Easy identification of generalized common and conserved nested intervals

In this paper we explain how to easily compute gene clusters, formalized by classical or generalized nested common or conserved intervals, between a set of K genomes represented as K permutations. A b-nested common (resp. conserved) interval I of size |I| is either an interval of size 1 or a common (resp. conserved) interval that contains another b-nested common (resp. conserved) interval of size at least |I|-b. When b=1, this corresponds to the classical notion of nested interval. We exhibit two simple algorithms to output all b-nested common or conserved intervals between K permutations in O(Kn+nocc) time, where nocc is the total number of such intervals. We also explain how to count all b-nested intervals in O(Kn) time. New properties of the family of conserved intervals are proposed to do so

Decomposing a Graph into Shortest Paths with Bounded Eccentricity

We introduce the problem of hub-laminar decomposition which generalizes that of computing a shortest path with minimum eccentricity (MESP). Intuitively, it consists in decomposing a graph into several paths that collectively have small eccentricity and meet only near their extremities. The problem is related to computing an isometric cycle with minimum eccentricity (MEIC). It is also linked to DNA reconstitution in the context of metagenomics in biology. We show that a graph having such a decomposition with long enough paths can be decomposed in polynomial time with approximated guaranties on the parameters of the decomposition. Moreover, such a decomposition with few paths allows to compute a compact representation of distances with additive distortion. We also show that having an isometric cycle with small eccentricity is related to the possibility of embedding the graph in a cycle with low distortion

Algorithmic Aspects of Switch Cographs

This paper introduces the notion of involution module, the first generalization of the modular decomposition of 2-structure which has a unique linear-sized decomposition tree. We derive an O(n^2) decomposition algorithm and we take advantage of the involution modular decomposition tree to state several algorithmic results. Cographs are the graphs that are totally decomposable w.r.t modular decomposition. In a similar way, we introduce the class of switch cographs, the class of graphs that are totally decomposable w.r.t involution modular decomposition. This class generalizes the class of cographs and is exactly the class of (Bull, Gem, Co-Gem, C_5)-free graphs. We use our new decomposition tool to design three practical algorithms for the maximum cut, vertex cover and vertex separator problems. The complexity of these problems was still unknown for this class of graphs. This paper also improves the complexity of the maximum clique, the maximum independant set, the chromatic number and the maximum clique cover problems by giving efficient algorithms, thanks to the decomposition tree. Eventually, we show that this class of graphs has Clique-Width at most 4 and that a Clique-Width expression can be computed in linear time

Optimisation de la bande passante dans un réseau pair-à-pair : la statégie BitTorrent face à ses challengers

Les protocoles d'échanges Pair-à-pair actuels incitent leurs clients à échanger les fichiers grâce à un système d'échanges de blocs rappelant l'économie libérale. Cette étude présente des algorithmes génétiques permettant de déterminer "la" meilleure stratégie de négociation des blocs dans un réseau Pair-à--pair de type BitTorrent, c'est-à-dire celle qui maximise la vitesse de téléchargement

Algorithmic Aspects of a General Modular Decomposition Theory

A new general decomposition theory inspired from modular graph decomposition is presented. This helps unifying modular decomposition on different structures, including (but not restricted to) graphs. Moreover, even in the case of graphs, the terminology ``module'' not only captures the classical graph modules but also allows to handle 2-connected components, star-cutsets, and other vertex subsets. The main result is that most of the nice algorithmic tools developed for modular decomposition of graphs still apply efficiently on our generalisation of modules. Besides, when an essential axiom is satisfied, almost all the important properties can be retrieved. For this case, an algorithm given by Ehrenfeucht, Gabow, McConnell and Sullivan 1994 is generalised and yields a very efficient solution to the associated decomposition problem

Minimum Eccentricity Shortest Path Problem: an Approximation Algorithm and Relation with the k-Laminarity Problem

The Minimum Eccentricity Shortest Path (MESP) Problem consists in determining a shortest path (a path whose length is the distance between its extremities) of minimum eccentricity in a graph. It was introduced by Dragan and Leitert [9] who described a linear-time algorithm which is an 8-approximation of the problem. In this paper, we study deeper the double-BFS procedure used in that algorithm and extend it to obtain a linear-time 3-approximation algorithm. We moreover study the link between the MESP problem and the notion of laminarity, introduced by Völkel et al [12], corresponding to its restriction to a diameter (i.e. a shortest path of maximum length), and show tight bounds between MESP and laminarity parameters

Stratification in P2P Networks - Application to BitTorrent

We introduce a model for decentralized networks with collaborating peers. The model is based on the stable matching theory which is applied to systems with a global ranking utility function. We consider the dynamics of peers searching for efficient collaborators and we prove that a unique stable solution exists. We prove that the system converges towards the stable solution and analyze its speed of convergence. We also study the stratification properties of the model, both when all collaborations are possible and for random possible collaborations. We present the corresponding fluid limit on the choice of collaborators in the random case. As a practical example, we study the BitTorrent Tit-for-Tat policy. For this system, our model provides an interesting insight on peer download rates and a possible way to optimize peer strategy

A Note On Computing Set Overlap Classes

Let ${\cal V}$ be a finite set of $n$ elements and ${\cal F}=\{X_1,X_2, >..., X_m\}$ a family of $m$ subsets of ${\cal V}.$ Two sets $X_i$ and $X_j$ of ${\cal F}$ overlap if $X_i \cap X_j \neq \emptyset,$ $X_j \setminus X_i \neq \emptyset,$ and $X_i \setminus X_j \neq \emptyset.$ Two sets $X,Y\in {\cal F}$ are in the same overlap class if there is a series $X=X_1,X_2, ..., X_k=Y$ of sets of ${\cal F}$ in which each $X_iX_{i+1}$ overlaps. In this note, we focus on efficiently identifying all overlap classes in $O(n+\sum_{i=1}^m |X_i|)$ time. We thus revisit the clever algorithm of Dahlhaus of which we give a clear presentation and that we simplify to make it practical and implementable in its real worst case complexity. An useful variant of Dahlhaus's approach is also explained