Related papers: Comparing Pedigree Graphs
Best match graphs (BMGs) are a class of colored digraphs that naturally appear in mathematical phylogenetics and can be approximated with the help of similarity measures between gene sequences, albeit not without errors. The corresponding…
Pedigree data contain family history information that is used to analyze hereditary diseases. These clinical data sets may contain duplicate records due to the same family visiting a clinic multiple times or a clinician entering multiple…
We study the computational complexity of the map redistricting problem (gerrymandering). Mathematically, the electoral district designer (gerrymanderer) attempts to partition a weighted graph into $k$ connected components (districts) such…
In multistage perfect matching problems we are given a sequence of graphs on the same vertex set and asked to find a sequence of perfect matchings, corresponding to the sequence of graphs, such that consecutive matchings are as similar as…
We consider the NP-hard Tree Containment problem that has important applications in phylogenetics. The problem asks if a given leaf-labeled network contains a subdivision of a given leaf-labeled tree. We develop a fast algorithm for the…
An evolutionary tree (phylogenetic tree) is a binary, rooted, unordered tree that models the evolutionary history of currently living species in which leaves are labeled by species. In this paper, we investigate the problem of finding the…
Phylogenetic networks are often constructed by merging multiple conflicting phylogenetic signals into a directed acyclic graph. It is interesting to explore whether a network constructed in this way induces biologically-relevant…
We study a well known noisy model of the graph isomorphism problem. In this model, the goal is to perfectly recover the vertex correspondence between two edge-correlated Erd\H{o}s-R\'{e}nyi random graphs, with an initial seed set of…
Discovering the underlying structures present in large real world graphs is a fundamental scientific problem. In this paper we show that a graph's clique tree can be used to extract a hyperedge replacement grammar. If we store an ordering…
Dual-tree algorithms are a widely used class of branch-and-bound algorithms. Unfortunately, developing dual-tree algorithms for use with different trees and problems is often complex and burdensome. We introduce a four-part logical split:…
I consider the problem of learning an optimal path graphical model from data and show the problem to be NP-hard for the maximum likelihood and minimum description length approaches and a Bayesian approach. This hardness result holds despite…
We study the complexity of testing if two given matroids are isomorphic. The problem is easily seen to be in $\Sigma_2^p$. In the case of linear matroids, which are represented over polynomially growing fields, we note that the problem is…
Historical linguistics aims at inferring the most likely language phylogenetic tree starting from information concerning the evolutionary relatedness of languages. The available information are typically lists of homologous (lexical,…
This thesis studies the graph alignment problem, the noisy version of the graph isomorphism problem, which aims to find a matching between the nodes of two graphs which preserves most of the edges. Focusing on the planted version where the…
Reciprocal best match graphs (RBMGs) are vertex colored graphs whose vertices represent genes and the colors the species where the genes reside. Edges identify pairs of genes that are most closely related with respect to an underlying…
In Polyamorous Scheduling, we are given an edge-weighted graph and must find a periodic schedule of matchings in this graph which minimizes the maximal weighted waiting time between consecutive occurrences of the same edge. This NP-hard…
An isomorphism between two graphs is a bijection between their vertices that preserves the edges. We consider the problem of determining whether two finite undirected weighted graphs are isomorphic, and finding an isomorphism relating them…
Phylogenetic trees describe the evolutionary history of a group of present-day species from a common ancestor. These trees are typically reconstructed from aligned DNA sequence data. In this paper we analytically address the following…
We investigate structural and algorithmic advantages of a directed version of the well-researched class of distance-hereditary graphs. Since the previously defined distance-hereditary digraphs do not permit a recursive structure, we define…
Phylogenetic trees illustrate the evolutionary history of genes and species. In most cases, although genes evolve along with the species they belong to, a species tree and gene tree are not identical, because of evolutionary events at the…