Mark Lewis

Amit Verma, Mark Lewis, Gary Kochenberger

Quadratic Unconstrained Binary Optimization (QUBO) is recognized as a unifying framework for modeling a wide range of problems. Problems can be solved with commercial solvers customized for solving QUBO and since QUBO have degree two, it is useful to have a method for transforming higher degree pseudo-Boolean problems to QUBO format. The standard transformation approach requires additional auxiliary variables supported by penalty terms for each higher degree term. This paper improves on the existing cubic-to-quadratic transformation approach by minimizing the number of additional variables as well as penalty coefficient. Extensive experimental testing on Max 3-SAT modeled as QUBO shows a near 100% reduction in the subproblem size used for minimization of the number of auxiliary variables.

Amit Verma, Mark Lewis

Quadratic Unconstrained Binary Optimization (QUBO) is a general-purpose modeling framework for combinatorial optimization problems and is a requirement for quantum annealers. This paper utilizes the eigenvalue decomposition of the underlying Q matrix to alter and improve the search process by extracting the information from dominant eigenvalues and eigenvectors to implicitly guide the search towards promising areas of the solution landscape. Computational results on benchmark datasets illustrate the efficacy of our routine demonstrating significant performance improvements on problems with dominant eigenvalues.

Mark W. Lewis, Amit Verma, Rick Hennig

The structure of an RNA molecule plays a significant role in its biological function. Predicting structure given a one dimensional sequence of RNA nucleotide bases is a difficult and important problem. Many computer programs (known as in silico) are available for predicting 2-dimensional (secondary) structures however 3-dimensional (tertiary) structure prediction is much more difficult mainly due to the far greater number of feasible solutions and fewer experimental data on the thermodynamic energies of 3D structures. It is also challenging to verify the most likely three dimensional structure even with the availability of sophisticated x-ray crystallography and nuclear magnetic resonance imaging technologies. In this paper we develop three dimensional RNA folding predictions by adding penalty and reward parameters to a previous two dimensional approach based on Quadratic Unconstrained Binary Optimization (QUBO) models. These parameters provide flexibility in the amount of three dimensional folding allowed. We address the problem of multiple near-optimal structures via a new weighted similarity structure measure and illustrate folding pathways via progressively improving local optimal solutions. The problems are solved via a new commercial QUBO solver AlphaQUBO (Meta-Analytics, 2020) that solves problems having hundreds of thousands of binary variables.

Amit Verma, Mark Lewis

The broad applicability of Quadratic Unconstrained Binary Optimization (QUBO) constitutes a general-purpose modeling framework for combinatorial optimization problems and are a required format for gate array and quantum annealing computers. QUBO annealers as well as other solution approaches benefit from starting with a diverse set of solutions with local optimality an additional benefit. This paper presents a new method for generating a set of one-flip local optima leveraging constraint programming. Further, as demonstrated in experimental testing, analysis of the solution set allows the generation of soft constraints to help guide the optimization process.

Mark Lewis, Gary Kochenberger, John Metcalfe

In this paper we focus on the unconstrained binary quadratic optimization model, maximize x^t Qx, x binary, and consider the problem of identifying optimal solutions that are robust with respect to perturbations in the Q matrix.. We are motivated to find robust, or stable, solutions because of the uncertainty inherent in the big data origins of Q and limitations in computer numerical precision, particularly in a new class of quantum annealing computers. Experimental design techniques are used to generate a diverse subset of possible scenarios, from which robust solutions are identified. An illustrative example with practical application to business decision making is examined. The approach presented also generates a surface response equation which is used to estimate upper bounds in constant time for Q instantiations within the scenario extremes. In addition, a theoretical framework for the robustness of individual x_i variables is considered by examining the range of Q values over which the x_i are predetermined.

Mark W. Lewis

Multi-start algorithms are a common and effective tool for metaheuristic searches. In this paper we amplify multi-start capabilities by employing the parallel processing power of the graphics processer unit (GPU) to quickly generate a diverse starting set of solutions for the Unconstrained Binary Quadratic Optimization Problem which are evaluated and used to implement screening methods to select solutions for further optimization. This method is implemented as an initial high quality solution generation phase prior to a secondary steepest ascent search and a comparison of results to best known approaches on benchmark unconstrained binary quadratic problems demonstrates that GPU-enabled diversified multi-start with screening quickly yields very good results.

Mark Lewis, Fred Glover

The Quadratic Unconstrained Binary Optimization problem (QUBO) has become a unifying model for representing a wide range of combinatorial optimization problems, and for linking a variety of disciplines that face these problems. A new class of quantum annealing computer that maps QUBO onto a physical qubit network structure with specific size and edge density restrictions is generating a growing interest in ways to transform the underlying QUBO structure into an equivalent graph having fewer nodes and edges. In this paper we present rules for reducing the size of the QUBO matrix by identifying variables whose value at optimality can be predetermined. We verify that the reductions improve both solution quality and time to solution and, in the case of metaheuristic methods where optimal solutions cannot be guaranteed, the quality of solutions obtained within reasonable time limits. We discuss the general QUBO structural characteristics that can take advantage of these reduction techniques and perform careful experimental design and analysis to identify and quantify the specific characteristics most affecting reduction. The rules make it possible to dramatically improve solution times on a new set of problems using both the exact Cplex solver and a tabu search metaheuristic.

Fred Glover, Mark Lewis, Gary Kochenberger

The quadratic unconstrained binary optimization (QUBO) problem arises in diverse optimization applications ranging from Ising spin problems to classical problems in graph theory and binary discrete optimization. The use of preprocessing to transform the graph representing the QUBO problem into a smaller equivalent graph is important for improving solution quality and time for both exact and metaheuristic algorithms and is a step towards mapping large scale QUBO to hardware graphs used in quantum annealing computers. In an earlier paper (Lewis and Glover, 2016) a set of rules was introduced that achieved significant QUBO reductions as verified through computational testing. Here this work is extended with additional rules that provide further reductions that succeed in exactly solving 10% of the benchmark QUBO problems. An algorithm and associated data structures to efficiently implement the entire set of rules is detailed and computational experiments are reported that demonstrate their efficacy.