Related papers: Comparing Pedigree Graphs
Reconstruction of evolutionary relationships between species is an important topic in the field of computational biology. Pairwise compatibility graphs (PCGs) are used to model such relationships. A graph is a PCG if its edges can be…
Subgraph matching is a compute-intensive problem that asks to enumerate all the isomorphic embeddings of a query graph within a data graph. This problem is generally solved with backtracking, which recursively evolves every possible partial…
A Supertree synthesizes the topologies of a set of phylogenetic trees carrying overlapping taxa set. In process, conflicts in the tree topologies are aimed to be resolved with the consensus clades. Such a problem is proved to be NP-hard.…
Many real world networks are considered temporal networks, in which the chronological ordering of the edges has importance to the meaning of the data. Performing temporal subgraph matching on such graphs requires the edges in the subgraphs…
We introduce a dynamic version of the NP-hard graph problem Cluster Editing. The essential point here is to take into account dynamically evolving input graphs: Having a cluster graph (that is, a disjoint union of cliques) that represents a…
Orthology and paralogy relations are often inferred by methods based on gene similarity, which usually yield a graph depicting the relationships between gene pairs. Such relation graphs are known to frequently contain errors, as they cannot…
Given two rooted, labeled trees $P$ and $T$ the tree path subsequence problem is to determine which paths in $P$ are subsequences of which paths in $T$. Here a path begins at the root and ends at a leaf. In this paper we propose this…
The inference of new information on the relatedness of species by phylogenetic trees based on DNA data is one of the main challenges of modern biology. But despite all technological advances, DNA sequencing is still a time-consuming and…
Finding the most parsimonious tree inside a phylogenetic network with respect to a given character is an NP-hard combinatorial optimization problem that for many network topologies is essentially inapproximable. In contrast, if the network…
Graphs are used in many disciplines to model the relationships that exist between objects in a complex discrete system. Researchers may wish to compare a network of interest to a "typical" graph from a family (or ensemble) of graphs which…
Most genes are part of larger families of evolutionary related genes. The history of gene families typically involves duplications and losses of genes as well as horizontal transfers into other organisms. The reconstruction of detailed gene…
We claimed that there is a polynomial algorithm to test if two graphs are isomorphic. But the algorithm is wrong. It only tests if the adjacency matrices of two graphs have the same eigenvalues. There is a counterexample of two…
The entities in directed networks arising from real-world interactions are often naturally organized under some hierarchical structure. Given a directed, weighted, graph with edges and node labels, we introduce ranking problem where the…
Graph similarity search is a common and fundamental operation in graph databases. One of the most popular graph similarity measures is the Graph Edit Distance (GED) mainly because of its broad applicability and high interpretability.…
Ancestral sequence reconstruction is a key task in computational biology. It consists in inferring a molecular sequence at an ancestral species of a known phylogeny, given descendant sequences at the tip of the tree. In addition to its many…
The problem of Distance Edge Labeling is a variant of Distance Vertex Labeling (also known as $L_{2,1}$ labeling) that has been studied for more than twenty years and has many applications, such as frequency assignment. The Distance Edge…
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…
Phylogenetics is the study of the evolutionary relationships between organisms. One of the main challenges in the field is to take biological data for a group of organisms and to infer an evolutionary tree, a graph that represents these…
The graph isomorphism, subgraph isomorphism, and graph edit distance problems are combinatorial problems with many applications. Heuristic exact and approximate algorithms for each of these problems have been developed for different kinds…
This paper introduces a novel hypergraph classification algorithm. The use of hypergraphs in this framework has been widely studied. In previous work, hypergraph models are typically constructed using distance or attribute based methods.…