DeepCare: A Deep Dynamic Memory Model for Predictive Medicine

Personalized predictive medicine necessitates modeling of patient illness and care processes, which inherently have long-term temporal dependencies. Healthcare observations, recorded in electronic medical records, are episodic and irregular in time. We introduce DeepCare, a deep dynamic neural network that reads medical records and predicts future medical outcomes. At the data level, DeepCare models patient health state trajectories with explicit memory of illness. Built on Long Short-Term Memory LSTM, DeepCare introduces time parameterizations to handle irregular timing by moderating the forgetting and consolidation of illness memory. DeepCare also incorporates medical interventions that change the course of illness and shape future medical risk. Moving upi¾źto the health state level, historical and present health states are then aggregated through multiscale temporal pooling, before passing through a neural network that estimates future outcomes. We demonstrate the efficacy of DeepCare for disease progression modeling and readmission prediction in diabetes, a chronic disease with large economic burden. The results show improved modeling and risk prediction accuracy.

[1]  Pierre Baldi,et al.  Understanding Dropout , 2013, NIPS.

[2]  Jürgen Schmidhuber,et al.  Long Short-Term Memory , 1997, Neural Computation.

[3]  C.J.H. Mann,et al.  Clinical Prediction Models: A Practical Approach to Development, Validation and Updating , 2009 .

[4]  Wei Luo,et al.  Stabilized sparse ordinal regression for medical risk stratification , 2014, Knowledge and Information Systems.

[5]  Jürgen Schmidhuber,et al.  Unconstrained On-line Handwriting Recognition with Recurrent Neural Networks , 2007, NIPS.

[6]  Geoffrey E. Hinton,et al.  Learning representations by back-propagating errors , 1986, Nature.

[7]  Elpida T. Keravnou,et al.  Temporal abstraction and temporal Bayesian networks in clinical domains: A survey , 2014, Artif. Intell. Medicine.

[8]  Hsinchun Chen,et al.  Prospective Infectious Disease Outbreak Detection Using Markov Switching Models , 2010, IEEE Transactions on Knowledge and Data Engineering.

[9]  Joseph Futoma,et al.  A comparison of models for predicting early hospital readmissions , 2015, J. Biomed. Informatics.

[10]  Quoc V. Le,et al.  Distributed Representations of Sentences and Documents , 2014, ICML.

[11]  Suchi Saria,et al.  Developing Predictive Models Using Electronic Medical Records: Challenges and Pitfalls , 2013, AMIA.

[12]  Tudor I. Oprea,et al.  Temporal disease trajectories condensed from population-wide registry data covering 6.2 million patients , 2014, Nature Communications.

[13]  Christian Osendorfer,et al.  On Fast Dropout and its Applicability to Recurrent Networks , 2013, ICLR.

[14]  Jeffrey Dean,et al.  Efficient Estimation of Word Representations in Vector Space , 2013, ICLR.

[15]  Huilong Duan,et al.  Similarity Measure Between Patient Traces for Clinical Pathway Analysis: Problem, Method, and Applications , 2014, IEEE Journal of Biomedical and Health Informatics.

[16]  A. Choudhary,et al.  Development of a 5 year life expectancy index in older adults using predictive mining of electronic health record data. , 2013, Journal of the American Medical Informatics Association : JAMIA.

[17]  Simon G. Thompson,et al.  Multistate Markov models for disease progression with classification error , 2003 .

[18]  Michael C. Mozer,et al.  Induction of Multiscale Temporal Structure , 1991, NIPS.

[19]  George Hripcsak,et al.  Defining and measuring completeness of electronic health records for secondary use , 2013, J. Biomed. Informatics.

[20]  Svetha Venkatesh,et al.  Graph-induced restricted Boltzmann machines for document modeling , 2016, Inf. Sci..

[21]  Ognjen Arandjelovic,et al.  Discovering hospital admission patterns using models learnt from electronic hospital records , 2015, Bioinform..

[22]  Wei Luo,et al.  An integrated framework for suicide risk prediction , 2013, KDD.

[23]  Svetha Venkatesh,et al.  Learning vector representation of medical objects via EMR-driven nonnegative restricted Boltzmann machines (eNRBM) , 2015, J. Biomed. Informatics.

[24]  Svetha Venkatesh,et al.  Learning Parts-based Representations with Nonnegative Restricted Boltzmann Machine , 2013, ACML.

[25]  Yoshua Bengio,et al.  Why Does Unsupervised Pre-training Help Deep Learning? , 2010, AISTATS.

