论文检索

Deep Learning/Graph Neural Networks

Tingting Dan, Jiaqi Ding, Ziquan Wei, Shahar Kovalsky, Minjeong Kim, Won Hwa Kim, Guorong Wu

Graphs are ubiquitous in various domains, such as social networks and biological systems. Despite the great successes of graph neural networks (GNNs) in modeling and analyzing complex graph data, the inductive bias of locality assumption, which involves exchanging information only within neighboring connected nodes, restricts GNNs in capturing long-range dependencies and global patterns in graphs. Inspired by the classic Brachistochrone problem, we seek how to devise a new inductive bias for cutting-edge graph application and present a general framework through the lens of variational analysis. The backbone of our framework is a two-way mapping between the discrete GNN model and continuous diffusion functional, which allows us to design application-specific objective function in the continuous domain and engineer discrete deep model with mathematical guarantees. First, we address over-smoothing in current GNNs. Specifically, our inference reveals that the existing layer-by-layer models of graph embedding learning are equivalent to a ${\ell _2}$-norm integral functional of graph gradients, which is the underlying cause of the over-smoothing problem. Similar to edge-preserving filters in image denoising, we introduce the total variation (TV) to promote alignment of the graph diffusion pattern with the global information present in community topologies. On top of this, we devise a new selective mechanism for inductive bias that can be easily integrated into existing GNNs and effectively address the trade-off between model depth and over-smoothing. Second, we devise a novel generative adversarial network (GAN) to predict the spreading flows in the graph through a neural transport equation. To avoid the potential issue of vanishing flows, we tailor the objective function to minimize the transportation within each community while maximizing the inter-community flows. Our new GNN models achieve state-of-the-art (SOTA) performance on graph learning benchmarks such as Cora, Citeseer, and Pubmed.

Deep Learning/Graph Neural Networks

Iulia Duta, Giulia Cassarà, Fabrizio Silvestri, Pietro Lió

Higher-order relations are widespread in nature, with numerous phenomena involving complex interactions that extend beyond simple pairwise connections. As a result, advancements in higher-order processing can accelerate the growth of various fields requiring structured data. Current approaches typically represent these interactions using hypergraphs.We enhance this representation by introducing cellular sheaves for hypergraphs, a mathematical construction that adds extra structure to the conventional hypergraph while maintaining their local, higher-order connectivity. Drawing inspiration from existing Laplacians in the literature, we develop two unique formulations of sheaf hypergraph Laplacians: linear and non-linear. Our theoretical analysis demonstrates that incorporating sheaves into the hypergraph Laplacian provides a more expressive inductive bias than standard hypergraph diffusion, creating a powerful instrument for effectively modelling complex data structures.We employ these sheaf hypergraph Laplacians to design two categories of models: Sheaf Hypergraph Neural Networks and Sheaf Hypergraph Convolutional Networks. These models generalize classical Hypergraph Networks often found in the literature. Through extensive experimentation, we show that this generalization significantly improves performance, achieving top results on multiple benchmark datasets for hypergraph node classification.

Deep Learning/Graph Neural Networks

Nicolas Keriven, Samuel Vaiter

We aim to deepen the theoretical understanding of Graph Neural Networks (GNNs) on large graphs, with a focus on their expressive power.Existing analyses relate this notion to the graph isomorphism problem, which is mostly relevant for graphs of small sizes, or studied graph classification or regression tasks, while prediction tasks on \emph{nodes} are far more relevant on large graphs. Recently, several works showed that, on very general random graphs models, GNNs converge to certains functions as the number of nodes grows.In this paper, we provide a more complete and intuitive description of the function space generated by equivariant GNNs for node-tasks, through general notions of convergence that encompass several previous examples. We emphasize the role of input node features, and study the impact of \emph{node Positional Encodings} (PEs), a recent line of work that has been shown to yield state-of-the-art results in practice. Through the study of several examples of PEs on large random graphs, we extend previously known universality results to significantly more general models. Our theoretical results hint at some normalization tricks, which is shown numerically to have a positive impact on GNN generalization on synthetic and real data. Our proofs contain new concentration inequalities of independent interest.

