Search results for "Monte Carlo method."
showing 10 items of 1217 documents
Importance sampling for Lambda-coalescents in the infinitely many sites model
2011
We present and discuss new importance sampling schemes for the approximate computation of the sample probability of observed genetic types in the infinitely many sites model from population genetics. More specifically, we extend the 'classical framework', where genealogies are assumed to be governed by Kingman's coalescent, to the more general class of Lambda-coalescents and develop further Hobolth et. al.'s (2008) idea of deriving importance sampling schemes based on 'compressed genetrees'. The resulting schemes extend earlier work by Griffiths and Tavar\'e (1994), Stephens and Donnelly (2000), Birkner and Blath (2008) and Hobolth et. al. (2008). We conclude with a performance comparison o…
Assessing the impact of copy number variants on miRNA genes in autism by Monte Carlo simulation.
2014
Autism Spectrum Disorders (ASDs) are childhood neurodevelopmental disorders with complex genetic origins. Previous studies have investigated the role of de novo Copy Number Variants (CNVs) and microRNAs as important but distinct etiological factors in ASD. We developed a novel computational procedure to assess the potential pathogenic role of microRNA genes overlapping de novo CNVs in ASD patients. Here we show that for chromosomes # 1, 2 and 22 the actual number of miRNA loci affected by de novo CNVs in patients was found significantly higher than that estimated by Monte Carlo simulation of random CNV events. Out of 24 miRNA genes over-represented in CNVs from these three chromosomes only …
Effect of inter-crystal scatter on estimation methods for random coincidences and subsequent correction.
2008
Random coincidences can contribute substantially to the background in positron emission tomography (PET). Several estimation methods are being used for correcting them. The goal of this study was to investigate the validity of techniques for random coincidence estimation, with various low-energy thresholds (LETs). Simulated singles list-mode data of the MADPET-II small animal PET scanner were used as input. The simulations have been performed using the GATE simulation toolkit. Several sources with different geometries have been employed. We evaluated the number of random events using three methods: delayed window (DW), singles rate (SR) and time histogram fitting (TH). Since the GATE simula…
Modeling Spatial Data Pooled over Time: Schematic Representation and Monte Carlo Evidences
2015
The spatial autocorrelation issue is now well established, and it is almost impossible to deal with spatial data without considering this reality. In addition, recent developments have been devoted to developing methods that deal with spatial autocorrelation in panel data. However, little effort has been devoted to dealing with spatial data (cross-section) pooled over time. This paper endeavours to bridge the gap between the theoretical modeling development and the application based on spatial data pooled over time. The paper presents a schematic representation of how spatial links can be expressed, depending on the nature of the variable, when combining the spatial multidirectional relatio…
OPKINE, a multipurpose program for kinetics
1991
The program OPKINE is presented for the study of reaction mechanisms and multicomponent analysis in dynamic conditions. This program is written in FORTRAN-77 for IBM 30/90 and VAX 8300 computers, and permits the simultaneous evaluation of both rate constants and initial reagent concentrations or, alternatively, rate constants and sensitivities. Up to 20 kinetic curves, with up to 400 points each, can be treated to evaluate up to 40 parameters. Integration of the system of differential equations is performed by means of the Runge–Kutta–Fehlberg method. OPKINE is provided with the Simplex, and modified versions of the Davidon–Fletcher–Powell and Gauss–Newton–Marquardt optimization methods. A …
PenRed: An extensible and parallel Monte-Carlo framework for radiation transport based on PENELOPE
2021
Monte Carlo methods provide detailed and accurate results for radiation transport simulations. Unfortunately, the high computational cost of these methods limits its usage in real-time applications. Moreover, existing computer codes do not provide a methodology for adapting these kinds of simulations to specific problems without advanced knowledge of the corresponding code system, and this restricts their applicability. To help solve these current limitations, we present PenRed, a general-purpose, stand-alone, extensible and modular framework code based on PENELOPE for parallel Monte Carlo simulations of electron-photon transport through matter. It has been implemented in C++ programming la…
Population Monte Carlo Schemes with Reduced Path Degeneracy
2017
Population Monte Carlo (PMC) algorithms are versatile adaptive tools for approximating moments of complicated distributions. A common problem of PMC algorithms is the so-called path degeneracy; the diversity in the adaptation is endangered due to the resampling step. In this paper we focus on novel population Monte Carlo schemes that present enhanced diversity, compared to the standard approach, while keeping the same implementation structure (sample generation, weighting and resampling). The new schemes combine different weighting and resampling strategies to reduce the path degeneracy and achieve a higher performance at the cost of additional low computational complexity cost. Computer si…
Monte Carlo Application in Brachytherapy Dosimetry
2009
This paper devoted to Monte-Carlo Applications in BT Dosimetry is organized in four parts: 1. Motivation of the use of Monte Carlo in brachytherapy 2. The use of Monte Carlo to obtain dose distribution around brachytherapy sources 3. Experimental dosimetry versus Monte Carlo 4. Others Monte Carlo applications in brachytherapy
Estimation of confidence limits for descriptive indexes derived from autoregressive analysis of time series: Methods and application to heart rate va…
2017
The growing interest in personalized medicine requires making inferences from descriptive indexes estimated from individual recordings of physiological signals, with statistical analyses focused on individual differences between/within subjects, rather than comparing supposedly homogeneous cohorts. To this end, methods to compute confidence limits of individual estimates of descriptive indexes are needed. This study introduces numerical methods to compute such confidence limits and perform statistical comparisons between indexes derived from autoregressive (AR) modeling of individual time series. Analytical approaches are generally not viable, because the indexes are usually nonlinear funct…
Sorting of Single Biomolecules based on Fourier Polar Representation of Surface Enhanced Raman Spectra
2016
AbstractSurface enhanced Raman scattering (SERS) spectroscopy becomes increasingly used in biosensors for its capacity to detect and identify single molecules. In practice, a large number of SERS spectra are acquired and reliable ranking methods are thus essential for analysing all these data. Supervised classification strategies, which are the most effective methods, are usually applied but they require pre-determined models or classes. In this work, we propose to sort SERS spectra in unknown groups with an alternative strategy called Fourier polar representation. This non-fitting method based on simple Fourier sine and cosine transforms produces a fast and graphical representation for sor…