FAQ - Revision history

Admin at 08:27, 17 March 2014

2014-03-17T08:27:33Z

Admin at 08:04, 17 March 2014

2014-03-17T08:04:25Z

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	* you need more modeling iterations or you need to build more models per iteration (see [[Running#Understanding_the_control_flow]]). This will result in a more extensive search of the model parameter space, but will take longer to run.		* you need more modeling iterations or you need to build more models per iteration (see [[Running#Understanding_the_control_flow]]). This will result in a more extensive search of the model parameter space, but will take longer to run.
	* you should switch to a different model parameter optimization algorithm (e.g., for example instead of the Pattern Search variant, try the Genetic Algorithm variant of your ~~AdaptiveModelBuilder~~.)		* you should switch to a different model parameter optimization algorithm (e.g., for example instead of the Pattern Search variant, try the Genetic Algorithm variant of your ModelBuilder.)
	* the model type you are using is not ideally suited to your data		* the model type you are using is not ideally suited to your data
	* there simply is not enough data, use a larger initial design or perform more sampling iterations to get more information per dimension		* there simply is not enough data, use a larger initial design or perform more sampling iterations to get more information per dimension
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	=== When running the SUMO Toolbox you get an error like "No component with id 'annpso' of type 'adaptive model builder' found in config file." ===		=== When running the SUMO Toolbox you get an error like "No component with id 'annpso' of type 'adaptive model builder' found in config file." ===

	This means you have specified to use a component with a certain id (in this case an ~~AdaptiveModelBuilder~~ component with id 'annpso') but a component with that id does not exist further down in the configuration file (in this particular case 'annpso' does not exist but 'anngenetic' or 'ann' does, as a quick search through the configuration file will show). So make sure you only declare components which have a definition lower down. So see which components are available, simply scroll down the configuration file and see which id's are specified. Please also refer to the [[Toolbox configuration#Declarations and Definitions \| Declarations and Definitions]] page.		This means you have specified to use a component with a certain id (in this case an ModelBuilder component with id 'annpso') but a component with that id does not exist further down in the configuration file (in this particular case 'annpso' does not exist but 'anngenetic' or 'ann' does, as a quick search through the configuration file will show). So make sure you only declare components which have a definition lower down. So see which components are available, simply scroll down the configuration file and see which id's are specified. Please also refer to the [[Toolbox configuration#Declarations and Definitions \| Declarations and Definitions]] page.

	=== When using NANN models I sometimes get "Runtime error in matrix library, Choldc failed. Matrix not positive definite" ===		=== When using NANN models I sometimes get "Runtime error in matrix library, Choldc failed. Matrix not positive definite" ===

Javdrher: /* What happened to the M3-Toolbox? */

2014-03-13T09:21:13Z

What happened to the M3-Toolbox?

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	=== What happened to the M3-Toolbox? ===		=== What happened to the M3-Toolbox? ===

	The M3 Toolbox project has been discontinued (Fall 2007) and superseded by the SUMO Toolbox. Please contact tom.dhaene@~~ua.ac~~.be for any inquiries and requests about the M3 Toolbox.		The M3 Toolbox project has been discontinued (Fall 2007) and superseded by the SUMO Toolbox. Please contact tom.dhaene@ugent.be for any inquiries and requests about the M3 Toolbox.

	=== How can I stay up to date with the latest news? ===		=== How can I stay up to date with the latest news? ===

Javdrher: /* What about dynamical, time dependent data? */

2014-03-13T09:20:55Z

What about dynamical, time dependent data?

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	The toolbox was originally not intended for this purpose. However, it is quite easy to add support for recurrent models. Automatic generation of dynamical models would involve adding a new model type (just like you would add a new regression technique) or require adapting an existing one. For example it would not be too much work to adapt the ANN or SVM models to support dynamic problems. The only extra work besides that would be to add a new [[Measures\|Measure]] that can evaluate the fidelity of the models' prediction.		The toolbox was originally not intended for this purpose. However, it is quite easy to add support for recurrent models. Automatic generation of dynamical models would involve adding a new model type (just like you would add a new regression technique) or require adapting an existing one. For example it would not be too much work to adapt the ANN or SVM models to support dynamic problems. The only extra work besides that would be to add a new [[Measures\|Measure]] that can evaluate the fidelity of the models' prediction.

	Naturally though, you would be unable to use sample selection (since it makes no sense in those problems). Unless of course there is a specialized need for it. In that case you would add a new [[~~SampleSelector~~]].		Naturally though, you would be unable to use sample selection (since it makes no sense in those problems). Unless of course there is a specialized need for it. In that case you would add a new [[Config:SequentialDesign\|SequentialDesign]].

