classification model for robust node classification. Extensive experiments on different datasets and GNN architectures demonstrate the effectiveness of PI-GNN, yielding a promising improvement over the state-of-the-art methods. Code is publicly available at https://github.com/TianBian95/pi-gnn.

PDF Details

ICLR Conference 2022 Conference Paper

Energy-Based Learning for Cooperative Games, with Applications to Valuation Problems in Machine Learning

  • Yatao An Bian
  • Yu Rong 0001
  • Tingyang Xu
  • Jiaxiang Wu 0001
  • Andreas Krause 0001
  • Junzhou Huang

Valuation problems, such as feature interpretation, data valuation and model valuation for ensembles, become increasingly more important in many machine learning applications. Such problems are commonly solved by well-known game-theoretic criteria, such as Shapley value or Banzhaf value. In this work, we present a novel energy-based treatment for cooperative games, with a theoretical justification by the maximum entropy framework. Surprisingly, by conducting variational inference of the energy-based model, we recover various game-theoretic valuation criteria through conducting one-step fixed point iteration for maximizing the mean-field ELBO objective. This observation also verifies the rationality of existing criteria, as they are all attempting to decouple the correlations among the players through the mean-field approach. By running fixed point iteration for multiple steps, we achieve a trajectory of the valuations, among which we define the valuation with the best conceivable decoupling error as the Variational Index. We prove that under uniform initializations, these variational valuations all satisfy a set of game-theoretic axioms. We experimentally demonstrate that the proposed Variational Index enjoys lower decoupling error and better valuation performance on certain synthetic and real-world valuation problems.

Details

NeurIPS Conference 2022 Conference Paper

Equivariant Graph Hierarchy-Based Neural Networks

  • Jiaqi Han
  • Wenbing Huang
  • Tingyang Xu
  • Yu Rong

Equivariant Graph neural Networks (EGNs) are powerful in characterizing the dynamics of multi-body physical systems. Existing EGNs conduct flat message passing, which, yet, is unable to capture the spatial/dynamical hierarchy for complex systems particularly, limiting substructure discovery and global information fusion. In this paper, we propose Equivariant Hierarchy-based Graph Networks (EGHNs) which consist of the three key components: generalized Equivariant Matrix Message Passing (EMMP), E-Pool and E-UnPool. In particular, EMMP is able to improve the expressivity of conventional equivariant message passing, E-Pool assigns the quantities of the low-level nodes into high-level clusters, while E-UnPool leverages the high-level information to update the dynamics of the low-level nodes. As their names imply, both E-Pool and E-UnPool are guaranteed to be equivariant to meet physic symmetry. Considerable experimental evaluations verify the effectiveness of our EGHN on several applications including multi-object dynamics simulation, motion capture, and protein dynamics modeling.

PDF Details

ICLR Conference 2022 Conference Paper

Equivariant Graph Mechanics Networks with Constraints

  • Wenbing Huang 0001
  • Jiaqi Han
  • Yu Rong 0001
  • Tingyang Xu
  • Fuchun Sun 0001
  • Junzhou Huang

Learning to reason about relations and dynamics over multiple interacting objects is a challenging topic in machine learning. The challenges mainly stem from that the interacting systems are exponentially-compositional, symmetrical, and commonly geometrically-constrained. Current methods, particularly the ones based on equivariant Graph Neural Networks (GNNs), have targeted on the first two challenges but remain immature for constrained systems. In this paper, we propose Graph Mechanics Network (GMN) which is combinatorially efficient, equivariant and constraint-aware. The core of GMN is that it represents, by generalized coordinates, the forward kinematics information (positions and velocities) of a structural object. In this manner, the geometrical constraints are implicitly and naturally encoded in the forward kinematics. Moreover, to allow equivariant message passing in GMN, we have developed a general form of orthogonality-equivariant functions, given that the dynamics of constrained systems are more complicated than the unconstrained counterparts. Theoretically, the proposed equivariant formulation is proved to be universally expressive under certain conditions. Extensive experiments support the advantages of GMN compared to the state-of-the-art GNNs in terms of prediction accuracy, constraint satisfaction and data efficiency on the simulated systems consisting of particles, sticks and hinges, as well as two real-world datasets for molecular dynamics prediction and human motion capture.

