Toby Kenney
YOU?
Author Swipe
View article: Evolutionary shift detection with ensemble variable selection
Evolutionary shift detection with ensemble variable selection Open
Abrupt environmental changes can lead to evolutionary shifts in trait evolution. Identifying these shifts is an important step in understanding the evolutionary history of phenotypes. The detection performances of different methods are inf…
View article: Detection of evolutionary shifts in variance under an Ornsten-Uhlenbeck model
Detection of evolutionary shifts in variance under an Ornsten-Uhlenbeck model Open
Sudden changes in environmental conditions can lead to evolutionary shifts not only in the optimal trait value, but also in the diffusion variance under the Ornstein-Uhlenbeck (OU) model. While several methods have been developed to detect…
View article: Rank selection for non‐negative matrix factorization
Rank selection for non‐negative matrix factorization Open
Non‐Negative Matrix Factorization (NMF) is a widely used dimension reduction method that factorizes a non‐negative data matrix into two lower dimensional non‐negative matrices: one is the basis or feature matrix which consists of the varia…
View article: Rank Selection for Non-negative Matrix Factorization
Rank Selection for Non-negative Matrix Factorization Open
Non-Negative Matrix Factorization (NMF) is a widely used dimension reduction method that factorizes a non-negative data matrix into two lower dimensional non-negative matrices: One is the basis or feature matrix which consists of the varia…
View article: The Community Coevolution Model with Application to the Study of Evolutionary Relationships between Genes Based on Phylogenetic Profiles
The Community Coevolution Model with Application to the Study of Evolutionary Relationships between Genes Based on Phylogenetic Profiles Open
Organismal traits can evolve in a coordinated way, with correlated patterns of gains and losses reflecting important evolutionary associations. Discovering these associations can reveal important information about the functional and ecolog…
View article: Evolutionary shift detection with ensemble variable selection
Evolutionary shift detection with ensemble variable selection Open
1. Abrupt environmental changes can lead to evolutionary shifts in trait evolution. Identifying these shifts is an important step in understanding the evolutionary history of phenotypes. 2. We propose an ensemble variable selection method …
View article: Stone Duality for Topological Convexity Spaces
Stone Duality for Topological Convexity Spaces Open
A convexity space is a set X with a chosen family of subsets (called convex subsets) that is closed under arbitrary intersections and directed unions. There is a lot of interest in spaces that have both a convexity space and a topological …
View article: Association between metabolic status and gut microbiome in obese populations
Association between metabolic status and gut microbiome in obese populations Open
Despite that obesity is associated with many metabolic diseases, a significant proportion (10–30 %) of obese individuals is recognized as ‘metabolically healthy obeses’ (MHOs). The aim of the current study is to characterize the gut microb…
View article: Deconvolution density estimation with penalised MLE
Deconvolution density estimation with penalised MLE Open
Deconvolution is the important problem of estimating the distribution of a quantity of interest from a sample with additive measurement error. Nearly all methods in the literature are based on Fourier transformation because it is mathemati…
View article: Stochastic Generalized Lotka-Volterra Model with An Application to Learning Microbial Community Structures
Stochastic Generalized Lotka-Volterra Model with An Application to Learning Microbial Community Structures Open
Inferring microbial community structure based on temporal metagenomics data is an important goal in microbiome studies. The deterministic generalized Lotka-Volterra differential (GLV) equations have been used to model the dynamics of micro…
View article: Application of OU processes to modelling temporal dynamics of the human microbiome, and calculating optimal sampling schemes.
Application of OU processes to modelling temporal dynamics of the human microbiome, and calculating optimal sampling schemes. Open
Background: The vast majority of microbiome research so far has focused on the structure of the microbiome at a single time-point. There have been several studies that measure the microbiome from a particular environment over time. A few m…
View article: Application of OU processes to modelling temporal dynamics of the human microbiome, and calculating optimal sampling schemes.
Application of OU processes to modelling temporal dynamics of the human microbiome, and calculating optimal sampling schemes. Open
Background: The vast majority of microbiome research so far has focused on the structure of the microbiome at a single time-point. There have been several studies that measure the microbiome from a particular environment over time. A few m…
View article: Application of OU processes to modelling temporal dynamics of the human microbiome, and calculating optimal sampling schemes.
Application of OU processes to modelling temporal dynamics of the human microbiome, and calculating optimal sampling schemes. Open
Background: The vast majority of Microbiome research so far has focused on the structure of the microbiome at a single time-point. There have been several studies that measure the microbiome from a particular environment over time. However…
View article: Temporal Dynamics of the Human Microbiome
Temporal Dynamics of the Human Microbiome Open
Background There has been a lot of research about the role of the microbiome in various processes. The research has focused almost exclusively on the structure of the microbiome at a single time-point. There have been several studies that …
View article: Discrepant gut microbiota markers for the classification of obesity-related metabolic abnormalities
Discrepant gut microbiota markers for the classification of obesity-related metabolic abnormalities Open
The gut microbiota (GM) is related to obesity and other metabolic diseases. To detect GM markers for obesity in patients with different metabolic abnormalities and investigate their relationships with clinical indicators, 1,914 Chinese adu…
View article: Consistency of Ranking Estimators
Consistency of Ranking Estimators Open
The ranking problem is to order a collection of units by some unobserved parameter, based on observations from the associated distribution. This problem arises naturally in a number of contexts, such as business, where we may want to rank …
View article: Learning Microbial Community Structures with Supervised and Unsupervised Non-negative Matrix Factorization
Learning Microbial Community Structures with Supervised and Unsupervised Non-negative Matrix Factorization Open
NMF is a powerful tool for identifying the key features of microbial communities. These identified features can not only be used to perform difficult classification problems with a high degree of accuracy, they are also very interpretable …
View article: Prior Distributions for Ranking Problems
Prior Distributions for Ranking Problems Open
The ranking problem is to order a collection of units by some unobserved parameter, based on observations from the associated distribution. This problem arises naturally in a number of contexts, such as business, where we may want to rank …
View article: The Adequate Bootstrap
The Adequate Bootstrap Open
There is a fundamental disconnect between what is tested in a model adequacy test, and what we would like to test. The usual approach is to test the null hypothesis "Model M is the true model." However, Model M is never the true model. A m…
View article: Partial-Sup Lattices
Partial-Sup Lattices Open
The study of sup lattices teaches us the important distinction between the algebraic part of the structure (in this case suprema) and the coincidental part of the structure (in this case infima). While a sup lattice happens to have all inf…