Learning a graph with a specific structure is essential for interpretability and identification of the relationships among data. It is well known that structured graph learning from observed samples is an NP-hard combinatorial problem. In this paper, we first show that for a set of important graph families it is possible to convert the structural constraints of structure into eigenvalue constraints of the graph Laplacian matrix. Then we introduce a unified graph learning framework, lying at the integration of the spectral properties of the Laplacian matrix with Gaussian graphical modeling that is capable of learning structures of a large class of graph families. The proposed algorithms are provably convergent and practically amenable for large-scale semi-supervised and unsupervised graph-based learning tasks. Extensive numerical experiments with both synthetic and real data sets demonstrate the effectiveness of the proposed methods. An R package containing code for all the experimental results is available at https://cran.r-project.org/package=spectralGraphTopology.
A panoply of multi-view clustering algorithms has been developed to deal with prevalent multi-view data. Among them, spectral clustering-based methods have drawn much attention and demonstrated promising results recently. Despite progress, there are still two fundamental questions that stay unanswered to date. First, how to fuse different views into one graph. More often than not, the similarities between samples may be manifested differently by different views. Many existing algorithms either simply take the average of multiple views or just learn a common graph. These simple approaches fail to consider the flexible local manifold structures of all views. Hence, the rich heterogeneous information is not fully exploited. Second, how to learn the explicit cluster structure. Most existing methods don't pay attention to the quality of the graphs and perform graph learning and spectral clustering separately. Those unreliable graphs might lead to suboptimal clustering results. To fill these gaps, in this paper, we propose a novel multi-view spectral clustering model which performs graph fusion and spectral clustering simultaneously. The fusion graph approximates the original graph of each individual view but maintains an explicit cluster structure. Experiments on four widely used data sets confirm the superiority of the proposed method.
To explore underlying complementary information from multiple views, in this paper, we propose a novel Latent Multi-view Semi-Supervised Classification (LMSSC) method. Unlike most existing multi-view semi-supervised classification methods that learn the graph using original features, our method seeks an underlying latent representation and performs graph learning and label propagation based on the learned latent representation. With the complementarity of multiple views, the latent representation could depict the data more comprehensively than every single view individually, accordingly making the graph more accurate and robust as well. Finally, LMSSC integrates latent representation learning, graph construction, and label propagation into a unified framework, which makes each subtask optimized. Experimental results on real-world benchmark datasets validate the effectiveness of our proposed method.
Advancing research in the emerging field of deep graph learning requires new tools to support tensor computation over graphs. In this paper, we present the design principles and implementation of Deep Graph Library (DGL). DGL distills the computational patterns of GNNs into a few generalized sparse tensor operations suitable for extensive parallelization. By advocating graph as the central programming abstraction, DGL can perform optimizations transparently. By cautiously adopting a framework-neutral design, DGL allows users to easily port and leverage the existing components across multiple deep learning frameworks. Our evaluation shows that DGL significantly outperforms other popular GNN-oriented frameworks in both speed and memory consumption over a variety of benchmarks and has little overhead for small scale workloads.
With the great success of graph embedding model on both academic and industry area, the robustness of graph embedding against adversarial attack inevitably becomes a central problem in graph learning domain. Regardless of the fruitful progress, most of the current works perform the attack in a white-box fashion: they need to access the model predictions and labels to construct their adversarial loss. However, the inaccessibility of model predictions in real systems makes the white-box attack impractical to real graph learning system. This paper promotes current frameworks in a more general and flexible sense -- we demand to attack various kinds of graph embedding model with black-box driven. To this end, we begin by investigating the theoretical connections between graph signal processing and graph embedding models in a principled way and formulate the graph embedding model as a general graph signal process with corresponding graph filter. As such, a generalized adversarial attacker: GF-Attack is constructed by the graph filter and feature matrix. Instead of accessing any knowledge of the target classifiers used in graph embedding, GF-Attack performs the attack only on the graph filter in a black-box attack fashion. To validate the generalization of GF-Attack, we construct the attacker on four popular graph embedding models. Extensive experimental results validate the effectiveness of our attacker on several benchmark datasets. Particularly by using our attack, even small graph perturbations like one-edge flip is able to consistently make a strong attack in performance to different graph embedding models.
