comp.ai.neural-nets FAQ, Part 5 of 7: Free software

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Archive-name: ai-faq/neural-nets/part5
Last-modified: 2002-07-27
URL: ftp://ftp.sas.com/pub/neural/FAQ5.html
Maintainer: sas...@unx.sas.com (Warren S. Sarle)

The copyright for the description of each product is held by the producer or
distributor of the product or whoever it was who supplied the description
for the FAQ, who by submitting it for the FAQ gives permission for the
description to be reproduced as part of the FAQ in any of the ways specified
in part 1 of the FAQ.

This is part 5 (of 7) of a monthly posting to the Usenet newsgroup
comp.ai.neural-nets. See the part 1 of this posting for full information
what it is all about.

========== Questions ==========
********************************

Part 1: Introduction
Part 2: Learning
Part 3: Generalization
Part 4: Books, data, etc.
Part 5: Free software

Source code on the web?
Freeware and shareware packages for NN simulation?

Part 6: Commercial software
Part 7: Hardware and miscellaneous

------------------------------------------------------------------------

Subject: Source code on the web?
================================

The following URLs are reputed to have source code for NNs. Use at your own
risk.

o C/C++
http://www.generation5.org/xornet.shtml
http://www.netwood.net/~edwin/Matrix/
http://www.netwood.net/~edwin/svmt/
http://www.geocities.com/Athens/Agora/7256/c-plus-p.html
http://www.cs.cmu.edu/afs/cs.cmu.edu/user/mitchell/ftp/faces.html
http://www.cog.brown.edu/~rodrigo/neural_nets_library.html
http://www.agt.net/public/bmarshal/aiparts/aiparts.htm
http://www.geocities.com/CapeCanaveral/1624/
http://www.neuroquest.com/ or http://www.grobe.org/LANE
http://www.neuro-fuzzy.de/
http://www.cs.cmu.edu/afs/cs/project/ai-repository/ai/areas/neural/systems/cascor/
http://www.cs.cmu.edu/afs/cs/project/ai-repository/ai/areas/neural/systems/qprop/
http://www.cs.cmu.edu/afs/cs/project/ai-repository/ai/areas/neural/systems/rcc/
etc.

o Java
http://rfhs8012.fh-regensburg.de/~saj39122/jfroehl/diplom/e-index.html
http://neuron.eng.wayne.edu/software.html
http://www.aist.go.jp/NIBH/~b0616/Lab/Links.html
http://www.aist.go.jp/NIBH/~b0616/Lab/BSOM1/
http://www.neuroinformatik.ruhr-uni-bochum.de/ini/PEOPLE/loos
http://www.neuroinformatik.ruhr-uni-bochum.de/ini/VDM/research/gsn/DemoGNG/GNG.html
http://www.isbiel.ch/I/Projects/janet/index.html
http://www.born-again.demon.nl/software.html
http://www.patol.com/java/NN/index.html
http://www-isis.ecs.soton.ac.uk/computing/neural/laboratory/laboratory.html
http://www.neuro-fuzzy.de/
http://sourceforge.net/projects/joone
http://www.geocities.com/aydingurel/neural/
http://www-eco.enst-bretagne.fr/~phan/emergence/complexe/neuron/mlp.html

o FORTRAN
http://www.cranfield.ac.uk/public/me/fo941992/mlpcode.htm

o Pascal
http://www.ibrtses.com/delphi/neuralnets.html

If you are using a small computer (PC, Mac, etc.) you may want to have a
look at the Central Neural System Electronic Bulletin Board (see question
"Other sources of information"). There are lots of small simulator packages.
Some of the CNS materials can also be found at
http://www.cs.cmu.edu/afs/cs.cmu.edu/project/ai-repository/ai/areas/neural/cns/0.html

------------------------------------------------------------------------

Subject: Freeware and shareware packages for NN
===============================================
simulation?
===========

Since the FAQ maintainer works for a software company, he does not recommend
or evaluate software in the FAQ. The descriptions below are provided by the
developers or distributors of the software.

Note for future submissions: Please restrict product descriptions to a
maximum of 60 lines of 72 characters, in either plain-text format or,
preferably, HTML format. If you include the standard header (name, company,
address, etc.), you need not count the header in the 60 line maximum. Please
confine your HTML to features that are supported by primitive browsers,
especially NCSA Mosaic 2.0; avoid tables, for example--use <pre> instead.
Try to make the descriptions objective, and avoid making implicit or
explicit assertions about competing products, such as "Our product is the
*only* one that does so-and-so." The FAQ maintainer reserves the right to
remove excessive marketing hype and to edit submissions to conform to size
requirements; if he is in a good mood, he may also correct your spelling and
punctuation.

The following simulators are described below:

1. JavaNNS
2. SNNS
3. PDP++
4. Rochester Connectionist Simulator
5. UCLA-SFINX
6. NeurDS
7. PlaNet (formerly known as SunNet)
8. GENESIS
9. Mactivation
10. Cascade Correlation Simulator
11. Quickprop
12. DartNet
13. Aspirin/MIGRAINES
14. ALN Workbench
15. Uts (Xerion, the sequel)
16. Multi-Module Neural Computing Environment (MUME)
17. LVQ_PAK, SOM_PAK
18. Nevada Backpropagation (NevProp)
19. Fuzzy ARTmap
20. PYGMALION
21. Basis-of-AI-NN Software
22. Matrix Backpropagation
23. BIOSIM
24. FuNeGen
25. NeuDL -- Neural-Network Description Language
26. NeoC Explorer
27. AINET
28. DemoGNG
29. Trajan 2.1 Shareware
30. Neural Networks at your Fingertips
31. NNFit
32. Nenet v1.0
33. Machine Consciousness Toolbox
34. NICO Toolkit (speech recognition)
35. SOM Toolbox for Matlab 5
36. FastICA package for MATLAB
37. NEXUS: Large-scale biological simulations
38. Netlab: Neural network software for Matlab
39. NuTank
40. Lens
41. Joone: Java Object Oriented Neural Engine
42. NV: Neural Viewer
43. EasyNN
44. Multilayer Perceptron - A Java Implementation

See also
http://www.emsl.pnl.gov:2080/proj/neuron/neural/systems/shareware.html

1. JavaNNS: Java Neural Network Simulator
+++++++++++++++++++++++++++++++++++++++++

http://www-ra.informatik.uni-tuebingen.de/forschung/JavaNNS/welcome_e.html
JavaNNS is the successor to SNNS. JavaNNS is based on the SNNS computing
kernel, but has a newly developed graphical user interface written in
Java set on top of it. Hence compatibility with SNNS is achieved while
platform-independence is increased.

