Graphs are often used to organize data because of their simple topological structure, and therefore play a key role in machine learning. And it turns out that the low-dimensional embedded representation obtained by graph representation learning are extremely useful in various typical tasks, such as node classification, content recommendation and link prediction. However, the existing methods mostly start from the microstructure (i.e., the edges) in the graph, ignoring the mesoscopic structure (high-order local structure). Here, we propose wGCN -- a novel framework that utilizes random walk to obtain the node-specific mesoscopic structures of the graph, and utilizes these mesoscopic structures to reconstruct the graph And organize the characteristic information of the nodes. Our method can effectively generate node embeddings for previously unseen data, which has been proven in a series of experiments conducted on citation networks and social networks (our method has advantages over baseline methods). We believe that combining high-order local structural information can more efficiently explore the potential of the network, which will greatly improve the learning efficiency of graph neural network and promote the establishment of new learning models.
Deep generative models have achieved great success in areas such as image, speech, and natural language processing in the past few years. Thanks to the advances in graph-based deep learning, and in particular graph representation learning, deep graph generation methods have recently emerged with new applications ranging from discovering novel molecular structures to modeling social networks. This paper conducts a comprehensive survey on deep learning-based graph generation approaches and classifies them into five broad categories, namely, autoregressive, autoencoder-based, RL-based, adversarial, and flow-based graph generators, providing the readers a detailed description of the methods in each class. We also present publicly available source codes, commonly used datasets, and the most widely utilized evaluation metrics. Finally, we highlight the existing challenges and discuss future research directions.
Modeling time-evolving knowledge graphs (KGs) has recently gained increasing interest. Here, graph representation learning has become the dominant paradigm for link prediction on temporal KGs. However, the embedding-based approaches largely operate in a black-box fashion, lacking the ability to interpret their predictions. This paper provides a link forecasting framework that reasons over query-relevant subgraphs of temporal KGs and jointly models the structural dependencies and the temporal dynamics. Especially, we propose a temporal relational attention mechanism and a novel reverse representation update scheme to guide the extraction of an enclosing subgraph around the query. The subgraph is expanded by an iterative sampling of temporal neighbors and by attention propagation. Our approach provides human-understandable evidence explaining the forecast. We evaluate our model on four benchmark temporal knowledge graphs for the link forecasting task. While being more explainable, our model obtains a relative improvement of up to 20% on Hits@1 compared to the previous best KG forecasting method. We also conduct a survey with 53 respondents, and the results show that the evidence extracted by the model for link forecasting is aligned with human understanding.
Graphs as a type of data structure have recently attracted significant attention. Representation learning of geometric graphs has achieved great success in many fields including molecular, social, and financial networks. It is natural to present proteins as graphs in which nodes represent the residues and edges represent the pairwise interactions between residues. However, 3D protein structures have rarely been studied as graphs directly. The challenges include: 1) Proteins are complex macromolecules composed of thousands of atoms making them much harder to model than micro-molecules. 2) Capturing the long-range pairwise relations for protein structure modeling remains under-explored. 3) Few studies have focused on learning the different attributes of proteins together. To address the above challenges, we propose a new graph neural network architecture to represent the proteins as 3D graphs and predict both distance geometric graph representation and dihedral geometric graph representation together. This gives a significant advantage because this network opens a new path from the sequence to structure. We conducted extensive experiments on four different datasets and demonstrated the effectiveness of the proposed method.
Graph Neural Networks (GNNs) are widely used in graph representation learning. However, most GNN methods are designed for either homogeneous or heterogeneous graphs. In this paper, we propose a new model, Hop-Hop Relation-aware Graph Neural Network (HHR-GNN), to unify representation learning for these two types of graphs. HHR-GNN learns a personalized receptive field for each node by leveraging knowledge graph embedding to learn relation scores between the central node's representations at different hops. In neighborhood aggregation, our model simultaneously allows for hop-aware projection and aggregation. This mechanism enables the central node to learn a hop-wise neighborhood mixing that can be applied to both homogeneous and heterogeneous graphs. Experimental results on five benchmarks show the competitive performance of our model compared to state-of-the-art GNNs, e.g., up to 13K faster in terms of time cost per training epoch on large heterogeneous graphs.
