VLSI layouts and DNA physical mappings

We show that an important problem ($k$-ICG) in computational biology is equivalent to a colored version of a well-known graph layout problem ($k$-CVS).Comment: 7 page

Activity recognition from videos with parallel hypergraph matching on GPUs

In this paper, we propose a method for activity recognition from videos based on sparse local features and hypergraph matching. We benefit from special properties of the temporal domain in the data to derive a sequential and fast graph matching algorithm for GPUs. Traditionally, graphs and hypergraphs are frequently used to recognize complex and often non-rigid patterns in computer vision, either through graph matching or point-set matching with graphs. Most formulations resort to the minimization of a difficult discrete energy function mixing geometric or structural terms with data attached terms involving appearance features. Traditional methods solve this minimization problem approximately, for instance with spectral techniques. In this work, instead of solving the problem approximatively, the exact solution for the optimal assignment is calculated in parallel on GPUs. The graphical structure is simplified and regularized, which allows to derive an efficient recursive minimization algorithm. The algorithm distributes subproblems over the calculation units of a GPU, which solves them in parallel, allowing the system to run faster than real-time on medium-end GPUs

Exact and Approximate Digraph Bandwidth

In this paper, we introduce a directed variant of the classical Bandwidth problem and study it from the view-point of moderately exponential time algorithms, both exactly and approximately. Motivated by the definitions of the directed variants of the classical Cutwidth and Pathwidth problems, we define Digraph Bandwidth as follows. Given a digraph D and an ordering sigma of its vertices, the digraph bandwidth of sigma with respect to D is equal to the maximum value of sigma(v)-sigma(u) over all arcs (u,v) of D going forward along sigma (that is, when sigma(u) < sigma (v)). The Digraph Bandwidth problem takes as input a digraph D and asks to output an ordering with the minimum digraph bandwidth. The undirected Bandwidth easily reduces to Digraph Bandwidth and thus, it immediately implies that Directed Bandwidth is {NP-hard}. While an O^*(n!) time algorithm for the problem is trivial, the goal of this paper is to design algorithms for Digraph Bandwidth which have running times of the form 2^O(n). In particular, we obtain the following results. Here, n and m denote the number of vertices and arcs of the input digraph D, respectively. - Digraph Bandwidth can be solved in O^*(3^n * 2^m) time. This result implies a 2^O(n) time algorithm on sparse graphs, such as graphs of bounded average degree. - Let G be the underlying undirected graph of the input digraph. If the treewidth of G is at most t, then Digraph Bandwidth can be solved in time O^*(2^(n + (t+2) log n)). This result implies a 2^(n+O(sqrt(n) log n)) algorithm for directed planar graphs and, in general, for the class of digraphs whose underlying undirected graph excludes some fixed graph H as a minor. - Digraph Bandwidth can be solved in min{O^*(4^n * b^n), O^*(4^n * 2^(b log b log n))} time, where b denotes the optimal digraph bandwidth of D. This allow us to deduce a 2^O(n) algorithm in many cases, for example when b <= n/(log^2n). - Finally, we give a (Single) Exponential Time Approximation Scheme for Digraph Bandwidth. In particular, we show that for any fixed real epsilon > 0, we can find an ordering whose digraph bandwidth is at most (1+epsilon) times the optimal digraph bandwidth, in time O^*(4^n * (ceil[4/epsilon])^n)