In addition to SNNS features, JavaNNS offers the capability of linking
HTML browsers to it. This provides for accessing the user manual
(available in HTML) or, optionally, a reference coursebook on neural
networks directly from within the program.

JavaNNS is available for Windows NT / Windows 2000, Solaris and RedHat
Linux. Additional ports are planed. JavaNNS is freely available and can
be downloaded from the URL shown above.

Contact: Igor Fischer, Phone: +49 7071 29-77176,
fis...@informatik.uni-tuebingen.de

2. SNNS 4.2
+++++++++++

SNNS (Stuttgart Neural Network Simulator) is a software simulator for
neural networks on Unix workstations developed at the Institute for
Parallel and Distributed High Performance Systems (IPVR) at the
University of Stuttgart. The goal of the SNNS project is to create an
efficient and flexible simulation environment for research on and
application of neural nets.

The SNNS simulator consists of two main components:

1. simulator kernel written in C
2. graphical user interface under X11R4 or X11R5

The simulator kernel operates on the internal network data structures of
the neural nets and performs all operations of learning and recall. It
can also be used without the other parts as a C program embedded in
custom applications. It supports arbitrary network topologies and, like
RCS, supports the concept of sites. SNNS can be extended by the user with
user defined activation functions, output functions, site functions and
learning procedures, which are written as simple C programs and linked to
the simulator kernel. C code can be generated from a trained network.

Currently the following network architectures and learning procedures are
included:

o Backpropagation (BP) for feedforward networks
o vanilla (online) BP
o BP with momentum term and flat spot elimination
o batch BP
o chunkwise BP
o Counterpropagation
o Quickprop
o Backpercolation 1
o RProp
o Generalized radial basis functions (RBF)
o ART1
o ART2
o ARTMAP
o Cascade Correlation
o Dynamic LVQ
o Backpropagation through time (for recurrent networks)
o Quickprop through time (for recurrent networks)
o Self-organizing maps (Kohonen maps)
o TDNN (time-delay networks) with Backpropagation
o Jordan networks
o Elman networks and extended hierarchical Elman networks
o Associative Memory
o TACOMA

The graphical user interface XGUI (X Graphical User Interface), built on
top of the kernel, gives a 2D and a 3D graphical representation of the
neural networks and controls the kernel during the simulation run. In
addition, the 2D user interface has an integrated network editor which
can be used to directly create, manipulate and visualize neural nets in
various ways.

SNNSv4.1 has been tested on SUN SparcSt ELC,IPC (SunOS 4.1.2, 4.1.3), SUN
SparcSt 2 (SunOS 4.1.2), SUN SparcSt 5, 10, 20 (SunOS 4.1.3, 5.2),
DECstation 3100, 5000 (Ultrix V4.2), DEC Alpha AXP 3000 (OSF1 V2.1),
IBM-PC 80486, Pentium (Linux), IBM RS 6000/320, 320H, 530H (AIX V3.1, AIX
V3.2), HP 9000/720, 730 (HP-UX 8.07), and SGI Indigo 2 (IRIX 4.0.5, 5.3).

The distributed kernel can spread one learning run over a workstation
cluster.

SNNS web page: http://www-ra.informatik.uni-tuebingen.de/SNNS
Ftp server: ftp://ftp.informatik.uni-tuebingen.de/pub/SNNS
o SNNSv4.1.Readme
o SNNSv4.1.tar.gz (1.4 MB, Source code)
o SNNSv4.1.Manual.ps.gz (1 MB, Documentation)
Mailing list:
http://www-ra.informatik.uni-tuebingen.de/SNNS/about-ml.html

3. PDP++
++++++++

URL: http://www.cnbc.cmu.edu/PDP++/PDP++.html

The PDP++ software is a neural-network simulation system written in C++.
It represents the next generation of the PDP software released with the
McClelland and Rumelhart "Explorations in Parallel Distributed Processing
Handbook", MIT Press, 1987. It is easy enough for novice users, but very
powerful and flexible for research use. PDP++ is featured in a new
textbook, Computational Explorations in Cognitive Neuroscience:
Understanding the Mind by Simulating the Brain, by Randall C. O'Reilly
and Yuko Munakata, MIT Press, 2000.

Supported algorithms include:

o Feedforward and recurrent error backpropagation. Recurrent BP includes
continuous, real-time models, and Almeida-Pineda.
o Constraint satisfaction algorithms and associated learning algorithms
including Boltzmann Machine, Hopfield models, mean-field networks
(DBM), Interactive Activation and Competition (IAC), and continuous
stochastic networks.
o Self-organizing learning including Competitive Learning, Soft
Competitive Learning, simple Hebbian, and Self-organizing Maps
("Kohonen Nets").
o Mixtures-of-experts using backpropagation experts, EM updating, and a
SoftMax gating module.
o Leabra algorithm that combines error-driven and Hebbian learning with
k-Winners-Take-All inhibitory competition.

