A Balanced Approach to Adaptive Probability Density Estimation

• Main Authors: Julio A. Kovacs, Cailee Helmick, Willy Wriggers
• Format: Article
• Language: English
• Published: Frontiers Media S.A. 2017-04-01
• Series: Frontiers in Molecular Biosciences
• Subjects: adaptive density estimation; covariance ellipsoid; covariance smoothing; optimal number of nearest neighbors; R*-tree; visual criterion
• Online Access: http://journal.frontiersin.org/article/10.3389/fmolb.2017.00025/full

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.