New App, Simulink Models, Runge-Kutta simulation method for TSP and GQKP, improved documentation, new examples, minor bugs and enhancements

Bug fixing:
#35 Checkpoint fails when using divide-conquer simulation method

Enhancements:
#10 Enable phase visualization in Divide-and-Conquer
#28 Create Hopfield Network for Simulink
#50 Update Hopfield Net TSP solver App
#51 Runge-Kutta simulation method
#52 energyplot function for HopfieldNetworkGQKP
#53 Improve documentation
#54 New examples for 2-opt, simulink models and GQKP

Tasks:
#23 TSPLIB help page not linked in User's Guide

Author: mathinking

Hopfield Net TSP solver.prj

@@ -5,20 +5,23 @@
     <param.email>lucasgarciarodriguez@ucm.es</param.email>
     <param.company>mathinking.github.com</param.company>
     <param.summary>A Hopfield Network Toolbox for MATLAB</param.summary>
-    <param.description>The Hopfield Network Toolbox can solve combinatorial optimization problems by using Hopfield Neural Networks. The Hopfield Network Toolbox is focused in Continuous Hopfield Networks.</param.description>
+    <param.description>The Hopfield Network Toolbox can solve combinatorial optimization problems by using Hopfield Neural Networks. The Hopfield Network Toolbox is mainly focused in Continuous Hopfield Networks.</param.description>
     <param.screenshot>${PROJECT_ROOT}\help\html\hopfieldnet.png</param.screenshot>
-    <param.version>1.1.2</param.version>
+    <param.version>2.0</param.version>
     <param.output>${PROJECT_ROOT}\Hopfield Network Toolbox.mltbx</param.output>
     <param.products.name>
       <item>MATLAB</item>
+      <item>Simulink</item>
       <item>Statistics and Machine Learning Toolbox</item>
     </param.products.name>
     <param.products.id>
       <item>1</item>
+      <item>2</item>
       <item>19</item>
     </param.products.id>
     <param.products.version>
       <item>9.2</item>
+      <item>8.9</item>
       <item>11.1</item>
     </param.products.version>
     <param.platforms />
@@ -48,10 +51,16 @@ help_source/
 Hopfield Net TSP solver_resources/
 README.md
 setup_hopfieldNetwork.m
-BuildInstructions.m</param.exclude.filters>
+BuildInstructions.m
+automateTests.m
+slprj
+tau
+Simulations
+runMultipleTSPLIBproblems.m
+script_runMultipleTSPLIBproblems.m</param.exclude.filters>
     <param.examples>&lt;?xml version="1.0" encoding="utf-8"?&gt;
 &lt;examples&gt;
-   &lt;exampleCategory name="Solving the Traveling Salesman Problem using Hopfield Networks"&gt;
+   &lt;exampleCategory name="Solving the Optimization problems using Hopfield Networks"&gt;
       &lt;example name="Solving the TSP with cities in Polygon Vertices" type="html"&gt;
          &lt;file type="source"&gt;/help/html/Example_tspUsingRegularPolygons.html&lt;/file&gt;
          &lt;file type="main"&gt;/help/Example_tspUsingRegularPolygons.m&lt;/file&gt;
@@ -78,6 +87,27 @@ BuildInstructions.m</param.exclude.filters>
          &lt;file type="main"&gt;/help/Example_tspUsingDistance.m&lt;/file&gt;
          &lt;file type="thumbnail"/&gt;
       &lt;/example&gt;
+      &lt;example name="Solving a GQKP problem using a Hopfield Network" type="html"&gt;
+         &lt;file type="source"&gt;/help/html/Example_GQKPusingCHN.html&lt;/file&gt;
