Wlodzislaw Duch

Red color = superpages.

Neural Networks | Neuroscience | Machine Learning + AI | Data Mining | Math & Statistics | Visualization of multidimensional data | Other software | Databases |

Gepetto list, from Amsterdam

Internet Analysis Tools Registry, supported by The Human Brain Project

Neural/AI Software - great list from Aston University

Neuroinformatics software tools

NN simulation tools - Franz Kurfess, Uni. Ulm, over 50 programs

Free & Shareware Simulators - about 100 programs, PNL Computational Intelligence list

Free & Shareware Simulators - over 40 programs, PNL Neural Networks list

Mathtools, many programs.

Neural Software - from Bristol, over 20 programs

Neural Networks and Fuzzy Systems, including Association Rule Induction, Regression, Trees, Bayes Classifier, Graphical Models, Network Training, Probabilistic and Fuzzy Clustering, Convex Hull Construction

Artificial Neural Networks Lab: Java applets and GIF-animation Many nice demonstrations: SVM, boosting, trees

DemoGNG, competitive learning (Loos, Fritzke)

Java demos of genetic and NN programs

Neural tutorial with Java applets

Java Applets for Neural Network and Artificial Life

RBF demo (Hong, MIT)

Virtual Minds Java demo

WebSim Java demo: neural, optimization, plots (Boston U.)

Sharky NN, nice 2D visualizations.

Deep Learning Software and info

Comparison of deep learning software - Wiki

KD nuggets, long list of software for data mining.

GASP, Globally Accessible Statistical Procedures, mostly applets.

Java Neural Network Simulator, JNNS (new version of SNNS)

KEEL - Knowledge Extraction Evolutionary Learning, 450 modułów!

KNIME, includes Weka and R-scripts.

LNKnet, MIT, neural, statistical, machine learning, dead project.

LENS, light, efficient network simulator

Orange, from Slovenia, component-based data mining software, includes SOM, MDS and other visualizations, 2006; some additional modules.

Pentaho data mining (based on Weka)

R-project, statistical computing | R Rattle, R for data mining |

SciViews open source, data acquisition, space-time series, image analysis etc.

Stuttgart Neural Network Simulator (SNNS), copy in Poland

WEKA, Machine Learning Project, many models | WEKA Metalearning

YALE, Yet Another Learning Environment, in Java, includes Weka models | now Rapid Miner

Efficient Learning, Large-scale Inference, and Optimization Toolkit

**General software packages**:

Matlab clones page: Scilab | Rlab | Octave |

**SOM software**:

EUDAPTICS - SOMine (demo)

ESO, Emergent SOM, Databionic tool.

WEBSOM for free-text browsing

JavaSOM

LVQ and SOM-PACK, HUT | SOM Toolbox in Matlab, Helsinki

SOM and LISSOM, with some programs for NLP, from UTCS Tx |

**Other software packages with neural models**:

DDlab, discrete dynamics networks

DDtools, data description toolbox, one-class problems.

Dynamics - program i tutorial |

DIBA, with interesting visualization.

ffnet, regularization, SA and other interesting things.

Joone, Java free NN engine

LENS, with good visualization.

LVQ visualization, Magdeburg |

Pajek, from Slovenia, social networks analysis | an introduction to Pajek |

Quantum clustering, D. Horn |

SimBrain, NN+MDS.

Another SimBrain, with integrate/fire neurons.

Spider, Matlab object-oriented machine learning, SVM-oriented.

Shogun, A Large Scale Machine Learning Toolbox

Netlab (Bishop, Nabney) - programs in Matlab for NN and Bayes nets, copy in Torun

Neural Networks at your Fingertips, program sources, K. Kutza.

Neuralogic Windows: Ultra High Performance NN (PC, Cray)

NODELIB, Neural Optimization Development Engine library (PC, Cray)

Oxlearn, Matlab-based Neural Network Simulator for Education.

PDP ++ 2003, new version from the PDP book of Rumelhart and McClelland | RNS++ 2005, even newer version based on PDP++

Semeion software, many types of networks from Italy

SNARLI, Java, by Simon D. Levy.

Sieci Neuronowe dla każdego! Z programami w C# (2007)

List: Neuroscience simulation software

List of computational neuroscience software

Brian spiking network simulator.

Emergent - extension of PDP++,Randall C. O'Reilly

GENESIS Simulator, biological neurons

EEGLAB, signal processing in Matlab , EEG, MEG and other electrophysiological signals.

ICAlab and NMFlab and ButIf bump analysis from Cichocki group, RIKEN BSI

Keenan's Software for Memory and Cognition, psychological experiments

LORETA software and papers, low resolution brain electromagnetic tomography.

Mantra - Neural Java, spiking neuron and other models (Gerstner)

NeuroGuide dynamic EEG

Nengo rapid spiking network simulator

NEST initiative

Delay Vector Variance (DVV) toolbox for time series (Mandic).

e-connectome, (Electrophysiological Connectome) is an open-source MATLAB software package for imaging brain functional connectivity from electrophysiological signals.

GhostMiner Software

GTech, brain signals in Matlab

Gensym Corporation, intelligent operations management, neural & AI software

LocBoost and other goodies, Java demo

FuzzyTech, fuzzy and neurofuzzy

IFS Limited, Amber i Onyx neuroforcasting

Orka, NN/GA software Arkus (Wroclaw), demo

NeuroSolutions Evaluation Edition

NeuroShell Easy and Gene Hunter demos, Ward Systems Group

Saxon, NN+MDS.