Deep Learning/Graph Neural Networks

Mingxuan Ju, Tong Zhao, Wenhao Yu, Neil Shah, Yanfang Ye

Recent studies have shown that graph neural networks (GNNs) exhibit strong biases towards the node degree: they usually perform satisfactorily on high-degree nodes with rich neighbor information but struggle with low-degree nodes. Existing works tackle this problem by deriving either designated GNN architectures or training strategies specifically for low-degree nodes. Though effective, these approaches unintentionally create an artificial out-of-distribution scenario, where models mainly or even only observe low-degree nodes during the training, leading to a downgraded performance for high-degree nodes that GNNs originally perform well at. In light of this, we propose a test-time augmentation framework, namely GraphPatcher, to enhance test-time generalization of any GNNs on low-degree nodes. Specifically, GraphPatcher iteratively generates virtual nodes to patch artificially created low-degree nodes via corruptions, aiming at progressively reconstructing target GNN's predictions over a sequence of increasingly corrupted nodes. Through this scheme, GraphPatcher not only learns how to enhance low-degree nodes (when the neighborhoods are heavily corrupted) but also preserves the original superior performance of GNNs on high-degree nodes (when lightly corrupted). Additionally, GraphPatcher is model-agnostic and can also mitigate the degree bias for either self-supervised or supervised GNNs. Comprehensive experiments are conducted over seven benchmark datasets and GraphPatcher consistently enhances common GNNs' overall performance by up to 3.6% and low-degree performance by up to 6.5%, significantly outperforming state-of-the-art baselines. The source code is publicly available at https://github.com/jumxglhf/GraphPatcher.

Deep Learning/Graph Neural Networks

Anton Tsitsulin, John Palowitch, Bryan Perozzi, Emmanuel Müller

Graph Neural Networks (GNNs) have achieved state-of-the-art results on many graph analysis tasks such as node classification and link prediction. However, important unsupervised problems on graphs, such as graph clustering, have proved more resistant to advances in GNNs. Graph clustering has the same overall goal as node pooling in GNNs—does this mean that GNN pooling methods do a good job at clustering graphs? Surprisingly, the answer is no—current GNN pooling methods often fail to recover the cluster structure in cases where simple baselines, such as k-means applied on learned representations, work well. We investigate further by carefully designing a set of experiments to study different signal-to-noise scenarios both in graph structure and attribute data. To address these methods' poor performance in clustering, we introduce Deep Modularity Networks (DMoN), an unsupervised pooling method inspired by the modularity measure of clustering quality, and show how it tackles recovery of the challenging clustering structure of real-world graphs. Similarly, on real-world data, we show that DMoN produces high quality clusters which correlate strongly with ground truth labels, achieving state-of-the-art results with over 40% improvement over other pooling methods across different metrics.

Deep Learning/Graph Neural Networks

Juanhui Li, Harry Shomer, Haitao Mao, Shenglai Zeng, Yao Ma, Neil Shah, Jiliang Tang, Dawei Yin

Link prediction attempts to predict whether an unseen edge exists based on only a portion of the graph. A flurry of methods has been created in recent years that attempt to make use of graph neural networks (GNNs) for this task. Furthermore, new and diverse datasets have also been created to better evaluate the effectiveness of these new models. However, multiple limitations currently exist that hinders our ability to properly evaluate these new methods. This includes, but is not limited to: (1) The underreporting of performance on multiple baselines, (2) A lack of a unified data split and evaluation metric on some datasets, (3) An unrealistic evaluation setting that produces negative samples that are easy to classify. To overcome these challenges we first conduct a fair comparison across prominent methods and datasets, utilizing the same dataset settings and hyperparameter settings. We then create a new real-world evaluation setting that samples difficult negative samples via multiple heuristics. The new evaluation setting helps promote new challenges and opportunities in link prediction by aligning the evaluation with real-world situations.

