Graphs are a powerful data structure for representing relational data, and Graph Neural Networks (GNNs) have emerged as effective tools for inference and learning on graph-structured data. Probabilistic Graphical Models (PGMs), which provide compact graphical representations of variable distributions, offer a complementary approach with well-developed methods for capturing relationships and conducting message passing. In this survey, we explore how PGMs can enhance GNNs. We discuss how GNNs benefit from structured representations in PGMs, generate explainable predictions, and infer relationships. We also examine how GNNs are used within PGMs for more efficient inference and structure learning.

Graph Neural Networks (GNNs) have demonstrated strong capabilities in processing structured data. While traditional GNNs typically treat each feature dimension equally important during graph convolution, we raise an important question: **Is the graph convolution operation equally beneficial for each feature?** If not, the convolution operation on certain feature dimensions can possibly lead to harmful effects, even worse than convolution-free models. Therefore, it is required to distinguish convolution-favored and convolution-disfavored features. Traditional feature selection methods mainly focus on identifying informative features or reducing redundancy, but they are not suitable for structured data as they overlook graph structures. In graph community, some studies have investigated the performance of GNN with respect to node features using feature homophily metrics, which assess feature consistency across graph topology. Unfortunately, these metrics do not effectively align with GNN performance and cannot be reliably used for feature selection in GNNs. To address these limitations, we introduce a novel metric, Topological Feature Informativeness (TFI), to distinguish GNN-favored and GNN-disfavored features, where its effectiveness is validated through both theoretical analysis and empirical observations. Based on TFI, we propose a simple yet effective Graph Feature Selection (GFS) method, which processes GNN-favored and GNN-disfavored features with GNNs and non-GNN models separately. Compared to original GNNs, GFS significantly improves the extraction of useful topological information from each feature with comparable computational costs. Extensive experiments show that after applying GFS to $\textbf{8}$ baseline and state-of-the-art (SOTA) GNN architectures across $\textbf{10}$ datasets, $\textbf{90\%}$ of the GFS-augmented cases show significant performance boosts. Furthermore, our proposed TFI metric outperforms other feature selection methods for GFS. These results verify the effectiveness of both GFS and TFI. Additionally, we demonstrate that GFS's improvements are robust to hyperparameter tuning, highlighting its potential as a universally valid method for enhancing various GNN architectures. To facilitate reproducibility and further research, we have made our code publicly available at https://github.com/KTTRCDL/graph-feature-selection.

Massive MIMO (multiple-input multiple-output) detection is an important topic in wireless communication and various machine learning based methods have been developed recently for this task. Expectation propagation (EP) and its variants are widely used for MIMO detection and have achieved the best performance. However, EP-based solvers fail to capture the correlation between unknown variables, leading to a loss of information, and in addition, they are computationally expensive. In this paper, we show that the real-valued system can be modeled as spectral signal convolution on graph, through which the correlation between unknown variables can be captured. Based on this analysis, we propose graph convolution-enhanced expectation propagation (GCEPNet). GCEPNet incorporates data-dependent attention scores into Chebyshev polynomial for powerful graph convolution with better generalization capacity. It enables a better estimation of the cavity distribution for EP and empirically achieves the state-of-the-art (SOTA) MIMO detection performance with much faster inference speed. To our knowledge, we are the first to shed light on the connection between the system model and graph convolution, and the first to design the data-dependent coefficients for graph convolution.

Enzymes, with their specific catalyzed reactions, are necessary for all aspects of life, enabling diverse biological processes and adaptations. Predicting enzyme functions is essential for understanding biological pathways, guiding drug development, enhancing bioproduct yields, and facilitating evolutionary studies.Addressing the inherent complexities, we introduce a new approach to annotating enzymes based on their catalyzed reactions. This method provides detailed insights into specific reactions and is adaptable to newly discovered reactions, diverging from traditional classifications by protein family or expert-derived reaction classes. We employ machine learning algorithms to analyze enzyme reaction datasets, delivering a much more refined view on the functionality of enzymes.Our evaluation leverages the largest enzyme-reaction dataset to date, derived from the SwissProt and Rhea databases with entries up to January 8, 2024. We frame the enzyme-reaction prediction as a retrieval problem, aiming to rank enzymes by their catalytic ability for specific reactions. With our model, we can recruit proteins for novel reactions and predict reactions in novel proteins, facilitating enzyme discovery and function annotation https://github.com/WillHua127/ReactZyme.

