Phase Transitions of the Typical Algorithmic Complexity of the Random Satisfiability Problem Studied with Linear Programming

Here we study the NP-complete $K$-SAT problem. Although the worst-case complexity of NP-complete problems is conjectured to be exponential, there exist parametrized random ensembles of problems where solutions can typically be found in polynomial time for suitable ranges of the parameter. In fact, random $K$-SAT, with $\alpha=M/N$ as control parameter, can be solved quickly for small enough values of $\alpha$. It shows a phase transition between a satisfiable phase and an unsatisfiable phase. For branch and bound algorithms, which operate in the space of feasible Boolean configurations, the empirically hardest problems are located only close to this phase transition. Here we study $K$-SAT ($K=3,4$) and the related optimization problem MAX-SAT by a linear programming approach, which is widely used for practical problems and allows for polynomial run time. In contrast to branch and bound it operates outside the space of feasible configurations. On the other hand, finding a solution within polynomial time is not guaranteed. We investigated several variants like including artificial objective functions, so called cutting-plane approaches, and a mapping to the NP-complete vertex-cover problem. We observed several easy-hard transitions, from where the problems are typically solvable (in polynomial time) using the given algorithms, respectively, to where they are not solvable in polynomial time. For the related vertex-cover problem on random graphs these easy-hard transitions can be identified with structural properties of the graphs, like percolation transitions. For the present random $K$-SAT problem we have investigated numerous structural properties also exhibiting clear transitions, but they appear not be correlated to the here observed easy-hard transitions. This renders the behaviour of random $K$-SAT more complex than, e.g., the vertex-cover problem.Comment: 11 pages, 5 figure

Polyhedral characteristics of balanced and unbalanced bipartite subgraph problems

We study the polyhedral properties of three problems of constructing an optimal complete bipartite subgraph (a biclique) in a bipartite graph. In the first problem we consider a balanced biclique with the same number of vertices in both parts and arbitrary edge weights. In the other two problems we are dealing with unbalanced subgraphs of maximum and minimum weight with nonnegative edges. All three problems are established to be NP-hard. We study the polytopes and the cone decompositions of these problems and their 1-skeletons. We describe the adjacency criterion in 1-skeleton of the polytope of the balanced complete bipartite subgraph problem. The clique number of 1-skeleton is estimated from below by a superpolynomial function. For both unbalanced biclique problems we establish the superpolynomial lower bounds on the clique numbers of the graphs of nonnegative cone decompositions. These values characterize the time complexity in a broad class of algorithms based on linear comparisons

Efficient Parallel Algorithms for some Tree Layout Problems

The minimum cut and minimum length linear arrangement problems usually occur in solving wiring problems and have a lot in common with job sequencing questions. Both problems are NP-complete for general graphs and in P for trees. We present here two algorithms in NC. The first solves the minimum length linear arrangement problem for unrooted trees in $O(\log^2 n)$ time and $O(n^2 3^{\log n})$ CREW PRAM processors. The second algorithm solves the minimum cut arrangement for unrooted trees of maximum degree $d$ in $O(d \log^2 n)$ time and $O(n^2 /\log n)$ CREW PRAM processors

The Distance and Median Problems in the Single-Cut-Or-Join Model with Single-Gene Duplications

Background. In the field of genome rearrangement algorithms, models accounting for gene duplication lead often to hard problems. For example, while computing the pairwise distance is tractable in most duplication-free models, the problem is NP-complete for most extensions of these models accounting for duplicated genes. Moreover, problems involving more than two genomes, such as the genome median and the Small Parsimony problem, are intractable for most duplication-free models, with some exceptions, for example the Single-Cut-or-Join (SCJ) model. Results. We introduce a variant of the SCJ distance that accounts for duplicated genes, in the context of directed evolution from an ancestral genome to a descendant genome where orthology relations between ancestral genes and their descendant are known. Our model includes two duplication mechanisms: single-gene tandem duplication and the creation of single-gene circular chromosomes. We prove that in this model, computing the directed distance and a parsimonious evolutionary scenario in terms of SCJ and single-gene duplication events can be done in linear time. We also show that the directed median problem is tractable for this distance, while the rooted median problem, where we assume that one of the given genomes is ancestral to the median, is NP-complete. We also describe an Integer Linear Program for solving this problem. We evaluate the directed distance and rooted median algorithms on simulated data. Conclusion. Our results provide a simple genome rearrangement model, extending the SCJ model to account for single-gene duplications, for which we prove a mix of tractability and hardness results. For the NP-complete rooted median problem, we design a simple Integer Linear Program. Our publicly available implementation of these algorithms for the directed distance and median problems allow to solve efficiently these problems on large instances

Linear-time Algorithms for Eliminating Claws in Graphs

Since many NP-complete graph problems have been shown polynomial-time solvable when restricted to claw-free graphs, we study the problem of determining the distance of a given graph to a claw-free graph, considering vertex elimination as measure. CLAW-FREE VERTEX DELETION (CFVD) consists of determining the minimum number of vertices to be removed from a graph such that the resulting graph is claw-free. Although CFVD is NP-complete in general and recognizing claw-free graphs is still a challenge, where the current best algorithm for a graph $G$ has the same running time of the best algorithm for matrix multiplication, we present linear-time algorithms for CFVD on weighted block graphs and weighted graphs with bounded treewidth. Furthermore, we show that this problem can be solved in linear time by a simpler algorithm on forests, and we determine the exact values for full $k$-ary trees. On the other hand, we show that CLAW-FREE VERTEX DELETION is NP-complete even when the input graph is a split graph. We also show that the problem is hard to approximate within any constant factor better than $2$, assuming the Unique Games Conjecture.Comment: 20 page