BNW using Octave instead of Matlab.

This version of BNW should perform the same as the original version. The only difference is that it uses Octave instead of Matlab when running BayesNet Toolbox during parameter learning.

I am calling this BNW_1.02. It can be accessed at:
compbio.uthsc.edu/BNW_1.02

1 files changed, 542 insertions, 0 deletions

diff --git a/sourcecodes/bnt-master/netlab3.3/demprgp.m b/sourcecodes/bnt-master/netlab3.3/demprgp.m
new file mode 100644
index 00000000..3cc7b8f5
--- /dev/null
+++ b/sourcecodes/bnt-master/netlab3.3/demprgp.m
@@ -0,0 +1,542 @@
+function demprgp(action);
+%DEMPRGP Demonstrate sampling from a Gaussian Process prior.
+%
+%	Description
+%	This function plots the functions represented by a Gaussian Process
+%	model. The hyperparameter values can be adjusted  on a linear scale
+%	using the sliders (though the exponential of the parameters is used
+%	in the covariance function), or  by typing values into the text boxes
+%	and pressing the return key. Both types of covariance function are
+%	supported.  An extra function specific parameter is needed for the
+%	rational quadratic function.
+%
+%	See also
+%	GP
+%
+
+%	Copyright (c) Ian T Nabney (1996-2001)
+
+if nargin<1,
+    action='initialize';
+end;
+
+if strcmp(action,'initialize')
+
+  % Bounds on hyperparameter values
+  biasminval = -3.0; biasmaxval = 3.0;
+  noiseminval = -20; noisemaxval = -2;
+  fparminval = 0.0; fparmaxval = 2.0;
+  inwminval = 0; inwmaxval = 8;
+  % Initial hyperparameter values
+  bias = (biasminval+biasmaxval)/2;
+  noise = (noiseminval+noisemaxval)/2;
+  inweights = (inwminval+inwmaxval)/2;
+  fpar = (fparminval+fparmaxval)/2;
+  fpar2 = (fparminval+fparmaxval)/2;
+  
+  gptype = 'sqexp';
+  
+  % Create FIGURE
+  fig=figure( ...
+    'Name','Sampling from a Gaussian Process prior', ...
+    'Position', [50 50 480 380], ...
+    'NumberTitle','off', ...
+    'Color', [0.8 0.8 0.8], ...
+    'Visible','on');
+
+  % List box for covariance function type
+  nettype_box = uicontrol(fig, ...
+    'Style', 'listbox', ...
+    'Units', 'normalized', ...
+    'HorizontalAlignment', 'center', ...
+    'Position', [0.52 0.77 0.40 0.12], ...
+    'String', 'Squared Exponential|Rational Quadratic', ...
+    'Max', 1, 'Min', 0, ... % Only allow one selection
+    'Value', 1, ... % Initial value is squared exponential
+    'BackgroundColor',[0.60 0.60 0.60],...
+    'CallBack', 'demprgp GPtype');
+
+  % Title for list box
+  uicontrol(fig, ...
+    'Style', 'text', ...
+    'Units', 'normalized', ...
+    'Position', [0.52 0.89 0.40 0.05], ...
+    'String', 'Covariance Function Type', ...
+    'BackgroundColor', get(fig, 'Color'), ...
+    'HorizontalAlignment', 'center');
+  
+  % Frames to enclose sliders
+  bottom_row = 0.04;
+  slider_frame_height = 0.15;
+  biasframe = uicontrol(fig, ...
+    'Style', 'frame', ...
+    'Units', 'normalized', ...
+    'BackgroundColor', [0.6 0.6 0.6], ...
+    'String', 'bias', ...
+    'HorizontalAlignment', 'left', ...
+    'Position', [0.05 bottom_row 0.35 slider_frame_height]);
+  
+  bpos = get(biasframe, 'Position');
+  noise_frame_bottom = bpos(2) + bpos(4) + 0.02;
+  noiseframe = uicontrol(fig, ...
+    'Style', 'frame', ...
+    'Units', 'normalized', ...
+    'BackgroundColor', [0.6 0.6 0.6], ...
+    'Position', [0.05 noise_frame_bottom 0.35 slider_frame_height]);
+   
+  npos = get(noiseframe, 'Position');
+  inw_frame_bottom = npos(2) + npos(4) + 0.02;
+  inwframe = uicontrol(fig, ...
+    'Style', 'frame', ...
+    'Units', 'normalized', ...
+    'BackgroundColor', [0.6 0.6 0.6], ...
