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About: BACKGROUND:Over the last decade several prediction methods have been developed for determining the structural and functional properties of individual protein residues using sequence and sequence-derived information. Most of these methods are based on support vector machines as they provide accurate and generalizable prediction models. RESULTS:We present a general purpose protein residue annotation toolkit (svmPRAT) to allow biologists to formulate residue-wise prediction problems. svmPRAT formulates the annotation problem as a classification or regression problem using support vector machines. One of the key features of svmPRAT is its ease of use in incorporating any user-provided information in the form of feature matrices. For every residue svmPRAT captures local information around the reside to create fixed length feature vectors. svmPRAT implements accurate and fast kernel functions, and also introduces a flexible window-based encoding scheme that accurately captures signals and pattern for training eective predictive models. CONCLUSIONS:In this work we evaluate svmPRAT on several classification and regression problems including disorder prediction, residue-wise contact order estimation, DNA-binding site prediction, and local structure alphabet prediction. svmPRAT has also been used for the development of state-of-the-art transmembrane helix prediction method called TOPTMH, and secondary structure prediction method called YASSPP. This toolkit developed provides practitioners an efficient and easy-to-use tool for a wide variety of annotation problems. Availability: http://www.cs.gmu.edu/~mlbio/svmprat/ Changes:Initial Announcement on mloss.org.
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About: dysii is a C++ library for distributed probabilistic inference and learning in large-scale dynamical systems. It provides methods such as the Kalman, unscented Kalman, and particle filters and [...] Changes:Initial Announcement on mloss.org.
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About: Hyperstream is a large-scale, flexible and robust software package for processing streaming data. Changes:python 3 support; new API; bug fixes and enhancements
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About: ClowdFlows is a web based platform for service oriented data mining publicly available at http://clowdflows.org . A web based interface allows users to construct data mining workflows that are hosted on the web and can be (if allowed by the author) accessed by anyone by following a URL of the workflow. Changes:Initial Announcement on mloss.org.
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About: This software is an implementation of Hidden Markov Support Vector Machines (HMSVMs). Changes:Initial Announcement on mloss.org.
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About: Multi-class vector classification based on cost function-driven learning vector quantization , minimizing misclassification. Changes:Initial Announcement on mloss.org.
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About: A Matlab implementation of Uncorrelated Multilinear Discriminant Analysis (UMLDA) for dimensionality reduction of tensor data via tensor-to-vector projection Changes:Initial Announcement on mloss.org.
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About: SVMlin: Fast Linear SVMs for Supervised and Semi-supervised Learning Changes:Initial Announcement on mloss.org.
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About: Fast Runtime-Flexible Multi-dimensional Arrays and Views for C++ Changes:Initial Announcement on mloss.org.
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About: Logic Forest Changes:Fetched by r-cran-robot on 2013-04-01 00:00:06.077571
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About: CVXOPT is a free software package for convex optimization based on the Python programming language. It can be used with the interactive Python interpreter, on the command line by executing Python [...] Changes:Initial Announcement on mloss.org.
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About: You can use the software in this package to efficiently sample from Changes:Initial Announcement on mloss.org.
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About: The original Random Forests implementation by Breiman and Cutler. Changes:Initial Announcement on mloss.org.
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About: PLEASD: A Matlab Toolbox for Structured Learning Changes:Initial Announcement on mloss.org.
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About: The incomplete Cholesky decomposition for a dense symmetric positive definite matrix A is a simple way of approximating A by a matrix of low rank (you can choose the rank). It has been used [...] Changes:Initial Announcement on mloss.org.
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About: A Java library to create, process and manage mixtures of exponential families. Changes:Initial Announcement on mloss.org.
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About: Matlab implementation of variational gaussian approximate inference for Bayesian Generalized Linear Models. Changes:Code restructure and bug fix.
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About: NetKit is an open-source Network Learning toolkit for statistical relational learning. Its architecture is extremely modular, making it easy to combine different learning algorithms. Changes:Initial Announcement on mloss.org.
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About: Fast Multidimensional GP Inference using Projected Additive Approximation Changes:Initial Announcement on mloss.org.
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About: We study the problem of robust feature extraction based on L21 regularized correntropy in both theoretical and algorithmic manner. In theoretical part, we point out that an L21-norm minimization can be justified from the viewpoint of half-quadratic (HQ) optimization, which facilitates convergence study and algorithmic development. In particular, a general formulation is accordingly proposed to unify L1-norm and L21-norm minimization within a common framework. In algorithmic part, we propose an L21 regularized correntropy algorithm to extract informative features meanwhile to remove outliers from training data. A new alternate minimization algorithm is also developed to optimize the non-convex correntropy objective. In terms of face recognition, we apply the proposed method to obtain an appearance-based model, called Sparse-Fisherfaces. Extensive experiments show that our method can select robust and sparse features, and outperforms several state-of-the-art subspace methods on largescale and open face recognition datasets. Changes:Initial Announcement on mloss.org. |