Optimal algorithms for haplotype assembly from whole-genome sequence data

Motivation: Haplotype inference is an important step for many types of analyses of genetic variation in the human genome. Traditional approaches for obtaining haplotypes involve collecting genotype information from a population of individuals and then applying a haplotype inference algorithm. The development of high-throughput sequencing technologies allows for an alternative strategy to obtain haplotypes by combining sequence fragments. The problem of ‘haplotype assembly’ is the problem of assembling the two haplotypes for a chromosome given the collection of such fragments, or reads, and their locations in the haplotypes, which are pre-determined by mapping the reads to a reference genome. Errors in reads significantly increase the difficulty of the problem and it has been shown that the problem is NP-hard even for reads of length 2. Existing greedy and stochastic algorithms are not guaranteed to find the optimal solutions for the haplotype assembly problem

Diversification and Intensification in Parallel {SAT} Solving

International audienceIn this paper, we explore the two well-known principles of diversification and intensification in portfolio-based parallel SAT solving. These dual concepts play an important role in several search algorithms including local search, and appear to be a key point in modern parallel SAT solvers. To study their trade-off, we define two roles for the computational units. Some of them classified as Masters perform an original search strategy, ensuring diversification. The remaining units, classified as Slaves are there to intensify their master's strategy. Several important questions have to be answered. The first one is what information should be given to a slave in order to intensify a given search effort? The second one is, how often, a subordinated unit has to receive such information? Finally, the question of finding the number of subordinated units along their connections with the search efforts has to be answered. Our results lead to an original intensification strategy which outperforms the best parallel SAT solver, and solves some open SAT instances

Boosting local search thanks to {CDCL}

International audienceIn this paper, a novel hybrid and complete approach for propositional satisfiability, called SAT HYS (Sat Hybrid Solver), is introduced. It efficiently combines the strength of both local search and CDCL based SAT solvers. Considering the consistent partial assignment under construction by the CDCL SAT solver, local search is used to extend it to a model of the Boolean formula, while the CDCL component is used by the local search one as a strategy to escape from a local minimum. Additionally, both solvers heavily cooperate thanks to relevant information gathered during search. Experimentations on SAT instances taken from the last competitions demonstrate the efficiency and the robustness of our hybrid solver with respect to the state-of-the-art CDCL based, local search and hybrid SAT solvers

Reducing chaos in SAT-like search: finding solutions close to a given one

Motivated by our own industrial users, we attack the following challenge that is crucial in many practical planning, scheduling or timetabling applications. Assume that a solver has found a solution for a given hard problem and, due to unforeseen circumstances (e.g., rescheduling), or after an analysis by a committee, a few more constraints have to be added and the solver has to be re-run. Then it is almost always important that the new solution is “close” to the original one. The activity-based variable selection heuristics used by SAT solvers make search chaotic, i.e., extremely sensitive to the initial conditions. Therefore, re-running with just one additional clause added at the end of the input usually gives a completely different solution. We show that naive approaches for finding close solutions do not work at all, and that solving the Boolean optimization problem is far too inefficient: to find a reasonably close solution, state-of-the-art tools typically require much more time than was needed to solve the original problem. Here we propose the first (to our knowledge) approach that obtains close solutions quickly. In fact, it typically finds the optimal (i.e., closest) solution in only 25% of the time the solver took in solving the original problem. Our approach requires no deep theoretical or conceptual innovations. Still, it is non-trivial to come up with and will certainly be valuable for researchers and practitioners facing the same problem.Postprint (published version

On Tackling the Limits of Resolution in SAT Solving

The practical success of Boolean Satisfiability (SAT) solvers stems from the CDCL (Conflict-Driven Clause Learning) approach to SAT solving. However, from a propositional proof complexity perspective, CDCL is no more powerful than the resolution proof system, for which many hard examples exist. This paper proposes a new problem transformation, which enables reducing the decision problem for formulas in conjunctive normal form (CNF) to the problem of solving maximum satisfiability over Horn formulas. Given the new transformation, the paper proves a polynomial bound on the number of MaxSAT resolution steps for pigeonhole formulas. This result is in clear contrast with earlier results on the length of proofs of MaxSAT resolution for pigeonhole formulas. The paper also establishes the same polynomial bound in the case of modern core-guided MaxSAT solvers. Experimental results, obtained on CNF formulas known to be hard for CDCL SAT solvers, show that these can be efficiently solved with modern MaxSAT solvers

Revisiting Clause Exchange in Parallel SAT Solving

International audienceManaging learnt clause database is known to be a tricky task in SAT solvers. In the portfolio framework, the collaboration between threads through learnt clause exchange makes this problem even more difficult to tackle. Several techniques have been proposed in the last few years, but practical results are still in favor of very limited collaboration, or even no collaboration at all. This is mainly due to the difficulty that each thread has to manage a large amount of learnt clauses generated by the other workers. In this paper, we propose new efficient techniques for clause exchanges within a parallel SAT solver. In contrast to most of the current clause exchange methods, our approach relies on both export and import policies, and makes use of recent techniques that proves very effective in the sequential case. Extensive experimentations show the practical interest of the proposed ideas