Projects running under cygwin.
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Logo WEKA 3.9.0

by mhall - April 15, 2016, 06:35:30 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 61795 views, 9137 downloads, 5 subscriptions

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About: The Weka workbench contains a collection of visualization tools and algorithms for data analysis and predictive modelling, together with graphical user interfaces for easy access to this [...]

Changes:

In core weka:

  • JAMA-based linear algebra routines replaced with MTJ. Faster operation with the option to use native libraries for even more speed
  • General efficiency improvements in core, filters and some classifiers
  • GaussianProcesses now handles instance weights
  • New Knowledge Flow implementation. Engine completely rewritten from scratch with a simplified API
  • New Workbench GUI
  • GUI package manager now has a search facility
  • FixedDictionaryStringToWordVector filter allows the use of an external dictionary for vectorization. DictionarySaver converter can be used to create a dictionary file

In packages:

  • Packages that were using JAMA are now using MTJ
  • New netlibNativeOSX, netlibNativeWindows and netlibNativeLinux packages providing native reference implementations (and system-optimized implementation in the case of OSX) of BLAS, LAPACK and ARPACK linear algebra
  • New elasticNet package, courtesy of Nikhil Kinshore
  • New niftiLoader package for loading a directory with MIR data in NIfTI format into Weka
  • New percentageErrorMetrics package - provides plugin evaluation metrics for root mean square percentage error and mean absolute percentage error
  • New iterativeAbsoluteErrorRegression package - provides a meta learner that fits a regression model to minimize absolute error
  • New largeScaleKernelLearning package - contains filters for large-scale kernel-based learning
  • discriminantAnalysis package now contains an implementation for LDA and QDA
  • New Knowledge Flow component implementations in various packages
  • newKnowledgeFlowStepExamples package - contains code examples for new Knowledge Flow API discussion in the Weka Manual
  • RPlugin updated to latest version of MLR
  • scatterPlot3D and associationRulesVisualizer packages updated with latest Java 3D libraries
  • Support for pluggable activation functions in the multiLayerPerceptrons package

Logo JMLR Jstacs 2.2

by keili - February 17, 2016, 11:57:56 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 23903 views, 5523 downloads, 3 subscriptions

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

Changes:

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 de.jstacs.tools 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 de.jstacs.utils.graphics 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 Libra 1.1.2d

by lowd - February 4, 2016, 08:51:50 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 22051 views, 4679 downloads, 3 subscriptions

About: The Libra Toolkit is a collection of algorithms for learning and inference with discrete probabilistic models, including Bayesian networks, Markov networks, dependency networks, sum-product networks, arithmetic circuits, and mixtures of trees.

Changes:

Version 1.1.2d (12/29/2015):

  • Minor fixes to scripts
  • Published in JMLR ML-OSS!

Logo jLDADMM 1.0

by dqnguyen - August 19, 2015, 12:52:36 CET [ Project Homepage BibTeX Download ] 1619 views, 411 downloads, 2 subscriptions

About: The Java package jLDADMM is released to provide alternative choices for topic modeling on normal or short texts. It provides implementations of the Latent Dirichlet Allocation topic model and the one-topic-per-document Dirichlet Multinomial Mixture model (i.e. mixture of unigrams), using collapsed Gibbs sampling. In addition, jLDADMM supplies a document clustering evaluation to compare topic models.

Changes:

Initial Announcement on mloss.org.


Logo JMLR libDAI 0.3.2

by jorism - July 17, 2015, 15:59:55 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 51363 views, 9584 downloads, 4 subscriptions

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About: libDAI provides free & open source implementations of various (approximate) inference methods for graphical models with discrete variables, including Bayesian networks and Markov Random Fields.

Changes:

Release 0.3.2 fixes various bugs and adds GLC (Generalized Loop Corrections) written by Siamak Ravanbakhsh.


Logo JMLR SHOGUN 4.0.0

by sonne - February 5, 2015, 09:09:37 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 115026 views, 16332 downloads, 6 subscriptions

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About: The SHOGUN machine learning toolbox's focus is on large scale learning methods with focus on Support Vector Machines (SVM), providing interfaces to python, octave, matlab, r and the command line.

