Document Type

Article

Publication Date

4-2017

DOI

10.3389/fmolb.2017.00025

Publication Title

Frontiers in Molecular Biosciences

Volume

4

Issue

(Article 25)

Pages

1-13

Abstract

Our development of a Fast (Mutual) Information Matching (FIM) of molecular dynamics time series data led us to the general problem of how to accurately estimate the probability density function of a random variable, especially in cases of very uneven samples. Here, we propose a novel Balanced Adaptive Density Estimation (BADE) method that effectively optimizes the amount of smoothing at each point. To do this, BADE relies on an efficient nearest-neighbor search which results in good scaling for large data sizes. Our tests on simulated data show that BADE exhibits equal or better accuracy than existing methods, and visual tests on univariate and bivariate experimental data show that the results are also aesthetically pleasing. This is due in part to the use of a visual criterion for setting the smoothing level of the density estimate. Our results suggest that BADE offers an attractive new take on the fundamental density estimation problem in statistics. We have applied it on molecular dynamics simulations of membrane pore formation. We also expect BADE to be generally useful for low-dimensional applications in other statistical application domains such as bioinformatics, signal processing and econometrics.

Comments

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY).

Original Publication Citation

Kovacs, J. A., Helmick, C., & Wriggers, W. (2017). A balanced approach to adaptive probability density estimation. Frontiers in Molecular Biosciences, 4(Article 25), 1-13. doi:10.3389/fmolb.2017.00025