Pancake Flipping is Hard

Pancake Flipping is the problem of sorting a stack of pancakes of different sizes (that is, a permutation), when the only allowed operation is to insert a spatula anywhere in the stack and to flip the pancakes above it (that is, to perform a prefix reversal). In the burnt variant, one side of each pancake is marked as burnt, and it is required to finish with all pancakes having the burnt side down. Computing the optimal scenario for any stack of pancakes and determining the worst-case stack for any stack size have been challenges over more than three decades. Beyond being an intriguing combinatorial problem in itself, it also yields applications, e.g. in parallel computing and computational biology. In this paper, we show that the Pancake Flipping problem, in its original (unburnt) variant, is NP-hard, thus answering the long-standing question of its computational complexity.Comment: Corrected reference

Systolic geometry and simplicial complexity for groups

Twenty years ago Gromov asked about how large is the set of isomorphism classes of groups whose systolic area is bounded from above. This article introduces a new combinatorial invariant for finitely presentable groups called {\it simplicial complexity} that allows to obtain a quite satisfactory answer to his question. Using this new complexity, we also derive new results on systolic area for groups that specify its topological behaviour.Comment: 35 pages, 9 figure

Decomposing Cubic Graphs into Connected Subgraphs of Size Three

Let $S=\{K_{1,3},K_3,P_4\}$ be the set of connected graphs of size 3. We study the problem of partitioning the edge set of a graph $G$ into graphs taken from any non-empty $S'\subseteq S$. The problem is known to be NP-complete for any possible choice of $S'$ in general graphs. In this paper, we assume that the input graph is cubic, and study the computational complexity of the problem of partitioning its edge set for any choice of $S'$. We identify all polynomial and NP-complete problems in that setting, and give graph-theoretic characterisations of $S'$-decomposable cubic graphs in some cases.Comment: to appear in the proceedings of COCOON 201

Beyond Adjacency Maximization: Scaffold Filling for New String Distances

International audienceIn Genomic Scaffold Filling, one aims at polishing in silico a draft genome, called scaffold. The scaffold is given in the form of an ordered set of gene sequences, called contigs. This is done by confronting the scaffold to an already complete reference genome from a close species. More precisely, given a scaffold S, a reference genome G and a score function f () between two genomes, the aim is to complete S by adding the missing genes from G so that the obtained complete genome S * optimizes f (S * , G). In this paper, we extend a model of Jiang et al. [CPM 2016] (i) by allowing the insertions of strings instead of single characters (i.e., some groups of genes may be forced to be inserted together) and (ii) by considering two alternative score functions: the first generalizes the notion of common adjacencies by maximizing the number of common k-mers between S * and G (k-Mer Scaffold Filling), the second aims at minimizing the number of breakpoints between S * and G (Min-Breakpoint Scaffold Filling). We study these problems from the parameterized complexity point of view, providing fixed-parameter (FPT) algorithms for both problems. In particular, we show that k-Mer Scaffold Filling is FPT wrt. parameter , the number of additional k-mers realized by the completion of S—this answers an open question of Jiang et al. [CPM 2016]. We also show that Min-Breakpoint Scaffold Filling is FPT wrt. a parameter combining the number of missing genes, the number of gene repetitions and the target distance

Some algorithmic results for [2]-sumset covers

International audienceLet X={xi:1≤i≤n}⊂N+X={xi:1≤i≤n}⊂N+, and h∈N+h∈N+. The h-iterated sumset of X , denoted hX , is the set {x1+x2+...+xh:x1,x2,...,xh∈X}{x1+x2+...+xh:x1,x2,...,xh∈X}, and the [h][h]-sumset of X , denoted [h]X[h]X, is the set View the MathML source⋃i=1hiX. A [h][h]-sumset cover of S⊂N+S⊂N+ is a set X⊂N+X⊂N+ such that S⊆[h]XS⊆[h]X. In this paper, we focus on the case h=2h=2, and study the APX-hardproblem of computing a minimum cardinality [2]-sumset cover X of S (i.e. computing a minimum cardinality set X⊂N+X⊂N+ such that every element of S is either an element of X , or the sum of two - non-necessarily distinct - elements of X ). We propose two new algorithmic results. First, we give a fixed-parameter tractable (FPT) algorithm that decides the existence of a [2]-sumset cover of size at most k of a given set S . Our algorithm runs in View the MathML sourceO(2(3logk−1.4)kpoly(k)) time, and thus outperforms the O(5k2(k+3)2k2log(k)) time FPT result presented in Fagnot et al. (2009) [6]. Second, we show that deciding whether a set S has a smaller [2]-sumset cover than itself is NP-hard

Finding a Small Number of Colourful Components

A partition (V_1,...,V_k) of the vertex set of a graph G with a (not necessarily proper) colouring c is colourful if no two vertices in any V_i have the same colour and every set V_i induces a connected graph. The Colourful Partition problem, introduced by Adamaszek and Popa, is to decide whether a coloured graph (G,c) has a colourful partition of size at most k. This problem is related to the Colourful Components problem, introduced by He, Liu and Zhao, which is to decide whether a graph can be modified into a graph whose connected components form a colourful partition by deleting at most p edges. Despite the similarities in their definitions, we show that Colourful Partition and Colourful Components may have different complexities for restricted instances. We tighten known NP-hardness results for both problems by closing a number of complexity gaps. In addition, we prove new hardness and tractability results for Colourful Partition. In particular, we prove that deciding whether a coloured graph (G,c) has a colourful partition of size 2 is NP-complete for coloured planar bipartite graphs of maximum degree 3 and path-width 3, but polynomial-time solvable for coloured graphs of treewidth 2. Rather than performing an ad hoc study, we use our classical complexity results to guide us in undertaking a thorough parameterized study of Colourful Partition. We show that this leads to suitable parameters for obtaining FPT results and moreover prove that Colourful Components and Colourful Partition may have different parameterized complexities, depending on the chosen parameter

Hardness of longest common subsequence for sequences with bounded run-lengths

International audienceThe longest common subsequence (LCS) problem is a classic and well-studied problem in computer science with extensive applications in diverse areas ranging from spelling error corrections to molecular biology. This paper focuses on LCS for fixed alphabet size and fixed run-lengths (i.e., maximum number of consecutive occurrences of the same symbol). We show that LCS is NP-complete even when restricted to (i) alphabets of size 3 and run-length at most 1, and (ii) alphabets of size 2 and run-length at most 2 (both results are tight). For the latter case, we show that the problem is approximable within ratio 3/5