On Finding Optimal Polytrees

Peer reviewe

Evolutionary branching in a stochastic population model with discrete mutational steps

Evolutionary branching is analysed in a stochastic, individual-based population model under mutation and selection. In such models, the common assumption is that individual reproduction and life career are characterised by values of a trait, and also by population sizes, and that mutations lead to small changes in trait value. Then, traditionally, the evolutionary dynamics is studied in the limit of vanishing mutational step sizes. In the present approach, small but non-negligible mutational steps are considered. By means of theoretical analysis in the limit of infinitely large populations, as well as computer simulations, we demonstrate how discrete mutational steps affect the patterns of evolutionary branching. We also argue that the average time to the first branching depends in a sensitive way on both mutational step size and population size.Comment: 12 pages, 8 figures. Revised versio

Subjectively interesting connecting trees and forests

Consider a large graph or network, and a user-provided set of query vertices between which the user wishes to explore relations. For example, a researcher may want to connect research papers in a citation network, an analyst may wish to connect organized crime suspects in a communication network, or an internet user may want to organize their bookmarks given their location in the world wide web. A natural way to do this is to connect the vertices in the form of a tree structure that is present in the graph. However, in sufficiently dense graphs, most such trees will be large or somehow trivial (e.g. involving high degree vertices) and thus not insightful. Extending previous research, we define and investigate the new problem of mining subjectively interesting trees connecting a set of query vertices in a graph, i.e., trees that are highly surprising to the specific user at hand. Using information theoretic principles, we formalize the notion of interestingness of such trees mathematically, taking in account certain prior beliefs the user has specified about the graph. A remaining problem is efficiently fitting a prior belief model. We show how this can be done for a large class of prior beliefs. Given a specified prior belief model, we then propose heuristic algorithms to find the best trees efficiently. An empirical validation of our methods on a large real graphs evaluates the different heuristics and validates the interestingness of the given trees

Efficiently Computing Directed Minimum Spanning Trees

Computing a directed minimum spanning tree, called arborescence, is a fundamental algorithmic problem, although not as common as its undirected counterpart. In 1967, Edmonds discussed an elegant solution. It was refined to run in $O(\min(n^2, m\log n))$ by Tarjan which is optimal for very dense and very sparse graphs. Gabow et al.~gave a version of Edmonds' algorithm that runs in $O(n\log n + m)$, thus asymptotically beating the Tarjan variant in the regime between sparse and dense. Despite the attention the problem received theoretically, there exists, to the best of our knowledge, no empirical evaluation of either of these algorithms. In fact, the version by Gabow et al.~has never been implemented and, aside from coding competitions, all readily available Tarjan implementations run in $O(n^2)$. In this paper, we provide the first implementation of the version by Gabow et al.~as well as five variants of Tarjan's version with different underlying data structures. We evaluate these algorithms and existing solvers on a large set of real-world and random graphs