Related papers: Maximizing Phylogenetic Diversity under Time Press…
Phylogenetic mixture models, in which the sites in sequences undergo different substitution processes along the same or different trees, allow the description of heterogeneous evolutionary processes. As data sets consisting of longer…
Phylogenomics is a new field which applies to tools in phylogenetics to genome data. Due to a new technology and increasing amount of data, we face new challenges to analyze them over a space of phylogenetic trees. Because a space of…
Evolutionary Biologists have long struggled with the challenge of developing analysis workflows in a flexible manner, thus facilitating the reuse of phylogenetic knowledge. An evolutionary biology workflow can be viewed as a plan which…
We consider the NP-hard Tree Containment problem that has important applications in phylogenetics. The problem asks if a given leaf-labeled network contains a subdivision of a given leaf-labeled tree. We develop a fast algorithm for the…
The branching structure of biological evolution confers statistical dependencies on phenotypic trait values in related organisms. For this reason, comparative macroevolutionary studies usually begin with an inferred phylogeny that describes…
Creating diverse sets of high quality solutions has become an important problem in recent years. Previous works on diverse solutions problems consider solutions' objective quality and diversity where one is regarded as the optimization goal…
In apparent contradiction to competition theory, the number of known, co-existing plankton species far exceeds their explicable biodiversity - a discrepancy termed the Paradox of the Plankton. We introduce a new game-theoretic model for…
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…
Reconstructing evolutionary trees from molecular sequence data is a fundamental problem in computational biology. Stochastic models of sequence evolution are closely related to spin systems that have been extensively studied in statistical…
In the small phylogeny problem we, are given a phylogenetic tree and gene orders of the extant species and our goal is to reconstruct all of the ancestral genomes so that the number of evolutionary operations is minimized. Algorithms for…
Structural parameters of graphs, such as treewidth, play a central role in the study of the parameterized complexity of graph problems. Motivated by the study of parametrized algorithms on phylogenetic networks, scanwidth was introduced…
There are multiple factors which can cause the phylogenetic inference process to produce two or more conflicting hypotheses of the evolutionary history of a set X of biological entities. That is: phylogenetic trees with the same set of leaf…
A popular line of research in evolutionary biology is the use of time-calibrated phylogenies for the inference of diversification processes. This requires computing the likelihood of a given ultrametric tree as the reconstructed tree…
Survival analysis concerns the task of predicting the time until an event occurs. Often used in the medical field, survival analysis deals with incomplete (i.e., censored) data, for instance, from patients who did not experience the event…
Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…
There are many classical problems in P whose time complexities have not been improved over the past decades. Recent studies of "Hardness in P" have revealed that, for several of such problems, the current fastest algorithm is the best…
Diversity, understood as the variety of different elements or configurations that an extensive system has, is a crucial property that allows maintaining the system's functionality in a changing environment, where failures, random events or…
Survival analysis studies and predicts the time of death, or other singular unrepeated events, based on historical data, while the true time of death for some instances is unknown. Survival trees enable the discovery of complex nonlinear…
In this study, we investigate the application of Semidefinite Programming (SDP) to phylogenetics. SDP is a powerful optimization framework that seeks to optimize a linear objective function over the cone of positive semidefinite matrices.…
Phylogenetic networks are a flexible model of evolution that can represent reticulate evolution and handle complex data. Tree-based networks, which are phylogenetic networks that have a spanning tree with the same root and leaf-set as the…