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Phytoplankton plays an important role in marine ecosystem. It is defined as a biological factor to assess marine quality. The identification of phytoplankton species has a high potential for monitoring environmental, climate changes and for…
Analyzing large datasets to select optimal features is one of the most important research areas in machine learning and data mining. This feature selection procedure involves dimensionality reduction which is crucial in enhancing the…
Social networks exhibit strikingly systematic patterns across a wide range of human contexts. While genetic variation accounts for a significant portion of the variation in many complex social behaviors, the heritability of egocentric…
Biogeographical regions (geographically distinct assemblages of species and communities) constitute a cornerstone for ecology, biogeography, evolution and conservation biology. Species turnover measures are often used to quantify…
Molecular and morphological characters, as important parts of biological taxonomy, are contradictory but need to be integrated. Organism's image recognition and bioinformatics are emerging and hot problems nowadays but with a gap between…
Multi-view datasets offer diverse forms of data that can enhance prediction models by providing complementary information. However, the use of multi-view data leads to an increase in high-dimensional data, which poses significant challenges…
In the biclustering problem, we seek to simultaneously group observations and features. While biclustering has applications in a wide array of domains, ranging from text mining to collaborative filtering, the problem of identifying…
In biodiversity conservation it is often necessary to prioritize the species to conserve. Existing approaches to prioritization, e.g. the Fair Proportion Index and the Shapley Value, are based on phylogenetic trees and rank species…
Phylogenetic networks provide a means of describing the evolutionary history of sets of species believed to have undergone hybridization or gene flow during their evolution. The mutation process for a set of such species can be modeled as a…
Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer.…
A phylogeny describes the evolutionary history of an evolving population. Evolutionary search algorithms can perfectly track the ancestry of candidate solutions, illuminating a population's trajectory through the search space. However,…
The association of a given human phenotype to a genetic variant remains a critical challenge for biology. We present a novel system called PhenoLinker capable of associating a score to a phenotype-gene relationship by using heterogeneous…
Resource allocation problems are a family of problems in which resources must be selected to satisfy given demands. This paper focuses on the two-stage stochastic generalization of resource allocation problems where future demands are…
Tree Containment is a fundamental problem in phylogenetics useful for verifying a proposed phylogenetic network, representing the evolutionary history of certain species. Tree Containment asks whether the given phylogenetic tree (for…
A computational challenge to validate the candidate disease genes identified in a high-throughput genomic study is to elucidate the associations between the set of candidate genes and disease phenotypes. The conventional gene set enrichment…
Typing methods are widely used in the surveillance of infectious diseases, outbreaks investigation and studies of the natural history of an infection. And their use is becoming standard, in particular with the introduction of High…
DNA microarray gene-expression data has been widely used to identify cancerous gene signatures. Microarray can increase the accuracy of cancer diagnosis and prognosis. However, analyzing the large amount of gene expression data from…
Genotyping errors are known to influence the power of both family-based and case-control studies in the genetics of complex disease. Estimating genotyping error rate in a given dataset can be complex, but when family information is…
Background: Continuous traits evolution of a group of taxa that are correlated through a phylogenetic tree is commonly modelled using parametric stochastic differential equations to represent deterministic change of trait through time,…
Generative models derived from large protein sequence alignments define complex fitness landscapes, but their utility for accurately modeling non-equilibrium evolutionary dynamics remains unclear. In this work, we perform a rigorous…