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Register a new userConvolutional Networks on Graphs for Learning Molecular Fingerprints
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David Duvenaud
Publication date
2015
fields
Informatics Engineering
and research's language is
English
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We introduce a convolutional neural network that operates directly on graphs. These networks allow end-to-end learning of prediction pipelines whose inputs are graphs of arbitrary size and shape. The architecture we present generalizes standard molecular feature extraction methods based on circular fingerprints. We show that these data-driven features are more interpretable, and have better predictive performance on a variety of tasks.
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Numerous important problems can be framed as learning from graph data. We propose a framework for learning convolutional neural networks for arbitrary graphs. These graphs may be undirected, directed, and with both discrete and continuous node and edge attributes. Analogous to image-based convolutional networks that operate on locally connected regions of the input, we present a general approach to extracting locally connected regions from graphs. Using established benchmark data sets, we demonstrate that the learned feature representations are competitive with state of the art graph kernels and that their computation is highly efficient.
The recently proposed self-ensembling methods have achieved promising results in deep semi-supervised learning, which penalize inconsistent predictions of unlabeled data under different perturbations. However, they only consider adding perturbations to each single data point, while ignoring the connections between data samples. In this paper, we propose a novel method, called Smooth Neighbors on Teacher Graphs (SNTG). In SNTG, a graph is constructed based on the predictions of the teacher model, i.e., the implicit self-ensemble of models. Then the graph serves as a similarity measure with respect to which the representations of similar neighboring points are learned to be smooth on the low-dimensional manifold. We achieve state-of-the-art results on semi-supervised learning benchmarks. The error rates are 9.89%, 3.99% for CIFAR-10 with 4000 labels, SVHN with 500 labels, respectively. In particular, the improvements are significant when the labels are fewer. For the non-augmented MNIST with only 20 labels, the error rate is reduced from previous 4.81% to 1.36%. Our method also shows robustness to noisy labels.
Graph representation learning resurges as a trending research subject owing to the widespread use of deep learning for Euclidean data, which inspire various creative designs of neural networks in the non-Euclidean domain, particularly graphs. With the success of these graph neural networks (GNN) in the static setting, we approach further practical scenarios where the graph dynamically evolves. Existing approaches typically resort to node embeddings and use a recurrent neural network (RNN, broadly speaking) to regulate the embeddings and learn the temporal dynamics. These methods require the knowledge of a node in the full time span (including both training and testing) and are less applicable to the frequent change of the node set. In some extreme scenarios, the node sets at different time steps may completely differ. To resolve this challenge, we propose EvolveGCN, which adapts the graph convolutional network (GCN) model along the temporal dimension without resorting to node embeddings. The proposed approach captures the dynamism of the graph sequence through using an RNN to evolve the GCN parameters. Two architectures are considered for the parameter evolution. We evaluate the proposed approach on tasks including link prediction, edge classification, and node classification. The experimental results indicate a generally higher performance of EvolveGCN compared with related approaches. The code is available at url{https://github.com/IBM/EvolveGCN}.
Graph Convolutional Network (GCN) has experienced great success in graph analysis tasks. It works by smoothing the node features across the graph. The current GCN models overwhelmingly assume that the node feature information is complete. However, real-world graph data are often incomplete and containing missing features. Traditionally, people have to estimate and fill in the unknown features based on imputation techniques and then apply GCN. However, the process of feature filling and graph learning are separated, resulting in degraded and unstable performance. This problem becomes more serious when a large number of features are missing. We propose an approach that adapts GCN to graphs containing missing features. In contrast to traditional strategy, our approach integrates the processing of missing features and graph learning within the same neural network architecture. Our idea is to represent the missing data by Gaussian Mixture Model (GMM) and calculate the expected activation of neurons in the first hidden layer of GCN, while keeping the other layers of the network unchanged. This enables us to learn the GMM parameters and network weight parameters in an end-to-end manner. Notably, our approach does not increase the computational complexity of GCN and it is consistent with GCN when the features are complete. We demonstrate through extensive experiments that our approach significantly outperforms the imputation-based methods in node classification and link prediction tasks. We show that the performance of our approach for the case with a low level of missing features is even superior to GCN for the case with complete features.
The conventional classification schemes -- notably multinomial logistic regression -- used in conjunction with convolutional networks (convnets) are classical in statistics, designed without consideration for the usual coupling with convnets, stochastic gradient descent, and backpropagation. In the specific application to supervised learning for convnets, a simple scale-invariant classification stage turns out to be more robust than multinomial logistic regression, appears to result in slightly lower errors on several standard test sets, has similar computational costs, and features precise control over the actual rate of learning. Scale-invariant means that multiplying the input values by any nonzero scalar leaves the output unchanged.
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