Improving SAT using 2SAT

This dissertation is to illustrate the current state of the art of DNA computing achievements, especially of new approaches to solve theoretical 3-SAT problems and the hitting-set problem. Beginning with Adleman’s breakthrough which is an molecular algorithm for the solution of a NP-complete, combinatorial problem, the directed Hamiltonian path problem (HPP). Today, many researchers all over the world concentrate on proposing new methods to solve engineering or application problems with a DNA computing approach. Satisfiability problem is given a Boolean formula, and decide if a satisfying truth assignment exists. ( ) ( ) … ( ) ( ) is an example of Boolean formula. k-SAT problem means that each clause has exactly k literals. Not-All-Equal (NAE) 3-SAT problem and One-In-Three (1IN3) 3-SAT problem are both NP-complete problems. In this dissertation, we present molecular solutions to find all true assignments (3-SAT problem) and furthermore find Not-All-Equal (NAE) solutions and One-In-Three (1IN3) solutions in DNA-based Supercomputing. Hitting-set problem assume that there exists a collection C of subsets of a finite set S, and a positive integer K  |S|, and we need to know if there is a subset  S with | |  K such that contains at least one element of each subset in C. In other words, is the subset that intersects every subset in C and is called the hitting-set. In this dissertation, a DNA-based algorithm is proposed to solve the small hitting-set problem. A small hitting-set is a hitting-set with the smallest K value, i.e., the hitting-set with the smallest number of elements. Furthermore, an algorithm is introduced to find the number of ones from 2n combinations and minimum numbers of ones represents the small hitting-set since K is expected to be as small as possible. The complexity of all the presented DNA-based algorithms is also discussed. We describe time complexity and volume complexity of three Algorithms, numbers of test tube used and the longest library strand in solution space of all three Algorithms. Finally, the simulated experiment is applied to verify correctness of the proposed DNA-based algorithm for solving the One-In-Three (1IN3) 3-SAT problem, and simulation of Not-All-Equal (NAE) 3-SAT problem is similar. Also, another simulated experiment is applied to our proposed DNA-based algorithm 6-2, in order to solve the well-known hitting-set problem. This research has been motivated by the benefit and the application of DNA computing and gives new methods to solve two 3-SAT problems and the hitting-set problem which are NP-complete.

Propositional Satisfiability (SAT) is a keystone in the history of computer science. SAT was the first problem shown to be NP-complete in 1971 by Stephen Cook. Having passed more than 40 years from then, SAT is now a lively research field where theory and practice have a natural intermixing. In this talk, we overview the use of SAT in practical domains, where SAT is thought in a broad sense, i.e. including SAT extensions such as Maximum Satisfiability (MaxSAT), Pseudo-Boolean Optimization (PBO) and Quantified Boolean Formulas (QBF).

Boolean satisfiability (SAT) solvers are at the core of efficient approaches for solving a vast multitude of practical problems. Moreover, albeit targeting an NP-complete problem, SAT solvers are increasingly used for tackling problems beyond NP. Despite the success of SAT in practice, modeling with SAT and more importantly implementing SAT-based problem solving solutions is often a difficult and error-prone task. This paper proposes the PySAT toolkit, which enables fast Python-based prototyping using SAT oracles and SAT-related technology. PySAT provides a simple API for working with a few state-of-the-art SAT oracles and also integrates a number of cardinality constraint encodings, all aiming at simplifying the prototyping process. Experimental results presented in the paper show that PySAT-based implementations can be as efficient as those written in a low-level language.

Chapter 2 Satisfiability Solvers

The exponential-time hypothesis (ETH) states that 3-SAT is not solvable in subexponential time, i.e. not solvable in O(c^n) time for arbitrary c > 1, where n denotes the number of variables. Problems like k-SAT can be viewed as special cases of the constraint satisfaction problem (CSP), which is the problem of determining whether a set of constraints is satisfiable. In this paper we study the worst-case time complexity of NP-complete CSPs. Our main interest is in the CSP problem parameterized by a constraint language Gamma (CSP(Gamma)), and how the choice of Gamma affects the time complexity. It is believed that CSP(Gamma) is either tractable or NP-complete, and the algebraic CSP dichotomy conjecture gives a sharp delineation of these two classes based on algebraic properties of constraint languages. Under this conjecture and the ETH, we first rule out the existence of subexponential algorithms for finite domain NP-complete CSP(Gamma) problems. This result also extends to certain infinite-domain CSPs and structurally restricted CSP(Gamma) problems. We then begin a study of the complexity of NP-complete CSPs where one is allowed to arbitrarily restrict the values of individual variables, which is a very well-studied subclass of CSPs. For such CSPs with finite domain D, we identify a relation SD such that (1) CSP({SD}) is NP-complete and (2) if CSP(Gamma) over D is NP-complete and solvable in O(c^n) time, then CSP({SD}) is solvable in O(c^n) time, too. Hence, the time complexity of CSP({SD}) is a lower bound for all CSPs of this particular kind. We also prove that the complexity of CSP({SD}) is decreasing when |D| increases, unless the ETH is false. This implies, for instance, that for every c>1 there exists a finite-domain Gamma such that CSP(Gamma) is NP complete and solvable in O(c^n) time.

