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Register a new userA Fast Exponential Time Algorithm for Max Hamming Distance X3SAT
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Frank Stephan
Publication date
2019
fields
Informatics Engineering
and research's language is
English
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X3SAT is the problem of whether one can satisfy a given set of clauses with up to three literals such that in every clause, exactly one literal is true and the others are false. A related question is to determine the maximal Hamming distance between two solutions of the instance. Dahllof provided an algorithm for Maximum Hamming Distance XSAT, which is more complicated than the same problem for X3SAT, with a runtime of $O(1.8348^n)$; Fu, Zhou and Yin considered Maximum Hamming Distance for X3SAT and found for this problem an algorithm with runtime $O(1.6760^n)$. In this paper, we propose an algorithm in $O(1.3298^n)$ time to solve the Max Hamming Distance X3SAT problem; the algorithm actually counts for each $k$ the number of pairs of solutions which have Hamming Distance $k$.
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In 2013, Orlin proved that the max flow problem could be solved in $O(nm)$ time. His algorithm ran in $O(nm + m^{1.94})$ time, which was the fastest for graphs with fewer than $n^{1.06}$ arcs. If the graph was not sufficiently sparse, the fastest running time was an algorithm due to King, Rao, and Tarjan. We describe a new variant of the excess scaling algorithm for the max flow problem whose running time strictly dominates the running time of the algorithm by King et al. Moreover, for graphs in which $m = O(n log n)$, the running time of our algorithm dominates that of King et al. by a factor of $O(loglog n)$.
MAX NAE-SAT is a natural optimization problem, closely related to its better-known relative MAX SAT. The approximability status of MAX NAE-SAT is almost completely understood if all clauses have the same size $k$, for some $kge 2$. We refer to this problem as MAX NAE-${k}$-SAT. For $k=2$, it is essentially the celebrated MAX CUT problem. For $k=3$, it is related to the MAX CUT problem in graphs that can be fractionally covered by triangles. For $kge 4$, it is known that an approximation ratio of $1-frac{1}{2^{k-1}}$, obtained by choosing a random assignment, is optimal, assuming $P e NP$. For every $kge 2$, an approximation ratio of at least $frac{7}{8}$ can be obtained for MAX NAE-${k}$-SAT. There was some hope, therefore, that there is also a $frac{7}{8}$-approximation algorithm for MAX NAE-SAT, where clauses of all sizes are allowed simultaneously. Our main result is that there is no $frac{7}{8}$-approximation algorithm for MAX NAE-SAT, assuming the unique games conjecture (UGC). In fact, even for almost satisfiable instances of MAX NAE-${3,5}$-SAT (i.e., MAX NAE-SAT where all clauses have size $3$ or $5$), the best approximation ratio that can be achieved, assuming UGC, is at most $frac{3(sqrt{21}-4)}{2}approx 0.8739$. Using calculus of variations, we extend the analysis of ODonnell and Wu for MAX CUT to MAX NAE-${3}$-SAT. We obtain an optimal algorithm, assuming UGC, for MAX NAE-${3}$-SAT, slightly improving on previous algorithms. The approximation ratio of the new algorithm is $approx 0.9089$. We complement our theoretical results with some experimental results. We describe an approximation algorithm for almost satisfiable instances of MAX NAE-${3,5}$-SAT with a conjectured approximation ratio of 0.8728, and an approximation algorithm for almost satisfiable instances of MAX NAE-SAT with a conjectured approximation ratio of 0.8698.
We present a (full) derandomization of HSSW algorithm for 3-SAT, proposed by Hofmeister, Schoning, Schuler, and Watanabe in [STACS02]. Thereby, we obtain an O(1.3303^n)-time deterministic algorithm for 3-SAT, which is currently fastest.
Recently, a framework considering RNA sequences and their RNA secondary structures as pairs, led to some information-theoretic perspectives on how the semantics encoded in RNA sequences can be inferred. In this context, the pairing arises naturally from the energy model of RNA secondary structures. Fixing the sequence in the pairing produces the RNA energy landscape, whose partition function was discovered by McCaskill. Dually, fixing the structure induces the energy landscape of sequences. The latter has been considered for designing more efficient inverse folding algorithms. We present here the Hamming distance filtered, dual partition function, together with a Boltzmann sampler using novel dynamic programming routines for the loop-based energy model. The time complexity of the algorithm is $O(h^2n)$, where $h,n$ are Hamming distance and sequence length, respectively, reducing the time complexity of samplers, reported in the literature by $O(n^2)$. We then present two applications, the first being in the context of the evolution of natural sequence-structure pairs of microRNAs and the second constructing neutral paths. The former studies the inverse fold rate (IFR) of sequence-structure pairs, filtered by Hamming distance, observing that such pairs evolve towards higher levels of robustness, i.e.,~increasing IFR. The latter is an algorithm that constructs neutral paths: given two sequences in a neutral network, we employ the sampler in order to construct short paths connecting them, consisting of sequences all contained in the neutral network.
The Exact Satisfiability problem, XSAT, is defined as the problem of finding a satisfying assignment to a formula in CNF such that there is exactly one literal in each clause assigned to be 1 and the other literals in the same clause are set to 0. If we restrict the length of each clause to be at most 3 literals, then it is known as the X3SAT problem. In this paper, we consider the problem of counting the number of satisfying assignments to the X3SAT problem, which is also known as #X3SAT. The current state of the art exact algorithm to solve #X3SAT is given by Dahllof, Jonsson and Beigel and runs in $O(1.1487^n)$, where $n$ is the number of variables in the formula. In this paper, we propose an exact algorithm for the #X3SAT problem that runs in $O(1.1120^n)$ with very few branching cases to consider, by using a result from Monien and Preis to give us a bisection width for graphs with at most degree 3.
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