Modern software systems rely on mining insights from business sensitive data stored in public clouds. A data breach usually incurs significant (monetary) loss for a commercial organization. Conceptually, cloud security heavily relies on Identity Access Management (IAM) policies that IT admins need to properly configure and periodically update. Security negligence and human errors often lead to misconfiguring IAM policies which may open a backdoor for attackers. To address these challenges, first, we develop a novel framework that encodes generating optimal IAM policies using constraint programming (CP). We identify reducing dark permissions of cloud users as an optimality criterion, which intuitively implies minimizing unnecessary datastore access permissions. Second, to make IAM policies interpretable, we use graph representation learning applied to historical access patterns of users to augment our CP model with similarity constraints: similar users should be grouped together and share common IAM policies. Third, we describe multiple attack models and show that our optimized IAM policies significantly reduce the impact of security attacks using real data from 8 commercial organizations, and synthetic instances.
Graph pooling has been increasingly considered for graph neural networks (GNNs) to facilitate hierarchical graph representation learning. Existing graph pooling methods commonly consist of two stages, i.e., selecting the top-ranked nodes and removing the rest nodes to construct a coarsened graph representation. However, local structural information of the removed nodes would be inevitably dropped in these methods, due to the inherent coupling of nodes (location) and their features (signals). In this paper, we propose an enhanced three-stage method via lifting, named LiftPool, to improve hierarchical graph representation by maximally preserving the local structural information in graph pooling. LiftPool introduces an additional stage of graph lifting before graph coarsening to preserve the local information of the removed nodes and decouple the processes of node removing and feature reduction. Specifically, for each node to be removed, its local information is obtained by subtracting the global information aggregated from its neighboring preserved nodes. Subsequently, this local information is aligned and propagated to the preserved nodes to alleviate information loss in graph coarsening. Furthermore, we demonstrate that the proposed LiftPool is localized and permutation-invariant. The proposed graph lifting structure is general to be integrated with existing downsampling-based graph pooling methods. Evaluations on benchmark graph datasets show that LiftPool substantially outperforms the state-of-the-art graph pooling methods in the task of graph classification.
We propose Graph Tree Networks (GTNets), a deep graph learning architecture with a new general message passing scheme that originates from the tree representation of graphs. In the tree representation, messages propagate upward from the leaf nodes to the root node, and each node preserves its initial information prior to receiving information from its child nodes (neighbors). We formulate a general propagation rule following the nature of message passing in the tree to update a node's feature by aggregating its initial feature and its neighbor nodes' updated features. Two graph representation learning models are proposed within this GTNet architecture - Graph Tree Attention Network (GTAN) and Graph Tree Convolution Network (GTCN), with experimentally demonstrated state-of-the-art performance on several popular benchmark datasets. Unlike the vanilla Graph Attention Network (GAT) and Graph Convolution Network (GCN) which have the "over-smoothing" issue, the proposed GTAN and GTCN models can go deep as demonstrated by comprehensive experiments and rigorous theoretical analysis.
To enable heterogeneous computing systems with autonomous programming and optimization capabilities, we propose a unified, end-to-end, programmable graph representation learning (PGL) framework that is capable of mining the complexity of high-level programs down to the universal intermediate representation, extracting the specific computational patterns and predicting which code segments would run best on a specific core in heterogeneous hardware platforms. The proposed framework extracts multi-fractal topological features from code graphs, utilizes graph autoencoders to learn how to partition the graph into computational kernels, and exploits graph neural networks (GNN) to predict the correct assignment to a processor type. In the evaluation, we validate the PGL framework and demonstrate a maximum speedup of 6.42x compared to the thread-based execution, and 2.02x compared to the state-of-the-art technique.
