Related papers: Heuristic Algorithms for Best Match Graph Editing
Best match graphs (BMGs) are vertex-colored directed graphs that were introduced to model the relationships of genes (vertices) from different species (colors) given an underlying evolutionary tree that is assumed to be unknown. In…
Best match graphs (BMG) are a key intermediate in graph-based orthology detection and contain a large amount of information on the gene tree. We provide a near-cubic algorithm to determine whether a BMG is binary-explainable, i.e., whether…
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…
Best match graphs (BMGs) are vertex-colored digraphs that naturally arise in mathematical phylogenetics to formalize the notion of evolutionary closest genes w.r.t. an a priori unknown phylogenetic tree. BMGs are explained by unique least…
Reciprocal best matches play an important role in numerous applications in computational biology, in particular as the basis of many widely used tools for orthology assessment. Nevertheless, very little is known about their mathematical…
2-colored best match graphs (2-BMGs) form a subclass of sink-free bi-transitive graphs that appears in phylogenetic combinatorics. There, 2-BMGs describe evolutionarily most closely related genes between a pair of species. They are…
A wide variety of problems in computational biology, most notably the assessment of orthology, are solved with the help of reciprocal best matches. Using an evolutionary definition of best matches that captures the intuition behind the…
THIS IS A CORRECTED VERSION INCLUDING AN APPENDED CORRIGENDUM. Best match graphs arise naturally as the first processing intermediate in algorithms for orthology detection. Let $T$ be a phylogenetic (gene) tree $T$ and $\sigma$ an…
The NP-complete mutual-visibility (MV) problem currently lacks empirical analysis on its practical behaviour despite theoretical studies. This paper addresses this gap by implementing and evaluating three distinct algorithms -- a direct…
In graph modification problems, one is given a graph G and the goal is to apply a minimum number of modification operations (such as edge deletions) to G such that the resulting graph fulfills a certain property. For example, the Cluster…
Many of the commonly used methods for orthology detection start from mutually most similar pairs of genes (reciprocal best hits) as an approximation for evolutionary most closely related pairs of genes (reciprocal best matches). This…
In metabolomics, small molecules are structurally elucidated using tandem mass spectrometry (MS/MS); this resulted in the computational Maximum Colorful Subtree problem, which is NP-hard. Unfortunately, data from a single metabolite…
Genome-scale orthology assignments are usually based on reciprocal best matches. In the absence of horizontal gene transfer (HGT), every pair of orthologs forms a reciprocal best match. Incorrect orthology assignments therefore are always…
Probabilistic graphical models (PGMs) are powerful tools for solving systems of complex relationships over a variety of probability distributions. However, while tree-structured PGMs always result in efficient and exact solutions, inference…
As two fundamental problems, graph cuts and graph matching have been investigated over decades, resulting in vast literature in these two topics respectively. However the way of jointly applying and solving graph cuts and matching receives…
Graphs provide a natural way to represent data by encoding information about objects and the relationships between them. With the ever-increasing amount of data collected and generated, locating specific patterns of relationships between…
Graph matching, also known as network alignment, refers to finding a bijection between the vertex sets of two given graphs so as to maximally align their edges. This fundamental computational problem arises frequently in multiple fields…
Probabilistic graphical models (PGMs) are tools for solving complex probabilistic relationships. However, suboptimal PGM structures are primarily used in practice. This dissertation presents three contributions to the PGM literature. The…
Unit disk graphs are intersection graphs of circles of unit radius in the plane. We present simple and provably good heuristics for a number of classical NP-hard optimization problems on unit disk graphs. The problems considered include…
Finding optimal matchings in dense graphs is of general interest and of particular importance in social, transportation and biological networks. While developing optimal solutions for various matching problems is important, the running…