	For more information on this topic [[Contact]] us.		For more information on this topic [[Contact]] us.

Javdrher: /* What is (adaptive) sampling? Why is it used? */

2014-03-13T09:20:35Z

What is (adaptive) sampling? Why is it used?

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	In classical Design of Experiments you need to specify the design of your experiment up-front. Or in other words, you have to say up-front how many data points you need and how they should be distributed. Two examples are Central Composite Designs and Latin Hypercube designs. However, if your data is expensive to generate (e.g., an expensive simulation code) it is not clear how many points are needed up-front. Instead data points are selected adaptively, only a couple at a time. This process of incrementally selecting new data points in regions that are the most interesting is called adaptive sampling, sequential design, or active learning. Of course the sampling process needs to start from somewhere so the very first set of points is selected based on a fixed, classic experimental design. See also [[Running#Understanding_the_control_flow]].		In classical Design of Experiments you need to specify the design of your experiment up-front. Or in other words, you have to say up-front how many data points you need and how they should be distributed. Two examples are Central Composite Designs and Latin Hypercube designs. However, if your data is expensive to generate (e.g., an expensive simulation code) it is not clear how many points are needed up-front. Instead data points are selected adaptively, only a couple at a time. This process of incrementally selecting new data points in regions that are the most interesting is called adaptive sampling, sequential design, or active learning. Of course the sampling process needs to start from somewhere so the very first set of points is selected based on a fixed, classic experimental design. See also [[Running#Understanding_the_control_flow]].
	SUMO provides a number of different sampling algorithms: [[~~SampleSelector~~]]		SUMO provides a number of different sampling algorithms: [[Config:SequentialDesign\|SequentialDesign]]

	Of course sometimes you dont want to do sampling. For example if you have a fixed dataset you just want to load all the data in one go and model that. For how to do this see [[FAQ#How_do_I_turn_off_adaptive_sampling_.28run_the_toolbox_for_a_fixed_set_of_samples.29.3F]].		Of course sometimes you dont want to do sampling. For example if you have a fixed dataset you just want to load all the data in one go and model that. For how to do this see [[FAQ#How_do_I_turn_off_adaptive_sampling_.28run_the_toolbox_for_a_fixed_set_of_samples.29.3F]].

Sprashant: /* What about classification problems? */

2014-03-05T08:46:18Z

What about classification problems?

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	=== What about classification problems? ===		=== What about classification problems? ===

	The main focus of the SUMO Toolbox is on regression/function approximation. However, the framework for hyperparameter optimization, model selection, etc. can also be used for classification. Starting from version 6.3 a demo file is included in the distribution that shows how this works on the well known two spiral test problem.		The main focus of the SUMO Toolbox is on regression/function approximation. However, the framework for hyperparameter optimization, model selection, etc. can also be used for classification. Starting from version 6.3 a demo file is included in the distribution that shows how this works on the well known two spiral test problem. It is possible to specify a run as a classification problem by setting the 'classificationMode' and 'numberOfClasses' option in ContextConfig in the configuration file. Classification models from WEKA are also available in SUMO. Please refer to the default configuration file for the explanation on usage of WEKA model types available through SUMO. The LOLA-Voronoi sample selection scheme also supports classification, and its usage is documented in the default configuration file as well.

	=== Does SUMO support discrete inputs/outputs ===		=== Does SUMO support discrete inputs/outputs ===

Mnguyen: /* What is XML? */

2012-02-13T16:43:07Z

What is XML?

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	XML stands for eXtensible Markup Language and is related to HTML (= the stuff web pages are written in). The first thing you have to understand is that '''does not do anything'''. Honest. Many engineers are not used to it and think it is some complicated computer programming language-stuff-thingy. This is of course not the case (we ignore some of the fancy stuff you can do with it for now). XML is a markup language meaning, it provides some rules how you can annotate or structure existing text.		XML stands for eXtensible Markup Language and is related to HTML (= the stuff web pages are written in). The first thing you have to understand is that '''does not do anything'''. Honest. Many engineers are not used to it and think it is some complicated computer programming language-stuff-thingy. This is of course not the case (we ignore some of the fancy stuff you can do with it for now). XML is a markup language meaning, it provides some rules how you can annotate or structure existing text.

	The way SUMO uses XML is really simple and there is not much to understand (for more information on how SUMO uses XML go this ~~page~~ [[Config:ToolboxConfiguration#Interpreting_the_configuration_file\|page]]). First some simple terminology. Take the following example:		The way SUMO uses XML is really simple and there is not much to understand (for more information on how SUMO uses XML go this [[Config:ToolboxConfiguration#Interpreting_the_configuration_file\|page]]).


