We investigate novel random graph embeddings that can be computed in expected polynomial time and that are able to distinguish all non-isomorphic graphs in expectation. Previous graph embeddings have limited expressiveness and either cannot distinguish all graphs or cannot be computed efficiently for every graph. To be able to approximate arbitrary functions on graphs, we are interested in efficient alternatives that become arbitrarily expressive with increasing resources. Our approach is based on Lov\'asz' characterisation of graph isomorphism through an infinite dimensional vector of homomorphism counts. Our empirical evaluation shows competitive results on several benchmark graph learning tasks.
Relational inference aims to identify interactions between parts of a dynamical system from the observed dynamics. Current state-of-the-art methods fit the dynamics with a graph neural network (GNN) on a learnable graph. They use one-step message-passing GNNs -- intuitively the right choice since non-locality of multi-step or spectral GNNs may confuse direct and indirect interactions. But the \textit{effective} interaction graph depends on the sampling rate and it is rarely localized to direct neighbors, leading to poor local optima for the one-step model. In this work, we propose a \textit{graph dynamics prior} (GDP) for relational inference. GDP constructively uses error amplification in non-local polynomial filters to steer the solution to the ground-truth graph. To deal with non-uniqueness, GDP simultaneously fits a ``shallow'' one-step model and a polynomial multi-step model with shared graph topology. Experiments show that GDP reconstructs graphs far more accurately than earlier methods, with remarkable robustness to under-sampling. Since appropriate sampling rates for unknown dynamical systems are not known a priori, this robustness makes GDP suitable for real applications in scientific machine learning. Reproducible code is available at https://github.com/DaDaCheng/GDP.
Recent advances and achievements of artificial intelligence (AI) as well as deep and graph learning models have established their usefulness in biomedical applications, especially in drug-drug interactions (DDIs). DDIs refer to a change in the effect of one drug to the presence of another drug in the human body, which plays an essential role in drug discovery and clinical research. DDIs prediction through traditional clinical trials and experiments is an expensive and time-consuming process. To correctly apply the advanced AI and deep learning, the developer and user meet various challenges such as the availability and encoding of data resources, and the design of computational methods. This review summarizes chemical structure based, network based, NLP based and hybrid methods, providing an updated and accessible guide to the broad researchers and development community with different domain knowledge. We introduce widely-used molecular representation and describe the theoretical frameworks of graph neural network models for representing molecular structures. We present the advantages and disadvantages of deep and graph learning methods by performing comparative experiments. We discuss the potential technical challenges and highlight future directions of deep and graph learning models for accelerating DDIs prediction.
Graphs are widely used to encapsulate a variety of data formats, but real-world networks often involve complex node relations beyond only being pairwise. While hypergraphs and hierarchical graphs have been developed and employed to account for the complex node relations, they cannot fully represent these complexities in practice. Additionally, though many Graph Neural Networks (GNNs) have been proposed for representation learning on higher-order graphs, they are usually only evaluated on simple graph datasets. Therefore, there is a need for a unified modelling of higher-order graphs, and a collection of comprehensive datasets with an accessible evaluation framework to fully understand the performance of these algorithms on complex graphs. In this paper, we introduce the concept of hybrid graphs, a unified definition for higher-order graphs, and present the Hybrid Graph Benchmark (HGB). HGB contains 23 real-world hybrid graph datasets across various domains such as biology, social media, and e-commerce. Furthermore, we provide an extensible evaluation framework and a supporting codebase to facilitate the training and evaluation of GNNs on HGB. Our empirical study of existing GNNs on HGB reveals various research opportunities and gaps, including (1) evaluating the actual performance improvement of hypergraph GNNs over simple graph GNNs; (2) comparing the impact of different sampling strategies on hybrid graph learning methods; and (3) exploring ways to integrate simple graph and hypergraph information. We make our source code and full datasets publicly available at https://zehui127.github.io/hybrid-graph-benchmark/.
Temporal graph clustering (TGC) is a crucial task in temporal graph learning. Its focus is on node clustering on temporal graphs, and it offers greater flexibility for large-scale graph structures due to the mechanism of temporal graph methods. However, the development of TGC is currently constrained by a significant problem: the lack of suitable and reliable large-scale temporal graph datasets to evaluate clustering performance. In other words, most existing temporal graph datasets are in small sizes, and even large-scale datasets contain only a limited number of available node labels. It makes evaluating models for large-scale temporal graph clustering challenging. To address this challenge, we build arXiv4TGC, a set of novel academic datasets (including arXivAI, arXivCS, arXivMath, arXivPhy, and arXivLarge) for large-scale temporal graph clustering. In particular, the largest dataset, arXivLarge, contains 1.3 million labeled available nodes and 10 million temporal edges. We further compare the clustering performance with typical temporal graph learning models on both previous classic temporal graph datasets and the new datasets proposed in this paper. The clustering performance on arXiv4TGC can be more apparent for evaluating different models, resulting in higher clustering confidence and more suitable for large-scale temporal graph clustering. The arXiv4TGC datasets are publicly available at: https://github.com/MGitHubL/arXiv4TGC.
