Biomarker Identification via EFS on the Grid
Created: 2013-08-13 17:23:30
Last updated: 2013-09-24 08:18:53
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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Workflow Components
Authors (0)
Titles (0)
Descriptions (0)
Dependencies (0)
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 |
ScriptString 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 |
Value0 |
| Cache_Size |
stringconstant |
Value100 |
| Epsilon_Loss |
stringconstant |
Value0.1 |
| Kernel_coef0 |
stringconstant |
Value0 |
| Kernel_Degree |
stringconstant |
Value3 |
| propability |
stringconstant |
Value0 |
| Shrink |
stringconstant |
Value1 |
| SVM_nu |
stringconstant |
Value0.5 |
| SVM_Type |
stringconstant |
Value0 |
| clac_ObjFunc |
activity |
|
| data_split |
activity |
|
| EFS |
activity |
|
Beanshells (1)
| Name |
Description |
Inputs |
Outputs |
| ExtractSeeds_and_Input |
|
in1
|
seeds
file_path
|
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 |
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Version 2 (latest)
(of 2)
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