Details

NeurIPS Conference 2022 Conference Paper

Learning Neural Set Functions Under the Optimal Subset Oracle

  • Zijing Ou
  • Tingyang Xu
  • Qinliang Su
  • Yingzhen Li
  • Peilin Zhao
  • Yatao Bian

Learning set functions becomes increasingly important in many applications like product recommendation and compound selection in AI-aided drug discovery. The majority of existing works study methodologies of set function learning under the function value oracle, which, however, requires expensive supervision signals. This renders it impractical for applications with only weak supervisions under the Optimal Subset (OS) oracle, the study of which is surprisingly overlooked. In this work, we present a principled yet practical maximum likelihood learning framework, termed as EquiVSet, that simultaneously meets the following desiderata of learning neural set functions under the OS oracle: i) permutation invariance of the set mass function being modeled; ii) permission of varying ground set; iii) minimum prior and iv) scalability. The main components of our framework involve: an energy-based treatment of the set mass function, DeepSet-style architectures to handle permutation invariance, mean-field variational inference, and its amortized variants. Thanks to the delicate combination of these advanced architectures, empirical studies on three real-world applications (including Amazon product recommendation, set anomaly detection, and compound selection for virtual screening) demonstrate that EquiVSet outperforms the baselines by a large margin.

PDF Details

ICML Conference 2022 Conference Paper

Local Augmentation for Graph Neural Networks

  • Songtao Liu
  • Rex Ying
  • Hanze Dong
  • Lanqing Li
  • Tingyang Xu
  • Yu Rong 0001
  • Peilin Zhao
  • Junzhou Huang

Graph Neural Networks (GNNs) have achieved remarkable performance on graph-based tasks. The key idea for GNNs is to obtain informative representation through aggregating information from local neighborhoods. However, it remains an open question whether the neighborhood information is adequately aggregated for learning representations of nodes with few neighbors. To address this, we propose a simple and efficient data augmentation strategy, local augmentation, to learn the distribution of the node representations of the neighbors conditioned on the central node’s representation and enhance GNN’s expressive power with generated features. Local augmentation is a general framework that can be applied to any GNN model in a plug-and-play manner. It samples feature vectors associated with each node from the learned conditional distribution as additional input for the backbone model at each training iteration. Extensive experiments and analyses show that local augmentation consistently yields performance improvement when applied to various GNN architectures across a diverse set of benchmarks. For example, experiments show that plugging in local augmentation to GCN and GAT improves by an average of 3. 4% and 1. 6% in terms of test accuracy on Cora, Citeseer, and Pubmed. Besides, our experimental results on large graphs (OGB) show that our model consistently improves performance over backbones. Code is available at https: //github. com/SongtaoLiu0823/LAGNN.

Details

ICLR Conference 2021 Conference Paper

Graph Information Bottleneck for Subgraph Recognition

  • Junchi Yu
  • Tingyang Xu
  • Yu Rong 0001
  • Yatao An Bian
  • Junzhou Huang
  • Ran He 0001

Given the input graph and its label/property, several key problems of graph learning, such as finding interpretable subgraphs, graph denoising and graph compression, can be attributed to the fundamental problem of recognizing a subgraph of the original one. This subgraph shall be as informative as possible, yet contains less redundant and noisy structure. This problem setting is closely related to the well-known information bottleneck (IB) principle, which, however, has less been studied for the irregular graph data and graph neural networks (GNNs). In this paper, we propose a framework of Graph Information Bottleneck (GIB) for the subgraph recognition problem in deep graph learning. Under this framework, one can recognize the maximally informative yet compressive subgraph, named IB-subgraph. However, the GIB objective is notoriously hard to optimize, mostly due to the intractability of the mutual information of irregular graph data and the unstable optimization process. In order to tackle these challenges, we propose: i) a GIB objective based-on a mutual information estimator for the irregular graph data; ii) a bi-level optimization scheme to maximize the GIB objective; iii) a connectivity loss to stabilize the optimization process. We evaluate the properties of the IB-subgraph in three application scenarios: improvement of graph classification, graph interpretation and graph denoising. Extensive experiments demonstrate that the information-theoretic IB-subgraph enjoys superior graph properties.