Efficient solutions to nonpolynomial (NP)-complete problems would significantly benefit both science and industry. However, such problems are intractable on digital computers based on the von Neumann architecture, thus creating the need for alternative solutions to tackle such problems. Recently, a deterministic, continuous-time dynamical system (CTDS) was proposed [1] to solve a representative NP-complete problem, Boolean Satisfiability (SAT). This solver shows polynomial analog time-complexity on even the hardest benchmark $k$ -SAT ( $k \geq 3$ ) formulas, but at an energy cost through exponentially driven auxiliary variables. This paper presents a novel analog hardware SAT solver, AC-SAT , implementing the CTDS via incorporating novel, analog circuit design ideas. AC-SAT is intended to be used as a coprocessor and is programmable for handling different problem specifications. It is especially effective for solving hard $k$ -SAT problem instances that are challenging for algorithms running on digital machines. Furthermore, with its modular design, AC-SAT can readily be extended to solve larger size problems, while the size of the circuit grows linearly with the product of the number of variables and the number of clauses. The circuit is designed and simulated based on a 32-nm CMOS technology. Simulation Program with Integrated Circuit Emphasis (SPICE) simulation results show speedup factors of ~104 on even the hardest 3-SAT problems, when compared with a state-of-the-art SAT solver on digital computers. As an example, for hard problems with $N=50$ variables and $M=212$ clauses, solutions are found within from a few nanoseconds to a few hundred nanoseconds.

We perform a comprehensive study of mappings between constraint satisfaction problems (CSPs) and propositional satisfiability (SAT). We analyse four different mappings of SAT problems into CSPs, and two of CSPs into SAT problems. For each mapping, we compare the impact of achieving arc-consistency on the CSP with unit propagation on the SAT problem. We then extend these results to CSP algorithms that maintain (some level of) arc-consistency during search like FC and MAC, and to the Davis-Putnam procedure (which performs unit propagation at each search node). Because of differences in the branching structure of their search, a result showing the dominance of achieving arc-consistency on the CSP over unit propagation on the SAT problem does not necessarily translate to the dominance of MAC over the Davis-Putnam procedure. These results provide insight into the relationship between propositional satisfiability and constraint satisfaction.

The partial string avoidability problem, also known as partial word avoidability, is stated as follows: given a finite set of strings with possible ``holes'' (undefined symbols), determine whether there exists any two-sided infinite string containing no substrings from this set, assuming that a hole matches every symbol. The problem is known to be NP-hard and in PSPACE, and this paper establishes its PSPACE-completeness. Next, string avoidability over the binary alphabet is interpreted as a version of conjunctive normal form (CNF) satisfiability problem (SAT), with each clause having infinitely many shifted variants. Non-satisfiability of these formulas can be proved using variants of classical propositional proof systems, augmented with derivation rules for shifting constraints (such as clauses, inequalities, polynomials, etc). Two results on their proof complexity are established. First, there is a particular formula that has a short refutation in Resolution with shift, but requires classical proofs of exponential size (Resolution, Cutting Plane, Polynomial Calculus, etc.). At the same time, exponential lower bounds for shifted versions of classical proof systems are established.

Quantum annealing device has shown a great potential in solving discrete problems that are theoretically and empirically hard. Boolean Satisfiability (SAT) problem, determining if there is an assignment of variables that satisfies a given Boolean function, is the first proven NP-complete problem widely used in various domains. Here, we present a novel mapping of the SAT problem to the quadratic unconstrained binary optimization problem (QUBO), and further develop a tool flow embedding the proposed QUBO to the architecture of the commercialized quantum computer D-Wave. By leveraging electronic design automation techniques including synthesis, placement and routing, this is not only the first work providing the detail flow that embeds the QUBO, but also a technique scalable for real world applications and some hard SAT problems with over 6000 variables in QUBO. Based on our results, we discuss the challenges in solving SAT using the current generation of annealing device, and explore the problem solving capability of future quantum annealing computers.

Many formal verification tools today are based on Boolean proof techniques. The two most powerful approaches in this context are binary decision diagrams (BDDs) and methods based on Boolean satisfiability (SAT). Recent studies have shown that BDDs and SAT are orthogonal, i.e. there exist problems where BDDs work well, while SAT solvers fail and vice versa. Beside this, the techniques are very different in general. E.g. SAT solvers try to find a single solution and BDDs represent all solutions in parallel. In this paper the first integrated approach is presented that combines BDDs and SAT within a single data structure. This hybrid approach combines the advantages of the two techniques, i.e. multiple solutions can be computed while the memory requirement remains small. First experimental results demonstrate the quality of the approach in comparison to BDDs and SAT solvers.

