Related papers: Unifying Parsimonious Tree Reconciliation
We propose a novel method for the inference of phylogenetic trees that utilises point configurations on hyperbolic space as its optimisation landscape. Each taxon corresponds to a point of the point configuration, while the evolutionary…
In this paper we present an evolutionary optimization approach to solve the risk parity portfolio selection problem. While there exist convex optimization approaches to solve this problem when long-only portfolios are considered, the…
A Supertree synthesizes the topologies of a set of phylogenetic trees carrying overlapping taxa set. In process, conflicts in the tree topologies are aimed to be resolved with the consensus clades. Such a problem is proved to be NP-hard.…
Modern software systems are increasingly designed to be highly configurable, which increases flexibility but can make programs harder to develop, test, and analyze, e.g., how configuration options are set to reach certain locations, what…
Natural phenomenon of coevolution is the reciprocally induced evolutionary change between two or more species or population. Though this biological occurrence is a natural fact, there are only few attempts to use this as a simile in…
Differential evolution possesses a multitude of various strategies for generating new trial solutions. Unfortunately, the best strategy is not known in advance. Moreover, this strategy usually depends on the problem to be solved. This paper…
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,…
We derive tractable criteria for the consistency of Bayesian tree reconstruction procedures, which constitute a central class of algorithms for inferring common ancestry among DNA sequence samples in phylogenetics. Our results encompass…
There are several tools available to infer phylogenetic trees, which depict the evolutionary relationships among biological entities such as viral and bacterial strains in infectious outbreaks, or cancerous cells in tumor progression trees.…
Recovering a tree that represents the evolutionary history of a group of species is a key task in phylogenetics. Performing this task using sequence data from multiple genetic markers poses two key challenges. The first is the discordance…
Tackling simulation optimization problems with non-convex objective functions remains a fundamental challenge in operations research. In this paper, we propose a class of random search algorithms, called Regular Tree Search, which…
Convolution trees, loopy belief propagation, and fast numerical p-convolution are combined for the first time to efficiently solve networks with several additive constraints between random variables. An implementation of this "convolution…
In phylogenetics, evolution is traditionally represented in a tree-like manner. However, phylogenetic networks can be more appropriate for representing evolutionary events such as hybridization, horizontal gene transfer, and others. In…
The phylogenetic tree construction is to infer the evolutionary relationship between species from the experimental data. However, the experimental data are often imperfect and conflicting each others. Therefore, it is important to extract…
In this paper, we consider a tree inference problem motivated by the critical problem in single-cell genomics of reconstructing dynamic cellular processes from sequencing data. In particular, given a population of cells sampled from such a…
Finding the most parsimonious tree inside a phylogenetic network with respect to a given character is an NP-hard combinatorial optimization problem that for many network topologies is essentially inapproximable. In contrast, if the network…
The history of gene families - which are equivalent to \emph{event-labeled} gene trees - can be reconstructed from empirically estimated evolutionary event-relations containing pairs of orthologous, paralogous or xenologous genes. The…
Algorithms for learning decision trees often include heuristic local-search operations such as (1) adjusting the threshold of a cut or (2) also exchanging the feature of that cut. We study minimizing the number of classification errors by…
Cartesian tree pattern matching consists of finding all the factors of a text that have the same Cartesian tree than a given pattern. There already exist theoretical and practical solutions for the exact case. In this paper, we propose the…
Evolutionary and ecosystem dynamics are often treated as different processes --operating at separate timescales-- even if evidence reveals that rapid evolutionary changes can feed back into ecological interactions. A recent long-term field…