Deep Learning/Graph Neural Networks

Fabian Jogl, Maximilian Thiessen, Thomas Gärtner

We systematically investigate graph transformations that enable standard message passing to simulate state-of-the-art graph neural networks (GNNs) without loss of expressivity. Using these, many state-of-the-art GNNs can be implemented with message passing operations from standard libraries, eliminating many sources of implementation issues and allowing for better code optimization. We distinguish between weak and strong simulation: weak simulation achieves the same expressivity only after several message passing steps while strong simulation achieves this after every message passing step. Our contribution leads to a direct way to translate common operations of non-standard GNNs to graph transformations that allow for strong or weak simulation. Our empirical evaluation shows competitive predictive performance of message passing on transformed graphs for various molecular benchmark datasets, in several cases surpassing the original GNNs.

Deep Learning/Graph Neural Networks

Yixiao Zhou, Ruiqi Jia, Hongxiang Lin, Hefeng Quan, Yumeng Zhao, Xiaoqing Lyu

Deriving from image matching and understanding, semantic keypoint matching aims at establishing correspondence between keypoint sets in images. As graphs are powerful tools to represent points and their complex relationships, graph matching provides an effective way to find desired semantic keypoint correspondences. Recent deep graph matching methods have shown excellent performance, but there is still a lack of exploration and utilization of spatial information of keypoints as nodes in graphs. More specifically, existing methods are insufficient to capture the relative spatial relations through current graph construction approaches from the locations of semantic keypoints. To address these issues, we introduce a positional reconstruction encoder-decoder (PR-EnDec) to model intrinsic graph spatial structure, and present an end-to-end graph matching network PREGM based on PR-EnDec. Our PR-EnDec consists of a positional encoder that learns effective node spatial embedding with the affine transformation invariance, and a spatial relation decoder that further utilizes the high-order spatial information by reconstructing the locational structure of graphs contained in the node coordinates. Extensive experimental results on three public keypoint matching datasets demonstrate the effectiveness of our proposed PREGM.

Deep Learning/Graph Neural Networks

Oleg Platonov, Denis Kuznedelev, Artem Babenko, Liudmila Prokhorenkova

Homophily is a graph property describing the tendency of edges to connect similar nodes; the opposite is called heterophily. It is often believed that heterophilous graphs are challenging for standard message-passing graph neural networks (GNNs), and much effort has been put into developing efficient methods for this setting. However, there is no universally agreed-upon measure of homophily in the literature. In this work, we show that commonly used homophily measures have critical drawbacks preventing the comparison of homophily levels across different datasets. For this, we formalize desirable properties for a proper homophily measure and verify which measures satisfy which properties. In particular, we show that a measure that we call adjusted homophily satisfies more desirable properties than other popular homophily measures while being rarely used in graph machine learning literature. Then, we go beyond the homophily-heterophily dichotomy and propose a new characteristic that allows one to further distinguish different sorts of heterophily. The proposed label informativeness (LI) characterizes how much information a neighbor's label provides about a node's label. We prove that this measure satisfies important desirable properties. We also observe empirically that LI better agrees with GNN performance compared to homophily measures, which confirms that it is a useful characteristic of the graph structure.

Deep Learning/Graph Neural Networks

Haoyu Han, Xiaorui Liu, Feng Shi, MohamadAli Torkamani, Charu Aggarwal, Jiliang Tang

Graph Neural Networks (GNNs) have emerged as a powerful tool for semi-supervised node classification tasks. However, recent studies have revealed various biases in GNNs stemming from both node features and graph topology. In this work, we uncover a new bias - label position bias, which indicates that the node closer to the labeled nodes tends to perform better. We introduce a new metric, the Label Proximity Score, to quantify this bias, and find that it is closely related to performance disparities. To address the label position bias, we propose a novel optimization framework for learning a label position unbiased graph structure, which can be applied to existing GNNs. Extensive experiments demonstrate that our proposed method not only outperforms backbone methods but also significantly mitigates the issue of label position bias in GNNs.