Changes:

This release features the work of our 8 GSoC 2014 students [student; mentors]:

  • OpenCV Integration and Computer Vision Applications [Abhijeet Kislay; Kevin Hughes]
  • Large-Scale Multi-Label Classification [Abinash Panda; Thoralf Klein]
  • Large-scale structured prediction with approximate inference [Jiaolong Xu; Shell Hu]
  • Essential Deep Learning Modules [Khaled Nasr; Sergey Lisitsyn, Theofanis Karaletsos]
  • Fundamental Machine Learning: decision trees, kernel density estimation [Parijat Mazumdar ; Fernando Iglesias]
  • Shogun Missionary & Shogun in Education [Saurabh Mahindre; Heiko Strathmann]
  • Testing and Measuring Variable Interactions With Kernels [Soumyajit De; Dino Sejdinovic, Heiko Strathmann]
  • Variational Learning for Gaussian Processes [Wu Lin; Heiko Strathmann, Emtiyaz Khan]

It also contains several cleanups and bugfixes:

Features

  • New Shogun project description [Heiko Strathmann]
  • ID3 algorithm for decision tree learning [Parijat Mazumdar]
  • New modes for PCA matrix factorizations: SVD & EVD, in-place or reallocating [Parijat Mazumdar]
  • Add Neural Networks with linear, logistic and softmax neurons [Khaled Nasr]
  • Add kernel multiclass strategy examples in multiclass notebook [Saurabh Mahindre]
  • Add decision trees notebook containing examples for ID3 algorithm [Parijat Mazumdar]
  • Add sudoku recognizer ipython notebook [Alejandro Hernandez]
  • Add in-place subsets on features, labels, and custom kernels [Heiko Strathmann]
  • Add Principal Component Analysis notebook [Abhijeet Kislay]
  • Add Multiple Kernel Learning notebook [Saurabh Mahindre]
  • Add Multi-Label classes to enable Multi-Label classification [Thoralf Klein]
  • Add rectified linear neurons, dropout and max-norm regularization to neural networks [Khaled Nasr]
  • Add C4.5 algorithm for multiclass classification using decision trees [Parijat Mazumdar]
  • Add support for arbitrary acyclic graph-structured neural networks [Khaled Nasr]
  • Add CART algorithm for classification and regression using decision trees [Parijat Mazumdar]
  • Add CHAID algorithm for multiclass classification and regression using decision trees [Parijat Mazumdar]
  • Add Convolutional Neural Networks [Khaled Nasr]
  • Add Random Forests algorithm for ensemble learning using CART [Parijat Mazumdar]
  • Add Restricted Botlzmann Machines [Khaled Nasr]
  • Add Stochastic Gradient Boosting algorithm for ensemble learning [Parijat Mazumdar]
  • Add Deep contractive and denoising autoencoders [Khaled Nasr]
  • Add Deep belief networks [Khaled Nasr]

Bugfixes

  • Fix reference counting bugs in CList when reference counting is on [Heiko Strathmann, Thoralf Klein, lambday]
  • Fix memory problem in PCA::apply_to_feature_matrix [Parijat Mazumdar]
  • Fix crash in LeastAngleRegression for the case D greater than N [Parijat Mazumdar]
  • Fix memory violations in bundle method solvers [Thoralf Klein]
  • Fix fail in library_mldatahdf5.cpp example when http://mldata.org is not working properly [Parijat Mazumdar]
  • Fix memory leaks in Vowpal Wabbit, LibSVMFile and KernelPCA [Thoralf Klein]
  • Fix memory and control flow issues discovered by Coverity [Thoralf Klein]
  • Fix R modular interface SWIG typemap (Requires SWIG >= 2.0.5) [Matt Huska]

Cleanup and API Changes

  • PCA now depends on Eigen3 instead of LAPACK [Parijat Mazumdar]
  • Removing redundant and fixing implicit imports [Thoralf Klein]
  • Hide many methods from SWIG, reducing compile memory by 500MiB [Heiko Strathmann, Fernando Iglesias, Thoralf Klein]

Logo JMLR MOA Massive Online Analysis Nov-13

by abifet - April 4, 2014, 03:50:20 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 18216 views, 6447 downloads, 1 subscription

About: Massive Online Analysis (MOA) is a real time analytic tool for data streams. It is a software environment for implementing algorithms and running experiments for online learning from evolving data streams. MOA includes a collection of offline and online methods as well as tools for evaluation. In particular, it implements boosting, bagging, and Hoeffding Trees, all with and without Naive Bayes classifiers at the leaves. MOA supports bi-directional interaction with WEKA, the Waikato Environment for Knowledge Analysis, and it is released under the GNU GPL license.