The software can be obtained by anonymous ftp from:
o ftp://grey.colorado.edu/pub/oreilly/pdp++ or
o ftp://cnbc.cmu.edu/pub/pdp++/ or
o ftp://unix.hensa.ac.uk/mirrors/pdp++/

4. Rochester Connectionist Simulator
++++++++++++++++++++++++++++++++++++

A versatile simulator program for arbitrary types of neural nets. Comes
with a backprop package and a X11/Sunview interface. Available via
anonymous FTP from
ftp://ftp.cs.rochester.edu/pub/packages/simulator/simulator_v4.2.tar.Z
There's also a patch available from
ftp://ftp.cs.rochester.edu/pub/packages/simulator/simulator_v4.2.patch.1

5. UCLA-SFINX
+++++++++++++

The UCLA-SFINX, a "neural" network simulator is now in public domain.
UCLA-SFINX (Structure and Function In Neural connec- tions) is an
interactive neural network simulation environment designed to provide the
investigative tools for studying the behavior of various neural
structures. It was designed to easily express and simulate the highly
regular patterns often found in large networks, but it is also general
enough to model parallel systems of arbitrary interconnectivity. For more
information, see
http://decus.acornsw.com/vs0121/AISIG/F90/NETS/UCLA_SIM.TXT

6. NeurDS
+++++++++

Neural Design and Simulation System. This is a general purpose tool for
building, running and analysing Neural Network Models in an efficient
manner. NeurDS will compile and run virtually any Neural Network Model
using a consistent user interface that may be either window or "batch"
oriented. HP-UX 8.07 source code is available from
http://hpux.u-aizu.ac.jp/hppd/hpux/NeuralNets/NeurDS-3.1/ or
http://askdonna.ask.uni-karlsruhe.de/hppd/hpux/NeuralNets/NeurDS-3.1/

7. PlaNet5.7 (formerly known as SunNet)
+++++++++++++++++++++++++++++++++++++++

A popular connectionist simulator with versions to run under X Windows,
and non-graphics terminals created by Yoshiro Miyata (Chukyo Univ.,
Japan). 60-page User's Guide in Postscript. Send any questions to
miy...@sccs.chukyo-u.ac.jp Available for anonymous ftp from
ftp.ira.uka.de as /pub/neuron/PlaNet5.7.tar.gz (800 kb)

8. GENESIS
++++++++++

GENESIS 2.0 (GEneral NEural SImulation System) is a general purpose
simulation platform which was developed to support the simulation of
neural systems ranging from complex models of single neurons to
simulations of large networks made up of more abstract neuronal
components. Most current GENESIS applications involve realistic
simulations of biological neural systems. Although the software can also
model more abstract networks, other simulators are more suitable for
backpropagation and similar connectionist modeling. Runs on most Unix
platforms. Graphical front end XODUS. Parallel version for networks of
workstations, symmetric multiprocessors, and MPPs also available. Further
information via WWW at http://www.genesis-sim.org/GENESIS/.

9. Mactivation
++++++++++++++

A neural network simulator for the Apple Macintosh. Available for ftp
from ftp.cs.colorado.edu as /pub/cs/misc/Mactivation-3.3.sea.hqx

10. Cascade Correlation Simulator
+++++++++++++++++++++++++++++++++

A simulator for Scott Fahlman's Cascade Correlation algorithm. Available
for ftp from ftp.cs.cmu.edu in directory
/afs/cs/project/connect/code/supported as the file cascor-v1.2.shar (223
KB) There is also a version of recurrent cascade correlation in the same
directory in file rcc1.c (108 KB).

11. Quickprop
+++++++++++++

A variation of the back-propagation algorithm developed by Scott Fahlman.
A simulator is available in the same directory as the cascade correlation
simulator above in file nevprop1.16.shar (137 KB)
(There is also an obsolete simulator called quickprop1.c (21 KB) in the
same directory, but it has been superseeded by NevProp. See also the
description of NevProp below.)

12. DartNet
+++++++++++

DartNet is a Macintosh-based backpropagation simulator, developed at
Dartmouth by Jamshed Bharucha and Sean Nolan as a pedagogical tool. It
makes use of the Mac's graphical interface, and provides a number of
tools for building, editing, training, testing and examining networks.
This program is available by anonymous ftp from ftp.dartmouth.edu as
/pub/mac/dartnet.sit.hqx (124 KB).

13. Aspirin/MIGRAINES
+++++++++++++++++++++

Aspirin/MIGRAINES 6.0 consists of a code generator that builds neural
network simulations by reading a network description (written in a
language called "Aspirin") and generates a C simulation. An interface
(called "MIGRAINES") is provided to export data from the neural network
to visualization tools. The system has been ported to a large number of
platforms. The goal of Aspirin is to provide a common extendible
front-end language and parser for different network paradigms. The
MIGRAINES interface is a terminal based interface that allows you to open
Unix pipes to data in the neural network. Users can display the data
using either public or commercial graphics/analysis tools. Example
filters are included that convert data exported through MIGRAINES to
formats readable by Gnuplot 3.0, Matlab, Mathematica, and xgobi.

The software is available from
http://www.elegant-software.com/software/aspirin/

14. ALN Workbench (a spreadsheet for Windows)
++++++++++++++++++++++++++++++++++++++++++++++

ALNBench is a free spreadsheet program for MS-Windows (NT, 95) that
allows the user to import training and test sets and predict a chosen
column of data from the others in the training set. It is an easy-to-use
program for research, education and evaluation of ALN technology. Anyone
who can use a spreadsheet can quickly understand how to use it. It
facilitates interactive access to the power of the Dendronic Learning
Engine (DLE), a product in commercial use.

An ALN consists of linear functions with adaptable weights at the leaves
of a tree of maximum and minimum operators. The tree grows automatically
during training: a linear piece splits if its error is too high. The
function computed by an ALN is piecewise linear and continuous. It can
learn to approximate any continuous function to arbitrarily high
accuracy.

Parameters allow the user to input knowledge about a function to promote
good generalization. In particular, bounds on the weights of the linear
functions can be directly enforced. Some parameters are chosen
automatically in standard mode, and are under user control in expert
mode.