Organ segmentation in CT volumes is an important pre-processing step in many computer assisted intervention and diagnosis methods. In recent years, convolutional neural networks have dominated the state of the art in this task. However, since this problem presents a challenging environment due to high variability in the organ's shape and similarity between tissues, the generation of false negative and false positive regions in the output segmentation is a common issue. Recent works have shown that the uncertainty analysis of the model can provide us with useful information about potential errors in the segmentation. In this context, we proposed a segmentation refinement method based on uncertainty analysis and graph convolutional networks. We employ the uncertainty levels of the convolutional network in a particular input volume to formulate a semi-supervised graph learning problem that is solved by training a graph convolutional network. To test our method we refine the initial output of a 2D U-Net. We validate our framework with the NIH pancreas dataset and the spleen dataset of the medical segmentation decathlon. We show that our method outperforms the state-of-the art CRF refinement method by improving the dice score by 1% for the pancreas and 2% for spleen, with respect to the original U-Net's prediction. Finally, we discuss the results and current limitations of the model for future work in this research direction. For reproducibility purposes, we make our code publicly available.
Recently, graph neural networks (GNNs) have proved to be suitable in tasks on unstructured data. Particularly in tasks as community detection, node classification, and link prediction. However, most GNN models still operate with static relationships. We propose the Graph Learning Network (GLN), a simple yet effective process to learn node embeddings and structure prediction functions. Our model uses graph convolutions to propose expected node features, and predict the best structure based on them. We repeat these steps recursively to enhance the prediction and the embeddings.
Graph learning from data represents a canonical problem that has received substantial attention in the literature. However, insufficient work has been done in incorporating prior structural knowledge onto the learning of underlying graphical models from data. Learning a graph with a specific structure is essential for interpretability and identification of the relationships among data. Useful structured graphs include the multi-component graph, bipartite graph, connected graph, sparse graph, and regular graph. In general, structured graph learning is an NP-hard combinatorial problem, therefore, designing a general tractable optimization method is extremely challenging. In this paper, we introduce a unified graph learning framework lying at the integration of Gaussian graphical models and spectral graph theory. To impose a particular structure on a graph, we first show how to formulate the combinatorial constraints as an analytical property of the graph matrix. Then we develop an optimization framework that leverages graph learning with specific structures via spectral constraints on graph matrices. The proposed algorithms are provably convergent, computationally efficient, and practically amenable for numerous graph-based tasks. Extensive numerical experiments with both synthetic and real data sets illustrate the effectiveness of the proposed algorithms. The code for all the simulations is made available as an open source repository.
Graph kernels based on the $1$-dimensional Weisfeiler-Leman algorithm and corresponding neural architectures recently emerged as powerful tools for (supervised) learning with graphs. However, due to the purely local nature of the algorithms, they might miss essential patterns in the given data and can only handle binary relations. The $k$-dimensional Weisfeiler-Leman algorithm addresses this by considering $k$-tuples, defined over the set of vertices, and defines a suitable notion of adjacency between these vertex tuples. Hence, it accounts for the higher-order interactions between vertices. However, it does not scale and may suffer from overfitting when used in a machine learning setting. Hence, it remains an important open problem to design WL-based graph learning methods that are simultaneously expressive, scalable, and non-overfitting. Here, we propose local variants and corresponding neural architectures, which consider a subset of the original neighborhood, making them more scalable, and less prone to overfitting. The expressive power of (one of) our algorithms is strictly higher than the original algorithm, in terms of ability to distinguish non-isomorphic graphs. Our experimental study confirms that the local algorithms, both kernel and neural architectures, lead to vastly reduced computation times, and prevent overfitting. The kernel version establishes a new state-of-the-art for graph classification on a wide range of benchmark datasets, while the neural version shows promising performance on large-scale molecular regression tasks.