+         &lt;file type="main"&gt;/help/Example_GQKPusingCHN.m&lt;/file&gt;
+         &lt;file type="thumbnail"&gt;/help/html/Example_GQKPusingCHN.png&lt;/file&gt;
+         &lt;file type="image"&gt;/help/html/Example_GQKPusingCHN_01.png&lt;/file&gt;
+      &lt;/example&gt;
+   &lt;/exampleCategory&gt;
+   &lt;exampleCategory name="Solving Hopfield Networks using Simulink"&gt;
+      &lt;example name="Solving Discrete Hopfield Networks using Simulink" type="html"&gt;
+         &lt;file type="source"&gt;/help/html/Example_SimulinkDiscrete.html&lt;/file&gt;
+         &lt;file type="main"&gt;/help/Example_SimulinkDiscrete.m&lt;/file&gt;
+         &lt;file type="thumbnail"&gt;/help/html/Example_SimulinkDiscrete.png&lt;/file&gt;
+         &lt;file type="image"&gt;/help/html/Example_SimulinkDiscrete_01.png&lt;/file&gt;
+         &lt;file type="image"&gt;/help/html/Example_SimulinkDiscrete_02.png&lt;/file&gt;
+      &lt;/example&gt;
+      &lt;example name="Solving Continuous Hopfield Networks using Simulink" type="html"&gt;
+         &lt;file type="source"&gt;/help/html/Example_SimulinkContinuous.html&lt;/file&gt;
+         &lt;file type="main"&gt;/help/Example_SimulinkContinuous.m&lt;/file&gt;
+         &lt;file type="thumbnail"&gt;/help/html/Example_SimulinkContinuous.png&lt;/file&gt;
+         &lt;file type="image"&gt;/help/html/Example_SimulinkContinuous_01.png&lt;/file&gt;
+      &lt;/example&gt;
    &lt;/exampleCategory&gt;
    &lt;exampleCategory name="Improving Hopfield Network performance when applied to the TSP"&gt;
       &lt;example name="Reduce the free parameter C" type="html"&gt;
@@ -99,6 +129,12 @@ BuildInstructions.m</param.exclude.filters>
          &lt;file type="thumbnail"&gt;/help/html/Example_tspDivideConquer.png&lt;/file&gt;
          &lt;file type="image"&gt;/help/html/Example_tspDivideConquer_01.png&lt;/file&gt;
       &lt;/example&gt;
+      &lt;example name="CHN as a 2-opt Algorithm" type="html"&gt;
+         &lt;file type="source"&gt;/help/html/Example_tsp2opt.html&lt;/file&gt;
+         &lt;file type="main"&gt;/help/Example_tsp2opt.m&lt;/file&gt;
+         &lt;file type="thumbnail"&gt;/help/html/Example_tsp2opt.png&lt;/file&gt;
+         &lt;file type="image"&gt;/help/html/Example_tsp2opt_01.png&lt;/file&gt;
+      &lt;/example&gt;
    &lt;/exampleCategory&gt;
 &lt;/examples&gt;</param.examples>
     <param.demosxml />
@@ -119,16 +155,12 @@ BuildInstructions.m</param.exclude.filters>
       <file>E:\Users\Lucas\Documents\GitHub\HopfieldNetworkToolbox</file>
     </fileset.rootdir>
     <fileset.rootfiles>
-      <file>${PROJECT_ROOT}\@hopfieldnet</file>
-      <file>${PROJECT_ROOT}\@hopfieldnetwork</file>
-      <file>${PROJECT_ROOT}\@tsphopfieldnet</file>
-      <file>${PROJECT_ROOT}\@tsphopfieldnetApp</file>
-      <file>${PROJECT_ROOT}\@tsplib</file>
+      <file>${PROJECT_ROOT}\chn</file>
+      <file>${PROJECT_ROOT}\data</file>
       <file>${PROJECT_ROOT}\help</file>
       <file>${PROJECT_ROOT}\Hopfield Net TSP solver.mlappinstall</file>
       <file>${PROJECT_ROOT}\LICENSE</file>
       <file>${PROJECT_ROOT}\setup_TSPLIB.m</file>
-      <file>${PROJECT_ROOT}\TSPFiles</file>
     </fileset.rootfiles>
     <fileset.depfun.included />
     <fileset.depfun.excluded />