The program can be downloaded from http://www.dendronic.com/main.htm

For further information please contact:

William W. Armstrong PhD, President
Dendronic Decisions Limited
3624 - 108 Street, NW
Edmonton, Alberta,
Canada T6J 1B4
Email: ar...@dendronic.com
URL: http://www.dendronic.com/
Tel. +1 403 421 0800
(Note: The area code 403 changes to 780 after Jan. 25, 1999)

15. Uts (Xerion, the sequel)
++++++++++++++++++++++++++++

Uts is a portable artificial neural network simulator written on top of
the Tool Control Language (Tcl) and the Tk UI toolkit. As result, the
user interface is readily modifiable and it is possible to simultaneously
use the graphical user interface and visualization tools and use scripts
written in Tcl. Uts itself implements only the connectionist paradigm of
linked units in Tcl and the basic elements of the graphical user
interface. To make a ready-to-use package, there exist modules which use
Uts to do back-propagation (tkbp) and mixed em gaussian optimization
(tkmxm). Uts is available in ftp.cs.toronto.edu in directory /pub/xerion.

16. Multi-Module Neural Computing Environment (MUME)
++++++++++++++++++++++++++++++++++++++++++++++++++++

MUME is a simulation environment for multi-modules neural computing. It
provides an object oriented facility for the simulation and training of
multiple nets with various architectures and learning algorithms. MUME
includes a library of network architectures including feedforward, simple
recurrent, and continuously running recurrent neural networks. Each
architecture is supported by a variety of learning algorithms. MUME can
be used for large scale neural network simulations as it provides support
for learning in multi-net environments. It also provide pre- and
post-processing facilities. For more information, see
http://www-2.cs.cmu.edu/afs/cs/project/ai-repository/ai/areas/neural/systems/mume/0.html

17. LVQ_PAK, SOM_PAK
++++++++++++++++++++

These are packages for Learning Vector Quantization and Self-Organizing
Maps, respectively. They have been built by the LVQ/SOM Programming Team
of the Helsinki University of Technology, Laboratory of Computer and
Information Science, Rakentajanaukio 2 C, SF-02150 Espoo, FINLAND There
are versions for Unix and MS-DOS available from
http://nucleus.hut.fi/nnrc/nnrc-programs.html

18. Nevada Backpropagation (NevProp)
++++++++++++++++++++++++++++++++++++

NevProp, version 3, is a relatively easy-to-use, feedforward
backpropagation multilayer perceptron simulator-that is, statistically
speaking, a multivariate nonlinear regression program. NevProp3 is
distributed for free under the terms of the GNU Public License and can be
downloaded from http://brain.cs.unr.edu/publications/NevProp.zip and
http://brain.cs.unr.edu/publications/NevPropManual.pdf

The program is distributed as C source code that should compile and run
on most platforms. In addition, precompiled executables are available for
Macintosh and DOS platforms. Limited support is available from Phil
Goodman (goo...@unr.edu), University of Nevada Center for Biomedical
Research.

MAJOR FEATURES OF NevProp3 OPERATION (* indicates feature new in version
3)
1. Character-based interface common to the UNIX, DOS, and Macintosh
platforms.
2. Command-line argument format to efficiently initiate NevProp3. For
Generalized Nonlinear Modeling (GNLM) mode, beginners may opt to use
an interactive interface.
3. Option to pre-standardize the training data (z-score or forced
range*).
4. Option to pre-impute missing elements in training data (case-wise
deletion, or imputation with mean, median, random selection, or
k-nearest neighbor).*
5. Primary error (criterion) measures include mean square error,
hyperbolic tangent error, and log likelihood (cross-entropy), as
penalized an unpenalized values.
6. Secondary measures include ROC-curve area (c-index), thresholded
classification, R-squared and Nagelkerke R-squared. Also reported at
intervals are the weight configuration, and the sum of square weights.
7. Allows simultaneous use of logistic (for dichotomous outputs) and
linear output activation functions (automatically detected to assign
activation and error function).*
8. 1-of-N (Softmax)* and M-of-N options for binary classification.
9. Optimization options: flexible learning rate (fixed global adaptive,
weight-specific, quickprop), split learn rate (inversely proportional
to number of incoming connections), stochastic (case-wise updating),
sigmoidprime offset (to prevent locking at logistic tails).
10. Regularization options: fixed weight decay, optional decay on bias
weights, Bayesian hyperpenalty* (partial and full Automatic Relevance
Determination-also used to select important predictors), automated
early stopping (full dataset stopping based on multiple subset
cross-validations) by error criterion.
11. Validation options: upload held-out validation test set; select subset
of outputs for joint summary statistics;* select automated
bootstrapped modeling to correct optimistically biased summary
statistics (with standard deviations) without use of hold-out.
12. Saving predictions: for training data and uploaded validation test
set, save file with identifiers, true targets, predictions, and (if
bootstrapped models selected) lower and upper 95% confidence limits*
for each prediction.
13. Inference options: determination of the mean predictor effects and
level effects (for multilevel predictor variables); confidence limits
within main model or across bootstrapped models.*
14. ANN-kNN (k-nearest neighbor) emulation mode options: impute missing
data elements and save to new data file; classify test data (with or
without missing elements) using ANN-kNN model trained on data with or
without missing elements (complete ANN-based expectation
maximization).*
15. AGE (ANN-Gated Ensemble) options: adaptively weight predictions (any
scale of scores) obtained from multiple (human or computational)
"experts"; validate on new prediction sets; optional internal
prior-probability expert.*

19. Fuzzy ARTmap
++++++++++++++++

This is just a small example program. Available for anonymous ftp from
park.bu.edu [128.176.121.56] ftp://cns-ftp.bu.edu/pub/fuzzy-artmap.tar.Z
(44 kB).

20. PYGMALION
+++++++++++++

This is a prototype that stems from an ESPRIT project. It implements
back-propagation, self organising map, and Hopfield nets. Avaliable for
ftp from ftp.funet.fi [128.214.248.6] as
/pub/sci/neural/sims/pygmalion.tar.Z (1534 kb). (Original site is
imag.imag.fr: archive/pygmalion/pygmalion.tar.Z).

21. Basis-of-AI-NN Software
+++++++++++++++++++++++++++

Non-GUI DOS and UNIX source code, DOS binaries and examples are available
in the following different program sets and the backprop package has a
Windows 3.x binary and a Unix/Tcl/Tk version:

[backprop, quickprop, delta-bar-delta, recurrent networks],
[simple clustering, k-nearest neighbor, LVQ1, DSM],
[Hopfield, Boltzman, interactive activation network],
[interactive activation network],
[feedforward counterpropagation],
[ART I],
[a simple BAM] and
[the linear pattern classifier]

For details see: http://www.dontveter.com/nnsoft/nnsoft.html

An improved professional version of backprop is also available; see Part
6 of the FAQ.

