Principal components analysis in the space of phylogenetic trees

Phylogenetic analysis of DNA or other data commonly gives rise to a collection or sample of inferred evolutionary trees. Principal Components Analysis (PCA) cannot be applied directly to collections of trees since the space of evolutionary trees on a fixed set of taxa is not a vector space. This paper describes a novel geometrical approach to PCA in tree-space that constructs the first principal path in an analogous way to standard linear Euclidean PCA. Given a data set of phylogenetic trees, a geodesic principal path is sought that maximizes the variance of the data under a form of projection onto the path. Due to the high dimensionality of tree-space and the nonlinear nature of this problem, the computational complexity is potentially very high, so approximate optimization algorithms are used to search for the optimal path. Principal paths identified in this way reveal and quantify the main sources of variation in the original collection of trees in terms of both topology and branch lengths. The approach is illustrated by application to simulated sets of trees and to a set of gene trees from metazoan (animal) species.Comment: Published in at http://dx.doi.org/10.1214/11-AOS915 the Annals of Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical Statistics (http://www.imstat.org

An Efficient Hybrid Ant Colony System for the Generalized Traveling Salesman Problem

The Generalized Traveling Salesman Problem (GTSP) is an extension of the well-known Traveling Salesman Problem (TSP), where the node set is partitioned into clusters, and the objective is to find the shortest cycle visiting each cluster exactly once. In this paper, we present a new hybrid Ant Colony System (ACS) algorithm for the symmetric GTSP. The proposed algorithm is a modification of a simple ACS for the TSP improved by an efficient GTSP-specific local search procedure. Our extensive computational experiments show that the use of the local search procedure dramatically improves the performance of the ACS algorithm, making it one of the most successful GTSP metaheuristics to date.Comment: 7 page

On green routing and scheduling problem

The vehicle routing and scheduling problem has been studied with much interest within the last four decades. In this paper, some of the existing literature dealing with routing and scheduling problems with environmental issues is reviewed, and a description is provided of the problems that have been investigated and how they are treated using combinatorial optimization tools

Transport optimization on complex networks

We present a comparative study of the application of a recently introduced heuristic algorithm to the optimization of transport on three major types of complex networks. The algorithm balances network traffic iteratively by minimizing the maximum node betweenness with as little path lengthening as possible. We show that by using this optimal routing, a network can sustain significantly higher traffic without jamming than in the case of shortest path routing. A formula is proved that allows quick computation of the average number of hops along the path and of the average travel times once the betweennesses of the nodes are computed. Using this formula, we show that routing optimization preserves the small-world character exhibited by networks under shortest path routing, and that it significantly reduces the average travel time on congested networks with only a negligible increase in the average travel time at low loads. Finally, we study the correlation between the weights of the links in the case of optimal routing and the betweennesses of the nodes connected by them.Comment: 19 pages, 7 figure