We provide an internal validation study of a recently published precise DNA mixture algorithm based on Hamiltonian Monte Carlo sampling (Susik et al., 2022). We provide results for all 428 mixtures analysed by Riman et al. (2021) and compare the results with two state-of-the-art software products: STRmix™ v2.6 and Euroformix v3.4.0. The comparison shows that the Hamiltonian Monte Carlo method provides reliable values of likelihood ratios (LRs) close to the other methods. We further propose a novel large-scale precision benchmark and quantify the precision of the Hamiltonian Monte Carlo method, indicating its improvements over existing solutions. Finally, we analyse the influence of the factors discussed by Buckleton et al. (2022).
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http://dx.doi.org/10.1016/j.fsigen.2023.102840 | DOI Listing |
Bull Math Biol
January 2025
Section of Epidemiology, University of Copenhagen, Copenhagen, Denmark.
Using genetic data to infer evolutionary distances between molecular sequence pairs based on a Markov substitution model is a common procedure in phylogenetics, in particular for selecting a good starting tree to improve upon. Many evolutionary patterns can be accurately modelled using substitution models that are available in closed form, including the popular general time reversible model (GTR) for DNA data. For more complex biological phenomena, such as variations in lineage-specific evolutionary rates over time (heterotachy), other approaches such as the GTR with rate variation (GTR ) are required, but do not admit analytical solutions and do not automatically allow for likelihood calculations crucial for Bayesian analysis.
View Article and Find Full Text PDFAm Stat
February 2024
Department of Biostatistics, UCLA.
This paper advocates proximal Markov Chain Monte Carlo (ProxMCMC) as a flexible and general Bayesian inference framework for constrained or regularized estimation. Originally introduced in the Bayesian imaging literature, ProxMCMC employs the Moreau-Yosida envelope for a smooth approximation of the total-variation regularization term, fixes variance and regularization strength parameters as constants, and uses the Langevin algorithm for the posterior sampling. We extend ProxMCMC to be fully Bayesian by providing data-adaptive estimation of all parameters including the regularization strength parameter.
View Article and Find Full Text PDFFront Public Health
December 2024
Department of Epidemiology and Biostatistics, Institute of Public Health, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia.
Background: The postnatal period is a critical period for both mothers and their newborns for their health. Lack of early postnatal care (PNC) services during a 2-day period is a life-threatening situation for both the mother and the babies. However, no data have been examined for PNCs in East Africa.
View Article and Find Full Text PDFJ Chem Phys
December 2024
Department of Chemistry, University of Colorado, Boulder, Colorado 80302, USA.
In this article, we combine the periodic sinc basis set with a curvilinear coordinate system for electronic structure calculations. This extension allows for variable resolution across the computational domain, with higher resolution close to the nuclei and lower resolution in the inter-atomic regions. We address two key challenges that arise while using basis sets obtained by such a coordinate transformation.
View Article and Find Full Text PDFEntropy (Basel)
October 2024
Department of Theoretical Physics and Astrophysics, Institute of Physics, Faculty of Science, Pavol Jozef Šafárik University in Košice, Park Angelinum 9, 041 54 Košice, Slovakia.
We propose spin models that can display an arbitrary number of phase transitions. The models are based on the standard XY model, which is generalized by including higher-order nematic terms with exponentially increasing order and linearly increasing interaction strength. By employing Monte Carlo simulation we demonstrate that under certain conditions the number of phase transitions in such models is equal to the number of terms in the generalized Hamiltonian and, thus, it can be predetermined by construction.
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