Questions to: Don Tveter, d...@dontveter.com

22. Matrix Backpropagation
++++++++++++++++++++++++++

MBP (Matrix Back Propagation) is a very efficient implementation of the
back-propagation algorithm for current-generation workstations. The
algorithm includes a per-epoch adaptive technique for gradient descent.
All the computations are done through matrix multiplications and make use
of highly optimized C code. The goal is to reach almost peak-performances
on RISCs with superscalar capabilities and fast caches. On some machines
(and with large networks) a 30-40x speed-up can be measured with respect
to conventional implementations. The software is available by anonymous
ftp from ftp.esng.dibe.unige.it as /neural/MBP/MBPv1.1.tar.Z (Unix
version), or /neural/MBP/MBPv11.zip (PC version)., For more information,
contact Davide Anguita (ang...@dibe.unige.it).

23. BIOSIM
++++++++++

BIOSIM is a biologically oriented neural network simulator. Public
domain, runs on Unix (less powerful PC-version is available, too), easy
to install, bilingual (german and english), has a GUI (Graphical User
Interface), designed for research and teaching, provides online help
facilities, offers controlling interfaces, batch version is available, a
DEMO is provided.

REQUIREMENTS (Unix version): X11 Rel. 3 and above, Motif Rel 1.0 and
above, 12 MB of physical memory, recommended are 24 MB and more, 20 MB
disc space. REQUIREMENTS (PC version): PC-compatible with MS Windows 3.0
and above, 4 MB of physical memory, recommended are 8 MB and more, 1 MB
disc space.

Four neuron models are implemented in BIOSIM: a simple model only
switching ion channels on and off, the original Hodgkin-Huxley model, the
SWIM model (a modified HH model) and the Golowasch-Buchholz model.
Dendrites consist of a chain of segments without bifurcation. A neural
network can be created by using the interactive network editor which is
part of BIOSIM. Parameters can be changed via context sensitive menus and
the results of the simulation can be visualized in observation windows
for neurons and synapses. Stochastic processes such as noise can be
included. In addition, biologically orientied learning and forgetting
processes are modeled, e.g. sensitization, habituation, conditioning,
hebbian learning and competitive learning. Three synaptic types are
predefined (an excitatatory synapse type, an inhibitory synapse type and
an electrical synapse). Additional synaptic types can be created
interactively as desired.

Available for ftp from ftp.uni-kl.de in directory /pub/bio/neurobio: Get
/pub/bio/neurobio/biosim.readme (2 kb) and /pub/bio/neurobio/biosim.tar.Z
(2.6 MB) for the Unix version or /pub/bio/neurobio/biosimpc.readme (2 kb)
and /pub/bio/neurobio/biosimpc.zip (150 kb) for the PC version.

Contact:
Stefan Bergdoll
Department of Software Engineering (ZXA/US)
BASF Inc.
D-67056 Ludwigshafen; Germany
berg...@zxa.basf-ag.de phone 0621-60-21372 fax 0621-60-43735

24. FuNeGen 1.0
+++++++++++++++

FuNeGen is a MLP based software program to generate fuzzy rule based
classifiers. For more information, see
http://www-2.cs.cmu.edu/afs/cs.cmu.edu/project/ai-repository/ai/areas/fuzzy/systems/funegen/

25. NeuDL -- Neural-Network Description Language
++++++++++++++++++++++++++++++++++++++++++++++++

NeuDL is a description language for the design, training, and operation
of neural networks. It is currently limited to the backpropagation
neural-network model; however, it offers a great deal of flexibility. For
example, the user can explicitly specify the connections between nodes
and can create or destroy connections dynamically as training progresses.
NeuDL is an interpreted language resembling C or C++. It also has
instructions dealing with training/testing set manipulation as well as
neural network operation. A NeuDL program can be run in interpreted mode
or it can be automatically translated into C++ which can be compiled and
then executed. The NeuDL interpreter is written in C++ and can be easly
extended with new instructions. For more information, see
http://www-2.cs.cmu.edu/afs/cs/project/ai-repository/ai/areas/neural/systems/neudl/0.html

26. NeoC Explorer (Pattern Maker included)
++++++++++++++++++++++++++++++++++++++++++

The NeoC software is an implementation of Fukushima's Neocognitron neural
network. Its purpose is to test the model and to facilitate interactivity
for the experiments. Some substantial features: GUI, explorer and tester
operation modes, recognition statistics, performance analysis, elements
displaying, easy net construction. PLUS, a pattern maker utility for
testing ANN: GUI, text file output, transformations. For more
information, see http://www.simtel.net/pub/pd/39893.html

27. AINET
+++++++++

AINET is a probabilistic neural network application which runs on Windows
95/NT. It was designed specifically to facilitate the modeling task in
all neural network problems. It is lightning fast and can be used in
conjunction with many different programming languages. It does not
require iterative learning, has no limits in variables (input and output
neurons), no limits in sample size. It is not sensitive toward noise in
the data. The database can be changed dynamically. It provides a way to
estimate the rate of error in your prediction. It has a graphical
spreadsheet-like user interface. The AINET manual (more than 100 pages)
is divided into: "User's Guide", "Basics About Modeling with the AINET",
"Examples", "The AINET DLL library" and "Appendix" where the theoretical
background is revealed. You can get a full working copy from:
http://www.ainet-sp.si/

28. DemoGNG
+++++++++++

This simulator is written in Java and should therefore run without
compilation on all platforms where a Java interpreter (or a browser with
Java support) is available. It implements the following algorithms and
neural network models:
o Hard Competitive Learning (standard algorithm)
o Neural Gas (Martinetz and Schulten 1991)
o Competitive Hebbian Learning (Martinetz and Schulten 1991, Martinetz
1993)
o Neural Gas with Competitive Hebbian Learning (Martinetz and Schulten
1991)
o Growing Neural Gas (Fritzke 1995)
DemoGNG is distributed under the GNU General Public License. It allows to
experiment with the different methods using various probability
distributions. All model parameters can be set interactively on the
graphical user interface. A teach modus is provided to observe the models
in "slow-motion" if so desired. It is currently not possible to
experiment with user-provided data, so the simulator is useful basically
for demonstration and teaching purposes and as a sample implementation of
the above algorithms.

