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Register a new userFederated and Differentially Private Learning for Electronic Health Records
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The use of collaborative and decentralized machine learning techniques such as federated learning have the potential to enable the development and deployment of clinical risk predictions models in low-resource settings without requiring sensitive data be shared or stored in a central repository. This process necessitates communication of model weights or updates between collaborating entities, but it is unclear to what extent patient privacy is compromised as a result. To gain insight into this question, we study the efficacy of centralized versus federated learning in both private and non-private settings. The clinical prediction tasks we consider are the prediction of prolonged length of stay and in-hospital mortality across thirty one hospitals in the eICU Collaborative Research Database. We find that while it is straightforward to apply differentially private stochastic gradient descent to achieve strong privacy bounds when training in a centralized setting, it is considerably more difficult to do so in the federated setting.
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Federated learning aims to protect data privacy by collaboratively learning a model without sharing private data among users. However, an adversary may still be able to infer the private training data by attacking the released model. Differential privacy provides a statistical protection against such attacks at the price of significantly degrading the accuracy or utility of the trained models. In this paper, we investigate a utility enhancement scheme based on Laplacian smoothing for differentially private federated learning (DP-Fed-LS), where the parameter aggregation with injected Gaussian noise is improved in statistical precision without losing privacy budget. Our key observation is that the aggregated gradients in federated learning often enjoy a type of smoothness, i.e. sparsity in the graph Fourier basis with polynomial decays of Fourier coefficients as frequency grows, which can be exploited by the Laplacian smoothing efficiently. Under a prescribed differential privacy budget, convergence error bounds with tight rates are provided for DP-Fed-LS with uniform subsampling of heterogeneous Non-IID data, revealing possible utility improvement of Laplacian smoothing in effective dimensionality and variance reduction, among others. Experiments over MNIST, SVHN, and Shakespeare datasets show that the proposed method can improve model accuracy with DP-guarantee and membership privacy under both uniform and Poisson subsampling mechanisms.
Today, despite decades of developments in medicine and the growing interest in precision healthcare, vast majority of diagnoses happen once patients begin to show noticeable signs of illness. Early indication and detection of diseases, however, can provide patients and carers with the chance of early intervention, better disease management, and efficient allocation of healthcare resources. The latest developments in machine learning (more specifically, deep learning) provides a great opportunity to address this unmet need. In this study, we introduce BEHRT: A deep neural sequence transduction model for EHR (electronic health records), capable of multitask prediction and disease trajectory mapping. When trained and evaluated on the data from nearly 1.6 million individuals, BEHRT shows a striking absolute improvement of 8.0-10.8%, in terms of Average Precision Score, compared to the existing state-of-the-art deep EHR models (in terms of average precision, when predicting for the onset of 301 conditions). In addition to its superior prediction power, BEHRT provides a personalised view of disease trajectories through its attention mechanism; its flexible architecture enables it to incorporate multiple heterogeneous concepts (e.g., diagnosis, medication, measurements, and more) to improve the accuracy of its predictions; and its (pre-)training results in disease and patient representations that can help us get a step closer to interpretable predictions.
Increasing volume of Electronic Health Records (EHR) in recent years provides great opportunities for data scientists to collaborate on different aspects of healthcare research by applying advanced analytics to these EHR clinical data. A key requirement however is obtaining meaningful insights from high dimensional, sparse and complex clinical data. Data science approaches typically address this challenge by performing feature learning in order to build more reliable and informative feature representations from clinical data followed by supervised learning. In this paper, we propose a predictive modeling approach based on deep learning based feature representations and word embedding techniques. Our method uses different deep architectures (stacked sparse autoencoders, deep belief network, adversarial autoencoders and variational autoencoders) for feature representation in higher-level abstraction to obtain effective and robust features from EHRs, and then build prediction models on top of them. Our approach is particularly useful when the unlabeled data is abundant whereas labeled data is scarce. We investigate the performance of representation learning through a supervised learning approach. Our focus is to present a comparative study to evaluate the performance of different deep architectures through supervised learning and provide insights in the choice of deep feature representation techniques. Our experiments demonstrate that for small data sets, stacked sparse autoencoder demonstrates a superior generality performance in prediction due to sparsity regularization whereas variational autoencoders outperform the competing approaches for large data sets due to its capability of learning the representation distribution.
An estimated 180 papers focusing on deep learning and EHR were published between 2010 and 2018. Despite the common workflow structure appearing in these publications, no trusted and verified software framework exists, forcing researchers to arduously repeat previous work. In this paper, we propose Cardea, an extensible open-source automated machine learning framework encapsulating common prediction problems in the health domain and allows users to build predictive models with their own data. This system relies on two components: Fast Healthcare Interoperability Resources (FHIR) -- a standardized data structure for electronic health systems -- and several AUTOML frameworks for automated feature engineering, model selection, and tuning. We augment these components with an adaptive data assembler and comprehensive data- and model- auditing capabilities. We demonstrate our framework via 5 prediction tasks on MIMIC-III and Kaggle datasets, which highlight Cardeas human competitiveness, flexibility in problem definition, extensive feature generation capability, adaptable automatic data assembler, and its usability.
While rich medical datasets are hosted in hospitals distributed across the world, concerns on patients privacy is a barrier against using such data to train deep neural networks (DNNs) for medical diagnostics. We propose Dopamine, a system to train DNNs on distributed datasets, which employs federated learning (FL) with differentially-private stochastic gradient descent (DPSGD), and, in combination with secure aggregation, can establish a better trade-off between differential privacy (DP) guarantee and DNNs accuracy than other approaches. Results on a diabetic retinopathy~(DR) task show that Dopamine provides a DP guarantee close to the centralized training counterpart, while achieving a better classification accuracy than FL with parallel DP where DPSGD is applied without coordination. Code is available at https://github.com/ipc-lab/private-ml-for-health.
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