Incorporating knowledge graph (KG) into recommender system is promising in improving the recommendation accuracy and explainability. However, existing methods largely assume that a KG is complete and simply transfer the "knowledge" in KG at the shallow level of entity raw data or embeddings. This may lead to suboptimal performance, since a practical KG can hardly be complete, and it is common that a KG has missing facts, relations, and entities. Thus, we argue that it is crucial to consider the incomplete nature of KG when incorporating it into recommender system. In this paper, we jointly learn the model of recommendation and knowledge graph completion. Distinct from previous KG-based recommendation methods, we transfer the relation information in KG, so as to understand the reasons that a user likes an item. As an example, if a user has watched several movies directed by (relation) the same person (entity), we can infer that the director relation plays a critical role when the user makes the decision, thus help to understand the user's preference at a finer granularity. Technically, we contribute a new translation-based recommendation model, which specially accounts for various preferences in translating a user to an item, and then jointly train it with a KG completion model by combining several transfer schemes. Extensive experiments on two benchmark datasets show that our method outperforms state-of-the-art KG-based recommendation methods. Further analysis verifies the positive effect of joint training on both tasks of recommendation and KG completion, and the advantage of our model in understanding user preference. We publish our project at https://github.com/TaoMiner/joint-kg-recommender.
Learning graphs from data automatically has shown encouraging performance on clustering and semisupervised learning tasks. However, real data are often corrupted, which may cause the learned graph to be inexact or unreliable. In this paper, we propose a novel robust graph learning scheme to learn reliable graphs from real-world noisy data by adaptively removing noise and errors in the raw data. We show that our proposed model can also be viewed as a robust version of manifold regularized robust PCA, where the quality of the graph plays a critical role. The proposed model is able to boost the performance of data clustering, semisupervised classification, and data recovery significantly, primarily due to two key factors: 1) enhanced low-rank recovery by exploiting the graph smoothness assumption, 2) improved graph construction by exploiting clean data recovered by robust PCA. Thus, it boosts the clustering, semi-supervised classification, and data recovery performance overall. Extensive experiments on image/document clustering, object recognition, image shadow removal, and video background subtraction reveal that our model outperforms the previous state-of-the-art methods.
Graphs are complex objects that do not lend themselves easily to typical learning tasks. Recently, a range of approaches based on graph kernels or graph neural networks have been developed for graph classification and for representation learning on graphs in general. As the developed methodologies become more sophisticated, it is important to understand which components of the increasingly complex methods are necessary or most effective. As a first step, we develop a simple yet meaningful graph representation, and explore its effectiveness in graph classification. We test our baseline representation for the graph classification task on a range of graph datasets. Interestingly, this simple representation achieves similar performance as the state-of-the-art graph kernels and graph neural networks for non-attributed graph classification. Its performance on classifying attributed graphs is slightly weaker as it does not incorporate attributes. However, given its simplicity and efficiency, we believe that it still serves as an effective baseline for attributed graph classification. Our graph representation is efficient (linear-time) to compute. We also provide a simple connection with the graph neural networks. Note that these observations are only for the task of graph classification while existing methods are often designed for a broader scope including node embedding and link prediction. The results are also likely biased due to the limited amount of benchmark datasets available. Nevertheless, the good performance of our simple baseline calls for the development of new, more comprehensive benchmark datasets so as to better evaluate and analyze different graph learning methods. Furthermore, given the computational efficiency of our graph summary, we believe that it is a good candidate as a baseline method for future graph classification (or even other graph learning) studies.
The Graph Convolutional Network (GCN) model and its variants are powerful graph embedding tools for facilitating classification and clustering on graphs. However, a major challenge is to reduce the complexity of layered GCNs and make them parallelizable and scalable on very large graphs -- state-of the art techniques are unable to achieve scalability without losing accuracy and efficiency. In this paper, we propose novel parallelization techniques for graph sampling-based GCNs that achieve superior scalable performance on very large graphs without compromising accuracy. Specifically, our GCN guarantees work-efficient training and produces order of magnitude savings in computation and communication. To scale GCN training on tightly-coupled shared memory systems, we develop parallelization strategies for the key steps in training: For the graph sampling step, we exploit parallelism within and across multiple sampling instances, and devise an efficient data structure for concurrent accesses that provides theoretical guarantee of near-linear speedup with number of processing units. For the feature propagation step within the sampled graph, we improve cache utilization and reduce DRAM communication by data partitioning. We prove that our partitioning strategy is a 2-approximation for minimizing the communication time compared to the optimal strategy. We demonstrate that our parallel graph embedding outperforms state-of-the-art methods in scalability (with respect to number of processors, graph size and GCN model size), efficiency and accuracy on several large datasets. On a 40-core Xeon platform, our parallel training achieves $64\times$ speedup (with AVX) in the sampling step and $25\times$ speedup in the feature propagation step, compared to the serial implementation, resulting in a net speedup of $21\times$.
