Notes on the Theory of Markov Chains in a Continuous State Space

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 …

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Efficient maximum likelihood parameterization of continuous-time Markov processes

This afternoon, I spoke on our recent work on arXiv on efficient estimation of continuous-time Markov processes (master equations) from discrete-time data. Check out the slide deck!

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What's new in MSMBuilder3!

The long awaited beta of MSMBuilder3 is here! I put together a short slide deck, which builds on some of Kyle Beauchamp slides, showing how the pieces fit together.

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Optimal Markov Models: Formulation & Pursuit

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!

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Cross-validating tICA and MSMs

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 …

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