			First some simple terminology. Take the following example:

	<source lang="xml">		<source lang="xml">

Mnguyen: /* Why does SUMO use XML? */

2012-02-10T15:58:23Z

Why does SUMO use XML?

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	XML is the de facto standard way of structuring information. This ranges from spreadsheet files (Microsoft Excel for example), to configuration data, to scientific data, ... There are even whole database systems based solely on XML. So basically, its an intuitive way to structure data and it is used everywhere. This makes that there are a very large number of libraries and programming languages available that can parse, and handle XML easily. That means less work for the programmer. Then of course there is stuff like XSLT, XQuery, etc that makes life even easier.		XML is the de facto standard way of structuring information. This ranges from spreadsheet files (Microsoft Excel for example), to configuration data, to scientific data, ... There are even whole database systems based solely on XML. So basically, its an intuitive way to structure data and it is used everywhere. This makes that there are a very large number of libraries and programming languages available that can parse, and handle XML easily. That means less work for the programmer. Then of course there is stuff like XSLT, XQuery, etc that makes life even easier.
	So basically, it would not make sense for SUMO to use any other format :). For more information on how SUMO uses XML go this ~~page~~ [[Config:ToolboxConfiguration#Interpreting_the_configuration_file\|page]].		So basically, it would not make sense for SUMO to use any other format :). For more information on how SUMO uses XML go this [[Config:ToolboxConfiguration#Interpreting_the_configuration_file\|page]].

	=== I get an error that SUMO is not yet activated ===		=== I get an error that SUMO is not yet activated ===

Mnguyen: /* Why does SUMO use XML? */

2012-02-10T15:58:10Z

Why does SUMO use XML?

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	=== Why does SUMO use XML? ===		=== Why does SUMO use XML? ===

	XML is the ~~defacto~~ standard way of structuring information. This ranges from spreadsheet files (Microsoft Excel for example), to configuration data, to scientific data, ... There are even whole database systems based solely on XML. So basically, its an intuitive way to structure data and it is used everywhere. This makes that there are a very large number of libraries and programming languages available that can parse, and handle XML easily. That means less work for the programmer. Then of course there is stuff like XSLT, XQuery, etc that makes life even easier.		XML is the de facto standard way of structuring information. This ranges from spreadsheet files (Microsoft Excel for example), to configuration data, to scientific data, ... There are even whole database systems based solely on XML. So basically, its an intuitive way to structure data and it is used everywhere. This makes that there are a very large number of libraries and programming languages available that can parse, and handle XML easily. That means less work for the programmer. Then of course there is stuff like XSLT, XQuery, etc that makes life even easier.
	So basically, it would not make sense for SUMO to use any other format :)		So basically, it would not make sense for SUMO to use any other format :). For more information on how SUMO uses XML go this page [[Config:ToolboxConfiguration#Interpreting_the_configuration_file\|page]].

	=== I get an error that SUMO is not yet activated ===		=== I get an error that SUMO is not yet activated ===

Mnguyen: /* What is XML? */

2012-02-10T15:57:05Z

What is XML?

← Older revision		Revision as of 15:57, 10 February 2012
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	XML stands for eXtensible Markup Language and is related to HTML (= the stuff web pages are written in). The first thing you have to understand is that '''does not do anything'''. Honest. Many engineers are not used to it and think it is some complicated computer programming language-stuff-thingy. This is of course not the case (we ignore some of the fancy stuff you can do with it for now). XML is a markup language meaning, it provides some rules how you can annotate or structure existing text.		XML stands for eXtensible Markup Language and is related to HTML (= the stuff web pages are written in). The first thing you have to understand is that '''does not do anything'''. Honest. Many engineers are not used to it and think it is some complicated computer programming language-stuff-thingy. This is of course not the case (we ignore some of the fancy stuff you can do with it for now). XML is a markup language meaning, it provides some rules how you can annotate or structure existing text.

	The way SUMO uses XML is really simple and there is not much to understand. First some simple terminology. Take the following example:		The way SUMO uses XML is really simple and there is not much to understand (for more information on how SUMO uses XML go this page [[Config:ToolboxConfiguration#Interpreting_the_configuration_file\|page]]). First some simple terminology. Take the following example:

	<source lang="xml">		<source lang="xml">

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	=== What is Java, why do I need it, do I have to install it, etc. ? ===		=== What is Java, why do I need it, do I have to install it, etc. ? ===