DemoGNG can be accessed most easily at
http://www.neuroinformatik.ruhr-uni-bochum.de/ in the file
/ini/VDM/research/gsn/DemoGNG/GNG.html where it is embedded as Java
applet into a Web page and is downloaded for immediate execution when you
visit this page. An accompanying paper entitled "Some competitive
learning methods" describes the implemented models in detail and is
available in html at the same server in the directory
ini/VDM/research/gsn/JavaPaper/.

It is also possible to download the complete source code and a Postscript
version of the paper via anonymous ftp from
ftp.neuroinformatik.ruhr-uni-bochum [134.147.176.16] in directory
/pub/software/NN/DemoGNG/. The software is in the file
DemoGNG-1.00.tar.gz (193 KB) and the paper in the file sclm.ps.gz (89
KB). There is also a README file (9 KB). Please send any comments and
questions to dem...@neuroinformatik.ruhr-uni-bochum.de which will reach
Hartmut Loos who has written DemoGNG as well as Bernd Fritzke, the author
of the accompanying paper.

29. Trajan 2.1 Shareware
++++++++++++++++++++++++

Trajan 2.1 Shareware is a Windows-based Neural Network simulation
package. It includes support for the two most popular forms of Neural
Network: Multilayer Perceptrons with Back Propagation and Kohonen
networks.

Trajan 2.1 Shareware concentrates on ease-of-use and feedback. It
includes Graphs, Bar Charts and Data Sheets presenting a range of
Statistical feedback in a simple, intuitive form. It also features
extensive on-line Help.

The Registered version of the package can support very large networks (up
to 128 layers with up to 8,192 units each, subject to memory limitations
in the machine), and allows simple Cut and Paste transfer of data to/from
other Windows-packages, such as spreadsheet programs. The Unregistered
version features limited network size and no Clipboard Cut-and-Paste.

There is also a Professional version of Trajan 2.1, which supports a
wider range of network models, training algorithms and other features.

See Trajan Software's Home Page at http://www.trajan-software.demon.co.uk
for further details, and a free copy of the Shareware version.

Alternatively, email and...@trajan-software.demon.co.uk for more details.

30. Neural Networks at your Fingertips
++++++++++++++++++++++++++++++++++++++

"Neural Networks at your Fingertips" is a package of ready-to-reuse
neural network simulation source code which was prepared for educational
purposes by Karsten Kutza. The package consists of eight programs, each
of which implements a particular network architecture together with an
embedded example application from a typical application domain.
Supported network architectures are
o Adaline,
o Backpropagation,
o Hopfield Model,
o Bidirectional Associative Memory,
o Boltzmann Machine,
o Counterpropagation,
o Self-Organizing Map, and
o Adaptive Resonance Theory.
The applications demonstrate use of the networks in various domains such
as pattern recognition, time-series forecasting, associative memory,
optimization, vision, and control and include e.g. a sunspot prediction,
the traveling salesman problem, and a pole balancer.
The programs are coded in portable, self-contained ANSI C and can be
obtained from the web pages at
http://www.geocities.com/CapeCanaveral/1624.

31. NNFit
+++++++++

NNFit (Neural Network data Fitting) is a user-friendly software that
allows the development of empirical correlations between input and output
data. Multilayered neural models have been implemented using a
quasi-newton method as learning algorithm. Early stopping method is
available and various tables and figures are provided to evaluate fitting
performances of the neural models. The software is available for most of
the Unix platforms with X-Windows (IBM-AIX, HP-UX, SUN, SGI, DEC, Linux).
Informations, manual and executable codes (english and french versions)
are available at http://www.gch.ulaval.ca/~nnfit
Contact: Bernard P.A. Grandjean, department of chemical engineering,
Laval University; Sainte-Foy (Quibec) Canada G1K 7P4;
gran...@gch.ulaval.ca

32. Nenet v1.0
++++++++++++++

Nenet v1.0 is a 32-bit Windows 95 and Windows NT 4.0 application designed
to facilitate the use of a Self-Organizing Map (SOM) algorithm.

The major motivation for Nenet was to create a user-friendly SOM
algorithm tool with good visualization capabilities and with a GUI
allowing efficient control of the SOM parameters. The use scenarios have
stemmed from the user's point of view and a considerable amount of work
has been placed on the ease of use and versatile visualization methods.

With Nenet, all the basic steps in map control can be performed. In
addition, Nenet also includes some more exotic and involved features
especially in the area of visualization.

Features in Nenet version 1.0:
o Implements the standard Kohonen SOM algorithm
o Supports 2 common data preprocessing methods
o 5 different visualization methods with rectangular or hexagonal
topology
o Capability to animate both train and test sequences in all
visualization methods
o Labelling
o Both neurons and parameter levels can be labelled
o Provides also autolabelling
o Neuron values can be inspected easily
o Arbitrary selection of parameter levels can be visualized with Umatrix
simultaneously
o Multiple views can be opened on the same map data
o Maps can be printed
o Extensive help system provides fast and accurate online help
o SOM_PAK compatible file formats
o Easy to install and uninstall
o Conforms to the common Windows 95 application style - all
functionality in one application

Nenet web site is at:
http://www.mbnet.fi/~phodju/nenet/Nenet/General.html The web site
contains further information on Nenet and also the downloadable Nenet
files (3 disks totalling about 3 Megs)

If you have any questions whatsoever, please contact: Nenet...@hut.fi
or phas...@cc.hut.fi

33. Machine Consciousness Toolbox
+++++++++++++++++++++++++++++++++

See listing for Machine Consciousness Toolbox in part 6 of the FAQ.

