24 papers · ranked by Valyu relevance
Ewelina Węglarz‐Tomczak, Jakub M. Tomczak, A. E. Eiben, Stanley Brul
Models in systems biology are mathematical descriptions of biological processes that are used to answer questions and gain a better understanding of biological phenomena. Dynamic models represent the network through rates of the production and consumption for the individual species. The ordinary differential equations…
N. A. Wardrop, W. C. Jochem, T. J. Bird, H. R. Chamberlain + 6 more
'D. Clarke' 'D. Kerr' 'L. Bengtsson' 'S. Juran' 'V. Seaman' 'A. J. Tatem'] Population numbers at local levels are fundamental data for many applications, including the delivery and planning of services, election preparation, and response to disasters. In resource-poor settings, recent and reliable demographic data at…
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 However, this data may become outdated during the intercensal period, which can stretch up to several decades.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…
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…
Mohammad-Reza Namazi-Rad, Payam Mokhtarian, Pascal Perez, Frederic Amblard
'Frederic Amblard'] Generating a reliable computer-simulated synthetic population is necessary for knowledge processing and decision-making analysis in agent-based systems in order to measure, interpret and describe each target area and the human activity patterns within it. In this paper, both synthetic reconstruction…
Scott Creel, Elias Rosenblatt
Estimates of population size are critical for conservation and management, but accurate estimates are difficult to obtain for many species. Noninvasive genetic methods are increasingly used to estimate population size, particularly in elusive species such as large carnivores, which are difficult to count by most other…
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…
Adrian E. Raftery, Leontine Alkema, Patrick Gerland
The United Nations regularly publishes projections of the populations of all the world's countries broken down by age and sex. These projections are the de facto standard and are widely used by international organizations, governments and researchers. Like almost all other population projections, they are produced…
Guillaume Péron, Mathieu Garel
We generalize the distance sampling protocol to accommodate three types of detection data in population surveys (population counts): distance to the observer, multiple observers, and time-to-detection. We also account for the effect of a partially-observed individual covariate, with the aim to account for the…
Kimberly F McManus
Background Sequencing and genotyping technology advancements have led to massive, growing repositories of spatially explicit genetic data and increasing quantities of temporal data (i.e., ancient DNA). These data will allow more complex and fine-scale inferences about population history than ever before; however, new…
Jahangheer S. Shaik, Asis Khan, Michael E. Grigg
The advent of new sequencing technologies has provided access to genome-wide markers which may be evaluated for their association with phenotypes. Recent studies have leveraged these technologies and sequenced hundreds and sometimes thousands of strains to improve the accuracy of genotype-phenotype predictions.…
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…
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…
Daniel J. Lawson
It is human nature to look for patterns in the natural world. One pattern is the grouping of individuals into populations based on observable features, be these anatomical, physiological, cultural, socio-economic, political or linguistic. Many of these groupings are for convenience – for example, we verbally group…
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…
Xin-Sheng Hu, Janika Simila, Sindey Schueler Platz, Stephen S. Moore + 3 more
Estimating animal abundance in industrial scale batches of ground meat is important for mapping meat products through the manufacturing process and for effectively tracing the finished product during a food safety recall. The processing of ground beef involves a potentially large number of animals from diverse sources…
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…
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…
Jaime Ashander, Peter Ralph, Evan McCartney-Melstad, H. Bradley Shaffer
In this paper, we study the general problem of extracting information from spatially explicit genomic data to inform inference of ecologically and geographically realistic population models. We describe methods and apply them to simulations motivated by the demography of the Mojave desert tortoise (Gopherus agassizii).…
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…
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…
Pier Francesco Palamara
Recent improvements in high-throughput genotyping and sequencing technologies have afforded the collection of massive, genome-wide datasets of DNA information from hundreds of thousands of individuals. These datasets, in turn, provide unprecedented opportunities to reconstruct the history of human populations and…
Authors not listed
People of color in the United States are disproportionately and unfairly exposed to air pollution. Equity-oriented scientific evaluations quantifying these disparities often use population-average exposure metrics to capture the overall inequality within a system. Utilizing these metrics involves choices about the…