Related papers: Polynomial-time completion of phylogenetic tree se…
We investigate parameterized algorithms for computing the average-tree phylogenetic diversity (APD) in rooted phylogenetic networks, studying the problem under different structural parameters that capture the deviation of a network from a…
This paper addresses the problem of finding a representation of a subtree distance, which is an extension of the tree metric. We show that a minimal representation is uniquely determined by a given subtree distance, and give a linear time…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
Phylogenetic networks are necessary to represent the tree of life expanded by edges to represent events such as horizontal gene transfers, hybridizations or gene flow. Not all species follow the paradigm of vertical inheritance of their…
Learning a Bayesian networks with bounded treewidth is important for reducing the complexity of the inferences. We present a novel anytime algorithm (k-MAX) method for this task, which scales up to thousands of variables. Through extensive…
In this paper, we investigate adaptive nonlinear regression and introduce tree based piecewise linear regression algorithms that are highly efficient and provide significantly improved performance with guaranteed upper bounds in an…
In evolutionary biology, biologists often face the problem of constructing a phylogenetic tree on a set $X$ of species from a multiset $\Pi$ of partitions corresponding to various attributes of these species. One approach that is used to…
Phylogenetic trees are a central tool in understanding evolution. They are typically inferred from sequence data, and capture evolutionary relationships through time. It is essential to be able to compare trees from different data sources…
We consider the polyhedral properties of two spanning tree problems with additional constraints. In the first problem, it is required to find a tree with a minimum sum of edge weights among all spanning trees with the number of leaves less…
Supertree methods are tree reconstruction techniques that combine several smaller gene trees (possibly on different sets of species) to build a larger species tree. The question of interest is whether the reconstructed supertree converges…
Phylogenetic networks are generalizations of phylogenetic trees that allow the representation of reticulation events such as horizontal gene transfer or hybridization, and can also represent uncertainty in inference. A subclass of these,…
A widely used method for determining the similarity of two labeled trees is to compute a maximum agreement subtree of the two trees. Previous work on this similarity measure is only concerned with the comparison of labeled trees of two…
In recent years, significant progress has been made on algorithms for learning optimal decision trees, primarily in the context of binary features. Extending these methods to continuous features remains substantially more challenging due to…
Large tree structures are ubiquitous and real-world relational datasets often have information associated with nodes (e.g., labels or other attributes) and edges (e.g., weights or distances) that need to be communicated to the viewers. Yet,…
The Hausdorff distance is a relatively new measure of similarity of graphs. The notion of the Hausdorff distance considers a special kind of a common subgraph of the compared graphs and depends on the structural properties outside of the…
We systematically study the computational complexity of a broad class of computational problems in phylogenetic reconstruction. The class contains for example the rooted triple consistency problem, forbidden subtree problems, the quartet…
Tree-based networks are a class of phylogenetic networks that attempt to formally capture what is meant by "tree-like" evolution. A given non-tree-based phylogenetic network, however, might appear to be very close to being tree-based, or…
Motivated by the problem of enumerating all tree decompositions of a graph, we consider in this article the problem of listing all the minimal chordal completions of a graph. In \cite{carmeli2020} (\textsc{Pods 2017}) Carmeli \emph{et al.}…
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 phylogenetic tree is a way to organize a finite set of species, individuals or other sources of related data. The species for which we have existing DNA data make up the set of leaves of the tree. The balanced minimal evolution method of…