Dropout Training of Matrix Factorization and Autoencoder for Link Prediction in Sparse Graphs

Matrix factorization (MF) and Autoencoder (AE) are among the most successful approaches of unsupervised learning. While MF based models have been extensively exploited in the graph modeling and link prediction literature, the AE family has not gained much attention. In this paper we investigate both MF and AE's application to the link prediction problem in sparse graphs. We show the connection between AE and MF from the perspective of multiview learning, and further propose MF+AE: a model training MF and AE jointly with shared parameters. We apply dropout to training both the MF and AE parts, and show that it can significantly prevent overfitting by acting as an adaptive regularization. We conduct experiments on six real world sparse graph datasets, and show that MF+AE consistently outperforms the competing methods, especially on datasets that demonstrate strong non-cohesive structures.Comment: Published in SDM 201

Predicting multicellular function through multi-layer tissue networks

Motivation: Understanding functions of proteins in specific human tissues is essential for insights into disease diagnostics and therapeutics, yet prediction of tissue-specific cellular function remains a critical challenge for biomedicine. Results: Here we present OhmNet, a hierarchy-aware unsupervised node feature learning approach for multi-layer networks. We build a multi-layer network, where each layer represents molecular interactions in a different human tissue. OhmNet then automatically learns a mapping of proteins, represented as nodes, to a neural embedding based low-dimensional space of features. OhmNet encourages sharing of similar features among proteins with similar network neighborhoods and among proteins activated in similar tissues. The algorithm generalizes prior work, which generally ignores relationships between tissues, by modeling tissue organization with a rich multiscale tissue hierarchy. We use OhmNet to study multicellular function in a multi-layer protein interaction network of 107 human tissues. In 48 tissues with known tissue-specific cellular functions, OhmNet provides more accurate predictions of cellular function than alternative approaches, and also generates more accurate hypotheses about tissue-specific protein actions. We show that taking into account the tissue hierarchy leads to improved predictive power. Remarkably, we also demonstrate that it is possible to leverage the tissue hierarchy in order to effectively transfer cellular functions to a functionally uncharacterized tissue. Overall, OhmNet moves from flat networks to multiscale models able to predict a range of phenotypes spanning cellular subsystemsComment: In Proceedings of the 25th International Conference on Intelligent Systems for Molecular Biology (ISMB), 201

node2vec: Scalable Feature Learning for Networks

Prediction tasks over nodes and edges in networks require careful effort in engineering features used by learning algorithms. Recent research in the broader field of representation learning has led to significant progress in automating prediction by learning the features themselves. However, present feature learning approaches are not expressive enough to capture the diversity of connectivity patterns observed in networks. Here we propose node2vec, an algorithmic framework for learning continuous feature representations for nodes in networks. In node2vec, we learn a mapping of nodes to a low-dimensional space of features that maximizes the likelihood of preserving network neighborhoods of nodes. We define a flexible notion of a node's network neighborhood and design a biased random walk procedure, which efficiently explores diverse neighborhoods. Our algorithm generalizes prior work which is based on rigid notions of network neighborhoods, and we argue that the added flexibility in exploring neighborhoods is the key to learning richer representations. We demonstrate the efficacy of node2vec over existing state-of-the-art techniques on multi-label classification and link prediction in several real-world networks from diverse domains. Taken together, our work represents a new way for efficiently learning state-of-the-art task-independent representations in complex networks.Comment: In Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 201

On the Implicit Bias of Dropout

Algorithmic approaches endow deep learning systems with implicit bias that helps them generalize even in over-parametrized settings. In this paper, we focus on understanding such a bias induced in learning through dropout, a popular technique to avoid overfitting in deep learning. For single hidden-layer linear neural networks, we show that dropout tends to make the norm of incoming/outgoing weight vectors of all the hidden nodes equal. In addition, we provide a complete characterization of the optimization landscape induced by dropout.Comment: 17 pages, 3 figures, In Proceedings of the Thirty-fifth International Conference on Machine Learning (ICML), 201