markovmodel / pyemma_tutorials

How to analyze molecular dynamics data with PyEMMA
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Systematic hyperparameter space search vs the current sequential approach #148

Closed cwehmeyer closed 6 years ago

cwehmeyer commented 6 years ago

Currently, we are choosing hyperparameters in a sequential manner. An alternative would be a fully systematic search in style of "Optimized parameter selection reveals trends in Markov state models for protein folding" (Husic et al, 2016).

We should briefly discuss both approaches and clearly describe how we are choosing our key hyperparameters.