Graph Neural networks (GNNs) have been applied in many scenarios due to the superior performance of graph learning. However, fairness is always ignored when designing GNNs. As a consequence, biased information in training data can easily affect vanilla GNNs, causing biased results toward particular demographic groups (divided by sensitive attributes, such as race and age). There have been efforts to address the fairness issue. However, existing fair techniques generally divide the demographic groups by raw sensitive attributes and assume that are fixed. The biased information correlated with raw sensitive attributes will run through the training process regardless of the implemented fair techniques. It is urgent to resolve this problem for training fair GNNs. To tackle this problem, we propose a brand new framework, FairMigration, which can dynamically migrate the demographic groups instead of keeping that fixed with raw sensitive attributes. FairMigration is composed of two training stages. In the first stage, the GNNs are initially optimized by personalized self-supervised learning, and the demographic groups are adjusted dynamically. In the second stage, the new demographic groups are frozen and supervised learning is carried out under the constraints of new demographic groups and adversarial training. Extensive experiments reveal that FairMigration balances model performance and fairness well.
The nature of heterophilous graphs is significantly different from that of homophilous graphs, which causes difficulties in early graph neural network models and suggests aggregations beyond the 1-hop neighborhood. In this paper, we develop a new way to implement multi-scale extraction via constructing Haar-type graph framelets with desired properties of permutation equivariance, efficiency, and sparsity, for deep learning tasks on graphs. We further design a graph framelet neural network model PEGFAN (Permutation Equivariant Graph Framelet Augmented Network) based on our constructed graph framelets. The experiments are conducted on a synthetic dataset and 9 benchmark datasets to compare performance with other state-of-the-art models. The result shows that our model can achieve the best performance on certain datasets of heterophilous graphs (including the majority of heterophilous datasets with relatively larger sizes and denser connections) and competitive performance on the remaining.
For robot-assisted surgery, an accurate surgical report reflects clinical operations during surgery and helps document entry tasks, post-operative analysis and follow-up treatment. It is a challenging task due to many complex and diverse interactions between instruments and tissues in the surgical scene. Although existing surgical report generation methods based on deep learning have achieved large success, they often ignore the interactive relation between tissues and instrumental tools, thereby degrading the report generation performance. This paper presents a neural network to boost surgical report generation by explicitly exploring the interactive relation between tissues and surgical instruments. We validate the effectiveness of our method on a widely-used robotic surgery benchmark dataset, and experimental results show that our network can significantly outperform existing state-of-the-art surgical report generation methods (e.g., 7.48% and 5.43% higher for BLEU-1 and ROUGE).
This paper proposes a blind detection problem for low pass graph signals. Without assuming knowledge of the exact graph topology, we aim to detect if a set of graph signal observations are generated from a low pass graph filter. Our problem is motivated by the widely adopted assumption of low pass (a.k.a.~smooth) signals required by many existing works in graph signal processing (GSP), as well as the longstanding problem of network dynamics identification. Focusing on detecting low pass graph signals on modular graphs whose cutoff frequency coincides with the number of clusters in the graph, we propose to leverage the unique spectral pattern exhibited by such low pass graph signals. We analyze the sample complexity of these detectors considering the effects of graph filter's properties, random delays, and other parameters. We show novel applications of the blind detector on robustifying graph learning, identifying antagonistic ties in opinion dynamics, and detecting anomalies in power systems. Numerical experiments validate our findings.
Vulnerability detection is a critical problem in software security and attracts growing attention both from academia and industry. Traditionally, software security is safeguarded by designated rule-based detectors that heavily rely on empirical expertise, requiring tremendous effort from software experts to generate rule repositories for large code corpus. Recent advances in deep learning, especially Graph Neural Networks (GNN), have uncovered the feasibility of automatic detection of a wide range of software vulnerabilities. However, prior learning-based works only break programs down into a sequence of word tokens for extracting contextual features of codes, or apply GNN largely on homogeneous graph representation (e.g., AST) without discerning complex types of underlying program entities (e.g., methods, variables). In this work, we are one of the first to explore heterogeneous graph representation in the form of Code Property Graph and adapt a well-known heterogeneous graph network with a dual-supervisor structure for the corresponding graph learning task. Using the prototype built, we have conducted extensive experiments on both synthetic datasets and real-world projects. Compared with the state-of-the-art baselines, the results demonstrate promising effectiveness in this research direction in terms of vulnerability detection performance (average F1 improvements over 10\% in real-world projects) and transferability from C/C++ to other programming languages (average F1 improvements over 11%).