[26]  Hui Xiong,et al.  Temporal Phenotyping from Longitudinal Electronic Health Records: A Graph Based Framework , 2015, KDD.

[27]  Peter Groves,et al.  The 'big data' revolution in healthcare: Accelerating value and innovation , 2016 .

[28]  A. Strauss,et al.  A nursing model for chronic illness management based upon the Trajectory Framework. , 1991, Scholarly inquiry for nursing practice.

[29]  Jürgen Schmidhuber,et al.  Learning to Forget: Continual Prediction with LSTM , 2000, Neural Computation.

[30]  B. Frey,et al.  Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning , 2015, Nature Biotechnology.

[31]  George Hripcsak,et al.  Next-generation phenotyping of electronic health records , 2012, J. Am. Medical Informatics Assoc..

[32]  Yoshua Bengio,et al.  Learning long-term dependencies with gradient descent is difficult , 1994, IEEE Trans. Neural Networks.

[33]  Razvan Pascanu,et al.  On the difficulty of training recurrent neural networks , 2012, ICML.

[34]  S. Brunak,et al.  Mining electronic health records: towards better research applications and clinical care , 2012, Nature Reviews Genetics.

[35]  Paul J. Werbos,et al.  Backpropagation Through Time: What It Does and How to Do It , 1990, Proc. IEEE.

[36]  Wojciech Zaremba,et al.  Recurrent Neural Network Regularization , 2014, ArXiv.

[37]  Wei Luo,et al.  A framework for feature extraction from hospital medical data with applications in risk prediction , 2014, BMC Bioinformatics.

[38]  Yoshua Bengio,et al.  Greedy Layer-Wise Training of Deep Networks , 2006, NIPS.

[39]  R. Snyderman,et al.  Prospective Medicine: The Next Health Care Transformation , 2003, Academic medicine : journal of the Association of American Medical Colleges.

[40]  M. D’Esposito Working memory. , 2008, Handbook of clinical neurology.

[41]  S. Henly,et al.  Health and illness over time: the trajectory perspective in nursing science. , 2011, Nursing research.

[42]  B. Granger,et al.  Caring for Patients with Chronic Heart Failure: The Trajectory Model , 2006, European journal of cardiovascular nursing : journal of the Working Group on Cardiovascular Nursing of the European Society of Cardiology.

[43]  Geoffrey E. Hinton,et al.  A time-delay neural network architecture for isolated word recognition , 1990, Neural Networks.

[44]  Yee Whye Teh,et al.  A Fast Learning Algorithm for Deep Belief Nets , 2006, Neural Computation.

[45]  Bozhkov Lachezar,et al.  Echo State Network , 2017, Encyclopedia of Machine Learning and Data Mining.

[46]  Yuval Shahar,et al.  Irregular-Time Bayesian Networks , 2010, UAI.

[47]  Quoc V. Le,et al.  Semi-supervised Sequence Learning , 2015, NIPS.

[48]  Nitish Srivastava,et al.  Unsupervised Learning of Video Representations using LSTMs , 2015, ICML.

[49]  Guigang Zhang,et al.  Deep Learning , 2016, Int. J. Semantic Comput..

[50]  Nitish Srivastava,et al.  Dropout: a simple way to prevent neural networks from overfitting , 2014, J. Mach. Learn. Res..

[51]  Geoffrey E. Hinton,et al.  Speech recognition with deep recurrent neural networks , 2013, 2013 IEEE International Conference on Acoustics, Speech and Signal Processing.

[52]  Yoshua Bengio,et al.  A Neural Probabilistic Language Model , 2003, J. Mach. Learn. Res..

[53]  Xiangji Huang,et al.  Deep learning for healthcare decision making with EMRs , 2014, 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

[54]  Xiang Wang,et al.  Unsupervised learning of disease progression models , 2014, KDD.

[55]  Quoc V. Le,et al.  Sequence to Sequence Learning with Neural Networks , 2014, NIPS.

[56]  Lukás Burget,et al.  Recurrent neural network based language model , 2010, INTERSPEECH.

[57]  Peter Tiño,et al.  Learning long-term dependencies in NARX recurrent neural networks , 1996, IEEE Trans. Neural Networks.

[58]  Cláudia Antunes,et al.  Generative modeling of repositories of health records for predictive tasks , 2014, Data Mining and Knowledge Discovery.

[59]  Alex Graves,et al.  Generating Sequences With Recurrent Neural Networks , 2013, ArXiv.