Details

NeurIPS Conference 2021 Conference Paper

Not All Low-Pass Filters are Robust in Graph Convolutional Networks

  • Heng Chang
  • Yu Rong
  • Tingyang Xu
  • Yatao Bian
  • Shiji Zhou
  • Xin Wang
  • Junzhou Huang
  • Wenwu Zhu

Graph Convolutional Networks (GCNs) are promising deep learning approaches in learning representations for graph-structured data. Despite the proliferation of such methods, it is well known that they are vulnerable to carefully crafted adversarial attacks on the graph structure. In this paper, we first conduct an adversarial vulnerability analysis based on matrix perturbation theory. We prove that the low- frequency components of the symmetric normalized Laplacian, which is usually used as the convolutional filter in GCNs, could be more robust against structural perturbations when their eigenvalues fall into a certain robust interval. Our results indicate that not all low-frequency components are robust to adversarial attacks and provide a deeper understanding of the relationship between graph spectrum and robustness of GCNs. Motivated by the theory, we present GCN-LFR, a general robust co-training paradigm for GCN-based models, that encourages transferring the robustness of low-frequency components with an auxiliary neural network. To this end, GCN-LFR could enhance the robustness of various kinds of GCN-based models against poisoning structural attacks in a plug-and-play manner. Extensive experiments across five benchmark datasets and five GCN-based models also confirm that GCN-LFR is resistant to the adversarial attacks without compromising on performance in the benign situation.

PDF Details

IJCAI Conference 2021 Conference Paper

On Self-Distilling Graph Neural Network

  • Yuzhao Chen
  • Yatao Bian
  • Xi Xiao
  • Yu Rong
  • Tingyang Xu
  • Junzhou Huang

Recently, the teacher-student knowledge distillation framework has demonstrated its potential in training Graph Neural Networks (GNNs). However, due to the difficulty of training over-parameterized GNN models, one may not easily obtain a satisfactory teacher model for distillation. Furthermore, the inefficient training process of teacher-student knowledge distillation also impedes its applications in GNN models. In this paper, we propose the first teacher-free knowledge distillation method for GNNs, termed GNN Self-Distillation (GNN-SD), that serves as a drop-in replacement of the standard training process. The method is built upon the proposed neighborhood discrepancy rate (NDR), which quantifies the non-smoothness of the embedded graph in an efficient way. Based on this metric, we propose the adaptive discrepancy retaining (ADR) regularizer to empower the transferability of knowledge that maintains high neighborhood discrepancy across GNN layers. We also summarize a generic GNN-SD framework that could be exploited to induce other distillation strategies. Experiments further prove the effectiveness and generalization of our approach, as it brings: 1) state-of-the-art GNN distillation performance with less training cost, 2) consistent and considerable performance enhancement for various popular backbones.

PDF Details DOI

AAAI Conference 2020 Conference Paper

A Restricted Black-Box Adversarial Framework Towards Attacking Graph Embedding Models

  • Heng Chang
  • Yu Rong
  • Tingyang Xu
  • Wenbing Huang
  • Honglei Zhang
  • Peng Cui
  • Wenwu Zhu
  • Junzhou Huang

With the great success of graph embedding model on both academic and industry area, the robustness of graph embedding against adversarial attack inevitably becomes a central problem in graph learning domain. Regardless of the fruitful progress, most of the current works perform the attack in a white-box fashion: they need to access the model predictions and labels to construct their adversarial loss. However, the inaccessibility of model predictions in real systems makes the white-box attack impractical to real graph learning system. This paper promotes current frameworks in a more general and flexible sense – we demand to attack various kinds of graph embedding model with black-box driven. To this end, we begin by investigating the theoretical connections between graph signal processing and graph embedding models in a principled way and formulate the graph embedding model as a general graph signal process with corresponding graph filter. As such, a generalized adversarial attacker: GF-Attack is constructed by the graph filter and feature matrix. Instead of accessing any knowledge of the target classifiers used in graph embedding, GF-Attack performs the attack only on the graph filter in a black-box attack fashion. To validate the generalization of GF-Attack, we construct the attacker on four popular graph embedding models. Extensive experimental results validate the effectiveness of our attacker on several benchmark datasets. Particularly by using our attack, even small graph perturbations like one-edge flip is able to consistently make a strong attack in performance to different graph embedding models.

