A Geometric Approach to Biomedical Time Series Analysis

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Biomedical time series are non-invasive windows through which we may observe human systems. Although a vast amount of information is hidden in the medical field's growing collection of long-term, high-resolution, and multi-modal biomedical time series, effective algorithms for extracting that information have not yet been developed. We are particularly interested in the physiological dynamics of a human system, namely the changes in state that the system experiences over time (which may be intrinsic or extrinsic in origin). We introduce a mathematical model for a particular class of biomedical time series, called the wave-shape oscillatory model, which quantifies the sense in which dynamics are hidden in those time series. There are two key ideas behind the new model. First, instead of viewing a biomedical time series as a sequence of measurements made at the sampling rate of the signal, we can often view it as a sequence of cycles occurring at irregularly-sampled time points. Second, the "shape" of an individual cycle is assumed to have a one-to-one correspondence with the state of the system being monitored; as such, changes in system state (dynamics) can be inferred by tracking changes in cycle shape. Since physiological dynamics are not random but are well-regulated (except in the most pathological of cases), we can assume that all of the system's states lie on a low-dimensional, abstract Riemannian manifold called the phase manifold. When we model the correspondence between the hidden system states and the observed cycle shapes using a diffeomorphism, we allow the topology of the phase manifold to be recovered by methods belonging to the field of unsupervised manifold learning. In particular, we prove that the physiological dynamics hidden in a time series adhering to the wave-shape oscillatory model can be well-recovered by applying the diffusion maps algorithm to the time series' set of oscillatory cycles. We provide several applications of the wave-shape oscillatory model and the associated algorithm for dynamics recovery, including unsupervised and supervised heartbeat classification, derived respiratory monitoring, intra-operative cardiovascular monitoring, supervised and unsupervised sleep stage classification, and f-wave extraction (a single-channel blind source separation problem).






Malik, John (2020). A Geometric Approach to Biomedical Time Series Analysis. Dissertation, Duke University. Retrieved from https://hdl.handle.net/10161/20998.


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