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Yizhou Sun

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57 papers
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57

AAAI Conference 2025 Conference Paper

Architecture-Aware Learning Curve Extrapolation via Graph Ordinary Differential Equation

  • Yanna Ding
  • Zijie Huang
  • Xiao Shou
  • Yihang Guo
  • Yizhou Sun
  • Jianxi Gao

Learning curve extrapolation predicts neural network performance from early training epochs and has been applied to accelerate AutoML, facilitating hyperparameter tuning and neural architecture search. However, existing methods typically model the evolution of learning curves in isolation, neglecting the impact of neural network (NN) architectures, which influence the loss landscape and learning trajectories. In this work, we explore whether incorporating neural network architecture improves learning curve modeling and how to effectively integrate this architectural information. Motivated by the dynamical system view of optimization, we propose a novel architecture-aware neural differential equation model to forecast learning curves continuously. We empirically demonstrate its ability to capture the general trend of fluctuating learning curves while quantifying uncertainty through variational parameters. Our model outperforms current state-of-the-art learning curve extrapolation methods and pure time-series modeling approaches for both MLP and CNN-based learning curves. Additionally, we explore the applicability of our method in Neural Architecture Search scenarios, such as training configuration ranking.

ICML Conference 2025 Conference Paper

Contradiction Retrieval via Contrastive Learning with Sparsity

  • Haike Xu
  • Zongyu Lin
  • Kai-Wei Chang 0001
  • Yizhou Sun
  • Piotr Indyk

Contradiction retrieval refers to identifying and extracting documents that explicitly disagree with or refute the content of a query, which is important to many downstream applications like fact checking and data cleaning. To retrieve contradiction argument to the query from large document corpora, existing methods such as similarity search and cross-encoder models exhibit different limitations. To address these challenges, we introduce a novel approach: SparseCL that leverages specially trained sentence embeddings designed to preserve subtle, contradictory nuances between sentences. Our method utilizes a combined metric of cosine similarity and a sparsity function to efficiently identify and retrieve documents that contradict a given query. This approach dramatically enhances the speed of contradiction detection by reducing the need for exhaustive document comparisons to simple vector calculations. We conduct contradiction retrieval experiments on Arguana, MSMARCO, and HotpotQA, where our method produces an average improvement of $11. 0%$ across different models. We also validate our method on downstream tasks like natural language inference and cleaning corrupted corpora. This paper outlines a promising direction for non-similarity-based information retrieval which is currently underexplored.

ICLR Conference 2025 Conference Paper

Do Contemporary Causal Inference Models Capture Real-World Heterogeneity? Findings from a Large-Scale Benchmark

  • Haining Yu
  • Yizhou Sun

We present unexpected findings from a large-scale benchmark study evaluating Conditional Average Treatment Effect (CATE) estimation algorithms. By running 16 modern CATE models across 43,200 datasets, we find that: (a) 62\% of CATE estimates have a higher Mean Squared Error (MSE) than a trivial zero-effect predictor, rendering them ineffective; (b) in datasets with at least one useful CATE estimate, 80\% still have higher MSE than a constant-effect model; and (c) Orthogonality-based models outperform other models only 30\% of the time, despite widespread optimism about their performance. These findings expose significant limitations in current CATE models and suggest ample opportunities for further research. Our findings stem from a novel application of \textit{observational sampling}, originally developed to evaluate Average Treatment Effect (ATE) estimates from observational methods with experiment data. To adapt observational sampling for CATE evaluation, we introduce a statistical parameter, $Q$, equal to MSE minus a constant and preserves the ranking of models by their MSE. We then derive a family of sample statistics, collectively called $\hat{Q}$, that can be computed from real-world data. We prove that $\hat{Q}$ is a consistent estimator of $Q$ under mild technical conditions. When used in observational sampling, $\hat{Q}$ is unbiased and asymptotically selects the model with the smallest MSE. To ensure the benchmark reflects real-world heterogeneity, we handpick datasets where outcomes come from field rather than simulation. By combining the new observational sampling method, new statistics, and real-world datasets, the benchmark provides a unique perspective on CATE estimator performance and uncover gaps in capturing real-world heterogeneity.

NeurIPS Conference 2025 Conference Paper

Don’t Forget the Enjoin: FocalLoRA for Instruction Hierarchical Alignment in Large Language Models

  • Zitong Shi
  • Frank Wan
  • Haixin Wang
  • Ruoyan Li
  • Zijie Huang
  • Wanjia Zhao
  • Yijia Xiao
  • Xiao Luo

Recent studies reveal that large language models (LLMs) often struggle to resolve conflicting instructions embedded within hierarchical prompts, resulting in decreased compliance with system-level directives and compromising the reliability of safety-critical applications. While earlier approaches attempt to improve instruction hierarchy awareness through prompt engineering or embedding-level modifications, they typically lack structural modeling and either offer limited gains or require extensive fine-tuning. In this work, we introduce $\textbf{FocalLoRA}$, a parameter-efficient and structure-aware framework that strengthens hierarchical instruction adherence by selectively optimizing structurally critical attention heads, referred to as $\textit{focal heads}$, which exhibit heightened sensitivity to instruction conflicts. Experiments across multiple models and a dedicated benchmark demonstrate that FocalLoRA markedly enhances system instruction compliance with minimal tuning cost. For instance, on Llama-8B, fine-tuning only 0. 0188\% of parameters yields a 35. 52\% $\uparrow$ in system instruction compliance.

AAAI Conference 2025 Conference Paper

Dynamic-Width Speculative Beam Decoding for LLM Inference

  • Zongyue Qin
  • Zifan He
  • Neha Prakriya
  • Jason Cong
  • Yizhou Sun

Large language models (LLMs) based on transformer architecture have shown outstanding performance across numerous real-world tasks. However, the autoregressive nature of these models makes the inference process slow and costly. Speculative decoding has emerged as a promising solution, leveraging a smaller auxiliary model to draft future tokens, which are then validated simultaneously by the larger model, achieving a speed-up of 1-2x. Although speculative decoding matches the same distribution as multinomial sampling, multinomial sampling itself is prone to suboptimal outputs, where as beam sampling is widely recognized for producing higher-quality results by maintaining multiple candidate sequences at each step. This paper explores the novel integration of speculative decoding with beam sampling. However, there are four key challenges: (1) how to generate multiple sequences from the larger model's distribution given drafts sequences from the small model; (2) how to dynamically optimize the number of beams to balance efficiency and accuracy; (3) how to efficiently verify the multiple drafts in parallel; and (4) how to address the extra memory costs inherent in beam sampling. To address these challenges, we propose dynamic-width speculative beam decoding (DSBD). Specifically, we first introduce a novel draft and verification scheme that generates multiple sequences following the large model's distribution based on beam sampling trajectories from the small model. Then, we introduce an adaptive mechanism to dynamically tune the number of beams based on the context, optimizing efficiency and effectiveness. Besides, we extend tree-based parallel verification to handle multiple trees simultaneously, accelerating the verification process. Finally, we illustrate a simple modification to our algorithm to mitigate the memory overhead of beam sampling. Experimental results show that our approach achieves a 1.5-1.9x speed-up and1.8-2.5x lower energy consumption compared to beam sampling, with no loss in downstream performance. Moreover, it can produce significantly higher-quality outputs than speculative decoding, while maintaining similar time, memory, and energy costs. In summary, our method offers a more efficient and effective inference process for LLMs.

NeurIPS Conference 2025 Conference Paper

Flow Field Reconstruction with Sensor Placement Policy Learning

  • Ruoyan Li
  • Frank Wan
  • Zijie Huang
  • Zixiao Liu
  • Haixin Wang
  • Xiao Luo
  • Wei Wang
  • Yizhou Sun

Flow‐field reconstruction from sparse sensor measurements remains a central challenge in modern fluid dynamics, as the need for high‐fidelity data often conflicts with practical limits on sensor deployment. Existing deep learning–based methods have demonstrated promising results, but they typically depend on simplifying assumptions such as two‐dimensional domains, predefined governing equations, synthetic datasets derived from idealized flow physics, and unconstrained sensor placement. In this work, we address these limitations by studying flow reconstruction under realistic conditions and introducing a \emph{directional transport‐aware Graph Neural Network (GNN)} that explicitly encodes both flow directionality and information transport. We further show that conventional sensor placement strategies frequently yield suboptimal configurations. To overcome this, we propose a novel \emph{Two‐Step Constrained PPO} procedure for Proximal Policy Optimization (PPO), which jointly optimizes sensor layouts by incorporating flow variability and accounts for reconstruction model's performance disparity with respect to sensor placement. We conduct comprehensive experiments under realistic assumptions to benchmark the performance of our reconstruction model and sensor placement policy. Together, they achieve significant improvements over existing methods.