Synapse by Peltarion, nice interface and many functions, 30 days demo

Universal Problem Solvers, Inc. (Transdimensional Learning, MPIL)

Neural Connection - SPSS

Vitalnet System for Analyzing Health Data

Z-solutions

## Artificial Intelligence (symbolic)

GNU/Linux AI & Alife HOWTO list of software packages

AI Planning Systems (Maryland)

AI Medical Systems in Routine Use

Soar (Newell, Simon, Laird, others) - expert system with some learning capabilities

See also Cognitive Architectures page

Lists of packages

CMU Software in ML list

Cagliari University list

Gaussian Processes, list of packages

T++, a C++ library of mathematical, signal processing, speech processing, and communications classes and functions.

KDnets Software - long list

KDnuggets Siftware - long list

Matlab CI software, Kevin Murphy.

Model and Mine, list of DM packages

ML-Net Software links

Machine Learning Library in C++, a bit hard to use (Silicon Graphics)

Machine Learning Open Source Software, long list

Neural/AI Software (from Aston)

Sciview list of software packages

Torch ML Library in C++, free

Tom Mitchell, NN + Bayes + Decision Tree software

CBA, Classification and Association Rules, NUS Singapore

Domrule, logical rules, Lin Min Fu

Emerald, AG and other ML software, Michalski's GMU lab

MLC++, Color GLDs

ML archive - University of Portsmouth AI Group

Tools for learning CI, for AI course;

ID3 Code with examples, decsion tree

NETLAB Bayesian Neural Networks (Bishop, Nabney), copy in Torun

N-body methods, fast O(N) learning;

RIPPER rule induction

Statistical Pattern Recognition Lib (from TU Delft)

TANAGRA, includes visualization, clustering, association, supervised learning.

TiMBL, Memory-Based Learning techniques

Forte (First Order Revision of Theories from Examples) machine learning system

GROBIAN project - user-friendly rough set software

Reduct & Lobbe Technologies (rough sets, Canada)

Rosetta (rough sets)

Rough Enough (Torvill Bjorvand)

ROSE Rough Set Software, II-PP

Rough Set software (Uni. Regina)

Rough Set systems, Inc.

Rough Set Exploration System (RSES)

Rseslib, library of machine learning data structures and algorithms implemented in Java.

CBR Software List

CBR Software, Haley Enterprise

Algorithm visualizations

Walrus - hyperbolic 3D vis.

C5.0, See5 & Cubist (Ross Quinlan, Rulequest Research) | C4.5 software and tutorial |

YaDT, fast tree and C4.5 improvements EC4.5 |

Occam tree from Visionary Tools |

Automated Reasoning, troubleshooting support

dmt - automatic identification

Free Statistical Software

Genetic Algorithms Digest

Generate new ideas creativity support software !

Partek Data Analysis & Modeling Software: PR, NN, Data Mining, demo

Machine Learning for Cancer Diagnosis and Prognosis

NeuroSoft SynthTalk, Gam, Regulus

Ahlea Systems Corp: Pattern Recognition in Matlab, Software Patches, commercial

caret: Classification and Regression Training, in R

SprLib and ANNLib, from Delft Technical University Pattern Recognition Group

PRTools - Pattern Recognition Tools (Heijden, Duin, de Ridder, Tax)

Statistical Pattern Recognition Toolbox

TOOLDIAG pattern recognition toolbox

FLANN, Fast Library for Approximate Nearest Neighbors

Data Mining Software List

Data Mining Software Vendors

Cognitive Processor - Molly Group support management software, data mining

Free and Commercial Data Mining Software

GMDH Shell: Data Mining & Forecasting Software (available for free download)

DM Review list (see Software Demos)

DM Maximizer, DMM demo | DMS on-line serwer, Inductive Learning by Logic Minimization (ILLM) | Galvano software, French group, many programs, with DM tutorial | GhostMiner Software | Statconsulting PL | IBM Quest (free) | Info-Fuzzy Network (IFN) (free) | Mine It Easyminer |

SAS Enterprise Miner | SGI MineSet | Xpert Rule Miner (Attar Software) | XELOPES library, embedded DM |

Business Miner (BusinessObjects) |

Molecular Mining (bioinformatics software GeneLinker)

Dragon Genome Explorer

Psychometric test |

Netlib - numerical software

Statlib - statistical software

Boost graphics library

JBoost for boosting clasification, with ADTrees.

Darren guide to statistical resources, software

Exact randomisation statistics software list

Free statistical software packages

Guide to mathematical software (NIST, excellent)

Sources of Math Software (NIST)

Statistical and Computational Software (RFE list)

Statistics.com tools, software, data

Anderson Hospital, biostatistics programs

Demo of genetic and NN algorithms in Java

GMM and MINZ packages in Matlab, spectral density, probit, logit (Mike Cliff)

Mathematical Programming in Machine Learning (Wisconsin)

Ordination software (for ecologist)

Provalis Research: MultiVariate Statistical + inne programy statystyczne.

Statistical Analysis and Graphics, Java Applets

Statistical Software Components from Boston College Department of Economics

Web Pages that Perform Statistical Calculations! also many free statistical packages.

Scientific software, Word2Tex etc (useful)

List from Statistics.com tools, software, data | list from recursive partitioning

AMELIA: A Program for Missing Data, statistical software, Gary King

AutoClass - Bayesian classification and clustering

CN2 decision tree

EMMIX, EM mixture model

Medcalc, statistics for biomedical research

Multiple imputation software

NEFCLASS< NEFCON< NEFPROX neurofuzzy software (Nauck)

SISA, Simple Interactive Statistical Analysis

SNOB MML unsupervised classification

TimeStat: freeware PCA, ARMA, FTT, spreadsheet style

ttests and other statitical tests from Paul Barrett

Trevor Hasti: SVMs, discriminant and prinicipal curves

Vista - visual statistics

**SVM and kernel methods**

Software list from Kernel-machines.org

Comparison of SVM software (getting old, 2005)

Kernel methods in Pattern Analysis list, John Shawe-Taylor & Nello Cristianini, 2004

Wikipedia SVM list

SVM On-line demonstration

BSVM, SVM solved by another method

Core Vector Machine, fastest SVM around?

