Classifying pairs with trees for supervised biological network inference

Networks are ubiquitous in biology and computational approaches have been largely investigated for their inference. In particular, supervised machine learning methods can be used to complete a partially known network by integrating various measurements. Two main supervised frameworks have been proposed: the local approach, which trains a separate model for each network node, and the global approach, which trains a single model over pairs of nodes. Here, we systematically investigate, theoretically and empirically, the exploitation of tree-based ensemble methods in the context of these two approaches for biological network inference. We first formalize the problem of network inference as classification of pairs, unifying in the process homogeneous and bipartite graphs and discussing two main sampling schemes. We then present the global and the local approaches, extending the later for the prediction of interactions between two unseen network nodes, and discuss their specializations to tree-based ensemble methods, highlighting their interpretability and drawing links with clustering techniques. Extensive computational experiments are carried out with these methods on various biological networks that clearly highlight that these methods are competitive with existing methods.Comment: 22 page

Algorithm selection on data streams

We explore the possibilities of meta-learning on data streams, in particular algorithm selection. In a first experiment we calculate the characteristics of a small sample of a data stream, and try to predict which classifier performs best on the entire stream. This yields promising results and interesting patterns. In a second experiment, we build a meta-classifier that predicts, based on measurable data characteristics in a window of the data stream, the best classifier for the next window. The results show that this meta-algorithm is very competitive with state of the art ensembles, such as OzaBag, OzaBoost and Leveraged Bagging. The results of all experiments are made publicly available in an online experiment database, for the purpose of verifiability, reproducibility and generalizability

Structured Learning of Tree Potentials in CRF for Image Segmentation

We propose a new approach to image segmentation, which exploits the advantages of both conditional random fields (CRFs) and decision trees. In the literature, the potential functions of CRFs are mostly defined as a linear combination of some pre-defined parametric models, and then methods like structured support vector machines (SSVMs) are applied to learn those linear coefficients. We instead formulate the unary and pairwise potentials as nonparametric forests---ensembles of decision trees, and learn the ensemble parameters and the trees in a unified optimization problem within the large-margin framework. In this fashion, we easily achieve nonlinear learning of potential functions on both unary and pairwise terms in CRFs. Moreover, we learn class-wise decision trees for each object that appears in the image. Due to the rich structure and flexibility of decision trees, our approach is powerful in modelling complex data likelihoods and label relationships. The resulting optimization problem is very challenging because it can have exponentially many variables and constraints. We show that this challenging optimization can be efficiently solved by combining a modified column generation and cutting-planes techniques. Experimental results on both binary (Graz-02, Weizmann horse, Oxford flower) and multi-class (MSRC-21, PASCAL VOC 2012) segmentation datasets demonstrate the power of the learned nonlinear nonparametric potentials.Comment: 10 pages. Appearing in IEEE Transactions on Neural Networks and Learning System