Two-sample tests utilizing a similarity graph on observations are useful for high-dimensional data and non-Euclidean data due to their flexibility and good performance under a wide range of alternatives. Existing works mainly focused on sparse graphs, such as graphs with the number of edges in the order of the number of observations. However, the tests have better performance with denser graphs under many settings. In this work, we establish the theoretical ground for graph-based tests with graphs that are much denser than those in existing works.
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Popular network models such as the mixed membership and standard stochastic block model are known to exhibit distinct geometric structure when embedded into $\mathbb{R}^{d}$ using spectral methods. The resulting point cloud concentrates around a simplex in the first model, whereas it separates into clusters in the second. By adopting the formalism of generalised random dot-product graphs, we demonstrate that both of these models, and different mixing regimes in the case of mixed membership, may be distinguished by the persistent homology of the underlying point distribution in the case of adjacency spectral embedding. Moreover, despite non-identifiability issues, we show that the persistent homology of the support of the distribution and its super-level sets can be consistently estimated. As an application of our consistency results, we provide a topological hypothesis test for distinguishing the standard and mixed membership stochastic block models.
The distance-geometric graph representation adopts a unified scheme (distance) for representing the geometry of three-dimensional(3D) graphs. It is invariant to rotation and translation of the graph and it reflects pair-wise node interactions and their generally local nature. To facilitate the incorporation of geometry in deep learning on 3D graphs, we propose a message-passing graph convolutional network based on the distance-geometric graph representation: DG-GCN (distance-geometric graph convolution network). It utilizes continuous-filter convolutional layers, with filter-generating networks, that enable learning of filter weights from distances, thereby incorporating the geometry of 3D graphs in graph convolutions. Our results for the ESOL and FreeSolv datasets show major improvement over those of standard graph convolutions. They also show significant improvement over those of geometric graph convolutions employing edge weight / edge distance power laws. Our work demonstrates the utility and value of DG-GCN for end-to-end deep learning on 3D graphs, particularly molecular graphs.
The aim of this work is to develop a fully-distributed algorithmic framework for training graph convolutional networks (GCNs). The proposed method is able to exploit the meaningful relational structure of the input data, which are collected by a set of agents that communicate over a sparse network topology. After formulating the centralized GCN training problem, we first show how to make inference in a distributed scenario where the underlying data graph is split among different agents. Then, we propose a distributed gradient descent procedure to solve the GCN training problem. The resulting model distributes computation along three lines: during inference, during back-propagation, and during optimization. Convergence to stationary solutions of the GCN training problem is also established under mild conditions. Finally, we propose an optimization criterion to design the communication topology between agents in order to match with the graph describing data relationships. A wide set of numerical results validate our proposal. To the best of our knowledge, this is the first work combining graph convolutional neural networks with distributed optimization.
Node classification is an important problem in graph data management. It is commonly solved by various label propagation methods that work iteratively starting from a few labeled seed nodes. For graphs with arbitrary compatibilities between classes, these methods crucially depend on knowing the compatibility matrix that must be provided by either domain experts or heuristics. Can we instead directly estimate the correct compatibilities from a sparsely labeled graph in a principled and scalable way? We answer this question affirmatively and suggest a method called distant compatibility estimation that works even on extremely sparsely labeled graphs (e.g., 1 in 10,000 nodes is labeled) in a fraction of the time it later takes to label the remaining nodes. Our approach first creates multiple factorized graph representations (with size independent of the graph) and then performs estimation on these smaller graph sketches. We define algebraic amplification as the more general idea of leveraging algebraic properties of an algorithm's update equations to amplify sparse signals. We show that our estimator is by orders of magnitude faster than an alternative approach and that the end-to-end classification accuracy is comparable to using gold standard compatibilities. This makes it a cheap preprocessing step for any existing label propagation method and removes the current dependence on heuristics.
Graph Convolutional Networks (GCNs) have recently become the primary choice for learning from graph-structured data, superseding hash fingerprints in representing chemical compounds. However, GCNs lack the ability to take into account the ordering of node neighbors, even when there is a geometric interpretation of the graph vertices that provides an order based on their spatial positions. To remedy this issue, we propose Geometric Graph Convolutional Network (geo-GCN) which uses spatial features to efficiently learn from graphs that can be naturally located in space. Our contribution is threefold: we propose a GCN-inspired architecture which (i) leverages node positions, (ii) is a proper generalisation of both GCNs and Convolutional Neural Networks (CNNs), (iii) benefits from augmentation which further improves the performance and assures invariance with respect to the desired properties. Empirically, geo-GCN outperforms state-of-the-art graph-based methods on image classification and chemical tasks.