TMLR Journal 2025 Journal Article

Graph Fourier Neural ODEs: Modeling Spatial-temporal Multi-scales in Molecular Dynamics

  • Fang Sun
  • Zijie Huang
  • Haixin Wang
  • Huacong Tang
  • Xiao Luo
  • Wei Wang
  • Yizhou Sun

Accurately predicting long-horizon molecular dynamics (MD) trajectories remains a significant challenge, as existing deep learning methods often struggle to retain fidelity over extended simulations. We hypothesize that one key factor limiting accuracy is the difficulty of capturing interactions that span distinct spatial and temporal scales—ranging from high-frequency local vibrations to low-frequency global conformational changes. To address these limitations, we propose **Graph Fourier Neural ODEs (GF-NODE)**, integrating a graph Fourier transform for spatial frequency decomposition with a Neural ODE framework for continuous-time evolution. Specifically, GF-NODE first decomposes molecular configurations into multiple spatial frequency modes using the graph Laplacian, then evolves the frequency components in time via a learnable Neural ODE module that captures both local and global dynamics, and finally reconstructs the updated molecular geometry through an inverse graph Fourier transform. By explicitly modeling high- and low-frequency phenomena in this unified pipeline, GF-NODE more effectively captures long-range correlations and local fluctuations alike. We provide theoretical insight through heat equation analysis on a simplified diffusion model, demonstrating how graph Laplacian eigenvalues can determine temporal dynamics scales, and crucially validate this correspondence through comprehensive empirical analysis on real molecular dynamics trajectories showing quantitative spatial-temporal correlations across diverse molecular systems. Experimental results on challenging MD benchmarks, including MD17 and alanine dipeptide, demonstrate that GF-NODE achieves state-of-the-art accuracy while preserving essential geometrical features over extended simulations. These findings highlight the promise of bridging spectral decomposition with continuous-time modeling to improve the robustness and predictive power of MD simulations. Our implementation is publicly available at https://github.com/FrancoTSolis/GF-NODE-code.

AAAI Conference 2025 Conference Paper

Hierarchical Mixture of Experts: Generalizable Learning for High-Level Synthesis

  • Weikai Li
  • Ding Wang
  • Zijian Ding
  • Atefeh Sohrabizadeh
  • Zongyue Qin
  • Jason Cong
  • Yizhou Sun

High-level synthesis (HLS) is a widely used tool in designing Field Programmable Gate Array (FPGA). HLS enables FPGA design with software programming languages by compiling the source code into an FPGA circuit. The source code includes a program (called ``kernel'') and several pragmas that instruct hardware synthesis, such as parallelization, pipeline, etc. While it is relatively easy for software developers to design the program, it heavily relies on hardware knowledge to design the pragmas, posing a big challenge for software developers. Recently, different machine learning algorithms, such as GNNs, have been proposed to automate the pragma design via performance prediction. However, when applying the trained model on new kernels, the significant domain shift often leads to unsatisfactory performance. We propose a more domain-generalizable model structure: a two-level hierarchical Mixture of Experts (MoE), that can be flexibly adapted to any GNN model. Different expert networks can learn to deal with different regions in the representation space, and they can utilize similar patterns between the old kernels and new kernels. In the low-level MoE, we apply MoE on three natural granularities of a program: node, basic block, and graph. The high-level MoE learns to aggregate the three granularities for the final decision. To stably train the hierarchical MoE, we further propose a two-stage training method. Extensive experiments verify the effectiveness of the hierarchical MoE.

ICLR Conference 2025 Conference Paper

Mixture of In-Context Prompters for Tabular PFNs

  • Derek Qiang Xu
  • F. Olcay Cirit
  • Reza Asadi
  • Yizhou Sun
  • Wei Wang 0010

Recent benchmarks find In-Context Learning (ICL) outperforms both deep learning and tree-based algorithms on small tabular datasets. However, on larger datasets, ICL for tabular learning suffers in both efficiency and effectiveness. In terms of efficiency, transformers incur linear space and quadratic time complexity w.r.t. context size. In terms of effectiveness, contexts at inference encounter distribution shift compared to contexts from pretraining. We propose MixturePFN, which extends Sparse Mixture of Experts to the state-of-the-art ICL for tabular learning model. Specifically, MixturePFN finetunes a specialized ICL expert on each cluster of tabular data and routes new test samples to appropriate experts at inference. MixturePFN supports constant-size contexts by splitting large training datasets into more manageable clusters. MixturePFN addresses distribution shift by finetuning an expert on each training dataset cluster via bootstrapping. Extensive experimental results shows MixturePFN outperforms 19 baselines both in mean rank and as the Condorcet winner across 36 diverse tabular datasets under both accuracy and F1 score with statistical significance.

ICLR Conference 2025 Conference Paper

Optimized Multi-Token Joint Decoding With Auxiliary Model for LLM Inference

  • Zongyue Qin
  • Ziniu Hu
  • Zifan He
  • Neha Prakriya
  • Jason Cong
  • Yizhou Sun

Large language models (LLMs) have achieved remarkable success across diverse tasks, yet their inference processes are hindered by substantial time and energy demands due to single-token generation at each decoding step. While previous methods such as speculative decoding mitigate these inefficiencies by producing multiple tokens per step, each token is still generated by its single-token distribution, thereby enhancing speed without improving effectiveness. In contrast, our work simultaneously enhances inference speed and improves the output effectiveness. We consider multi-token joint decoding (MTJD), which generates multiple tokens from their joint distribution at each iteration, theoretically reducing perplexity and enhancing task performance. However, MTJD suffers from the high cost of sampling from the joint distribution of multiple tokens. Inspired by speculative decoding, we introduce multi-token assisted decoding (MTAD), a novel framework designed to accelerate MTJD. MTAD leverages a smaller auxiliary model to approximate the joint distribution of a larger model, incorporating a verification mechanism that not only ensures the accuracy of this approximation, but also improves the decoding efficiency over conventional speculative decoding. Theoretically, we demonstrate that MTAD closely approximates exact MTJD with bounded error. Empirical evaluations using Llama-2 and OPT models ranging from 13B to 70B parameters across various tasks reveal that MTAD reduces perplexity by 21.2% and improves downstream performance compared to standard single-token sampling. Furthermore, MTAD achieves a 1.42× speed-up and consumes 1.54× less energy than conventional speculative decoding methods. These results highlight MTAD’s ability to make multi-token joint decoding both effective and efficient, promoting more sustainable and high-performance deployment of LLMs.

ICML Conference 2025 Conference Paper

QLASS: Boosting Language Agent Inference via Q-Guided Stepwise Search

  • Zongyu Lin
  • Yao Tang
  • Xingcheng Yao
  • Da Yin
  • Ziniu Hu
  • Yizhou Sun
  • Kai-Wei Chang 0001

Language agents have become a promising solution to complex interactive tasks. One of the key ingredients to the success of language agents is the reward model on the trajectory of the agentic workflow, which provides valuable guidance during training or inference. However, due to the lack of annotations of intermediate interactions, most existing works use an outcome reward model to optimize policies across entire trajectories. This may lead to sub-optimal policies and hinder the overall performance. To address this, we propose QLASS (Q-guided Language Agent Stepwise Search), to automatically generate annotations by estimating Q-values in a stepwise manner for open language agents. By introducing a reasoning tree and performing process reward modeling, QLASS provides effective intermediate guidance for each step. With the stepwise guidance, we propose a Q-guided generation strategy to enable language agents to better adapt to long-term value, resulting in significant performance improvement during model inference on complex interactive agent tasks. Notably, even with almost half the annotated data, QLASS retains strong performance, demonstrating its efficiency in handling limited supervision. We also empirically demonstrate that QLASS can lead to more effective decision making through qualitative analysis.

ICML Conference 2025 Conference Paper

Rethink GraphODE Generalization within Coupled Dynamical System

  • Guancheng Wan
  • Zijie Huang 0002
  • Wanjia Zhao
  • Xiao Luo 0001
  • Yizhou Sun
  • Wei Wang 0010

Coupled dynamical systems govern essential phenomena across physics, biology, and engineering, where components interact through complex dependencies. While Graph Ordinary Differential Equations (GraphODE) offer a powerful framework to model these systems, their generalization capabilities degrade severely under limited observational training data due to two fundamental flaws: (i) the entanglement of static attributes and dynamic states in the initialization process, and (ii) the reliance on context-specific coupling patterns during training, which hinders performance in unseen scenarios. In this paper, we propose a Generalizable GraphODE with disentanglement and regularization (GREAT) to address these challenges. Through systematic analysis via the Structural Causal Model, we identify backdoor paths that undermine generalization and design two key modules to mitigate their effects. The Dynamic-Static Equilibrium Decoupler (DyStaED) disentangles static and dynamic states via orthogonal subspace projections, ensuring robust initialization. Furthermore, the Causal Mediation for Coupled Dynamics (CMCD) employs variational inference to estimate latent causal factors, reducing spurious correlations and enhancing universal coupling dynamics. Extensive experiments across diverse dynamical systems demonstrate that ours outperforms state-of-the-art methods within both in-distribution and out-of-distribution.

NeurIPS Conference 2025 Conference Paper

Symmetry-Preserving Conformer Ensemble Networks for Molecular Representation Learning

  • Yanqiao Zhu
  • Yidan Shi
  • Yuanzhou Chen
  • Fang Sun
  • Yizhou Sun
  • Wei Wang

Molecular representation learning has emerged as a promising approach for modeling molecules with deep learning in chemistry and beyond. While 3D geometric models effectively capture molecular structure, they typically process single static conformers, overlooking the inherent flexibility and dynamics of molecules. In reality, many molecular properties depend on distributions of thermodynamically accessible conformations rather than single structures. Recent works show that learning from conformer ensembles can improve molecular representations, but existing approaches either produce unphysical structures through averaging or require restrictive molecular alignment. In this paper, we propose SymmetryPreserving Conformer Ensemble networks (SPiCE), which introduces two key innovations: (1) geometric mixture-of-experts for selective processing of scalar and vector features, and (2) hierarchical ensemble encoding that combines ensemblelevel representation with cross-conformer integration. Crucially, SPiCE ensures physically meaningful representations by maintaining joint equivariance to geometric transformations of individual conformers and conformer permutations. Extensive experiments demonstrate that SPiCE consistently outperforms existing conformer ensemble methods and state-of-the-art structural aggregation models across quantum mechanical and biological property prediction tasks.

