4,365 research outputs found
A Fast Algorithm for Computing Geodesic Distances in Tree Space
Comparing and computing distances between phylogenetic trees are important biological problems, especially for models where edge lengths play an important role. The geodesic distance measure between two phylogenetic trees with edge lengths is the length of the shortest path between them in the continuous tree space introduced by Billera, Holmes, and Vogtmann. This tree space provides a powerful tool for studying and comparing phylogenetic trees, both in exhibiting a natural distance measure and in providing a Euclidean-like structure for solving optimization problems on trees. An important open problem is to find a polynomial time algorithm for finding geodesics in tree space. This paper gives such an algorithm, which starts with a simple initial path and moves through a series of successively shorter paths until the geodesic is attained
Fast approximation of centrality and distances in hyperbolic graphs
We show that the eccentricities (and thus the centrality indices) of all
vertices of a -hyperbolic graph can be computed in linear
time with an additive one-sided error of at most , i.e., after a
linear time preprocessing, for every vertex of one can compute in
time an estimate of its eccentricity such that
for a small constant . We
prove that every -hyperbolic graph has a shortest path tree,
constructible in linear time, such that for every vertex of ,
. These results are based on an
interesting monotonicity property of the eccentricity function of hyperbolic
graphs: the closer a vertex is to the center of , the smaller its
eccentricity is. We also show that the distance matrix of with an additive
one-sided error of at most can be computed in
time, where is a small constant. Recent empirical studies show that
many real-world graphs (including Internet application networks, web networks,
collaboration networks, social networks, biological networks, and others) have
small hyperbolicity. So, we analyze the performance of our algorithms for
approximating centrality and distance matrix on a number of real-world
networks. Our experimental results show that the obtained estimates are even
better than the theoretical bounds.Comment: arXiv admin note: text overlap with arXiv:1506.01799 by other author
Exact Computation of a Manifold Metric, via Lipschitz Embeddings and Shortest Paths on a Graph
Data-sensitive metrics adapt distances locally based the density of data
points with the goal of aligning distances and some notion of similarity. In
this paper, we give the first exact algorithm for computing a data-sensitive
metric called the nearest neighbor metric. In fact, we prove the surprising
result that a previously published -approximation is an exact algorithm.
The nearest neighbor metric can be viewed as a special case of a
density-based distance used in machine learning, or it can be seen as an
example of a manifold metric. Previous computational research on such metrics
despaired of computing exact distances on account of the apparent difficulty of
minimizing over all continuous paths between a pair of points. We leverage the
exact computation of the nearest neighbor metric to compute sparse spanners and
persistent homology. We also explore the behavior of the metric built from
point sets drawn from an underlying distribution and consider the more general
case of inputs that are finite collections of path-connected compact sets.
The main results connect several classical theories such as the conformal
change of Riemannian metrics, the theory of positive definite functions of
Schoenberg, and screw function theory of Schoenberg and Von Neumann. We develop
novel proof techniques based on the combination of screw functions and
Lipschitz extensions that may be of independent interest.Comment: 15 page
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
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