Publications related to Comparing genomes with rearrangements and segmental duplications

New Genome Similarity Measures based on Conserved Gene Adjacencies

Bernard Moret, Shachi Shailesh Deshpande

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, ...

Mary Ann Liebert2017

LP-Based Algorithms For Capacitated Facility Location

Ola Nils Anders Svensson, Hyung Chan An

Linear programming (LP) has played a key role in the study of algorithms for combinatorial optimization problems. In the field of approximation algorithms, this is well illustrated by the uncapacitated facility location problem. A variety of algorithmic me ...

Society for Industrial and Applied Mathematics2017

Strengths and Limitations of Linear Programming Relaxations

Abbas Bazzi

Many of the currently best-known approximation algorithms for NP-hard optimization problems are based on Linear Programming (LP) and Semi-definite Programming (SDP) relaxations. Given its power, this class of algorithms seems to contain the most favourable ...

EPFL2017

Dynamic Facility Location via Exponential Clocks

Ola Nils Anders Svensson, Ashkan Norouzi Fard, Hyung Chan An

The dynamic facility location problem is a generalization of the classic facility location problem proposed by Eisenstat, Mathieu, and Schabanel to model the dynamics of evolving social/infrastructure networks. The generalization lies in that the distance ...

Association for Computing Machinery2017

Dynamic clustering and propagation of congestion in heterogeneously congested urban traffic networks

Nikolaos Geroliminis, Mohammadreza Saeedmanesh

The problem of clustering in urban traffic networks has been mainly studied in static framework by considering traffic conditions at a given time. Nevertheless, it is important to underline that traffic is a strongly time-variant process and it needs to be ...

2017

The multi-objective railway timetable rescheduling problem

Michel Bierlaire, Mohammad Yousef Maknoon, Stefan Yves Gabriel Binder

Unexpected disruptions occur for many reasons in railway networks and cause delays, cancelations, and, eventually, passenger inconvenience. This research focuses on the railway timetable rescheduling problem from a macroscopic point of view in case of larg ...

Pergamon-Elsevier Science Ltd2017

Maximizing Symmetric Submodular Functions

Moran Feldman

Symmetric submodular functions are an important family of submodular functions capturing many interesting cases, including cut functions of graphs and hypergraphs. Maximization of such functions subject to various constraints receives little attention by c ...

Association for Computing Machinery2017

Memetic Viability Evolution for Constrained Optimization

Dario Floreano, Andrea Maesani, Giovanni Iacca

The performance of evolutionary algorithms can be heavily undermined when constraints limit the feasible areas of the search space. For instance, while Covariance Matrix Adapta- tion Evolution Strategy is one of the most efficient algorithms for unconstrai ...

Institute of Electrical and Electronics Engineers2016

Exact Algorithms for $ L ^{ 1 } $ -TV Regularization of Real-Valued or Circle-Valued Signals

Michaël Unser, Martin Kurt Storath

We consider

L ^{ 1 }

-TV regularization of univariate signals with values on the real line or on the unit circle. While the real data space leads to a convex optimization problem, the problem is nonconvex for circle-valued data. In this paper, we deriv ...

SIAM2016

A Fast and Exact Algorithm for the Exemplar Breakpoint Distance

Bernard Moret, Mingfu Shao

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 ...

Mary Ann Liebert, Inc2016

Comparing genomes with rearrangements and segmental duplications

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New Genome Similarity Measures based on Conserved Gene Adjacencies

LP-Based Algorithms For Capacitated Facility Location

Strengths and Limitations of Linear Programming Relaxations

Dynamic Facility Location via Exponential Clocks

Dynamic clustering and propagation of congestion in heterogeneously congested urban traffic networks

The multi-objective railway timetable rescheduling problem

Maximizing Symmetric Submodular Functions

Memetic Viability Evolution for Constrained Optimization

Exact Algorithms for $ L ^{ 1 } $ -TV Regularization of Real-Valued or Circle-Valued Signals

A Fast and Exact Algorithm for the Exemplar Breakpoint Distance

Dynamic Facility Location via Exponential Clocks

Dynamic clustering and propagation of congestion in heterogeneously congested urban traffic networks

LP-Based Algorithms For Capacitated Facility Location

Strengths and Limitations of Linear Programming Relaxations

Exact Algorithms for $ L ^{ 1 } $ -TV Regularization of Real-Valued or Circle-Valued Signals

Memetic Viability Evolution for Constrained Optimization

The multi-objective railway timetable rescheduling problem

Maximizing Symmetric Submodular Functions

A Fast and Exact Algorithm for the Exemplar Breakpoint Distance

New Genome Similarity Measures based on Conserved Gene Adjacencies