Related papers: Concepts of Classification and Taxonomy. Phylogene…
Orthology is a central concept in evolutionary and comparative genomics, used to relate corresponding genes in different species. In particular, orthologs are needed to infer species trees. In this chapter, we introduce the fundamental…
Classification is an important supervised machine learning method, which is necessary and challenging issue for ecological research. It offers a way to classify a dataset into subsets that share common patterns. Notably, there are many…
Tuffley and Steel (1997) proved that Maximum Likelihood and Maximum Parsimony methods in phylogenetics are equivalent for sequences of characters under a simple symmetric model of substitution with no common mechanism. This result has been…
One of the main aims in phylogenetics is the estimation of ancestral sequences based on present-day data like, for instance, DNA alignments. One way to estimate the data of the last common ancestor of a given set of species is to first…
Clustering is a fundamental analysis tool aiming at classifying data points into groups based on their similarity or distance. It has found successful applications in all natural and social sciences, including biology, physics, economics,…
Metagenomics provides a powerful new tool set for investigating evolutionary interactions with the environment. However, an absence of model-based statistical methods means that researchers are often not able to make full use of this…
In recent years, automated, supervised classification techniques have been fruitfully applied to labeling and organizing large astronomical databases. These methods require off-line classifier training, based on labeled examples from each…
This paper introduces a variational formulation of natural selection, paying special attention to the nature of "things" and the way that different "kinds" of "things" are individuated from - and influence - each other. We use the Bayesian…
The taxonomy of galaxy morphology is critical in astrophysics as the morphological properties are powerful tracers of galaxy evolution. With the upcoming Large-scale Imaging Surveys, billions of galaxy images challenge astronomers to…
Phages are one of the most present groups of organisms in the biosphere. Their identification continues and their taxonomies are divergent. However, due to their evolution mode and the complexity of their species ecosystem, their…
In an effort to catalog insect biodiversity, we propose a new large dataset of hand-labelled insect images, the BIOSCAN-Insect Dataset. Each record is taxonomically classified by an expert, and also has associated genetic information…
We compare three basic kinds of discrete mathematical models used to portray phylogenetic relationships among species and higher taxa: phylogenetic trees, Hennig trees and Nelson cladograms. All three models are trees, as that term is…
Clustering is an unsupervised technique of Data Mining. It means grouping similar objects together and separating the dissimilar ones. Each object in the data set is assigned a class label in the clustering process using a distance measure.…
Biological systems reach organizational complexity that far exceeds the complexity of any known inanimate objects. Biological entities undoubtedly obey the laws of quantum physics and statistical mechanics. However, is modern physics…
Data classification, the process of analyzing data and organizing it into categories, is a fundamental computing problem of natural and artificial information processing systems. Ideally, the performance of classifier models would be…
Machine learning classifiers are widely used to make decisions with a major impact on people's lives (e.g. accepting or denying a loan, hiring decisions, etc). In such applications,the learned classifiers need to be both accurate and fair…
Clustering is an unsupervised machine learning methodology where unlabeled elements/objects are grouped together aiming to the construction of well-established clusters that their elements are classified according to their similarity. The…
Although taxonomy is often used informally to evaluate the results of phylogenetic inference and find the root of phylogenetic trees, algorithmic methods to do so are lacking. In this paper we formalize these procedures and develop…
Probabilistic programming frameworks are powerful tools for statistical modelling and inference. They are not immediately generalisable to phylogenetic problems due to the particular computational properties of the phylogenetic tree object.…
One thing that discriminates living things from inanimate matter is their ability to generate similarly complex or non-random architectures in a large abundance. From DNA sequences to folded protein structures, living cells, microbial…