GiniSVM, SVM for regression

GIST, SVM and kernel PCA (Unix only)

HeroSVM

LIBSVM, SVM for large classification and regression

LIBLINEAR: A Library for Large Linear Classification.

LSSVMlab, least squares SVM, Matlab toolbox + tutorials

P-SVM software

Multivariate Relevance Vector Machine (MVRVM)

Shogun - A Large Scale Machine Learning Toolbox

SVM-Light, SVM software for regresion and classification

SVM in the primal, Matlab code

BMR: Bayesian Multinomial Regression Software

DTREG: SVM, decision tree + logistic regression (commercial, demo available)

**Clustering**

Affinity propagation

COMPACT - Comparative Package for Clustering Assessment, D. Horn

CLUSION, Cluster Analysis and Cluster Ensemble Software

CLUTO, Clustering High-Dim data, texts

Dendrograms data clustering

Fuzzy Clustering

G-means, C++ program

Joining clustering algorithms, dendrograms and other

KlustaKwik, Automatic Clustering

MCL - a cluster algorithm for graphs

MIXMOD (MIXture MODelling), fits mixture models

Multi-dimensional Clustering and Outlier Detection

PermutMatrix, seriation analysis.

Quantum clustering, D. Horn |

SP-means, C++ program

Parallel Performance Group, Inc., High-Technology Commercial Software

CART | MARS | GMAX-DM, genetic system (Salford Systems)

Data Desk (Majih)

AccuROC for Windows | GraphROC for Windows

Minitab (Minitab Inc)

Predictive Data Mining, Weiss S, Indurkhya, book and software

Simstat for Windows StatSoft Polska Sp. z o.o. - STATISTICA

StatSol, missing data, statistical software

Stata statistical software

Statgraphics (Manugistics Inc), STATG-PL

CSS STATISTICA (StatSoft Inc.)

SPSS (SPSS Inc.), pakiet Systat

SAS Institute - DSS, data mining

S-Plus (Mathsoft)

StatXact, LogXact (Cytel)

Larger lists of software pacakges:

**MDS software**: Collection of MDS-like programs | Taguchi MDS programs collection | HiT-MDS, fast MDS | MDS, multidimensional scaling | MDS Alscal | HiT-MDS, using correlation coefficient | New MDSX, multidimensional scaling | Permap MDS | ALSCAL - old MDS Program several MDS packages, from Granular.com | HMDS: Hyperbolic Multidimensional Scaling | HMDS project | HMDS paper (2004) |

Proximity visualization, W. Basalaj, interesting thesis

CAIDA Visualization Tools, Internet data visualization.

COVIAGRA, Learning Coordinate Covariances via Gradients, Matlab code.

Davis - PCA, parallel, dendrograms, touring ...

Facet Analysis, Smallest Space Analysis, Multidimensional Scalogram Analysis, Partial Order Scalogram Analysis

GCSVIS - Growing Cell Structures.

Ggobi for Windows- many visualizations |

GE Data visualization collection

GTM - Bishop and Svensen.

Hierarchical Clustering Explorer for Interactive Exploration of Multidimensional Data.

HiSee project, Scott Hotton and Jeff Yoshimi.

Hyperplane animator

KNOT Tools for Pathfinder Network Analysis |

Levenstein Software

Locally Linear Embedding

MaxdView, bioinfo data

MANIfold learning, Matlab for ISOMAP, LLE, Hessian LLE, Laplacian, and LTSA.

Orange, from Slovenia, includes parallel coordinates, multigrams, SOM, MDS ...

Pathfinder Networks Wiki

PhiVis, hierarchical visualization - Bishop and Tipping

Parvis, a tool for parallel coordinates

Radviz visualization

Spotfire - clustering, visualization

SigViewer, visualization of biosignals

Visalix, Visual Interactive System for Annotation and LearnIng at Xerox.

Visual insights, methods and software for e-Business.

WheelVue visualization - Excel, tree-like diagrams

XDAT - A free software for multidimensional data analysis and visualization

Xgobi, XGvis - many visualizations | tutorial, gene expression data |

Principal curves page | Local principal curves in R

Reccurrence plots (N. Marwan and others)

PyCogent - a software library for genomic biology, good FastMDS program

More visualization algorithms

LEDA, Library of Efficient Data types and Algorithms

Benchin Software Reviews - also for statistical/ AI/ neural software

Jadex BDI Agents Java software

Software in Mental Health

Intel probabilistic network library | Audio-Visual Speech Recognition | Intel Open Source Computer Vision

Visumap - Relational Perspective Maps (free trial)

Dimensionality reduction, many embedding methods, Matlab package.

MMPI/MMPI-2 Adult Interpretive Report | Psychological Assessment Resources | Psychological Science net |

INFORMS OR/MS Resource Collection.

ASA, Ingber Lester - Adaptive Simmulated Annealing code

Global Optimization: Software, Events, Publications, Home Pages

Merlin - multidimensional optimization

NEOS Guide: Optimization Software

Multisimplex methods, demo.

Simulated Annealing info i software.

Bayes Belief Networks + HMM + MDP + Kalman filter, Kevin Murphy.

Bayesian Knowledge Discovery

Bayesia Lab, Bayesia.

