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.
@cite_31 developed and applied the local approach with support vector machines to predict the PPI and MN networks and show that it was superior to several previous works @cite_16 @cite_21 . They only consider @math predictions and used 5-fold CV. Although they exploited yeast-two-hybrid data as additional features for the prediction of the PPI network, we obtain very similar performances with the local multiple output approach (see Table ). @cite_22 use ensembles of output kernel trees to infer the MN and PPI networks with the same input data as @cite_31 . With the global approach, we obtain similar or inferior results as @cite_22 in terms of AUROC but much better results in terms of AUPR, especially on the MN data.
@cite_31 @cite_16 @cite_21 @cite_22
2743620784 2179596243 2051177122 2171662214
The region-based Convolutional Neural Network (CNN) detectors such as Faster R-CNN or R-FCN have already shown promising results for object detection by combining the region proposal subnetwork and the classification subnetwork together. Although R-FCN has achieved higher detection speed while keeping the detection performance, the global structure information is ignored by the position-sensitive score maps. To fully explore the local and global properties, in this paper, we propose a novel fully convolutional network, named as CoupleNet, to couple the global structure with local parts for object detection. Specifically, the object proposals obtained by the Region Proposal Network (RPN) are fed into the the coupling module which consists of two branches. One branch adopts the position-sensitive RoI (PSRoI) pooling to capture the local part information of the object, while the other employs the RoI pooling to encode the global and context information. Next, we design different coupling strategies and normalization ways to make full use of the complementary advantages between the global and local branches. Extensive experiments demonstrate the effectiveness of our approach. We achieve state-of-the-art results on all three challenging datasets, i.e. a mAP of 82.7 on VOC07, 80.4 on VOC12, and 34.4 on COCO. Codes will be made publicly available. We propose a new method for creating computationally efficient convolutional neural networks (CNNs) by using low-rank representations of convolutional filters. Rather than approximating filters in previously-trained networks with more efficient versions, we learn a set of small basis filters from scratch; during training, the network learns to combine these basis filters into more complex filters that are discriminative for image classification. To train such networks, a novel weight initialization scheme is used. This allows effective initialization of connection weights in convolutional layers composed of groups of differently-shaped filters. We validate our approach by applying it to several existing CNN architectures and training these networks from scratch using the CIFAR, ILSVRC and MIT Places datasets. Our results show similar or higher accuracy than conventional CNNs with much less compute. Applying our method to an improved version of VGG-11 network using global max-pooling, we achieve comparable validation accuracy using 41 less compute and only 24 of the original VGG-11 model parameters; another variant of our method gives a 1 percentage point increase in accuracy over our improved VGG-11 model, giving a top-5 center-crop validation accuracy of 89.7 while reducing computation by 16 relative to the original VGG-11 model. Applying our method to the GoogLeNet architecture for ILSVRC, we achieved comparable accuracy with 26 less compute and 41 fewer model parameters. Applying our method to a near state-of-the-art network for CIFAR, we achieved comparable accuracy with 46 less compute and 55 fewer parameters. Summary Background—Most machine learning approaches only provide a classification for binary responses. However, probabilities are required for risk estimation using individual patient characteristics. It has been shown recently that every statistical learning machine known to be consistent for a nonparametric regression problem is a probability machine that is provably consistent for this estimation problem. Objectives—The aim of this paper is to show how random forests and nearest neighbors can be used for consistent estimation of individual probabilities. Methods—Two random forest algorithms and two nearest neighbor algorithms are described in detail for estimation of individual probabilities. We discuss the consistency of random forests, nearest neighbors and other learning machines in detail. We conduct a simulation study to illustrate the validity of the methods. We exemplify the algorithms by analyzing two well-known data sets on the diagnosis of appendicitis and the diagnosis of diabetes in Pima Indians. Results—Simulations demonstrate the validity of the method. With the real data application, we show the accuracy and practicality of this approach. We provide sample code from R packages in which the probability estimation is already available. This means that all calculations can be performed using existing software. Conclusions—Random forest algorithms as well as nearest neighbor approaches are valid machine learning methods for estimating individual probabilities for binary responses. Freely available implementations are available in R and may be used for applications. Motivation: With the exponential growth of expression and protein–protein interaction (PPI) data, the frontier of research in systems biology shifts more and more to the integrated analysis of these large datasets. Of particular interest is the identification of functional modules in PPI networks, sharing common cellular function beyond the scope of classical pathways, by means of detecting differentially expressed regions in PPI networks. This requires on the one hand an adequate scoring of the nodes in the network to be identified and on the other hand the availability of an effective algorithm to find the maximally scoring network regions. Various heuristic approaches have been proposed in the literature. Results: Here we present the first exact solution for this problem, which is based on integer-linear programming and its connection to the well-known prize-collecting Steiner tree problem from Operations Research. Despite the NP-hardness of the underlying combinatorial problem, our method typically computes provably optimal subnetworks in large PPI networks in a few minutes. An essential ingredient of our approach is a scoring function defined on network nodes. We propose a new additive score with two desirable properties: (i) it is scalable by a statistically interpretable parameter and (ii) it allows a smooth integration of data from various sources. We apply our method to a well-established lymphoma microarray dataset in combination with associated survival data and the large interaction network of HPRD to identify functional modules by computing optimal-scoring subnetworks. In particular, we find a functional interaction module associated with proliferation over-expressed in the aggressive ABC subtype as well as modules derived from non-malignant by-stander cells. Availability: Our software is available freely for non-commercial purposes at http: www.planet-lisa.net. Contact: tobias.mueller@biozentrum.uni-wuerzburg.de