Related papers: From Best Hits to Best Matches
Evolutionary scenarios describing the evolution of a family of genes within a collection of species comprise the mapping of the vertices of a gene tree $T$ to vertices and edges of a species tree $S$. The relative timing of the last common…
Random graph matching refers to recovering the underlying vertex correspondence between two random graphs with correlated edges; a prominent example is when the two random graphs are given by Erd\H{o}s-R\'{e}nyi graphs $G(n,\frac{d}{n})$.…
Ontology matching is the process of automatically determining the semantic equivalences between the concepts of two ontologies. Most ontology matching algorithms are based on two types of strategies: terminology-based strategies, which…
Orthology is a central concept in evolutionary and comparative genomics, used to relate corresponding genes in different species. In particular, orthologs are needed to infer species trees. In this chapter, we introduce the fundamental…
Reconstructing the evolutionary past of a family of genes is an important aspect of many genomic studies. To help with this, simple operations on a set of sequences called orthology relations may be employed. In addition to being…
This work addresses approximate nearest neighbor search applied in the domain of large-scale image retrieval. Within the group testing framework we propose an efficient off-line construction of the search structures. The linear-time…
We consider a novel approach of measuring the homology of DNA sequences based of the variety of optimal alignments in the longest common subsequence sense. The proposed approach is compared with BLAST in measuring the homology of four…
Accurate estimation of evolutionary distances between taxa is important for many phylogenetic reconstruction methods. In the case of bacteria, distances can be estimated using a range of different evolutionary models, from single nucleotide…
When searching for exoplanets, one wants to count how many planets orbit a given star, and to determine what their characteristics are. If the estimated planet characteristics are too far from those of a planet truly present, this should be…
A widely used method for determining the similarity of two labeled trees is to compute a maximum agreement subtree of the two trees. Previous work on this similarity measure is only concerned with the comparison of labeled trees of two…
Ear recognition task is known as predicting whether two ear images belong to the same person or not. In this paper, we present a novel metric learning method for ear recognition. This method is formulated as a pairwise constrained…
Although the applications of Non-Homogeneous Poisson Processes to model and study the threshold overshoots of interest in different time series of measurements have proven to provide good results, they needed to be complemented with an…
We propose an efficient algorithm for graph matching based on similarity scores constructed from counting a certain family of weighted trees rooted at each vertex. For two Erd\H{o}s-R\'enyi graphs $\mathcal{G}(n,q)$ whose edges are…
This paper considers pairs of optimization problems that are defined from a single input and for which it is desired to find a good approximation to either one of the problems. In many instances, it is possible to efficiently find an…
Ontology alignment is widely-used to find the correspondences between different ontologies in diverse fields.After discovering the alignments,several performance scores are available to evaluate them.The scores typically require the…
We consider a similarity measure between two sets $A$ and $B$ of vectors, that balances the average and maximum cosine distance between pairs of vectors, one from set $A$ and one from set $B$. As a motivation for this measure, we present…
Fast exact algorithms are known for Hamiltonian paths in undirected and directed bipartite graphs through elegant though involved algorithms that are quite different from each other. We devise algorithms that are simple and similar to each…
Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…
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…
Optimal search strategies where targets are observed at several different angles are found. Targets are assumed to exhibit rectangular symmetry and have a uniformly-distributed orientation. By rectangular symmetry, it is meant that one side…