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Expression Predictor Quick Start Guide

1.1 Training/Testing Set Validation Over a Single Run

1. Double click on ExP.bat

2. Click on Project and select Load Data

Select Load Data

3. Select Input file

Select file and then "open" button

4. Click Open

Select the training set in the original set panel

5. Select the Training Set

Click on the "Insert" button

6. Click on the "Insert>>" button on the Training Set Panel

Select the testing set

7. Select the Testing Set

Click on the "Insert" button

8. Click on the "Insert>>" button on the Testing Set Panel

Select the vigilance value

9. Select a vigilance value from the slider

Click the "Submit" button at the bottom of the window

10. Click on the "Submit button

Click on the Prediction Tab in the upper left hand corner

11. Click on the Prediction Tab to view the confusion matrix

Confusion matrix

12. Click on one of the numbers in the confusion matrix to view the list of samples that corresponds the prediction in the selected cell from the matrix

Prediction: Clofibrate highlighted in the confusion matrix
Prediction: Clofibrate

1.2 Training/Testing Set Validation over the Entire Vigilance Spectrum

1. Repeat steps 1 to 8 from Section 1.1

2. Click on the checkbox that says "Apply All Values in Vigilance Spectrum"

Check "Apply All Values in Vigilance Spectrum"

3. Repeat steps 10 from Section 1.1
4. Click on Prediction Tab to view the prediction results using vigilance values from 0 to 1 with 0.01 increment at each cycle

Prediction tab

5. Click on "Save As Text (Tab delimited), enter the filename, and click Save.

Enter filename in the text field

2.1 Leave One Out Cross Validation a Single Run

1. Repeat steps 1 to 4 from Section 1.1

2. Select Leave One Out Cross Validation

Select "Leave One Out Cross Validation" under Validation

3. Click on the Submit button

Click on the "Submit" button

4. Click on the Prediction Tab to view the confusion matrix

Confusion matrix

5. Click on one of the numbers in the confusion matrix to view the list of samples that corresponds to the prediction in the selected cell from the matrix.

In the prediction tab, a value from Clofibrate is selected
Prediction: Clofibrate

2.2 Leave One Out Cross Validation over the Entire Vigilance Spectrum

1. Repeat steps 1 and 2 from Section 2.1

2. Click on the checkbox that says “Apply All Values in Vigilance Spectrum”

Click on "Apply All Values in Vigilance Spectrum" in the Parameters tab

3. Repeat steps 3 Section 2.1

4. Click on Prediction Tab to view the prediction results using vigilance values from 0 to 1 with 0.01 increment at each cycle

Under Predictions tab, save prediction as tab-delimited text file

5. Repeat step 5 from Section 1.2 to save prediction as tab-delimited text file.

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