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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)
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 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)
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)
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)
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)
A general framework is proposed for gradient boosting in supervised learning problems where the loss function is defined using a kernel over the output space. It extends boosting in a principled way to complex output spaces (images, text, graphs etc.) and can be applied to a general class of base learners working in kernelized output spaces. Empirical(More)
SUMMARY CycSim is a web application dedicated to in silico experiments with genome-scale metabolic models coupled to the exploration of knowledge from BioCyc and KEGG. Specifically, CycSim supports the design of knockout experiments: simulation of growth phenotypes of single or multiple gene deletions mutants on specified media, comparison of these(More)