Boolean Satisfiability (SAT), the first problem proven to be NP-complete, is intractable on digital computers based on the von Neumann architecture. An efficient SAT solver can benefit many applications such as artificial intelligence, circuit design, and functional verification. Recently, a SAT solver approach based on a deterministic, continuous-time dynamical system (CTDS) was introduced [1]. This approach shows polynomial analog time-complexity on even the hardest k-SAT (k ≥ 3) problem instances, but at an energy cost dependent on exponentially growing auxiliary variables. This paper reports a novel analog hardware SAT solver, AC-SAT, implementing the CTDS via incorporating novel, analog circuit design ideas. AC-SAT is intended to be used as a co-processor and is programmable for handling different problem specifications. Furthermore, with its modular design, AC-SAT can be readily extended to solve larger size problems. SPICE simulation results show that AC-SAT can indeed solve the SAT problems, and it has speedup factors of ~10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sup> on even the hardest 3-SAT problems, when compared with a state-of-the-art SAT solver on digital computers.

Boolean Satisfiability (SAT) solvers are popular engines used throughout the verification world. Bounded sequential problems such as bounded model checking and bounded sequential equivalence checking rely on fast and robust SAT solvers. In this work, we introduce a technique that improves the performance of the underlying SAT solver for bounded sequential problems by taking advantage of a design's don't care states. We develop cost effective methods of filtering, replicating and applying the don't care states to the original problem thus reducing the search space. Experiments demonstrate the effectiveness of the proposed method on ISCAS'89 benchmarks.

Multi-agent pathfinding (MAPF) is an NP-hard problem. As such, dense maps may be very hard to solve optimally. In such scenarios, compilation-based approaches, via Boolean satisfiability (SAT) and answer set programming (ASP), have been shown to outperform heuristic-search-based approaches, such as conflict-based search (CBS). In this paper, we propose a new Boolean encoding for MAPF, and show how to implement it in ASP and MaxSAT. A feature that distinguishes our encoding from existing ones is that swap and follow conflicts are encoded using binary clauses, which can be exploited by current conflict-driven clause learning (CDCL) solvers. In addition, the number of clauses used to encode swap and follow conflicts do not depend on the number of agents, allowing us to scale better. For MaxSAT, we study different ways in which we may combine the MSU3 and LSU algorithms for maximum performance. In our experimental evaluation, we used square grids, ranging from 20 x 20 to 50 x 50 cells, and warehouse maps, with a varying number of agents and obstacles. We compared against representative solvers of the state-of-the-art, including the search-based algorithm CBS, the ASP-based solver ASP-MAPF, and the branch-and-cut-and-price hybrid solver, BCP. We observe that the ASP implementation of our encoding, ASP-MAPF2 outperforms other solvers in most of our experiments. The MaxSAT implementation of our encoding, MtMS shows best performance in relatively small warehouse maps when the number of agents is large, which are the instances with closer resemblance to hard puzzle-like problems.

We present a genetic-based approach to solve SAT problem and NP-complete problems. The main idea of the approach presented here is to exploit the fact that, although all NP-complete problems are equally difficult in a general computational sense, some have much better genetic representations than others, leading to much more successful use of genetic-based algorithm on some NP-complete problems than on others. Since any NP-complete problem can be mapped into any other one in polynomial time by a transformation, the approach described here consists of identifying and finding a canonical or generic NP-complete problem on which genetic algorithm work well, and solving other NP-complete problems indirectly by translating them onto the canonical problem. We presented some initial results where we have the Boolean Satisfiability Problem (SAT) as a canonical problem, and results on Hamiltonian Circuit problem which represent a family of NP-complete problems, it can be solved efficiently by mapping them first onto SAT problems.KeywordsSATGenetic AlgorithmNP-complete ProblemHamiltonian Circuit

Learning is a general concept, playing an important role in many Artificial intelligence domains. In this paper, we address the learning paradigm used to explain failures or conflicts encountered during search. This explanation, derived by conflict analysis, and generally expressed as a new constraint, is usually used to dynamically avoid future occurrences of similar situations. Before focusing on clause learning in Boolean satisfiability (SAT), we first overview some important works on this powerful reasoning tool in other domains such as constraint satisfaction and truth maintenance systems. Then, we present a comprehensive survey of the most important works having led to what is called today—conflict driven clause learning—which is one of the key components of modern SAT solvers. We also overview some of the original extensions or variants of clauses learning. In theory, current SAT solvers with clause learning are as powerful as general resolution proof systems. In practice, real-world SAT instances with millions of variables and clauses are now in the scope of this solving paradigm.