We introduce quantum utility , a new approach to evaluating quantum performance that aims to capture the user experience by considering the overhead costs associated with a quantum computation. A demonstration of quantum utility by the quantum processing unit (QPU) shows that the QPU can outperform classical solvers at some tasks of interest to practitioners, when considering the costs of computational overheads. A milestone is a test of quantum utility that is restricted to a specific subset of overhead costs and input types. We illustrate this approach with a benchmark study of a D-Wave annealing-based QPU versus seven classical solvers for a variety of problems in heuristic optimization. We consider overhead costs that arise in standalone use of the D-Wave QPU (as opposed to a hybrid computation). We define three early milestones on the path to broad-scale quantum utility. Milestone 0 is the purely quantum computation with no overhead costs and is demonstrated implicitly by positive results on other milestones. We evaluate the performance of a D-Wave Advantage QPU with respect to milestones 1 and 2: For milestone 1, the QPU outperformed all classical solvers in 99% of our tests. For milestone 2, the QPU outperformed all classical solvers in 19% of our tests, and the scenarios in which the QPU found success correspond to cases where classical solvers most frequently failed. This approach of isolating subsets of overheads for separate analysis reveals distinct mechanisms in quantum versus classical performance, which explain the observed differences in patterns of success and failure. We present evidence-based arguments that these distinctions bode well for annealing quantum processors to support demonstrations of quantum utility on ever-expanding classes of inputs and with more challenging milestones in the very near future.

Quantum processing units (QPUs) executing annealing algorithms have shown promise in optimization and simulation applications. Hybrid algorithms are a natural bridge to larger applications. We present a simple greedy method for solving larger-than-QPU lattice-structured Ising optimization problems. The method, implemented in the open source D-Wave Hybrid framework, uses a QPU coprocessor operating with generic parameters. Performance is evaluated for standard spin-glass problems on two lattice types with up to 11,616 spin variables, double the size that is directly programmable on any available QPU. The proposed method is shown to converge to low-energy solutions faster than an open source simulated annealing method that is either directly employed or substituted as a coprocessor in the hybrid method. Using newer Advantage QPUs in place of D-Wave 2000Q QPUs is shown to enhance convergence of the hybrid method to low energies and to achieve a lower final energy.

We define the quantum utility performance metric and three milestones, which define quantum utility as measured in some limited context. Current and previous-generation annealing quantum systems can outperform classical solvers on a variety of input classes, on Milestones 0 and 1; our tests of Milestone 2 show positive results on a small set of inputs. Characterization of the input properties that drive these outcomes suggests that future tests will yield more widespread successes on these and more challenging milestones.

In this paper we propose an API to pause and resume task execution depending on external events. We leverage this generic API to improve the interoperability between MPI synchronous communication primitives and tasks. When an MPI operation blocks, the task running is paused so that the runtime system can schedule a new task on the core that became idle. Once the MPI operation is completed, the paused task is put again on the runtime system's ready queue. We expose our proposal through a new MPI threading level which we implement through two approaches.

The packaging of DNA inside a nucleus shows complex structure stabilized by a host of DNA-bound factors. Both the distribution of these factors and the contacts between different genomic locations of the DNA can now be measured on a genome-wide scale. This has advanced the development of models aimed at predicting the conformation of DNA given only the locations of bound factors-the chromatin folding problem. Here we present a maximum-entropy model that is able to predict a contact map representation of structure given a sequence of bound factors. Non-local effects due to the sequence neighborhood around contacting sites are found to be important for making accurate predictions. Lastly, we show that the model can be used to infer a sequence of bound factors given only a measurement of structure. This opens up the possibility for efficiently predicting sequence regions that may play a role in generating cell-type specific structural differences.

BACKGROUND: A variety of DNA binding proteins are involved in regulating and shaping the packing of chromatin. They aid the formation of loops in the DNA that function to isolate different structural domains. A recent experimental technique, Hi-C, provides a method for determining the frequency of such looping between all distant parts of the genome. Given that the binding locations of many chromatin associated proteins have also been measured, it has been possible to make estimates for their influence on the long-range interactions as measured by Hi-C. However, a challenge in this analysis is the predominance of non-specific contacts that mask out the specific interactions of interest. RESULTS: We show that transforming the Hi-C contact frequencies into free energies gives a natural method for separating out the distance dependent non-specific interactions. In particular we apply Principal Component Analysis (PCA) to the transformed free energy matrix to identify the dominant modes of interaction. PCA identifies systematic effects as well as high frequency spatial noise in the Hi-C data which can be filtered out. Thus it can be used as a data driven approach for normalizing Hi-C data. We assess this PCA based normalization approach, along with several other normalization schemes, by fitting the transformed Hi-C data using a pairwise interaction model that takes as input the known locations of bound chromatin factors. The result of fitting is a set of predictions for the coupling energies between the various chromatin factors and their effect on the energetics of looping. We show that the quality of the fit can be used as a means to determine how much PCA filtering should be applied to the Hi-C data. CONCLUSIONS: We find that the different normalizations of the Hi-C data vary in the quality of fit to the pairwise interaction model. PCA filtering can improve the fit, and the predicted coupling energies lead to biologically meaningful insights for how various chromatin bound factors influence the stability of DNA loops in chromatin.