Representation Learning on Graphs: Methods and Applications

Machine learning on graphs is an important and ubiquitous task with applications ranging from drug design to friendship recommendation in social networks. The primary challenge in this domain is finding a way to represent, or encode, graph structure so that it can be easily exploited by machine learning models. Traditionally, machine learning approaches relied on user-defined heuristics to extract features encoding structural information about a graph (e.g., degree statistics or kernel functions). However, recent years have seen a surge in approaches that automatically learn to encode graph structure into low-dimensional embeddings, using techniques based on deep learning and nonlinear dimensionality reduction. Here we provide a conceptual review of key advancements in this area of representation learning on graphs, including matrix factorization-based methods, random-walk based algorithms, and graph neural networks. We review methods to embed individual nodes as well as approaches to embed entire (sub)graphs. In doing so, we develop a unified framework to describe these recent approaches, and we highlight a number of important applications and directions for future work.Comment: Published in the IEEE Data Engineering Bulletin, September 2017; version with minor correction

Deep Representation Learning for Social Network Analysis

Social network analysis is an important problem in data mining. A fundamental step for analyzing social networks is to encode network data into low-dimensional representations, i.e., network embeddings, so that the network topology structure and other attribute information can be effectively preserved. Network representation leaning facilitates further applications such as classification, link prediction, anomaly detection and clustering. In addition, techniques based on deep neural networks have attracted great interests over the past a few years. In this survey, we conduct a comprehensive review of current literature in network representation learning utilizing neural network models. First, we introduce the basic models for learning node representations in homogeneous networks. Meanwhile, we will also introduce some extensions of the base models in tackling more complex scenarios, such as analyzing attributed networks, heterogeneous networks and dynamic networks. Then, we introduce the techniques for embedding subgraphs. After that, we present the applications of network representation learning. At the end, we discuss some promising research directions for future work

Can Graph Neural Networks Go "Online"? An Analysis of Pretraining and Inference

Large-scale graph data in real-world applications is often not static but dynamic, i. e., new nodes and edges appear over time. Current graph convolution approaches are promising, especially, when all the graph's nodes and edges are available during training. When unseen nodes and edges are inserted after training, it is not yet evaluated whether up-training or re-training from scratch is preferable. We construct an experimental setup, in which we insert previously unseen nodes and edges after training and conduct a limited amount of inference epochs. In this setup, we compare adapting pretrained graph neural networks against retraining from scratch. Our results show that pretrained models yield high accuracy scores on the unseen nodes and that pretraining is preferable over retraining from scratch. Our experiments represent a first step to evaluate and develop truly online variants of graph neural networks.Comment: 5 pages, 1 figure, Representation Learning on Graphs and Manifolds Workshop of the International Conference on Learning Representations (ICLR), 201

Adversarial Defense Framework for Graph Neural Network

Graph neural network (GNN), as a powerful representation learning model on graph data, attracts much attention across various disciplines. However, recent studies show that GNN is vulnerable to adversarial attacks. How to make GNN more robust? What are the key vulnerabilities in GNN? How to address the vulnerabilities and defense GNN against the adversarial attacks? In this paper, we propose DefNet, an effective adversarial defense framework for GNNs. In particular, we first investigate the latent vulnerabilities in every layer of GNNs and propose corresponding strategies including dual-stage aggregation and bottleneck perceptron. Then, to cope with the scarcity of training data, we propose an adversarial contrastive learning method to train the GNN in a conditional GAN manner by leveraging the high-level graph representation. Extensive experiments on three public datasets demonstrate the effectiveness of DefNet in improving the robustness of popular GNN variants, such as Graph Convolutional Network and GraphSAGE, under various types of adversarial attacks

Deep Structured Models For Group Activity Recognition

This paper presents a deep neural-network-based hierarchical graphical model for individual and group activity recognition in surveillance scenes. Deep networks are used to recognize the actions of individual people in a scene. Next, a neural-network-based hierarchical graphical model refines the predicted labels for each class by considering dependencies between the classes. This refinement step mimics a message-passing step similar to inference in a probabilistic graphical model. We show that this approach can be effective in group activity recognition, with the deep graphical model improving recognition rates over baseline methods

Graph Convolutional Reinforcement Learning

Learning to cooperate is crucially important in multi-agent environments. The key is to understand the mutual interplay between agents. However, multi-agent environments are highly dynamic, where agents keep moving and their neighbors change quickly. This makes it hard to learn abstract representations of mutual interplay between agents. To tackle these difficulties, we propose graph convolutional reinforcement learning, where graph convolution adapts to the dynamics of the underlying graph of the multi-agent environment, and relation kernels capture the interplay between agents by their relation representations. Latent features produced by convolutional layers from gradually increased receptive fields are exploited to learn cooperation, and cooperation is further improved by temporal relation regularization for consistency. Empirically, we show that our method substantially outperforms existing methods in a variety of cooperative scenarios.Comment: ICLR'2

