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Logo JMLR GPML Gaussian Processes for Machine Learning Toolbox 4.0

by hn - October 19, 2016, 10:15:05 CET [ Project Homepage BibTeX Download ] 37090 views, 8414 downloads, 4 subscriptions

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About: The GPML toolbox is a flexible and generic Octave/Matlab implementation of inference and prediction with Gaussian process models. The toolbox offers exact inference, approximate inference for non-Gaussian likelihoods (Laplace's Method, Expectation Propagation, Variational Bayes) as well for large datasets (FITC, VFE, KISS-GP). A wide range of covariance, likelihood, mean and hyperprior functions allows to create very complex GP models.


A major code restructuring effort did take place in the current release unifying certain inference functions and allowing more flexibility in covariance function composition. We also redesigned the whole derivative computation pipeline to strongly improve the overall runtime. We finally include grid-based covariance approximations natively.

More generic sparse approximation using Power EP

  • unified treatment of FITC approximation, variational approaches VFE and hybrids

  • inducing input optimisation for all (compositions of) covariance functions dropping the previous limitation to a few standard examples

  • infFITC is now covered by the more generic infGaussLik function

Approximate covariance object unifying sparse approximations, grid-based approximations and exact covariance computations

  • implementation in cov/apx, cov/apxGrid, cov/apxSparse

  • generic infGaussLik unifies infExact, infFITC and infGrid

  • generic infLaplace unifies infLaplace, infFITC_Laplace and infGrid_Laplace

Hiearchical structure of covariance functions

  • clear hierachical compositional implementation

  • no more code duplication as present in covSEiso and covSEard pairs

  • two mother covariance functions

    • covDot for dot-product-based covariances and

    • covMaha for Mahalanobis-distance-based covariances

  • a variety of modifiers: eye, iso, ard, proj, fact, vlen

  • more flexibility as more variants are available and possible

  • all covariance functions offer derivatives w.r.t. inputs

Faster derivative computations for mean and cov functions

  • switched from partial derivatives to directional derivatives

  • simpler and more concise interface of mean and cov functions

  • much faster marginal likelihood derivative computations

  • simpler and more compact code

New mean functions

  • new mean/meanWSPC (Weighted Sum of Projected Cosines or Random Kitchen Sink features) following a suggestion by William Herlands

  • new mean/meanWarp for constructing a new mean from an existing one by means of a warping function adapted from William Herlands

New optimizer

  • added a new minimize_minfunc, contributed by Truong X. Nghiem

New GLM link function

  • added the twice logistic link function util/glm_invlink_logistic2

Smaller fixes

  • two-fold speedup of util/elsympol used by covADD by Truong X. Nghiem

  • bugfix in util/logphi as reported by John Darby

Logo AMIDST Toolbox 0.6.0

by ana - October 14, 2016, 19:35:27 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 4291 views, 656 downloads, 4 subscriptions

About: A Java Toolbox for Scalable Probabilistic Machine Learning.

  • Added sparklink module implementing the integration with Apache Spark. More information here.
  • Fluent pattern in latent-variable-models
  • Predefined model implementing the concept drift detection

Detailed information can be found in the toolbox's web page

Logo revrand 0.7.0

by dsteinberg - October 14, 2016, 08:31:02 CET [ Project Homepage BibTeX Download ] 6526 views, 1228 downloads, 3 subscriptions

About: A library of scalable Bayesian generalised linear models with fancy features

  • Ability to set the random state in all random basis functions, optimisers and the generalised linear model
  • Numerous numerical bug fixes
  • small performance optimisations

Logo KeLP 2.1.0

by kelpadmin - August 11, 2016, 10:40:38 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 11313 views, 2562 downloads, 3 subscriptions

About: Kernel-based Learning Platform (KeLP) is Java framework that supports the implementation of kernel-based learning algorithms, as well as an agile definition of kernel functions over generic data representation, e.g. vectorial data or discrete structures. The framework has been designed to decouple kernel functions and learning algorithms, through the definition of specific interfaces. Once a new kernel function has been implemented, it can be automatically adopted in all the available kernel-machine algorithms. KeLP includes different Online and Batch Learning algorithms for Classification, Regression and Clustering, as well as several Kernel functions, ranging from vector-based to structural kernels. It allows to build complex kernel machine based systems, leveraging on JSON/XML interfaces to instantiate prediction models without writing a single line of code.