ICLR Conference 2025 Conference Paper

VideoPhy: Evaluating Physical Commonsense for Video Generation

  • Hritik Bansal
  • Zongyu Lin
  • Tianyi Xie
  • Zeshun Zong
  • Michal Yarom
  • Yonatan Bitton
  • Chenfanfu Jiang
  • Yizhou Sun

Recent advances in internet-scale video data pretraining have led to the development of text-to-video generative models that can create high-quality videos across a broad range of visual concepts, synthesize realistic motions and render complex objects. Hence, these generative models have the potential to become general-purpose simulators of the physical world. However, it is unclear how far we are from this goal with the existing text-to-video generative models. To this end, we present VideoPhy, a benchmark designed to assess whether the generated videos follow physical commonsense for real-world activities (e.g. marbles will roll down when placed on a slanted surface). Specifically, we curate diverse prompts that involve interactions between various material types in the physical world (e.g., solid-solid, solid-fluid, fluid-fluid). We then generate videos conditioned on these captions from diverse state-of-the-art text-to-video generative models, including open models (e.g., CogVideoX) and closed models (e.g., Lumiere, Dream Machine). Our human evaluation reveals that the existing models severely lack the ability to generate videos adhering to the given text prompts, while also lack physical commonsense. Specifically, the best performing model, CogVideoX-5B, generates videos that adhere to the caption and physical laws for 39.6% of the instances. VideoPhy thus highlights that the video generative models are far from accurately simulating the physical world. Finally, we propose an auto-evaluator, VideoCon-Physics, to assess the performance reliably for the newly released models. The code is available here: https://github.com/Hritikbansal/videophy.

IJCAI Conference 2024 Conference Paper

A Single Vector Is Not Enough: Taxonomy Expansion via Box Embeddings (Extended Abstract)

  • Song Jiang
  • Qiyue Yao
  • Qifan Wang
  • Yizhou Sun

Taxonomies support various practical web applications such as product navigation in online shopping and user profile tagging on social platforms. Most existing methods for expanding taxonomies encode entities into vector embeddings (i. e. , single points). However, we argue that vectors are insufficient to model the ``is-a'' hierarchy in taxonomy (asymmetrical relation), because two points can only represent pairwise similarity (symmetrical relation). To this end, we propose to project taxonomy entities into boxes (i. e. , hyperrectangles). Two boxes can be "contained", "disjoint" and "intersecting", thus naturally representing an asymmetrical taxonomic hierarchy. Upon box embeddings, we propose a novel model BoxTaxo for taxonomy expansion. The core of BoxTaxo is to learn boxes for entities to capture their child-parent hierarchies. Extensive experiments on two benchmarks demonstrate the effectiveness of BoxTaxo compared to vector based models.

NeurIPS Conference 2024 Conference Paper

Integrating Deep Metric Learning with Coreset for Active Learning in 3D Segmentation

  • Arvind M. Vepa
  • Zukang Yang
  • Andrew Choi
  • Jungseock Joo
  • Fabien Scalzo
  • Yizhou Sun

Deep learning has seen remarkable advancements in machine learning, yet it often demands extensive annotated data. Tasks like 3D semantic segmentation impose a substantial annotation burden, especially in domains like medicine, where expert annotations drive up the cost. Active learning (AL) holds great potential to alleviate this annotation burden in 3D medical segmentation. The majority of existing AL methods, however, are not tailored to the medical domain. While weakly-supervised methods have been explored to reduce annotation burden, the fusion of AL with weak supervision remains unexplored, despite its potential to significantly reduce annotation costs. Additionally, there is little focus on slice-based AL for 3D segmentation, which can also significantly reduce costs in comparison to conventional volume-based AL. This paper introduces a novel metric learning method for Coreset to perform slice-based active learning in 3D medical segmentation. By merging contrastive learning with inherent data groupings in medical imaging, we learn a metric that emphasizes the relevant differences in samples for training 3D medical segmentation models. We perform comprehensive evaluations using both weak and full annotations across four datasets (medical and non-medical). Our findings demonstrate that our approach surpasses existing active learning techniques on both weak and full annotations and obtains superior performance with low-annotation budgets which is crucial in medical imaging. Source code for this project is available in the supplementary materials and on GitHub: https: //github. com/arvindmvepa/al-seg.

ICLR Conference 2024 Conference Paper

Learning Over Molecular Conformer Ensembles: Datasets and Benchmarks

  • Yanqiao Zhu 0001
  • Jeehyun Hwang
  • Keir Adams
  • Zhen Liu 0069
  • Bozhao Nan
  • Brock Stenfors
  • Yuanqi Du
  • Jatin Chauhan

Molecular Representation Learning (MRL) has proven impactful in numerous biochemical applications such as drug discovery and enzyme design. While Graph Neural Networks (GNNs) are effective at learning molecular representations from a 2D molecular graph or a single 3D structure, existing works often overlook the flexible nature of molecules, which continuously interconvert across conformations via chemical bond rotations and minor vibrational perturbations. To better account for molecular flexibility, some recent works formulate MRL as an ensemble learning problem, focusing on explicitly learning from a set of conformer structures. However, most of these studies have limited datasets, tasks, and models. In this work, we introduce the first MoleculAR Conformer Ensemble Learning (MARCEL) benchmark to thoroughly evaluate the potential of learning on con- former ensembles and suggest promising research directions. MARCEL includes four datasets covering diverse molecule- and reaction-level properties of chemically diverse molecules including organocatalysts and transition-metal catalysts, extending beyond the scope of common GNN benchmarks that are confined to drug-like molecules. In addition, we conduct a comprehensive empirical study, which benchmarks representative 1D, 2D, and 3D MRL models, along with two strategies that explicitly incorporate conformer ensembles into 3D models. Our findings reveal that direct learning from an accessible conformer space can improve performance on a variety of tasks and models.

ICML Conference 2024 Conference Paper

Networked Inequality: Preferential Attachment Bias in Graph Neural Network Link Prediction

  • Arjun Subramonian
  • Levent Sagun
  • Yizhou Sun

Graph neural network (GNN) link prediction is increasingly deployed in citation, collaboration, and online social networks to recommend academic literature, collaborators, and friends. While prior research has investigated the dyadic fairness of GNN link prediction, the within-group (e. g. , queer women) fairness and "rich get richer" dynamics of link prediction remain underexplored. However, these aspects have significant consequences for degree and power imbalances in networks. In this paper, we shed light on how degree bias in networks affects Graph Convolutional Network (GCN) link prediction. In particular, we theoretically uncover that GCNs with a symmetric normalized graph filter have a within-group preferential attachment bias. We validate our theoretical analysis on real-world citation, collaboration, and online social networks. We further bridge GCN’s preferential attachment bias with unfairness in link prediction and propose a new within-group fairness metric. This metric quantifies disparities in link prediction scores within social groups, towards combating the amplification of degree and power disparities. Finally, we propose a simple training-time strategy to alleviate within-group unfairness, and we show that it is effective on citation, social, and credit networks.

NeurIPS Conference 2024 Conference Paper

Non-Euclidean Mixture Model for Social Network Embedding

  • Roshni G. Iyer
  • Yewen Wang
  • Wei Wang
  • Yizhou Sun

It is largely agreed that social network links are formed due to either homophily or social influence. Inspired by this, we aim at understanding the generation of links via providing a novel embedding-based graph formation model. Different from existing graph representation learning, where link generation probabilities are defined as a simple function of the corresponding node embeddings, we model the link generation as a mixture model of the two factors. In addition, we model the homophily factor in spherical space and the influence factor in hyperbolic space to accommodate the fact that (1) homophily results in cycles and (2) influence results in hierarchies in networks. We also design a special projection to align these two spaces. We call this model Non-Euclidean Mixture Model, i. e. , NMM. We further integrate NMM with our non-Euclidean graph variational autoencoder (VAE) framework, NMM-GNN. NMM-GNN learns embeddings through a unified framework which uses non-Euclidean GNN encoders, non-Euclidean Gaussian priors, a non-Euclidean decoder, and a novel space unification loss component to unify distinct non-Euclidean geometric spaces. Experiments on public datasets show NMM-GNN significantly outperforms state-of-the-art baselines on social network generation and classification tasks, demonstrating its ability to better explain how the social network is formed.

ICML Conference 2024 Conference Paper

PGODE: Towards High-quality System Dynamics Modeling

  • Xiao Luo 0001
  • Yiyang Gu
  • Huiyu Jiang
  • Hang Zhou 0008
  • Jinsheng Huang
  • Wei Ju 0001
  • Zhiping Xiao 0001
  • Ming Zhang 0004

This paper studies the problem of modeling multi-agent dynamical systems, where agents could interact mutually to influence their behaviors. Recent research predominantly uses geometric graphs to depict these mutual interactions, which are then captured by powerful graph neural networks (GNNs). However, predicting interacting dynamics in challenging scenarios such as out-of-distribution shift and complicated underlying rules remains unsolved. In this paper, we propose a new approach named Prototypical Graph ODE (PGODE) to address the problem. The core of PGODE is to incorporate prototype decomposition from contextual knowledge into a continuous graph ODE framework. Specifically, PGODE employs representation disentanglement and system parameters to extract both object-level and system-level contexts from historical trajectories, which allows us to explicitly model their independent influence and thus enhances the generalization capability under system changes. Then, we integrate these disentangled latent representations into a graph ODE model, which determines a combination of various interacting prototypes for enhanced model expressivity. The entire model is optimized using an end-to-end variational inference framework to maximize the likelihood. Extensive experiments in both in-distribution and out-of-distribution settings validate the superiority of PGODE compared to various baselines.

