An Exact Algorithm to Compute the DCJ Distance for Genomes with Duplicate Genes
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Motivation: Large-scale evolutionary events such as genomic rearrange. ments and segmental duplications form an important part of the evolution of genomes and are widely studied from both biological and computational perspectives. A basic computational pro ...
The fully connected conditional random field (CRF) with Gaussian pairwise potentials has proven popular and effective for multi-class semantic segmentation. While the energy of a dense CRF can be minimized accurately using a linear programming (LP) relaxat ...
The deluge of sequenced whole-genome data has motivated the study of comparative genomics, which provides global views on genome evolution, and also offers practical solutions in deciphering the functional roles of components of genomes. A fundamental comp ...
Many important questions in molecular biology, evolution, and biomedicine can be addressed by comparative genomic approaches. One of the basic tasks when comparing genomes is the definition of measures of similarity (or dissimilarity) between two genomes, ...
A fundamental problem in comparative genomics is to compute the distance between two genomes. For two genomes without duplicate genes, we can easily compute a variety of distance measures in linear time, but the problem is NP-hard under most models when ge ...
Group-based sparsity models are proven instrumental in linear regression problems for recovering signals from much fewer measurements than standard compressive sensing. The main promise of these models is the recovery of ``interpretable" signals along with ...
Institute of Electrical and Electronics Engineers2016
Computing the edit distance between two genomes is a basic problem in the study of genome evolution. The double-cut-and-join (DCJ) model has formed the basis for most algorithmic research on rearrangements over the last few years. The edit distance under t ...
Polyploid taxa represent excellent models to address the underpinnings of genome evolution and the building up of new species in heterogeneous environments. Here, we present an overview of recent works in the alpine Biscutella laevigata autopolyploid compl ...
A fundamental problem in comparative genomics is to compute the distance between two genomes. For two genomes without duplicate genes, we can easily compute a variety of distance measures in linear time, but the problem is NP-hard under most models when ge ...
The vertex cover problem is one of the most important and intensively studied combinatorial optimization problems. Khot and Regevproved that the problem is NP-hard to approximate within a factor2 - ∈, assuming the Unique Games Conjecture (UGC). This is tig ...