Bayesware Discoverer (commercial)

Bayesian Network Repository

Bayesian Net Library (Norsys)

Bayes net Matlab toolbox (K. Murphy)

Bayesware Ltd Discoverer

Belief Network (BN) PowerConstructor

Elvira project | and more on the Elvira project.

GeNIe and SMILE- building graphical decision-theoretic models, Bayesian networks, influence diagrams, and structural equation models.

Netica, "the world's most widely used Bayesian network development software".

Rectified Gaussian Belief Networks (MIT), Matlab Program

Software for Manipulating Belief Networks (> 10 packages) and for Learning Belief Networks from Data

GA Archive

NeuCom - A Neuro-computing Decision Support Enviroment (KEDRI)

Jerzy Korczak, Strassbourg group, several packages.

HMMER - hidden Markov models of DNA and protein consensusHMM + MDP, Kevin Murphy.

Blind Source Separation Using Temporal Predictability, Matlab code

Several ICA algorithms, Matlab code (DK)

ICA Lab, Matlab code, RIKEN

Tree-Dependent CA, Matlab code

MISEP Linear and Nonlinear ICA Toolbox

Empirical Mode Decomposition.

See also NLP tools on the AI in IR list.

NLP Tools list

list of NLP software from Uni. Mass..

Proxem NLP Resources

Bow and Rainbow Toolkit, with C source code.

CLUTO, Clustering High-Dim data, texts.

Ellogon, a multi-lingual, cross-platform, general-purpose language engineering environment.

LingPipe, Java NLP tools, with MedLine support.

Mallet project, in Java

Megaputer PolyAnalyst, TextAnalyst, WebAnalyst

Natural Language Toolkit, Python libraries

OpenNLP, center for NLP open source projects, including MaxEnt.

Stanford Java NLP

VisualText Pro, free!

WEBSOM for free-text browsing

WordStat text mining, works with QDA Miner

Bixo open source web mining toolkit.

Visual Text 2 Pro

Text-Garden - Text-Mining Software Tools

Cognitive & Psychology Software

CTI Psychology: Software

Computers in Mental Health

Repertory Grids - Techwiki with many links to software

Software Archives in Psychology

Software for visual psychophysics

Tlearn - Kim Plunkett and Jeff Elman | Walnut - CALM, Hopfield, other | Rethinking Innateness: A Connectionist Perspective on Development

Natural Language Software Registry

Neural Translator (EN-PL)

Some NLP tools

CSLU Speech Tools, Spectrogram

Speech Toys

Speech corpora: CSLU Corpora | Linguistic Data Consortium | Machine Readable Spoken English Corpus

Attrasoft Neural Network Applications - stock predictions, image classfication etc

CodEc - Programs for Economics and Econometrics

ELSA, Econometrics Laboratory Software Archive (Berkeley)

LBS Model Building Software

Lista z NUMA

Reg-X, freeware (Stephen Hall, LBS)

Software from CTI Centre Economics

SORITEC, power tools for econometric and statistical analysis

Winsolve - package for solving nonlinear macroeconomic models

free POPLOG, POP11, LISP, Prolog and ML.

AITECH (Katowice) RL-Glue, interconnecting reinforcement learning agents and environments.

Comparison of classfication results | Comparison of logical rules extracted from data |

CBMR list of data sources - great list from WWW Virtual Library

GMD Repository and their

ML-Net Data links

RISE - Repository of online Information Sources used in information Extraction tasks

Brain-Computer Interface (BCI) competitions

New UCI Machine Learning Repository | old UCI | unofficial copy in Torun | UCI KDD Archive | use https://ftp.ics.uci.edu/pub/machine-learning-databases/ instead of ftp!

TuneIT, Testing Machine Learning & Data Mining Algorithms - Automated Tests, Repeatable Experiments, Meaningful Results.

ExpDB, experiment database, automatic comparison of results on various datasesets and algorithms.

CMU Artificial Intelligence Repository

CMU Machine Learning RepositoryDASL. The Data and (Statistical) Story Library

Bob Duin links to data

Data hub (links to many data types)

UCLA data and their cases studies

List of benchmark data from Czestochowa

Data Mining Institute, Wisconsin, software and data

KONECT, the Koblenz Network Collection of large network datasets

**Neuroscience data**

1000 connectom project

Autism Brain Imaging Data Exchange

**Bioinformatics data**

Bacterial Genomes Functional Annotation Benchmark Dataset

Biologia molekularna (molecular biology)

Kent Ridge bioinformatics |

Expected Fold-Protein classes (DEF)

UPITT Cancer Gene Expression Data (Pittsburg)

Data and systematic comparison of results (Leuven)

Protein Folding prediction, 27 classes, multiple kernels.

Stanford Microarray Database

KEDRI, gene expressions (large zip file!)

Bladder Cancer Microarray data (Leuven)

**Time series**: Econometric data (ELSA, Berkeley) | FinWeb Databases | Financial Data Finder | Global Financial Data | Investment data collection (FTP) | Time Series Data Library | Simple Time Series data |

Climate Modeling data

Census database, USA

DASL, The Data and Story Library (StatLib)

DELVE - Data for Evaluating Learning in Valid Experiments

Dr. B's Wide World of Web Data

International Association for Statistical Computing | datasets from IASC | few links to IASC databases

IEEE Neural Networks Council Standards Committee, Working Group on Data Modeling Benchmarks

National Space Science Data Center, NASA datasets)

Statistical Reference Datasets (NIST)

StatLog datasets (Portugal) Statlib, software and over 100 datasets

LLIAC datasets (Portugal)

SCDS - create your own syntethic data

SIMBAD astronomical database

Semi-supervised learning benchmarks

**Images:**

Curvlets |

Waveatom transforms |

Rice wavelet toolbox |

Morphological Component Analysis |

SPARCO: sparse reconstruction algorithms toolbox |

Cytopathology

**Texts:**

The Oxford Text Archive

List of corpora (from UC SD)

Reuters-21578 Text Categorization Collection | Reuters-21578 Test Collection | Tools for Reuters-21578 Dataset |

Ohsumed data collection

Cytopathology

NIPS 2000 competition data

Algoval - a system for evaluating algorithms on datasets.