Photonic neural networks perform brain-inspired computations using photons instead of electrons that can achieve substantially improved computing performance. However, existing architectures can only handle data with regular structures, e.g., images or videos, but fail to generalize to graph-structured data beyond Euclidean space, e.g., social networks or document co-citation networks. Here, we propose an all-optical graph representation learning architecture, termed diffractive graph neural network (DGNN), based on the integrated diffractive photonic computing units (DPUs) to address this limitation. Specifically, DGNN optically encodes node attributes into strip optical waveguides, which are transformed by DPUs and aggregated by on-chip optical couplers to extract their feature representations. Each DPU comprises successive passive layers of metalines to modulate the electromagnetic optical field via diffraction, where the metaline structures are learnable parameters shared across graph nodes. DGNN captures complex dependencies among the node neighborhoods and eliminates the nonlinear transition functions during the light-speed optical message passing over graph structures. We demonstrate the use of DGNN extracted features for node and graph-level classification tasks with benchmark databases and achieve superior performance. Our work opens up a new direction for designing application-specific integrated photonic circuits for high-efficiency processing of large-scale graph data structures using deep learning.
Graph Neural Networks (GNNs) are powerful tools for graph representation learning. Despite their rapid development, GNNs also face some challenges, such as over-fitting, over-smoothing, and non-robustness. Previous works indicate that these problems can be alleviated by random dropping methods, which integrate augmented data into models by randomly masking parts of the input. However, some open problems of random dropping on GNNs remain to be solved. First, it is challenging to find a universal method that are suitable for all cases considering the divergence of different datasets and models. Second, augmented data introduced to GNNs causes the incomplete coverage of parameters and unstable training process. Third, there is no theoretical analysis on the effectiveness of random dropping methods on GNNs. In this paper, we propose a novel random dropping method called DropMessage, which performs dropping operations directly on the propagated messages during the message-passing process. More importantly, we find that DropMessage provides a unified framework for most existing random dropping methods, based on which we give theoretical analysis of their effectiveness. Furthermore, we elaborate the superiority of DropMessage: it stabilizes the training process by reducing sample variance; it keeps information diversity from the perspective of information theory, enabling it become a theoretical upper bound of other methods. To evaluate our proposed method, we conduct experiments that aims for multiple tasks on five public datasets and two industrial datasets with various backbone models. The experimental results show that DropMessage has the advantages of both effectiveness and generalization, and can significantly alleviate the problems mentioned above.
Graph representation learning methods have mostly been limited to the modelling of node-wise interactions. Recently, there has been an increased interest in understanding how higher-order structures can be utilised to further enhance the learning abilities of graph neural networks (GNNs) in combinatorial spaces. Simplicial Neural Networks (SNNs) naturally model these interactions by performing message passing on simplicial complexes, higher-dimensional generalisations of graphs. Nonetheless, the computations performed by most existent SNNs are strictly tied to the combinatorial structure of the complex. Leveraging the success of attention mechanisms in structured domains, we propose Simplicial Attention Networks (SAT), a new type of simplicial network that dynamically weighs the interactions between neighbouring simplicies and can readily adapt to novel structures. Additionally, we propose a signed attention mechanism that makes SAT orientation equivariant, a desirable property for models operating on (co)chain complexes. We demonstrate that SAT outperforms existent convolutional SNNs and GNNs in two image and trajectory classification tasks.
Graph Representation Learning (GRL) has become central for characterizing structures of complex networks and performing tasks such as link prediction, node classification, network reconstruction, and community detection. Whereas numerous generative GRL models have been proposed, many approaches have prohibitive computational requirements hampering large-scale network analysis, fewer are able to explicitly account for structure emerging at multiple scales, and only a few explicitly respect important network properties such as homophily and transitivity. This paper proposes a novel scalable graph representation learning method named the Hierarchical Block Distance Model (HBDM). The HBDM imposes a multiscale block structure akin to stochastic block modeling (SBM) and accounts for homophily and transitivity by accurately approximating the latent distance model (LDM) throughout the inferred hierarchy. The HBDM naturally accommodates unipartite, directed, and bipartite networks whereas the hierarchy is designed to ensure linearithmic time and space complexity enabling the analysis of very large-scale networks. We evaluate the performance of the HBDM on massive networks consisting of millions of nodes. Importantly, we find that the proposed HBDM framework significantly outperforms recent scalable approaches in all considered downstream tasks. Surprisingly, we observe superior performance even imposing ultra-low two-dimensional embeddings facilitating accurate direct and hierarchical-aware network visualization and interpretation.