Hopfield Network Toolbox.prj

@@ -5,13 +5,13 @@ The Continuous Hopfield Network (CHN) is a **recurrent neural network** with an
 As the Lyapunov function is associated with an objective function of the optimization problem (i.e. the mapping process), the equilibrium, or stable point, helps identify a local optimum for the optimization problem.
 The dynamics of the CHN is described by a **differential equation**:
 
-![\frac{du}{dt} = - \frac{u}{\Lambda} + T v + i^b](http://mathurl.com/hzhnzj5.png) 
+![\frac{du}{dt} = - \frac{u}{\lambda} + T v + i^b](http://mathurl.com/ycfv6hhd.png) 
 
 and the output function is a hyperbolic tangent:
 
 ![v_i = g(u_i) = \frac{1}{2} \left( 1 + \tanh \left( \frac{u_i}{u_0} \right) \right), \qquad u_0 > 0](http://mathurl.com/zdeg52h.png)
 
-The existence of an equilibrium point is guaranteed if a Lyapunov or energy function exists. The idea is that the network's Lyapunov function, when ![\Lambda \rightarrow{} \infty](http://mathurl.com/hl2t4by.png), is associated with the cost function to be minimized in the combinatorial problem.
+The existence of an equilibrium point is guaranteed if a Lyapunov or energy function exists. The idea is that the network's Lyapunov function, when ![\lambda \rightarrow{} \infty](http://mathurl.com/ydye9fha.png), is associated with the cost function to be minimized in the combinatorial problem.
 
 The CHN will solve those combinatorial problems which can be expressed as the constrained minimization of: 
 
@@ -37,11 +37,12 @@ Want to contribute? Great! Feel free to fork the repository and contact us for i
 ## Questions?
 Open a new Issue and label it as a question. We will get back to you.
 
-## References
+## Major References
   - [“Neural” computation of decisions in optimization problems](http://www.ams.org/mathscinet-getitem?mr=824597)
   - [A continuous Hopfield network equilibrium points algorithm](http://www.sciencedirect.com/science/article/pii/S0305054804000243)
   - [Parameter setting of the Hopfield network applied to TSP](http://www.sciencedirect.com/science/article/pii/S0893608002000217)
   - [Improving the Hopfield model performance when applied to the traveling salesman problem: A divide-and-conquer scheme](http://link.springer.com/article/10.1007/s00500-016-2039-8)
+  - [Attractor basin analysis of the Hopfield model: The Generalized Quadratic Knapsack Problem. In International Work-Conference on Artificial Neural Networks (2017)](https://link.springer.com/chapter/10.1007%2F978-3-319-59153-7_37)
 
 ## Contact us
 Send us an [Email](mailto:lucasgarciarodriguez@ucm.es) with your comments/suggestions.

README.md

@@ -26,7 +26,8 @@
         tabOtherCoordinates;
         tabOtherDistance;
 
-        simulation;      
+        simulation; 
+        schemeMenu;
         simFcnMenu;
 
         ExecutionEnvironment;
@@ -83,7 +84,7 @@
         function app = HopfieldNetworkTSPApp()
             createFigure(app);
             defaultSettings(app);
-            drawnow nocallbacks;
+%             drawnow;
             app.figure.Visible = 'on';
         end
     end
@@ -100,9 +101,13 @@
         cb_parameterCEdit(app);
         cb_findTour(app);
         cb_simFcn(app);
+        cb_scheme(app);
         timeElapsed(app,obj,event);
         cleanState(app);
         createTspHopfieldNet(app,varargin);
         updateTspHopfieldNet(app,C);
+        problemIsSelected = verifyProblemIsSelected(app);
+        cb_closeApp(app);
     end
+    
 end