PDF Details

NeurIPS Conference 2020 Conference Paper

Deep Multimodal Fusion by Channel Exchanging

  • Yikai Wang
  • Wenbing Huang
  • Fuchun Sun
  • Tingyang Xu
  • Yu Rong
  • Junzhou Huang

Deep multimodal fusion by using multiple sources of data for classification or regression has exhibited a clear advantage over the unimodal counterpart on various applications. Yet, current methods including aggregation-based and alignment-based fusion are still inadequate in balancing the trade-off between inter-modal fusion and intra-modal processing, incurring a bottleneck of performance improvement. To this end, this paper proposes Channel-Exchanging-Network (CEN), a parameter-free multimodal fusion framework that dynamically exchanges channels between sub-networks of different modalities. Specifically, the channel exchanging process is self-guided by individual channel importance that is measured by the magnitude of Batch-Normalization (BN) scaling factor during training. The validity of such exchanging process is also guaranteed by sharing convolutional filters yet keeping separate BN layers across modalities, which, as an add-on benefit, allows our multimodal architecture to be almost as compact as a unimodal network. Extensive experiments on semantic segmentation via RGB-D data and image translation through multi-domain input verify the effectiveness of our CEN compared to current state-of-the-art methods. Detailed ablation studies have also been carried out, which provably affirm the advantage of each component we propose. Our code is available at https: //github. com/yikaiw/CEN.

PDF Details

ICLR Conference 2020 Conference Paper

DropEdge: Towards Deep Graph Convolutional Networks on Node Classification

  • Yu Rong 0001
  • Wenbing Huang 0001
  • Tingyang Xu
  • Junzhou Huang

Over-fitting and over-smoothing are two main obstacles of developing deep Graph Convolutional Networks (GCNs) for node classification. In particular, over-fitting weakens the generalization ability on small dataset, while over-smoothing impedes model training by isolating output representations from the input features with the increase in network depth. This paper proposes DropEdge, a novel and flexible technique to alleviate both issues. At its core, DropEdge randomly removes a certain number of edges from the input graph at each training epoch, acting like a data augmenter and also a message passing reducer. Furthermore, we theoretically demonstrate that DropEdge either reduces the convergence speed of over-smoothing or relieves the information loss caused by it. More importantly, our DropEdge is a general skill that can be equipped with many other backbone models (e.g. GCN, ResGCN, GraphSAGE, and JKNet) for enhanced performance. Extensive experiments on several benchmarks verify that DropEdge consistently improves the performance on a variety of both shallow and deep GCNs. The effect of DropEdge on preventing over-smoothing is empirically visualized and validated as well. Codes are released on~https://github.com/DropEdge/DropEdge.

Details

AAAI Conference 2020 Conference Paper

Rumor Detection on Social Media with Bi-Directional Graph Convolutional Networks

  • Tian Bian
  • Xi Xiao
  • Tingyang Xu
  • Peilin Zhao
  • Wenbing Huang
  • Yu Rong
  • Junzhou Huang

Social media has been developing rapidly in public due to its nature of spreading new information, which leads to rumors being circulated. Meanwhile, detecting rumors from such massive information in social media is becoming an arduous challenge. Therefore, some deep learning methods are applied to discover rumors through the way they spread, such as Recursive Neural Network (RvNN) and so on. However, these deep learning methods only take into account the patterns of deep propagation but ignore the structures of wide dispersion in rumor detection. Actually, propagation and dispersion are two crucial characteristics of rumors. In this paper, we propose a novel bi-directional graph model, named Bi-Directional Graph Convolutional Networks (Bi-GCN), to explore both characteristics by operating on both top-down and bottom-up propagation of rumors. It leverages a GCN with a top-down directed graph of rumor spreading to learn the patterns of rumor propagation; and a GCN with an opposite directed graph of rumor diffusion to capture the structures of rumor dispersion. Moreover, the information from source post is involved in each layer of GCN to enhance the influences from the roots of rumors. Encouraging empirical results on several benchmarks confirm the superiority of the proposed method over the state-of-the-art approaches.

