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 first two components split the original data set into several sub-sampling sets. The EFS component performs the machine learning approach by executing several instances of a SVM, each of which consuming one sub-sample data set. Another level of SVM execution is added by taking bootstapping into account. The execution of all SVMs takes place in a distributed computing environment using the UNICORE-Taverna plugin. The calc_objFunc component calculates the F-measure of the ranked gene list compared to a 'gold standard'

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Inputs (8)

Name	Description
Input_file
number_iterations
gold_standard
RFE_Remove_Percentage
RFE_Cost
RFE_Epsilon_Tolerance
gamma
EFS_Bootstraps

Processors (13)

Name	Type	Description
ExtractSeeds_and_Input	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";
Kernel_Type	stringconstant	Value 0
Cache_Size	stringconstant	Value 100
Epsilon_Loss	stringconstant	Value 0.1
Kernel_coef0	stringconstant	Value 0
Kernel_Degree	stringconstant	Value 3
propability	stringconstant	Value 0
Shrink	stringconstant	Value 1
SVM_nu	stringconstant	Value 0.5
SVM_Type	stringconstant	Value 0
clac_ObjFunc	activity
data_split	activity
EFS	activity

Beanshells (1)

Name	Description	Inputs	Outputs
ExtractSeeds_and_Input		in1	seeds file_path

Outputs (1)

Name	Description
ES_out

Datalinks (22)

Source	Sink
data_split:stdout	ExtractSeeds_and_Input:in1
gold_standard	clac_ObjFunc:Gold_standard
EFS:EFSOutput	clac_ObjFunc:Input_files
Input_file	data_split:Input_file
number_iterations	data_split:Number_it
SVM_Type:value	EFS:SVM_Type
Kernel_coef0:value	EFS:Kernel_coef0
Kernel_Degree:value	EFS:Kernel_Degree
propability:value	EFS:propability
Shrink:value	EFS:Shrink
SVM_nu:value	EFS:SVM_nu
Cache_Size:value	EFS:Cache_Size
Epsilon_Loss:value	EFS:Epsilon_Loss
Kernel_Type:value	EFS:Kernel_Type
RFE_Remove_Percentage	EFS:Remove_Percentage
RFE_Epsilon_Tolerance	EFS:Epsilon_Tolerance
gamma	EFS:Kernel_Gamma
RFE_Cost	EFS:Cost
EFS_Bootstraps	EFS:Bootstraps
ExtractSeeds_and_Input:seeds	EFS:Seed
data_split:Data	EFS:Input
clac_ObjFunc:SimpleES	ES_out