34. NICO Toolkit (speech recognition)
+++++++++++++++++++++++++++++++++++++

Name: NICO Artificial Neural Network Toolkit
Author: Nikko Strom
Address: Speech, Music and Hearing, KTH, S-100 44, Stockholm, Sweden
Email: ni...@speech.kth.se
URL: http://www.speech.kth.se/NICO/index.html
Platforms: UNIX, ANSI C; Source code tested on: HPUX, SUN Solaris, Linux
Price: Free

The NICO Toolkit is an artificial neural network toolkit designed and
optimized for automatic speech recognition applications. Networks with
both recurrent connections and time-delay windows are easily constructed.
The network topology is very flexible -- any number of layers is allowed
and layers can be arbitrarily connected. Sparse connectivity between
layers can be specified. Tools for extracting input-features from the
speech signal are included as well as tools for computing target values
from several standard phonetic label-file formats.

Algorithms:
o Back-propagation through time,
o Speech feature extraction (Mel cepstrum coefficients, filter-bank)

35. SOM Toolbox for Matlab 5
++++++++++++++++++++++++++++

SOM Toolbox, a shareware Matlab 5 toolbox for data analysis with
self-organizing maps is available at the URL
http://www.cis.hut.fi/projects/somtoolbox/. If you are interested in
practical data analysis and/or self-organizing maps and have Matlab 5 in
your computer, be sure to check this out!

Highlights of the SOM Toolbox include the following:
o Tools for all the stages of data analysis: besides the basic SOM
training and visualization tools, the package includes also tools for
data preprocessing and model validation and interpretation.
o Graphical user interface (GUI): the GUI first guides the user through
the initialization and training procedures, and then offers a variety
of different methods to visualize the data on the trained map.
o Modular programming style: the Toolbox code utilizes Matlab
structures, and the functions are constructed in a modular manner,
which makes it convenient to tailor the code for each user's specific
needs.
o Advanced graphics: building on the Matlab's strong graphics
capabilities, attractive figures can be easily produced.
o Compatibility with SOM_PAK: import/export functions for SOM_PAK
codebook and data files are included in the package.
o Component weights and names: the input vector components may be given
different weights according to their relative importance, and the
components can be given names to make the figures easier to read.
o Batch or sequential training: in data analysis applications, the speed
of training may be considerably improved by using the batch version.
o Map dimension: maps may be N-dimensional (but visualization is not
supported when N > 2 ).

36. FastICA package for MATLAB
++++++++++++++++++++++++++++++

The FastICA algorithm for independent component analysis.

Independent component analysis, or ICA, is neural network or signal
processing technique that represents a multidimensional random vector as
a linear combination of nongaussian random variables ('independent
components') that are as independent as possible. ICA is a nongaussian
version of factor analysis, and somewhat similar to principal component
analysis. ICA has many applications in data analysis, source separation,
and feature extraction.

The FastICA algorithm is a computationally optimized method for
performing the estimation of ICA. It uses a fixed-point iteration scheme
that has been found in independent experiments to be 10-100 times faster
than conventional gradient descent methods for ICA. Another advantage of
the FastICA algorithm is that it can be used to estimate the independent
components one-by-one, as in projection pursuit, which is very practical
in exploratory data analysis.

The FastICA package for MATLAB (versions 5 or 4) is freeware package with
a graphical user interface that implements the fixed-point algorithm for
ICA. The package is available on the Web at
http://www.cis.hut.fi/projects/ica/fastica/.
Email contact: Aapo Hyvarinen <Aapo.Hy...@hut.fi>

37. NEXUS: Large-scale biological simulations
+++++++++++++++++++++++++++++++++++++++++++++

Large-scale biological neural network simulation engine. Includes
automated network construction tool that allows extremely complex
networks to be generated according to user-supplied architectural
specifications.

The network engine is an attempt at creating a biological neural network
simulator. It consists of a C++ class, called "network". A network object
houses a set of objects of another C++ class, called "neuron". The neuron
class is a detailed functional simulation of a neuron (i.e. the actual
chemical processes that lead to a biological neuron's behavior are not
modeled explicitly, but the behavior itself is). The simulation of the
neuron is handled entirely by the neuron class. The network class
coordinates the functioning of the neurons that make up the neural
network, as well as providing addressing services that allow the neurons
to interact. It is also responsible for facilitating the interface of the
neural network it houses onto any existing software into which the neural
network is to be integrated.

Since a simulated neural network consisting of a large number of heavily
interconnected neurons is extremely difficult to generate manually, NEXUS
was developed. To create a network with NEXUS, one need only describe the
network in general terms, in terms of groups of sets of specifically
arranged neurons, and how the groups interface onto each other and onto
themselves. This information constitutes a network architecture
descriptor. A network architecture descriptor is read by NEXUS, and NEXUS
uses the information to generate a network, building all the neurons and
connecting them together appropriately. This system is analogous to
nature's brain construction system. For example, human brains, in
general, are very similar. The basic design is stored in human DNA. Since
it is certainly not possible to record information about each neuron and
its connections, DNA must instead contain (in some form) what is
essentially a set of guidelines, a set of rules about how the brain is to
be laid out. These guidelines are used to build the brain, just like
NEXUS uses the guidelines set out in the network architecture descriptor
to build the simulated neural network.

NEXUS and the network engine have deliberately been engineered to be
highly efficient and very compact. Even so, large, complex networks
require tremendous amounts of memory and processing power.