PDF Details

NeurIPS Conference 2020 Conference Paper

Self-Supervised Graph Transformer on Large-Scale Molecular Data

  • Yu Rong
  • Yatao Bian
  • Tingyang Xu
  • Weiyang Xie
  • Ying Wei
  • Wenbing Huang
  • Junzhou Huang

How to obtain informative representations of molecules is a crucial prerequisite in AI-driven drug design and discovery. Recent researches abstract molecules as graphs and employ Graph Neural Networks (GNNs) for molecular representation learning. Nevertheless, two issues impede the usage of GNNs in real scenarios: (1) insufficient labeled molecules for supervised training; (2) poor generalization capability to new-synthesized molecules. To address them both, we propose a novel framework, GROVER, which stands for Graph Representation frOm self-superVised mEssage passing tRansformer. With carefully designed self-supervised tasks in node-, edge- and graph-level, GROVER can learn rich structural and semantic information of molecules from enormous unlabelled molecular data. Rather, to encode such complex information, GROVER integrates Message Passing Networks into the Transformer-style architecture to deliver a class of more expressive encoders of molecules. The flexibility of GROVER allows it to be trained efficiently on large-scale molecular dataset without requiring any supervision, thus being immunized to the two issues mentioned above. We pre-train GROVER with 100 million parameters on 10 million unlabelled molecules---the biggest GNN and the largest training dataset in molecular representation learning. We then leverage the pre-trained GROVER for molecular property prediction followed by task-specific fine-tuning, where we observe a huge improvement (more than 6% on average) from current state-of-the-art methods on 11 challenging benchmarks. The insights we gained are that well-designed self-supervision losses and largely-expressive pre-trained models enjoy the significant potential on performance boosting.

PDF Details

NeurIPS Conference 2019 Conference Paper

DTWNet: a Dynamic Time Warping Network

  • Xingyu Cai
  • Tingyang Xu
  • Jinfeng Yi
  • Junzhou Huang
  • Sanguthevar Rajasekaran

Dynamic Time Warping (DTW) is widely used as a similarity measure in various domains. Due to its invariance against warping in the time axis, DTW provides more meaningful discrepancy measurements between two signals than other dis- tance measures. In this paper, we propose a novel component in an artificial neural network. In contrast to the previous successful usage of DTW as a loss function, the proposed framework leverages DTW to obtain a better feature extraction. For the first time, the DTW loss is theoretically analyzed, and a stochastic backpropogation scheme is proposed to improve the accuracy and efficiency of the DTW learning. We also demonstrate that the proposed framework can be used as a data analysis tool to perform data decomposition.

PDF Details

AAAI Conference 2018 Conference Paper

Latent Sparse Modeling of Longitudinal Multi-Dimensional Data

  • Ko-Shin Chen
  • Tingyang Xu
  • Jinbo Bi

We propose a tensor-based approach to analyze multidimensional data describing sample subjects. It simultaneously discovers patterns in features and reveals past temporal points that have impact on current outcomes. The model coefficient, a k-mode tensor, is decomposed into a summation of k tensors of the same dimension. To accomplish feature selection, we introduce the tensor ‘latent LF, 1 norm’ as a grouped penalty in our formulation. Furthermore, the proposed model takes into account within-subject correlations by developing a tensor-based quadratic inference function. We provide an asymptotic analysis of our model when the sample size approaches to infinity. To solve the corresponding optimization problem, we develop a linearized block coordinate descent algorithm and prove its convergence for a fixed sample size. Computational results on synthetic datasets and real- file fMRI and EEG problems demonstrate the superior performance of the proposed approach over existing techniques.

PDF Details

ICML Conference 2015 Conference Paper

Multi-view Sparse Co-clustering via Proximal Alternating Linearized Minimization

  • Jiangwen Sun
  • Jin Lu 0001
  • Tingyang Xu
  • Jinbo Bi

When multiple views of data are available for a set of subjects, co-clustering aims to identify subject clusters that agree across the different views. We explore the problem of co-clustering when the underlying clusters exist in different subspaces of each view. We propose a proximal alternating linearized minimization algorithm that simultaneously decomposes multiple data matrices into sparse row and columns vectors. This approach is able to group subjects consistently across the views and simultaneously identify the subset of features in each view that are associated with the clusters. The proposed algorithm can globally converge to a critical point of the problem. A simulation study validates that the proposed algorithm can identify the hypothesized clusters and their associated features. Comparison with several latest multi-view co-clustering methods on benchmark datasets demonstrates the superior performance of the proposed approach.

Details
v2026.09.13