Deep Learning/Graph Neural Networks

Hezhe Qiao, Guansong Pang

We reveal a one-class homophily phenomenon, which is one prevalent property we find empirically in real-world graph anomaly detection (GAD) datasets, i.e., normal nodes tend to have strong connection/affinity with each other, while the homophily in abnormal nodes is significantly weaker than normal nodes. However, this anomaly-discriminative property is ignored by existing GAD methods that are typically built using a conventional anomaly detection objective, such as data reconstruction.In this work, we explore this property to introduce a novel unsupervised anomaly scoring measure for GAD -- local node affinity-- that assigns a larger anomaly score to nodes that are less affiliated with their neighbors, with the affinity defined as similarity on node attributes/representations. We further propose Truncated Affinity Maximization (TAM) that learns tailored node representations for our anomaly measure by maximizing the local affinity of nodes to their neighbors. Optimizing on the original graph structure can be biased by non-homophily edges(i.e., edges connecting normal and abnormal nodes). Thus, TAM is instead optimized on truncated graphs where non-homophily edges are removed iteratively to mitigate this bias. The learned representations result in significantly stronger local affinity for normal nodes than abnormal nodes. Extensive empirical results on 10 real-world GAD datasets show that TAM substantially outperforms seven competing models, achieving over 10% increase in AUROC/AUPRC compared to the best contenders on challenging datasets. Our code is available at https://github.com/mala-lab/TAM-master/.

Deep Learning/Graph Neural Networks

Zhihao Wu, Zhao Zhang, Jicong Fan

Graph convolutional networks (GCN) with one or two hidden layers have been widely used in handling graph data that are prevalent in various disciplines. Many studies showed that the gain of making GCNs deeper is tiny or even negative. This implies that the complexity of graph data is often limited and shallow models are often sufficient to extract expressive features for various tasks such as node classification. Therefore, in this work, we present a framework called graph convolutional kernel machine (GCKM) for graph-based machine learning. GCKMs are built upon kernel functions integrated with graph convolution. An example is the graph convolutional kernel support vector machine (GCKSVM) for node classification, for which we analyze the generalization error bound and discuss the impact of the graph structure. Compared to GCNs, GCKMs require much less effort in architecture design, hyperparameter tuning, and optimization. More importantly, GCKMs are guaranteed to obtain globally optimal solutions and have strong generalization ability and high interpretability. GCKMs are composable, can be extended to large-scale data, and are applicable to various tasks (e.g., node or graph classification, clustering, feature extraction, dimensionality reduction). The numerical results on benchmark datasets show that, besides the aforementioned advantages, GCKMs have at least competitive accuracy compared to GCNs.

Deep Learning/Graph Neural Networks

Lorenzo Brusca, Lars C.P.M. Quaedvlieg, Stratis Skoulakis, Grigorios Chrysos, Volkan Cevher

This work presents a graph neural network (GNN) framework for solving the maximum independent set (MIS) problem, inspired by dynamic programming (DP). Specifically, given a graph, we propose a DP-like recursive algorithm based on GNNs that firstly constructs two smaller sub-graphs, predicts the one with the larger MIS, and then uses it in the next recursive call. To train our algorithm, we require annotated comparisons of different graphs concerning their MIS size. Annotating the comparisons with the output of our algorithm leads to a self-training process that results in more accurate self-annotation of the comparisons and vice versa. We provide numerical evidence showing the superiority of our method vs prior methods in multiple synthetic and real-world datasets.