The network engine:
o flexible and elegant design; highly customizable simulation
parameters; extremely efficient
o throughout, nonlinear magnitude decay modeling
o dendritic tree complexity and network connection density limited only
by the computer hardware
o simulation of dendritic logic gate behaviors via a sophisticated
excitation thresholding and conduction model
o detailed simulation of backprop, allowing realistic simulation of
associated memory formation processes
o simulation of all known postsynaptic memory formation mechanisms (STP,
STD, LTP, LTD)
o dynamic presynaptic output pattern modeling, including excitation
magnitude dependent output pattern selection
o simulation of all known presynaptic activity-based output modifiers
(PPF, PTP, depression)

NEXUS:
o allows networks to be designed concisely and as precisely as is
necessary
o makes massively complex large-scale neural network design and
construction possible
o allows existing networks to be augmented without disturbing existing
network structure
o UNIX and Win32 compatible

URL: http://www.sfu.ca/~loryan/neural.html
Email: Lawrence O. Ryan <lor...@sfu.ca>

38. Netlab: Neural network software for Matlab
++++++++++++++++++++++++++++++++++++++++++++++

http://www.ncrg.aston.ac.uk/netlab/index.html

The Netlab simulation software is designed to provide the central tools
necessary for the simulation of theoretically well founded neural network
algorithms for use in teaching, research and applications development. It
consists of a library of Matlab functions and scripts based on the
approach and techniques described in Neural Networks for Pattern
Recognition by Christopher M. Bishop, (Oxford University Press, 1995).
The functions come with on-line help, and further explanation is
available via HTML files.

The Netlab library includes software implementations of a wide range of
data analysis techniques. Netlab works with Matlab version 5.0 and
higher. It is not compatible with earlier versions of Matlab.

39. NuTank
++++++++++

NuTank stands for NeuralTank. It is educational and entertainment
software. In this program one is given the shell of a 2 dimentional
robotic tank. The tank has various I/O devices like wheels, whiskers,
optical sensors, smell, fuel level, sound and such. These I/O sensors are
connected to Neurons. The player/designer uses more Neurons to
interconnect the I/O devices. One can have any level of complexity
desired (memory limited) and do subsumptive designs. More complex design
take slightly more fuel, so life is not free. All movement costs fuel
too. One can also tag neuron connections as "adaptable" that adapt their
weights in acordance with the target neuron. This allows neurons to
learn. The Neuron editor can handle 3 dimention arrays of neurons as
single entities with very flexible interconect patterns.

One can then design a scenario with walls, rocks, lights, fat (fuel)
sources (that can be smelled) and many other such things. Robot tanks are
then introduced into the Scenario and allowed interact or battle it out.
The last one alive wins, or maybe one just watches the motion of the
robots for fun. While the scenario is running it can be stopped, edited,
zoom'd, and can track on any robot.

The entire program is mouse and graphicly based. It uses DOS and VGA and
is written in TurboC++. There will also be the ability to download
designs to another computer and source code will be available for the
core neural simulator. This will allow one to design neural systems and
download them to real robots. The design tools can handle three
dimentional networks so will work with video camera inputs and such.

NuTank source code is free from
http://www.xmission.com/~rkeene/NuTankSrc.ZIP
Contact: Richard Keene; Keene Educational Software
Email: rke...@xmission.com or r.k...@center7.com

40. Lens
++++++++

http://www.cs.cmu.edu/~dr/Lens

Lens (the light, efficient network simulator) is a fast, flexible, and
customizable neural network package written primarily in C. It currently
handles standard backpropagation networks, simple recurrent (including
Jordan and Elman) and fully recurrent nets, deterministic Boltzmann
machines, self-organizing maps, and interactive-activation models.

Lens runs under Windows as well as a variety of Unix platforms. It
includes a graphical interface and an embedded script language (Tcl). The
key to the speed of Lens is its use of tight inner-loops that minimize
memory references when traversing links. Frequently accessed values are
stored in contiguous memory to achieve good cache performance. It is also
able to do batch-level parallel training on multiple processors.

Because it is recognized that no simulator will satisfy sophisticated
users out of the box, Lens was designed to facilitate code modification.
Users can create and register such things as new network or group types,
new weight update algorithms, or new shell commands without altering the
main body of code. Therefore, modifications can be easily transferred to
new releases.

Lens is available free-of-charge to those conducting research at academic
or non-profit institutions. Other users should contact Douglas Rohde for
licensing information at dr+...@cs.cmu.edu.

41. Joone: Java Object Oriented Neural Engine
+++++++++++++++++++++++++++++++++++++++++++++

http://sourceforge.net/projects/joone

Joone is a neural net engine written in Java. It's a modular, scalable,
multitasking and extensible engine. It can be extended by writing new
modules to implement new algorithms or new architectures starting from
simple base components. It's an Open Source project and everybody can
contribute to its development.

Contact: Paolo Marrone, pa...@marrone.org

42. NV: Neural Viewer
+++++++++++++++++++++

http://www.btinternet.com/~cfinnie/

A free software application for modelling and visualizing complex
recurrent neural networks in 3D.

43. EasyNN
++++++++++

URL: http://www.easynn.com/

EasyNN is a neural network system for Microsoft Windows. It can generate
multi layer neural networks from text files or grids with minimal user
intervention. The networks can then be trained, validated and queried.
Network diagrams, graphs, input/output data and all the network details
can be displayed and printed. Nodes can be added or deleted while the
network is learning. The graph, grid, network and detail displays are
updated dynamically so you can see how the neural networks work. EasyNN
runs on Windows 95, 98, ME, NT 4.0, 2000 or XP.

44. Multilayer Perceptron - A Java Implementation
++++++++++++++++++++++++++++++++++++++++++++++++++

Download java from: http://www.geocities.com/aydingurel/neural/

What can you exactly do with it? You can:
o Build nets with any number of layers and units. Layers are connected
to each other consecutively, each unit in a layer is connected to all
of the units on the next layer (and vice versa) if there is one,
o Set units with linear and sigmoid activation functions and set them
separately for each layer,
o Set parameters for sigmoid functions and set them separately for each
layer,
o Use momentum, set different momentum parameters for each layer,
o Initialize the net using your own set of weights,
o Train the net using backpropagation and with any training rate.

Contact: Aydin Gurel, aydin...@lycos.com

------------------------------------------------------------------------

For some of these simulators there are user mailing lists. Get the packages
and look into their documentation for further info.

------------------------------------------------------------------------

Next part is part 6 (of 7). Previous part is part 4.

--

Warren S. Sarle SAS Institute Inc. The opinions expressed here
sas...@unx.sas.com SAS Campus Drive are mine and not necessarily
(919) 677-8000 Cary, NC 27513, USA those of SAS Institute.

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