The Robotics Data Set Repository

SMS Spam data

Wlodzislaw Duch; my local homepage

##

Red color = superpages.

Neural Networks | Neuroscience | Machine Learning + AI | Data Mining | Math & Statistics | Visualization of multidimensional data | Other software | Databases |

- Separate pages

AI and Machine Learning | AI in Information Retrieval | Cognitive science | Computational Intelligence | Neuroscience | Software & Databases | Science & Fringes | Comparison of classfication results | Logical rules extracted from data |

## Neural Networks |

Lists of links: |

Internet Analysis Tools Registry, supported by The Human Brain Project

Neural/AI Software - great list from Aston University

Neuroinformatics software tools

NN simulation tools - Franz Kurfess, Uni. Ulm, over 50 programs

Free & Shareware Simulators - about 100 programs, PNL Computational Intelligence list

Free & Shareware Simulators - over 40 programs, PNL Neural Networks list

Mathtools, many programs.

Neural Software - from Bristol, over 20 programs

Neural Networks and Fuzzy Systems, including Association Rule Induction, Regression, Trees, Bayes Classifier, Graphical Models, Network Training, Probabilistic and Fuzzy Clustering, Convex Hull Construction

On-line neural demos: |

DemoGNG, competitive learning (Loos, Fritzke)

Java demos of genetic and NN programs

Neural tutorial with Java applets

Java Applets for Neural Network and Artificial Life

RBF demo (Hong, MIT)

Virtual Minds Java demo

WebSim Java demo: neural, optimization, plots (Boston U.)

Sharky NN, nice 2D visualizations.

Large software packages |

Comparison of deep learning software - Wiki

KD nuggets, long list of software for data mining.

GASP, Globally Accessible Statistical Procedures, mostly applets.

Java Neural Network Simulator, JNNS (new version of SNNS)

KEEL - Knowledge Extraction Evolutionary Learning, 450 modułów!

KNIME, includes Weka and R-scripts.

LNKnet, MIT, neural, statistical, machine learning, dead project.

LENS, light, efficient network simulator

Orange, from Slovenia, component-based data mining software, includes SOM, MDS and other visualizations, 2006; some additional modules.

Pentaho data mining (based on Weka)

R-project, statistical computing | R Rattle, R for data mining |

SciViews open source, data acquisition, space-time series, image analysis etc.

Stuttgart Neural Network Simulator (SNNS), copy in Poland

WEKA, Machine Learning Project, many models | WEKA Metalearning

YALE, Yet Another Learning Environment, in Java, includes Weka models | now Rapid Miner

Efficient Learning, Large-scale Inference, and Optimization Toolkit

Matlab clones page: Scilab | Rlab | Octave |

EUDAPTICS - SOMine (demo)

ESO, Emergent SOM, Databionic tool.

WEBSOM for free-text browsing

JavaSOM

LVQ and SOM-PACK, HUT | SOM Toolbox in Matlab, Helsinki

SOM and LISSOM, with some programs for NLP, from UTCS Tx |

DDlab, discrete dynamics networks

DDtools, data description toolbox, one-class problems.

Dynamics - program i tutorial |

DIBA, with interesting visualization.

ffnet, regularization, SA and other interesting things.

Joone, Java free NN engine

LENS, with good visualization.

LVQ visualization, Magdeburg |

Pajek, from Slovenia, social networks analysis | an introduction to Pajek |

Quantum clustering, D. Horn |

SimBrain, NN+MDS.

Another SimBrain, with integrate/fire neurons.

Spider, Matlab object-oriented machine learning, SVM-oriented.

Shogun, A Large Scale Machine Learning Toolbox

Netlab (Bishop, Nabney) - programs in Matlab for NN and Bayes nets, copy in Torun

Neural Networks at your Fingertips, program sources, K. Kutza.

Neuralogic Windows: Ultra High Performance NN (PC, Cray)

NODELIB, Neural Optimization Development Engine library (PC, Cray)

Oxlearn, Matlab-based Neural Network Simulator for Education.

PDP ++ 2003, new version from the PDP book of Rumelhart and McClelland | RNS++ 2005, even newer version based on PDP++

Semeion software, many types of networks from Italy

SNARLI, Java, by Simon D. Levy.

Sieci Neuronowe dla każdego! Z programami w C# (2007)

## Neuroscience |

List of computational neuroscience software

Brian spiking network simulator.

Emergent - extension of PDP++,Randall C. O'Reilly

GENESIS Simulator, biological neurons

EEGLAB, signal processing in Matlab , EEG, MEG and other electrophysiological signals.

ICAlab and NMFlab and ButIf bump analysis from Cichocki group, RIKEN BSI

Keenan's Software for Memory and Cognition, psychological experiments

LORETA software and papers, low resolution brain electromagnetic tomography.

Mantra - Neural Java, spiking neuron and other models (Gerstner)

NeuroGuide dynamic EEG

Nengo rapid spiking network simulator

NEST initiative

Delay Vector Variance (DVV) toolbox for time series (Mandic).

e-connectome, (Electrophysiological Connectome) is an open-source MATLAB software package for imaging brain functional connectivity from electrophysiological signals.

