Related papers: Reconstructing Ultrametric Trees from Noisy Experi…
Tree rotations (left and right) are basic local deformations allowing to transform between two unlabeled binary trees of the same size. Hence, there is a natural problem of practically finding such transformation path with low number of…
Network reconstruction lies at the heart of phylogenetic research. Two well studied classes of phylogenetic networks include tree-child networks and level-$k$ networks. In a tree-child network, every non-leaf node has a child that is a tree…
The presence of reticulate evolutionary events in phylogenies turn phylogenetic trees into phylogenetic networks. These events imply in particular that there may exist multiple evolutionary paths from a non-extant species to an extant one,…
Phylogenetic trees are frequently used to model evolution. Such trees are typically reconstructed from data like DNA, RNA, or protein alignments using methods based on criteria like maximum parsimony (amongst others). Maximum parsimony has…
A major problem for inferring species trees from gene trees is that evolutionary processes can sometimes favour gene tree topologies that conflict with an underlying species tree. In the case of incomplete lineage sorting, this phenomenon…
Good representations for phylogenetic trees and networks are important for optimizing storage efficiency and implementation of scalable methods for the inference and analysis of evolutionary trees for genes, genomes and species. We…
In phylogenetics, phylogenetic trees are rooted binary trees, whereas phylogenetic networks are rooted arbitrary acyclic digraphs. Edges are directed away from the root and leaves are uniquely labeled with taxa in phylogenetic networks. For…
The algebraic properties of flattenings and subflattenings provide direct methods for identifying edges in the true phylogeny -- and by extension the complete tree -- using pattern counts from a sequence alignment. The relatively small…
We consider the in-plane motion of elastic strings on tree-like network, observed from the 'leaves'. We investigate the inverse problem of recovering not only the physical properties i.e. the 'optical lengths' of each string, but also the…
Selective inference is considered for testing trees and edges in phylogenetic tree selection from molecular sequences. This improves the previously proposed approximately unbiased test by adjusting the selection bias when testing many trees…
The well-known trace reconstruction problem is the problem of inferring an unknown source string $x \in \{0,1\}^n$ from independent "traces", i.e. copies of $x$ that have been corrupted by a $\delta$-deletion channel which independently…
Many biological studies involve inferring the evolutionary history of a sample of individuals from a large population and interpreting the reconstructed tree. Such an ascertained tree typically represents only a small part of a…
Tree shape statistics quantify some aspect of the shape of a phylogenetic tree. They are commonly used to compare reconstructed trees to evolutionary models and to find evidence of tree reconstruction bias. Historically, to find a useful…
Computational inference of dated evolutionary histories relies upon various hypotheses about RNA, DNA, and protein sequence mutation rates. Using mutation rates to infer these dated histories is referred to as molecular clock assumption.…
Decision trees are popular classification models, providing high accuracy and intuitive explanations. However, as the tree size grows the model interpretability deteriorates. Traditional tree-induction algorithms, such as C4.5 and CART,…
The inference of the evolutionary history of a collection of organisms is a problem of fundamental importance in evolutionary biology. The abundance of DNA sequence data arising from genome sequencing projects has led to significant…
We provide high probability finite sample complexity guarantees for hidden non-parametric structure learning of tree-shaped graphical models, whose hidden and observable nodes are discrete random variables with either finite or countable…
It is common in phylogenetics to have some, perhaps partial, information about the overall evolutionary tree of a group of organisms and wish to find an evolutionary tree of a specific gene for those organisms. There may not be enough…
We consider the problem of reconstructing the intrinsic geometry of a manifold from noisy pairwise distance observations. Specifically, let $M$ denote a diameter 1 d-dimensional manifold and $\mu$ a probability measure on $M$ that is…
The purpose of this paper is to analyze certain statistics of a recently introduced non-uniform random tree model, biased recursive trees. This model is based on constructing a random tree by establishing a correspondence with non-uniform…