Low probability of detection (LPD) has recently emerged as a means to enhance the privacy and security of wireless networks. Unlike existing wireless security techniques, LPD measures aim to conceal the entire existence of wireless communication instead of safeguarding the information transmitted from users. Motivated by LPD communication, in this paper, we study a privacy-preserving and distributed framework based on graph neural networks to minimise the detectability of a wireless ad-hoc network as a whole and predict an optimal communication region for each node in the wireless network, allowing them to communicate while remaining undetected from external actors. We also demonstrate the effectiveness of the proposed method in terms of two performance measures, i.e., mean absolute error and median absolute error.
Transformers use the dense self-attention mechanism which gives a lot of flexibility for long-range connectivity. Over multiple layers of a deep transformer, the number of possible connectivity patterns increases exponentially. However, very few of these contribute to the performance of the network, and even fewer are essential. We hypothesize that there are sparsely connected sub-networks within a transformer, called information pathways which can be trained independently. However, the dynamic (i.e., input-dependent) nature of these pathways makes it difficult to prune dense self-attention during training. But the overall distribution of these pathways is often predictable. We take advantage of this fact to propose Stochastically Subsampled self-Attention (SSA) - a general-purpose training strategy for transformers that can reduce both the memory and computational cost of self-attention by 4 to 8 times during training while also serving as a regularization method - improving generalization over dense training. We show that an ensemble of sub-models can be formed from the subsampled pathways within a network, which can achieve better performance than its densely attended counterpart. We perform experiments on a variety of NLP, computer vision and graph learning tasks in both generative and discriminative settings to provide empirical evidence for our claims and show the effectiveness of the proposed method.
Label errors have been found to be prevalent in popular text, vision, and audio datasets, which heavily influence the safe development and evaluation of machine learning algorithms. Despite increasing efforts towards improving the quality of generic data types, such as images and texts, the problem of mislabel detection in graph data remains underexplored. To bridge the gap, we explore mislabelling issues in popular real-world graph datasets and propose GraphCleaner, a post-hoc method to detect and correct these mislabelled nodes in graph datasets. GraphCleaner combines the novel ideas of 1) Synthetic Mislabel Dataset Generation, which seeks to generate realistic mislabels; and 2) Neighborhood-Aware Mislabel Detection, where neighborhood dependency is exploited in both labels and base classifier predictions. Empirical evaluations on 6 datasets and 6 experimental settings demonstrate that GraphCleaner outperforms the closest baseline, with an average improvement of 0.14 in F1 score, and 0.16 in MCC. On real-data case studies, GraphCleaner detects real and previously unknown mislabels in popular graph benchmarks: PubMed, Cora, CiteSeer and OGB-arxiv; we find that at least 6.91% of PubMed data is mislabelled or ambiguous, and simply removing these mislabelled data can boost evaluation performance from 86.71% to 89.11%.
Heterogeneous Graph Neural Networks (HGNNs) have gained significant popularity in various heterogeneous graph learning tasks. However, most existing HGNNs rely on spatial domain-based methods to aggregate information, i.e., manually selected meta-paths or some heuristic modules, lacking theoretical guarantees. Furthermore, these methods cannot learn arbitrary valid heterogeneous graph filters within the spectral domain, which have limited expressiveness. To tackle these issues, we present a positive spectral heterogeneous graph convolution via positive noncommutative polynomials. Then, using this convolution, we propose PSHGCN, a novel Positive Spectral Heterogeneous Graph Convolutional Network. PSHGCN offers a simple yet effective method for learning valid heterogeneous graph filters. Moreover, we demonstrate the rationale of PSHGCN in the graph optimization framework. We conducted an extensive experimental study to show that PSHGCN can learn diverse heterogeneous graph filters and outperform all baselines on open benchmarks. Notably, PSHGCN exhibits remarkable scalability, efficiently handling large real-world graphs comprising millions of nodes and edges. Our codes are available at https://github.com/ivam-he/PSHGCN.
With the growing popularity of various mobile devices, user targeting has received a growing amount of attention, which aims at effectively and efficiently locating target users that are interested in specific services. Most pioneering works for user targeting tasks commonly perform similarity-based expansion with a few active users as seeds, suffering from the following major issues: the unavailability of seed users for newcoming services and the unfriendliness of black-box procedures towards marketers. In this paper, we design an Entity Graph Learning (EGL) system to provide explainable user targeting ability meanwhile applicable to addressing the cold-start issue. EGL System follows the hybrid online-offline architecture to satisfy the requirements of scalability and timeliness. Specifically, in the offline stage, the system focuses on the heavyweight entity graph construction and user entity preference learning, in which we propose a Three-stage Relation Mining Procedure (TRMP), breaking loose from the expensive seed users. At the online stage, the system offers the ability of user targeting in real-time based on the entity graph from the offline stage. Since the user targeting process is based on graph reasoning, the whole process is transparent and operation-friendly to marketers. Finally, extensive offline experiments and online A/B testing demonstrate the superior performance of the proposed EGL System.
