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On the DCJ Median Problem

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Coordination and Sampling in Distributed Constraint Optimization

Brammert Ottens

The Distributed Constraint Optimization (DCOP) framework can be used to model a wide range of optimization problems that are inherently distributed. A distributed optimization problem can be viewed as a problem distributed over a set of agents, where agent ...

EPFL2012

A Metric for Phylogenetic Trees Based on Matching

Bernard Moret, Yu Lin, Vaibhav Rajan

Comparing two or more phylogenetic trees is a fundamental task in computational biology. The simplest outcome of such a comparison is a pairwise measure of similarity, dissimilarity, or distance. A large number of such measures have been proposed, but so f ...

2012

Reconstruction of Large-Scale Phylogenies

Vaibhav Rajan

The evolutionary relationships between organisms or phylogenies are fundamental to biology. They are invaluable as guiding tools to mine, organize and exploit the enormous amounts of biological data in the post-genomic era. The advent of high-throughput se ...

EPFL2012

Efficient Interior Point Methods for Multistage Problems Arising in Receding Horizon Control

Colin Neil Jones, Melanie Nicole Zeilinger

Receding horizon control requires the solution of an optimization problem at every sampling instant. We present efficient interior point methods tailored to convex multistage problems, a problem class which most relevant MPC problems with linear dynamics c ...

2012

Bootstrapping phylogenies inferred from rearrangement data

Bernard Moret, Yu Lin, Vaibhav Rajan

Large-scale sequencing of genomes has enabled the inference of phylogenies based on the evolution of genomic architecture, under such events as rearrangements, duplications, and losses. Many evolutionary models and associated algorithms have been designed ...

Springer Verlag2011

Container Terminal Management

Ilaria Vacca

This thesis deals with models and methods for large scale optimization problems; in particular, we focus on decision problems arising in the context of seaport container terminals for the efficient management of terminal operations. Large-scale optimizatio ...

EPFL2011

Fast and accurate phylogenetic reconstruction from high-resolution whole-genome data and a novel robustness estimator

Bernard Moret, Yu Lin, Vaibhav Rajan

The rapid accumulation of whole-genome data has renewed interest in the study of genomic rearrangements. Comparative genomics, evolutionary biology, and cancer research all require models and algorithms to elucidate the mechanisms, history, and consequence ...

2011

A metric for phylogenetic trees based on matching

Bernard Moret, Yu Lin, Vaibhav Rajan

Springer Verlag2011

Transcriptional Regulatory Networks across Species

Xiuwei Zhang

The determination of transcriptional regulatory networks is key to the understanding of biological systems. However, the experimental determination of transcriptional regulatory networks in the laboratory remains difficult and time-consuming, while current ...

EPFL2011

Fast and accurate phylogenetic reconstruction from high-resolution whole-genome data and a novel robustness estimator

Bernard Moret, Yu Lin, Vaibhav Rajan

Springer2010