+    'Position', [0.05 inw_frame_bottom 0.35 slider_frame_height]);
+   
+  inwpos = get(inwframe, 'Position');
+  fpar_frame_bottom = inwpos(2) + inwpos(4) + 0.02;
+  % This frame sometimes has multiple parameters
+  uicontrol(fig, ...
+    'Style', 'frame', ...
+    'Units', 'normalized', ...
+    'BackgroundColor', [0.6 0.6 0.6], ...
+    'Position', [0.05 fpar_frame_bottom 0.35 2*slider_frame_height]);
+   
+  % Frame text
+  slider_text_height = 0.05;
+  slider_text_voffset = 0.08;
+  uicontrol(fig, ...
+    'Style', 'text', ...
+    'Units', 'normalized', ...
+    'HorizontalAlignment', 'left', ...
+    'BackgroundColor', [0.6 0.6 0.6], ...
+    'Position', [0.07 bottom_row+slider_text_voffset ...
+      0.06 slider_text_height], ...
+    'String', 'bias');
+
+  % Frame text
+  noiseframe = uicontrol(fig, ...
+    'Style', 'text', ...
+    'Units', 'normalized', ...
+    'HorizontalAlignment', 'left', ...
+    'BackgroundColor', [0.6 0.6 0.6], ...
+    'Position', [0.07 noise_frame_bottom+slider_text_voffset ...
+      0.08 slider_text_height], ...
+    'String', 'noise');
+
+  % Frame text
+  uicontrol(fig, ...
+    'Style', 'text', ...
+    'Units', 'normalized', ...
+    'HorizontalAlignment', 'left', ...
+    'BackgroundColor', [0.6 0.6 0.6], ...
+    'Position', [0.07 inw_frame_bottom+slider_text_voffset ...
+      0.14 slider_text_height], ...
+    'String', 'inweights');
+
+  % Frame text
+  uicontrol(fig, ...
+    'Style', 'text', ...
+    'Units', 'normalized', ...
+    'HorizontalAlignment', 'left', ...
+    'BackgroundColor', [0.6 0.6 0.6], ...
+    'Position', [0.07 fpar_frame_bottom+slider_frame_height+ ...
+       slider_text_voffset 0.06 slider_text_height], ...
+    'String', 'fpar');
+
+ uicontrol(fig, ...
+    'Style', 'text', ...
+    'Units', 'normalized', ...
+    'HorizontalAlignment', 'left', ...
+    'BackgroundColor', [0.6 0.6 0.6], ...
+    'Position', [0.07 fpar_frame_bottom+slider_text_voffset ...
+       0.06 slider_text_height], ...
+    'String', 'fpar2', ...
+    'Tag', 'fpar2text', ...
+    'Enable', 'off');
+   
+  % Slider
+  slider_left = 0.07;
+  slider_width = 0.31;
+  slider_frame_voffset = 0.02;
+  biasslide = uicontrol(fig, ...
+    'Style', 'slider', ...
+    'Units', 'normalized', ...
+    'Value', bias, ...
+    'BackgroundColor', [0.8 0.8 0.8], ...
+    'Position', [slider_left bottom_row+slider_frame_voffset ...
+      slider_width 0.05], ...
+    'Min', biasminval, 'Max', biasmaxval, ...
+    'Callback', 'demprgp update');
+  
+  % Slider
+  noiseslide = uicontrol(fig, ...
+    'Style', 'slider', ...
+    'Units', 'normalized', ...
+    'Value', noise, ...
+    'BackgroundColor', [0.8 0.8 0.8], ...
+    'Position', [slider_left noise_frame_bottom+slider_frame_voffset ...
+      slider_width 0.05], ...
+    'Min', noiseminval, 'Max', noisemaxval, ...
+    'Callback', 'demprgp update');
+  
+  % Slider
+  inweightsslide = uicontrol(fig, ...
+    'Style', 'slider', ...
+    'Units', 'normalized', ...
+    'Value', inweights, ...
+    'BackgroundColor', [0.8 0.8 0.8], ...
+    'Position', [slider_left inw_frame_bottom+slider_frame_voffset ...
+      slider_width 0.05], ...
+    'Min', inwminval, 'Max', inwmaxval, ...
+    'Callback', 'demprgp update');
+  
+  % Slider
+  fparslide = uicontrol(fig, ...
+    'Style', 'slider', ...
+    'Units', 'normalized', ...
+    'Value', fpar, ...
+    'BackgroundColor', [0.8 0.8 0.8], ...
+    'Position', [slider_left fpar_frame_bottom+slider_frame_height+ ...
