Solution Path Algorithm for Twin Multi-class Support Vector Machine

The twin support vector machine and its extensions have made great achievements in dealing with binary classification problems, however, which is faced with some difficulties such as model selection and solving multi-classification problems quickly. This paper is devoted to the fast regularization parameter tuning algorithm for the twin multi-class support vector machine. A new sample dataset division method is adopted and the Lagrangian multipliers are proved to be piecewise linear with respect to the regularization parameters by combining the linear equations and block matrix theory. Eight kinds of events are defined to seek for the starting event and then the solution path algorithm is designed, which greatly reduces the computational cost. In addition, only few points are combined to complete the initialization and Lagrangian multipliers are proved to be 1 as the regularization parameter tends to infinity. Simulation results based on UCI datasets show that the proposed method can achieve good classification performance with reducing the computational cost of grid search method from exponential level to the constant level

Applicability of semi-supervised learning assumptions for gene ontology terms prediction

Gene Ontology (GO) is one of the most important resources in bioinformatics, aiming to provide a unified framework for the biological annotation of genes and proteins across all species. Predicting GO terms is an essential task for bioinformatics, but the number of available labelled proteins is in several cases insufficient for training reliable machine learning classifiers. Semi-supervised learning methods arise as a powerful solution that explodes the information contained in unlabelled data in order to improve the estimations of traditional supervised approaches. However, semi-supervised learning methods have to make strong assumptions about the nature of the training data and thus, the performance of the predictor is highly dependent on these assumptions. This paper presents an analysis of the applicability of semi-supervised learning assumptions over the specific task of GO terms prediction, focused on providing judgment elements that allow choosing the most suitable tools for specific GO terms. The results show that semi-supervised approaches significantly outperform the traditional supervised methods and that the highest performances are reached when applying the cluster assumption. Besides, it is experimentally demonstrated that cluster and manifold assumptions are complimentary to each other and an analysis of which GO terms can be more prone to be correctly predicted with each assumption, is provided.Postprint (published version

QCD simulations with staggered fermions on GPUs

We report on our implementation of the RHMC algorithm for the simulation of lattice QCD with two staggered flavors on Graphics Processing Units, using the NVIDIA CUDA programming language. The main feature of our code is that the GPU is not used just as an accelerator, but instead the whole Molecular Dynamics trajectory is performed on it. After pointing out the main bottlenecks and how to circumvent them, we discuss the obtained performances. We present some preliminary results regarding OpenCL and multiGPU extensions of our code and discuss future perspectives.Comment: 22 pages, 14 eps figures, final version to be published in Computer Physics Communication