Deep Learning/Graph Neural Networks

Namyong Park, Ryan Rossi, Xing Wang, Antoine Simoulin, Nesreen K. Ahmed, Christos Faloutsos

The choice of a graph learning (GL) model (i.e., a GL algorithm and its hyperparameter settings) has a significant impact on the performance of downstream tasks. However, selecting the right GL model becomes increasingly difficult and time consuming as more and more GL models are developed. Accordingly, it is of great significance and practical value to equip users of GL with the ability to perform a near-instantaneous selection of an effective GL model without manual intervention. Despite the recent attempts to tackle this important problem, there has been no comprehensive benchmark environment to evaluate the performance of GL model selection methods. To bridge this gap, we present GLEMOS in this work, a comprehensive benchmark for instantaneous GL model selection that makes the following contributions. (i) GLEMOS provides extensive benchmark data for fundamental GL tasks, i.e., link prediction and node classification, including the performances of 366 models on 457 graphs on these tasks. (ii) GLEMOS designs multiple evaluation settings, and assesses how effectively representative model selection techniques perform in these different settings. (iii) GLEMOS is designed to be easily extended with new models, new graphs, and new performance records. (iv) Based on the experimental results, we discuss the limitations of existing approaches and highlight future research directions. To promote research on this significant problem, we make the benchmark data and code publicly available at https://namyongpark.github.io/glemos.

Deep Learning/Graph Neural Networks

Sangwoo Seo, Sungwon Kim, Chanyoung Park

The success of Graph Neural Networks (GNNs) has led to a need for understanding their decision-making process and providing explanations for their predictions, which has given rise to explainable AI (XAI) that offers transparent explanations for black-box models. Recently, the use of prototypes has successfully improved the explainability of models by learning prototypes to imply training graphs that affect the prediction. However, these approaches tend to provide prototypes with excessive information from the entire graph, leading to the exclusion of key substructures or the inclusion of irrelevant substructures, which can limit both the interpretability and the performance of the model in downstream tasks. In this work, we propose a novel framework of explainable GNNs, called interpretable Prototype-based Graph Information Bottleneck (PGIB) that incorporates prototype learning within the information bottleneck framework to provide prototypes with the key subgraph from the input graph that is important for the model prediction. This is the first work that incorporates prototype learning into the process of identifying the key subgraphs that have a critical impact on the prediction performance. Extensive experiments, including qualitative analysis, demonstrate that PGIB outperforms state-of-the-art methods in terms of both prediction performance and explainability.

Deep Learning/Graph Neural Networks

Yannik Mahlau, Lukas Berg, Leonie Kayser

Yuan et al. claim their proposed method SubgraphX achieves (i) higher fidelity in explaining models for graph- and node classification tasks compared to other explanation techniques, namely GNNExplainer. Additionally, (ii) the computational effort of SubgraphX is at a 'reasonable level', which is not further specified by the original authors. We define this as at most ten times slower than GNNExplainer. We reimplemented the proposed algorithm in PyTorch. Then, we replicated the experiments performed by the authors on a smaller scale due to resource constraints. Additionally, we checked the performance on a new dataset and investigated the influence of hyperparameters. Lastly, we improved SubgraphX using greedy initialization and utilizing fidelity as a score function. We were able to reproduce the main claims on the MUTAG dataset, where SubgraphX has a better performance than GNNExplainer. Furthermore, SubgraphX has a reasonable runtime of about seven times longer than GNNExplainer. We successfully employed SubgraphX on the Karate Club dataset, where it outperforms GNNExplainer as well. The hyperparameter study revealed that the number of Monte-Carlo Tree search iterations and Monte-Carlo sampling steps are the most important hyperparameters and directly trade performance for runtime. Lastly, we show that our proposed improvements to SubgraphX significantly enhance fidelity and runtime. The authors' description of the algorithm was clear and concise. The original implementation is available in the DIG-library as a reference to our implementation. The authors performed extensive experiments, which we could not replicate in their full scale due to resource constraints. However, we were able to achieve similar results on a subset of the datasets used. Another issue was that despite the original code of the authors and datasets being publicly available, there were many compatibility issues. The original authors briefly reviewed our work and agreed with the findings.