Knowledge Graphs have been one of the fundamental methods for integrating heterogeneous data sources. Integrating heterogeneous data sources is crucial, especially in the biomedical domain, where central data-driven tasks such as drug discovery rely on incorporating information from different biomedical databases. These databases contain various biological entities and relations such as proteins (PDB), genes (Gene Ontology), drugs (DrugBank), diseases (DDB), and protein-protein interactions (BioGRID). The process of semantically integrating heterogeneous biomedical databases is often riddled with imperfections. The quality of data-driven drug discovery relies on the accuracy of the mining methods used and the data's quality as well. Thus, having complete and refined biomedical knowledge graphs is central to achieving more accurate drug discovery outcomes. Here we propose using the latest graph representation learning and embedding models to refine and complete biomedical knowledge graphs. This preliminary work demonstrates learning discrete representations of the integrated biomedical knowledge graph Chem2Bio2RD [3]. We perform a knowledge graph completion and refinement task using a simple top-K cosine similarity measure between the learned embedding vectors to predict missing links between drugs and targets present in the data. We show that this simple procedure can be used alternatively to binary classifiers in link prediction.
Graph representation learning has many real-world applications, from super-resolution imaging, 3D computer vision to drug repurposing, protein classification, social networks analysis. An adequate representation of graph data is vital to the learning performance of a statistical or machine learning model for graph-structured data. In this paper, we propose a novel multiscale representation system for graph data, called decimated framelets, which form a localized tight frame on the graph. The decimated framelet system allows storage of the graph data representation on a coarse-grained chain and processes the graph data at multi scales where at each scale, the data is stored at a subgraph. Based on this, we then establish decimated G-framelet transforms for the decomposition and reconstruction of the graph data at multi resolutions via a constructive data-driven filter bank. The graph framelets are built on a chain-based orthonormal basis that supports fast graph Fourier transforms. From this, we give a fast algorithm for the decimated G-framelet transforms, or FGT, that has linear computational complexity O(N) for a graph of size N. The theory of decimated framelets and FGT is verified with numerical examples for random graphs. The effectiveness is demonstrated by real-world applications, including multiresolution analysis for traffic network, and graph neural networks for graph classification tasks.
Graph Neural Networks (GNNs) are a framework for graph representation learning, where a model learns to generate low dimensional node embeddings that encapsulate structural and feature-related information. GNNs are usually trained in an end-to-end fashion, leading to highly specialized node embeddings. However, generating node embeddings that can be used to perform multiple tasks (with performance comparable to single-task models) is an open problem. We propose a novel meta-learning strategy capable of producing multi-task node embeddings. Our method avoids the difficulties arising when learning to perform multiple tasks concurrently by, instead, learning to quickly (i.e. with a few steps of gradient descent) adapt to multiple tasks singularly. We show that the embeddings produced by our method can be used to perform multiple tasks with comparable or higher performance than classically trained models. Our method is model-agnostic and task-agnostic, thus applicable to a wide variety of multi-task domains.
Low-dimension graph embeddings have proved extremely useful in various downstream tasks in large graphs, e.g., link-related content recommendation and node classification tasks, etc. Most existing embedding approaches take nodes as the basic unit for information aggregation, e.g., node perception fields in GNN or con-textual nodes in random walks. The main drawback raised by such node-view is its lack of support for expressing the compound relationships between nodes, which results in the loss of a certain degree of graph information during embedding. To this end, this paper pro-poses PairE(Pair Embedding), a solution to use "pair", a higher level unit than a "node" as the core for graph embeddings. Accordingly, a multi-self-supervised auto-encoder is designed to fulfill two pretext tasks, to reconstruct the feature distribution for respective pairs and their surrounding context. PairE has three major advantages: 1) Informative, embedding beyond node-view are capable to preserve richer information of the graph; 2) Simple, the solutions provided by PairE are time-saving, storage-efficient, and require the fewer hyper-parameters; 3) High adaptability, with the introduced translator operator to map pair embeddings to the node embeddings, PairE can be effectively used in both the link-based and the node-based graph analysis. Experiment results show that PairE consistently outperforms the state of baselines in all four downstream tasks, especially with significant edges in the link-prediction and multi-label node classification tasks.
