Computing the blocks of a quasi-median graph

Quasi-median graphs are a tool commonly used by evolutionary biologists to visualise the evolution of molecular sequences. As with any graph, a quasi-median graph can contain cut vertices, that is, vertices whose removal disconnect the graph. These vertices induce a decomposition of the graph into blocks, that is, maximal subgraphs which do not contain any cut vertices. Here we show that the special structure of quasi-median graphs can be used to compute their blocks without having to compute the whole graph. In particular we present an algorithm that, for a collection of $n$ aligned sequences of length $m$, can compute the blocks of the associated quasi-median graph together with the information required to correctly connect these blocks together in run time $\mathcal O(n^2m^2)$, independent of the size of the sequence alphabet. Our primary motivation for presenting this algorithm is the fact that the quasi-median graph associated to a sequence alignment must contain all most parsimonious trees for the alignment, and therefore precomputing the blocks of the graph has the potential to help speed up any method for computing such trees.Comment: 17 pages, 2 figure

Lagrangian Relaxation and Partial Cover

Lagrangian relaxation has been used extensively in the design of approximation algorithms. This paper studies its strengths and limitations when applied to Partial Cover.Comment: 20 pages, extended abstract appeared in STACS 200

Approximate Clustering via Metric Partitioning

In this paper we consider two metric covering/clustering problems - \textit{Minimum Cost Covering Problem} (MCC) and $k$-clustering. In the MCC problem, we are given two point sets $X$ (clients) and $Y$ (servers), and a metric on $X \cup Y$. We would like to cover the clients by balls centered at the servers. The objective function to minimize is the sum of the $\alpha$-th power of the radii of the balls. Here $\alpha \geq 1$ is a parameter of the problem (but not of a problem instance). MCC is closely related to the $k$-clustering problem. The main difference between $k$-clustering and MCC is that in $k$-clustering one needs to select $k$ balls to cover the clients. For any \eps > 0, we describe quasi-polynomial time (1 + \eps) approximation algorithms for both of the problems. However, in case of $k$-clustering the algorithm uses (1 + \eps)k balls. Prior to our work, a $3^{\alpha}$ and a ${c}^{\alpha}$ approximation were achieved by polynomial-time algorithms for MCC and $k$-clustering, respectively, where $c > 1$ is an absolute constant. These two problems are thus interesting examples of metric covering/clustering problems that admit (1 + \eps)-approximation (using (1+\eps)k balls in case of $k$-clustering), if one is willing to settle for quasi-polynomial time. In contrast, for the variant of MCC where $\alpha$ is part of the input, we show under standard assumptions that no polynomial time algorithm can achieve an approximation factor better than $O(\log |X|)$ for $\alpha \geq \log |X|$.Comment: 19 page

Model-based clustering for populations of networks

Until recently obtaining data on populations of networks was typically rare. However, with the advancement of automatic monitoring devices and the growing social and scientific interest in networks, such data has become more widely available. From sociological experiments involving cognitive social structures to fMRI scans revealing large-scale brain networks of groups of patients, there is a growing awareness that we urgently need tools to analyse populations of networks and particularly to model the variation between networks due to covariates. We propose a model-based clustering method based on mixtures of generalized linear (mixed) models that can be employed to describe the joint distribution of a populations of networks in a parsimonious manner and to identify subpopulations of networks that share certain topological properties of interest (degree distribution, community structure, effect of covariates on the presence of an edge, etc.). Maximum likelihood estimation for the proposed model can be efficiently carried out with an implementation of the EM algorithm. We assess the performance of this method on simulated data and conclude with an example application on advice networks in a small business.Comment: The final (published) version of the article can be downloaded for free (Open Access) from the editor's website (click on the DOI link below

Truss Decomposition in Massive Networks

The k-truss is a type of cohesive subgraphs proposed recently for the study of networks. While the problem of computing most cohesive subgraphs is NP-hard, there exists a polynomial time algorithm for computing k-truss. Compared with k-core which is also efficient to compute, k-truss represents the "core" of a k-core that keeps the key information of, while filtering out less important information from, the k-core. However, existing algorithms for computing k-truss are inefficient for handling today's massive networks. We first improve the existing in-memory algorithm for computing k-truss in networks of moderate size. Then, we propose two I/O-efficient algorithms to handle massive networks that cannot fit in main memory. Our experiments on real datasets verify the efficiency of our algorithms and the value of k-truss.Comment: VLDB201