On space efficiency of algorithms working on structural decompositions of graphs

Dynamic programming on path and tree decompositions of graphs is a technique that is ubiquitous in the field of parameterized and exponential-time algorithms. However, one of its drawbacks is that the space usage is exponential in the decomposition's width. Following the work of Allender et al. [Theory of Computing, '14], we investigate whether this space complexity explosion is unavoidable. Using the idea of reparameterization of Cai and Juedes [J. Comput. Syst. Sci., '03], we prove that the question is closely related to a conjecture that the Longest Common Subsequence problem parameterized by the number of input strings does not admit an algorithm that simultaneously uses XP time and FPT space. Moreover, we complete the complexity landscape sketched for pathwidth and treewidth by Allender et al. by considering the parameter tree-depth. We prove that computations on tree-depth decompositions correspond to a model of non-deterministic machines that work in polynomial time and logarithmic space, with access to an auxiliary stack of maximum height equal to the decomposition's depth. Together with the results of Allender et al., this describes a hierarchy of complexity classes for polynomial-time non-deterministic machines with different restrictions on the access to working space, which mirrors the classic relations between treewidth, pathwidth, and tree-depth.Comment: An extended abstract appeared in the proceedings of STACS'16. The new version is augmented with a space-efficient algorithm for Dominating Set using the Chinese remainder theore

On the Extended TSP Problem

We initiate the theoretical study of Ext-TSP, a problem that originates in the area of profile-guided binary optimization. Given a graph $G=(V, E)$ with positive edge weights $w: E \rightarrow R^+$, and a non-increasing discount function $f(\cdot)$ such that $f(1) = 1$ and $f(i) = 0$ for $i > k$, for some parameter $k$ that is part of the problem definition. The problem is to sequence the vertices $V$ so as to maximize $\sum_{(u, v) \in E} f(|d_u - d_v|)\cdot w(u,v)$, where $d_v \in \{1, \ldots, |V| \}$ is the position of vertex~$v$ in the sequence. We show that \prob{Ext-TSP} is APX-hard to approximate in general and we give a $(k+1)$-approximation algorithm for general graphs and a PTAS for some sparse graph classes such as planar or treewidth-bounded graphs. Interestingly, the problem remains challenging even on very simple graph classes; indeed, there is no exact $n^{o(k)}$ time algorithm for trees unless the ETH fails. We complement this negative result with an exact $n^{O(k)}$ time algorithm for trees.Comment: 17 page

Retracting Graphs to Cycles

We initiate the algorithmic study of retracting a graph into a cycle in the graph, which seeks a mapping of the graph vertices to the cycle vertices so as to minimize the maximum stretch of any edge, subject to the constraint that the restriction of the mapping to the cycle is the identity map. This problem has its roots in the rich theory of retraction of topological spaces, and has strong ties to well-studied metric embedding problems such as minimum bandwidth and 0-extension. Our first result is an O(min{k, sqrt{n}})-approximation for retracting any graph on n nodes to a cycle with k nodes. We also show a surprising connection to Sperner\u27s Lemma that rules out the possibility of improving this result using certain natural convex relaxations of the problem. Nevertheless, if the problem is restricted to planar graphs, we show that we can overcome these integrality gaps by giving an optimal combinatorial algorithm, which is the technical centerpiece of the paper. Building on our planar graph algorithm, we also obtain a constant-factor approximation algorithm for retraction of points in the Euclidean plane to a uniform cycle

Approximation algorithms for low-distortion embeddings into low-dimensional spaces

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2005.Includes bibliographical references (p. 33-35).We present several approximation algorithms for the problem of embedding metric spaces into a line, and into the two-dimensional plane. We give an O([square root] n)-approximation algorithm for the problem of finding a line embedding of a metric induced by a given unweighted graph, that minimizes the (standard) multiplicative distortion. For the same problem, we give an exact algorithm, with running-time exponential in the distortion. We complement these results by showing that the problem is NP-hard to [alpha]-approximate, for some constant [alpha] > 1. For the two-dimensional case, we show a O([square root] n) upper bound for the distortion required to embed an n-point subset of the two-dimensional sphere, into the plane. We prove that this bound is asymptotically tight, by exhibiting n-point subsets such that any embedding into the plane has distortion [omega]([square root] n). These techniques yield a O(1)-approximation algorithm for the problem of embedding an n-point subset of the sphere into the plane.by Anastasios Sidiropoulos.S.M