Hristo Djidjev

Aaron Barbosa, Elijah Pelofske, Georg Hahn et al.

Quantum annealers, such as the device built by D-Wave Systems, Inc., offer a way to compute solutions of NP-hard problems that can be expressed in Ising or QUBO (quadratic unconstrained binary optimization) form. Although such solutions are typically of very high quality, problem instances are usually not solved to optimality due to imperfections of the current generations quantum annealers. In this contribution, we aim to understand some of the factors contributing to the hardness of a problem instance, and to use machine learning models to predict the accuracy of the D-Wave 2000Q annealer for solving specific problems. We focus on the Maximum Clique problem, a classic NP-hard problem with important applications in network analysis, bioinformatics, and computational chemistry. By training a machine learning classification model on basic problem characteristics such as the number of edges in the graph, or annealing parameters such as D-Wave's chain strength, we are able to rank certain features in the order of their contribution to the solution hardness, and present a simple decision tree which allows to predict whether a problem will be solvable to optimality with the D-Wave 2000Q. We extend these results by training a machine learning regression model that predicts the clique size found by D-Wave.

Aaron Barbosa, Elijah Pelofske, Georg Hahn et al.

Quantum annealers have been designed to propose near-optimal solutions to NP-hard optimization problems. However, the accuracy of current annealers such as the ones of D-Wave Systems, Inc., is limited by environmental noise and hardware biases. One way to deal with these imperfections and to improve the quality of the annealing results is to apply a variety of pre-processing techniques such as spin reversal (SR), anneal offsets (AO), or chain weights (CW). Maximizing the effectiveness of these techniques involves performing optimizations over a large number of parameters, which would be too costly if needed to be done for each new problem instance. In this work, we show that the aforementioned parameter optimization can be done for an entire class of problems, given each instance uses a previously chosen fixed embedding. Specifically, in the training phase, we fix an embedding E of a complete graph onto the hardware of the annealer, and then run an optimization algorithm to tune the following set of parameter values: the set of bits to be flipped for SR, the specific qubit offsets for AO, and the distribution of chain weights, optimized over a set of training graphs randomly chosen from that class, where the graphs are embedded onto the hardware using E. In the testing phase, we estimate how well the parameters computed during the training phase work on a random selection of other graphs from that class. We investigate graph instances of varying densities for the Maximum Clique, Maximum Cut, and Graph Partitioning problems. Our results indicate that, compared to their default behavior, substantial improvements of the annealing results can be achieved by using the optimized parameters for SR, AO, and CW.

Nasrin Akhter, Gopinath Chennupati, Hristo Djidjev et al.

Identifying one or more biologically-active/native decoys from millions of non-native decoys is one of the major challenges in computational structural biology. The extreme lack of balance in positive and negative samples (native and non-native decoys) in a decoy set makes the problem even more complicated. Consensus methods show varied success in handling the challenge of decoy selection despite some issues associated with clustering large decoy sets and decoy sets that do not show much structural similarity. Recent investigations into energy landscape-based decoy selection approaches show promises. However, lack of generalization over varied test cases remains a bottleneck for these methods. We propose a novel decoy selection method, ML-Select, a machine learning framework that exploits the energy landscape associated with the structure space probed through a template-free decoy generation. The proposed method outperforms both clustering and energy ranking-based methods, all the while consistently offering better performance on varied test-cases. Moreover, ML-Select shows promising results even for the decoy sets consisting of mostly low-quality decoys. ML-Select is a useful method for decoy selection. This work suggests further research in finding more effective ways to adopt machine learning frameworks in achieving robust performance for decoy selection in template-free protein structure prediction.