NeurIPS Conference 2024 Conference Paper

Physics-Informed Regularization for Domain-Agnostic Dynamical System Modeling

  • Zijie Huang
  • Wanjia Zhao
  • Jingdong Gao
  • Ziniu Hu
  • Xiao Luo
  • Yadi Cao
  • Yuanzhou Chen
  • Yizhou Sun

Learning complex physical dynamics purely from data is challenging due to the intrinsic properties of systems to be satisfied. Incorporating physics-informed priors, such as in Hamiltonian Neural Networks (HNNs), achieves high-precision modeling for energy-conservative systems. However, real-world systems often deviate from strict energy conservation and follow different physical priors. To address this, we present a framework that achieves high-precision modeling for a wide range of dynamical systems from the numerical aspect, by enforcing Time-Reversal Symmetry (TRS) via a novel regularization term. It helps preserve energies for conservative systems while serving as a strong inductive bias for non-conservative, reversible systems. While TRS is a domain-specific physical prior, we present the first theoretical proof that TRS loss can universally improve modeling accuracy by minimizing higher-order Taylor terms in ODE integration, which is numerically beneficial to various systems regardless of their properties, even for irreversible systems. By integrating the TRS loss within neural ordinary differential equation models, the proposed model TREAT demonstrates superior performance on diverse physical systems. It achieves a significant 11. 5% MSE improvement in a challenging chaotic triple-pendulum scenario, underscoring TREAT’s broad applicability and effectiveness.

ICML Conference 2024 Conference Paper

Predicting and Interpreting Energy Barriers of Metallic Glasses with Graph Neural Networks

  • Haoyu Li
  • Shichang Zhang
  • Longwen Tang
  • Mathieu Bauchy
  • Yizhou Sun

Metallic Glasses (MGs) are widely used materials that are stronger than steel while being shapeable as plastic. While understanding the structure-property relationship of MGs remains a challenge in materials science, studying their energy barriers (EBs) as an intermediary step shows promise. In this work, we utilize Graph Neural Networks (GNNs) to model MGs and study EBs. We contribute a new dataset for EB prediction and a novel Symmetrized GNN (SymGNN) model that is E(3)-invariant in expectation. SymGNN handles invariance by aggregating over orthogonal transformations of the graph structure. When applied to EB prediction, SymGNN are more accurate than molecular dynamics (MD) local-sampling methods and other machine-learning models. Compared to precise MD simulations, SymGNN reduces the inference time on new MGs from roughly 41 days to less than one second. We apply explanation algorithms to reveal the relationship between structures and EBs. The structures that we identify through explanations match the medium-range order (MRO) hypothesis and possess unique topological properties. Our work enables effective prediction and interpretation of MG EBs, bolstering material science research.

ICML Conference 2024 Conference Paper

SciBench: Evaluating College-Level Scientific Problem-Solving Abilities of Large Language Models

  • Xiaoxuan Wang
  • Ziniu Hu
  • Pan Lu
  • Yanqiao Zhu 0001
  • Jieyu Zhang 0001
  • Satyen Subramaniam
  • Arjun R. Loomba
  • Shichang Zhang

Most existing Large Language Model (LLM) benchmarks on scientific problem reasoning focus on problems grounded in high-school subjects and are confined to elementary algebraic operations. To systematically examine the reasoning capabilities required for solving complex scientific problems, we introduce an expansive benchmark suite SciBench for LLMs. SciBench contains a carefully curated dataset featuring a range of collegiate-level scientific problems from mathematics, chemistry, and physics domains. Based on the dataset, we conduct an in-depth benchmarking study of representative open-source and proprietary LLMs with various prompting strategies. The results reveal that current LLMs fall short of delivering satisfactory performance, with the best overall score of merely 43. 22%. Furthermore, through a detailed user study, we categorize the errors made by LLMs into ten problem-solving abilities. Our analysis indicates that no single prompting strategy significantly outperforms the others and some strategies that demonstrate improvements in certain problem-solving skills could result in declines in other skills. We envision that SciBench will catalyze further developments in the reasoning abilities of LLMs, thereby ultimately contributing to scientific research and discovery.

NeurIPS Conference 2024 Conference Paper

Theoretical and Empirical Insights into the Origins of Degree Bias in Graph Neural Networks

  • Arjun Subramonian
  • Jian Kang
  • Yizhou Sun

Graph Neural Networks (GNNs) often perform better for high-degree nodes than low-degree nodes on node classification tasks. This degree bias can reinforce social marginalization by, e. g. , privileging celebrities and other high-degree actors in social networks during social and content recommendation. While researchers have proposed numerous hypotheses for why GNN degree bias occurs, we find via a survey of 38 degree bias papers that these hypotheses are often not rigorously validated, and can even be contradictory. Thus, we provide an analysis of the origins of degree bias in message-passing GNNs with different graph filters. We prove that high-degree test nodes tend to have a lower probability of misclassification regardless of how GNNs are trained. Moreover, we show that degree bias arises from a variety of factors that are associated with a node's degree (e. g. , homophily of neighbors, diversity of neighbors). Furthermore, we show that during training, some GNNs may adjust their loss on low-degree nodes more slowly than on high-degree nodes; however, with sufficiently many epochs of training, message-passing GNNs can achieve their maximum possible training accuracy, which is not significantly limited by their expressive power. Throughout our analysis, we connect our findings to previously-proposed hypotheses for the origins of degree bias, supporting and unifying some while drawing doubt to others. We validate our theoretical findings on 8 common real-world networks, and based on our theoretical and empirical insights, describe a roadmap to alleviate degree bias.

NeurIPS Conference 2023 Conference Paper

Amazon-M2: A Multilingual Multi-locale Shopping Session Dataset for Recommendation and Text Generation

  • Wei Jin
  • Haitao Mao
  • Zheng Li
  • Haoming Jiang
  • Chen Luo
  • Hongzhi Wen
  • Haoyu Han
  • Hanqing Lu

Modeling customer shopping intentions is a crucial task for e-commerce, as it directly impacts user experience and engagement. Thus, accurately understanding customer preferences is essential for providing personalized recommendations. Session-based recommendation, which utilizes customer session data to predict their next interaction, has become increasingly popular. However, existing session datasets have limitations in terms of item attributes, user diversity, and dataset scale. As a result, they cannot comprehensively capture the spectrum of user behaviors and preferences. To bridge this gap, we present the Amazon Multilingual Multi-locale Shopping Session Dataset, namely Amazon-M2. It is the first multilingual dataset consisting of millions of user sessions from six different locales, where the major languages of products are English, German, Japanese, French, Italian, and Spanish. Remarkably, the dataset can help us enhance personalization and understanding of user preferences, which can benefit various existing tasks as well as enable new tasks. To test the potential of the dataset, we introduce three tasks in this work: (1) next-product recommendation, (2) next-product recommendation with domain shifts, and (3) next-product title generation. With the above tasks, we benchmark a range of algorithms on our proposed dataset, drawing new insights for further research and practice. In addition, based on the proposed dataset and tasks, we hosted a competition in the KDD CUP 2023 https: //www. aicrowd. com/challenges/amazon-kdd-cup-23-multilingual-recommendation-challenge and have attracted thousands of users and submissions. The winning solutions and the associated workshop can be accessed at our website~https: //kddcup23. github. io/.

NeurIPS Conference 2023 Conference Paper

AVIS: Autonomous Visual Information Seeking with Large Language Model Agent

  • Ziniu Hu
  • Ahmet Iscen
  • Chen Sun
  • Kai-Wei Chang
  • Yizhou Sun
  • David Ross
  • Cordelia Schmid
  • Alireza Fathi

In this paper, we propose an autonomous information seeking visual question answering framework, AVIS. Our method leverages a Large Language Model (LLM) to dynamically strategize the utilization of external tools and to investigate their outputs via tree search, thereby acquiring the indispensable knowledge needed to provide answers to the posed questions. Responding to visual questions that necessitate external knowledge, such as "What event is commemorated by the building depicted in this image? ", is a complex task. This task presents a combinatorial search space that demands a sequence of actions, including invoking APIs, analyzing their responses, and making informed decisions. We conduct a user study to collect a variety of instances of human decision-making when faced with this task. This data is then used to design a system comprised of three components: an LLM-powered planner that dynamically determines which tool to use next, an LLM-powered reasoner that analyzes and extracts key information from the tool outputs, and a working memory component that retains the acquired information throughout the process. The collected user behavior serves as a guide for our system in two key ways. First, we create a transition graph by analyzing the sequence of decisions made by users. This graph delineates distinct states and confines the set of actions available at each state. Second, we use examples of user decision-making to provide our LLM-powered planner and reasoner with relevant contextual instances, enhancing their capacity to make informed decisions. We show that AVIS achieves state-of-the-art results on knowledge-based visual question answering benchmarks such as Infoseek and OK-VQA.