Graphs representation learning has been a very active research area in recent years. The goal of graph representation learning is to generate graph representation vectors that capture the structure and features of large graphs accurately. This is especially important because the quality of the graph representation vectors will affect the performance of these vectors in downstream tasks such as node classification, link prediction and anomaly detection. Many techniques are proposed for generating effective graph representation vectors. Two of the most prevalent categories of graph representation learning are graph embedding methods without using graph neural nets (GNN), which we denote as non-GNN based graph embedding methods, and graph neural nets (GNN) based methods. Non-GNN graph embedding methods are based on techniques such as random walks, temporal point processes and neural network learning methods. GNN-based methods, on the other hand, are the application of deep learning on graph data. In this survey, we provide an overview of these two categories and cover the current state-of-the-art methods for both static and dynamic graphs. Finally, we explore some open and ongoing research directions for future work.
Graph Contrastive Learning (GCL) has shown promising performance in graph representation learning (GRL) without the supervision of manual annotations. GCL can generate graph-level embeddings by maximizing the Mutual Information (MI) between different augmented views of the same graph (positive pairs). However, the GCL is limited by dimensional collapse, i.e., embedding vectors only occupy a low-dimensional subspace. In this paper, we show that the smoothing effect of the graph pooling and the implicit regularization of the graph convolution are two causes of the dimensional collapse in GCL. To mitigate the above issue, we propose a non-maximum removal graph contrastive learning approach (nmrGCL), which removes "prominent'' dimensions (i.e., contribute most in similarity measurement) for positive pair in the pre-text task. Comprehensive experiments on various benchmark datasets are conducted to demonstrate the effectiveness of nmrGCL, and the results show that our model outperforms the state-of-the-art methods. Source code will be made publicly available.
The identification of drug-target binding affinity (DTA) has attracted increasing attention in the drug discovery process due to the more specific interpretation than binary interaction prediction. Recently, numerous deep learning-based computational methods have been proposed to predict the binding affinities between drugs and targets benefiting from their satisfactory performance. However, the previous works mainly focus on encoding biological features and chemical structures of drugs and targets, with a lack of exploiting the essential topological information from the drug-target affinity network. In this paper, we propose a novel hierarchical graph representation learning model for the drug-target binding affinity prediction, namely HGRL-DTA. The main contribution of our model is to establish a hierarchical graph learning architecture to incorporate the intrinsic properties of drug/target molecules and the topological affinities of drug-target pairs. In this architecture, we adopt a message broadcasting mechanism to integrate the hierarchical representations learned from the global-level affinity graph and the local-level molecular graph. Besides, we design a similarity-based embedding map to solve the cold start problem of inferring representations for unseen drugs and targets. Comprehensive experimental results under different scenarios indicate that HGRL-DTA significantly outperforms the state-of-the-art models and shows better model generalization among all the scenarios.
Graph representation learning has attracted tremendous attention due to its remarkable performance in many real-world applications. However, prevailing supervised graph representation learning models for specific tasks often suffer from label sparsity issue as data labeling is always time and resource consuming. In light of this, few-shot learning on graphs (FSLG), which combines the strengths of graph representation learning and few-shot learning together, has been proposed to tackle the performance degradation in face of limited annotated data challenge. There have been many studies working on FSLG recently. In this paper, we comprehensively survey these work in the form of a series of methods and applications. Specifically, we first introduce FSLG challenges and bases, then categorize and summarize existing work of FSLG in terms of three major graph mining tasks at different granularity levels, i.e., node, edge, and graph. Finally, we share our thoughts on some future research directions of FSLG. The authors of this survey have contributed significantly to the AI literature on FSLG over the last few years.