+       slider_frame_voffset slider_width 0.05], ...
+    'Min', fparminval, 'Max', fparmaxval, ...
+    'Callback', 'demprgp update');
+ 
+ fpar2slide = uicontrol(fig, ...
+    'Style', 'slider', ...
+    'Units', 'normalized', ...
+    'Value', fpar2, ...
+    'BackgroundColor', [0.8 0.8 0.8], ...
+    'Position', [slider_left fpar_frame_bottom+slider_frame_voffset ...
+       slider_width 0.05], ...
+    'Min', fparminval, 'Max', fparmaxval, ...
+    'Callback', 'demprgp update', ...
+    'Tag', 'fpar2slider', ...
+    'Enable', 'off');
+  
+  % Text display of hyper-parameter values
+  
+  format = '%8f';
+
+  hp_left = 0.20;
+  hp_width = 0.17;
+  biasval = uicontrol(fig, ...
+    'Style', 'edit', ...
+    'Units', 'normalized', ...
+    'Position', [hp_left bottom_row+slider_text_voffset ...
+      hp_width slider_text_height], ...
+    'String', sprintf(format, bias), ...
+    'Callback', 'demprgp newval');
+  
+  noiseval = uicontrol(fig, ...
+    'Style', 'edit', ...
+    'Units', 'normalized', ...
+    'Position', [hp_left noise_frame_bottom+slider_text_voffset ...
+      hp_width slider_text_height], ...
+    'String', sprintf(format, noise), ...
+    'Callback', 'demprgp newval');
+  
+  inweightsval = uicontrol(fig, ...
+    'Style', 'edit', ...
+    'Units', 'normalized', ...
+    'Position', [hp_left inw_frame_bottom+slider_text_voffset ...
+      hp_width slider_text_height], ...
+    'String', sprintf(format, inweights), ...
+    'Callback', 'demprgp newval');
+  
+  fparval = uicontrol(fig, ...
+    'Style', 'edit', ...
+    'Units', 'normalized', ...
+    'Position', [hp_left fpar_frame_bottom+slider_frame_height+ ...
+       slider_text_voffset hp_width slider_text_height], ...
+    'String', sprintf(format, fpar), ...
+    'Callback', 'demprgp newval');
+ 
+  fpar2val = uicontrol(fig, ...
+    'Style', 'edit', ...
+    'Units', 'normalized', ...
+    'Position', [hp_left fpar_frame_bottom+slider_text_voffset ...
+       hp_width slider_text_height], ...
+    'String', sprintf(format, fpar), ...
+    'Callback', 'demprgp newval', ...
+    'Enable', 'off', ...
+    'Tag', 'fpar2val');
+   
+  
+  % The graph box
+  haxes = axes('Position', [0.5 0.28 0.45 0.45], ...
+    'Units', 'normalized', ...
+    'Visible', 'on');
+
+  % The SAMPLE button
+  uicontrol(fig, ...
+    'Style','push', ...
+    'Units','normalized', ...
+    'BackgroundColor', [0.6 0.6 0.6], ...
+    'Position',[0.5 bottom_row 0.13 0.1], ...
+    'String','Sample', ...
+    'Callback','demprgp replot');
+  
+  % The CLOSE button
+  uicontrol(fig, ...
+    'Style','push', ...
+    'Units','normalized', ...
+    'BackgroundColor', [0.6 0.6 0.6], ...
+    'Position',[0.82 bottom_row 0.13 0.1], ...
+    'String','Close', ...
+    'Callback','close(gcf)');
+  
+  % The HELP button
+  uicontrol(fig, ...
+    'Style','push', ...
+    'Units','normalized', ...
+    'BackgroundColor', [0.6 0.6 0.6], ...
+    'Position',[0.66 bottom_row 0.13 0.1], ...
+    'String','Help', ...
+    'Callback','demprgp help');
+  
+   % Save handles to objects
+  
+   hndlList=[fig biasslide noiseslide inweightsslide fparslide ...
+         biasval noiseval inweightsval ...
+      fparval haxes nettype_box];
+  set(fig, 'UserData', hndlList);
+  
+  demprgp('replot')
+  
+  
+elseif strcmp(action, 'update'),
+  
+  % Update when a slider is moved.
