About: Epistatic miniarray profiles (EMAPs) are a highthroughput approach capable of quantifying aggravating or alleviating genetic interactions between gene pairs. The datasets resulting from EMAP experiments typically take the form of a symmetric pairwise matrix of interaction scores. These datasets have a significant number of missing values  up to 35%  that can reduce the effectiveness of some data analysis techniques and prevent the use of others. This project contains nearest neighbor based tools for the imputation and prediction of these missing values. The code is implemented in Python and uses a nearest neighbor based approach. Two variants are used  a simple weighted nearest neighbors, and a local least squares based regression. Changes:Initial Announcement on mloss.org.

About: OpenGM is a free C++ template library, a command line tool and a set of MATLAB functions for optimization in higher order graphical models. Graphical models of any order and structure can be built either in C++ or in MATLAB, using simple and intuitive commands. These models can be stored in HDF5 files and subjected to stateoftheart optimization algorithms via the OpenGM command line optimizer. All library functions can also be called directly from C++ code. OpenGM realizes the Inference Algorithm Interface (IAI), a concept that makes it easy for programmers to use their own algorithms and factor classes with OpenGM. Changes:Initial Announcement on mloss.org.

About: Pyriel is a Python system for learning classification rules from data. Unlike other rule learning systems, it is designed to learn rule lists that maximize the area under the ROC curve (AUC) instead of accuracy. Pyriel is mostly an experimental research tool, but it's robust and fast enough to be used for lightweight industrial data mining. Changes:1.5 Changed CF (confidence factor) to do LaPlace smoothing of estimates. New flag "scoreforclass C" causes scores to be computed relative to a given (positive) class. For twoclass problems. Fixed bug in example sampling code (sample n) Fixed bug keeping oldstyle example formats (terminated by dot) from working. More code restructuring.

About: This Java software implements Profile Hidden Markov Models (PHMMs) for protein classification for the WEKA workbench. Standard PHMMs and newly introduced binary PHMMs are used. In addition the software allows propositionalisation of PHMMs. Changes:description changed

About: The gmm toolbox contains code for density estimation using mixtures of Gaussians: Starting from simple kernel density estimation with spherical and diagonal Gaussian kernels over manifold Parzen window until mixtures of penalised full Gaussians with only a few components. The toolbox covers many Gaussian mixture model parametrisations from the recent literature. Most prominently, the package contains code to use the Gaussian Process Latent Variable Model for density estimation. Most of the code is written in Matlab 7.x including some MEX files. Changes:Initial Announcement on mloss.org

About: A collection of clustering algorithms implemented in Javascript. Changes:Initial Announcement on mloss.org.

About: PSVM  Support vector classification, regression and feature extraction for nonsquare dyadic data, nonMercer kernels. Changes:Initial Announcement on mloss.org.

About: Implementation of LSTM for biological sequence analysis (classification, regression, motif discovery, remote homology detection). Additionally a LSTM as logistic regression with spectrum kernel is included. Changes:Spectrum LSTM package included

About: Investigation of dependencies between multiple data sources allows the discovery of regularities and interactions that are not seen in individual data sets. The demand for such methods is increasing with the availability and size of cooccurring observations in computational biology, open data initiatives, and in other domains. We provide practical, open access implementations of generalpurpose algorithms that help to realize the full potential of these information sources. Changes:Three independent modules (drCCA, pint, MultiWayCCA) have been added.

About: dANN is an Artificial Intelligence and Artificial Genetics library targeted at employing conventional techniques as well as acting as a platform for research & development of novel techniques. As new techniques are developed and proven to be effective they will be integrated into the core library. It is currently written in Java, C++, and C#. However only the java version is currently in active development. If you want to obtain a version other than the java version you will need to get it directly from GIT. Changes:Please get the version in GIT only, the released version is old.

About: RLS2 is an instance of multiple kernel learning algorithm to simultaneously learn a regularized predictor and the kernel function. RLS2LIN is a version of RLS2 specialized to linear kernels on each feature. The package contains a set of scripts that implements RLS2 and RLS2LIN, together with a Graphic User Interface to load data, perform training, validation, and plot results. Changes:

About: ALGLIB is an open source numerical analysis library distributed under GPL 2+. It implements both general numerical algorithms and machine learning algorithms. ALGLIB can be used from C#, C++, FreePascal, VBA and other languages. It is the only numerical analysis library which uses automatic translation to generate source code written in different programming languages with 100% identical functionality. Changes:

About: The open source ErrorCorrecting Output Codes (ECOC) library contains both stateoftheart coding and decoding designs, as well as the option to include your own coding, decoding, and base classifier. Changes:Initial Announcement on mloss.org.

About: The Universal Java Matrix Package (UJMP) is a data processing tool for Java. Unlike JAMA and Colt, it supports multithreading and is therefore much faster on current hardware. It does not only support matrices with double values, but instead handles every type of data as a matrix through a common interface, e.g. CSV files, Excel files, images, WAVE audio files, tables in SQL data bases, and much more. Changes:Meta data updated.

About: OXlearn is a free neural network simulation software that enables you to build, train, test and analyse connectionist neural network models. Because OXlearn is implemented as a Matlab toolbox you can run it on all operation systems (Windows, Linux, MAC, etc.), and there is a compiled version for XP. Changes:Initial Announcement on mloss.org.

About: A set of Perl programs for generating and manipulating ROC curves. Changes:Initial Announcement on mloss.org.

About: A fast implementation of several stochastic gradient descent learners for classification, ranking, and ROC area optimization, suitable for large, sparse data sets. Includes Pegasos SVM, SGDSVM, PassiveAggressive Perceptron, Perceptron with Margins, Logistic Regression, and ROMMA. Commandline utility and API libraries are provided. Changes:Initial Announcement on mloss.org.

About: Matlab code for semisupervised regression and dimensionality reduction using Hessian energy. Changes:Initial Announcement on mloss.org.
