论文检索

Deep Learning/Graph Neural Networks

Seiyun Shin, Ilan Shomorony, Han Zhao

Graph Neural Networks (GNNs) are a powerful class of machine learning models with applications in recommender systems, drug discovery, social network analysis, and computer vision. One challenge with their implementation is that GNNs often take large-scale graphs as inputs, which imposes significant computational/storage costs in the training and testing phases. In particular, the message passing operations of a GNN require multiplication of the graph adjacency matrix $A \in \mathbb{R}^{n \times n}$ and the data matrix $X \in \mathbb{R}^{n \times d}$, and the $O(n^2 d)$ time complexity can be prohibitive for large $n$. Thus, a natural question is whether it is possible to perform the GNN operations in (quasi-)linear time by avoiding the full computation of $A X$. To study this question, we consider the setting of a regression task on a two-layer Linear Graph Convolutional Network (GCN). We develop an efficient training algorithm based on (1) performing node subsampling, (2) estimating the leverage scores of $A X$ based on the subsampled graph, and (3) performing leverage score sampling on $A X$. We show that our proposed scheme learns the regression model observing only $O(nd\epsilon^{-2}\log n)$ entries of $A$ in time $O(nd^2 \epsilon^{-2}\log n)$, with the guarantee that the learned weights deviate by at most $\epsilon$ under the $\ell_2$ norm from the model learned using the entire adjacency matrix $A$. We present empirical results for regression problems on real-world graphs and show that our algorithm significantly outperforms other baseline sampling strategies that exploit the same number of observations.

Deep Learning/Graph Neural Networks

Tianyu Liu, Qitan Lv, Jie Wang, Shuling Yang, Hanzhu Chen

Inductive relation prediction (IRP)---where entities can be different during training and inference---has shown great power for completing evolving knowledge graphs. Existing works mainly focus on using graph neural networks (GNNs) to learn the representation of the subgraph induced from the target link, which can be seen as an implicit rule-mining process to measure the plausibility of the target link. However, these methods are not able to differentiate the target link and other links during message passing, hence the final subgraph representation will contain irrelevant rule information to the target link, which reduces the reasoning performance and severely hinders the applications for real-world scenarios. To tackle this problem, we propose a novel $\textit{single-source edge-wise}$ GNN model to learn the $\textbf{R}$ule-induc$\textbf{E}$d $\textbf{S}$ubgraph represen$\textbf{T}$ations $(\textbf{REST}$), which encodes relevant rules and eliminates irrelevant rules within the subgraph. Specifically, we propose a $\textit{single-source}$ initialization approach to initialize edge features only for the target link, which guarantees the relevance of mined rules and target link. Then we propose several RNN-based functions for $\textit{edge-wise}$ message passing to model the sequential property of mined rules. REST is a simple and effective approach with theoretical support to learn the $\textit{rule-induced subgraph representation}$. Moreover, REST does not need node labeling, which significantly accelerates the subgraph preprocessing time by up to $\textbf{11.66}\times$. Experiments on inductive relation prediction benchmarks demonstrate the effectiveness of our REST.

Deep Learning/Graph Neural Networks

Yizhou Chen, Anxiang Zeng, Qingtao Yu, Kerui Zhang, Cao Yuanpeng, Kangle Wu, Guangda Huzhang, Han Yu, Zhiming Zhou

Temporal graphs offer more accurate modeling of many real-world scenarios than static graphs. However, neighbor aggregation, a critical building block of graph networks, for temporal graphs, is currently straightforwardly extended from that of static graphs. It can be computationally expensive when involving all historical neighbors during such aggregation. In practice, typically only a subset of the most recent neighbors are involved. However, such subsampling leads to incomplete and biased neighbor information. To address this limitation, we propose a novel framework for temporal neighbor aggregation that uses the recurrent neural network with node-wise hidden states to integrate information from all historical neighbors for each node to acquire the complete neighbor information. We demonstrate the superior theoretical expressiveness of the proposed framework as well as its state-of-the-art performance in real-world applications. Notably, it achieves a significant +9.4% improvement on averaged precision in a real-world Ecommerce dataset over existing methods on 2-layer models.

