Paradigms for Parameterized Enumeration

The aim of the paper is to examine the computational complexity and algorithmics of enumeration, the task to output all solutions of a given problem, from the point of view of parameterized complexity. First we define formally different notions of efficient enumeration in the context of parameterized complexity. Second we show how different algorithmic paradigms can be used in order to get parameter-efficient enumeration algorithms in a number of examples. These paradigms use well-known principles from the design of parameterized decision as well as enumeration techniques, like for instance kernelization and self-reducibility. The concept of kernelization, in particular, leads to a characterization of fixed-parameter tractable enumeration problems.Comment: Accepted for MFCS 2013; long version of the pape

Letter graphs and geometric grid classes of permutations: characterization and recognition

In this paper, we reveal an intriguing relationship between two seemingly unrelated notions: letter graphs and geometric grid classes of permutations. An important property common for both of them is well-quasi-orderability, implying, in a non-constructive way, a polynomial-time recognition of geometric grid classes of permutations and $k$-letter graphs for a fixed $k$. However, constructive algorithms are available only for $k=2$. In this paper, we present the first constructive polynomial-time algorithm for the recognition of $3$-letter graphs. It is based on a structural characterization of graphs in this class.Comment: arXiv admin note: text overlap with arXiv:1108.6319 by other author

Fast Arc-Annotated Subsequence Matching in Linear Space

An arc-annotated string is a string of characters, called bases, augmented with a set of pairs, called arcs, each connecting two bases. Given arc-annotated strings $P$ and $Q$ the arc-preserving subsequence problem is to determine if $P$ can be obtained from $Q$ by deleting bases from $Q$. Whenever a base is deleted any arc with an endpoint in that base is also deleted. Arc-annotated strings where the arcs are ``nested'' are a natural model of RNA molecules that captures both the primary and secondary structure of these. The arc-preserving subsequence problem for nested arc-annotated strings is basic primitive for investigating the function of RNA molecules. Gramm et al. [ACM Trans. Algorithms 2006] gave an algorithm for this problem using $O(nm)$ time and space, where $m$ and $n$ are the lengths of $P$ and $Q$, respectively. In this paper we present a new algorithm using $O(nm)$ time and $O(n + m)$ space, thereby matching the previous time bound while significantly reducing the space from a quadratic term to linear. This is essential to process large RNA molecules where the space is likely to be a bottleneck. To obtain our result we introduce several novel ideas which may be of independent interest for related problems on arc-annotated strings.Comment: To appear in Algoritmic

On retracts, absolute retracts, and folds in cographs

Let G and H be two cographs. We show that the problem to determine whether H is a retract of G is NP-complete. We show that this problem is fixed-parameter tractable when parameterized by the size of H. When restricted to the class of threshold graphs or to the class of trivially perfect graphs, the problem becomes tractable in polynomial time. The problem is also soluble when one cograph is given as an induced subgraph of the other. We characterize absolute retracts of cographs.Comment: 15 page

Partial Covering Arrays: Algorithms and Asymptotics

A covering array $\mathsf{CA}(N;t,k,v)$ is an $N\times k$ array with entries in $\{1, 2, \ldots , v\}$, for which every $N\times t$ subarray contains each $t$-tuple of $\{1, 2, \ldots , v\}^t$ among its rows. Covering arrays find application in interaction testing, including software and hardware testing, advanced materials development, and biological systems. A central question is to determine or bound $\mathsf{CAN}(t,k,v)$, the minimum number $N$ of rows of a $\mathsf{CA}(N;t,k,v)$. The well known bound $\mathsf{CAN}(t,k,v)=O((t-1)v^t\log k)$ is not too far from being asymptotically optimal. Sensible relaxations of the covering requirement arise when (1) the set $\{1, 2, \ldots , v\}^t$ need only be contained among the rows of at least $(1-\epsilon)\binom{k}{t}$ of the $N\times t$ subarrays and (2) the rows of every $N\times t$ subarray need only contain a (large) subset of $\{1, 2, \ldots , v\}^t$. In this paper, using probabilistic methods, significant improvements on the covering array upper bound are established for both relaxations, and for the conjunction of the two. In each case, a randomized algorithm constructs such arrays in expected polynomial time

Examining the influence of turbulence on viscosity measurements of molten germanium under reduced gravity

The thermophysical properties of liquid germanium were recently measured both in parabolic flight experiments and on the ISS in the ISS-EML facility. The viscosity measurements differed between the reduced gravity experiments and the literature values. Since the oscillating drop method has been widely used in EML, further exploration into this phenomenon was of interest. Models of the magnetohydrodynamic flow indicated that turbulence was present during the measurement in the ISS-EML facility, which accounts for the observed difference