NeurIPS Conference 2023 Conference Paper

CARE: Modeling Interacting Dynamics Under Temporal Environmental Variation

  • Xiao Luo
  • Haixin Wang
  • Zijie Huang
  • Huiyu Jiang
  • Abhijeet Gangan
  • Song Jiang
  • Yizhou Sun

Modeling interacting dynamical systems, such as fluid dynamics and intermolecular interactions, is a fundamental research problem for understanding and simulating complex real-world systems. Many of these systems can be naturally represented by dynamic graphs, and graph neural network-based approaches have been proposed and shown promising performance. However, most of these approaches assume the underlying dynamics does not change over time, which is unfortunately untrue. For example, a molecular dynamics can be affected by the environment temperature over the time. In this paper, we take an attempt to provide a probabilistic view for time-varying dynamics and propose a model Context-attended Graph ODE (CARE) for modeling time-varying interacting dynamical systems. In our CARE, we explicitly use a context variable to model time-varying environment and construct an encoder to initialize the context variable from historical trajectories. Furthermore, we employ a neural ODE model to depict the dynamic evolution of the context variable inferred from system states. This context variable is incorporated into a coupled ODE to simultaneously drive the evolution of systems. Comprehensive experiments on four datasets demonstrate the effectiveness of our proposed CARE compared with several state-of-the-art approaches.

ICML Conference 2023 Conference Paper

HOPE: High-order Graph ODE For Modeling Interacting Dynamics

  • Xiao Luo 0001
  • Jingyang Yuan
  • Zijie Huang 0002
  • Huiyu Jiang
  • Yifang Qin
  • Wei Ju 0001
  • Ming Zhang 0004
  • Yizhou Sun

Leading graph ordinary differential equation (ODE) models have offered generalized strategies to model interacting multi-agent dynamical systems in a data-driven approach. They typically consist of a temporal graph encoder to get the initial states and a neural ODE-based generative model to model the evolution of dynamical systems. However, existing methods have severe deficiencies in capacity and efficiency due to the failure to model high-order correlations in long-term temporal trends. To tackle this, in this paper, we propose a novel model named High-order graph ODE (HOPE) for learning from dynamic interaction data, which can be naturally represented as a graph. It first adopts a twin graph encoder to initialize the latent state representations of nodes and edges, which consists of two branches to capture spatio-temporal correlations in complementary manners. More importantly, our HOPE utilizes a second-order graph ODE function which models the dynamics for both nodes and edges in the latent space respectively, which enables efficient learning of long-term dependencies from complex dynamical systems. Experiment results on a variety of datasets demonstrate both the effectiveness and efficiency of our proposed method.

ICLR Conference 2023 Conference Paper

Neural Compositional Rule Learning for Knowledge Graph Reasoning

  • Kewei Cheng
  • Nesreen K. Ahmed
  • Yizhou Sun

Learning logical rules is critical to improving reasoning in KGs. This is due to their ability to provide logical and interpretable explanations when used for predictions, as well as their ability to generalize to other tasks, domains, and data. While recent methods have been proposed to learn logical rules, the majority of these methods are either restricted by their computational complexity and can not handle the large search space of large-scale KGs, or show poor generalization when exposed to data outside the training set. In this paper, we propose an end-to-end neural model for learning compositional logical rules called NCRL. NCRL detects the best compositional structure of a rule body, and breaks it into small compositions in order to infer the rule head. By recurrently merging compositions in the rule body with a recurrent attention unit, NCRL finally predicts a single rule head. Experimental results show that NCRL learns high-quality rules, as well as being generalizable. Specifically, we show that NCRL is scalable, efficient, and yields state-of-the-art results for knowledge graph completion on large-scale KGs. Moreover, we test NCRL for systematic generalization by learning to reason on small-scale observed graphs and evaluating on larger unseen ones.

AAAI Conference 2023 Conference Paper

Prototypical Fine-Tuning: Towards Robust Performance under Varying Data Sizes

  • Yiqiao Jin
  • Xiting Wang
  • Yaru Hao
  • Yizhou Sun
  • Xing Xie

In this paper, we move towards combining large parametric models with non-parametric prototypical networks. We propose prototypical fine-tuning, a novel prototypical framework for fine-tuning pretrained language models (LM), which automatically learns a bias to improve predictive performance for varying data sizes, especially low-resource settings. Our prototypical fine-tuning approach can automatically adjust the model capacity according to the number of data points and the model's inherent attributes. Moreover, we propose four principles for effective prototype fine-tuning towards the optimal solution. Experimental results across various datasets show that our work achieves significant performance improvements under various low-resource settings, as well as comparable and usually better performances in high-resource scenarios.

TMLR Journal 2023 Journal Article

RIGNN: A Rationale Perspective for Semi-supervised Open-world Graph Classification

  • Xiao Luo
  • Yusheng Zhao
  • Zhengyang Mao
  • Yifang Qin
  • Wei Ju
  • Ming Zhang
  • Yizhou Sun

Graph classification has gained growing attention in the graph machine learning community and a variety of semi-supervised methods have been developed to reduce the high cost of annotation. They usually combine graph neural networks (GNNs) and extensive semi-supervised techniques such as knowledge distillation. However, they adhere to the close-set assumption that unlabeled graphs all belong to known classes, limiting their applications in the real world. This paper goes further, investigating a practical problem of semi-supervised open-world graph classification where these unlabeled graph data could come from unseen classes. A novel approach named Rationale-Informed GNN (RIGNN) is proposed, which takes a rationale view to detect components containing the most information related to the label space and classify unlabeled graphs into a known class or an unseen class. In particular, RIGNN contains a relational detector and a feature extractor to produce effective rationale features, which maximize the mutual information with label information and exhibit sufficient disentanglement with non-rationale elements. Furthermore, we construct a graph-of-graph based on geometrical relationships, which gives instructions on enhancing rationale representations. In virtue of effective rationale representations, we can provide accurate and balanced predictions for unlabeled graphs. An extension is also made to accomplish effective open-set graph classification. We verify our proposed methods on four benchmark datasets in various settings and experimental results reveal the effectiveness of our proposed RIGNN compared with state-of-the-art methods.

NeurIPS Conference 2023 Conference Paper

Towards a Comprehensive Benchmark for High-Level Synthesis Targeted to FPGAs

  • Yunsheng Bai
  • Atefeh Sohrabizadeh
  • Zongyue Qin
  • Ziniu Hu
  • Yizhou Sun
  • Jason Cong

High-level synthesis (HLS) aims to raise the abstraction layer in hardware design, enabling the design of domain-specific accelerators (DSAs) like field-programmable gate arrays (FPGAs) using C/C++ instead of hardware description languages (HDLs). Compiler directives in the form of pragmas play a crucial role in modifying the microarchitecture within the HLS framework. However, the space of possible microarchitectures grows exponentially with the number of pragmas. Moreover, the evaluation of each candidate design using the HLS tool consumes significant time, ranging from minutes to hours, leading to a time-consuming optimization process. To accelerate this process, machine learning models have been used to predict design quality in milliseconds. However, existing open-source datasets for training such models are limited in terms of design complexity and available optimizations. In this paper, we present HLSyn, the first benchmark that addresses these limitations. It contains more complex programs with a wider range of optimization pragmas, making it a comprehensive dataset for training and evaluating design quality prediction models. The HLSyn benchmark consists of 42 unique programs/kernels, resulting in over 42, 000 labeled designs. We conduct an extensive comparison of state-of-the-art baselines to assess their effectiveness in predicting design quality. As an ongoing project, we anticipate expanding the HLSyn benchmark in terms of both quantity and variety of programs to further support the development of this field.

AAAI Conference 2022 Conference Paper

Blindfolded Attackers Still Threatening: Strict Black-Box Adversarial Attacks on Graphs

  • Jiarong Xu
  • Yizhou Sun
  • Xin Jiang
  • Yanhao Wang
  • Chunping Wang
  • Jiangang Lu
  • Yang Yang

Adversarial attacks on graphs have attracted considerable research interests. Existing works assume the attacker is either (partly) aware of the victim model, or able to send queries to it. These assumptions are, however, unrealistic. To bridge the gap between theoretical graph attacks and real-world scenarios, in this work, we propose a novel and more realistic setting: strict black-box graph attack, in which the attacker has no knowledge about the victim model at all and is not allowed to send any queries. To design such an attack strategy, we first propose a generic graph filter to unify different families of graph-based models. The strength of attacks can then be quantified by the change in the graph filter before and after attack. By maximizing this change, we are able to find an effective attack strategy, regardless of the underlying model. To solve this optimization problem, we also propose a relaxation technique and approximation theories to reduce the difficulty as well as the computational expense. Experiments demonstrate that, even with no exposure to the model, the Macro-F1 drops 5. 5% in node classification and 29. 5% in graph classification, which is a significant result compared with existent works.

