ShortFuse: Biomedical Time Series Representations in the Presence of Structured Information


Madalina Fiterau, Suvrat Bhooshan, Jason Fries, Charles Bournhonesque, Jennifer Hicks, Eni Halilaj, Christopher Re, Scott Delp ;
Proceedings of the 2nd Machine Learning for Healthcare Conference, PMLR 68:59-74, 2017.


In healthcare applications, temporal variables that encode movement, health status, and longitudinal patient evolution are often accompanied by rich structured information such as demographics, diagnostics and medical exam data. However, current methods do not jointly optimize over structured covariates and time series in the feature extraction process. We present ShortFuse, a method that boosts the accuracy of deep learning models for time series by explicitly modeling temporal interactions and dependencies with structured covariates. ShortFuse introduces hybrid convolutional and LSTM cells that incorporate the covariates via weights that are shared across the temporal domain. ShortFuse outperforms competing models by 3% on two biomedical applications, forecasting osteoarthritis-related cartilage degeneration and predicting surgical outcomes for cerebral palsy patients.

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