Graphs are fundamental mathematical structures used in various fields to represent data, signals and processes. In this paper, we propose a novel framework for learning/estimating graphs from data. The proposed framework includes (i) formulation of various graph learning problems, (ii) their probabilistic interpretations and (iii) associated algorithms. Specifically, graph learning problems are posed as estimation of graph Laplacian matrices from some observed data under given structural constraints (e.g., graph connectivity and sparsity level). From a probabilistic perspective, the problems of interest correspond to maximum a posteriori (MAP) parameter estimation of Gaussian-Markov random field (GMRF) models, whose precision (inverse covariance) is a graph Laplacian matrix. For the proposed graph learning problems, specialized algorithms are developed by incorporating the graph Laplacian and structural constraints. The experimental results demonstrate that the proposed algorithms outperform the current state-of-the-art methods in terms of accuracy and computational efficiency.
Graph signals offer a very generic and natural representation for data that lives on networks or irregular structures. The actual data structure is however often unknown a priori but can sometimes be estimated from the knowledge of the application domain. If this is not possible, the data structure has to be inferred from the mere signal observations. This is exactly the problem that we address in this paper, under the assumption that the graph signals can be represented as a sparse linear combination of a few atoms of a structured graph dictionary. The dictionary is constructed on polynomials of the graph Laplacian, which can sparsely represent a general class of graph signals composed of localized patterns on the graph. We formulate a graph learning problem, whose solution provides an ideal fit between the signal observations and the sparse graph signal model. As the problem is non-convex, we propose to solve it by alternating between a signal sparse coding and a graph update step. We provide experimental results that outline the good graph recovery performance of our method, which generally compares favourably to other recent network inference algorithms.
Most existing neural networks for learning graphs address permutation invariance by conceiving of the network as a message passing scheme, where each node sums the feature vectors coming from its neighbors. We argue that this imposes a limitation on their representation power, and instead propose a new general architecture for representing objects consisting of a hierarchy of parts, which we call Covariant Compositional Networks (CCNs). Here, covariance means that the activation of each neuron must transform in a specific way under permutations, similarly to steerability in CNNs. We achieve covariance by making each activation transform according to a tensor representation of the permutation group, and derive the corresponding tensor aggregation rules that each neuron must implement. Experiments show that CCNs can outperform competing methods on standard graph learning benchmarks.
Digital presence in the world of online social media entails significant privacy risks. In this work we consider a privacy threat to a social network in which an attacker has access to a subset of random walk-based node similarities, such as effective resistances (i.e., commute times) or personalized PageRank scores. Using these similarities, the attacker's goal is to infer as much information as possible about the underlying network, including any remaining unknown pairwise node similarities and edges. For the effective resistance metric, we show that with just a small subset of measurements, the attacker can learn a large fraction of edges in a social network, even when the measurements are noisy. We also show that it is possible to learn a graph which accurately matches the underlying network on all other effective resistances. This second observation is interesting from a data mining perspective, since it can be expensive to accurately compute all effective resistances. As an alternative, our graphs learned from just a subset of approximate effective resistances can be used as surrogates in a wide range of applications that use effective resistances to probe graph structure, including for graph clustering, node centrality evaluation, and anomaly detection. We obtain our results by formalizing the graph learning objective mathematically, using two optimization problems. One formulation is convex and can be solved provably in polynomial time. The other is not, but we solve it efficiently with projected gradient and coordinate descent. We demonstrate the effectiveness of these methods on a number of social networks obtained from Facebook. We also discuss how our methods can be generalized to other random walk-based similarities, such as personalized PageRank. Our code is available at https://github.com/cnmusco/graph-similarity-learning.