Graph Neural Networks (GNNs) have emerged as prominent models for representation learning on graph structured data. GNNs follow an approach of message passing analogous to 1-dimensional Weisfeiler Lehman (1-WL) test for graph isomorphism and consequently are limited by the distinguishing power of 1-WL. More expressive higher-order GNNs which operate on k-tuples of nodes need increased computational resources in order to process higher-order tensors. Instead of the WL approach, in this work, we follow the classical approach of Individualization and Refinement (IR), a technique followed by most practical isomorphism solvers. Individualization refers to artificially distinguishing a node in the graph and refinement is the propagation of this information to other nodes through message passing. We learn to adaptively select nodes to individualize and to aggregate the resulting graphs after refinement to help handle the complexity. Our technique lets us learn richer node embeddings while keeping the computational complexity manageable. Theoretically, we show that our procedure is more expressive than the 1-WL test. Experiments show that our method outperforms prominent 1-WL GNN models as well as competitive higher-order baselines on several benchmark synthetic and real datasets. Furthermore, our method opens new doors for exploring the paradigm of learning on graph structures with individualization and refinement.
Graph neural networks (GNNs) have been extensively developed for graph representation learning in various application domains. However, similar to all other neural networks models, GNNs suffer from the black-box problem as people cannot understand the mechanism underlying them. To solve this problem, several GNN explainability methods have been proposed to explain the decisions made by GNNs. In this survey, we give an overview of the state-of-the-art GNN explainability methods and how they are evaluated. Furthermore, we propose a new evaluation metric and conduct thorough experiments to compare GNN explainability methods on real world datasets. We also suggest future directions for GNN explainability.
The online social platforms, like Twitter, Facebook, LinkedIn and WeChat, have grown really fast in last decade and have been one of the most effective platforms for people to communicate and share information with each other. Due to the "word of mouth" effects, information usually can spread rapidly on these social media platforms. Therefore, it is important to study the mechanisms driving the information diffusion and quantify the consequence of information spread. A lot of efforts have been focused on this problem to help us better understand and achieve higher performance in viral marketing and advertising. On the other hand, the development of neural networks has blossomed in the last few years, leading to a large number of graph representation learning (GRL) models. Compared to traditional models, GRL methods are often shown to be more effective. In this paper, we present a comprehensive review for existing works using GRL methods for popularity prediction problem, and categorize related literatures into two big classes, according to their mainly used model and techniques: embedding-based methods and deep learning methods. Deep learning method is further classified into six small classes: convolutional neural networks, graph convolutional networks, graph attention networks, graph neural networks, recurrent neural networks, and reinforcement learning. We compare the performance of these different models and discuss their strengths and limitations. Finally, we outline the challenges and future chances for popularity prediction problem.
Benefiting from the powerful expressive capability of graphs, graph-based approaches have been popularly applied to handle multi-modal medical data and achieved impressive performance in various biomedical applications. For disease prediction tasks, most existing graph-based methods tend to define the graph manually based on specified modality (e.g., demographic information), and then integrated other modalities to obtain the patient representation by Graph Representation Learning (GRL). However, constructing an appropriate graph in advance is not a simple matter for these methods. Meanwhile, the complex correlation between modalities is ignored. These factors inevitably yield the inadequacy of providing sufficient information about the patient's condition for a reliable diagnosis. To this end, we propose an end-to-end Multi-modal Graph Learning framework (MMGL) for disease prediction with multi-modality. To effectively exploit the rich information across multi-modality associated with the disease, modality-aware representation learning is proposed to aggregate the features of each modality by leveraging the correlation and complementarity between the modalities. Furthermore, instead of defining the graph manually, the latent graph structure is captured through an effective way of adaptive graph learning. It could be jointly optimized with the prediction model, thus revealing the intrinsic connections among samples. Our model is also applicable to the scenario of inductive learning for those unseen data. An extensive group of experiments on two disease prediction tasks demonstrates that the proposed MMGL achieves more favorable performance. The code of MMGL is available at \url{https://github.com/SsGood/MMGL}.