Graph Neural Networks (GNNs) have exhibited impressive performance in many graph learning tasks. Nevertheless, the performance of GNNs can deteriorate when the input graph data suffer from weak information, i.e., incomplete structure, incomplete features, and insufficient labels. Most prior studies, which attempt to learn from the graph data with a specific type of weak information, are far from effective in dealing with the scenario where diverse data deficiencies exist and mutually affect each other. To fill the gap, in this paper, we aim to develop an effective and principled approach to the problem of graph learning with weak information (GLWI). Based on the findings from our empirical analysis, we derive two design focal points for solving the problem of GLWI, i.e., enabling long-range propagation in GNNs and allowing information propagation to those stray nodes isolated from the largest connected component. Accordingly, we propose D$^2$PT, a dual-channel GNN framework that performs long-range information propagation not only on the input graph with incomplete structure, but also on a global graph that encodes global semantic similarities. We further develop a prototype contrastive alignment algorithm that aligns the class-level prototypes learned from two channels, such that the two different information propagation processes can mutually benefit from each other and the finally learned model can well handle the GLWI problem. Extensive experiments on eight real-world benchmark datasets demonstrate the effectiveness and efficiency of our proposed methods in various GLWI scenarios.
Learning expressive representations for high-dimensional yet sparse features has been a longstanding problem in information retrieval. Though recent deep learning methods can partially solve the problem, they often fail to handle the numerous sparse features, particularly those tail feature values with infrequent occurrences in the training data. Worse still, existing methods cannot explicitly leverage the correlations among different instances to help further improve the representation learning on sparse features since such relational prior knowledge is not provided. To address these challenges, in this paper, we tackle the problem of representation learning on feature-sparse data from a graph learning perspective. Specifically, we propose to model the sparse features of different instances using hypergraphs where each node represents a data instance and each hyperedge denotes a distinct feature value. By passing messages on the constructed hypergraphs based on our Hypergraph Transformer (HyperFormer), the learned feature representations capture not only the correlations among different instances but also the correlations among features. Our experiments demonstrate that the proposed approach can effectively improve feature representation learning on sparse features.
Graph neural networks (GNNs) have shown promising results across various graph learning tasks, but they often assume homophily, which can result in poor performance on heterophilic graphs. The connected nodes are likely to be from different classes or have dissimilar features on heterophilic graphs. In this paper, we propose a novel GNN that incorporates the principle of heterophily by modeling the flow of information on nodes using the convection-diffusion equation (CDE). This allows the CDE to take into account both the diffusion of information due to homophily and the ``convection'' of information due to heterophily. We conduct extensive experiments, which suggest that our framework can achieve competitive performance on node classification tasks for heterophilic graphs, compared to the state-of-the-art methods. The code is available at \url{https://github.com/zknus/Graph-Diffusion-CDE}.
This paper investigates a missing feature imputation problem for graph learning tasks. Several methods have previously addressed learning tasks on graphs with missing features. However, in cases of high rates of missing features, they were unable to avoid significant performance degradation. To overcome this limitation, we introduce a novel concept of channel-wise confidence in a node feature, which is assigned to each imputed channel feature of a node for reflecting certainty of the imputation. We then design pseudo-confidence using the channel-wise shortest path distance between a missing-feature node and its nearest known-feature node to replace unavailable true confidence in an actual learning process. Based on the pseudo-confidence, we propose a novel feature imputation scheme that performs channel-wise inter-node diffusion and node-wise inter-channel propagation. The scheme can endure even at an exceedingly high missing rate (e.g., 99.5\%) and it achieves state-of-the-art accuracy for both semi-supervised node classification and link prediction on various datasets containing a high rate of missing features. Codes are available at https://github.com/daehoum1/pcfi.
Influence operations are large-scale efforts to manipulate public opinion. The rapid detection and disruption of these operations is critical for healthy public discourse. Emergent AI technologies may enable novel operations which evade current detection methods and influence public discourse on social media with greater scale, reach, and specificity. New methods with inductive learning capacity will be needed to identify these novel operations before they indelibly alter public opinion and events. We develop an inductive learning framework which: 1) determines content- and graph-based indicators that are not specific to any operation; 2) uses graph learning to encode abstract signatures of coordinated manipulation; and 3) evaluates generalization capacity by training and testing models across operations originating from Russia, China, and Iran. We find that this framework enables strong cross-operation generalization while also revealing salient indicators$\unicode{x2013}$illustrating a generic approach which directly complements transductive methodologies, thereby enhancing detection coverage.