Homology Computation of Large Point Clouds using Quantum Annealing

Homology is a tool in topological data analysis which measures the shape of the data. In many cases, these measurements translate into new insights which are not available by other means. To compute homology, we rely on mathematical constructions which scale exponentially with the size of the data. Therefore, for large point clouds, the computation is infeasible using classical computers. In this paper, we present a quantum annealing pipeline for computation of homology of large point clouds. The pipeline takes as input a graph approximating the given point cloud. It uses quantum annealing to compute a clique covering of the graph and then uses this cover to construct a Mayer-Vietoris complex. The pipeline terminates by performing a simplified homology computation of the Mayer-Vietoris complex. We have introduced three different clique coverings and their quantum annealing formulation. Our pipeline scales polynomially in the size of the data, once the covering step is solved. To prove correctness of our algorithm, we have also included tests using D-Wave 2X quantum processor

Computing Wasserstein Distance for Persistence Diagrams on a Quantum Computer

Persistence diagrams are a useful tool from topological data analysis which can be used to provide a concise description of a filtered topological space. What makes them even more useful in practice is that they come with a notion of a metric, the Wasserstein distance (closely related to but not the same as the homonymous metric from probability theory). Further, this metric provides a notion of stability; that is, small noise in the input causes at worst small differences in the output. In this paper, we show that the Wasserstein distance for persistence diagrams can be computed through quantum annealing. We provide a formulation of the problem as a Quadratic Unconstrained Binary Optimization problem, or QUBO, and prove correctness. Finally, we test our algorithm, exploring parameter choices and problem size capabilities, using a D-Wave 2000Q quantum annealing computer

The Topology of Mutated Driver Pathways

Much progress has been made, and continues to be made, towards identifying candidate mutated driver pathways in cancer. However, no systematic approach to understanding how candidate pathways relate to each other for a given cancer (such as Acute myeloid leukemia), and how one type of cancer may be similar or different from another with regard to their respective pathways (Acute myeloid leukemia vs. Glioblastoma multiforme for instance), has emerged thus far. Our work attempts to contribute to the understanding of {\em space of pathways} through a novel topological framework. We illustrate our approach, using mutation data (obtained from TCGA) of two types of tumors: Acute myeloid leukemia (AML) and Glioblastoma multiforme (GBM). We find that the space of pathways for AML is homotopy equivalent to a sphere, while that of GBM is equivalent to a genus-2 surface. We hope to trigger new types of questions (i.e., allow for novel kinds of hypotheses) towards a more comprehensive grasp of cancer.Comment: Key words: topological data analysis, cancer genomics, mutation data, acute myeloid leukemia, glioblastoma multiforme, persistent homology, simplicial complex, Betti numbers, algebraic topolog

Quantum Computing: An Overview Across the System Stack

Quantum computers, if fully realized, promise to be a revolutionary technology. As a result, quantum computing has become one of the hottest areas of research in the last few years. Much effort is being applied at all levels of the system stack, from the creation of quantum algorithms to the development of hardware devices. The quantum age appears to be arriving sooner rather than later as commercially useful small-to-medium sized machines have already been built. However, full-scale quantum computers, and the full-scale algorithms they would perform, remain out of reach for now. It is currently uncertain how the first such computer will be built. Many different technologies are competing to be the first scalable quantum computer

Finding universal structures in quantum many-body dynamics via persistent homology

Inspired by topological data analysis techniques, we introduce persistent homology observables and apply them in a geometric analysis of the dynamics of quantum field theories. As a prototype application, we consider simulated data of a two-dimensional Bose gas far from equilibrium. We discover a continuous spectrum of dynamical scaling exponents, which provides a refined classification of nonequilibrium universal phenomena. A possible explanation of the underlying processes is provided in terms of mixing wave turbulence and vortex kinetics components in point clouds. We find that the persistent homology scaling exponents are inherently linked to the geometry of the system, as the derivation of a packing relation reveals. The approach opens new ways of analyzing quantum many-body dynamics in terms of robust topological structures beyond standard field theoretic techniques.Comment: 21 pages, 18 figure