Related papers: Concepts of Classification and Taxonomy. Phylogene…
We introduce a novel approach for discriminative classification using evolutionary algorithms. We first propose an algorithm to optimize the total loss value using a modified 0-1 loss function in a one-dimensional space for classification.…
We here introduce a novel classification approach adopted from the nonlinear model identification framework, which jointly addresses the feature selection and classifier design tasks. The classifier is constructed as a polynomial expansion…
Phylogenetic trees are widely used to display estimates of how groups of species evolved. Each phylogenetic tree can be seen as a collection of clusters, subgroups of the species that evolved from a common ancestor. When phylogenetic trees…
We introduce a model for simulating mutation of prokaryote DNA sequences. Using that model we can then evaluated traditional techniques like parsimony and maximum likelihood methods for computing phylogenetic relationships. We also use the…
The determination of cluster centers generally depends on the scale that we use to analyze the data to be clustered. Inappropriate scale usually leads to unreasonable cluster centers and thus unreasonable results. In this study, we first…
We often wish to classify objects by their shapes. Indeed, the study of shapes is an important part of many scientific fields such as evolutionary biology, structural biology, image processing, and archaeology. The most widely-used method…
There have been many studies to examine whether one trait is correlated with another trait across a group of present-day species (for example, do species with larger brains tend to have longer gestation times. Since the introduction of the…
Quantitative morphological classification of galaxies is important for understanding the origin of type frequency and correlations with environment. But galaxy morphological classification is still mainly done visually by dedicated…
Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…
As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic…
Bi-clustering is a useful approach in analyzing biological data when observations come from heterogeneous groups and have a large number of features. We outline a general Bayesian approach in tackling bi-clustering problems in moderate to…
Biological cells, by definition, are the basic units which contain the fundamental molecules of life of which all living things are composed. Understanding how they function and differentiating cells from one another therefore is of…
Discovering evolutionary traits that are heritable across species on the tree of life (also referred to as a phylogenetic tree) is of great interest to biologists to understand how organisms diversify and evolve. However, the measurement of…
A phylogenetic birth-and-death model is a probabilistic graphical model for a so-called phylogenetic profile, i.e., the size distribution for a homolog gene family at the terminal nodes of a phylogeny. Profile datasets are used in…
Automatic classification of aquatic microorganisms is based on the morphological features extracted from individual images. The current works on their classification do not consider the inter-class similarity and intra-class variance that…
Phylogenetic reconstruction aims at finding plausible hypotheses of the evolutionary history of genes or species based on genomic sequence information. The distinction of orthologous genes (genes that having a common ancestry and diverged…
The objective of the paper is to study accuracy of multi-class classification in high-dimensional setting, where the number of classes is also large ("large $L$, large $p$, small $n$" model). While this problem arises in many practical…
A highly comparative, feature-based approach to time series classification is introduced that uses an extensive database of algorithms to extract thousands of interpretable features from time series. These features are derived from across…
Scientific names of organisms consist of a genus name and a species epithet, with the latter often reflecting aspects such as morphology, ecology, distribution, and cultural background. Traditionally, researchers have manually labeled…
Physics analysis in astroparticle experiments requires the capability of recognizing new phenomena; in order to establish what is new, it is important to develop tools for automatic classification, able to compare the final result with data…