+  
+  hndlList   = get(gcf, 'UserData');
+  biasslide   = hndlList(2);
+  noiseslide = hndlList(3);
+  inweightsslide  = hndlList(4);
+  fparslide = hndlList(5);
+  biasval = hndlList(6);
+  noiseval = hndlList(7);
+  inweightsval = hndlList(8);
+  fparval = hndlList(9);
+  haxes = hndlList(10);
+  nettype_box = hndlList(11);
+
+  
+  bias = get(biasslide, 'Value');
+  noise = get(noiseslide, 'Value');
+  inweights = get(inweightsslide, 'Value');
+  fpar = get(fparslide, 'Value');
+  fpar2 = get(findobj('Tag', 'fpar2slider'), 'Value');
+    
+  format = '%8f';
+  set(biasval, 'String', sprintf(format, bias));
+  set(noiseval, 'String', sprintf(format, noise));
+  set(inweightsval, 'String', sprintf(format, inweights));
+  set(fparval, 'String', sprintf(format, fpar));
+  set(findobj('Tag', 'fpar2val'), 'String', ...
+     sprintf(format, fpar2));
+  
+  demprgp('replot');
+  
+elseif strcmp(action, 'newval'),
+  
+  % Update when text is changed.
+  
+  hndlList   = get(gcf, 'UserData');
+  biasslide   = hndlList(2);
+  noiseslide = hndlList(3);
+  inweightsslide  = hndlList(4);
+  fparslide = hndlList(5);
+  biasval = hndlList(6);
+  noiseval = hndlList(7);
+  inweightsval = hndlList(8);
+  fparval = hndlList(9);
+  haxes = hndlList(10);
+    
+  bias = sscanf(get(biasval, 'String'), '%f');
+  noise = sscanf(get(noiseval, 'String'), '%f');
+  inweights = sscanf(get(inweightsval, 'String'), '%f');
+  fpar = sscanf(get(fparval, 'String'), '%f');
+  fpar2 = sscanf(get(findobj('Tag', 'fpar2val'), 'String'), '%f');
+  
+  set(biasslide, 'Value', bias);
+  set(noiseslide, 'Value', noise);
+  set(inweightsslide, 'Value', inweights);
+  set(fparslide, 'Value', fpar);
+  set(findobj('Tag', 'fpar2slider'), 'Value', fpar2);
+  
+  demprgp('replot');
+  
+elseif strcmp(action, 'GPtype')
+  hndlList   = get(gcf, 'UserData');
+  nettype_box = hndlList(11);
+  gptval = get(nettype_box, 'Value');
+  if gptval == 1
+     % Squared exponential, so turn off fpar2
+     set(findobj('Tag', 'fpar2text'), 'Enable', 'off');
+     set(findobj('Tag', 'fpar2slider'), 'Enable', 'off');
+     set(findobj('Tag', 'fpar2val'), 'Enable', 'off');
+  else
+     % Rational quadratic, so turn on fpar2
+     set(findobj('Tag', 'fpar2text'), 'Enable', 'on');
+     set(findobj('Tag', 'fpar2slider'), 'Enable', 'on');
+     set(findobj('Tag', 'fpar2val'), 'Enable', 'on');
+  end
+  demprgp('replot');
+  
+elseif strcmp(action, 'replot'),
+  
+  % Re-sample from the prior and plot graphs.
+ 
+  oldFigNumber=watchon;
+
+  hndlList   = get(gcf, 'UserData');
+  biasslide   = hndlList(2);
+  noiseslide = hndlList(3);
+  inweightsslide  = hndlList(4);
+  fparslide = hndlList(5);
+  haxes = hndlList(10);
+  nettype_box = hndlList(11);
+  gptval = get(nettype_box, 'Value');
+  if gptval == 1
+    gptype = 'sqexp';
+  else
+    gptype = 'ratquad';
+  end
+  
+  bias = get(biasslide, 'Value');
+  noise = get(noiseslide, 'Value');
+  inweights = get(inweightsslide, 'Value');
+  fpar = get(fparslide, 'Value');
+  
+ 
+  axes(haxes);
+  cla
+  set(gca, ...
+    'Box', 'on', ...
+    'Color', [0 0 0], ...
+    'XColor', [0 0 0], ...
+    'YColor', [0 0 0], ...
+    'FontSize', 14);
+  ymin = -10;
+  ymax = 10;
+  axis([-1 1 ymin ymax]);  
+  set(gca,'DefaultLineLineWidth', 2);
+
+  xvals = (-1:0.01:1)';
+  nsample = 10;    % Number of samples from prior.
