26 papers · ranked by Valyu relevance
Daniel Gaissmaier, Matthias van den Borg, Donato Fantauzzi, Timo Jacob
In this work, we demonstrate the superior exploration capabilities of the population-based methods over the sequential one-parameter parabolic interpolation (SOPPI) approach to optimise ReaxFF force field parameters. Evolutionary algorithms (EAs) are heuristic-based approaches using a population of concurrent models in…
Kemin Zhu, Ling Yin, Kang Liu, Junli Liu + 5 more
'Hongyang Zou' 'Huibin Du' 'Benjamin Althouse'] Agent-based models have gained traction in exploring the intricate processes governing the spread of infectious diseases, particularly due to their proficiency in capturing nonlinear interaction dynamics. The fidelity of agent-based models in replicating real-world…
Gianluca Boo, Edith Darin, Douglas R. Leasure, Claire A. Dooley + 10 more
The national census is an essential data source to support decision-making in many areas of public interest. However, this data may become outdated during the intercensal period, which can stretch up to several decades. In this study, we develop a Bayesian hierarchical model leveraging recent household surveys and…
Dhruv Vyas, Erik Jørgensen, Yu-Hsiang Wu, Octav Chipara
Adults with mild-to-moderate hearing loss can use over-the-counter hearing aids to treat their hearing loss at a fraction of traditional hearing care costs. These products incorporate self-fitting methods that allow end-users to configure their hearing aids without the help of an audiologist. A self-fitting method…
Travis J. Struck, Andrew H. Vaughn, Austin Daigle, Dylan D. Ray + 13 more
Evaluating population genetic inference methods is challenging due to the complexity of evolutionary histories, potential model misspecification, and unconscious biases in self-assessment. The Genomic History Inference Strategies Tournament (GHIST) is a community-driven competition designed to evaluate methods for…
Brianna Greenstein, Danielle Elsey, Geoffrey Hutchison
Genetic algorithms (GAs) are a powerful tool to search large chemical spaces for inverse molecular design. However, GAs have multiple hyperparameters that have not been thoroughly investigated for chemical space searches. In this work, we examine the general effects of a number of hyperparameters, such as population…
Enrique Santiago, Carlos Köpke, Armando Caballero
Linkage disequilibrium methods for demographic inference usually rely on panmictic population models. However, the structure of natural populations is generally complex and the quality of the genotyping data is often suboptimal. We present two software tools that implement theoretical developments to estimate the…
Pascal Jutras-Dubé, Mohammad B. Al-Khasawneh, Zhichao Yang, Javier Bas + 2 more
'Javier Bas' 'Fabian Bastin' 'Cinzia Cirillo'] Population synthesis consists of generating synthetic but realistic representations of a target population of micro-agents for the purpose of behavioral modeling and simulation. We introduce a new framework based on copulas to generate synthetic data for a target…
Gianluca Boo, Édith Darin, Douglas R. Leasure, Claire Dooley + 10 more
'Heather Chamberlain' 'Attila N. Lázár' 'Kevin Tschirhart' 'Cyrus Sinai' 'Nicole A. Hoff' 'Trevon Fuller' 'Kamy Musene' 'Arly Batumbo' 'Anne W. Rimoin' 'Andrew J. Tatem'] 1WorldPop, School of Geography and Environmental Science, University of Southampton, Southampton, UK 2Center for International Earth Science…
Piotr Chlebicki, Maciej Beręsewicz
Population size estimation is a major challenge in official statistics, social sciences, and natural sciences. The problem can be tackled by applying capture-recapture methods, which vary depending on the number of sources used, particularly on whether a single or multiple sources are involved. This paper focuses on…
Vladimir Shchur, Débora Y. C. Brandt, Anna Ilina, Rasmus Nielsen
The estimation of effective population sizes (N_e_) through time is of fundamental interest in population genetics, but the interpretation of N_e_ as the effective number of breeding individuals in the population is challenged by the effect of population structure. In fact, variation in N_e_ reported in many studies…
Robin S. Waples
The Wright-Fisher model, which directs how matings occur and how genes are transmitted across generations, has long been a lynchpin of evolutionary biology. This model is elegantly simple, analytically tractable, and easy to implement, but it has one serious limitation: essentially no real species satisfies its many…
Imran Mahmood, Nicholas Bishop, Anisoara Calinescu, Michael Wooldridge + 1 more
hierarchical population synthesis Authors: ['Imran Mahmood' 'Nicholas Bishop' 'Anisoara Calinescu' 'Michael Wooldridge' 'Ioannis Zachos'] In agent-based simulations, synthetic populations of agents are commonly used to represent the structure, behaviour, and interactions of individuals. However, generating a synthetic…