Complex heterogeneous dynamic networks like knowledge graphs are powerful constructs that can be used in modeling data provenance from computer systems. From a security perspective, these attributed graphs enable causality analysis and tracing for analyzing a myriad of cyberattacks. However, there is a paucity in systematic development of pipelines that transform system executions and provenance into usable graph representations for machine learning tasks. This lack of instrumentation severely inhibits scientific advancement in provenance graph machine learning by hindering reproducibility and limiting the availability of data that are critical for techniques like graph neural networks. To fulfill this need, we present Flurry, an end-to-end data pipeline which simulates cyberattacks, captures provenance data from these attacks at multiple system and application layers, converts audit logs from these attacks into data provenance graphs, and incorporates this data with a framework for training deep neural models that supports preconfigured or custom-designed models for analysis in real-world resilient systems. We showcase this pipeline by processing data from multiple system attacks and performing anomaly detection via graph classification using current benchmark graph representational learning frameworks. Flurry provides a fast, customizable, extensible, and transparent solution for providing this much needed data to cybersecurity professionals.
Large-scale perturbations in the microbiome constitution are strongly correlated, whether as a driver or a consequence, with the health and functioning of human physiology. However, understanding the difference in the microbiome profiles of healthy and ill individuals can be complicated due to the large number of complex interactions among microbes. We propose to model these interactions as a time-evolving graph whose nodes are microbes and edges are interactions among them. Motivated by the need to analyse such complex interactions, we develop a method that learns a low-dimensional representation of the time-evolving graph and maintains the dynamics occurring in the high-dimensional space. Through our experiments, we show that we can extract graph features such as clusters of nodes or edges that have the highest impact on the model to learn the low-dimensional representation. This information can be crucial to identify microbes and interactions among them that are strongly correlated with clinical diseases. We conduct our experiments on both synthetic and real-world microbiome datasets.
Unsupervised graph representation learning aims to distill various graph information into a downstream task-agnostic dense vector embedding. However, existing graph representation learning approaches are designed mainly under the node homophily assumption: connected nodes tend to have similar labels and optimize performance on node-centric downstream tasks. Their design is apparently against the task-agnostic principle and generally suffers poor performance in tasks, e.g., edge classification, that demands feature signals beyond the node-view and homophily assumption. To condense different feature signals into the embeddings, this paper proposes PairE, a novel unsupervised graph embedding method using two paired nodes as the basic unit of embedding to retain the high-frequency signals between nodes to support node-related and edge-related tasks. Accordingly, a multi-self-supervised autoencoder is designed to fulfill two pretext tasks: one retains the high-frequency signal better, and another enhances the representation of commonality. Our extensive experiments on a diversity of benchmark datasets clearly show that PairE outperforms the unsupervised state-of-the-art baselines, with up to 101.1\% relative improvement on the edge classification tasks that rely on both the high and low-frequency signals in the pair and up to 82.5\% relative performance gain on the node classification tasks.
An emerging trend in representation learning over knowledge graphs (KGs) moves beyond transductive link prediction tasks over a fixed set of known entities in favor of inductive tasks that imply training on one graph and performing inference over a new graph with unseen entities. In inductive setups, node features are often not available and training shallow entity embedding matrices is meaningless as they cannot be used at inference time with unseen entities. Despite the growing interest, there are not enough benchmarks for evaluating inductive representation learning methods. In this work, we introduce ILPC 2022, a novel open challenge on KG inductive link prediction. To this end, we constructed two new datasets based on Wikidata with various sizes of training and inference graphs that are much larger than existing inductive benchmarks. We also provide two strong baselines leveraging recently proposed inductive methods. We hope this challenge helps to streamline community efforts in the inductive graph representation learning area. ILPC 2022 follows best practices on evaluation fairness and reproducibility, and is available at https://github.com/pykeen/ilpc2022.