Recent years have witnessed the emergence and flourishing of hierarchical graph pooling neural networks (HGPNNs) which are effective graph representation learning approaches for graph level tasks such as graph classification. However, current HGPNNs do not take full advantage of the graph's intrinsic structures (e.g., community structure). Moreover, the pooling operations in existing HGPNNs are difficult to be interpreted. In this paper, we propose a new interpretable graph pooling framework - CommPOOL, that can capture and preserve the hierarchical community structure of graphs in the graph representation learning process. Specifically, the proposed community pooling mechanism in CommPOOL utilizes an unsupervised approach for capturing the inherent community structure of graphs in an interpretable manner. CommPOOL is a general and flexible framework for hierarchical graph representation learning that can further facilitate various graph-level tasks. Evaluations on five public benchmark datasets and one synthetic dataset demonstrate the superior performance of CommPOOL in graph representation learning for graph classification compared to the state-of-the-art baseline methods, and its effectiveness in capturing and preserving the community structure of graphs.
We introduce the Graph Mixture Density Networks, a new family of machine learning models that can fit multimodal output distributions conditioned on graphs of arbitrary topology. By combining ideas from mixture models and graph representation learning, we address a broader class of challenging conditional density estimation problems that rely on structured data. In this respect, we evaluate our method on a new benchmark application that leverages random graphs for stochastic epidemic simulations. We show a significant improvement in the likelihood of epidemic outcomes when taking into account both multimodality and structure. The empirical analysis is complemented by two real-world regression tasks showing the effectiveness of our approach in modeling the output prediction uncertainty. Graph Mixture Density Networks open appealing research opportunities in the study of structure-dependent phenomena that exhibit non-trivial conditional output distributions.
Unsupervised/self-supervised pre-training methods for graph representation learning have recently attracted increasing research interests, and they are shown to be able to generalize to various downstream applications. Yet, the adversarial robustness of such pre-trained graph learning models remains largely unexplored. More importantly, most existing defense techniques designed for end-to-end graph representation learning methods require pre-specified label definitions, and thus cannot be directly applied to the pre-training methods. In this paper, we propose an unsupervised defense technique to robustify pre-trained deep graph models, so that the perturbations on the input graph can be successfully identified and blocked before the model is applied to different downstream tasks. Specifically, we introduce a mutual information-based measure, \textit{graph representation vulnerability (GRV)}, to quantify the robustness of graph encoders on the representation space. We then formulate an optimization problem to learn the graph representation by carefully balancing the trade-off between the expressive power and the robustness (\emph{i.e.}, GRV) of the graph encoder. The discrete nature of graph topology and the joint space of graph data make the optimization problem intractable to solve. To handle the above difficulty and to reduce computational expense, we further relax the problem and thus provide an approximate solution. Additionally, we explore a provable connection between the robustness of the unsupervised graph encoder and that of models on downstream tasks. Extensive experiments demonstrate that even without access to labels and tasks, our model is still able to enhance robustness against adversarial attacks on three downstream tasks (node classification, link prediction, and community detection) by an average of +16.5% compared with existing methods.
Heterogeneous graphs (HGs) also known as heterogeneous information networks have become ubiquitous in real-world scenarios; therefore, HG embedding, which aims to learn representations in a lower-dimension space while preserving the heterogeneous structures and semantics for downstream tasks (e.g., node/graph classification, node clustering, link prediction), has drawn considerable attentions in recent years. In this survey, we perform a comprehensive review of the recent development on HG embedding methods and techniques. We first introduce the basic concepts of HG and discuss the unique challenges brought by the heterogeneity for HG embedding in comparison with homogeneous graph representation learning; and then we systemically survey and categorize the state-of-the-art HG embedding methods based on the information they used in the learning process to address the challenges posed by the HG heterogeneity. In particular, for each representative HG embedding method, we provide detailed introduction and further analyze its pros and cons; meanwhile, we also explore the transformativeness and applicability of different types of HG embedding methods in the real-world industrial environments for the first time. In addition, we further present several widely deployed systems that have demonstrated the success of HG embedding techniques in resolving real-world application problems with broader impacts. To facilitate future research and applications in this area, we also summarize the open-source code, existing graph learning platforms and benchmark datasets. Finally, we explore the additional issues and challenges of HG embedding and forecast the future research directions in this field.
