Zhengping Che

Deep Computational Phenotyping

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.

Recurrent Neural Networks for Multivariate Time Series with Missing Values

Multivariate time series data in practical applications, such as health care, geoscience, and biology, are characterized by a variety of missing values. In time series prediction and other related tasks, it has been noted that missing values and their missing patterns are often correlated with the target labels, a.k.a., informative missingness. There is very limited work on exploiting the missing patterns for effective imputation and improving prediction performance. In this paper, we develop novel deep learning models, namely GRU-D, as one of the early attempts. GRU-D is based on Gated Recurrent Unit (GRU), a state-of-the-art recurrent neural network. It takes two representations of missing patterns, i.e., masking and time interval, and effectively incorporates them into a deep model architecture so that it not only captures the long-term temporal dependencies in time series, but also utilizes the missing patterns to achieve better prediction results. Experiments of time series classification tasks on real-world clinical datasets (MIMIC-III, PhysioNet) and synthetic datasets demonstrate that our models achieve state-of-the-art performance and provide useful insights for better understanding and utilization of missing values in time series analysis.

An Examination of Multivariate Time Series Hashing with Applications to Health Care

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.

Time Series Feature Learning with Applications to Health Care

Exponential growth in mobile health devices and electronic health records has resulted in a surge of large-scale time series data, which demands effective and fast machine learning models for analysis and discovery. In this chapter, we discuss a novel framework based on deep learning which automatically performs feature learning from heterogeneous time series data. It is well-suited for healthcare applications, where available data have many sparse outputs (e.g., rare diagnoses) and exploitable structures (e.g., temporal order and relationships between labels). Furthermore, we introduce a simple yet effective knowledge-distillation approach to learn an interpretable model while achieving the prediction performance of deep models. We conduct experiments on several real-world datasets and show the empirical efficacy of our framework and the interpretability of the mimic models.