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Machine Learning on Graphs: A Model and Comprehensive Taxonomy
TL;DR: A comprehensive taxonomy of representation learning methods for graph-structured data is proposed, aiming to unify several disparate bodies of work and provide a solid foundation for understanding the intuition behind these methods, and enables future research in the area.
Abstract: There has been a surge of recent interest in learning representations for graph-structured data. Graph representation learning methods have generally fallen into three main categories, based on the availability of labeled data. The first, network embedding (such as shallow graph embedding or graph auto-encoders), focuses on learning unsupervised representations of relational structure. The second, graph regularized neural networks, leverages graphs to augment neural network losses with a regularization objective for semi-supervised learning. The third, graph neural networks, aims to learn differentiable functions over discrete topologies with arbitrary structure. However, despite the popularity of these areas there has been surprisingly little work on unifying the three paradigms. Here, we aim to bridge the gap between graph neural networks, network embedding and graph regularization models. We propose a comprehensive taxonomy of representation learning methods for graph-structured data, aiming to unify several disparate bodies of work. Specifically, we propose a Graph Encoder Decoder Model (GRAPHEDM), which generalizes popular algorithms for semi-supervised learning on graphs (e.g. GraphSage, Graph Convolutional Networks, Graph Attention Networks), and unsupervised learning of graph representations (e.g. DeepWalk, node2vec, etc) into a single consistent approach. To illustrate the generality of this approach, we fit over thirty existing methods into this framework. We believe that this unifying view both provides a solid foundation for understanding the intuition behind these methods, and enables future research in the area.
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TL;DR: A detailed review over existing graph neural network models is provided, systematically categorize the applications, and four open problems for future research are proposed.
Abstract: 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.
2,494 citations
01 Jan 2020
TL;DR: In this paper, the authors 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.
Abstract: 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.
1,266 citations
Posted Content•
TL;DR: A reproducible GNN benchmarking framework is introduced, with the facility for researchers to add new models conveniently for arbitrary datasets, and a principled investigation into the recent Weisfeiler-Lehman GNNs (WL-GNNs) compared to message passing-based graph convolutional networks (GCNs).
Abstract: 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.
481 citations
Journal Article•
TL;DR: A reproducible GNN benchmarking framework is introduced, with the facility for researchers to add new models conveniently for arbitrary datasets, and a principled investigation into the recent Weisfeiler-Lehman GNNs (WL-GNNs) compared to message passing-based graph convolutional networks (GCNs).
Abstract: 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.
353 citations
Posted Content•
TL;DR: The TUDataset for graph classification and regression is introduced, which consists of over 120 datasets of varying sizes from a wide range of applications and provides Python-based data loaders, kernel and graph neural network baseline implementations, and evaluation tools.
Abstract: Recently, there has been an increasing interest in (supervised) learning with graph data, especially using graph neural networks. However, the development of meaningful benchmark datasets and standardized evaluation procedures is lagging, consequently hindering advancements in this area. To address this, we introduce the TUDataset for graph classification and regression. The collection consists of over 120 datasets of varying sizes from a wide range of applications. We provide Python-based data loaders, kernel and graph neural network baseline implementations, and evaluation tools. Here, we give an overview of the datasets, standardized evaluation procedures, and provide baseline experiments. All datasets are available at this http URL. The experiments are fully reproducible from the code available at this http URL.
346 citations
References
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TL;DR: A novel, efficient, gradient based method called long short-term memory (LSTM) is introduced, which can learn to bridge minimal time lags in excess of 1000 discrete-time steps by enforcing constant error flow through constant error carousels within special units.
Abstract: Learning to store information over extended time intervals by recurrent backpropagation takes a very long time, mostly because of insufficient, decaying error backflow. We briefly review Hochreiter's (1991) analysis of this problem, then address it by introducing a novel, efficient, gradient based method called long short-term memory (LSTM). Truncating the gradient where this does not do harm, LSTM can learn to bridge minimal time lags in excess of 1000 discrete-time steps by enforcing constant error flow through constant error carousels within special units. Multiplicative gate units learn to open and close access to the constant error flow. LSTM is local in space and time; its computational complexity per time step and weight is O. 1. Our experiments with artificial data involve local, distributed, real-valued, and noisy pattern representations. In comparisons with real-time recurrent learning, back propagation through time, recurrent cascade correlation, Elman nets, and neural sequence chunking, LSTM leads to many more successful runs, and learns much faster. LSTM also solves complex, artificial long-time-lag tasks that have never been solved by previous recurrent network algorithms.
72,897 citations
"Machine Learning on Graphs: A Model..." refers methods in this paper
...[17] introduced NGM and showed that the regularization objective in Equation 26 generalizes to more complex neural architectures than feed-forward neural networks (FF-NN), such as Long short-term memory (LSTM) networks [54] or CNNs [68]....
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Proceedings Article•
12 Jun 2017TL;DR: This paper proposed a simple network architecture based solely on an attention mechanism, dispensing with recurrence and convolutions entirely and achieved state-of-the-art performance on English-to-French translation.
Abstract: The dominant sequence transduction models are based on complex recurrent orconvolutional neural networks in an encoder and decoder configuration. The best performing such models also connect the encoder and decoder through an attentionm echanisms. We propose a novel, simple network architecture based solely onan attention mechanism, dispensing with recurrence and convolutions entirely.Experiments on two machine translation tasks show these models to be superiorin quality while being more parallelizable and requiring significantly less timeto train. Our single model with 165 million parameters, achieves 27.5 BLEU onEnglish-to-German translation, improving over the existing best ensemble result by over 1 BLEU. On English-to-French translation, we outperform the previoussingle state-of-the-art with model by 0.7 BLEU, achieving a BLEU score of 41.1.
52,856 citations
20 Jun 2009
TL;DR: A new database called “ImageNet” is introduced, a large-scale ontology of images built upon the backbone of the WordNet structure, much larger in scale and diversity and much more accurate than the current image datasets.
Abstract: The explosion of image data on the Internet has the potential to foster more sophisticated and robust models and algorithms to index, retrieve, organize and interact with images and multimedia data. But exactly how such data can be harnessed and organized remains a critical problem. We introduce here a new database called “ImageNet”, a large-scale ontology of images built upon the backbone of the WordNet structure. ImageNet aims to populate the majority of the 80,000 synsets of WordNet with an average of 500-1000 clean and full resolution images. This will result in tens of millions of annotated images organized by the semantic hierarchy of WordNet. This paper offers a detailed analysis of ImageNet in its current state: 12 subtrees with 5247 synsets and 3.2 million images in total. We show that ImageNet is much larger in scale and diversity and much more accurate than the current image datasets. Constructing such a large-scale database is a challenging task. We describe the data collection scheme with Amazon Mechanical Turk. Lastly, we illustrate the usefulness of ImageNet through three simple applications in object recognition, image classification and automatic object clustering. We hope that the scale, accuracy, diversity and hierarchical structure of ImageNet can offer unparalleled opportunities to researchers in the computer vision community and beyond.
49,639 citations
"Machine Learning on Graphs: A Model..." refers background in this paper
...with one terabyte size) but does not fit on RAM, how can a researcher apply a learning method on such a large graphs, using just a personal computer? Contrast this with a computer vision task by considering a large image dataset [33, 67]....
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01 Oct 2014
TL;DR: A new global logbilinear regression model that combines the advantages of the two major model families in the literature: global matrix factorization and local context window methods and produces a vector space with meaningful substructure.
Abstract: Recent methods for learning vector space representations of words have succeeded in capturing fine-grained semantic and syntactic regularities using vector arithmetic, but the origin of these regularities has remained opaque. We analyze and make explicit the model properties needed for such regularities to emerge in word vectors. The result is a new global logbilinear regression model that combines the advantages of the two major model families in the literature: global matrix factorization and local context window methods. Our model efficiently leverages statistical information by training only on the nonzero elements in a word-word cooccurrence matrix, rather than on the entire sparse matrix or on individual context windows in a large corpus. The model produces a vector space with meaningful substructure, as evidenced by its performance of 75% on a recent word analogy task. It also outperforms related models on similarity tasks and named entity recognition.
30,558 citations
"Machine Learning on Graphs: A Model..." refers methods in this paper
...4 Outer product-based: Skip-gram methods Skip-gram graph embedding models were inspired by efficient NLP methods modeling probability distributions over words for learning word embeddings [80, 89]....
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Journal Article•
TL;DR: A new technique called t-SNE that visualizes high-dimensional data by giving each datapoint a location in a two or three-dimensional map, a variation of Stochastic Neighbor Embedding that is much easier to optimize, and produces significantly better visualizations by reducing the tendency to crowd points together in the center of the map.
Abstract: We present a new technique called “t-SNE” that visualizes high-dimensional data by giving each datapoint a location in a two or three-dimensional map. The technique is a variation of Stochastic Neighbor Embedding (Hinton and Roweis, 2002) that is much easier to optimize, and produces significantly better visualizations by reducing the tendency to crowd points together in the center of the map. t-SNE is better than existing techniques at creating a single map that reveals structure at many different scales. This is particularly important for high-dimensional data that lie on several different, but related, low-dimensional manifolds, such as images of objects from multiple classes seen from multiple viewpoints. For visualizing the structure of very large datasets, we show how t-SNE can use random walks on neighborhood graphs to allow the implicit structure of all of the data to influence the way in which a subset of the data is displayed. We illustrate the performance of t-SNE on a wide variety of datasets and compare it with many other non-parametric visualization techniques, including Sammon mapping, Isomap, and Locally Linear Embedding. The visualizations produced by t-SNE are significantly better than those produced by the other techniques on almost all of the datasets.
30,124 citations
"Machine Learning on Graphs: A Model..." refers methods in this paper
...Note that unsupervised graph embedding methods are also used for visualization purposes: by first training an encoder-decoder model (corresponding to a shallow embedding or graph convolution network), and then mapping every node representation onto a two-dimensional space using, t-distributed stochastic neighbor embeddings (t-SNE) [77] or PCA [58]....
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