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 sequencederived 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 residuewise 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 userprovided 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 windowbased 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, residuewise contact order estimation, DNAbinding site prediction, and local structure alphabet prediction. svmPRAT has also been used for the development of stateoftheart transmembrane helix prediction method called TOPTMH, and secondary structure prediction method called YASSPP. This toolkit developed provides practitioners an efficient and easytouse tool for a wide variety of annotation problems. Availability: http://www.cs.gmu.edu/~mlbio/svmprat/ Changes:Initial Announcement on mloss.org.

About: JOP is a Java virtual machine implemented in hardware. It is a hard realtime open source multicore processor capable of worst case execution time analysis of Java code. Changes:Initial Announcement on mloss.org.

About: A Java library to create, process and manage mixtures of exponential families. Changes:Initial Announcement on mloss.org.

About: SHARK is a modular C++ library for the design and optimization of adaptive systems. It provides various machine learning and computational intelligence techniques. Changes:

About: Elefant is an open source software platform for the Machine Learning community licensed under the Mozilla Public License (MPL) and developed using Python, C, and C++. We aim to make it the platform [...] Changes:This release contains the Stream module as a first step in the direction of providing C++ library support. Stream aims to be a software framework for the implementation of large scale online learning algorithms. Large scale, in this context, should be understood as something that does not fit in the memory of a standard desktop computer. Added Bundle Methods for Regularized Risk Minimization (BMRM) allowing to choose from a list of loss functions and solvers (linear and quadratic). Added the following loss classes: BinaryClassificationLoss, HingeLoss, SquaredHingeLoss, ExponentialLoss, LogisticLoss, NoveltyLoss, LeastMeanSquareLoss, LeastAbsoluteDeviationLoss, QuantileRegressionLoss, EpsilonInsensitiveLoss, HuberRobustLoss, PoissonRegressionLoss, MultiClassLoss, WinnerTakesAllMultiClassLoss, ScaledSoftMarginMultiClassLoss, SoftmaxMultiClassLoss, MultivariateRegressionLoss Graphical User Interface provides now extensive documentation for each component explaining state variables and port descriptions. Changed saving and loading of experiments to XML (thereby avoiding storage of large input data structures). Unified automatic input checking via new static typing extending Python properties. Full support for recursive composition of larger components containing arbitrary statically typed state variables.

About: EANT Without Structural Optimization is used to learn a policy in either complete or partially observable reinforcement learning domains of continuous state and action space. Changes:Initial Announcement on mloss.org.

About: BioSig is a software library for biomedical signal processings. Besides several other modules, one modul (t400) provides a common interface (train_sc.m and test_sc.m) to various classification [...] Changes:Update of project information: machine learning and classification tools are moved to the NaNtoolbox.

About: The Computational Infrastructure for Operations Research (COINOR) project is an initiative to spur the development of opensource software for the operations research community. Changes:Initial Announcement on mloss.org.

About: SeDuMi is a software package to solve optimization problems over symmetric cones. This includes linear, quadratic, second order conic and semidefinite optimization, and any combination of these. Changes:Initial Announcement on mloss.org.

About: A desktop planetarium and sky map program which shows the sky from anywhere on Earth at any time. Changes:Removed erroneous topocentric code. Increased maximum zoom for detail on planets.

About: CMixSim is an open source package written in C for simulating finite mixture models with Gaussian components. With a vast number of clustering algorithms, evaluating performance is important. CMixSim provides an easy and convenient way of generating datasets from Gaussian mixture models with different levels of clustering complexity. CMixSim is released under the GNU GPL license. Changes:Initial Announcement on mloss.org.

About: This package contains functions to estimate linear and nonlinear regression methods with Penalized Partial Least Squares. Changes:

About: Nieme is a C++ machine learning library for largescale classification, regression and ranking. It provides a simple interface available in C++, Python and Java and a user interface for visualization. Changes:Released Nieme 1.0

About: CoFiRank is a Collaborative Filtering system based on matrix factorization. CoFiRank is based on the idea that it is better to predict the relative order of preferences (ranking) instead of the absolute rating. Changes:Initial Announcement on mloss.org.

About: CRFSuite is a speedoriented implementation of Conditional Random Fields (CRFs). This software features: parameter estimation using SGD and LBFGS, l1/l2 regularization, simple data I/O format, etc. Changes:Initial Announcement on mloss.org.

About: Pebl is a python library and command line application for learning the structure of a Bayesian network given prior knowledge and observations. Changes:Updated version to 1.0.1

About: SVQP1 and SVQP2 are QP solvers for training SVM. Changes:Initial Announcement on mloss.org.

About: A library for fast computation of Gauss transforms in multiple dimensions, using the Improved Fast Gauss Transform and a tree data structure. This library is useful for efficient Kernel Density [...] Changes:Initial Announcement on mloss.org.

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.

About: Intended for .NET developers wanting to implement algorithms directly in a common .NET language (recommended: C#). Support for ndim generic arrays, LAPACK, FFT, cells, logicals, 2D&3D plotting [...] Changes:Initial Announcement on mloss.org.
