Time Series

Adams, Roy J., Edison Thomaz, and Benjamin M. Marlin. "Hierarchical Nested CRFs for Segmentation and Labeling of Physiological Time Series." NIPS Workshop on Machine Learning in Healthcare. 2015. Abstractadams-nips-heath2015.pdf

In this paper, we address the problem of nested hierarchical segmentation
and labeling of time series data. We present a hierarchical
span-based conditional random field framework for this problem that
leverages higher-order factors to enforce the nesting constraints. The framework can
incorporate a variety of additional factors including higher order cardinality
factors. This research is motivated by hierarchical activity recognition problems
in the field of mobile Health (mHealth). We show that the specific model of interest in the mHealth setting supports exact MAP inference in quadratic time. Learning is accomplished in the structured support vector machine framework. We show positive results on real and synthetic data sets.

Natarajan, Annamalai, Edward Gaiser, Gustavo Angarita, Robert Malison, Deepak Ganesan, and Benjamin Marlin. "Conditional Random Fields for Morphological Analysis of Wireless ECG Signals." Proceedings of the 5th Annual conference on Bioinformatics, Computational Biology and Health Informatics. Newport Beach, CA: ACM, 2014. Abstractcrf_bcb2014.pdf

Thanks to advances in mobile sensing technologies, it has recently become practical to deploy wireless electrocardiograph sensors for continuous recording of ECG signals. This capability has diverse applications in the study of human health and behavior, but to realize its full potential, new computational tools are required to effectively deal with the uncertainty that results from the noisy and highly non-stationary signals collected using these devices. In this work, we present a novel approach to the problem of extracting the morphological structure of ECG signals based on the use of dynamically structured conditional random field (CRF) models. We apply this framework to the problem of extracting morphological structure from wireless ECG sensor data collected in a lab-based study of habituated cocaine users. Our results show that the proposed CRF-based approach significantly out-performs independent prediction models using the same features, as well as a widely cited open source toolkit.

Natarajan, Annamalai, Abhinav Parate, Edward Gaiser, Gustavo Angarita, Robert Malison, Benjamin M. Marlin, and Deepak Ganesan. "Detecting cocaine use with wearable electrocardiogram sensors." UbiComp. 2013. 123-132. Abstractcocaine_ubicomp13_paper.pdf

Ubiquitous physiological sensing has the potential to profoundly improve our understanding of human behavior, leading to more targeted treatments for a variety of disorders. The long term goal of this work is development of novel computational tools to support the study of addiction in the context of cocaine use. The current paper takes the first step in this important direction by posing a simple, but crucial question: Can cocaine use be reliably detected using wearable electrocardiogram (ECG) sensors? The main contributions in this paper include the presentation of a novel clinical study of cocaine use, the development of a computational pipeline for inferring morphological features from noisy ECG waveforms, and the evaluation of feature sets for cocaine use detection. Our results show that 32mg/70kg doses of cocaine can be detected with the area under the receiver operating characteristic curve levels above 0.9 both within and between-subjects.

Parate, Abhinav, Matthias Böhmer, David Chu, Deepak Ganesan, and Benjamin M. Marlin. "Practical prediction and prefetch for faster access to applications on mobile phones." UbiComp. 2013. 275-284. Abstractprefetch_ubicomp13_paper.pdf

Mobile phones have evolved from communication devices to indispensable accessories with access to real-time content. The increasing reliance on dynamic content comes at the cost of increased latency to pull the content from the Internet before the user can start using it. While prior work has explored parts of this problem, they ignore the bandwidth costs of prefetching, incur significant training overhead, need several sensors to be turned on, and do not consider practical systems issues that arise from the limited background processing capability supported by mobile operating systems. In this paper, we make app prefetch practical on mobile phones. Our contributions are two-fold. First, we design an app prediction algorithm, APPM, that requires no prior training, adapts to usage dynamics, predicts not only which app will be used next but also when it will be used, and provides high accuracy without requiring additional sensor context. Second, we perform parallel prefetch on screen unlock, a mechanism that leverages the benefits of prediction while operating within the constraints of mobile operating systems. Our experiments are conducted on long-term traces, live deployments on the Android Play Market, and user studies, and show that we outperform prior approaches to predicting app usage, while also providing practical ways to prefetch application content on mobile phones.

Parate, Abhinav, Meng-Chieh Chiu, Deepak Ganesan, and Benjamin M. Marlin. "Leveraging graphical models to improve accuracy and reduce privacy risks of mobile sensing." MobiSys. 2013. 83-96. Abstractsensing_mobisys13_paper.pdf

The proliferation of sensors on mobile phones and wearables has led to a plethora of context classifiers designed to sense the individual's context. We argue that a key missing piece in mobile inference is a layer that fuses the outputs of several classifiers to learn deeper insights into an individual's habitual patterns and associated correlations between contexts, thereby enabling new systems optimizations and opportunities. In this paper, we design CQue, a dynamic bayesian network that operates over classifiers for individual contexts, observes relations across these outputs across time, and identifies opportunities for improving energy-efficiency and accuracy by taking advantage of relations. In addition, such a layer provides insights into privacy leakage that might occur when seemingly innocuous user context revealed to different applications on a phone may be combined to reveal more information than originally intended. In terms of system architecture, our key contribution is a clean separation between the detection layer and the fusion layer, enabling classifiers to solely focus on detecting the context, and leverage temporal smoothing and fusion mechanisms to further boost performance by just connecting to our higher-level inference engine. To applications and users, CQue provides a query interface, allowing a) applications to obtain more accurate context results while remaining agnostic of what classifiers/sensors are used and when, and b) users to specify what contexts they wish to keep private, and only allow information that has low leakage with the private context to be revealed. We implemented CQue in Android, and our results show that CQue can i) improve activity classification accuracy up to 42%, ii) reduce energy consumption in classifying social, location and activity contexts with high accuracy(>90%) by reducing the number of required classifiers by at least 33%, and iii) effectively detect and suppress contexts that reveal private information.

Marlin, Benjamin M., David C. Kale, Robinder G. Khemani, and Randall C. Wetzel. "Unsupervised pattern discovery in electronic health care data using probabilistic clustering models." IHI. 2012. 389-398. Abstractehr_clustering_ihi2012_paper.pdf

Bedside clinicians routinely identify temporal patterns in physiologic data in the process of choosing and administering treatments intended to alter the course of critical illness for individual patients. Our primary interest is the study of unsupervised learning techniques for automatically uncovering such patterns from the physiologic time series data contained in electronic health care records. This data is sparse, high-dimensional and often both uncertain and incomplete. In this paper, we develop and study a probabilistic clustering model designed to mitigate the effects of temporal sparsity inherent in electronic health care records data. We evaluate the model qualitatively by visualizing the learned cluster parameters and quantitatively in terms of its ability to predict mortality outcomes associated with patient episodes. Our results indicate that the model can discover distinct, recognizable physiologic patterns with prognostic significance.