Acquiring commonsense knowledge and reasoning is recognized as an important frontier in achieving general Artificial Intelligence (AI). Recent research in the Natural Language Processing (NLP) community has demonstrated significant progress in this problem setting. Despite this progress, which is mainly on multiple-choice question answering tasks in limited settings, there is still a lack of understanding (especially at scale) of the nature of commonsense knowledge itself. In this paper, we propose and conduct a systematic study to enable a deeper understanding of commonsense knowledge by doing an empirical and structural analysis of the ConceptNet knowledge base. ConceptNet is a freely available knowledge base containing millions of commonsense assertions presented in natural language. Detailed experimental results on three carefully designed research questions, using state-of-the-art unsupervised graph representation learning ('embedding') and clustering techniques, reveal deep substructures in ConceptNet relations, allowing us to make data-driven and computational claims about the meaning of phenomena such as 'context' that are traditionally discussed only in qualitative terms. Furthermore, our methodology provides a case study in how to use data-science and computational methodologies for understanding the nature of an everyday (yet complex) psychological phenomenon that is an essential feature of human intelligence.
Graph Neural Networks (GNNs) have achieved tremendous success in various real-world applications due to their strong ability in graph representation learning. GNNs explore the graph structure and node features by aggregating and transforming information within node neighborhoods. However, through theoretical and empirical analysis, we reveal that the aggregation process of GNNs tends to destroy node similarity in the original feature space. There are many scenarios where node similarity plays a crucial role. Thus, it has motivated the proposed framework SimP-GCN that can effectively and efficiently preserve node similarity while exploiting graph structure. Specifically, to balance information from graph structure and node features, we propose a feature similarity preserving aggregation which adaptively integrates graph structure and node features. Furthermore, we employ self-supervised learning to explicitly capture the complex feature similarity and dissimilarity relations between nodes. We validate the effectiveness of SimP-GCN on seven benchmark datasets including three assortative and four disassorative graphs. The results demonstrate that SimP-GCN outperforms representative baselines. Further probe shows various advantages of the proposed framework. The implementation of SimP-GCN is available at \url{https://github.com/ChandlerBang/SimP-GCN}.
In many numerical schemes, the computational complexity scales non-linearly with the problem size. Solving a linear system of equations using direct methods or most iterative methods is a typical example. Algebraic multi-grid (AMG) methods are numerical methods used to solve large linear systems of equations efficiently. One of the main differences between AMG methods is how the coarser grid is constructed from a given fine grid. There are two main classes of AMG methods; graph and aggregation based coarsening methods. Here we propose an aggregation-based coarsening framework leveraging graph representation learning and clustering algorithms. Our method introduces the power of machine learning into the AMG research field and opens a new perspective for future researches. The proposed method uses graph representation learning techniques to learn latent features of the graph obtained from the underlying matrix of coefficients. Using these extracted features, we generated a coarser grid from the fine grid. The proposed method is highly capable of parallel computations. Our experiments show that the proposed method's efficiency in solving large systems is closely comparable with other aggregation-based methods, demonstrating the high capability of graph representation learning in designing multi-grid solvers.
