The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues. Here we describe the integrative analysis of 111 reference human epigenomes generated as part of the programme, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression. We establish global maps of regulatory elements, define regulatory modules of coordinated activity, and their likely activators and repressors. We show that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease. Our results demonstrate the central role of epigenomic information for understanding gene regulation, cellular differentiation and human disease.

Integrative analysis of 111 reference human epigenomes

Lots of learning tasks require dealing with graph data which contains rich relation information among elements. Modeling physics systems, learning molecular fingerprints, predicting protein interface, and classifying diseases demand a model to learn from graph inputs. In other domains such as learning from non-structural data like texts and images, reasoning on extracted structures (like the dependency trees of sentences and the scene graphs of images) is an important research topic which also needs graph reasoning models. Graph neural networks (GNNs) are neural models that capture the dependence of graphs via message passing between the nodes of graphs. In recent years, variants of GNNs such as graph convolutional network (GCN), graph attention network (GAT), graph recurrent network (GRN) have demonstrated ground-breaking performances on many deep learning tasks. In this survey, we propose a general design pipeline for GNN models and discuss the variants of each component, systematically categorize the applications, and propose four open problems for future research.

Graph Neural Networks: A Review of Methods and Applications

Graphs naturally appear in numerous application domains, ranging from social analysis, bioinformatics to computer vision. The unique capability of graphs enables capturing the structural relations among data, and thus allows to harvest more insights compared to analyzing data in isolation. However, it is often very challenging to solve the learning problems on graphs, because (1) many types of data are not originally structured as graphs, such as images and text data, and (2) for graph-structured data, the underlying connectivity patterns are often complex and diverse. On the other hand, the representation learning has achieved great successes in many areas. Thereby, a potential solution is to learn the representation of graphs in a low-dimensional Euclidean space, such that the graph properties can be preserved. Although tremendous efforts have been made to address the graph representation learning problem, many of them still suffer from their shallow learning mechanisms. Deep learning models on graphs (e.g., graph neural networks) have recently emerged in machine learning and other related areas, and demonstrated the superior performance in various problems. In this survey, despite numerous types of graph neural networks, we conduct a comprehensive review specifically on the emerging field of graph convolutional networks, which is one of the most prominent graph deep learning models. First, we group the existing graph convolutional network models into two categories based on the types of convolutions and highlight some graph convolutional network models in details. Then, we categorize different graph convolutional networks according to the areas of their applications. Finally, we present several open challenges in this area and discuss potential directions for future research.

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Graph convolutional networks: a comprehensive review

Graph neural networks (GNNs) have become the standard toolkit for analyzing and learning from data on graphs. As the field grows, it becomes critical to identify key architectures and validate new ideas that generalize to larger, more complex datasets. Unfortunately, it has been increasingly difficult to gauge the effectiveness of new models in the absence of a standardized benchmark with consistent experimental settings. In this paper, we introduce a reproducible GNN benchmarking framework, with the facility for researchers to add new models conveniently for arbitrary datasets. We demonstrate the usefulness of our framework by presenting a principled investigation into the recent Weisfeiler-Lehman GNNs (WL-GNNs) compared to message passing-based graph convolutional networks (GCNs) for a variety of graph tasks, i.e. graph regression/classification and node/link prediction, with medium-scale datasets.

Benchmarking Graph Neural Networks

Social media are nowadays one of the main news sources for millions of people around the globe due to their low cost, easy access and rapid dissemination. This however comes at the cost of dubious trustworthiness and significant risk of exposure to 'fake news', intentionally written to mislead the readers. Automatically detecting fake news poses challenges that defy existing content-based analysis approaches. One of the main reasons is that often the interpretation of the news requires the knowledge of political or social context or 'common sense', which current NLP algorithms are still missing. Recent studies have shown that fake and real news spread differently on social media, forming propagation patterns that could be harnessed for the automatic fake news detection. Propagation-based approaches have multiple advantages compared to their content-based counterparts, among which is language independence and better resilience to adversarial attacks. In this paper we show a novel automatic fake news detection model based on geometric deep learning. The underlying core algorithms are a generalization of classical CNNs to graphs, allowing the fusion of heterogeneous data such as content, user profile and activity, social graph, and news propagation. Our model was trained and tested on news stories, verified by professional fact-checking organizations, that were spread on Twitter. Our experiments indicate that social network structure and propagation are important features allowing highly accurate (92.7% ROC AUC) fake news detection. Second, we observe that fake news can be reliably detected at an early stage, after just a few hours of propagation. Third, we test the aging of our model on training and testing data separated in time. Our results point to the promise of propagation-based approaches for fake news detection as an alternative or complementary strategy to content-based approaches.

Fake News Detection on Social Media using Geometric Deep Learning

Graph Neural Networks (GNNs) have recently become increasingly popular due to their ability to learn complex systems of relations or interactions arising in a broad spectrum of problems ranging from biology and particle physics to social networks and recommendation systems Despite the plethora of different models for deep learning on graphs, few approaches have been proposed thus far for dealing with graphs that present some sort of dynamic nature (eg evolving features or connectivity over time) In this paper, we present Temporal Graph Networks (TGNs), a generic, efficient framework for deep learning on dynamic graphs represented as sequences of timed events Thanks to a novel combination of memory modules and graph-based operators, TGNs are able to significantly outperform previous approaches being at the same time more computationally efficient We furthermore show that several previous models for learning on dynamic graphs can be cast as specific instances of our framework We perform a detailed ablation study of different components of our framework and devise the best configuration that achieves state-of-the-art performance on several transductive and inductive prediction tasks for dynamic graphs

Temporal Graph Networks for Deep Learning on Dynamic Graphs.

Graph representation learning has recently been applied to a broad spectrum of problems ranging from computer graphics and chemistry to high energy physics and social media. The popularity of graph neural networks has sparked interest, both in academia and in industry, in developing methods that scale to very large graphs such as Facebook or Twitter social networks. In most of these approaches, the computational cost is alleviated by a sampling strategy retaining a subset of node neighbors or subgraphs at training time. In this paper we propose a new, efficient and scalable graph deep learning architecture which sidesteps the need for graph sampling by using graph convolutional filters of different size that are amenable to efficient precomputation, allowing extremely fast training and inference. Our architecture allows using different local graph operators (e.g. motif-induced adjacency matrices or Personalized Page Rank diffusion matrix) to best suit the task at hand. We conduct extensive experimental evaluation on various open benchmarks and show that our approach is competitive with other state-of-the-art architectures, while requiring a fraction of the training and inference time. Moreover, we obtain state-of-the-art results on ogbn-papers100M, the largest public graph dataset, with over 110 million nodes and 1.5 billion edges.

SIGN: Scalable Inception Graph Neural Networks

While Graph Neural Networks (GNNs) have achieved remarkable results in a variety of applications, recent studies exposed important shortcomings in their ability to capture the structure of the underlying graph. It has been shown that the expressive power of standard GNNs is bounded by the Weisfeiler-Lehman (WL) graph isomorphism test, from which they inherit proven limitations such as the inability to detect and count graph substructures. On the other hand, there is significant empirical evidence, e.g. in network science and bioinformatics, that substructures are often informative for downstream tasks, suggesting that it is desirable to design GNNs capable of leveraging this important source of information. To this end, we propose a novel topologically-aware message passing scheme based on substructure encoding. We show that our architecture allows incorporating domain-specific inductive biases and that it is strictly more expressive than the WL test. Importantly, in contrast to recent works on the expressivity of GNNs, we do not attempt to adhere to the WL hierarchy; this allows us to retain multiple attractive properties of standard GNNs such as locality and linear network complexity, while being able to disambiguate even hard instances of graph isomorphism. We extensively evaluate our method on graph classification and regression tasks and show state-of-the-art results on multiple datasets including molecular graphs and social networks.

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Improving Graph Neural Network Expressivity via Subgraph Isomorphism Counting

Subgraph GNNs are a recent class of expressive Graph Neural Networks (GNNs) which model graphs as collections of subgraphs. So far, the design space of possible Subgraph GNN architectures as well as their basic theoretical properties are still largely unexplored. In this paper, we study the most prominent form of subgraph methods, which employs node-based subgraph selection policies such as ego-networks or node marking and deletion. We address two central questions: (1) What is the upper-bound of the expressive power of these methods? and (2) What is the family of equivariant message passing layers on these sets of subgraphs?. Our first step in answering these questions is a novel symmetry analysis which shows that modelling the symmetries of node-based subgraph collections requires a significantly smaller symmetry group than the one adopted in previous works. This analysis is then used to establish a link between Subgraph GNNs and Invariant Graph Networks (IGNs). We answer the questions above by first bounding the expressive power of subgraph methods by 3-WL, and then proposing a general family of message-passing layers for subgraph methods that generalises all previous node-based Subgraph GNNs. Finally, we design a novel Subgraph GNN dubbed SUN, which theoretically unifies previous architectures while providing better empirical performance on multiple benchmarks.

Fabrizio Frasca

Papers

Fake News Detection on Social Media using Geometric Deep Learning

Temporal Graph Networks for Deep Learning on Dynamic Graphs.

SIGN: Scalable Inception Graph Neural Networks

Improving Graph Neural Network Expressivity via Subgraph Isomorphism Counting

Understanding and Extending Subgraph GNNs by Rethinking Their Symmetries