Reference Guide


The BrainWave Reference Guide provides the information needed to use the BrainWave neural network simulator. It is organised in a question - answer format (in the style of a structured Frequently Asked Questions, FAQ, list). The questions are divided into the following sections:
  1. Getting Started
  2. Basic Objects: Units, Weights, Labels, Values and Graphs
  3. Editing Networks
  4. Sets
  5. Running the Network: Using Buttons
  6. File Operations: Saving, Loading and Printing
  7. Interface Options
  8. Network Specific Actions

To find the information your require either select a category and look for the appropriate question or use the Find option of your browser and search for a key term.

Questions

  1. Getting Started

  2. How do I download and install the BrainWave software?
  3. How do I execute BrainWave?
  4. How do I exit BrainWave?
  5. What menus are there in the BrainWave simulator?
  6. How do I clear the BrainWave workspace?
  7. How do I find out the authorship and version details for my copy of BrainWave?

    Basic Objects: Units, Weights, Labels, Values and Graphs

  8. How do I select a tool?
  9. How do I create a unit?
  10. How do I create a weight?
  11. How do I create a label?
  12. How do I create a value?
  13. How do I create a graph?
  14. How do I resize a graph?
  15. I want to compare graphs from two different runs. When I start the second run the first graph keeps changing. What should I do?

    Editing Networks

  16. How do I undo the last change to the set of objects?
  17. How do I move an object?
  18. How do I delete an object?
  19. How do I select an object?
  20. How do I double select an object?
  21. How do I deselect an object?
  22. How do I select multiple objects?
  23. How do I select all objects?
  24. How do I select all units?
  25. How do I select all weights?
  26. How do I deselect currently selected objects?
  27. How do I cut a set of objects into the paste buffer?
  28. How do I copy a set of objects into the paste buffer?
  29. How do I paste a set of objects from the paste buffer?
  30. How do I change the parameters of an object?
  31. How do I toggle a unit?

    Sets

  32. How do I create a set?
  33. How do I add a pattern to a set?
  34. How do I select a pattern from a set?
  35. How do I delete a pattern from a set?
  36. How do I create an input or output layer of units?

    Running the Network

  37. How do I run the network?
  38. How do I stop a network cycling or learning?

    File Operations: Saving, Loading and Printing

  39. How do I load a default network?
  40. How do I save a network?
  41. How do I load a network from disk?
  42. How do I load a network from a URL?
  43. How do I print a network?

    Interface Options

  44. The weights are cluttering up the screen. How can I make them invisible?
  45. How do you get things to line up on the workspace?
  46. I have a black and white screen and can't see the colour graphics. What should I do?
  47. When I save to a postscript file I want encapsulated postscript rather than normal postscript (so I can import the file into another package). How do I get BrainWave to save encapsulated postscript?
  48. How do I save postscript in landscape rather than portrait mode?

Answers to Questions

  1. Getting Started

  2. How do I download and install BrainWave?
  3. How do I execute BrainWave?

    Using a browser: Once you have extracted the files use the "Open File" or "Open File in Browser" option in the File menu to open BrainWave.html (or which ever html file you are interested in).

    Using a appletviewer: Different appletviewers work slightly differently and you should refer to the documentation that comes with the appletviewer. In general, to use an appletviewer you should ensure that your CLASSPATH variable contains the directory in which BrainWave resides. Then use a command like to folowing:

    appletviewer BrainWave.html

    Using BrainWave as an application: Again, different java machines can operate differently, so you should refer to the documentation that comes with your package. In general, however a line like the following is needed:

    java BrainWave.BWMain

    To open a BrainWave with a network use:

    java BrainWave <network name>

  4. How do I exit BrainWave?

    To exit the BrainWave application select the Exit box (top right hand corner in Windows 95).

  5. What menus are there in the BrainWave simulator?

    BrainWave uses two types of menu. The first is the main menu which is activated by pressing the right mouse button while the pointer is located over a blank segment of the simulator (hold down the Apple key and press on the Macintosh). This menu contains the object, file, edit, option submenus (see later for a description). The second sort of menu is an object menu which is activated by pressing the right mouse button while the pointer is located over one of the objects in the simulator (such as a unit or a weight). This menu contains the parameters and operations that can be performed on that object.

