Related papers: Ordered Leaf Attachment (OLA) Vectors can Identify…
Linkage Tree Genetic Algorithm (LTGA) is an effective Evolutionary Algorithm (EA) to solve complex problems using the linkage information between problem variables. LTGA performs well in various kinds of single-task optimization and yields…
Phylogenomics commonly aims to construct evolutionary trees from genomic sequence information. One way to approach this problem is to first estimate event-labeled gene trees (i.e., rooted trees whose non-leaf vertices are labeled by…
This paper deals with the multiobjective version of the optimal spanning tree problem. More precisely, we are interested in determining the optimal spanning tree according to an Ordered Weighted Average (OWA) of its objective values. We…
A chief problem in phylogenetics and database theory is the computation of a maximum consistent tree from a set of rooted or unrooted trees. A standard input are triplets, rooted binary trees on three leaves, or quartets, unrooted binary…
The Bundle Adjustment (BA) model is commonly optimized using a nonlinear least squares method, with the Levenberg-Marquardt (L-M) algorithm being a typical choice. However, despite the L-M algorithm's effectiveness, its sensitivity to…
Trees have long been used as a graphical representation of species relationships. However complex evolutionary events, such as genetic reassortments or hybrid speciations which occur commonly in viruses, bacteria and plants, do not fit into…
Dynamic techniques are a scalable and effective way to analyze concurrent programs. Instead of analyzing all behaviors of a program, these techniques detect errors by focusing on a single program execution. Often a crucial step in these…
The reconstruction of a species phylogeny from genomic data faces two significant hurdles: 1) the trees describing the evolution of each individual gene--i.e., the gene trees--may differ from the species phylogeny and 2) the molecular…
When performing an analysis on a collection of molecular sequences, it can be convenient to reduce the number of sequences under consideration while maintaining some characteristic of a larger collection of sequences. For example, one may…
We present improved learning-augmented algorithms for finding an approximate minimum spanning tree (MST) for points in an arbitrary metric space. Our work follows a recent framework called metric forest completion (MFC), where the learned…
An evolutionary tree is a rooted tree where each internal vertex has at least two children and where the leaves are labeled with distinct symbols representing species. Evolutionary trees are useful for modeling the evolutionary history of…
Phylogenetic networks are used to represent the evolutionary history of species. Recently, the new class of orchard networks was introduced, which were later shown to be interpretable as trees with additional horizontal arcs. This makes the…
We study the complexity of finding communication trees with the lowest possible completion time for rooted, irregular gather and scatter collective communication operations in fully connected, $k$-ported communication networks under a…
We propose a new arrangement problem on directed graphs, Maximum Directed Linear Arrangement (MaxDLA). This is a directed variant of a similar problem for undirected graphs, in which however one seeks maximum and not minimum; this problem…
In 1989 Erd\H{o}s and Sz\'ekely showed that there is a bijection between (i) the set of rooted trees with $n+1$ vertices whose leaves are bijectively labeled with the elements of $[\ell]=\{1,2,\dots,\ell\}$ for some $\ell \leq n$, and (ii)…
The reconstruction of large phylogenetic trees from data that violates clocklike evolution (or as a supertree constructed from any m input trees) raises a difficult question for biologists - how can one assign relative dates to the vertices…
Rooted phylogenetic networks provide an explicit representation of the evolutionary history of a set $X$ of sampled species. In contrast to phylogenetic trees which show only speciation events, networks can also accommodate reticulate…
Complex data objects arise in many areas of modern science including evolutionary biology, nueroscience, dynamics of gene expression and medical imaging. Object oriented data analysis (OODA) is the statistical analysis of datasets of…
We present $O(\log^2 \log n)$ time 3-coloring, maximal independent set and maximal matching algorithms for trees in the Massively Parallel Computation (MPC) model. Our algorithms are deterministic, apply to arbitrary-degree trees and work…
We present the first fixed-parameter algorithm for constructing a tree-child phylogenetic network that displays an arbitrary number of binary input trees and has the minimum number of reticulations among all such networks. The algorithm…