Trace Reconstruction: Generalized and Parameterized

In the beautifully simple-to-state problem of trace reconstruction, the goal is to reconstruct an unknown binary string x given random "traces" of x where each trace is generated by deleting each coordinate of x independently with probability p<1. The problem is well studied both when the unknown string is arbitrary and when it is chosen uniformly at random. For both settings, there is still an exponential gap between upper and lower sample complexity bounds and our understanding of the problem is still surprisingly limited. In this paper, we consider natural parameterizations and generalizations of this problem in an effort to attain a deeper and more comprehensive understanding. Perhaps our most surprising results are: 1) We prove that exp(O(n^(1/4) sqrt{log n})) traces suffice for reconstructing arbitrary matrices. In the matrix version of the problem, each row and column of an unknown sqrt{n} x sqrt{n} matrix is deleted independently with probability p. Our results contrasts with the best known results for sequence reconstruction where the best known upper bound is exp(O(n^(1/3))). 2) An optimal result for random matrix reconstruction: we show that Theta(log n) traces are necessary and sufficient. This is in contrast to the problem for random sequences where there is a super-logarithmic lower bound and the best known upper bound is exp({O}(log^(1/3) n)). 3) We show that exp(O(k^(1/3) log^(2/3) n)) traces suffice to reconstruct k-sparse strings, providing an improvement over the best known sequence reconstruction results when k = o(n/log^2 n). 4) We show that poly(n) traces suffice if x is k-sparse and we additionally have a "separation" promise, specifically that the indices of 1\u27s in x all differ by Omega(k log n)

Vertex Cover Kernelization Revisited: Upper and Lower Bounds for a Refined Parameter

An important result in the study of polynomial-time preprocessing shows that there is an algorithm which given an instance (G,k) of Vertex Cover outputs an equivalent instance (G',k') in polynomial time with the guarantee that G' has at most 2k' vertices (and thus O((k')^2) edges) with k' <= k. Using the terminology of parameterized complexity we say that k-Vertex Cover has a kernel with 2k vertices. There is complexity-theoretic evidence that both 2k vertices and Theta(k^2) edges are optimal for the kernel size. In this paper we consider the Vertex Cover problem with a different parameter, the size fvs(G) of a minimum feedback vertex set for G. This refined parameter is structurally smaller than the parameter k associated to the vertex covering number vc(G) since fvs(G) <= vc(G) and the difference can be arbitrarily large. We give a kernel for Vertex Cover with a number of vertices that is cubic in fvs(G): an instance (G,X,k) of Vertex Cover, where X is a feedback vertex set for G, can be transformed in polynomial time into an equivalent instance (G',X',k') such that |V(G')| <= 2k and |V(G')| <= O(|X'|^3). A similar result holds when the feedback vertex set X is not given along with the input. In sharp contrast we show that the Weighted Vertex Cover problem does not have a polynomial kernel when parameterized by the cardinality of a given vertex cover of the graph unless NP is in coNP/poly and the polynomial hierarchy collapses to the third level.Comment: Published in "Theory of Computing Systems" as an Open Access publicatio