Commercial and demos |

GTech, brain signals in Matlab

Gensym Corporation, intelligent operations management, neural & AI software

LocBoost and other goodies, Java demo

FuzzyTech, fuzzy and neurofuzzy

IFS Limited, Amber i Onyx neuroforcasting

Orka, NN/GA software Arkus (Wroclaw), demo

NeuroSolutions Evaluation Edition

NeuroShell Easy and Gene Hunter demos, Ward Systems Group

Saxon, NN+MDS.

Synapse by Peltarion, nice interface and many functions, 30 days demo

Universal Problem Solvers, Inc. (Transdimensional Learning, MPIL)

Neural Connection - SPSS

Vitalnet System for Analyzing Health Data

Z-solutions

GNU/Linux AI & Alife HOWTO list of software packages

AI Planning Systems (Maryland)

AI Medical Systems in Routine Use

Soar (Newell, Simon, Laird, others) - expert system with some learning capabilities

See also Cognitive Architectures page

## Machine Learning & Data Mining |

CMU Software in ML list

Cagliari University list

Gaussian Processes, list of packages

T++, a C++ library of mathematical, signal processing, speech processing, and communications classes and functions.

KDnets Software - long list

KDnuggets Siftware - long list

Matlab CI software, Kevin Murphy.

Model and Mine, list of DM packages

ML-Net Software links

Machine Learning Library in C++, a bit hard to use (Silicon Graphics)

Machine Learning Open Source Software, long list

Neural/AI Software (from Aston)

Sciview list of software packages

Torch ML Library in C++, free

Tom Mitchell, NN + Bayes + Decision Tree software

CBA, Classification and Association Rules, NUS Singapore

Domrule, logical rules, Lin Min Fu

Emerald, AG and other ML software, Michalski's GMU lab

MLC++, Color GLDs

ML archive - University of Portsmouth AI Group

Tools for learning CI, for AI course;

ID3 Code with examples, decsion tree

NETLAB Bayesian Neural Networks (Bishop, Nabney), copy in Torun

N-body methods, fast O(N) learning;

RIPPER rule induction

Statistical Pattern Recognition Lib (from TU Delft)

TANAGRA, includes visualization, clustering, association, supervised learning.

TiMBL, Memory-Based Learning techniques

Forte (First Order Revision of Theories from Examples) machine learning system

Rough sets: |

Reduct & Lobbe Technologies (rough sets, Canada)

Rosetta (rough sets)

Rough Enough (Torvill Bjorvand)

ROSE Rough Set Software, II-PP

Rough Set software (Uni. Regina)

Rough Set systems, Inc.

Rough Set Exploration System (RSES)

Rseslib, library of machine learning data structures and algorithms implemented in Java.

CBR, Case-Based: |

CBR Software, Haley Enterprise

Varia: |

Walrus - hyperbolic 3D vis.

C5.0, See5 & Cubist (Ross Quinlan, Rulequest Research) | C4.5 software and tutorial |

YaDT, fast tree and C4.5 improvements EC4.5 |

Occam tree from Visionary Tools |

Automated Reasoning, troubleshooting support

dmt - automatic identification

Free Statistical Software

Genetic Algorithms Digest

Generate new ideas creativity support software !

Partek Data Analysis & Modeling Software: PR, NN, Data Mining, demo

Machine Learning for Cancer Diagnosis and Prognosis

NeuroSoft SynthTalk, Gam, Regulus

Pattern recognition |

caret: Classification and Regression Training, in R

SprLib and ANNLib, from Delft Technical University Pattern Recognition Group

PRTools - Pattern Recognition Tools (Heijden, Duin, de Ridder, Tax)

Statistical Pattern Recognition Toolbox

TOOLDIAG pattern recognition toolbox

FLANN, Fast Library for Approximate Nearest Neighbors

## Data mining |

Data Mining Software Vendors

Cognitive Processor - Molly Group support management software, data mining

Free and Commercial Data Mining Software

GMDH Shell: Data Mining & Forecasting Software (available for free download)

DM Review list (see Software Demos)

DM Maximizer, DMM demo | DMS on-line serwer, Inductive Learning by Logic Minimization (ILLM) | Galvano software, French group, many programs, with DM tutorial | GhostMiner Software | Statconsulting PL | IBM Quest (free) | Info-Fuzzy Network (IFN) (free) | Mine It Easyminer |

SAS Enterprise Miner | SGI MineSet | Xpert Rule Miner (Attar Software) | XELOPES library, embedded DM |

Business Miner (BusinessObjects) |

Molecular Mining (bioinformatics software GeneLinker)

Dragon Genome Explorer

Psychometric test |

## Math & Statistics - lists |

Statlib - statistical software

Boost graphics library

JBoost for boosting clasification, with ADTrees.

Darren guide to statistical resources, software

Exact randomisation statistics software list

Free statistical software packages

Guide to mathematical software (NIST, excellent)

Sources of Math Software (NIST)

Statistical and Computational Software (RFE list)

Statistics.com tools, software, data

Anderson Hospital, biostatistics programs

Demo of genetic and NN algorithms in Java

GMM and MINZ packages in Matlab, spectral density, probit, logit (Mike Cliff)

Mathematical Programming in Machine Learning (Wisconsin)

Ordination software (for ecologist)

Provalis Research: MultiVariate Statistical + inne programy statystyczne.

Statistical Analysis and Graphics, Java Applets

Statistical Software Components from Boston College Department of Economics

Web Pages that Perform Statistical Calculations! also many free statistical packages.

