Related papers: A Theory of Taxonomy
The evolutionary dynamics of molecular populations are strongly dependent on the structure of genotype spaces. The map between genotype and phenotype determines how easily genotype spaces can be navigated and the accessibility of…
The discovery of new and interesting patterns in large datasets, known as data mining, draws more and more interest as the quantities of available data are exploding. Data mining techniques may be applied to different domains and fields…
Information hierarchies are organizational structures that often used to organize and present large and complex information as well as provide a mechanism for effective human navigation. Fortunately, many statistical and computational…
The species-area relationship is one of the central generalizations in ecology however its origin has remained a puzzle. Since ecosystems are understood as energy transduction systems, the regularities in species richness are considered to…
This report presents a taxonomy of vulnerabilities created as a part of an effort to develop a framework for deriving verification and validation strategies to assess software security. This taxonomy is grounded in a theoretical model of…
Topic models are popular models for analyzing a collection of text documents. The models assert that documents are distributions over latent topics and latent topics are distributions over words. A nested document collection is where…
Joint species distribution models are popular in ecology for modeling covariate effects on species occurrence, while characterizing cross-species dependence. Data consist of multivariate binary indicators of the occurrences of different…
This paper describes a framework for a systematic classification of spreadsheet errors. This classification or taxonomy of errors is aimed at facilitating analysis and comprehension of the different types of spreadsheet errors. The taxonomy…
A computational theory for clustering and a semi-supervised clustering algorithm is presented. Clustering is defined to be the obtainment of groupings of data such that each group contains no anomalies with respect to a chosen grouping…
Empirical studies of graphs have contributed enormously to our understanding of complex systems. Known today as network science, what was originally a theoretical study of graphs has grown into a more scientific exploration of communities…
Selection, the tendency of some traits to become more frequent than others in a population under the influence of some (natural or artificial) agency, is a key component of Darwinian evolution and countless other natural and social…
Scientific journals are the repositories of the gradually accumulating knowledge of mankind about the world surrounding us. Just as our knowledge is organised into classes ranging from major disciplines, subjects and fields to increasingly…
Biological sequences do not come at random. Instead, they appear with particular frequencies that reflect properties of the associated system or phenomenon. Knowing how biological sequences are distributed in sequence space is thus a…
An operation on species corresponding to the inner plethysm of their associated cycle index series is constructed. This operation, the inner plethysm of species, is generalized to n-sorted species. Polynomial maps on species are studied and…
Multivariate count data are defined as the number of items of different categories issued from sampling within a population, which individuals are grouped into categories. The analysis of multivariate count data is a recurrent and crucial…
When we think of model ensembling or ensemble modeling, there are many possibilities that come to mind in different disciplines. For example, one might think of a set of descriptions of a phenomenon in the world, perhaps a time series or a…
Diversification models describe the random growth of evolutionary trees, modeling the historical relationships of species through speciation and extinction events. One class of such models allows for independently changing traits, or types,…
Written to be contributed as the "mathematical modeling" chapter of a book, edited by Elaine Landry, to be titled "Categories for the Working Philosopher". In this chapter, category theory is presented as a mathematical modeling framework…
Anomalies are occurrences in a dataset that are in some way unusual and do not fit the general patterns. The concept of the anomaly is typically ill-defined and perceived as vague and domain-dependent. Moreover, despite some 250 years of…
Disordered systems theory provides powerful tools to analyze the generic behaviors of highdimensional systems, such as species-rich ecological communities or neural networks. By assuming randomness in their interactions, universality…