Amit Verma

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.