  6. How do I clear the BrainWave workspace?

    To clear the BrainWave workspace select the New item from the File menu. Note this removes all of the objects and reverts the Objectmenu to a standard set.

  7. How do I find out the authorship and version details for my copy of BrainWave? To find out the authorship and version details of your version of BrainWave select the About item from the File menu.

    Basic Objects: Units, Weights, Labels, Values and Graphs

  8. How do I select a tool?

    To select a tool select an item from the Object menu.

  9. How do I create a unit?

    To create a unit, select the unit tool, move the mouse cursor to the position on the workspace where you wish the unit to appear and click.

  10. How do I create a weight?

    To create a weight select the weight tool, select the unit(s) from which you want the weights to originate and double select the unit(s) to which the weights should be connected. Then click on any open segment of the workspace. The weight will appear as a line linking the two units. The value of the weight is represented by the colour of the line. Red lines indicate positive weights and blue lines indicate negative weights.

  11. How do I create a label?

    To create a label, select the label tool, move the cursor to the position on the workspace where you would like the place the label, and click.

  12. How do I create a bound value?

    Sometimes it is necessary to be able to track a value of an object as it changes during learning or cycling. To create a value, select the object you want the value to be bound to select the bound value tool, move the mouse cursor to the position on the workspace where you wish the value to appear and click. Many objects have more than one value associated with them. To select which of these values you want to track set the bound value name in the object menu of the bound value. The bound value will be updated whenever that object is updated.

  13. How do I create a graph?

    To create a graph, select the object to be graphed, select the graph tool and click on an unoccupied portion of the workspace. Like the bound value the graph can be attached to different values. Select the value you wish to graph in the graphs object menu.

  14. How do I resize a graph?

    To resize a graph select the graph and click down on the bottom right hand corner and drag until the graph is the required size.

  15. I want to compare graphs from two different runs. When I start the second run the first graph keeps changing. What should I do?

    To stop the first graph from changing select unfrozen from the graphs object menu. This freezes the graph so that it will not alter. The graph can be "unfrozen" by selecting "frozen".

    Editing Networks

  16. How do I undo the last change to the set of objects?

    [not yet operational] Select the Undo item from the Edit menu. Note this can only undo changes to the set of objects on the workspace. it cannot be used to undo changes to object parameters.

  17. How do I move an object?

    To move an object (unit, weight, label, value, graph, set, or group), move the cursor over the object you want to move, click down, drag the cursor to the new position for the object and release the mouse button.

  18. How do I delete an object?

    To delete an object, hold down control, move the cursor over the object that you want to delete and click.

  19. How do I select an object?

    To select an object, hold down shift, move the cursor over the object you want to select and click. A selected item will have green "handles" on its corners.

  20. How do I double select an object?

    To double select an object, just select an already selected item again. A double selected item will have yellow "handles" on its corners.

  21. How do I deselect an object?

    To deselect select a double selected object.

  22. How do I select multiple objects?

    To select multiple objects and hold the shift key down when you are selecting additional objects.

  23. How do I select all objects?

    Select the "Select All" item from the Edit menu.

  24. How do I select all units?

    Select the "Select Units" item from the Edit menu.

  25. How do I select all weights?

    Select the "Select Weights" item from the Edit menu.

  26. How do I deselect currently selected objects?

    To deselect currently selected objects, hold down shift, and then click on any unoccupied part of the workspace.

  27. How do I cut a set of objects into the paste buffer?

    Select the objects you wish to cut and select the Cut item from the Edit menu.

  28. How do I copy a set of objects into the paste buffer?

    Select the objects you wish to copy and select the Copy item from the Edit menu.

  29. How do I paste a set of objects from the paste buffer?

    Select the Paste item from the Edit menu.

  30. How do I change the parameters of an object?

    To change the parameters of an object right click on the object to popup the object menu and select the parameter you wish to change. Typically, a dialog will appear and allow you to change the value. In some cases, however, a special editor can be instantiated (see editing pattern sets). In the case, of boolean variables the value is toggled. Important: by changing parameters in the parameter panel, you are changing the parameters of all selected objects of that type.

