How did you determine the threshold "0.335"

[HarveyYan]

Kudos for the nice work.
One lttle question I have wondered whilst reading your paper was about that threshold which converts probabilities to basepairs.
Would you mind clarifying a bit how it was chosen?

[jaswindersingh2]

Hi Yan,

The threshold was determined by maximizing the Matthews Correlation Coefficient (MCC) on validation set (VL1). MCC was calculated for 1000 values between 0 and 1 at sampling rate 0.001. MCC on validation set was maximum at 0.335, therefore, we selected this value. All the model parameters were optimized for the validation sets.

Jaswinder

[HarveyYan]

Thanks for the prompt reply!