Unconventional machine learning of genome-wide human cancer data

Recent advances in high-throughput genomic technologies coupled with exponential increases in computer processing and memory have allowed us to interrogate the complex aberrant molecular underpinnings of human disease from a genome-wide perspective. While the deluge of genomic information is expected to increase, a bottleneck in conventional high-performance computing is rapidly approaching. Inspired in part by recent advances in physical quantum processors, we evaluated several unconventional machine learning (ML) strategies on actual human tumor data. Here we show for the first time the efficacy of multiple annealing-based ML algorithms for classification of high-dimensional, multi-omics human cancer data from the Cancer Genome Atlas. To assess algorithm performance, we compared these classifiers to a variety of standard ML methods. Our results indicate the feasibility of using annealing-based ML to provide competitive classification of human cancer types and associated molecular subtypes and superior performance with smaller training datasets, thus providing compelling empirical evidence for the potential future application of unconventional computing architectures in the biomedical sciences

Multiple Query Optimization on the D-Wave 2X Adiabatic Quantum Computer

The D-Wave adiabatic quantum annealer solves hard combinatorial optimization problems leveraging quantum physics. The newest version features over 1000 qubits and was released in August 2015. We were given access to such a machine, currently hosted at NASA Ames Research Center in California, to explore the potential for hard optimization problems that arise in the context of databases. In this paper, we tackle the problem of multiple query optimization (MQO). We show how an MQO problem instance can be transformed into a mathematical formula that complies with the restrictive input format accepted by the quantum annealer. This formula is translated into weights on and between qubits such that the configuration minimizing the input formula can be found via a process called adiabatic quantum annealing. We analyze the asymptotic growth rate of the number of required qubits in the MQO problem dimensions as the number of qubits is currently the main factor restricting applicability. We experimentally compare the performance of the quantum annealer against other MQO algorithms executed on a traditional computer. While the problem sizes that can be treated are currently limited, we already find a class of problem instances where the quantum annealer is three orders of magnitude faster than other approaches

The Quantum Adiabatic Algorithm applied to random optimization problems: the quantum spin glass perspective

Among various algorithms designed to exploit the specific properties of quantum computers with respect to classical ones, the quantum adiabatic algorithm is a versatile proposition to find the minimal value of an arbitrary cost function (ground state energy). Random optimization problems provide a natural testbed to compare its efficiency with that of classical algorithms. These problems correspond to mean field spin glasses that have been extensively studied in the classical case. This paper reviews recent analytical works that extended these studies to incorporate the effect of quantum fluctuations, and presents also some original results in this direction.Comment: 151 pages, 21 figure

Advances in quantum machine learning

Here we discuss advances in the field of quantum machine learning. The following document offers a hybrid discussion; both reviewing the field as it is currently, and suggesting directions for further research. We include both algorithms and experimental implementations in the discussion. The field's outlook is generally positive, showing significant promise. However, we believe there are appreciable hurdles to overcome before one can claim that it is a primary application of quantum computation.Comment: 38 pages, 17 Figure

Duality approach to quantum annealing of the 3-XORSAT problem

Classical models with complex energy landscapes represent a perspective avenue for the near-term application of quantum simulators. Until now, many theoretical works studied the performance of quantum algorithms for models with a unique ground state. However, when the classical problem is in a so-called clustering phase, the ground state manifold is highly degenerate. As an example, we consider a 3-XORSAT model defined on simple hypergraphs. The degeneracy of classical ground state manifold translates into the emergence of an extensive number of $Z_2$ symmetries, which remain intact even in the presence of a quantum transverse magnetic field. We establish a general duality approach that restricts the quantum problem to a given sector of conserved $Z_2$ charges and use it to study how the outcome of the quantum adiabatic algorithm depends on the hypergraph geometry. We show that the tree hypergraph which corresponds to a classically solvable instance of the 3-XORSAT problem features a constant gap, whereas the closed hypergraph encounters a second-order phase transition with a gap vanishing as a power-law in the problem size. The duality developed in this work provides a practical tool for studies of quantum models with classically degenerate energy manifold and reveals potential connections between glasses and gauge theories