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Universal sample size invariant measures for uncertainty quantification in density estimation
Title
Universal sample size invariant measures for uncertainty quantification in density estimation
Author
Jacobs, Donald J., Farmer, Jenny, Merino, Zach, Merino, Zach
Date Created
2019
Subjects--Topical
Statistics, Entropy
Description
Previously, we developed a high throughput non-parametric maximum entropy method (PLOS ONE, 13(5): e0196937, 2018) that employs a log-likelihood scoring function to characterize uncertainty in trial probability density estimates through a scaled q...
Statistical measures to quantify similarity between molecular dynamics simulation trajectories
Title
Statistical measures to quantify similarity between molecular dynamics simulation trajectories
Author
Jacobs, Donald J., Farmer, Jenny, Kanwal, Fareeha, Nikulsin, Nikita
Date Created
2017
Subjects--Topical
Molecular dynamics, Statistics
Description
Molecular dynamics simulation is commonly employed to explore protein dynamics. Despite the disparate timescales between functional mechanisms and molecular dynamics (MD) trajectories, functional differences are often inferred from differences in ...
New Algorithms for Protein Structure Analysis: From Nonparametric Density Estimation to Characterization of Molecular Volume Spatial Distributions
Title
New Algorithms for Protein Structure Analysis: From Nonparametric Density Estimation to Characterization of Molecular Volume Spatial Distributions
Author
Farmer, Jenny
Date Created
2018
Subjects--Topical
Bioinformatics, Biophysics, Physics
Description
The Flexibility and Stability Test (FAST) is a C++ class library designed in the early 2000’s to execute free energy decomposition and reconstitution operations applied to protein structures. The library has been substantially expanded to include ...
MATLAB tool for probability density assessment and nonparametric estimation
Title
MATLAB tool for probability density assessment and nonparametric estimation
Author
Jacobs, Donald J., Farmer, Jenny
Date Created
2022
Subjects--Topical
Statistics, Entropy
Description
A MATLAB function is presented for nonparametric probability density estimation, based on an iterative method that employs the principle of maximum entropy and characteristic properties of single order statistics. Featuring a robust and adaptive d...
High throughput nonparametric probability density estimation
Title
High throughput nonparametric probability density estimation
Author
Jacobs, Donald J., Farmer, Jenny
Date Created
2018
Subjects--Topical
Statistics, Probabilities
Description
In high throughput applications, such as those found in bioinformatics and finance, it is important to determine accurate probability distribution functions despite only minimal information about data characteristics, and without using human subje...