+  hold on
+  plot([-1 0; 1 0], [0 ymin; 0 ymax], 'b--');
+  net = gp(1, gptype);
+  net.bias = bias;
+  net.noise = noise;
+  net.inweights = inweights;
+  if strcmp(gptype, 'sqexp')
+    net.fpar = fpar;
+  else
+    fpar2 = get(findobj('Tag', 'fpar2slider'), 'Value');
+    net.fpar = [fpar fpar2];
+  end
+  cn = gpcovar(net, xvals);
+  cninv = inv(cn);
+  cnchol = chol(cn);
+  set(gca, 'DefaultLineLineWidth', 1);
+  for n = 1:nsample
+    y = (cnchol') * randn(size(xvals));
+    plot(xvals, y, 'y');
+  end
+ 
+  watchoff(oldFigNumber);
+ 
+elseif strcmp(action, 'help'),
+  
+  % Provide help to user.
+
+  oldFigNumber=watchon;
+
+  helpfig = figure('Position', [100 100 480 400], ...
+    'Name', 'Help', ...
+    'NumberTitle', 'off', ...
+    'Color', [0.8 0.8 0.8], ...
+    'Visible','on');
+  
+    % The HELP TITLE BAR frame
+  uicontrol(helpfig,  ...
+    'Style','frame', ...
+    'Units','normalized', ...
+    'HorizontalAlignment', 'center', ...
+    'Position', [0.05 0.82 0.9 0.1], ...
+    'BackgroundColor',[0.60 0.60 0.60]);
+  
+  % The HELP TITLE BAR text
+  uicontrol(helpfig, ...
+    'Style', 'text', ...
+    'Units', 'normalized', ...
+    'BackgroundColor', [0.6 0.6 0.6], ...
+    'Position', [0.26 0.85 0.6 0.05], ...
+    'HorizontalAlignment', 'left', ...
+    'String', 'Help: Sampling from a Gaussian Process Prior');
+  
+  helpstr1 = strcat(...
+    'This demonstration shows the effects of sampling from a Gaussian', ...
+     ' process prior. The parameters bias, noise, inweights and fpar', ...
+     ' control the corresponding terms in the covariance function of the',...
+     ' Gaussian process. Their values can be adjusted on a linear scale',...
+     ' using the sliders, or by typing values into the text boxes and',...
+     ' pressing the return key.  After setting these values, press the',...
+     ' ''Sample'' button to see a new sample from the prior.');
+
+   helpstr2 = strcat(...
+      'Observe how inweights controls horizontal length-scale of the',...
+       ' variation in the functions, noise controls the roughness of the',...
+       ' functions, and the bias controls the size of the', ...
+       ' vertical offset of the signal.');
+   helpstr3 = strcat(...
+       'There are two types of covariance function supported by', ...
+       ' Netlab which can be selected using the ''Covariance Function', ...
+       ' Type'' menu.');
+   helpstr4 = strcat(...
+       'The squared exponential has a single fpar which', ...
+       ' controls the vertical scale of the process.');
+   helpstr5 = strcat(...
+      'The rational quadratic has two fpar values.  The first is', ...
+      ' is a scale parameter inside the rational function like the',...
+      ' first fpar for the squared exponential covariance, while the', ...
+      ' second gives the exponent of the rational function (i.e. the',...
+      ' rate of decay of the covariance function.');
+   % Set up cell array with help strings
+   hstr(1) = {helpstr1};
+   hstr(2) = {''};
+   hstr(3) = {helpstr2};
+   hstr(4) = {''};
+   hstr(5) = {helpstr3};
+   hstr(6) = {''};
+   hstr(7) = {helpstr4};
+   hstr(8) = {''};
+   hstr(9) = {helpstr5};
+
+  % The HELP text
+  helpui = uicontrol(helpfig, ...
+    'Style', 'Text', ...
+    'Units', 'normalized', ...
+    'ForegroundColor', [0 0 0], ...
+    'HorizontalAlignment', 'left', ...
+    'BackgroundColor', [1 1 1], ...
+    'Min', 0, ...
+    'Max', 2, ...
+    'Position', [0.05 0.2 0.9 0.57]);
+  [hstrw, newpos] = textwrap(helpui, hstr);
+  set(helpui, 'String', hstrw, 'Position', [0.05, 0.2, 0.9 newpos(4)]);
+	     
+  % The CLOSE button
+  uicontrol(helpfig, ...
+    'Style','push', ...
+    'Units','normalized', ...
+    'BackgroundColor', [0.6 0.6 0.6], ...
+    'Position',[0.4 0.05 0.2 0.1], ...
+    'String','Close', ...
+    'Callback','close(gcf)');
+
+   watchoff(oldFigNumber);
+
+end;
+