Scientific software, Word2Tex etc (useful)

Free software: |

AMELIA: A Program for Missing Data, statistical software, Gary King

AutoClass - Bayesian classification and clustering

CN2 decision tree

EMMIX, EM mixture model

Medcalc, statistics for biomedical research

Multiple imputation software

NEFCLASS< NEFCON< NEFPROX neurofuzzy software (Nauck)

SISA, Simple Interactive Statistical Analysis

SNOB MML unsupervised classification

TimeStat: freeware PCA, ARMA, FTT, spreadsheet style

ttests and other statitical tests from Paul Barrett

Trevor Hasti: SVMs, discriminant and prinicipal curves

Vista - visual statistics

Software list from Kernel-machines.org

Comparison of SVM software (getting old, 2005)

Kernel methods in Pattern Analysis list, John Shawe-Taylor & Nello Cristianini, 2004

Wikipedia SVM list

SVM On-line demonstration

BSVM, SVM solved by another method

Core Vector Machine, fastest SVM around?

GiniSVM, SVM for regression

GIST, SVM and kernel PCA (Unix only)

HeroSVM

LIBSVM, SVM for large classification and regression

LIBLINEAR: A Library for Large Linear Classification.

LSSVMlab, least squares SVM, Matlab toolbox + tutorials

P-SVM software

Multivariate Relevance Vector Machine (MVRVM)

Shogun - A Large Scale Machine Learning Toolbox

SVM-Light, SVM software for regresion and classification

SVM in the primal, Matlab code

BMR: Bayesian Multinomial Regression Software

DTREG: SVM, decision tree + logistic regression (commercial, demo available)

Affinity propagation

COMPACT - Comparative Package for Clustering Assessment, D. Horn

CLUSION, Cluster Analysis and Cluster Ensemble Software

CLUTO, Clustering High-Dim data, texts

Dendrograms data clustering

Fuzzy Clustering

G-means, C++ program

Joining clustering algorithms, dendrograms and other

KlustaKwik, Automatic Clustering

MCL - a cluster algorithm for graphs

MIXMOD (MIXture MODelling), fits mixture models

Multi-dimensional Clustering and Outlier Detection

PermutMatrix, seriation analysis.

Quantum clustering, D. Horn |

SP-means, C++ program

Commercial Statistical Software: |

CART | MARS | GMAX-DM, genetic system (Salford Systems)

Data Desk (Majih)

AccuROC for Windows | GraphROC for Windows

Minitab (Minitab Inc)

Predictive Data Mining, Weiss S, Indurkhya, book and software

Simstat for Windows StatSoft Polska Sp. z o.o. - STATISTICA

StatSol, missing data, statistical software

Stata statistical software

Statgraphics (Manugistics Inc), STATG-PL

CSS STATISTICA (StatSoft Inc.)

SPSS (SPSS Inc.), pakiet Systat

SAS Institute - DSS, data mining

S-Plus (Mathsoft)

StatXact, LogXact (Cytel)

## Visualization of multidimensional data |

- IVS - Information Visualization Software Repository, many interesting algorithms
- Info Visualizations at Infovis-Wiki
- Graphics and data analysis software
- Information Visualization, T. Cribbin.
- Long list of packages from UBC
- On-line Library of Information Visualization Environments.

Proximity visualization, W. Basalaj, interesting thesis

CAIDA Visualization Tools, Internet data visualization.

COVIAGRA, Learning Coordinate Covariances via Gradients, Matlab code.

Davis - PCA, parallel, dendrograms, touring ...

Facet Analysis, Smallest Space Analysis, Multidimensional Scalogram Analysis, Partial Order Scalogram Analysis

GCSVIS - Growing Cell Structures.

Ggobi for Windows- many visualizations |

GE Data visualization collection

GTM - Bishop and Svensen.

Hierarchical Clustering Explorer for Interactive Exploration of Multidimensional Data.

HiSee project, Scott Hotton and Jeff Yoshimi.

Hyperplane animator

KNOT Tools for Pathfinder Network Analysis |

Levenstein Software

Locally Linear Embedding

MaxdView, bioinfo data

MANIfold learning, Matlab for ISOMAP, LLE, Hessian LLE, Laplacian, and LTSA.

Orange, from Slovenia, includes parallel coordinates, multigrams, SOM, MDS ...

Pathfinder Networks Wiki

PhiVis, hierarchical visualization - Bishop and Tipping

Parvis, a tool for parallel coordinates

Radviz visualization

Spotfire - clustering, visualization

SigViewer, visualization of biosignals

Visalix, Visual Interactive System for Annotation and LearnIng at Xerox.

Visual insights, methods and software for e-Business.

WheelVue visualization - Excel, tree-like diagrams

XDAT - A free software for multidimensional data analysis and visualization

Xgobi, XGvis - many visualizations | tutorial, gene expression data |

Principal curves page | Local principal curves in R

Reccurrence plots (N. Marwan and others)

PyCogent - a software library for genomic biology, good FastMDS program

More visualization algorithms

## Other software |

Benchin Software Reviews - also for statistical/ AI/ neural software

Jadex BDI Agents Java software

Software in Mental Health

Intel probabilistic network library | Audio-Visual Speech Recognition | Intel Open Source Computer Vision

Visumap - Relational Perspective Maps (free trial)

Dimensionality reduction, many embedding methods, Matlab package.

Psychometric programs: |

Optimization: |

ASA, Ingber Lester - Adaptive Simmulated Annealing code

Global Optimization: Software, Events, Publications, Home Pages

Merlin - multidimensional optimization

NEOS Guide: Optimization Software

Multisimplex methods, demo.

Simulated Annealing info i software.

Belief (Bayesian) networks: |

Bayesian Knowledge Discovery

Bayesia Lab, Bayesia.

