Synthetic Health-related Longitudinal Data with Mixed-type Variables Generated using Diffusion Models

This paper presents a novel approach to simulating electronic health records (EHRs) using diffusion probabilistic models (DPMs). Specifically, we demonstrate the effectiveness of DPMs in synthesising longitudinal EHRs that capture mixed-type variables, including numeric, binary, and categorical variables. To our knowledge, this represents the first use of DPMs for this purpose. We compared our DPM-simulated datasets to previous state-of-the-art results based on generative adversarial networks (GANs) for two clinical applications: acute hypotension and human immunodeficiency virus (ART for HIV). Given the lack of similar previous studies in DPMs, a core component of our work involves exploring the advantages and caveats of employing DPMs across a wide range of aspects. In addition to assessing the realism of the synthetic datasets, we also trained reinforcement learning (RL) agents on the synthetic data to evaluate their utility for supporting the development of downstream machine learning models. Finally, we estimated that our DPM-simulated datasets are secure and posed a low patient exposure risk for public access.

Generating Synthetic Clinical Data that Capture Class Imbalanced Distributions with Generative Adversarial Networks: Example using Antiretroviral Therapy for HIV

Clinical data usually cannot be freely distributed due to their highly confidential nature and this hampers the development of machine learning in the healthcare domain. One way to mitigate this problem is by generating realistic synthetic datasets using generative adversarial networks (GANs). However, GANs are known to suffer from mode collapse and thus creating outputs of low diveristy. In this paper, we extend the classic GAN setup with an external memory to replay features from real samples. Using antiretroviral therapy for human immunodeficiency virus (ART for HIV) as a case study, we show that our extended setup increases convergence and more importantly, it is effective in capturing the severe class imbalanced distributions common to real world clinical data.

The Health Gym: Synthetic Health-Related Datasets for the Development of Reinforcement Learning Algorithms

In recent years, the machine learning research community has benefited tremendously from the availability of openly accessible benchmark datasets. Clinical data are usually not openly available due to their highly confidential nature. This has hampered the development of reproducible and generalisable machine learning applications in health care. Here we introduce the Health Gym - a growing collection of highly realistic synthetic medical datasets that can be freely accessed to prototype, evaluate, and compare machine learning algorithms, with a specific focus on reinforcement learning. The three synthetic datasets described in this paper present patient cohorts with acute hypotension and sepsis in the intensive care unit, and people with human immunodeficiency virus (HIV) receiving antiretroviral therapy in ambulatory care. The datasets were created using a novel generative adversarial network (GAN). The distributions of variables, and correlations between variables and trends over time in the synthetic datasets mirror those in the real datasets. Furthermore, the risk of sensitive information disclosure associated with the public distribution of the synthetic datasets is estimated to be very low.

Synthetic Acute Hypotension and Sepsis Datasets Based on MIMIC-III and Published as Part of the Health Gym Project

These two synthetic datasets comprise vital signs, laboratory test results, administered fluid boluses and vasopressors for 3,910 patients with acute hypotension and for 2,164 patients with sepsis in the Intensive Care Unit (ICU). The patient cohorts were built using previously published inclusion and exclusion criteria and the data were created using Generative Adversarial Networks (GANs) and the MIMIC-III Clinical Database. The risk of identity disclosure associated with the release of these data was estimated to be very low (0.045%). The datasets were generated and published as part of the Health Gym, a project aiming to publicly distribute synthetic longitudinal health data for developing machine learning algorithms (with a particular focus on offline reinforcement learning) and for educational purposes.

Learning to Continually Learn Rapidly from Few and Noisy Data

Neural networks suffer from catastrophic forgetting and are unable to sequentially learn new tasks without guaranteed stationarity in data distribution. Continual learning could be achieved via replay -- by concurrently training externally stored old data while learning a new task. However, replay becomes less effective when each past task is allocated with less memory. To overcome this difficulty, we supplemented replay mechanics with meta-learning for rapid knowledge acquisition. By employing a meta-learner, which \textit{learns a learning rate per parameter per past task}, we found that base learners produced strong results when less memory was available. Additionally, our approach inherited several meta-learning advantages for continual learning: it demonstrated strong robustness to continually learn under the presence of noises and yielded base learners to higher accuracy in less updates.

MTL2L: A Context Aware Neural Optimiser

Learning to learn (L2L) trains a meta-learner to assist the learning of a task-specific base learner. Previously, it was shown that a meta-learner could learn the direct rules to update learner parameters; and that the learnt neural optimiser updated learners more rapidly than handcrafted gradient-descent methods. However, we demonstrate that previous neural optimisers were limited to update learners on one designated dataset. In order to address input-domain heterogeneity, we introduce Multi-Task Learning to Learn (MTL2L), a context aware neural optimiser which self-modifies its optimisation rules based on input data. We show that MTL2L is capable of updating learners to classify on data of an unseen input-domain at the meta-testing phase.