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Efficient solution of Boolean satisfiability problems with digital memcomputing.

ABSTRACT: Boolean satisfiability is a propositional logic problem of interest in multiple fields, e.g., physics, mathematics, and computer science. Beyond a field of research, instances of the SAT problem, as it is known, require efficient solution methods in a variety of applications. It is the decision problem of determining whether a Boolean formula has a satisfying assignment, believed to require exponentially growing time for an algorithm to solve for the worst-case instances. Yet, the efficient solution of many classes of Boolean formulae eludes even the most successful algorithms, not only for the worst-case scenarios, but also for typical-case instances. Here, we introduce a memory-assisted physical system (a digital memcomputing machine) that, when its non-linear ordinary differential equations are integrated numerically, shows evidence for polynomially-bounded scalability while solving "hard" planted-solution instances of SAT, known to require exponential time to solve in the typical case for both complete and incomplete algorithms. Furthermore, we analytically demonstrate that the physical system can efficiently solve the SAT problem in continuous time, without the need to introduce chaos or an exponentially growing energy. The efficiency of the simulations is related to the collective dynamical properties of the original physical system that persist in the numerical integration to robustly guide the solution search even in the presence of numerical errors. We anticipate our results to broaden research directions in physics-inspired computing paradigms ranging from theory to application, from simulation to hardware implementation.

SUBMITTER: Bearden SRB

PROVIDER: S-EPMC7665037 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

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Efficient solution of Boolean satisfiability problems with digital memcomputing.

Bearden Sean R B SRB Pei Yan Ru YR Di Ventra Massimiliano M

Scientific reports 20201112 1

Boolean satisfiability is a propositional logic problem of interest in multiple fields, e.g., physics, mathematics, and computer science. Beyond a field of research, instances of the SAT problem, as it is known, require efficient solution methods in a variety of applications. It is the decision problem of determining whether a Boolean formula has a satisfying assignment, believed to require exponentially growing time for an algorithm to solve for the worst-case instances. Yet, the efficient solu ...[more]

PMID: 33184386

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Project description:BACKGROUND: Various computational models have been of interest due to their use in the modelling of gene regulatory networks (GRNs). As a logical model, probabilistic Boolean networks (PBNs) consider molecular and genetic noise, so the study of PBNs provides significant insights into the understanding of the dynamics of GRNs. This will ultimately lead to advances in developing therapeutic methods that intervene in the process of disease development and progression. The applications of PBNs, however, are hindered by the complexities involved in the computation of the state transition matrix and the steady-state distribution of a PBN. For a PBN with n genes and N Boolean networks, the complexity to compute the state transition matrix is O(nN22n) or O(nN2n) for a sparse matrix. RESULTS: This paper presents a novel implementation of PBNs based on the notions of stochastic logic and stochastic computation. This stochastic implementation of a PBN is referred to as a stochastic Boolean network (SBN). An SBN provides an accurate and efficient simulation of a PBN without and with random gene perturbation. The state transition matrix is computed in an SBN with a complexity of O(nL2n), where L is a factor related to the stochastic sequence length. Since the minimum sequence length required for obtaining an evaluation accuracy approximately increases in a polynomial order with the number of genes, n, and the number of Boolean networks, N, usually increases exponentially with n, L is typically smaller than N, especially in a network with a large number of genes. Hence, the computational efficiency of an SBN is primarily limited by the number of genes, but not directly by the total possible number of Boolean networks. Furthermore, a time-frame expanded SBN enables an efficient analysis of the steady-state distribution of a PBN. These findings are supported by the simulation results of a simplified p53 network, several randomly generated networks and a network inferred from a T cell immune response dataset. An SBN can also implement the function of an asynchronous PBN and is potentially useful in a hybrid approach in combination with a continuous or single-molecule level stochastic model. CONCLUSIONS: Stochastic Boolean networks (SBNs) are proposed as an efficient approach to modelling gene regulatory networks (GRNs). The SBN approach is able to recover biologically-proven regulatory behaviours, such as the oscillatory dynamics of the p53-Mdm2 network and the dynamic attractors in a T cell immune response network. The proposed approach can further predict the network dynamics when the genes are under perturbation, thus providing biologically meaningful insights for a better understanding of the dynamics of GRNs. The algorithms and methods described in this paper have been implemented in Matlab packages, which are attached as Additional files.

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Efficient solution of Boolean satisfiability problems with digital memcomputing.

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Efficient solution of Boolean satisfiability problems with digital memcomputing.

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