byun-jinyoung / sml_cv

Using supervised machine learning to build collective variables for accelerated sampling

Supervised Machine Learning + Enhanced sampling

Using supervised machine learning to build starting collective variables for accelerated sampling

This project is designed to answer the following question: Given sampling in state A and state B, how does one go about picking some collective variable capable of going between them via an ennhanced sampling framework. We argue that the decision function from any differentiable supervised machine learning algorithm represents a good starting CV. This repo contains the necessary details for reproducing the results from our manuscript showing that :

Sultan et al: Decision functions from supervised machine learning algorithms as collective variables for accelerating molecular simulations, arXiv preprint

The general idea can be summarized using the picture below:

Given some sampling in the start and end states, a SML algorithm such as a Support Vector Machine can find a hyper plane that maximally divides those states. Then the distance to this plane can be used as a collective variable in molecular dynamics and enhanced sampling calculations.

We can compute this decision function, which basically measures this distance, in a variety of different ways. For example, in logistic regression methods, this is done via a sigmoid of the linear weights. SML based CVs can use non-linearity via kernels or neural network based classifiers. Multiple states can be incorporated via bias-exchange. For more details, please see the manuscript. At its core, if any classification algorithm can distinguish between start and end states, then its decision function is a good starting point for acclerating sampling between those states.

The full algorithm is rather simple as shown below:

The repo requires several other python and non-python packages including MSMBuilder, MSMExplorer, tica_metadynamics, scikit-learn, Plumed, and OpenMM .

1). The folders contains the ipython notebooks + setup scripts needed to reproduce the main results of the paper. It also contains a step-by-step guide on how to generate input files needed for Plumed to able to run Metadynamics using the SML's decision function as the collective variable.