Related papers: Towards a Data Reduction for the Minimum Flip Supe…
This paper characterizes and discusses devolutionary genetic algorithms and evaluates their performances in solving the minimum labeling Steiner tree (MLST) problem. We define devolutionary algorithms as the process of reaching a feasible…
Computing an optimal classification tree that provably maximizes training performance within a given size limit, is NP-hard, and in practice, most state-of-the-art methods do not scale beyond computing optimal trees of depth three.…
We investigate the complexity of finding a transformation from a given spanning tree in a graph to another given spanning tree in the same graph via a sequence of edge flips. The exchange property of the matroid bases immediately yields…
This paper proposes an algorithmic framework for various reconfiguration problems using zero-suppressed binary decision diagrams (ZDDs), a data structure for families of sets. In general, a reconfiguration problem checks if there is a…
The problem Parsimony Haplotyping (PH) asks for the smallest set of haplotypes which can explain a given set of genotypes, and the problem Minimum Perfect Phylogeny Haplotyping (MPPH) asks for the smallest such set which also allows the…
Spanning tree problems with specialized constraints can be difficult to solve in real-world scenarios, often requiring intricate algorithmic design and exponential time. Recently, there has been growing interest in end-to-end deep neural…
Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…
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…
Phylogenetic Diversity (PD) is a measure of the overall biodiversity of a set of present-day species (taxa) within a phylogenetic tree. In Maximize Phylogenetic Diversity (MPD) one is asked to find a set of taxa (of bounded size/cost) for…
We present an axiomatic framework for analyzing the algorithmic properties of decision trees. This framework supports the classification of decision tree problems through structural and ancestral constraints within a rigorous mathematical…
The reconstruction of phylogenetic trees from mixed populations has become important in the study of cancer evolution, as sequencing is often performed on bulk tumor tissue containing mixed populations of cells. Recent work has shown how to…
Phylogenetic networks are used to represent the evolutionary history of species. They are versatile when compared to traditional phylogenetic trees, as they capture more complex evolutionary events such as hybridization and horizontal gene…
The statistical estimation of phylogenies is always associated with uncertainty, and accommodating this uncertainty is an important component of modern phylogenetic comparative analysis. The birth-death polytomy resolver is a method of…
Given a rooted, binary phylogenetic network and a rooted, binary phylogenetic tree, can the tree be embedded into the network? This problem, called \textsc{Tree Containment}, arises when validating networks constructed by phylogenetic…
We consider the problems of computing maximal palindromes and distinct palindromes in a trie. A trie is a natural generalization of a string, which can be seen as a single-path tree. There is a linear-time offline algorithm to compute…
In this paper, we introduce a specific type of Euclidean tree called LED (Leaves of Equal Depth) tree. LED trees can be used in computational phylogeny, since they are a natural representative of the time evolution of a set of species in a…
Genetic and comparative genomic studies indicate that extant genomes are more properly considered to be a fusion product of random mutations over generations and genomic material transfers between individuals of different lineages. This has…
Reconstructing the evolutionary history of a set of species is a central task in computational biology. In real data, it is often the case that some information is missing: the Incomplete Directed Perfect Phylogeny (IDPP) problem asks,…
In this paper we propose and study a new complexity model for approximation algorithms. The main motivation are practical problems over large data sets that need to be solved many times for different scenarios, e.g., many multicast trees…
Phylogenetic tree shapes capture fundamental signatures of evolution. We consider ``ranked'' tree shapes, which are equipped with a total order on the internal nodes compatible with the tree graph. Recent work has established an elegant…