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 $\delta$-hyperbolic graph $G=(V,E)$ can be computed in linear time with an additive one-sided error of at most $c\delta$, i.e., after a linear time preprocessing, for every vertex $v$ of $G$ one can compute in $O(1)$ time an estimate $\hat{e}(v)$ of its eccentricity $ecc_G(v)$ such that $ecc_G(v)\leq \hat{e}(v)\leq ecc_G(v)+ c\delta$ for a small constant $c$. We prove that every $\delta$-hyperbolic graph $G$ has a shortest path tree, constructible in linear time, such that for every vertex $v$ of $G$, $ecc_G(v)\leq ecc_T(v)\leq ecc_G(v)+ c\delta$. 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 $G$, the smaller its eccentricity is. We also show that the distance matrix of $G$ with an additive one-sided error of at most $c'\delta$ can be computed in $O(|V|^2\log^2|V|)$ time, where $c'< c$ 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