Changes:

New version November 2013


Logo JMLR CARP 3.3

by volmeln - November 7, 2013, 15:48:06 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 22368 views, 6971 downloads, 1 subscription

About: CARP: The Clustering Algorithms’ Referee Package

Changes:

Generalized overlap error and some bugs have been fixed


Logo JMLR LPmade 1.2.2

by rlichten - April 2, 2012, 17:11:59 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 27034 views, 9269 downloads, 1 subscription

About: Link Prediction Made Easy

Changes:

v1.2.2

  • Fixed MAJOR issue related to github migration several months ago. The original github commit neglected to import empty folders. This caused parts of the project compilation procedure to fail. Any users of LPmade who downloaded the most recent version from github over the last several months would have encountered this build error and should download the most recent version. This change updates the network library makefile to create the empty folders and gets around the issue. Very sorry to anybody that this may have inconvenienced, but thanks for hanging in there if you diagnosed and solved it yourself.

  • Fixed issue with auroc on 32-bit architectures that caused integer wraparounds that produced incorrect results.


Logo SGD 2.0

by leonbottou - October 11, 2011, 20:59:41 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 14235 views, 2227 downloads, 5 subscriptions

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About: The SGD-2.0 package contains implementations of the SGD and ASGD algorithms for linear SVMs and linear CRFs.

Changes:

Version 2.0 features ASGD.


Logo Moses Decoder 2010-08-13

by oliver_wilson - September 3, 2010, 13:49:43 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 6435 views, 1981 downloads, 0 comments, 1 subscription

About: Moses is a statistical machine translation system that allows you to automatically train translation models for any language pair. All you need is a collection of translated texts (parallel corpus). An efficient search algorithm finds quickly the highest probability translation among the exponential number of choices.

Changes:

Initial Announcement on mloss.org.


Logo jblas 1.1.1

by mikio - September 1, 2010, 13:53:51 CET [ Project Homepage BibTeX Download ] 16464 views, 3966 downloads, 1 subscription

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About: jblas is a fast linear algebra library for Java. jblas is based on BLAS and LAPACK, the de-facto industry standard for matrix computations, and uses state-of-the-art implementations like ATLAS for all its computational routines, making jBLAS very fast.

Changes:

Changes from 1.0:

  • Added singular value decomposition
  • Fixed bug with returning complex values
  • Many other minor improvements

Logo asp 0.3

by sonne - May 7, 2010, 10:25:39 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 10474 views, 2080 downloads, 1 subscription

About: Accurate splice site predictor for a variety of genomes.

Changes:

Asp now supports three formats:

-g fname for gff format

-s fname for spf format

-b dir for a binary format compatible with mGene.

And a new switch

-t which switches on a sigmoid-based transformation of the svm scores to get scores between 0 and 1.


Logo LIBSVM 2.9

by cjlin - February 27, 2010, 01:09:23 CET [ Project Homepage BibTeX Download ] 13367 views, 2793 downloads, 1 subscription

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About: LIBSVM is an integrated software for support vector classification, (C-SVC, nu-SVC ), regression (epsilon-SVR, nu-SVR) and distribution estimation (one-class SVM). It supports multi-class [...]

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.


Logo JMLR RL Glue and Codecs -- Glue 3.x and Codecs

by btanner - October 12, 2009, 07:50:03 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 21110 views, 2375 downloads, 1 subscription

About: RL-Glue allows agents, environments, and experiments written in Java, C/C++, Matlab, Python, and Lisp to inter operate, accelerating research by promoting software re-use in the community.

Changes:

RL-Glue paper has been published in JMLR.


Logo LibSGDQN 1.1

by antojne - July 2, 2009, 15:02:44 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 9331 views, 1882 downloads, 1 subscription

About: LibSGDQN proposes an implementation of SGD-QN, a carefully designed quasi-Newton stochastic gradient descent solver for linear SVMs.

Changes:

small bug fix (thx nicolas ;)


Logo OLaRankGreedy 1.0

by antojne - June 24, 2009, 17:07:57 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 5805 views, 1236 downloads, 1 subscription

About: OLaRankGreedy is an online solver of the dual formulation of support vector machines for sequence labeling using greedy inference.

Changes:

Initial Announcement on mloss.org.


Logo OLaRankExact 1.0

by antojne - June 24, 2009, 17:03:48 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 5501 views, 1279 downloads, 1 subscription

About: OLaRank is an online solver of the dual formulation of support vector machines for sequence labeling using viterbi decoding.

Changes:

Initial Announcement on mloss.org.


Logo C MixSim 0.5

by volmeln - June 10, 2009, 19:37:42 CET [ Project Homepage BibTeX Download ] 6876 views, 1673 downloads, 1 subscription

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About: C-MixSim 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. C-MixSim provides an easy and convenient way of generating datasets from Gaussian mixture models with different levels of clustering complexity. C-MixSim is released under the GNU GPL license.

Changes:

Initial Announcement on mloss.org.


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