Deep Learning/Graph Neural Networks

weitao Du, Yuanqi Du, Limei Wang, Dieqiao Feng, Guifeng Wang, Shuiwang Ji, Carla Gomes, Zhi-Ming Ma

Geometric deep learning enables the encoding of physical symmetries in modeling 3D objects. Despite rapid progress in encoding 3D symmetries into Graph Neural Networks (GNNs), a comprehensive evaluation of the expressiveness of these network architectures through a local-to-global analysis lacks today. In this paper, we propose a local hierarchy of 3D isomorphism to evaluate the expressive power of equivariant GNNs and investigate the process of representing global geometric information from local patches. Our work leads to two crucial modules for designing expressive and efficient geometric GNNs; namely local substructure encoding (\textbf{LSE}) and frame transition encoding (\textbf{FTE}). To demonstrate the applicability of our theory, we propose LEFTNet which effectively implements these modules and achieves state-of-the-art performance on both scalar-valued and vector-valued molecular property prediction tasks. We further point out future design space for 3D equivariant graph neural networks. Our codes are available at \url{https://github.com/yuanqidu/LeftNet}.

Deep Learning/Graph Neural Networks

Xinyi Wu, Amir Ajorlou, Zihui Wu, Ali Jadbabaie

Oversmoothing in Graph Neural Networks (GNNs) refers to the phenomenon where increasing network depth leads to homogeneous node representations. While previous work has established that Graph Convolutional Networks (GCNs) exponentially lose expressive power, it remains controversial whether the graph attention mechanism can mitigate oversmoothing. In this work, we provide a definitive answer to this question through a rigorous mathematical analysis, by viewing attention-based GNNs as nonlinear time-varying dynamical systems and incorporating tools and techniques from the theory of products of inhomogeneous matrices and the joint spectral radius. We establish that, contrary to popular belief, the graph attention mechanism cannot prevent oversmoothing and loses expressive power exponentially. The proposed framework extends the existing results on oversmoothing for symmetric GCNs to a significantly broader class of GNN models, including random walk GCNs, Graph Attention Networks (GATs) and (graph) transformers. In particular, our analysis accounts for asymmetric, state-dependent and time-varying aggregation operators and a wide range of common nonlinear activation functions, such as ReLU, LeakyReLU, GELU and SiLU.

Deep Learning/Graph Neural Networks

Hiren Madhu, Sundeep Prabhakar Chepuri

In this paper, we introduce $\texttt{TopoSRL}$, a novel self-supervised learning (SSL) method for simplicial complexes to effectively capture higher-order interactions and preserve topology in the learned representations. $\texttt{TopoSRL}$ addresses the limitations of existing graph-based SSL methods that typically concentrate on pairwise relationships, neglecting long-range dependencies crucial to capture topological information. We propose a new simplicial augmentation technique that generates two views of the simplicial complex that enriches the representations while being efficient. Next, we propose a new simplicial contrastive loss function that contrasts the generated simplices to preserve local and global information present in the simplicial complexes. Extensive experimental results demonstrate the superior performance of $\texttt{TopoSRL}$ compared to state-of-the-art graph SSL techniques and supervised simplicial neural models across various datasets corroborating the efficacy of $\texttt{TopoSRL}$ in processing simplicial complex data in a self-supervised setting.

Deep Learning/Graph Neural Networks

Zixing Song, Yifei Zhang, Irwin King

Graph Neural Networks (GNNs) are crucial for machine learning applications with graph-structured data, but their success depends on sufficient labeled data. We present a novel active learning (AL) method for GNNs, extending the Expected Model Change Maximization (EMCM) principle to improve prediction performance on unlabeled data. By presenting a Bayesian interpretation for the node embeddings generated by GNNs under the semi-supervised setting, we efficiently compute the closed-form EMCM acquisition function as the selection criterion for AL without re-training. Our method establishes a direct connection with expected prediction error minimization, offering theoretical guarantees for AL performance. Experiments demonstrate our method's effectiveness compared to existing approaches, in terms of both accuracy and efficiency.

Deep Learning/Graph Neural Networks

Yixin Liu, Kaize Ding, Qinghua Lu, Fuyi Li, Leo Yu Zhang, Shirui Pan

Graph-level anomaly detection (GLAD) aims to identify graphs that exhibit notable dissimilarity compared to the majority in a collection. However, current works primarily focus on evaluating graph-level abnormality while failing to provide meaningful explanations for the predictions, which largely limits their reliability and application scope. In this paper, we investigate a new challenging problem, explainable GLAD, where the learning objective is to predict the abnormality of each graph sample with corresponding explanations, i.e., the vital subgraph that leads to the predictions. To address this challenging problem, we propose a Self-Interpretable Graph aNomaly dETection model (SIGNET for short) that detects anomalous graphs as well as generates informative explanations simultaneously. Specifically, we first introduce the multi-view subgraph information bottleneck (MSIB) framework, serving as the design basis of our self-interpretable GLAD approach. This way SIGNET is able to not only measure the abnormality of each graph based on cross-view mutual information but also provide informative graph rationales by extracting bottleneck subgraphs from the input graph and its dual hypergraph in a self-supervised way. Extensive experiments on 16 datasets demonstrate the anomaly detection capability and self-interpretability of SIGNET.

Deep Learning/Graph Neural Networks

Cai Zhou, Xiyuan Wang, Muhan Zhang

Node-level random walk has been widely used to improve Graph Neural Networks. However, there is limited attention to random walk on edge and, more generally, on $k$-simplices. This paper systematically analyzes how random walk on different orders of simplicial complexes (SC) facilitates GNNs in their theoretical expressivity. First, on $0$-simplices or node level, we establish a connection between existing positional encoding (PE) and structure encoding (SE) methods through the bridge of random walk. Second, on $1$-simplices or edge level, we bridge edge-level random walk and Hodge $1$-Laplacians and design corresponding edge PE respectively. In spatial domain, we directly make use of edge level random walk to construct EdgeRWSE. Based on spectral analysis of Hodge $1$-Laplcians, we propose Hodge1Lap, a permutation equivariant and expressive edge-level positional encoding. Third, we generalize our theory to random walk on higher-order simplices and propose the general principle to design PE on simplices based on random walk and Hodge Laplacians. Inter-level random walk is also introduced to unify a wide range of simplicial networks. Extensive experiments verify the effectiveness of our random walk-based methods.

Deep Learning/Graph Neural Networks

Qitian Wu, Wentao Zhao, Chenxiao Yang, Hengrui Zhang, Fan Nie, Haitian Jiang, Yatao Bian, Junchi Yan

Learning representations on large-sized graphs is a long-standing challenge due to the inter-dependence nature involved in massive data points. Transformers, as an emerging class of foundation encoders for graph-structured data, have shown promising performance on small graphs due to its global attention capable of capturing all-pair influence beyond neighboring nodes. Even so, existing approaches tend to inherit the spirit of Transformers in language and vision tasks, and embrace complicated models by stacking deep multi-head attentions. In this paper, we critically demonstrate that even using a one-layer attention can bring up surprisingly competitive performance across node property prediction benchmarks where node numbers range from thousand-level to billion-level. This encourages us to rethink the design philosophy for Transformers on large graphs, where the global attention is a computation overhead hindering the scalability. We frame the proposed scheme as Simplified Graph Transformers (SGFormer), which is empowered by a simple attention model that can efficiently propagate information among arbitrary nodes in one layer. SGFormer requires none of positional encodings, feature/graph pre-processing or augmented loss. Empirically, SGFormer successfully scales to the web-scale graph ogbn-papers100M and yields up to 141x inference acceleration over SOTA Transformers on medium-sized graphs. Beyond current results, we believe the proposed methodology alone enlightens a new technical path of independent interest for building Transformers on large graphs.

Deep Learning/Graph Neural Networks

Hao Yan, Chaozhuo Li, Ruosong Long, Chao Yan, Jianan Zhao, Wenwen Zhuang, Jun Yin, Peiyan Zhang, Weihao Han, Hao Sun 等

Text-attributed graphs (TAGs) are prevalent in various real-world scenarios, where each node is associated with a text description. The cornerstone of representation learning on TAGs lies in the seamless integration of textual semantics within individual nodes and the topological connections across nodes. Recent advancements in pre-trained language models (PLMs) and graph neural networks (GNNs) have facilitated effective learning on TAGs, garnering increased research interest. However, the absence of meaningful benchmark datasets and standardized evaluation procedures for TAGs has impeded progress in this field. In this paper, we propose CS-TAG, a comprehensive and diverse collection of challenging benchmark datasets for TAGs. The CS-TAG datasets are notably large in scale and encompass a wide range of domains, spanning from citation networks to purchase graphs. In addition to building the datasets, we conduct extensive benchmark experiments over CS-TAG with various learning paradigms, including PLMs, GNNs, PLM-GNN co-training methods, and the proposed novel topological pre-training of language models. In a nutshell, we provide an overview of the CS-TAG datasets, standardized evaluation procedures, and present baseline experiments. The entire CS-TAG project is publicly accessible at \url{https://github.com/sktsherlock/TAG-Benchmark}.

Deep Learning/Graph Neural Networks

Senzhang Wang, Jun Yin, Chaozhuo Li, Xing Xie, Jianxin Wang

GNN explanation method aims to identify an explanatory subgraph which contains the most informative components of the full graph. However, a major limitation of existing GNN explainers is that they are not robust to the structurally corrupted graphs, e.g., graphs with noisy or adversarial edges. On the one hand, existing GNN explainers mostly explore explanations based on either the raw graph features or the learned latent representations, both of which can be easily corrupted. On the other hand, the corruptions in graphs are irregular in terms of the structural properties, e.g., the size or connectivity of graphs, which makes the rigorous constraints used by previous GNN explainers unfeasible. To address these issues, we propose a robust GNN explainer called V-InfoR. Specifically, a robust graph representation extractor, which takes insights of variational inference, is proposed to infer the latent distribution of graph representations. Instead of directly using the corrupted raw features or representations of each single graph, we sample the graph representations from the inferred distribution for the downstream explanation generator, which can effectively eliminate the minor corruption. We next formulate the explanation exploration as a graph information bottleneck (GIB) optimization problem. As a more general method that does not need any rigorous structural constraints, our GIB-based method can adaptively capture both the regularity and irregularity of the severely corrupted graphs for explanation. Extensive evaluations on both synthetic and real-world datasets indicate that V-InfoR significantly improves the GNN explanation performance for the structurally corrupted graphs. Code and dataset are available at https://anonymous.4open.science/r/V-InfoR-EF88

Deep Learning/Graph Neural Networks

Anwar Said, Roza Bayrak, Tyler Derr, Mudassir Shabbir, Daniel Moyer, Catie Chang, Xenofon Koutsoukos

Machine learning provides a valuable tool for analyzing high-dimensional functional neuroimaging data, and is proving effective in predicting various neurological conditions, psychiatric disorders, and cognitive patterns. In functional magnetic resonance imaging (MRI) research, interactions between brain regions are commonly modeled using graph-based representations. The potency of graph machine learning methods has been established across myriad domains, marking a transformative step in data interpretation and predictive modeling. Yet, despite their promise, the transposition of these techniques to the neuroimaging domain has been challenging due to the expansive number of potential preprocessing pipelines and the large parameter search space for graph-based dataset construction. In this paper, we introduce NeuroGraph, a collection of graph-based neuroimaging datasets, and demonstrated its utility for predicting multiple categories of behavioral and cognitive traits. We delve deeply into the dataset generation search space by crafting 35 datasets that encompass static and dynamic brain connectivity, running in excess of 15 baseline methods for benchmarking. Additionally, we provide generic frameworks for learning on both static and dynamic graphs. Our extensive experiments lead to several key observations. Notably, using correlation vectors as node features, incorporating larger number of regions of interest, and employing sparser graphs lead to improved performance. To foster further advancements in graph-based data driven neuroimaging analysis, we offer a comprehensive open-source Python package that includes the benchmark datasets, baseline implementations, model training, and standard evaluation.

Deep Learning/Graph Neural Networks

Zun Wang, Guoqing Liu, Yichi Zhou, Tong Wang, Bin Shao

Machine learning force fields (MLFFs) have instigated a groundbreaking shift in molecular dynamics (MD) simulations across a wide range of fields, such as physics, chemistry, biology, and materials science. Incorporating higher order many-body interactions can enhance the expressiveness and accuracy of models. Recent models have achieved this by explicitly including up to four-body interactions. However, five-body interactions, which have relevance in various fields, are still challenging to incorporate efficiently into MLFFs. In this work, we propose the quintuple network (QuinNet), an end-to-end graph neural network that efficiently expresses many-body interactions up to five-body interactions with \emph{ab initio} accuracy. By analyzing the topology of diverse many-body interactions, we design the model architecture to efficiently and explicitly represent these interactions. We evaluate QuinNet on public datasets of small molecules, such as MD17 and its revised version, and show that it is compatible with other state-of-the-art models on these benchmarks. Moreover, QuinNet surpasses many leading models on larger and more complex molecular systems, such as MD22 and Chignolin, without increasing the computational complexity. We also use QuinNet as a force field for molecular dynamics (MD) simulations to demonstrate its accuracy and stability, and conduct an ablation study to elucidate the significance of five-body interactions. We open source our implementation at https://github.com/Zun-Wang/QuinNet.

Deep Learning/Graph Neural Networks

Langzhang Liang, Xiangjing Hu, Zenglin Xu, Zixing Song, Irwin King

Graph Neural Networks (GNNs) have been shown to achieve remarkable performance on node classification tasks by exploiting both graph structures and node features. The majority of existing GNNs rely on the implicit homophily assumption. Recent studies have demonstrated that GNNs may struggle to model heterophilous graphs where nodes with different labels are more likely connected. To address this issue, we propose a generic GNN applicable to both homophilous and heterophilous graphs, namely Low-Rank Graph Neural Network (LRGNN). Our analysis demonstrates that a signed graph's global label relationship matrix has a low rank. This insight inspires us to predict the label relationship matrix by solving a robust low-rank matrix approximation problem, as prior research has proven that low-rank approximation could achieve perfect recovery under certain conditions. The experimental results reveal that the solution bears a strong resemblance to the label relationship matrix, presenting two advantages for graph modeling: a block diagonal structure and varying distributions of within-class and between-class entries.

Deep Learning/Graph Neural Networks

Ningyi Liao, Siqiang Luo, Xiang Li, Jieming Shi

Heterophilous Graph Neural Network (GNN) is a family of GNNs that specializes in learning graphs under heterophily, where connected nodes tend to have different labels. Most existing heterophilous models incorporate iterative non-local computations to capture node relationships. However, these approaches have limited application to large-scale graphs due to their high computational costs and challenges in adopting minibatch schemes. In this work, we study the scalability issues of heterophilous GNN and propose a scalable model, LD2, which simplifies the learning process by decoupling graph propagation and generating expressive embeddings prior to training. Theoretical analysis demonstrates that LD2 achieves optimal time complexity in training, as well as a memory footprint that remains independent of the graph scale. We conduct extensive experiments to showcase that our model is capable of lightweight minibatch training on large-scale heterophilous graphs, with up to $15\times$ speed improvement and efficient memory utilization, while maintaining comparable or better performance than the baselines.

Deep Learning/Graph Neural Networks

Yue Yu, Xiao Wang, Mengmei Zhang, Nian Liu, Chuan Shi

Graph Contrastive Learning (GCL) has emerged as a popular training approach for learning node embeddings from augmented graphs without labels. Despite the key principle that maximizing the similarity between positive node pairs while minimizing it between negative node pairs is well established, some fundamental problems are still unclear. Considering the complex graph structure, are some nodes consistently well-trained and following this principle even with different graph augmentations? Or are there some nodes more likely to be untrained across graph augmentations and violate the principle? How to distinguish these nodes and further guide the training of GCL? To answer these questions, we first present experimental evidence showing that the training of GCL is indeed imbalanced across all nodes. To address this problem, we propose the metric "node compactness", which is the lower bound of how a node follows the GCL principle related to the range of augmentations. We further derive the form of node compactness theoretically through bound propagation, which can be integrated into binary cross-entropy as a regularization. To this end, we propose the PrOvable Training (POT) for GCL, which regularizes the training of GCL to encode node embeddings that follows the GCL principle better. Through extensive experiments on various benchmarks, POT consistently improves the existing GCL approaches, serving as a friendly plugin.

