Likelihood-based inference for discretely observed birth-death-shift processes, with applications to evolution of mobile genetic elements
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Publication:2809527
DOI10.1111/BIOM.12352zbMATH Open1419.62481arXiv1411.0031OpenAlexW2963297750WikidataQ40289220 ScholiaQ40289220MaRDI QIDQ2809527FDOQ2809527
Authors: Jason Xu, Peter Guttorp, Midori Kato-Maeda, Vladimir N. Minin 
Publication date: 30 May 2016
Published in: Biometrics (Search for Journal in Brave)
Abstract: Continuous-time birth-death-shift (BDS) processes are frequently used in stochastic modeling, with many applications in ecology and epidemiology. In particular, such processes can model evolutionary dynamics of transposable elements - important genetic markers in molecular epidemiology. Estimation of the effects of individual covariates on the birth, death, and shift rates of the process can be accomplished by analyzing patient data, but inferring these rates in a discretely and unevenly observed setting presents computational challenges. We propose a mutli-type branching process approximation to BDS processes and develop a corresponding expectation maximization (EM) algorithm, where we use spectral techniques to reduce calculation of expected sufficient statistics to low dimensional integration. These techniques yield an efficient and robust optimization routine for inferring the rates of the BDS process, and apply more broadly to multi-type branching processes where rates can depend on many covariates. After rigorously testing our methodology in simulation studies, we apply our method to study intrapatient time evolution of IS6110 transposable element, a frequently used element during estimation of epidemiological clusters of Mycobacterium tuberculosis infections.
Full work available at URL: https://arxiv.org/abs/1411.0031
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Markov processes: estimation; hidden Markov models (62M05) Applications of statistics to biology and medical sciences; meta analysis (62P10) Applications of branching processes (60J85) Continuous-time Markov processes on discrete state spaces (60J27)
Cites Work
- Estimating the dimension of a model
- Title not available (Why is that?)
- Transition probabilities for general birth-death processes with applications in ecology, genetics, and evolution
- Maximum likelihood estimation in the birth-and-death process
- Bayesian inference in a hidden stochastic two-compartment model for feline hematopoiesis
- Fast Fourier Methods in Computational Complex Analysis
- Spatial birth-death swap chains
- Statistical inference in a two-compartment model for hematopoiesis
- Estimation for general birth-death processes
- Estimating change rates of genetic markers using serial samples: applications to the transposon IS6110 in Mycobacterium tuberculosis
- Counting labeled transitions in continuous-time Markov models of evolution
- Fitting birth-death processes to panel data with applications to bacterial DNA fingerprinting
Cited In (11)
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- Birth/birth-death processes and their computable transition probabilities with biological applications
- Computational methods for birth-death processes
- Extinction probabilities and stationary distributions of mobile genetic elements in prokaryotes: the birth-death-diversification model
- Likelihood-Based Inference for Partially Observed Epidemics on Dynamic Networks
- Gain-loss-duplication models for copy number evolution on a phylogeny: exact algorithms for computing the likelihood and its gradient
- A numerical approach for evaluating the time-dependent distribution of a quasi birth-death process
- Parameter estimation for discretely observed linear birth‐and‐death processes
- Fitting birth-death processes to panel data with applications to bacterial DNA fingerprinting
- Computational tools for assessing gene therapy under branching process models of mutation
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