This paper focuses on the discrimination capacity of aggregation functions: these are the permutation invariant functions used by graph neural networks to combine the features of nodes. Realizing that the most powerful aggregation functions suffer from a dimensionality curse, we consider a restricted setting. In particular, we show that the standard sum and a novel histogram-based function have the capacity to discriminate between any fixed number of inputs chosen by an adversary. Based on our insights, we design a graph neural network aiming, not to maximize discrimination capacity, but to learn discriminative graph representations that generalize well. Our empirical evaluation provides evidence that our choices can yield benefits to the problem of structural graph classification.
Network embedding aims to learn a latent, low-dimensional vector representations of network nodes, effective in supporting various network analytic tasks. While prior arts on network embedding focus primarily on preserving network topology structure to learn node representations, recently proposed attributed network embedding algorithms attempt to integrate rich node content information with network topological structure for enhancing the quality of network embedding. In reality, networks often have sparse content, incomplete node attributes, as well as the discrepancy between node attribute feature space and network structure space, which severely deteriorates the performance of existing methods. In this paper, we propose a unified framework for attributed network embedding-attri2vec-that learns node embeddings by discovering a latent node attribute subspace via a network structure guided transformation performed on the original attribute space. The resultant latent subspace can respect network structure in a more consistent way towards learning high-quality node representations. We formulate an optimization problem which is solved by an efficient stochastic gradient descent algorithm, with linear time complexity to the number of nodes. We investigate a series of linear and non-linear transformations performed on node attributes and empirically validate their effectiveness on various types of networks. Another advantage of attri2vec is its ability to solve out-of-sample problems, where embeddings of new coming nodes can be inferred from their node attributes through the learned mapping function. Experiments on various types of networks confirm that attri2vec is superior to state-of-the-art baselines for node classification, node clustering, as well as out-of-sample link prediction tasks. The source code of this paper is available at //github.com/daokunzhang/attri2vec.
We study object recognition under the constraint that each object class is only represented by very few observations. In such cases, naive supervised learning would lead to severe over-fitting in deep neural networks due to limited training data. We tackle this problem by creating much more training data through label propagation from the few labeled examples to a vast collection of unannotated images. Our main insight is that such a label propagation scheme can be highly effective when the similarity metric used for propagation is learned and transferred from other related domains with lots of data. We test our approach on semi-supervised learning, transfer learning and few-shot recognition, where we learn our similarity metric using various supervised/unsupervised pretraining methods, and transfer it to unlabeled data across different data distributions. By taking advantage of unlabeled data in this way, we achieve significant improvements on all three tasks. Notably, our approach outperforms current state-of-the-art techniques by an absolute $20\%$ for semi-supervised learning on CIFAR10, $10\%$ for transfer learning from ImageNet to CIFAR10, and $6\%$ for few-shot recognition on mini-ImageNet, when labeled examples are limited.
Random walks are at the heart of many existing network embedding methods. However, such algorithms have many limitations that arise from the use of random walks, e.g., the features resulting from these methods are unable to transfer to new nodes and graphs as they are tied to vertex identity. In this work, we introduce the Role2Vec framework which uses the flexible notion of attributed random walks, and serves as a basis for generalizing existing methods such as DeepWalk, node2vec, and many others that leverage random walks. Our proposed framework enables these methods to be more widely applicable for both transductive and inductive learning as well as for use on graphs with attributes (if available). This is achieved by learning functions that generalize to new nodes and graphs. We show that our proposed framework is effective with an average AUC improvement of 16:55% while requiring on average 853x less space than existing methods on a variety of graphs.
We address the problem of learning vector representations for entities and relations in Knowledge Graphs (KGs) for Knowledge Base Completion (KBC). This problem has received significant attention in the past few years and multiple methods have been proposed. Most of the existing methods in the literature use a predefined characteristic scoring function for evaluating the correctness of KG triples. These scoring functions distinguish correct triples (high score) from incorrect ones (low score). However, their performance vary across different datasets. In this work, we demonstrate that a simple neural network based score function can consistently achieve near start-of-the-art performance on multiple datasets. We also quantitatively demonstrate biases in standard benchmark datasets, and highlight the need to perform evaluation spanning various datasets.
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