In addition to minor bug fixes, this release includes:

  • a flexible system to manipulate example-pairs
  • new manipulators for performing tree pruning
  • new examples for the usage of kelp

Check out this new version from our repositories. API Javadoc is already available. Your suggestions will be very precious for us, so download and try KeLP 2.1.0!

Logo JMLR MLPACK 2.0.3

by rcurtin - July 22, 2016, 00:39:12 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 66205 views, 11873 downloads, 6 subscriptions

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About: A scalable, fast C++ machine learning library, with emphasis on usability.

  • Standardize some parameter names for programs (old names are kept for reverse compatibility, but warnings will now be issued).
  • RectangleTree optimizations (#721).
  • Fix memory leak in NeighborSearch (#731).
  • Documentation fix for k-means tutorial (#730).
  • Fix TreeTraits for BallTree (#727).
  • Fix incorrect parameter checks for some command-line programs.
  • Fix error in HMM training with probabilities for each point (#636).

Logo MLweb 0.1.4

by lauerfab - June 28, 2016, 16:00:52 CET [ Project Homepage BibTeX Download ] 5770 views, 1321 downloads, 3 subscriptions

About: MLweb is an open source project that aims at bringing machine learning capabilities into web pages and web applications, while maintaining all computations on the client side. It includes (i) a javascript library to enable scientific computing within web pages, (ii) a javascript library implementing machine learning algorithms for classification, regression, clustering and dimensionality reduction, (iii) a web application providing a matlab-like development environment.

  • Add Logistic Regression
  • Add support for sparse input in fast training of linear SVM
  • Better support for sparse vectors/matrices
  • Fix plot windows in IE
  • Minor bug fixes

About: Nowadays this is very popular to use the deep architectures in machine learning. Deep Belief Networks (DBNs) are deep architectures that use a stack of Restricted Boltzmann Machines (RBM) to create a powerful generative model using training data. DBNs have many abilities such as feature extraction and classification that are used in many applications including image processing, speech processing, text categorization, etc. This paper introduces a new object oriented toolbox with the most important abilities needed for the implementation of DBNs. According to the results of the experiments conducted on the MNIST (image), ISOLET (speech), and the 20 Newsgroups (text) datasets, it was shown that the toolbox can learn automatically a good representation of the input from unlabeled data with better discrimination between different classes. Also on all the aforementioned datasets, the obtained classification errors are comparable to those of the state of the art classifiers. In addition, the toolbox supports different sampling methods (e.g. Gibbs, CD, PCD and our new FEPCD method), different sparsity methods (quadratic, rate distortion and our new normal method), different RBM types (generative and discriminative), GPU based, etc. The toolbox is a user-friendly open source software in MATLAB and Octave and is freely available on the website.


New in toolbox

  • Using GPU in Backpropagation
  • Revision of some demo scripts
  • Function approximation with multiple outputs
  • Feature extraction with GRBM in first layer


Logo SparklingGraph 0.0.6

by riomus - June 17, 2016, 14:49:46 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 3522 views, 686 downloads, 3 subscriptions

About: Large scale, distributed graph processing made easy.


Bug fixes, Graph generators

Logo JMLR GPstuff 4.7

by avehtari - June 9, 2016, 17:45:15 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 36899 views, 8900 downloads, 3 subscriptions

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About: The GPstuff toolbox is a versatile collection of Gaussian process models and computational tools required for inference. The tools include, among others, various inference methods, sparse approximations and model assessment methods.


2016-06-09 Version 4.7

Development and release branches available at

New features

  • Simple Bayesian Optimization demo


  • Improved use of PSIS
  • More options added to gp_monotonic
  • Monotonicity now works for additive covariance functions with selected variables
  • Possibility to use gpcf_squared.m-covariance function with derivative observations/monotonicity
  • Default behaviour made more robust by changing default jitter from 1e-9 to 1e-6
  • LA-LOO uses the cavity method as the default (see Vehtari et al (2016). Bayesian leave-one-out cross-validation approximations for Gaussian latent variable models. JMLR, accpeted for publication)
  • Selected variables -option works now better with monotonicity


  • small error in derivative observation computation fixed
  • several minor bug fixes

Logo ELKI 0.7.1

by erich - March 14, 2016, 13:44:02 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 22422 views, 4037 downloads, 4 subscriptions

About: ELKI is a framework for implementing data-mining algorithms with support for index structures, that includes a wide variety of clustering and outlier detection methods.