	The short answer is: no, dont worry about it. The long answer is: Some of the code of the SUMO Toolbox is written in [http://en.wikipedia.org/wiki/Java_(programming_language) Java], since it makes a lot more sense in many situations and is a proper programming language instead of a scripting language like Matlab. Since Matlab automatically includes a JVM to run Java code there is nothing you need to do or worry about (see the previous FAQ entry). Unless its not working of course, in that case see [[FAQ#When_running_the_toolbox_you_get_something_like_.27.3F.3F.3F_Undefined_variable_.~~22ibbt~~.22_or_class_.~~22ibbt~~.sumo.config.ContextConfig.setRootDirectory.22.27]].		The short answer is: no, dont worry about it. The long answer is: Some of the code of the SUMO Toolbox is written in [http://en.wikipedia.org/wiki/Java_(programming_language) Java], since it makes a lot more sense in many situations and is a proper programming language instead of a scripting language like Matlab. Since Matlab automatically includes a JVM to run Java code there is nothing you need to do or worry about (see the previous FAQ entry). Unless its not working of course, in that case see [[FAQ#When_running_the_toolbox_you_get_something_like_.27.3F.3F.3F_Undefined_variable_.22iminds.22_or_class_.22iminds.sumo.config.ContextConfig.setRootDirectory.22.27]].

	=== What is XML? ===		=== What is XML? ===
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	=== I get an error that SUMO is not yet activated ===		=== I get an error that SUMO is not yet activated ===

	Make sure you installed the activation file that was mailed to you as is explained in the [[Installation]] instructions. Also double check your system meets the [[System requirements]] and that [http://www.sumowiki.intec.ugent.be/index.php/FAQ#When_running_the_toolbox_you_get_something_like_.27.3F.3F.3F_Undefined_variable_.~~22ibbt~~.22_or_class_.~~22ibbt~~.sumo.config.ContextConfig.setRootDirectory.22.27\|java java is enabled]. To fully verify that the activation file installation is correct ensure that the file ContextConfig.class is present in the directory ''<SUMO installation directory>/bin/java/~~ibbt~~/sumo/config''.		Make sure you installed the activation file that was mailed to you as is explained in the [[Installation]] instructions. Also double check your system meets the [[System requirements]] and that [http://www.sumowiki.intec.ugent.be/index.php/FAQ#When_running_the_toolbox_you_get_something_like_.27.3F.3F.3F_Undefined_variable_.22iminds.22_or_class_.22iminds.sumo.config.ContextConfig.setRootDirectory.22.27\|java java is enabled]. To fully verify that the activation file installation is correct ensure that the file ContextConfig.class is present in the directory ''<SUMO installation directory>/bin/java/iminds/sumo/config''.

	Please note that more flexible research licenses are available if it is possible to [[FAQ#What_are_collaboration_options.3F\|collaborate in any way]].		Please note that more flexible research licenses are available if it is possible to [[FAQ#What_are_collaboration_options.3F\|collaborate in any way]].
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	You forgot to build the SVM mex files for your platform. For windows they are pre-compiled for you, on other systems you have to compile them yourself with the makefile.		You forgot to build the SVM mex files for your platform. For windows they are pre-compiled for you, on other systems you have to compile them yourself with the makefile.

	=== When running the toolbox you get something like '??? Undefined variable "~~ibbt~~" or class "~~ibbt~~.sumo.config.ContextConfig.setRootDirectory"' ===		=== When running the toolbox you get something like '??? Undefined variable "iminds" or class "iminds.sumo.config.ContextConfig.setRootDirectory"' ===

	First see [[FAQ#What_is_the_relationship_between_Matlab_and_Java.3F \| this FAQ entry]].		First see [[FAQ#What_is_the_relationship_between_Matlab_and_Java.3F \| this FAQ entry]].
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	(*) This is normal if you are using a measure like cross validation that is less reliable on little data than on more data. However, in some cases you may wish to override this behavior if you are using a measure that is independent of the number of samples the model is trained with (e.g., a dense, external validation set). In this case you can force a monotonic decrease by setting the 'keepOldModels' option in the SUMO tag to true. Use with caution!		(*) This is normal if you are using a measure like cross validation that is less reliable on little data than on more data. However, in some cases you may wish to override this behavior if you are using a measure that is independent of the number of samples the model is trained with (e.g., a dense, external validation set). In this case you can force a monotonic decrease by setting the 'keepOldModels' option in the SUMO tag to true. Use with caution!

	=== At the end of a run I get Undefined variable "~~ibbt~~" or class "~~ibbt~~.sumo.util.JpegImagesToMovie.createMovie" ===		=== At the end of a run I get Undefined variable "iminds" or class "iminds.sumo.util.JpegImagesToMovie.createMovie" ===

	This is normal, the warning printed out before the error explains why:		This is normal, the warning printed out before the error explains why: