Related papers: Information Content of a Phylogenetic Tree in a Da…
Phylogenetic networks extend phylogenetic trees to model non-vertical inheritance, by which a lineage inherits material from multiple parents. The computational complexity of estimating phylogenetic networks from genome-wide data with…
Attempting to recognize a tree inside a phylogenetic network is a fundamental undertaking in evolutionary analysis. In the last few years, therefore, tree-based phylogenetic networks, which are defined by a spanning tree called a…
Phylogenomics heavily relies on well-curated sequence data sets that consist, for each gene, exclusively of 1:1-orthologous. Paralogs are treated as a dangerous nuisance that has to be detected and removed. We show here that this severe…
Phylogenetic networks are a generalisation of phylogenetic trees that allow for more complex evolutionary histories that include hybridisation-like processes. It is of considerable interest whether a network can be considered `tree-like' or…
In this paper, we consider the problem of distributed inference in tree based networks. In the framework considered in this paper, distributed nodes make a 1-bit local decision regarding a phenomenon before sending it to the fusion center…
Highly dynamic networks are characterized by frequent changes in the availability of communication links. These networks are often partitioned into several components, which split and merge unpredictably. We present a distributed algorithm…
Cluster analysis is one of the essential tasks in data mining and knowledge discovery. Each type of data poses unique challenges in achieving relatively efficient partitioning of the data into homogeneous groups. While the algorithms for…
Neuronal dendrites form densely branched tree architectures through which mitochondria must be distributed to supply the cell's energetic needs. Dendritic mitochondria circulate through the tree, undergoing fusion and fission to form…
A phylogenetic tree is an important way in Bioinformatics to find the evolutionary relationship among biological species. In this research, a proposed model is described for the estimation of a phylogenetic tree for a given set of data. To…
Phylogenetic inference can potentially result in a more accurate tree using data from multiple loci. However, if the loci are incongruent--due to events such as incomplete lineage sorting or horizontal gene transfer--it can be misleading to…
Phylogenetic trees elucidate evolutionary relationships among species, but phylogenetic inference remains challenging due to the complexity of combining continuous (branch lengths) and discrete parameters (tree topology). Traditional Markov…
The objective of clustering is to discover natural groups in datasets and to identify geometrical structures which might reside there, without assuming any prior knowledge on the characteristics of the data. The problem can be seen as…
Phylogenetic networks are rooted acyclic directed graphs in which the leaves are identified with members of a set X of species. The cluster of a vertex is the set of leaves that are descendants of the vertex. A network is "distinct-cluster"…
In classification and forecasting with tabular data, one often utilizes tree-based models. Those can be competitive with deep neural networks on tabular data and, under some conditions, explainable. The explainability depends on the depth…
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…
Succinct data structures give space-efficient representations of large amounts of data without sacrificing performance. They rely one cleverly designed data representations and algorithms. We present here the formalization in Coq/SSReflect…
Measures of tree balance play an important role in different research areas such as mathematical phylogenetics or theoretical computer science. The balance of a tree is usually quantified in a single number, called a balance or imbalance…
Rare events have played an increasing role in molecular phylogenetics as potentially homoplasy-poor characters.In this contribution we analyze the phylogenetic information content from a combinatorial point of view by consid-ering the…
The relative importance of the intrinsic and extrinsic factors determining the variety of geometric shapes exhibited by dendritic trees remains unclear. This question was addressed by developing a model of the growth of dendritic trees…
Contour trees describe the topology of level sets in scalar fields and are widely used in topological data analysis and visualization. A main challenge of utilizing contour trees for large-scale scientific data is their computation at scale…