Bayesware Discoverer (commercial)

Bayesian Network Repository

Bayesian Net Library (Norsys)

Bayes net Matlab toolbox (K. Murphy)

Bayesware Ltd Discoverer

Belief Network (BN) PowerConstructor

Elvira project | and more on the Elvira project.

GeNIe and SMILE- building graphical decision-theoretic models, Bayesian networks, influence diagrams, and structural equation models.

Netica, "the world's most widely used Bayesian network development software".

Rectified Gaussian Belief Networks (MIT), Matlab Program

Software for Manipulating Belief Networks (> 10 packages) and for Learning Belief Networks from Data

Genetic/evolutionary optimization software: |

NeuCom - A Neuro-computing Decision Support Enviroment (KEDRI)

Jerzy Korczak, Strassbourg group, several packages.

HMM: |

ICA, Independent Component Analysis + variants |

Several ICA algorithms, Matlab code (DK)

ICA Lab, Matlab code, RIKEN

Tree-Dependent CA, Matlab code

MISEP Linear and Nonlinear ICA Toolbox

Empirical Mode Decomposition.

Text Processing, retrieval, clusterization, classification: |

NLP Tools list

list of NLP software from Uni. Mass..

Proxem NLP Resources

Bow and Rainbow Toolkit, with C source code.

CLUTO, Clustering High-Dim data, texts.

Ellogon, a multi-lingual, cross-platform, general-purpose language engineering environment.

LingPipe, Java NLP tools, with MedLine support.

Mallet project, in Java

Megaputer PolyAnalyst, TextAnalyst, WebAnalyst

Natural Language Toolkit, Python libraries

OpenNLP, center for NLP open source projects, including MaxEnt.

Stanford Java NLP

VisualText Pro, free!

WEBSOM for free-text browsing

WordStat text mining, works with QDA Miner

Bixo open source web mining toolkit.

Visual Text 2 Pro

Text-Garden - Text-Mining Software Tools

Psychology and cognitive science software: |

CTI Psychology: Software

Computers in Mental Health

Repertory Grids - Techwiki with many links to software

Software Archives in Psychology

Software for visual psychophysics

Tlearn - Kim Plunkett and Jeff Elman | Walnut - CALM, Hopfield, other | Rethinking Innateness: A Connectionist Perspective on Development

Linguistics: |

Neural Translator (EN-PL)

Some NLP tools

Speech-related tools: |

Speech Toys

Speech corpora: CSLU Corpora | Linguistic Data Consortium | Machine Readable Spoken English Corpus

Financial and econometric software: |

CodEc - Programs for Economics and Econometrics

ELSA, Econometrics Laboratory Software Archive (Berkeley)

LBS Model Building Software

Lista z NUMA

Reg-X, freeware (Stephen Hall, LBS)

Software from CTI Centre Economics

SORITEC, power tools for econometric and statistical analysis

Winsolve - package for solving nonlinear macroeconomic models

Expert Systems and AI Software: |

AITECH (Katowice) RL-Glue, interconnecting reinforcement learning agents and environments.

## Datasets |

Lists of data sources: |

GMD Repository and their

ML-Net Data links

RISE - Repository of online Information Sources used in information Extraction tasks

Brain-Computer Interface (BCI) competitions

Data: |

TuneIT, Testing Machine Learning & Data Mining Algorithms - Automated Tests, Repeatable Experiments, Meaningful Results.

ExpDB, experiment database, automatic comparison of results on various datasesets and algorithms.

CMU Artificial Intelligence Repository

CMU Machine Learning RepositoryDASL. The Data and (Statistical) Story Library

Bob Duin links to data

Data hub (links to many data types)

UCLA data and their cases studies

List of benchmark data from Czestochowa

Data Mining Institute, Wisconsin, software and data

KONECT, the Koblenz Network Collection of large network datasets

1000 connectom project

Autism Brain Imaging Data Exchange

Bacterial Genomes Functional Annotation Benchmark Dataset

Biologia molekularna (molecular biology)

Kent Ridge bioinformatics |

Expected Fold-Protein classes (DEF)

UPITT Cancer Gene Expression Data (Pittsburg)

Data and systematic comparison of results (Leuven)

Protein Folding prediction, 27 classes, multiple kernels.

Stanford Microarray Database

KEDRI, gene expressions (large zip file!)

Bladder Cancer Microarray data (Leuven)

Climate Modeling data

Census database, USA

DASL, The Data and Story Library (StatLib)

DELVE - Data for Evaluating Learning in Valid Experiments

Dr. B's Wide World of Web Data

International Association for Statistical Computing | datasets from IASC | few links to IASC databases

IEEE Neural Networks Council Standards Committee, Working Group on Data Modeling Benchmarks

National Space Science Data Center, NASA datasets)

Statistical Reference Datasets (NIST)

StatLog datasets (Portugal) Statlib, software and over 100 datasets

LLIAC datasets (Portugal)

SCDS - create your own syntethic data

SIMBAD astronomical database

Semi-supervised learning benchmarks

Curvlets |

Waveatom transforms |

Rice wavelet toolbox |

Morphological Component Analysis |

SPARCO: sparse reconstruction algorithms toolbox |

Cytopathology

The Oxford Text Archive

List of corpora (from UC SD)

Reuters-21578 Text Categorization Collection | Reuters-21578 Test Collection | Tools for Reuters-21578 Dataset |

Ohsumed data collection

Cytopathology

NIPS 2000 competition data

Algoval - a system for evaluating algorithms on datasets.

The Robotics Data Set Repository

SMS Spam data

Wlodzislaw Duch; my local homepage