Additions and improvements from ELKI 0.7.0 to 0.7.1:

Algorithm additions:

  • GriDBSCAN: DBSCAN using grid partitioning (Minkowski distances only)

  • Compare-Means and Sort-Means k-means variations (much faster than traditional k-means)

  • Visualization of dendrograms.

Important bug fixes:

  • Classes with no package ("default package") would cause errors.

  • The fast power function implementation was sometimes returning incorrect results.

  • Random sampling was sometimes not sampling from the full data set.

UI improvements:

  • The file input source will now automatically choose the Arff parser for .arff files.

  • MiniGUI now allows choosing other applications.

  • MiniGUI now displays the command line in a separate field.

  • MiniGUI displays an error message, if an incorrect classpath or JAyatana (on Ubuntu) is detected.

  • Export to png now works, we added a work-around for an open Batik bug.

Smaller changes:

  • Many smaller bug fixes.

  • C-Index for cluster evaluation now can process larger data sets.

  • OPTICS output of undefined reachability fixed.

  • External distance matrixes are easier to use and perform additional checks.

  • Precomputed distance matrixes can answer range and kNN queries.

  • Voronoi visualization can be switched in the menu now.

  • Improved backwards command line compatibility with additional aliases.

  • Added generated @since annotations in JavaDoc.

  • Many new unit tests, renamed to the Java conventions.

  • Low-level reading of service files, to have faster startup.

Logo MDLText 1

by renatoms88 - March 3, 2016, 19:31:25 CET [ BibTeX Download ] 666 views, 255 downloads, 2 subscriptions

About: testing


Initial Announcement on

Logo APCluster 1.4.3

by UBod - February 25, 2016, 16:22:36 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 35493 views, 6146 downloads, 3 subscriptions

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About: The apcluster package implements Frey's and Dueck's Affinity Propagation clustering in R. The package further provides leveraged affinity propagation, exemplar-based agglomerative clustering, and various tools for visual analysis of clustering results.

  • added optional color legend to heatmap plotting; in line with this change, some minor changes to the interface of the heatmap() function
  • corresponding updates of help pages and vignette

Logo JMLR Jstacs 2.2

by keili - February 17, 2016, 11:57:56 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 24391 views, 5621 downloads, 3 subscriptions

About: A Java framework for statistical analysis and classification of biological sequences


New classes and packages:

  • CorreationCoefficient: PerformanceMeasure
  • de.jstacs.clustering: package with classes for hierarchical clustering
  • DeBruijnGraphSequenceGenerator and DeBruijnSequenceGenerator for generating De Buijn sequences
  • CyclicSequenceAdaptor for representing cyclic sequences
  • PlotGeneratorResult for representing results that plot images to a Graphics2D object
  • TextResult for results that may be stored as text files
  • package de.jstacs.results.savers for generic classes that store results to disk
  • LimitedSparseLocalInhomogeneousMixtureDiffSM_higherOrder for sparse local inhomogeneous mixture (Slim) models
  • PFMWrapperTrainSM for representing position frequency matrices and position weight matrices from databases
  • package with classes for generic Jstacs tools that may be used in different user interfaces (command line, Galaxy, JavaFX)
  • Compression for ZIP compression of Strings
  • package with generic GraphicsAdaptor using Apache XML commons
  • projects: Dimont, GeMoMa, Slim, TALEN, motif comparison

New features and improvements:

  • Major restructuring of Alignment for better efficiency
  • Alignment Costs and StringAlignment now Storable
  • New constructor of DataSet allowing a specified percentage of sequences to mismatch the given alphabet
  • BioJavaAdapter ported to BioJava 1.9
  • XMLParser now also allows for storing Sequences
  • New method for parsing HMMer profile HMMs in HMMFactory
  • Several minor improvements and bugfixes in many classes
  • Improvements of documentation of several classes

Logo KeBABS 1.4.1

by UBod - November 3, 2015, 11:33:46 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 14342 views, 2627 downloads, 3 subscriptions

