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This article deals with the identification of gene regulatory networks from experimental data using a statistical machine learning approach. A stochastic model of gene interactions capable of handling missing variables is proposed. It can be described as a dynamic Bayesian network particularly well suited to tackle the stochastic nature of gene regulation… (More)

In many discrimination problems a large amount of data is available but only a few of them are labeled. This provides a strong motivation to improve or develop methods for semi-supervised learning. In this paper, boosting is generalized to this task within the optimization framework of MarginBoost. We extend the margin definition to unlabeled data and… (More)

Link prediction is addressed as an output kernel learning task through semi-supervised Output Kernel Regression. Working in the framework of RKHS theory with vector-valued functions, we establish a new repre-senter theorem devoted to semi-supervised least square regression. We then apply it to get a new model (POKR: Penalized Output Kernel Regression) and… (More)

We propose to solve a text categorization task using a new metric between documents, based on a priori semantic knowledge about words. This metric can be incorporated into the definition of radial basis kernels of Support Vector Machines or directly used in a K-nearest neighbors algorithm. Both SVM and KNN are tested and compared on the 20-newsgroups… (More)

We consider the question of predicting nonlinear time series. Kernel Dy-namical Modeling (KDM), a new method based on kernels, is proposed as an extension to linear dynamical models. The kernel trick is used twice: first, to learn the parameters of the model, and second, to compute preimages of the time series predicted in the feature space by means of… (More)

In this paper, we propose and study a new on-line algorithm for learning a SVM based on Radial Basis Function Kernel: Local Incremental Learning of SVM or LISVM. Our method exploits the " locality " of RBF kernels to update current machine by only considering a subset of support candidates in the neighbourhood of the input. The determination of this subset… (More)

MOTIVATION
Statistical inference of biological networks such as gene regulatory networks, signaling pathways and metabolic networks can contribute to build a picture of complex interactions that take place in the cell. However, biological systems considered as dynamical, non-linear and generally partially observed processes may be difficult to estimate even… (More)

We extend tree-based methods to the prediction of structured outputs using a kernelization of the algorithm that allows one to grow trees as soon as a kernel can be defined on the output space. The resulting algorithm, called output kernel trees (OK3), generalizes classification and regression trees as well as tree-based ensemble methods in a principled… (More)

Neural trees are constructive algorithms which build decision trees whose nodes are binary neurons. We propose a new learning scheme, "trio-learning," which leads to a significant reduction in the tree complexity. In this strategy, each node of the tree is optimized by taking into account the knowledge that it will be followed by two son nodes. Moreover,… (More)

BACKGROUND
Elucidating biological networks between proteins appears nowadays as one of the most important challenges in systems biology. Computational approaches to this problem are important to complement high-throughput technologies and to help biologists in designing new experiments. In this work, we focus on the completion of a biological network from… (More)