A temporal prognostic model based on dynamic Bayesian networks: mining medical insurance data

A prognostic model is a formal combination of multiple predictors from which risk probability of a specific diagnosis can be modelled for patients. Prognostic models have become essential instruments in medicine. The models are used for prediction purposes of guiding doctors to make a smart diagnosis, patient-specific decisions or help in planning the utilization of resources for patient groups who have similar prognostic paths. Dynamic Bayesian networks theoretically provide a very expressive and flexible model to solve temporal problems in medicine. However, this involves various challenges due both to the nature of the clinical domain, and the nature of the DBN modelling and inference process itself. The challenges from the clinical domain include insufficient knowledge of temporal interactions of processes in the medical literature, the sparse nature and variability of medical data collection, and the difficulty in preparing and abstracting clinical data in a suitable format without losing valuable information in the process. Challenges about the DBN methodology and implementation include the lack of tools that allow easy modelling of temporal processes. Overcoming this challenge will help to solve various clinical temporal reasoning problems. In this thesis, we addressed these challenges while building a temporal network with explanations of the effects of predisposing factors, such as age and gender, and the progression information of all diagnoses using claims data from an insurance company in Kenya. We showed that our network could differentiate the possible probability exposure to a diagnosis given the age and gender and possible paths given a patient's history. We also presented evidence that the more patient history is provided, the better the prediction of future diagnosis

DeepCare: A Deep Dynamic Memory Model for Predictive Medicine

Personalized predictive medicine necessitates the 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, an end-to-end deep dynamic neural network that reads medical records, stores previous illness history, infers current illness states and predicts future medical outcomes. At the data level, DeepCare represents care episodes as vectors in space, models patient health state trajectories through explicit memory of historical records. Built on Long Short-Term Memory (LSTM), DeepCare introduces time parameterizations to handle irregular timed events by moderating the forgetting and consolidation of memory cells. DeepCare also incorporates medical interventions that change the course of illness and shape future medical risk. Moving up to 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, intervention recommendation, and future risk prediction. On two important cohorts with heavy social and economic burden -- diabetes and mental health -- the results show improved modeling and risk prediction accuracy.Comment: Accepted at JBI under the new name: "Predicting healthcare trajectories from medical records: A deep learning approach

Robust training of recurrent neural networks to handle missing data for disease progression modeling

Disease progression modeling (DPM) using longitudinal data is a challenging task in machine learning for healthcare that can provide clinicians with better tools for diagnosis and monitoring of disease. Existing DPM algorithms neglect temporal dependencies among measurements and make parametric assumptions about biomarker trajectories. In addition, they do not model multiple biomarkers jointly and need to align subjects' trajectories. In this paper, recurrent neural networks (RNNs) are utilized to address these issues. However, in many cases, longitudinal cohorts contain incomplete data, which hinders the application of standard RNNs and requires a pre-processing step such as imputation of the missing values. We, therefore, propose a generalized training rule for the most widely used RNN architecture, long short-term memory (LSTM) networks, that can handle missing values in both target and predictor variables. This algorithm is applied for modeling the progression of Alzheimer's disease (AD) using magnetic resonance imaging (MRI) biomarkers. The results show that the proposed LSTM algorithm achieves a lower mean absolute error for prediction of measurements across all considered MRI biomarkers compared to using standard LSTM networks with data imputation or using a regression-based DPM method. Moreover, applying linear discriminant analysis to the biomarkers' values predicted by the proposed algorithm results in a larger area under the receiver operating characteristic curve (AUC) for clinical diagnosis of AD compared to the same alternatives, and the AUC is comparable to state-of-the-art AUCs from a recent cross-sectional medical image classification challenge. This paper shows that built-in handling of missing values in LSTM network training paves the way for application of RNNs in disease progression modeling.Comment: 9 pages, 1 figure, MIDL conferenc