Learning from Graphs with Heterophily: Progress and Future

Graphs are structured data that models complex relations between real-world entities. Heterophilous graphs, where linked nodes are prone to be with different labels or dissimilar features, have recently attracted significant attention and found many applications. Meanwhile, increasing efforts have been made to advance learning from heterophilous graphs. Although there exist surveys on the relevant topic, they focus on heterophilous GNNs, which are only sub-topics of heterophilous graph learning. In this survey, we comprehensively overview existing works on learning from graphs with heterophily.First, we collect over 180 publications and introduce the development of this field. Then, we systematically categorize existing methods based on a hierarchical taxonomy including learning strategies, model architectures and practical applications. Finally, we discuss the primary challenges of existing studies and highlight promising avenues for future research.More publication details and corresponding open-source codes can be accessed and will be continuously updated at our repositories:https://github.com/gongchenghua/Awesome-Survey-Graphs-with-Heterophily.

AdaMedGraph: Adaboosting Graph Neural Networks for Personalized Medicine

Precision medicine tailored to individual patients has gained significant attention in recent times. Machine learning techniques are now employed to process personalized data from various sources, including images, genetics, and assessments. These techniques have demonstrated good outcomes in many clinical prediction tasks. Notably, the approach of constructing graphs by linking similar patients and then applying graph neural networks (GNNs) stands out, because related information from analogous patients are aggregated and considered for prediction. However, selecting the appropriate edge feature to define patient similarity and construct the graph is challenging, given that each patient is depicted by high-dimensional features from diverse sources. Previous studies rely on human expertise to select the edge feature, which is neither scalable nor efficient in pinpointing crucial edge features for complex diseases. In this paper, we propose a novel algorithm named \ours, which can automatically select important features to construct multiple patient similarity graphs, and train GNNs based on these graphs as weak learners in adaptive boosting. \ours{} is evaluated on two real-world medical scenarios and shows superiors performance.

Prioritized Propagation in Graph Neural Networks

Graph neural networks (GNNs) have recently received significant attention. Learning node-wise message propagation in GNNs aims to set personalized propagation steps for different nodes in the graph. Despite the success, existing methods ignore node priority that can be reflected by node influence and heterophily. In this paper, we propose a versatile framework PPro, which can be integrated with most existing GNN models and aim to learn prioritized node-wise message propagation in GNNs. Specifically, the framework consists of three components: a backbone GNN model, a propagation controller to determine the optimal propagation steps for nodes, and a weight controller to compute the priority scores for nodes. We design a mutually enhanced mechanism to compute node priority, optimal propagation step and label prediction. We also propose an alternative optimization strategy to learn the parameters in the backbone GNN model and two parametric controllers. We conduct extensive experiments to compare our framework with other 11 state-of-the-art competitors on 8 benchmark datasets. Experimental results show that our framework can lead to superior performance in terms of propagation strategies and node representations.

Label Propagation for Graph Label Noise

Label noise is a common challenge in large datasets, as it can significantly degrade the generalization ability of deep neural networks. Most existing studies focus on noisy labels in computer vision; however, graph models encompass both node features and graph topology as input, and become more susceptible to label noise through message-passing mechanisms. Recently, only a few works have been proposed to tackle the label noise on graphs. One major limitation is that they assume the graph is homophilous and the labels are smoothly distributed. Nevertheless, real-world graphs may contain varying degrees of heterophily or even be heterophily-dominated, leading to the inadequacy of current methods. In this paper, we study graph label noise in the context of arbitrary heterophily, with the aim of rectifying noisy labels and assigning labels to previously unlabeled nodes. We begin by conducting two empirical analyses to explore the impact of graph homophily on graph label noise. Following observations, we propose a simple yet efficient algorithm, denoted as LP4GLN. Specifically, LP4GLN is an iterative algorithm with three steps: (1) reconstruct the graph to recover the homophily property, (2) utilize label propagation to rectify the noisy labels, (3) select high-confidence labels to retain for the next iteration. By iterating these steps, we obtain a set of correct labels, ultimately achieving high accuracy in the node classification task. The theoretical analysis is also provided to demonstrate its remarkable denoising "effect". Finally, we conduct experiments on 10 benchmark datasets under varying graph heterophily levels and noise types, comparing the performance of LP4GLN with 7 typical baselines. Our results illustrate the superior performance of the proposed LP4GLN.

Learning to Optimize LSM-trees: Towards A Reinforcement Learning based Key-Value Store for Dynamic Workloads

LSM-trees are widely adopted as the storage backend of key-value stores. However, optimizing the system performance under dynamic workloads has not been sufficiently studied or evaluated in previous work. To fill the gap, we present RusKey, a key-value store with the following new features: (1) RusKey is a first attempt to orchestrate LSM-tree structures online to enable robust performance under the context of dynamic workloads; (2) RusKey is the first study to use Reinforcement Learning (RL) to guide LSM-tree transformations; (3) RusKey includes a new LSM-tree design, named FLSM-tree, for an efficient transition between different compaction policies -- the bottleneck of dynamic key-value stores. We justify the superiority of the new design with theoretical analysis; (4) RusKey requires no prior workload knowledge for system adjustment, in contrast to state-of-the-art techniques. Experiments show that RusKey exhibits strong performance robustness in diverse workloads, achieving up to 4x better end-to-end performance than the RocksDB system under various settings.