Graph homophily refers to the phenomenon that connected nodes tend to share similar characteristics. Understanding this concept and its related metrics is crucial for designing effective Graph Neural Networks (GNNs). The most widely used homophily metrics, such as edge or node homophily, quantify such "similarity" as label consistency across the graph topology. These metrics are believed to be able to reflect the performance of GNNs, especially on node-level tasks. However, many recent studies have empirically demonstrated that the performance of GNNs does not always align with homophily metrics, and how homophily influences GNNs still remains unclear and controversial. Then, a crucial question arises: What is missing in our current understanding of homophily? To figure out the missing part, in this paper, we disentangle the graph homophily into three aspects: label, structural, and feature homophily, which are derived from the three basic elements of graph data. We argue that the synergy of the three homophily can provide a more comprehensive understanding of GNN performance. Our new proposed structural and feature homophily consider the neighborhood consistency and feature dependencies among nodes, addressing the previously overlooked structural and feature aspects in graph homophily. To investigate their synergy, we propose a Contextual Stochastic Block Model with three types of Homophily (CSBM-3H), where the topology and feature generation are controlled by the three metrics. Based on the theoretical analysis of CSBM-3H, we derive a new composite metric, named Tri-Hom, that considers all three aspects and overcomes the limitations of conventional homophily metrics. The theoretical conclusions and the effectiveness of Tri-Hom have been verified through synthetic experiments on CSBM-3H. In addition, we conduct experiments on $31$ real-world benchmark datasets and calculate the correlations between homophily metrics and model performance. Tri-Hom has significantly higher correlation values than $17$ existing metrics that only focus on a single homophily aspect, demonstrating its superiority and the importance of homophily synergy. Our code is available at https://github.com/zylMozart/Disentangle_GraphHom.

Homophily principle, i.e., nodes with the same labels are more likely to be connected, has been believed to be the main reason for the performance superiority of Graph Neural Networks (GNNs) over Neural Networks on node classification tasks. Recent research suggests that, even in the absence of homophily, the advantage of GNNs still exists as long as nodes from the same class share similar neighborhood patterns. However, this argument only considers intra-class Node Distinguishability (ND) but neglects inter-class ND, which provides incomplete understanding of homophily on GNNs. In this paper, we first demonstrate such deficiency with examples and argue that an ideal situation for ND is to have smaller intra-class ND than inter-class ND. To formulate this idea and study ND deeply, we propose Contextual Stochastic Block Model for Homophily (CSBM-H) and define two metrics, Probabilistic Bayes Error (PBE) and negative generalized Jeffreys divergence, to quantify ND. With the metrics, we visualize and analyze how graph filters, node degree distributions and class variances influence ND, and investigate the combined effect of intra- and inter-class ND. Besides, we discovered the mid-homophily pitfall, which occurs widely in graph datasets. Furthermore, we verified that, in real-work tasks, the superiority of GNNs is indeed closely related to both intra- and inter-class ND regardless of homophily levels. Grounded in this observation, we propose a new hypothesis-testing based performance metric beyond homophily, which is non-linear, feature-based and can provide statistical threshold value for GNNs' the superiority. Experiments indicate that it is significantly more effective than the existing homophily metrics on revealing the advantage and disadvantage of graph-aware modes on both synthetic and benchmark real-world datasets.

Graph Neural Networks (GNNs) extend basic Neural Networks (NNs) by using graph structures based on the relational inductive bias (homophily assumption). While GNNs have been commonly believed to outperform NNs in real-world tasks, recent work has identified a non-trivial set of datasets where their performance compared to NNs is not satisfactory. Heterophily has been considered the main cause of this empirical observation and numerous works have been put forward to address it. In this paper, we first revisit the widely used homophily metrics and point out that their consideration of only graph-label consistency is a shortcoming. Then, we study heterophily from the perspective of post-aggregation node similarity and define new homophily metrics, which are potentially advantageous compared to existing ones. Based on this investigation, we prove that some harmful cases of heterophily can be effectively addressed by local diversification operation. Then, we propose the Adaptive Channel Mixing (ACM), a framework to adaptively exploit aggregation, diversification and identity channels to extract richer localized information in each baseline GNN layer. ACM is more powerful than the commonly used uni-channel framework for node classification tasks on heterophilic graphs. When evaluated on 10 benchmark node classification tasks, ACM-augmented baselines consistently achieve significant performance gain, exceeding state-of-the-art GNNs on most tasks without incurring significant computational burden. (Code: https://github.com/SitaoLuan/ACM-GNN)

We present an end-to-end, model-based deep reinforcement learning agent which dynamically attends to relevant parts of its state during planning. The agent uses a bottleneck mechanism over a set-based representation to force the number of entities to which the agent attends at each planning step to be small. In experiments, we investigate the bottleneck mechanism with several sets of customized environments featuring different challenges. We consistently observe that the design allows the planning agents to generalize their learned task-solving abilities in compatible unseen environments by attending to the relevant objects, leading to better out-of-distribution generalization performance.

Recently, neural network based approaches have achieved significant progress for solving large, complex, graph-structured problems. Nevertheless, the advantages of multi-scale information and deep architectures have not been sufficiently exploited. In this paper, we first analyze key factors constraining the expressive power of existing Graph Convolutional Networks (GCNs), including the activation function and shallow learning mechanisms. Then, we generalize spectral graph convolution and deep GCN in block Krylov subspace forms, upon which we devise two architectures, both scalable in depth however making use of multi-scale information differently. On several node classification tasks, the proposed architectures achieve state-of-the-art performance.