A Survey on Deep Learning for Neuroimaging-based Brain Disorder Analysis

Deep learning has been recently used for the analysis of neuroimages, such as structural magnetic resonance imaging (MRI), functional MRI, and positron emission tomography (PET), and has achieved significant performance improvements over traditional machine learning in computer-aided diagnosis of brain disorders. This paper reviews the applications of deep learning methods for neuroimaging-based brain disorder analysis. We first provide a comprehensive overview of deep learning techniques and popular network architectures, by introducing various types of deep neural networks and recent developments. We then review deep learning methods for computer-aided analysis of four typical brain disorders, including Alzheimer's disease, Parkinson's disease, Autism spectrum disorder, and Schizophrenia, where the first two diseases are neurodegenerative disorders and the last two are neurodevelopmental and psychiatric disorders, respectively. More importantly, we discuss the limitations of existing studies and present possible future directions.Comment: 30 pages, 7 figure

ChestX-ray8: Hospital-scale Chest X-ray Database and Benchmarks on Weakly-Supervised Classification and Localization of Common Thorax Diseases

The chest X-ray is one of the most commonly accessible radiological examinations for screening and diagnosis of many lung diseases. A tremendous number of X-ray imaging studies accompanied by radiological reports are accumulated and stored in many modern hospitals' Picture Archiving and Communication Systems (PACS). On the other side, it is still an open question how this type of hospital-size knowledge database containing invaluable imaging informatics (i.e., loosely labeled) can be used to facilitate the data-hungry deep learning paradigms in building truly large-scale high precision computer-aided diagnosis (CAD) systems. In this paper, we present a new chest X-ray database, namely "ChestX-ray8", which comprises 108,948 frontal-view X-ray images of 32,717 unique patients with the text-mined eight disease image labels (where each image can have multi-labels), from the associated radiological reports using natural language processing. Importantly, we demonstrate that these commonly occurring thoracic diseases can be detected and even spatially-located via a unified weakly-supervised multi-label image classification and disease localization framework, which is validated using our proposed dataset. Although the initial quantitative results are promising as reported, deep convolutional neural network based "reading chest X-rays" (i.e., recognizing and locating the common disease patterns trained with only image-level labels) remains a strenuous task for fully-automated high precision CAD systems. Data download link: https://nihcc.app.box.com/v/ChestXray-NIHCCComment: CVPR 2017 spotlight;V1: CVPR submission+supplementary; V2: Statistics and benchmark results on published ChestX-ray14 dataset are updated in Appendix B V3: Minor correction V4: new data download link upated: https://nihcc.app.box.com/v/ChestXray-NIHCC V5: Update benchmark results on the published data split in the appendi

A Collaborative Computer Aided Diagnosis (C-CAD) System with Eye-Tracking, Sparse Attentional Model, and Deep Learning

There are at least two categories of errors in radiology screening that can lead to suboptimal diagnostic decisions and interventions:(i)human fallibility and (ii)complexity of visual search. Computer aided diagnostic (CAD) tools are developed to help radiologists to compensate for some of these errors. However, despite their significant improvements over conventional screening strategies, most CAD systems do not go beyond their use as second opinion tools due to producing a high number of false positives, which human interpreters need to correct. In parallel with efforts in computerized analysis of radiology scans, several researchers have examined behaviors of radiologists while screening medical images to better understand how and why they miss tumors, how they interact with the information in an image, and how they search for unknown pathology in the images. Eye-tracking tools have been instrumental in exploring answers to these fundamental questions. In this paper, we aim to develop a paradigm shift CAD system, called collaborative CAD (C-CAD), that unifies both of the above mentioned research lines: CAD and eye-tracking. We design an eye-tracking interface providing radiologists with a real radiology reading room experience. Then, we propose a novel algorithm that unifies eye-tracking data and a CAD system. Specifically, we present a new graph based clustering and sparsification algorithm to transform eye-tracking data (gaze) into a signal model to interpret gaze patterns quantitatively and qualitatively. The proposed C-CAD collaborates with radiologists via eye-tracking technology and helps them to improve diagnostic decisions. The C-CAD learns radiologists' search efficiency by processing their gaze patterns. To do this, the C-CAD uses a deep learning algorithm in a newly designed multi-task learning platform to segment and diagnose cancers simultaneously.Comment: Submitted to Medical Image Analysis Journal (MedIA

Structure Inference Net: Object Detection Using Scene-Level Context and Instance-Level Relationships

Context is important for accurate visual recognition. In this work we propose an object detection algorithm that not only considers object visual appearance, but also makes use of two kinds of context including scene contextual information and object relationships within a single image. Therefore, object detection is regarded as both a cognition problem and a reasoning problem when leveraging these structured information. Specifically, this paper formulates object detection as a problem of graph structure inference, where given an image the objects are treated as nodes in a graph and relationships between the objects are modeled as edges in such graph. To this end, we present a so-called Structure Inference Network (SIN), a detector that incorporates into a typical detection framework (e.g. Faster R-CNN) with a graphical model which aims to infer object state. Comprehensive experiments on PASCAL VOC and MS COCO datasets indicate that scene context and object relationships truly improve the performance of object detection with more desirable and reasonable outputs.Comment: published in CVPR 201