Fast branching algorithm for Cluster Vertex Deletion

In the family of clustering problems, we are given a set of objects (vertices of the graph), together with some observed pairwise similarities (edges). The goal is to identify clusters of similar objects by slightly modifying the graph to obtain a cluster graph (disjoint union of cliques). Hueffner et al. [Theory Comput. Syst. 2010] initiated the parameterized study of Cluster Vertex Deletion, where the allowed modification is vertex deletion, and presented an elegant O(2^k * k^9 + n * m)-time fixed-parameter algorithm, parameterized by the solution size. In our work, we pick up this line of research and present an O(1.9102^k * (n + m))-time branching algorithm

Environmental changes during the onset of the Late Pliensbachian Event (Early Jurassic) in the Cardigan Bay Basin, Wales

The Late Pliensbachian Event (LPE), in the Early Jurassic, is associated with a perturbation in the global carbon cycle (positive carbon isotope excursion (CIE) of ∼2 ‰), cooling of ∼5 ∘C, and the deposition of widespread regressive facies. Cooling during the late Pliensbachian has been linked to enhanced organic matter burial and/or disruption of thermohaline ocean circulation due to a sea level lowstand of at least regional extent. Orbital forcing had a strong influence on the Pliensbachian environments and recent studies show that the terrestrial realm and the marine realm in and around the Cardigan Bay Basin, UK, were strongly influenced by orbital climate forcing. In the present study we build on the previously published data for long eccentricity cycle E459 ± 1 and extend the palaeoenvironmental record to include E458 ± 1. We explore the environmental and depositional changes on orbital timescales for the Llanbedr (Mochras Farm) core during the onset of the LPE. Clay mineralogy, X-ray fluorescence (XRF) elemental analysis, isotope ratio mass spectrometry, and palynology are combined to resolve systematic changes in erosion, weathering, fire, grain size, and riverine influx. Our results indicate distinctively different environments before and after the onset of the LPE positive CIE and show increased physical erosion relative to chemical weathering. We also identify five swings in the climate, in tandem with the 405 kyr eccentricity minima and maxima. Eccentricity maxima are linked to precessionally repeated occurrences of a semi-arid monsoonal climate with high fire activity and relatively coarser sediment from terrestrial runoff. In contrast, 405 kyr minima in the Mochras core are linked to a more persistent, annually wet climate, low fire activity, and relatively finer-grained deposits across multiple precession cycles. The onset of the LPE positive CIE did not impact the expression of the 405 kyr cycle in the proxy records; however, during the second pulse of heavier carbon (13C) enrichment, the clay minerals record a change from dominant chemical weathering to dominant physical erosion

Longest Increasing Subsequence under Persistent Comparison Errors

We study the problem of computing a longest increasing subsequence in a sequence $S$ of $n$ distinct elements in the presence of persistent comparison errors. In this model, every comparison between two elements can return the wrong result with some fixed (small) probability $p$, and comparisons cannot be repeated. Computing the longest increasing subsequence exactly is impossible in this model, therefore, the objective is to identify a subsequence that (i) is indeed increasing and (ii) has a length that approximates the length of the longest increasing subsequence. We present asymptotically tight upper and lower bounds on both the approximation factor and the running time. In particular, we present an algorithm that computes an $O(\log n)$-approximation in time $O(n\log n)$, with high probability. This approximation relies on the fact that that we can approximately sort $n$ elements in $O(n\log n)$ time such that the maximum dislocation of an element is at most $O(\log n)$. For the lower bounds, we prove that (i) there is a set of sequences, such that on a sequence picked randomly from this set every algorithm must return an $\Omega(\log n)$-approximation with high probability, and (ii) any $O(\log n)$-approximation algorithm for longest increasing subsequence requires $\Omega(n \log n)$ comparisons, even in the absence of errors

Parameterized Complexity of 1-Planarity

We consider the problem of finding a 1-planar drawing for a general graph, where a 1-planar drawing is a drawing in which each edge participates in at most one crossing. Since this problem is known to be NP-hard we investigate the parameterized complexity of the problem with respect to the vertex cover number, tree-depth, and cyclomatic number. For these parameters we construct fixed-parameter tractable algorithms. However, the problem remains NP-complete for graphs of bounded bandwidth, pathwidth, or treewidth.Comment: WADS 201