chn/+apps/@HopfieldNetworkTSPApp/HopfieldNetworkTSPApp.m

@@ -0,0 +1,14 @@
+function cb_closeApp(app,~)
+
+    selection = questdlg('Close Hopfield Net TSP solver App?',...
+        'Close App?',...
+        'Yes','No','Yes'); 
+    switch selection
+        case 'Yes'
+            warning('on','tsphopfieldnet:NotSimulated');
+            warning('on','MATLAB:MKDIR:DirectoryExists');
+            delete(app.figure);
+        case 'No'
+            return;
+    end
+end

chn/+apps/@HopfieldNetworkTSPApp/cb_closeApp.m

@@ -18,15 +18,9 @@ function cb_findTour(app,~)
     end
 end
 
-if app.simFcnMenu.Value == 1
-    msgbox('Please choose an algorithm for the Hopfield Network simulation', 'Error', 'error');
+if app.schemeMenu.Value == 1
+    msgbox('Please choose a scheme for the Hopfield Network simulation', 'Error', 'error');
 	return;
-else
-    algorithms = app.simFcnMenu.String;
-    setSimFcn(app.net,algorithms{app.simFcnMenu.Value});
-    if strcmp(algorithms{app.simFcnMenu.Value},'divide-conquer')
-        setCities(app.net,'Tau',max(3,round(getTrainParam(app.net,'N')/10))); %#TODO Bring to APP
-    end
 end
 
 u0 = str2double(app.settings_u0Edit.String);
@@ -35,6 +29,7 @@ function cb_findTour(app,~)
 dt = str2double(app.settings_dtEdit.String);
 e = str2double(app.settings_eEdit.String);
 q = str2double(app.settings_qEdit.String);
+tau = str2double(app.cities_tauEdit.String);
 
 try
     setSetting(app.net,'U0',u0)
@@ -43,6 +38,7 @@ function cb_findTour(app,~)
     setSetting(app.net,'Dt',dt)
     setSetting(app.net,'E',e)
     setSetting(app.net,'Q',q)
+    setCities(app.net,'Tau',tau)
 catch me
 	msgbox(me.message)
     return;

chn/+apps/@HopfieldNetworkTSPApp/cb_findTour.m

@@ -0,0 +1,37 @@
+function cb_scheme(app,~)
+
+    problemIsSelected = verifyProblemIsSelected(app);
+    if ~problemIsSelected
+        msgbox('Please select first the problem to solve', 'Error', 'error');
+        app.schemeMenu.Value = 1;
+        return;
+    end
+    schemes = app.schemeMenu.String;
+
+    chosenScheme = schemes{app.schemeMenu.Value};
+
+    if strncmp(chosenScheme,'divide-conquer',14)
+        app.cities_tauEdit.Enable = 'on';
+        tau = max(3,round(getTrainParam(app.net,'N')/10));
+        setCities(app.net,'Tau',tau); 
+        app.cities_tauEdit.String = num2str(tau);
+        
+        train(app.net);
+        trainParams = getTrainParam(app.net);
+
+        app.parameterAEdit.String = num2str(trainParams.A);
+        app.parameterBEdit.String = num2str(trainParams.B);
+        app.parameterDEdit.String = num2str(1/trainParams.dUaux);
+        
+        app.parameterNEdit.String = num2str(trainParams.N);
+        app.parameterNpEdit.String = num2str(trainParams.Np);
+        app.cities_tauEdit.String = num2str(getCities(app.net,'Tau'));        
+    else
+        app.cities_tauEdit.Enable = 'off';
+    end
+    
+    if ~isempty(app.net) && ~strcmp(chosenScheme,'Scheme')
+        setScheme(app.net, chosenScheme)
+    end
+
+end

chn/+apps/@HopfieldNetworkTSPApp/cb_scheme.m

@@ -1,21 +1,32 @@
 function cb_simFcn(app,~)
 
