Biomarker Identification via EFS on the Grid

Created: 2013-08-13 17:23:30 Last updated: 2013-09-24 08:18:53

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The workflow splits the data set into several sub-sampling sets, which are then used as input forEnsemble Feature Selection (support vector machine) . The objective function is calculated by taking a 'gold standard' into account. The execution of the EFS is performed on the Grid by using the Taverna UNICORE Plugin.

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Workflow Components

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Inputs (18)

Name	Description
file
number_iterations
out_folder
gold_standard
Bootstraps
Cache_Size
Cost
Epsilon_Loss
coef0
Epsilon_Tolerance
Kernel_Degree
Kernel_Gamma
Kernel_Type
propability
Remove_Percentage
Shrink
SVM_nu
SVM_Type

Processors (5)

Name	Type	Description
DataSplit_And_Seed	externaltool
ExtractSeeds	beanshell	Script String a = in1; int d= a.indexOf("Seed values:"); int f= a.indexOf("Importing and splitting completed.")-2; String b=a.substring(d+13,f); String [] seeds= b.split(" "); int e= a.indexOf("Done."); int g= a.indexOf("total")-1; String file_path=a.substring(e+6,g)+File.separator+"data.ser";
EFS	activity
get_Value	beanshell	Script out1=in1;
clac_ObjFunc_2	activity

Beanshells (2)

Name	Description	Inputs	Outputs
ExtractSeeds		in1	seeds file_path
get_Value		in1	out1

Outputs (1)

Name	Description
CalculateObjectiveFunction

Datalinks (24)

Source	Sink
file	DataSplit_And_Seed:file
number_iterations	DataSplit_And_Seed:number_iterations
out_folder	DataSplit_And_Seed:out_folder
DataSplit_And_Seed:STDOUT	ExtractSeeds:in1
ExtractSeeds:seeds	EFS:Seed
Bootstraps	EFS:Bootstraps
ExtractSeeds:file_path	EFS:Input
Cache_Size	EFS:Cache_Size
Cost	EFS:Cost
Epsilon_Loss	EFS:Epsilon_Loss
coef0	EFS:Kernel_coef0
Epsilon_Tolerance	EFS:Epsilon_Tolerance
Kernel_Degree	EFS:Kernel_Degree
Kernel_Gamma	EFS:Kernel_Gamma
Kernel_Type	EFS:Kernel_Type
propability	EFS:propability
Remove_Percentage	EFS:Remove_Percentage
Shrink	EFS:Shrink
SVM_nu	EFS:SVM_nu
SVM_Type	EFS:SVM_Type
clac_ObjFunc_2:SimpleES	get_Value:in1
EFS:EFSOutput	clac_ObjFunc_2:Input_files
gold_standard	clac_ObjFunc_2:Gold_standard
get_Value:out1	CalculateObjectiveFunction

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Information Workflow Type

Taverna 2

Information Uploader

Sonja Holl

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Information Version 1 (earliest) (of 2)

Information Credits (1)

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Sonja Holl

Information Attributions (1)

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Biomarker Identification via RFE on the Grid

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Biomarker Identification via RFE on the Grid

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Information Statistics

1108 viewings

690 downloads

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Version History

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Biomarker Identification via EFS on the Grid

Created by Sonja Holl on Tuesday 13 August 2013 17:23:30 (UTC)

Last edited by Sonja Holl on Wednesday 04 September 2013 07:21:27 (UTC)
Biomarker Identification via EFS on the Grid

Created by Sonja Holl on Tuesday 24 September 2013 08:15:44 (UTC)

Last edited by Sonja Holl on Tuesday 24 September 2013 08:18:53 (UTC)