Deep Learning/Graph Neural Networks

Erik Arakelyan, Pasquale Minervini, Daniel Daza, Michael Cochez, Isabelle Augenstein

Answering complex queries on incomplete knowledge graphs is a challenging task where a model needs to answer complex logical queries in the presence of missing knowledge. Prior work in the literature has proposed to address this problem by designing architectures trained end-to-end for the complex query answering task with a reasoning process that is hard to interpret while requiring data and resource-intensive training. Other lines of research have proposed re-using simple neural link predictors to answer complex queries, reducing the amount of training data by orders of magnitude while providing interpretable answers. The neural link predictor used in such approaches is not explicitly optimised for the complex query answering task, implying that its scores are not calibrated to interact together. We propose to address these problems via CQD$^{\mathcal{A}}$, a parameter-efficient score \emph{adaptation} model optimised to re-calibrate neural link prediction scores for the complex query answering task. While the neural link predictor is frozen, the adaptation component -- which only increases the number of model parameters by $0.03\%$ -- is trained on the downstream complex query answering task. Furthermore, the calibration component enables us to support reasoning over queries that include atomic negations, which was previously impossible with link predictors. In our experiments, CQD$^{\mathcal{A}}$ produces significantly more accurate results than current state-of-the-art methods, improving from $34.4$ to $35.1$ Mean Reciprocal Rank values averaged across all datasets and query types while using $\leq 30\%$ of the available training query types. We further show that CQD$^{\mathcal{A}}$ is data-efficient, achieving competitive results with only $1\%$ of the complex training queries and robust in out-of-domain evaluations. Source code and datasets are available at https://github.com/EdinburghNLP/adaptive-cqd.

Deep Learning/Graph Neural Networks

Chanakya Ekbote, Ajinkya Deshpande, Arun Iyer, SUNDARARAJAN SELLAMANICKAM, Ramakrishna Bairi

Unsupervised node representations learnt using contrastive learning-based methods have shown good performance on downstream tasks. However, these methods rely on augmentations that mimic low-pass filters, limiting their performance on tasks requiring different eigen-spectrum parts. This paper presents a simple filter-based augmentation method to capture different parts of the eigen-spectrum. We show significant improvements using these augmentations. Further, we show that sharing the same weights across these different filter augmentations is possible, reducing the computational load. In addition, previous works have shown that good performance on downstream tasks requires high dimensional representations. Working with high dimensions increases the computations, especially when multiple augmentations are involved. We mitigate this problem and recover good performance through lower dimensional embeddings using simple random Fourier feature projections. Our method, FiGURe, achieves an average gain of up to 4.4\%, compared to the state-of-the-art unsupervised models, across all datasets in consideration, both homophilic and heterophilic. Our code can be found at: https://github.com/Microsoft/figure.

Deep Learning/Graph Neural Networks

David Ruhe, Johannes Brandstetter, Patrick Forré

We introduce Clifford Group Equivariant Neural Networks: a novel approach for constructing $\mathrm{O}(n)$- and $\mathrm{E}(n)$-equivariant models. We identify and study the *Clifford group*: a subgroup inside the Clifford algebra tailored to achieve several favorable properties. Primarily, the group's action forms an orthogonal automorphism that extends beyond the typical vector space to the entire Clifford algebra while respecting the multivector grading. This leads to several non-equivalent subrepresentations corresponding to the multivector decomposition. Furthermore, we prove that the action respects not just the vector space structure of the Clifford algebra but also its multiplicative structure, i.e., the geometric product. These findings imply that every polynomial in multivectors, including their grade projections, constitutes an equivariant map with respect to the Clifford group, allowing us to parameterize equivariant neural network layers. An advantage worth mentioning is that we obtain expressive layers that can elegantly generalize to inner-product spaces of any dimension. We demonstrate, notably from a single core implementation, state-of-the-art performance on several distinct tasks, including a three-dimensional $n$-body experiment, a four-dimensional Lorentz-equivariant high-energy physics experiment, and a five-dimensional convex hull experiment.