+    problemIsSelected = verifyProblemIsSelected(app);
+    if ~problemIsSelected
+        msgbox('Please select first the problem to solve', 'Error', 'error');
+        app.simFcnMenu.Value = 1;
+        return;
+    end
+    if app.schemeMenu.Value == 1
+        msgbox('Please select first the Hopfield Network scheme to solve the problem', 'Error', 'error');
+        app.simFcnMenu.Value = 1;
+        return;
+    end
+    
     algorithms = app.simFcnMenu.String;
 
-    chosenAlgorithm = algorithms(app.simFcnMenu.Value);
+    chosenAlgorithm = algorithms{app.simFcnMenu.Value};
 
     app.elapsedTime.String = '';
-
-    if strcmp(chosenAlgorithm,'euler')
+       
+    if strcmp(chosenAlgorithm,'euler') || strcmp(chosenAlgorithm,'runge-kutta')
         app.settings_u0Edit.Enable = 'on';
         app.settings_dtEdit.Enable = 'on';
         app.settings_maxIterEdit.Enable = 'on';
         app.settings_eEdit.Enable = 'on';
         app.settings_R_ITEREdit.Enable = 'on';
         app.settings_qEdit.Enable = 'on';
-        app.cities_tauEdit.Enable = 'off';
         if ~isempty(app.net)
-            setSimFcn(app.net,'euler')
+            setSimFcn(app.net,chosenAlgorithm)
         end
 
     elseif strcmp(chosenAlgorithm,'talavan-yanez')
@@ -25,31 +36,16 @@ function cb_simFcn(app,~)
         app.settings_eEdit.Enable = 'on';
         app.settings_R_ITEREdit.Enable = 'on';
         app.settings_qEdit.Enable = 'on';
-        app.cities_tauEdit.Enable = 'off';
         if ~isempty(app.net)
             setSimFcn(app.net,'talavan-yanez')
-        end    
-
-    elseif strcmp(chosenAlgorithm,'divide-conquer')
-        app.settings_u0Edit.Enable = 'on';
-        app.settings_dtEdit.Enable = 'off';
-        app.settings_maxIterEdit.Enable = 'on';
-        app.settings_eEdit.Enable = 'on';
-        app.settings_R_ITEREdit.Enable = 'on';
-        app.settings_qEdit.Enable = 'on';
-        app.cities_tauEdit.Enable = 'on';
-        if ~isempty(app.net)
-            setSimFcn(app.net,'divide-conquer')
-        end 
-
+        end
     else
         app.settings_u0Edit.Enable = 'off';
         app.settings_dtEdit.Enable = 'off';
         app.settings_maxIterEdit.Enable = 'off';
         app.settings_eEdit.Enable = 'off';
         app.settings_R_ITEREdit.Enable = 'off';
         app.settings_qEdit.Enable = 'off';
-        app.cities_tauEdit.Enable = 'off';
     end
-
+   
 end

chn/+apps/@HopfieldNetworkTSPApp/cb_simFcn.m

@@ -1,5 +1,5 @@
 function cb_tabPolygonNcities(app)
-    
+   
     N = str2double(app.tabPolygonnCitiesEdit.String);
     if isnan(N) || N < 2
         msgbox('You must provide a value for number of cities greater than 2', 'Error', 'error');

chn/+apps/@HopfieldNetworkTSPApp/cb_tabPolygonNcities.m

@@ -3,6 +3,10 @@ function cb_tabTSPLIBmenu(app)
 problems = app.tabTSPLIBmenu.String;
 problemSelected = app.tabTSPLIBmenu.Value;
 
+app.schemeMenu.Value = 1;
+app.simFcnMenu.Value = 1;
+app.cities_tauEdit.Enable = 'off';
+
 % Useful for problems that take longer to compute tsplib
 % and training
 app.tabTSPLIBnCitiesEdit.String = '- - - ';