AAAI Conference 2022 Conference Paper

Fuzzy Logic Based Logical Query Answering on Knowledge Graphs

  • Xuelu Chen
  • Ziniu Hu
  • Yizhou Sun

Answering complex First-Order Logical (FOL) queries on large-scale incomplete knowledge graphs (KGs) is an important yet challenging task. Recent advances embed logical queries and KG entities in the same space and conduct query answering via dense similarity search. However, most logical operators designed in previous studies do not satisfy the axiomatic system of classical logic, limiting their performance. Moreover, these logical operators are parameterized and thus require many complex FOL queries as training data, which are often arduous to collect or even inaccessible in most real-world KGs. We thus present FuzzQE, a fuzzy logic based logical query embedding framework for answering FOL queries over KGs. FuzzQE follows fuzzy logic to define logical operators in a principled and learningfree manner, where only entity and relation embeddings require learning. FuzzQE can further benefit from labeled complex logical queries for training. Extensive experiments on two benchmark datasets demonstrate that FuzzQE provides significantly better performance in answering FOL queries compared to state-of-the-art methods. In addition, FuzzQE trained with only KG link prediction can achieve comparable performance to those trained with extra complex query data.

ICLR Conference 2022 Conference Paper

Graph-less Neural Networks: Teaching Old MLPs New Tricks Via Distillation

  • Shichang Zhang
  • Yozen Liu
  • Yizhou Sun
  • Neil Shah

Graph Neural Networks (GNNs) are popular for graph machine learning and have shown great results on wide node classification tasks. Yet, they are less popular for practical deployments in the industry owing to their scalability challenges incurred by data dependency. Namely, GNN inference depends on neighbor nodes multiple hops away from the target, and fetching them burdens latency-constrained applications. Existing inference acceleration methods like pruning and quantization can speed up GNNs by reducing Multiplication-and-ACcumulation (MAC) operations, but the improvements are limited given the data dependency is not resolved. Conversely, multi-layer perceptrons (MLPs) have no graph dependency and infer much faster than GNNs, even though they are less accurate than GNNs for node classification in general. Motivated by these complementary strengths and weaknesses, we bring GNNs and MLPs together via knowledge distillation (KD). Our work shows that the performance of MLPs can be improved by large margins with GNN KD. We call the distilled MLPs Graph-less Neural Networks (GLNNs) as they have no inference graph dependency. We show that GLNNs with competitive accuracy infer faster than GNNs by 146X-273X and faster than other acceleration methods by 14X-27X. Under a production setting involving both transductive and inductive predictions across 7 datasets, GLNN accuracies improve over stand-alone MLPs by 12.36% on average and match GNNs on 6/7 datasets. Comprehensive analysis shows when and why GLNNs can achieve competitive accuracies to GNNs and suggests GLNN as a handy choice for latency-constrained applications.

AAAI Conference 2022 Short Paper

GRU4RecBE: A Hybrid Session-Based Movie Recommendation System (Student Abstract)

  • Michael Potter
  • Hamlin Liu
  • Yash Lala
  • Christian Loanzon
  • Yizhou Sun

We present a novel movie recommendation system, GRU4RecBE, which extends the GRU4Rec architecture with rich item features extracted by the pre-trained BERT model. GRU4RecBE outperforms state-of-the-art sessionbased models over the benchmark MovieLens 1m and Movie- Lens 20m datasets.

NeurIPS Conference 2022 Conference Paper

GStarX: Explaining Graph Neural Networks with Structure-Aware Cooperative Games

  • Shichang Zhang
  • Yozen Liu
  • Neil Shah
  • Yizhou Sun

Explaining machine learning models is an important and increasingly popular area of research interest. The Shapley value from game theory has been proposed as a prime approach to compute feature importance towards model predictions on images, text, tabular data, and recently graph neural networks (GNNs) on graphs. In this work, we revisit the appropriateness of the Shapley value for GNN explanation, where the task is to identify the most important subgraph and constituent nodes for GNN predictions. We claim that the Shapley value is a non-ideal choice for graph data because it is by definition not structure-aware. We propose a Graph Structure-aware eXplanation (GStarX) method to leverage the critical graph structure information to improve the explanation. Specifically, we define a scoring function based on a new structure-aware value from the cooperative game theory proposed by Hamiache and Navarro (HN). When used to score node importance, the HN value utilizes graph structures to attribute cooperation surplus between neighbor nodes, resembling message passing in GNNs, so that node importance scores reflect not only the node feature importance, but also the node structural roles. We demonstrate that GStarX produces qualitatively more intuitive explanations, and quantitatively improves explanation fidelity over strong baselines on chemical graph property prediction and text graph sentiment classification. Code: https: //github. com/ShichangZh/GStarX

NeurIPS Conference 2022 Conference Paper

Improving Multi-Task Generalization via Regularizing Spurious Correlation

  • Ziniu Hu
  • Zhe Zhao
  • Xinyang Yi
  • Tiansheng Yao
  • Lichan Hong
  • Yizhou Sun
  • Ed Chi

Multi-Task Learning (MTL) is a powerful learning paradigm to improve generalization performance via knowledge sharing. However, existing studies find that MTL could sometimes hurt generalization, especially when two tasks are less correlated. One possible reason that hurts generalization is spurious correlation, i. e. , some knowledge is spurious and not causally related to task labels, but the model could mistakenly utilize them and thus fail when such correlation changes. In MTL setup, there exist several unique challenges of spurious correlation. First, the risk of having non-causal knowledge is higher, as the shared MTL model needs to encode all knowledge from different tasks, and causal knowledge for one task could be potentially spurious to the other. Second, the confounder between task labels brings in a different type of spurious correlation to MTL. Given such label-label confounders, we theoretically and empirically show that MTL is prone to taking non-causal knowledge from other tasks. To solve this problem, we propose Multi-Task Causal Representation Learning (MT-CRL) framework. MT-CRL aims to represent multi-task knowledge via disentangled neural modules, and learn which module is causally related to each task via MTL-specific invariant regularization. Experiments show that MT-CRL could enhance MTL model's performance by 5. 5% on average over Multi-MNIST, MovieLens, Taskonomy, CityScape, and NYUv2, and show it could indeed alleviate spurious correlation problem.

NeurIPS Conference 2022 Conference Paper

On the Discrimination Risk of Mean Aggregation Feature Imputation in Graphs

  • Arjun Subramonian
  • Kai-Wei Chang
  • Yizhou Sun

In human networks, nodes belonging to a marginalized group often have a disproportionate rate of unknown or missing features. This, in conjunction with graph structure and known feature biases, can cause graph feature imputation algorithms to predict values for unknown features that make the marginalized group's feature values more distinct from the the dominant group's feature values than they are in reality. We call this distinction the discrimination risk. We prove that a higher discrimination risk can amplify the unfairness of a machine learning model applied to the imputed data. We then formalize a general graph feature imputation framework called mean aggregation imputation and theoretically and empirically characterize graphs in which applying this framework can yield feature values with a high discrimination risk. We propose a simple algorithm to ensure mean aggregation-imputed features provably have a low discrimination risk, while minimally sacrificing reconstruction error (with respect to the imputation objective). We evaluate the fairness and accuracy of our solution on synthetic and real-world credit networks.

AAAI Conference 2022 Conference Paper

Towards Fine-Grained Reasoning for Fake News Detection

  • Yiqiao Jin
  • Xiting Wang
  • Ruichao Yang
  • Yizhou Sun
  • Wei Wang
  • Hao Liao
  • Xing Xie

The detection of fake news often requires sophisticated reasoning skills, such as logically combining information by considering word-level subtle clues. In this paper, we move towards fine-grained reasoning for fake news detection by better reflecting the logical processes of human thinking and enabling the modeling of subtle clues. In particular, we propose a fine-grained reasoning framework by following the human’s information-processing model, introduce a mutualreinforcement-based method for incorporating human knowledge about which evidence is more important, and design a prior-aware bi-channel kernel graph network to model subtle differences between pieces of evidence. Extensive experiments show that our model outperforms the state-of-the-art methods and demonstrate the explainability of our approach.

AAAI Conference 2022 Conference Paper

Unsupervised Adversarially Robust Representation Learning on Graphs

  • Jiarong Xu
  • Yang Yang
  • Junru Chen
  • Xin Jiang
  • Chunping Wang
  • Jiangang Lu
  • Yizhou Sun

Unsupervised/self-supervised pre-training methods for graph representation learning have recently attracted increasing research interests, and they can be generalized to various downstream applications. Yet, the adversarial robustness of such pre-trained graph learning models remains largely unexplored. More importantly, most existing defense techniques for endto-end graph representation learning methods require prespecified label definitions, and thus cannot be directly applied to the pre-training methods. In this paper, we propose an unsupervised defense technique to robustify pre-trained deep graph models, so that the perturbations on the input graph can be successfully identified and blocked before the model is applied to different downstream tasks. Specifically, we introduce a mutual information-based measure, graph representation vulnerability (GRV), to quantify the robustness of graph encoders on the representation space. We then formulate an optimization problem to learn the graph representation by carefully balancing the trade-off between the expressive power and the robustness (i. e. , GRV) of the graph encoder. The discrete nature of graph topology and the joint space of graph data make the optimization problem intractable to solve. To handle the above difficulty and to reduce computational expense, we further relax the problem and thus provide an approximate solution. Additionally, we explore a provable connection between the robustness of the unsupervised graph encoder and that of models on downstream tasks. Extensive experiments demonstrate that even without access to labels and tasks, our model is still able to enhance robustness against adversarial attacks on three downstream tasks (i. e. , node classification, link prediction, and community detection) by an average of +16. 5% compared with existing methods.

