Related papers: Complimentary Phylogenetic Signals for Morphologic…
This thesis concerns multivariate phylogenetic comparative methods. We investigate two aspects of them. The first is the bias caused by measurement error in regression studies of comparative data. We calculate the formula for the bias and…
The last few million years on planet Earth have witnessed two remarkable phases of hominid development, starting with a phase of biological evolution characterised by rather rapid increase of the size of the brain. This has been followed by…
A recent paper (Manceau and Lambert, 2016) developed a novel approach for describing two well-defined notions of 'species' based on a phylogenetic tree and a phenotypic partition. In this paper, we explore some further combinatorial…
Drosophila melanogaster, a small dipteran of African origin, represents one of the best-studied model organisms. Early work in this system has uniquely shed light on the basic principles of genetics and resulted in a versatile collection of…
Biological phenotypes are products of complex evolutionary processes in which selective forces influence multiple biological trait measurements in unknown ways. Phylogenetic factor analysis disentangles these relationships across the…
Data-driven brain parcellations aim to provide a more accurate representation of an individual's functional connectivity, since they are able to capture individual variability that arises due to development or disease. This renders…
We compare the phylogenetic tensors for various trees and networks for two, three and four taxa. If the probability spaces between one tree or network and another are not identical then there will be phylogenetic tensors that could have…
Species trees represent the historical divergences of populations or species, while gene trees trace the ancestry of individual gene copies sampled within those populations. In cases involving rapid speciation, gene trees with topologies…
The inference of evolutionary histories is a central problem in evolutionary biology. The analysis of a sample of phylogenetic trees can be conducted in Billera-Holmes-Vogtmann tree space, which is a CAT(0) metric space of phylogenetic…
A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called…
Despite the common misconception of nearly static organisms, plants do interact continuously with the environment and with each other. It is fair to assume that during their evolution they developed particular features to overcome problems…
Computational topologists recently developed a method, called persistent homology to analyze data presented in terms of similarity or dissimilarity. Indeed, persistent homology studies the evolution of topological features in terms of a…
Testing fit of data to model is fundamentally important to any science, but publications in the field of phylogenetics rarely do this. Such analyses discard fundamental aspects of science as prescribed by Karl Popper. Indeed, not without…
The Hubble tuning fork diagram, based on morphology and established in the 1930s, has always been the preferred scheme for classification of galaxies. However, the current large amount of data up to higher and higher redshifts asks for more…
Online genealogy datasets contain extensive information about millions of people and their past and present family connections. This vast amount of data can assist in identifying various patterns in human population. In this study, we…
Distance-based phylogenetic algorithms attempt to solve the NP-hard least squares phylogeny problem by mapping an arbitrary dissimilarity map representing biological data to a tree metric. The set of all dissimilarity maps is a Euclidean…
Conversational human-likeness plays a central role in human-AI interaction, yet it has remained difficult to define, measure, and optimize. As a result, improvements in human-like behavior are largely driven by scale or broad supervised…
Large Language Models (LLMs) have emerged as dominant foundational models in modern NLP. However, the understanding of their prediction processes and internal mechanisms, such as feed-forward networks (FFN) and multi-head self-attention…
Describing a complex system is in many ways a problem akin to identifying an object, in that it involves defining boundaries, constituent parts and their relationships by the use of grouping laws. Here we propose a novel method which…
Phenomics is an emerging branch of modern biology that uses high throughput phenotyping tools to capture multiple environmental and phenotypic traits, often at massive spatial and temporal scales. The resulting high dimensional data…