More links on: 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 |

Maintained by Wlodzislaw Duch

Red color = superpages. Older version of this page in Polish.

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

Neural Networks


Lists of links:
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

On-line neural demos:
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.

Large software packages
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)

Neuroscience

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.
Commercial and demos
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

Machine Learning & Data Mining

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

Rough sets:
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, Case-Based:
CBR Software List
CBR Software, Haley Enterprise

Varia:
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

Pattern recognition
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

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 |

Math & Statistics - lists

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)

Free software:
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

Commercial Statistical Software:
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)

Visualization of multidimensional data

Larger lists of software pacakges:
  1. IVS - Information Visualization Software Repository, many interesting algorithms
  2. Info Visualizations at Infovis-Wiki
  3. Graphics and data analysis software
  4. Information Visualization, T. Cribbin.
  5. Long list of packages from UBC
  6. On-line Library of Information Visualization Environments.

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

Other software

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.

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

Optimization:
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.

Belief (Bayesian) networks:
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

Genetic/evolutionary optimization software:
GA Archive
NeuCom - A Neuro-computing Decision Support Enviroment (KEDRI)
Jerzy Korczak, Strassbourg group, several packages.

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

ICA, Independent Component Analysis + variants
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.

Text Processing, retrieval, clusterization, classification:
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

Psychology and cognitive science software:
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

Linguistics:
Natural Language Software Registry
Neural Translator (EN-PL)
Some NLP tools

Speech-related tools:
CSLU Speech Tools, Spectrogram
Speech Toys
Speech corpora: CSLU Corpora | Linguistic Data Consortium | Machine Readable Spoken English Corpus

Financial and econometric software:
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

Expert Systems and AI Software:
free POPLOG, POP11, LISP, Prolog and ML.
AITECH (Katowice) RL-Glue, interconnecting reinforcement learning agents and environments.




Datasets

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

Lists of data sources:
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
Data:
New UCI Machine Learning Repository | old UCI | unofficial copy in Torun | UCI KDD Archive | use http://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


Other pages: AI in IR | AI & ML | Computational Intelligence | Cognitive Science | Neuroscience and brains | Software and data | Science & Fringes | Comparison of classfication results | Logical rules extracted from data |
Last modification 18.03.2016, by Wlodzislaw Duch; my local homepage