Deep Learning/Graph Neural Networks

Nimrah Mustafa, Aleksandar Bojchevski, Rebekka Burkholz

While the expressive power and computational capabilities of graph neural networks (GNNs) have been theoretically studied, their optimization and learning dynamics, in general, remain largely unexplored. Our study undertakes the Graph Attention Network (GAT), a popular GNN architecture in which a node's neighborhood aggregation is weighted by parameterized attention coefficients. We derive a conservation law of GAT gradient flow dynamics, which explains why a high portion of parameters in GATs with standard initialization struggle to change during training. This effect is amplified in deeper GATs, which perform significantly worse than their shallow counterparts. To alleviate this problem, we devise an initialization scheme that balances the GAT network. Our approach i) allows more effective propagation of gradients and in turn enables trainability of deeper networks, and ii) attains a considerable speedup in training and convergence time in comparison to the standard initialization. Our main theorem serves as a stepping stone to studying the learning dynamics of positive homogeneous models with attention mechanisms.

Deep Learning/Graph Neural Networks

Qian Huang, Hongyu Ren, Peng Chen, Gregor Kržmanc, Daniel Zeng, Percy Liang, Jure Leskovec

In-context learning is the ability of a pretrained model to adapt to novel and diverse downstream tasks by conditioning on prompt examples, without optimizing any parameters. While large language models have demonstrated this ability, how in-context learning could be performed over graphs is unexplored. In this paper, we develop \textbf{Pr}etraining \textbf{O}ver \textbf{D}iverse \textbf{I}n-Context \textbf{G}raph S\textbf{y}stems (PRODIGY), the first pretraining framework that enables in-context learning over graphs. The key idea of our framework is to formulate in-context learning over graphs with a novel \emph{prompt graph} representation, which connects prompt examples and queries. We then propose a graph neural network architecture over the prompt graph and a corresponding family of in-context pretraining objectives. With PRODIGY, the pretrained model can directly perform novel downstream classification tasks on unseen graphs via in-context learning. We provide empirical evidence of the effectiveness of our framework by showcasing its strong in-context learning performance on tasks involving citation networks and knowledge graphs. Our approach outperforms the in-context learning accuracy of contrastive pretraining baselines with hard-coded adaptation by 18\% on average across all setups. Moreover, it also outperforms standard finetuning with limited data by 33\% on average with in-context learning.

Deep Learning/Graph Neural Networks

Junliang Li, Yang Yajun, Qinghua Hu, Xin Wang, Hong Gao

Trending topic diffusion and prediction analysis is an important problem and has been well studied in social networks. Representation learning is an effective way to extract node embeddings, which can help for topic propagation analysis by completing downstream tasks such as link prediction and node classification. In real world, there are often several trending topics or opinion leaders in public opinion space at the same time and they can be regarded as different centers of public opinion. A public opinion field will be formed surrounding every center. These public opinion fields compete for public's attention and it will potentially affect the development of public opinion. However, the existing methods do not consider public opinion field effect for trending topics diffusion. In this paper, we introduce three well-known observations about public opinion field effect in media and communication studies, and propose a novel and effective heterogeneous representation learning framework to incorporate public opinion field effect and social circle influence effect. To the best of our knowledge, our work is the first to consider these effects in representation learning for trending topic diffusion. Extensive experiments on real-world datasets validate the superiority of our model.

Deep Learning/Graph Neural Networks

Derek Lim, Joshua Robinson, Stefanie Jegelka, Haggai Maron

Recent work has shown the utility of developing machine learning models that respect the structure and symmetries of eigenvectors. These works promote sign invariance, since for any eigenvector v the negation -v is also an eigenvector. However, we show that sign invariance is theoretically limited for tasks such as building orthogonally equivariant models and learning node positional encodings for link prediction in graphs. In this work, we demonstrate the benefits of sign equivariance for these tasks. To obtain these benefits, we develop novel sign equivariant neural network architectures. Our models are based on a new analytic characterization of sign equivariant polynomials and thus inherit provable expressiveness properties. Controlled synthetic experiments show that our networks can achieve the theoretically predicted benefits of sign equivariant models.