With the rapid emergence of graph representation learning, the construction of new large-scale datasets is necessary to distinguish model capabilities and accurately assess the strengths and weaknesses of each technique. By carefully analyzing existing graph databases, we identify 3 critical components important for advancing the field of graph representation learning: (1) large graphs, (2) many graphs, and (3) class diversity. To date, no single graph database offers all these desired properties. We introduce MalNet, the largest public graph database ever constructed, representing a large-scale ontology of malicious software function call graphs. MalNet contains over 1.2 million graphs, averaging over 15k nodes and 35k edges per graph, across a hierarchy of 47 types and 696 families. Compared to the popular REDDIT-12K database, MalNet offers 105x more graphs, 39x larger graphs on average, and 63x more classes. We provide a detailed analysis of MalNet, discussing its properties and provenance, along with the evaluation of state-of-the-art machine learning and graph neural network techniques. The unprecedented scale and diversity of MalNet offers exciting opportunities to advance the frontiers of graph representation learning--enabling new discoveries and research into imbalanced classification, explainability and the impact of class hardness. The database is publicly available at www.mal-net.org.
In this study, we present a dynamic graph representation learning model on weighted graphs to accurately predict the network capacity of connections between viewers in a live video streaming event. We propose EGAD, a neural network architecture to capture the graph evolution by introducing a self-attention mechanism on the weights between consecutive graph convolutional networks. In addition, we account for the fact that neural architectures require a huge amount of parameters to train, thus increasing the online inference latency and negatively influencing the user experience in a live video streaming event. To address the problem of the high online inference of a vast number of parameters, we propose a knowledge distillation strategy. In particular, we design a distillation loss function, aiming to first pretrain a teacher model on offline data, and then transfer the knowledge from the teacher to a smaller student model with less parameters. We evaluate our proposed model on the link prediction task on three real-world datasets, generated by live video streaming events. The events lasted 80 minutes and each viewer exploited the distribution solution provided by the company Hive Streaming AB. The experiments demonstrate the effectiveness of the proposed model in terms of link prediction accuracy and number of required parameters, when evaluated against state-of-the-art approaches. In addition, we study the distillation performance of the proposed model in terms of compression ratio for different distillation strategies, where we show that the proposed model can achieve a compression ratio up to 15:100, preserving high link prediction accuracy. For reproduction purposes, our evaluation datasets and implementation are publicly available at https://stefanosantaris.github.io/EGAD.
Live video streaming has become a mainstay as a standard communication solution for several enterprises worldwide. To efficiently stream high-quality live video content to a large amount of offices, companies employ distributed video streaming solutions which rely on prior knowledge of the underlying evolving enterprise network. However, such networks are highly complex and dynamic. Hence, to optimally coordinate the live video distribution, the available network capacity between viewers has to be accurately predicted. In this paper we propose a graph representation learning technique on weighted and dynamic graphs to predict the network capacity, that is the weights of connections/links between viewers/nodes. We propose VStreamDRLS, a graph neural network architecture with a self-attention mechanism to capture the evolution of the graph structure of live video streaming events. VStreamDRLS employs the graph convolutional network (GCN) model over the duration of a live video streaming event and introduces a self-attention mechanism to evolve the GCN parameters. In doing so, our model focuses on the GCN weights that are relevant to the evolution of the graph and generate the node representation, accordingly. We evaluate our proposed approach on the link prediction task on two real-world datasets, generated by enterprise live video streaming events. The duration of each event lasted an hour. The experimental results demonstrate the effectiveness of VStreamDRLS when compared with state-of-the-art strategies. Our evaluation datasets and implementation are publicly available at https://github.com/stefanosantaris/vstreamdrls
Dynamic graph representation learning strategies are based on different neural architectures to capture the graph evolution over time. However, the underlying neural architectures require a large amount of parameters to train and suffer from high online inference latency, that is several model parameters have to be updated when new data arrive online. In this study we propose Distill2Vec, a knowledge distillation strategy to train a compact model with a low number of trainable parameters, so as to reduce the latency of online inference and maintain the model accuracy high. We design a distillation loss function based on Kullback-Leibler divergence to transfer the acquired knowledge from a teacher model trained on offline data, to a small-size student model for online data. Our experiments with publicly available datasets show the superiority of our proposed model over several state-of-the-art approaches with relative gains up to 5% in the link prediction task. In addition, we demonstrate the effectiveness of our knowledge distillation strategy, in terms of number of required parameters, where Distill2Vec achieves a compression ratio up to 7:100 when compared with baseline approaches. For reproduction purposes, our implementation is publicly available at https://stefanosantaris.github.io/Distill2Vec.