These are lecture notes that were delivered as a seminar (chalk talk) at the Pande Group lab meeting on February 12, 2016. They introduce some aspects theory of reversible Markov chains in a continuous state space, with an orientation towards models of the classical conformational dynamics of molecular systems.

The …

Last week, I started work on a new open source software project whose goal is to streamline hyperparameter optimization for machine learning algorithms. The tool is called osprey, and it's available on github, pypi, and readthedocs. It integrates closely with scikit-learn.

Osprey is designed to make hyperparameter optimization as easy …

I spoke this afternoon about our recent work [on arXiv] on the parameterization and cross-validation of Markovian models of molecular kinetics. The talk focus on the theory for a variational formulation of low-rank approximations to the kinetics of reversible dynamical systems. Check out the slide deck!

Some of our new work at the intersection of chemical physics and machine learning on the construction of Markov models is now out on arXiv and under review. The title of our manuscript is "Variational cross-validation of slow dynamical modes in molecular kinetics".

The question that lead down this road …