Biological Factor Regulatory Neural Network

Genes are fundamental for analyzing biological systems and many recent works proposed to utilize gene expression for various biological tasks by deep learning models. Despite their promising performance, it is hard for deep neural networks to provide biological insights for humans due to their black-box nature. Recently, some works integrated biological knowledge with neural networks to improve the transparency and performance of their models. However, these methods can only incorporate partial biological knowledge, leading to suboptimal performance. In this paper, we propose the Biological Factor Regulatory Neural Network (BFReg-NN), a generic framework to model relations among biological factors in cell systems. BFReg-NN starts from gene expression data and is capable of merging most existing biological knowledge into the model, including the regulatory relations among genes or proteins (e.g., gene regulatory networks (GRN), protein-protein interaction networks (PPI)) and the hierarchical relations among genes, proteins and pathways (e.g., several genes/proteins are contained in a pathway). Moreover, BFReg-NN also has the ability to provide new biologically meaningful insights because of its white-box characteristics. Experimental results on different gene expression-based tasks verify the superiority of BFReg-NN compared with baselines. Our case studies also show that the key insights found by BFReg-NN are consistent with the biological literature.

SeeGera: Self-supervised Semi-implicit Graph Variational Auto-encoders with Masking

Generative graph self-supervised learning (SSL) aims to learn node representations by reconstructing the input graph data. However, most existing methods focus on unsupervised learning tasks only and very few work has shown its superiority over the state-of-the-art graph contrastive learning (GCL) models, especially on the classification task. While a very recent model has been proposed to bridge the gap, its performance on unsupervised learning tasks is still unknown. In this paper, to comprehensively enhance the performance of generative graph SSL against other GCL models on both unsupervised and supervised learning tasks, we propose the SeeGera model, which is based on the family of self-supervised variational graph auto-encoder (VGAE). Specifically, SeeGera adopts the semi-implicit variational inference framework, a hierarchical variational framework, and mainly focuses on feature reconstruction and structure/feature masking. On the one hand, SeeGera co-embeds both nodes and features in the encoder and reconstructs both links and features in the decoder. Since feature embeddings contain rich semantic information on features, they can be combined with node embeddings to provide fine-grained knowledge for feature reconstruction. On the other hand, SeeGera adds an additional layer for structure/feature masking to the hierarchical variational framework, which boosts the model generalizability. We conduct extensive experiments comparing SeeGera with 9 other state-of-the-art competitors. Our results show that SeeGera can compare favorably against other state-of-the-art GCL methods in a variety of unsupervised and supervised learning tasks.

RuDi: Explaining Behavior Sequence Models by Automatic Statistics Generation and Rule Distillation

Risk scoring systems have been widely deployed in many applications, which assign risk scores to users according to their behavior sequences. Though many deep learning methods with sophisticated designs have achieved promising results, the black-box nature hinders their applications due to fairness, explainability, and compliance consideration. Rule-based systems are considered reliable in these sensitive scenarios. However, building a rule system is labor-intensive. Experts need to find informative statistics from user behavior sequences, design rules based on statistics and assign weights to each rule. In this paper, we bridge the gap between effective but black-box models and transparent rule models. We propose a two-stage method, RuDi, that distills the knowledge of black-box teacher models into rule-based student models. We design a Monte Carlo tree search-based statistics generation method that can provide a set of informative statistics in the first stage. Then statistics are composed into logical rules with our proposed neural logical networks by mimicking the outputs of teacher models. We evaluate RuDi on three real-world public datasets and an industrial dataset to demonstrate its effectiveness.

RendNet: Unified 2D/3D Recognizer With Latent Space Rendering

Vector graphics (VG) have been ubiquitous in our daily life with vast applications in engineering, architecture, designs, etc. The VG recognition process of most existing methods is to first render the VG into raster graphics (RG) and then conduct recognition based on RG formats. However, this procedure discards the structure of geometries and loses the high resolution of VG. Recently, another category of algorithms is proposed to recognize directly from the original VG format. But it is affected by the topological errors that can be filtered out by RG rendering. Instead of looking at one format, it is a good solution to utilize the formats of VG and RG together to avoid these shortcomings. Besides, we argue that the VG-to-RG rendering process is essential to effectively combine VG and RG information. By specifying the rules on how to transfer VG primitives to RG pixels, the rendering process depicts the interaction and correlation between VG and RG. As a result, we propose RendNet, a unified architecture for recognition on both 2D and 3D scenarios, which considers both VG/RG representations and exploits their interaction by incorporating the VG-to-RG rasterization process. Experiments show that RendNet can achieve state-of-the-art performance on 2D and 3D object recognition tasks on various VG datasets.

Finding Global Homophily in Graph Neural Networks When Meeting Heterophily

We investigate graph neural networks on graphs with heterophily. Some existing methods amplify a node's neighborhood with multi-hop neighbors to include more nodes with homophily. However, it is a significant challenge to set personalized neighborhood sizes for different nodes. Further, for other homophilous nodes excluded in the neighborhood, they are ignored for information aggregation. To address these problems, we propose two models GloGNN and GloGNN++, which generate a node's embedding by aggregating information from global nodes in the graph. In each layer, both models learn a coefficient matrix to capture the correlations between nodes, based on which neighborhood aggregation is performed. The coefficient matrix allows signed values and is derived from an optimization problem that has a closed-form solution. We further accelerate neighborhood aggregation and derive a linear time complexity. We theoretically explain the models' effectiveness by proving that both the coefficient matrix and the generated node embedding matrix have the desired grouping effect. We conduct extensive experiments to compare our models against 11 other competitors on 15 benchmark datasets in a wide range of domains, scales and graph heterophilies. Experimental results show that our methods achieve superior performance and are also very efficient.