Biomarker Identification via RFE on the Grid
Created: 2013-08-13 17:18:58
Last updated: 2013-09-24 08:17:01
The first two components split the original data set into several sub-sampling sets. The RFE component performs the machine learning approach by executing several instances of a SVM, each of which consuming one sub-sample data set. The execution of the SVM takes place in a distributed computing environment. 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 (6)
| Name |
Description |
| Input_file |
|
| number_iterations |
|
| gold_standard |
|
| RFE_Remove_Percentage |
|
| RFE_Cost |
|
| RFE_Epsilon_Tolerance |
|
Processors (16)
| Name |
Type |
Description |
| DataSplit_And_Seed |
externaltool |
|
| 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";
|
| RFE |
activity |
|
| out_folder_value |
stringconstant |
Value. |
| Kernel_Type |
stringconstant |
Value0 |
| Cache_Size |
stringconstant |
Value100 |
| Epsilon_Loss |
stringconstant |
Value0.001 |
| Kernel_coef0 |
stringconstant |
Value0 |
| Kernel_Degree |
stringconstant |
Value3 |
| Kernel_Gamma |
stringconstant |
Value0.25 |
| propability |
stringconstant |
Value0 |
| Shrink |
stringconstant |
Value1 |
| SVM_nu |
stringconstant |
Value0.5 |
| SVM_Type |
stringconstant |
Value0 |
| Beanshell_2 |
beanshell |
|
| clac_ObjFunc_2 |
activity |
|
Beanshells (2)
| Name |
Description |
Inputs |
Outputs |
| ExtractSeeds_and_Input |
|
in1
|
seeds
file_path
|
| Beanshell_2 |
|
in1
|
out1
|
Outputs (1)
| Name |
Description |
| Beanshell_2_out1 |
|
Datalinks (23)
| Source |
Sink |
| Input_file |
DataSplit_And_Seed:file |
| number_iterations |
DataSplit_And_Seed:number_iterations |
| out_folder_value:value |
DataSplit_And_Seed:out_folder |
| DataSplit_And_Seed:STDOUT |
ExtractSeeds_and_Input:in1 |
| ExtractSeeds_and_Input:seeds |
RFE:Seed |
| ExtractSeeds_and_Input:file_path |
RFE:Input |
| RFE_Remove_Percentage |
RFE:Remove_Percentage |
| RFE_Cost |
RFE:Cost |
| Kernel_Type:value |
RFE:Kernel_Type |
| Cache_Size:value |
RFE:Cache_Size |
| Kernel_coef0:value |
RFE:Kernel_coef0 |
| Kernel_Degree:value |
RFE:Kernel_Degree |
| Kernel_Gamma:value |
RFE:Kernel_Gamma |
| propability:value |
RFE:propability |
| Shrink:value |
RFE:Shrink |
| SVM_nu:value |
RFE:SVM_nu |
| SVM_Type:value |
RFE:SVM_Type |
| Epsilon_Loss:value |
RFE:Epsilon_Loss |
| RFE_Epsilon_Tolerance |
RFE:Epsilon_Tolerance |
| clac_ObjFunc_2:SimpleES |
Beanshell_2:in1 |
| RFE:RFEOutput |
clac_ObjFunc_2:Input_files |
| gold_standard |
clac_ObjFunc_2:Gold_standard |
| Beanshell_2:out1 |
Beanshell_2_out1 |
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