Metric learning pairwise kernel for graph inference

Much recent work in bioinformatics has focused on the inference of various types of biological networks, representing gene regulation, metabolic processes, protein-protein interactions, etc. A common setting involves inferring network edges in a supervised fashion from a set of high-confidence edges, possibly characterized by multiple, heterogeneous data sets (protein sequence, gene expression, etc.). Here, we distinguish between two modes of inference in this setting: direct inference based upon similarities between nodes joined by an edge, and indirect inference based upon similarities between one pair of nodes and another pair of nodes. We propose a supervised approach for the direct case by translating it into a distance metric learning problem. A relaxation of the resulting convex optimization problem leads to the support vector machine (SVM) algorithm with a particular kernel for pairs, which we call the metric learning pairwise kernel (MLPK). We demonstrate, using several real biological networks, that this direct approach often improves upon the state-of-the-art SVM for indirect inference with the tensor product pairwise kernel

Network Model Selection for Task-Focused Attributed Network Inference

Networks are models representing relationships between entities. Often these relationships are explicitly given, or we must learn a representation which generalizes and predicts observed behavior in underlying individual data (e.g. attributes or labels). Whether given or inferred, choosing the best representation affects subsequent tasks and questions on the network. This work focuses on model selection to evaluate network representations from data, focusing on fundamental predictive tasks on networks. We present a modular methodology using general, interpretable network models, task neighborhood functions found across domains, and several criteria for robust model selection. We demonstrate our methodology on three online user activity datasets and show that network model selection for the appropriate network task vs. an alternate task increases performance by an order of magnitude in our experiments