  31. How do I toggle a unit?

    To toggle a unit, move the mouse cursor over the unit you wish to toggle and click. If the value of a unit is near 0 it will become 1 and if it is near 1 it will become 0.

    Sets

  32. How do I create a set?

    To create a set select the objects you wish to be in the set (typically these are units although other objects can be included also), select the set tool, move the mouse cursor to the position on the workspace where you wish the set to appear and click.

  33. How do I add a pattern to a set?

    To add a pattern to a set, specify the values of the objects in the set (by using the toggle tool for units, or by changing the value parameter of an object), and select Add Pattern option from the set you wish to add the pattern to. The label for the new pattern will appear under the set(s) to which it has been added. alternatively, you can use the pattern set editor by selecting "Edit patterns" from the set's object menu.

  34. How do I select a pattern from a set?

    To select a pattern from a set, click on the label of the pattern which you wish to select. The label will change colour and the pattern will be instantiated on its objects.

  35. How do I delete a pattern from a set?

    Select the "Delete Pattern" option from the set's object menu.

  36. How do I create an input or output layer of units?

    To create an input layer of units create the units you wish to be in the layer. Next select these units and only these units. Now create a pattern set using the set tool.

    Running the Network: Cycling and Learning

  37. How do I run the network?

    Exactly what has to be done to run a netowrk depends on the type of network. Typically, cycling activations or initiating the learning algorithm will invovle clicking on a button. The names of these buttons change from architecture to architecture. In addition, buttons are used to initiate other network operations such as reseting all units to zero, or randomizing weights.

  38. How do I stop a network cycling or learning?

    To stop a network cycling or learning click on the Stop button.

    File Operations: Saving, Loading and Printing

  39. How do I load a default network?

    When BrainWave is run as an applet from within a web page you can load a default network by specifying the InitialNetwork parameter. For instance, the following html loads the JetsAndSharks network when the page is accessed.

    <center>
    <applet code="BrainWave/BWMain.class" archive="BrainWave.jar" width=600 height=400>
    <PARAM NAME="InitialNetwork" VALUE="JetsAndSharks.net">
    <applet>
    <center>

  40. How do I save a network?

    To save a network select the "Save As" option from the File menu. A dialog will appear allowing you to specify where you would like the file saved and what its name should be. Note that when running BrainWave through Netscape, the save options are not available for security reasons.

  41. How do I load a network from disk?

    To load a network from disk select the "Open" option from the File menu. A dialog will appear allowing you to select the file to load.

  42. How do I load a network from a URL?

    To load a network from a URL select the "Open URL" option from the File menu. A dialog will appear to allow you to type in the URL of the file you wish to load.

  43. How do I print a network? To print a network use the Export to Postscript option to save a postscript file. The print this file using the method appropriate to your platform. On unix machines this involves the lpr command:

    lpr MyNetwork.ps

    Note that the Landscape item in the Options menu can be used to change the aspect of the printed network. Also the Eps option makes "Export to Postscript" produce an encapsulated postscript file which can be imported into other packages.

    Interface Options

  44. The weights are cluttering up the screen. How can I make them invisible?

    To make the weights invisible select the "Weights Visible" item from the Options menu. To make them visible again select the item again.

  45. How do you get things to line up on the workspace?

    You can bring up a grid on the screen by selecting the "Grid" option from the Options menu. When the grid is showing any object created or moved will align with the grid.

  46. I have a black and white screen and can't see the colour graphics. What should I do?

    BrainWave comes with a black and white option which causes all graphics to be displayed in black and white. You can select it from the Options menu. Units with positive activations are represented by a white square on a black background. Negative activations are represented by a a black square on a white background. As a consequence zero which is represented by just a black background can look very similar to -1 which is a large black square on a white background - so beware.

  47. When I save to a postscript file I want encapsulated postscript rather than normal postscript (so I can import the file into another package). How do I get BrainWave to save encapsulated postscript?

    You can select the eps item from the Options menu to make the "Export to Postscript" option save encapsulated postscript.

  48. How do I save postscript in landscape rather than portrait mode?

    You can select the landscape item from the Options menu to make the "Export to Postscript" option save in landscape mode rather than portrait.

The BrainWave homepage.