Efficient Inference of Gaussian Process Modulated Renewal Processes with Application to Medical Event Data

The episodic, irregular and asynchronous nature of medical data render them difficult substrates for standard machine learning algorithms. We would like to abstract away this difficulty for the class of time-stamped categorical variables (or events) by modeling them as a renewal process and inferring a probability density over continuous, longitudinal, nonparametric intensity functions modulating that process. Several methods exist for inferring such a density over intensity functions, but either their constraints and assumptions prevent their use with our potentially bursty event streams, or their time complexity renders their use intractable on our long-duration observations of high-resolution events, or both. In this paper we present a new and efficient method for inferring a distribution over intensity functions that uses direct numeric integration and smooth interpolation over Gaussian processes. We demonstrate that our direct method is up to twice as accurate and two orders of magnitude more efficient than the best existing method (thinning). Importantly, the direct method can infer intensity functions over the full range of bursty to memoryless to regular events, which thinning and many other methods cannot. Finally, we apply the method to clinical event data and demonstrate the face-validity of the abstraction, which is now amenable to standard learning algorithms.Comment: 8 pages, 4 figure

Finite-dimensional Gaussian approximation with linear inequality constraints

International audienceGaussian process (GP) modulated Cox processes are widely used to model point patterns. Existing approaches require a mapping (link function) between the unconstrained GP and the positive intensity function. This commonly yields solutions that do not have a closed form or that are restricted to specific covariance functions. We introduce a novel finite approximation of GP-modulated Cox processes where positiveness conditions can be imposed directly on the GP, with no restrictions on the covariance function. Our approach can also ensure other types of inequality constraints e.g. monotonicity, convexity), resulting in more versatile models that can be used for other classes of point processes (e.g. renewal processes). We demonstrate on both synthetic and real-world data that our framework accurately infers the intensity functions. Where monotonicity is a feature of the process, our ability to include this in the inference improves results

Event series prediction via non-homogeneous Poisson process modelling

Data streams whose events occur at random arrival times rather than at the regular, tick-tock intervals of traditional time series are increasingly prevalent. Event series are continuous, irregular and often highly sparse, differing greatly in nature to the regularly sampled time series traditionally the concern of hard sciences. As mass sets of such data have become more common, so interest in predicting future events in them has grown. Yet repurposing of traditional forecasting approaches has proven ineffective, in part due to issues such as sparsity, but often due to inapplicable underpinning assumptions such as stationarity and ergodicity. In this paper we derive a principled new approach to forecasting event series that avoids such assumptions, based upon: 1. the processing of event series datasets in order to produce a parameterized mixture model of non-homogeneous Poisson processes; and 2. application of a technique called parallel forecasting that uses these processes’ rate functions to directly generate accurate temporal predictions for new query realizations. This approach uses forerunners of a stochastic process to shed light on the distribution of future events, not for themselves, but for realizations that subsequently follow in their footsteps

Methods for event time series prediction and anomaly detection

Event time series are sequences of events occurring in continuous time. They arise in many real-world problems and may represent, for example, posts in social media, administrations of medications to patients, or adverse events, such as episodes of atrial fibrillation or earthquakes. In this work, we study and develop methods for prediction and anomaly detection on event time series. We study two general approaches. The first approach converts event time series to regular time series of counts via time discretization. We develop methods relying on (a) nonparametric time series decomposition and (b) dynamic linear models for regular time series. The second approach models the events in continuous time directly. We develop methods relying on point processes. For prediction, we develop a new model based on point processes to combine the advantages of existing models. It is flexible enough to capture complex dependency structures between events, while not sacrificing applicability in common scenarios. For anomaly detection, we develop methods that can detect new types of anomalies in continuous time and that show advantages compared to time discretization