Players across the health ecosystem are initiating studies of thousands, even millions, of participants to gather diverse types of data, including biomedical, behavioral, and lifestyle in order to advance medical research. These efforts to collect multi-modal data sets on large cohorts coincide with the rise of broad activity and behavior tracking across industries, particularly in healthcare and the growing field of mobile health (mHealth). Government and pharmaceutical sponsored, as well as patient-driven group studies in this arena leverage the ability of mobile technology to continuously track behaviors and environmental factors with minimal participant burden. However, the adoption of mHealth has been constrained by the lack of robust solutions for large-scale data collection in free-living conditions and concerns around data quality. In this work, we describe the infrastructure Evidation Health has developed to collect mHealth data from millions of users through hundreds of different mobile devices and apps. Additionally, we provide evidence of the utility of the data for inferring individual traits pertaining to health, wellness, and behavior. To this end, we introduce and evaluate deep neural network models that achieve high prediction performance without requiring any feature engineering when trained directly on the densely sampled multivariate mHealth time series data. We believe that the present work substantiates both the feasibility and the utility of creating a very large mHealth research cohort, as envisioned by the many large cohort studies currently underway across therapeutic areas and conditions.

While generative models such as Latent Dirichlet Allocation (LDA) have proven fruitful in topic modeling, they often require detailed assumptions and careful specification of hyperparameters. Such model complexity issues only compound when trying to generalize generative models to incorporate human input. We introduce Correlation Explanation (CorEx), an alternative approach to topic modeling that does not assume an underlying generative model, and instead learns maximally informative topics through an information-theoretic framework. This framework naturally generalizes to hierarchical and semi-supervised extensions with no additional modeling assumptions. In particular, word-level domain knowledge can be flexibly incorporated within CorEx through anchor words, allowing topic separability and representation to be promoted with minimal human intervention. Across a variety of datasets, metrics, and experiments, we demonstrate that CorEx produces topics that are comparable in quality to those produced by unsupervised and semi-supervised variants of LDA.

Functional data, where samples are random functions, are increasingly common and important in a variety of applications, such as health care and traffic analysis. They are naturally high dimensional and lie along complex manifolds. These properties warrant use of the subspace assumption, but most state-of-the-art subspace learning algorithms are limited to linear or other simple settings. To address these challenges, we propose a new framework called Functional Subspace Clustering (FSC). FSC assumes that functional samples lie in deformed linear subspaces and formulates the subspace learning problem as a sparse regression over operators. The resulting problem can be efficiently solved via greedy variable selection, given access to a fast deformation oracle. We provide theoretical guarantees for FSC and show how it can be applied to time series with warped alignments. Experimental results on both synthetic data and real clinical time series show that FSC outperforms both standard time series clustering and state-of-the-art subspace clustering.

We apply deep learning to the problem of discovery and detection of characteristic patterns of physiology in clinical time series data. We propose two novel modifications to standard neural net training that address challenges and exploit properties that are peculiar, if not exclusive, to medical data. First, we examine a general framework for using prior knowledge to regularize parameters in the topmost layers. This framework can leverage priors of any form, ranging from formal ontologies (e.g., ICD9 codes) to data-derived similarity. Second, we describe a scalable procedure for training a collection of neural networks of different sizes but with partially shared architectures. Both of these innovations are well-suited to medical applications, where available data are not yet Internet scale and have many sparse outputs (e.g., rare diagnoses) but which have exploitable structure (e.g., temporal order and relationships between labels). However, both techniques are sufficiently general to be applied to other problems and domains. We demonstrate the empirical efficacy of both techniques on two real-world hospital data sets and show that the resulting neural nets learn interpretable and clinically relevant features.

We describe a unified active transfer learning framework called Hierarchical Active Transfer Learning (HATL). HATL exploits cluster structure shared between different data domains to perform transfer learning by imputing labels for unlabeled target data and to generate effective label queries during active learning. The resulting framework is flexible enough to perform not only adaptive transfer learning and accelerated active learning but also unsupervised and semi-supervised transfer learning. We derive an intuitive and useful upper bound on HATL's error when used to infer labels for unlabeled target points. We also present results on synthetic data that confirm both intuition and our analysis. Finally, we demonstrate HATL's empirical effectiveness on a benchmark data set for sentiment classification.

As large-scale multivariate time series data become increasingly common in application domains, such as health care and traffic analysis, researchers are challenged to build efficient tools to analyze it and provide useful insights. Similarity search, as a basic operator for many machine learning and data mining algorithms, has been extensively studied before, leading to several efficient solutions. However, similarity search for multivariate time series data is intrinsically challenging because (1) there is no conclusive agreement on what is a good similarity metric for multivariate time series data and (2) calculating similarity scores between two time series is often computationally expensive. In this paper, we address this problem by applying a generalized hashing framework, namely kernelized locality sensitive hashing, to accelerate time series similarity search with a series of representative similarity metrics. Experiment results on three large-scale clinical data sets demonstrate the effectiveness of the proposed approach.

Active learning, transfer learning, and related techniques are unified by a core theme: efficient and effective use of available data. Active learning offers scalable solutions for building effective supervised learning models while minimizing annotation effort. Transfer learning utilizes existing labeled data from one task to help learning related tasks for which limited labeled data are available. There has been limited research, however, on how to combine these two techniques. In this paper, we present a simple and principled transfer active learning framework that leverages pre-existing labeled data from related tasks to improve the performance of an active learner. We derive an intuitive bound on generalization error for the classifiers learned by this algorithm that provides insight into the algorithm's behavior and the problem in general. Experimental results using several well-known transfer learning data sets confirm our theoretical analysis and demonstrate the effectiveness of our approach.

The Laura P. and Leland K. Whittier Virtual Pediatric Intensive Care Unit (VPICU) is an ambitious research network focused on building online databases for improving decision-making in pediatric intensive care units. Increasingly, there is a need to unify previously distributed and heterogeneous information captured in these databases to support both traditional retrospective support ad-hoc studies, and ad-hoc analyses. VPICU and NASA's Jet Propulsion Laboratory have constructed a reference architecture and implementation framework that addresses these needs. The architecture is unobtrusive, scalable, and secure, with a strong focus on rapid deployment and integration. This paper reports on the current status of our efforts and details the strength of the framework via our recent work in unsupervised discovery of patient similarity within the hospital.