Related papers: A tool for computing diversity and consideration o…
In this paper, we describe a Graphical User Interface (GUI) designed to manage large quantities of image data of a biological system. After setting the design requirements for the system, we developed an ecology quantification GUI that…
The applicability of computational models to the biological world is an active topic of debate. We argue that a useful path forward results from abandoning hard boundaries between categories and adopting an observer-dependent, pragmatic…
Until recently, much of the microbial world was hidden from view. A global research effort has changed this, unveiling and quantifying microbial diversity across enormous range of critically-important contexts, from the human microbiome, to…
The distribution of objective vectors in a Pareto Front Approximation (PFA) is crucial for representing the associated manifold accurately. Distribution Indicators (DIs) assess the distribution of a PFA numerically, utilizing concepts like…
The explosion in known microbial diversity in the last two decades has made it abundantly clear that microbes in the environment do not exist in isolation; they are members of communities. Accordingly, omics approaches such as metagenomics…
Insects play such a crucial role in ecosystems that a shift in demography of just a few species can have devastating consequences at environmental, social and economic levels. Despite this, evaluation of insect demography is strongly…
Phylogenetic Diversity (PD) is a prominent quantitative measure of the biodiversity of a collection of present-day species (taxa). This measure is based on the evolutionary distance among the species in the collection. Loosely speaking, if…
Background: Plant breeders are utilising an increasingly diverse range of data types in order to identify lines that have desirable characteristics which are suitable to be taken forward in plant breeding programmes. There are a number of…
We consider a problem of data integration. Consider determining which genes affect a disease. The genes, which we call predictor objects, can be measured in different experiments on the same individual. We address the question of finding…
Text-to-image (T2I) models are rapidly gaining popularity, yet their outputs often lack geographical diversity, reinforce stereotypes, and misrepresent regions. Given their broad reach, it is critical to rigorously evaluate how these models…
Polyploidization is an important evolutionary process which affects organisms ranging from plants to fish and fungi. The signal left behind by it is in the form of a species' ploidy level (number of complete chromosome sets found in a cell)…
Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer, and comparative-genomics…
Several factors affect the structure of communities, including biological, physical and chemical phenomena, impacting the quantification of biodiversity, measured by diversity indexes such as Shannon's entropy. Then, once a point estimate…
Diversification in a set of solutions has become a hot research topic in the evolutionary computation community. It has been proven beneficial for optimisation problems in several ways, such as computing a diverse set of high-quality…
Monitoring biodiversity is paramount to manage and protect natural resources. Collecting images of organisms over large temporal or spatial scales is a promising practice to monitor the biodiversity of natural ecosystems, providing large…
Phylogenetic diversity indices provide a formal way to apportion 'evolutionary heritage' across species. Two natural diversity indices are Fair Proportion (FP) and Equal Splits (ES). FP is also called 'evolutionary distinctiveness' and, for…
This paper describes a cascading multimodal pipeline for high-resolution biodiversity mapping across Europe, integrating species distribution modeling, biodiversity indicators, and habitat classification. The proposed pipeline first…
Measuring diversity accurately is important for many scientific fields, including machine learning (ML), ecology, and chemistry. The Vendi Score was introduced as a generic similarity-based diversity metric that extends the Hill number of…
Evolutionary algorithms have been successfully applied to a variety of optimisation problems in stationary environments. However, many real world optimisation problems are set in dynamic environments where the success criteria shifts…
The system decomposition theory has recently been developed for the dynamic analysis of nonlinear compartmental systems. The application of this theory to the ecosystem analysis has also been introduced in a separate article. Based on this…