AAAI Conference 2021 Conference Paper

Clinical Temporal Relation Extraction with Probabilistic Soft Logic Regularization and Global Inference

  • Yichao Zhou
  • Yu Yan
  • Rujun Han
  • J. Harry Caufield
  • Kai-Wei Chang
  • Yizhou Sun
  • Peipei Ping
  • Wei Wang

There has been a steady need in the medical community to precisely extract the temporal relations between clinical events. In particular, temporal information can facilitate a variety of downstream applications such as case report retrieval and medical question answering. However, existing methods either require expensive feature engineering or are incapable of modeling the global relational dependencies among the events. In this paper, we propose Clinical Temporal ReLation Exaction with Probabilistic Soft Logic Regularization and Global Inference (CTRL-PG), a novel method to tackle the problem at the document level. Extensive experiments on two benchmark datasets, I2B2-2012 and TB-Dense, demonstrate that CTRL-PG significantly outperforms baseline methods for temporal relation extraction.

ICML Conference 2021 Conference Paper

GLSearch: Maximum Common Subgraph Detection via Learning to Search

  • Yunsheng Bai
  • Derek Xu
  • Yizhou Sun
  • Wei Wang 0010

Detecting the Maximum Common Subgraph (MCS) between two input graphs is fundamental for applications in drug synthesis, malware detection, cloud computing, etc. However, MCS computation is NP-hard, and state-of-the-art MCS solvers rely on heuristic search algorithms which in practice cannot find good solution for large graph pairs given a limited computation budget. We propose GLSearch, a Graph Neural Network (GNN) based learning to search model. Our model is built upon the branch and bound algorithm, which selects one pair of nodes from the two input graphs to expand at a time. We propose a novel GNN-based Deep Q-Network (DQN) to select the node pair, making the search process much faster. Experiments on synthetic and real-world graph pairs demonstrate that our model learns a search strategy that is able to detect significantly larger common subgraphs than existing MCS solvers given the same computation budget. GLSearch can be potentially extended to solve many other combinatorial problems with constraints on graphs.

ICML Conference 2020 Conference Paper

Differentiable Product Quantization for End-to-End Embedding Compression

  • Ting Chen 0007
  • Lala Li
  • Yizhou Sun

Embedding layers are commonly used to map discrete symbols into continuous embedding vectors that reflect their semantic meanings. Despite their effectiveness, the number of parameters in an embedding layer increases linearly with the number of symbols and poses a critical challenge on memory and storage constraints. In this work, we propose a generic and end-to-end learnable compression framework termed differentiable product quantization (DPQ). We present two instantiations of DPQ that leverage different approximation techniques to enable differentiability in end-to-end learning. Our method can readily serve as a drop-in alternative for any existing embedding layer. Empirically, DPQ offers significant compression ratios (14-238X) at negligible or no performance cost on 10 datasets across three different language tasks.

IJCAI Conference 2020 Conference Paper

Heterogeneous Network Representation Learning

  • Yuxiao Dong
  • Ziniu Hu
  • Kuansan Wang
  • Yizhou Sun
  • Jie Tang

Representation learning has offered a revolutionary learning paradigm for various AI domains. In this survey, we examine and review the problem of representation learning with the focus on heterogeneous networks, which consists of different types of vertices and relations. The goal of this problem is to automatically project objects, most commonly, vertices, in an input heterogeneous network into a latent embedding space such that both the structural and relational properties of the network can be encoded and preserved. The embeddings (representations) can be then used as the features to machine learning algorithms for addressing corresponding network tasks. To learn expressive embeddings, current research developments can fall into two major categories: shallow embedding learning and graph neural networks. After a thorough review of the existing literature, we identify several critical challenges that remain unaddressed and discuss future directions. Finally, we build the Heterogeneous Graph Benchmark to facilitate open research for this rapidly-developing topic.

NeurIPS Conference 2020 Conference Paper

Learning Continuous System Dynamics from Irregularly-Sampled Partial Observations

  • Zijie Huang
  • Yizhou Sun
  • Wei Wang

Many real-world systems, such as moving planets, can be considered as multi-agent dynamic systems, where objects interact with each other and co-evolve along with the time. Such dynamics is usually difficult to capture, and understanding and predicting the dynamics based on observed trajectories of objects become a critical research problem in many domains. Most existing algorithms, however, assume the observations are regularly sampled and all the objects can be fully observed at each sampling time, which is impractical for many applications. In this paper, we pro-pose to learn system dynamics from irregularly-sampled and partial observations with underlying graph structure for the first time. To tackle the above challenge, we present LG-ODE, a latent ordinary differential equation generative model for modeling multi-agent dynamic system with known graph structure. It can simultaneously learn the embedding of high dimensional trajectories and infer continuous latent system dynamics. Our model employs a novel encoder parameterized by a graph neural network that can infer initial states in an unsupervised way from irregularly-sampled partial observations of structural objects and utilizes neuralODE to infer arbitrarily complex continuous-time latent dynamics. Experiments on motion capture, spring system, and charged particle datasets demonstrate the effectiveness of our approach.

AAAI Conference 2020 Conference Paper

Learning-Based Efficient Graph Similarity Computation via Multi-Scale Convolutional Set Matching

  • Yunsheng Bai
  • Hao Ding
  • Ken Gu
  • Yizhou Sun
  • Wei Wang

Graph similarity computation is one of the core operations in many graph-based applications, such as graph similarity search, graph database analysis, graph clustering, etc. Since computing the exact distance/similarity between two graphs is typically NP-hard, a series of approximate methods have been proposed with a trade-off between accuracy and speed. Recently, several data-driven approaches based on neural networks have been proposed, most of which model the graphgraph similarity as the inner product of their graph-level representations, with different techniques proposed for generating one embedding per graph. However, using one fixeddimensional embedding per graph may fail to fully capture graphs in varying sizes and link structures—a limitation that is especially problematic for the task of graph similarity computation, where the goal is to find the fine-grained difference between two graphs. In this paper, we address the problem of graph similarity computation from another perspective, by directly matching two sets of node embeddings without the need to use fixed-dimensional vectors to represent whole graphs for their similarity computation. The model, GRAPH- SIM, achieves the state-of-the-art performance on four realworld graph datasets under six out of eight settings (here we count a specific dataset and metric combination as one setting), compared to existing popular methods for approximate Graph Edit Distance (GED) and Maximum Common Subgraph (MCS) computation.

AAAI Conference 2019 Conference Paper

Embedding Uncertain Knowledge Graphs

  • Xuelu Chen
  • Muhao Chen
  • Weijia Shi
  • Yizhou Sun
  • Carlo Zaniolo

Embedding models for deterministic Knowledge Graphs (KG) have been extensively studied, with the purpose of capturing latent semantic relations between entities and incorporating the structured knowledge they contain into machine learning. However, there are many KGs that model uncertain knowledge, which typically model the inherent uncertainty of relations facts with a confidence score, and embedding such uncertain knowledge represents an unresolved challenge. The capturing of uncertain knowledge will benefit many knowledge-driven applications such as question answering and semantic search by providing more natural characterization of the knowledge. In this paper, we propose a novel uncertain KG embedding model UKGE, which aims to preserve both structural and uncertainty information of relation facts in the embedding space. Unlike previous models that characterize relation facts with binary classification techniques, UKGE learns embeddings according to the confidence scores of uncertain relation facts. To further enhance the precision of UKGE, we also introduce probabilistic soft logic to infer confidence scores for unseen relation facts during training. We propose and evaluate two variants of UKGE based on different confidence score modeling strategies. Experiments are conducted on three real-world uncertain KGs via three tasks, i. e. confidence prediction, relation fact ranking, and relation fact classification. UKGE shows effectiveness in capturing uncertain knowledge by achieving promising results, and it consistently outperforms baselines on these tasks.

NeurIPS Conference 2019 Conference Paper

Layer-Dependent Importance Sampling for Training Deep and Large Graph Convolutional Networks

  • Difan Zou
  • Ziniu Hu
  • Yewen Wang
  • Song Jiang
  • Yizhou Sun
  • Quanquan Gu

Graph convolutional networks (GCNs) have recently received wide attentions, due to their successful applications in different graph tasks and different domains. Training GCNs for a large graph, however, is still a challenge. Original full-batch GCN training requires calculating the representation of all the nodes in the graph per GCN layer, which brings in high computation and memory costs. To alleviate this issue, several sampling-based methods are proposed to train GCNs on a subset of nodes. Among them, the node-wise neighbor-sampling method recursively samples a fixed number of neighbor nodes, and thus its computation cost suffers from exponential growing neighbor size across layers; while the layer-wise importance-sampling method discards the neighbor-dependent constraints, and thus the nodes sampled across layer suffer from sparse connection problem. To deal with the above two problems, we propose a new effective sampling algorithm called LAyer-Dependent ImportancE Sampling (LADIES). Based on the sampled nodes in the upper layer, LADIES selects nodes that are in the neighborhood of these nodes and uses the constructed bipartite graph to compute the importance probability. Then, it samples a fixed number of nodes according to the probability for the whole layer, and recursively conducts such procedure per layer to construct the whole computation graph. We prove theoretically and experimentally, that our proposed sampling algorithm outperforms the previous sampling methods regarding both time and memory. Furthermore, LADIES is shown to have better generalization accuracy than original full-batch GCN, due to its stochastic nature.