Meaghan I. Clark, Sarah W. Fitzpatrick, Gideon S. Bradburd
Detecting recent demographic changes is a crucial component of species conservation and management, as many natural populations face declines due to anthropogenic habitat alteration and climate change. Genetic methods allow researchers to detect changes in effective population size (Ne) from sampling at a single…
Jerzy Wieczorek, Grayson W. White, Zachariah W. Cody, Emily X. Tan + 4 more
'Jacqueline O. Chistolini' 'Kelly S. McConville' 'Tracey S. Frescino' 'Gretchen G. Moisen'] Comparing and evaluating small area estimation (SAE) models for a given application is inherently difficult. Typically, we do not have enough data in many areas to check unit-level modeling assumptions or to assess unit-level…
Mirjam J Borger, Jan Komdeur, David S Richardson, Franz J Weissing + 1 more
'Peter Buston'] Title: Abstract Quantifying fitness is important to understand adaptive evolution. Reproductive values are useful for making fitness comparisons involving different categories of individuals, like males and females. By definition, the reproductive value of a category is the expected per capita…
Stephanie M. Wu, Briana Joy K. Stephenson
Understanding how and why certain communities bear a disproportionate burden of disease is challenging due to the scarcity of data on these communities. Surveys provide a useful avenue for accessing hard-to-reach populations, as many surveys specifically oversample understudied and vulnerable populations. When survey…
Tiziana Tuoto, Davide Di Cecco, Andrea Tancredi
The identification and treatment of “one-inflation” in estimating the size of an elusive population has received increasing attention in capture-recapture literature in recent years. The phenomenon occurs when the number of units captured exactly once clearly exceeds the expectation under a baseline count distribution.…
Robert Arbon, Yanchen Zhu, Antonia S. J. S. Mey
Markov state models (MSM) are a popular statistical method for analyzing the conformational dynamics of proteins, including protein folding. With all statistical and machine learning (ML) models choices must be made about the modeling pipeline that cannot be directly learned from the data. These choices, or…
Authors not listed
Finding the most stable adsorption geometry of a flexible molecule on a catalytic surface remains a key challenge due to the high dimensionality and ruggedness of the potential energy surface. We present a Gradient-Enhanced Genetic Algorithm (GE-GA) for the global optimization of adsorbate–surface configurations…
Felix T. Petersma, Len Thomas, Danielle Harris, Darcy Bradley + 1 more
'Yannis P. Papastamatiou'] Title: Abstract Population size is a key parameter for the conservation of animal species. Close-kin mark-recapture (CKMR) relies on the observed frequency and type of kinship among individuals sampled from the population to estimate population size. Knowledge of the age of the individuals…
Charles W. Champ, Andrew V. Sills
A case is made that researchers are interested in studying processes. Often the inferences they are interested in making are about the process and its associated population. On other occasions, a researcher may be interested in making an inference about the collection of individuals the process has generated. We will…
Ruoyi Cai, Brian L. Browning, Sharon R. Browning
Effective population size (N_e_) in the recent past can be estimated through analysis of identity-by-descent (IBD) segments. Several methods have been developed for estimating N_e_ from autosomal IBD segments, but no such effort has been made with X chromosome IBD segments. In this work, we propose a method to estimate…
Armando Caballero, Santiago C. González-Martínez, Enrique Santiago
Estimation of the effective size (N_e_) of large populations with a continuous distribution across wide geographic areas and limited dispersal of individuals has been elusive so far. Estimates of the contemporary N_e_ from genetic markers for such large, structured populations, typically of plant and marine species…
Robin S. Waples
Researchers often use more than one genetic method to estimate contemporary effective population size (N_e_), but few formally combine multiple estimates despite the potential benefits for increasing precision. Maximizing these benefits requires an optimal, inverse-variance weighting scheme. A precondition for…
David Lundberg, Landon Kilgallon, Julian Cooper, Francesca Starvaggi + 2 more
An understanding of monomer sequence is required to predict and engineer the properties of copolymers. Typically, comonomer sequence is inferred or determined from reactivity ratios, which are measured through copolymerization experiments. The accurate determination of reactivity ratios from copolymerizations where one…