Kernelization Lower Bounds By Cross-Composition

We introduce the cross-composition framework for proving kernelization lower bounds. A classical problem L AND/OR-cross-composes into a parameterized problem Q if it is possible to efficiently construct an instance of Q with polynomially bounded parameter value that expresses the logical AND or OR of a sequence of instances of L. Building on work by Bodlaender et al. (ICALP 2008) and using a result by Fortnow and Santhanam (STOC 2008) with a refinement by Dell and van Melkebeek (STOC 2010), we show that if an NP-hard problem OR-cross-composes into a parameterized problem Q then Q does not admit a polynomial kernel unless NP \subseteq coNP/poly and the polynomial hierarchy collapses. Similarly, an AND-cross-composition for Q rules out polynomial kernels for Q under Bodlaender et al.'s AND-distillation conjecture. Our technique generalizes and strengthens the recent techniques of using composition algorithms and of transferring the lower bounds via polynomial parameter transformations. We show its applicability by proving kernelization lower bounds for a number of important graphs problems with structural (non-standard) parameterizations, e.g., Clique, Chromatic Number, Weighted Feedback Vertex Set, and Weighted Odd Cycle Transversal do not admit polynomial kernels with respect to the vertex cover number of the input graphs unless the polynomial hierarchy collapses, contrasting the fact that these problems are trivially fixed-parameter tractable for this parameter. After learning of our results, several teams of authors have successfully applied the cross-composition framework to different parameterized problems. For completeness, our presentation of the framework includes several extensions based on this follow-up work. For example, we show how a relaxed version of OR-cross-compositions may be used to give lower bounds on the degree of the polynomial in the kernel size.Comment: A preliminary version appeared in the proceedings of the 28th International Symposium on Theoretical Aspects of Computer Science (STACS 2011) under the title "Cross-Composition: A New Technique for Kernelization Lower Bounds". Several results have been strengthened compared to the preliminary version (http://arxiv.org/abs/1011.4224). 29 pages, 2 figure

Cross-Composition: A New Technique for Kernelization Lower Bounds

We introduce a new technique for proving kernelization lower bounds, called cross-composition. A classical problem L cross-composes into a parameterized problem Q if an instance of Q with polynomially bounded parameter value can express the logical OR of a sequence of instances of L. Building on work by Bodlaender et al. (ICALP 2008) and using a result by Fortnow and Santhanam (STOC 2008) we show that if an NP-complete problem cross-composes into a parameterized problem Q then Q does not admit a polynomial kernel unless the polynomial hierarchy collapses. Our technique generalizes and strengthens the recent techniques of using OR-composition algorithms and of transferring the lower bounds via polynomial parameter transformations. We show its applicability by proving kernelization lower bounds for a number of important graphs problems with structural (non-standard) parameterizations, e.g., Chromatic Number, Clique, and Weighted Feedback Vertex Set do not admit polynomial kernels with respect to the vertex cover number of the input graphs unless the polynomial hierarchy collapses, contrasting the fact that these problems are trivially fixed-parameter tractable for this parameter. We have similar lower bounds for Feedback Vertex Set.Comment: Updated information based on final version submitted to STACS 201

Revisiting the Complexity of Stability of Continuous and Hybrid Systems

We develop a framework to give upper bounds on the "practical" computational complexity of stability problems for a wide range of nonlinear continuous and hybrid systems. To do so, we describe stability properties of dynamical systems using first-order formulas over the real numbers, and reduce stability problems to the delta-decision problems of these formulas. The framework allows us to obtain a precise characterization of the complexity of different notions of stability for nonlinear continuous and hybrid systems. We prove that bounded versions of the stability problems are generally decidable, and give upper bounds on their complexity. The unbounded versions are generally undecidable, for which we give upper bounds on their degrees of unsolvability

On Sparsification for Computing Treewidth

We investigate whether an n-vertex instance (G,k) of Treewidth, asking whether the graph G has treewidth at most k, can efficiently be made sparse without changing its answer. By giving a special form of OR-cross-composition, we prove that this is unlikely: if there is an e > 0 and a polynomial-time algorithm that reduces n-vertex Treewidth instances to equivalent instances, of an arbitrary problem, with O(n^{2-e}) bits, then NP is in coNP/poly and the polynomial hierarchy collapses to its third level. Our sparsification lower bound has implications for structural parameterizations of Treewidth: parameterizations by measures that do not exceed the vertex count, cannot have kernels with O(k^{2-e}) bits for any e > 0, unless NP is in coNP/poly. Motivated by the question of determining the optimal kernel size for Treewidth parameterized by vertex cover, we improve the O(k^3)-vertex kernel from Bodlaender et al. (STACS 2011) to a kernel with O(k^2) vertices. Our improved kernel is based on a novel form of treewidth-invariant set. We use the q-expansion lemma of Fomin et al. (STACS 2011) to find such sets efficiently in graphs whose vertex count is superquadratic in their vertex cover number.Comment: 21 pages. Full version of the extended abstract presented at IPEC 201