AAAI Conference 2019 Conference Paper

Personalized Question Routing via Heterogeneous Network Embedding

  • Zeyu Li
  • Jyun-Yu Jiang
  • Yizhou Sun
  • Wei Wang

Question Routing (QR) on Community-based Question Answering (CQA) websites aims at recommending answerers that have high probabilities of providing the “accepted answers” to new questions. The existing question routing algorithms simply predict the ranking of users based on query content. As a consequence, the question raiser information is ignored. On the other hand, they lack learnable scoring functions to explicitly compute ranking scores. To tackle these challenges, we propose NeRank that (1) jointly learns representations of question content, question raiser, and question answerers by a heterogeneous information network embedding algorithm and a long short-term memory (LSTM) model. The embeddings of the three types of entities are unified in the same latent space, and (2) conducts question routing for personalized queries, i. e. , queries with two entities (question content, question raiser), by a convolutional scoring function taking the learned embeddings of all three types of entities as input. Using the scores, NeRank routes new questions to high-ranking answerers that are skillfulness in the question domain and have similar backgrounds to the question raiser. Experimental results show that NeRank significantly outperforms competitive baseline question routing models that ignore the raiser information in three ranking metrics. In addition, NeRank is convergeable in several thousand iterations and insensitive to parameter changes, which prove its effectiveness, scalability, and robustness.

IJCAI Conference 2019 Conference Paper

Unsupervised Inductive Graph-Level Representation Learning via Graph-Graph Proximity

  • Yunsheng Bai
  • Hao Ding
  • Yang Qiao
  • Agustin Marinovic
  • Ken Gu
  • Ting Chen
  • Yizhou Sun
  • Wei Wang

We introduce a novel approach to graph-level representation learning, which is to embed an entire graph into a vector space where the embeddings of two graphs preserve their graph-graph proximity. Our approach, UGraphEmb, is a general framework that provides a novel means to performing graph-level embedding in a completely unsupervised and inductive manner. The learned neural network can be considered as a function that receives any graph as input, either seen or unseen in the training set, and transforms it into an embedding. A novel graph-level embedding generation mechanism called Multi-Scale Node Attention (MSNA), is proposed. Experiments on five real graph datasets show that UGraphEmb achieves competitive accuracy in the tasks of graph classification, similarity ranking, and graph visualization.

ICML Conference 2018 Conference Paper

Learning K-way D-dimensional Discrete Codes for Compact Embedding Representations

  • Ting Chen 0007
  • Martin Renqiang Min
  • Yizhou Sun

Conventional embedding methods directly associate each symbol with a continuous embedding vector, which is equivalent to applying a linear transformation based on a “one-hot” encoding of the discrete symbols. Despite its simplicity, such approach yields the number of parameters that grows linearly with the vocabulary size and can lead to overfitting. In this work, we propose a much more compact K-way D-dimensional discrete encoding scheme to replace the “one-hot" encoding. In the proposed “KD encoding”, each symbol is represented by a $D$-dimensional code with a cardinality of $K$, and the final symbol embedding vector is generated by composing the code embedding vectors. To end-to-end learn semantically meaningful codes, we derive a relaxed discrete optimization approach based on stochastic gradient descent, which can be generally applied to any differentiable computational graph with an embedding layer. In our experiments with various applications from natural language processing to graph convolutional networks, the total size of the embedding layer can be reduced up to 98% while achieving similar or better performance.

IJCAI Conference 2017 Conference Paper

Semi-supervised Learning over Heterogeneous Information Networks by Ensemble of Meta-graph Guided Random Walks

  • He Jiang
  • Yangqiu Song
  • Chenguang Wang
  • Ming Zhang
  • Yizhou Sun

Heterogeneous information networks (HINs) is a general representation of many real world applications. The difference between HIN and traditional homogeneous graphs is that the nodes and edges in HIN are with types. Then in the many applications, we need to consider the types to make the approach more semantically meaningful. For the applications that annotation is expensive, on natural way is to consider semi-supervised learning over HIN. In this paper, we present a semi-supervised learning algorithm constrained by the types of HINs. We first decompose the original HIN into several semantically meaningful sub-graphs based the meta-graphs composed of entity and relation types. Then we perform random walk over the sub-graphs to propagate the labels from labeled data to unlabeled data. After we obtain all the labels propagated by different trials of random walk guided by meta-graphs, we use an ensemble algorithm to vote for the final labeling results. We use two public available datasets, 20-newsgroups and RCV1 datasets to test our algorithm. Experimental results show that our algorithm is better than the traditional semi-supervised learning algorithms for HINs. One particular by-product of this work is that we show that previous random walk approach guided by meta-paths can be non-stationary, which is the major reason we propose a meta-graph guide random walk for semi-supervised learning over HINs.

TIST Journal 2017 Journal Article

ST-SAGE

  • Weiqing Wang
  • Hongzhi Yin
  • Ling Chen
  • Yizhou Sun
  • Shazia Sadiq
  • Xiaofang Zhou

With the rapid development of location-based social networks (LBSNs), spatial item recommendation has become an important mobile application, especially when users travel away from home. However, this type of recommendation is very challenging compared to traditional recommender systems. A user may visit only a limited number of spatial items, leading to a very sparse user-item matrix. This matrix becomes even sparser when the user travels to a distant place, as most of the items visited by a user are usually located within a short distance from the user’s home. Moreover, user interests and behavior patterns may vary dramatically across different time and geographical regions. In light of this, we propose ST-SAGE, a spatial-temporal sparse additive generative model for spatial item recommendation in this article. ST-SAGE considers both personal interests of the users and the preferences of the crowd in the target region at the given time by exploiting both the co-occurrence patterns and content of spatial items. To further alleviate the data-sparsity issue, ST-SAGE exploits the geographical correlation by smoothing the crowd’s preferences over a well-designed spatial index structure called the spatial pyramid. To speed up the training process of ST-SAGE, we implement a parallel version of the model inference algorithm on the GraphLab framework. We conduct extensive experiments; the experimental results clearly demonstrate that ST-SAGE outperforms the state-of-the-art recommender systems in terms of recommendation effectiveness, model training efficiency, and online recommendation efficiency.

IJCAI Conference 2016 Conference Paper

Entity Embedding-Based Anomaly Detection for Heterogeneous Categorical Events

  • Ting Chen
  • Lu-An Tang
  • Yizhou Sun
  • Zhengzhang Chen
  • Kai Zhang

Anomaly detection plays an important role in modern data-driven security applications, such as detecting suspicious access to a socket from a process. In many cases, such events can be described as a collection of categorical values that are considered as entities of different types, which we call heterogeneous categorical events. Due to the lack of intrinsic distance measures among entities, and the exponentially large event space, most existing work relies heavily on heuristics to calculate abnormal scores for events. Different from previous work, we propose a principled and unified probabilistic model APE (Anomaly detection via Probabilistic pairwise interaction and Entity embedding) that directly models the likelihood of events. In this model, we embed entities into a common latent space using their observed co-occurrence in different events. More specifically, we first model the compatibility of each pair of entities according to their embeddings. Then we utilize the weighted pairwise interactions of different entity types to define the event probability. Using Noise-Contrastive Estimation with "context-dependent" noise distribution, our model can be learned efficiently regardless of the large event space. Experimental results on real enterprise surveillance data show that our methods can accurately detect abnormal events compared to other state-of-the-art abnormal detection techniques.

AAAI Conference 2015 Conference Paper

RAIN: Social Role-Aware Information Diffusion

  • Yang Yang
  • Jie Tang
  • Cane Leung
  • Yizhou Sun
  • Qicong Chen
  • Juanzi Li
  • Qiang Yang

Information diffusion, which studies how information is propagated in social networks, has attracted considerable research effort recently. However, most existing approaches do not distinguish social roles that nodes may play in the diffusion process. In this paper, we study the interplay between users’ social roles and their influence on information diffusion. We propose a Role-Aware INformation diffusion model (RAIN) that integrates social role recognition and diffusion modeling into a unified framework. We develop a Gibbssampling based algorithm to learn the proposed model using historical diffusion data. The proposed model can be applied to different scenarios. For instance, at the micro-level, the proposed model can be used to predict whether an individual user will repost a specific message; while at the macro-level, we can use the model to predict the scale and the duration of a diffusion process. We evaluate the proposed model on a real social media data set. Our model performs much better in both micro- and macro-level prediction than several alternative methods.

NeurIPS Conference 2009 Conference Paper

Graph-based Consensus Maximization among Multiple Supervised and Unsupervised Models

  • Jing Gao
  • Feng Liang
  • Wei Fan
  • Yizhou Sun
  • Jiawei Han

Little work has been done to directly combine the outputs of multiple supervised and unsupervised models. However, it can increase the accuracy and applicability of ensemble methods. First, we can boost the diversity of classification ensemble by incorporating multiple clustering outputs, each of which provides grouping constraints for the joint label predictions of a set of related objects. Secondly, ensemble of supervised models is limited in applications which have no access to raw data but to the meta-level model outputs. In this paper, we aim at calculating a consolidated classification solution for a set of objects by maximizing the consensus among both supervised predictions and unsupervised grouping constraints. We seek a global optimal label assignment for the target objects, which is different from the result of traditional majority voting and model combination approaches. We cast the problem into an optimization problem on a bipartite graph, where the objective function favors smoothness in the conditional probability estimates over the graph, as well as penalizes deviation from initial labeling of supervised models. We solve the problem through iterative propagation of conditional probability estimates among neighboring nodes, and interpret the method as conducting a constrained embedding in a transformed space, as well as a ranking on the graph. Experimental results on three real applications demonstrate the benefits of the proposed method over existing alternatives.

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