File: /u/tld/programming/matlab/work/cortex/README

Introduction:

The code in this archive (Cortex Version 2.0.1) has been tested in
Matlab Version 7.1.0.183 (R14) Service Pack 3 and Version 7.0.4 -
(R14) Service Pack 2 - January 29, 2005.  Cortex 2.0.1 also depends on
Kevin Murphy's Bayes Net Toolbox (BNT).  BNT can be downloaded from
http://bnt.sourceforge.net/ or from Murphy's web site at the
University of British Columbia http://www.cs.ubc.ca/~murphyk/Software/
and is well worth looking into if you work with Matlab and graphical
models.  Since the sourceforge BNT project is relatively new and the
developers are still getting coordinated I've included a slightly
modified 2004 version of BNT with this archive. The modifications were
made for compatability with Matlab 7.1 and are detailed in CHANGES.

Directory structure:

   ./cortex/README                    % This README file
            CHANGES                   % Version history for this code
            startup.m                 % Modify to suit root directory
   ./cortex/examples/demo_synth.m     % Experiments with synthetic data
                     demo_mnist.m     % Experiments with MNIST data (1)
                     demo_dmb.m       % Distributed-memory broker 1.0
                     demo_aaai/       % Generative model for AAAI 2005
   ./data/MNIST/readMNIST.m           % MNIST format reader (2)
                *-images.idx3-ubyte   % MNIST training/test images (3)
                *-labels.idx1-ubyte   % MNIST training/test labels (3)
   ./cortex/image_filters/            % Filtered MNIST digit images
   ./output/README                    % Summary of MNIST experiments
            MNIST/*.txt               % Details of MNIST experiments
   ./local/FullBNT/                   % Minor BNT modifications
   ../FullBNT/                        % Version of Murphy's BNT (4)

___________

 1. The 'demo_mnist.m' script uses MNIST data set in ./../data/MNIST/.

 2. Available from Kevin Murphy at http://www.cs.ubc.ca/~murphyk/.

 3. Available from Yann LeCun at http://yann.lecun.com/exdb/mnist/.  
    The files uncompress as, e.g., train-images.idx1-ubytes, instead 
    of, e.g., train-images-idx-ubytes, as one might have expected 
    from the corresponding anchor text on LeCunn's web site.  Note 
    that Kevin Murphy's readMNIST assumes the latter format, so check 
    this and modify readMNIST.m or the data file names as you prefer.

 4. This version of Murphy's code was last updated on 9 June 2004. 
    BNT is distributed under the GNU Library GPL as is the code 
    contained in this archive - see ../FullBNT/BNT/license.gpl.txt.
___________

Installation instructions:

Here is how the Cortex archive was created. 

% cd /u/tld/programming/projects/
% tar -cvf cortex.tar ./cortex/ ./data/MNIST/ ./output/ ./local/ ../FullBNT

Here is one way to decant the archive in csh.

% if ( ! -e projects ) mkdir projects
% cd projects
% tar -xvf cortex.tar
% mv FullBNT ..

Now modify the file-system-specific directories in ./cortex/startup.m, run the
script 'startup' and you should be able to run the demos in ./cortex/examples/.