About: Kernel-Based Analysis of Biological Sequences

  • new method to compute prediction profiles from models trained with mixture kernels
  • correction for position specific kernel with offsets
  • corrections for prediction profile of motif kernel
  • additional hint on help page of kbsvm

Logo BayesPy 0.4.1

by jluttine - November 2, 2015, 13:40:09 CET [ Project Homepage BibTeX Download ] 15781 views, 3529 downloads, 3 subscriptions

About: Variational Bayesian inference tools for Python

  • Define extra dependencies needed to build the documentation

Logo Cognitive Foundry 3.4.2

by Baz - October 30, 2015, 06:53:03 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 29584 views, 5008 downloads, 4 subscriptions

About: The Cognitive Foundry is a modular Java software library of machine learning components and algorithms designed for research and applications.

  • General:
    • Upgraded MTJ to 1.0.3.
  • Common:
    • Added package for hash function computation including Eva, FNV-1a, MD5, Murmur2, Prime, SHA1, SHA2
    • Added callback-based forEach implementations to Vector and InfiniteVector, which can be faster for iterating through some vector types.
    • Optimized DenseVector by removing a layer of indirection.
    • Added method to compute set of percentiles in UnivariateStatisticsUtil and fixed issue with percentile interpolation.
    • Added utility class for enumerating combinations.
    • Adjusted ScalarMap implementation hierarchy.
    • Added method for copying a map to VectorFactory and moved createVectorCapacity up from SparseVectorFactory.
    • Added method for creating square identity matrix to MatrixFactory.
    • Added Random implementation that uses a cached set of values.
  • Learning:
    • Implemented feature hashing.
    • Added factory for random forests.
    • Implemented uniform distribution over integer values.
    • Added Chi-squared similarity.
    • Added KL divergence.
    • Added general conditional probability distribution.
    • Added interfaces for Regression, UnivariateRegression, and MultivariateRegression.
    • Fixed null pointer exception that can happen in K-means with an empty cluster.
    • Fixed name of maxClusters property on AgglomerativeClusterer (was called maxMinDistance).
  • Text:
    • Improvements to LDA Gibbs sampler.

Logo KEEL Knowledge Extraction based on Evolutionary Learning 3.0

by keel - September 18, 2015, 12:38:54 CET [ Project Homepage BibTeX Download ] 1839 views, 472 downloads, 1 subscription

About: KEEL (Knowledge Extraction based on Evolutionary Learning) is an open source (GPLv3) Java software tool that can be used for a large number of different knowledge data discovery tasks. KEEL provides a simple GUI based on data flow to design experiments with different datasets and computational intelligence algorithms (paying special attention to evolutionary algorithms) in order to assess the behavior of the algorithms. It contains a wide variety of classical knowledge extraction algorithms, preprocessing techniques (training set selection, feature selection, discretization, imputation methods for missing values, among others), computational intelligence based learning algorithms, hybrid models, statistical methodologies for contrasting experiments and so forth. It allows to perform a complete analysis of new computational intelligence proposals in comparison to existing ones. Moreover, KEEL has been designed with a two-fold goal: research and educational. KEEL is also coupled with KEEL-dataset: a webpage that aims at providing to the machine learning researchers a set of benchmarks to analyze the behavior of the learning methods. Concretely, it is possible to find benchmarks already formatted in KEEL format for classification (such as standard, multi instance or imbalanced data), semi-supervised classification, regression, time series and unsupervised learning. Also, a set of low quality data benchmarks is maintained in the repository.


Initial Announcement on

Logo Java Data Mining Package 0.3.0

by arndt - August 19, 2015, 15:44:46 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 2433 views, 491 downloads, 3 subscriptions

About: A Java library for machine learning and data analytics


Initial Announcement on

Logo Universal Java Matrix Package 0.3.0

by arndt - July 31, 2015, 14:23:14 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 14453 views, 2746 downloads, 3 subscriptions

About: The Universal Java Matrix Package (UJMP) is a data processing tool for Java. Unlike JAMA and Colt, it supports multi-threading 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.


Updated to version 0.3.0

About: R package implementing statistical test and post hoc tests to compare multiple algorithms in multiple problems.


Initial Announcement on

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