Data Pre-Processing Using Neural Processes for Modeling Personalized Vital-Sign Time-Series Data

Pulkit Sharma, Farah E. Shamout, Vinayak Abrol, David A. Clifton

Research output: Contribution to journalArticlepeer-review


Clinical time-series data retrieved from electronic medical records are widely used to build predictive models of adverse events to support resource management. Such data is often sparse and irregularly-sampled, which makes it challenging to use many common machine learning methods. Missing values may be interpolated by carrying the last value forward, or through linear regression. Gaussian process (GP) regression is also used for performing imputation, and often re-sampling of time-series at regular intervals. The use of GPs can require extensive, and likely adhoc, investigation to determine model structure, such as an appropriate covariance function. This can be challenging for multivariate real-world clinical data, in which time-series variables exhibit different dynamics to one another. In this work, we construct generative models to estimate missing values in clinical time-series data using a neural latent variable model, known as a Neural Process (NP). The NP model employs a conditional prior distribution in the latent space to learn global uncertainty in the data by modelling variations at a local level. In contrast to conventional generative modelling, this prior is not fixed and is itself learned during the training process. Thus, NP model provides the flexibility to adapt to the dynamics of the available clinical data. We propose a variant of the NP framework for efficient modelling of the mutual information between the latent and input spaces, ensuring meaningful learned priors. Experiments using the MIMIC III dataset demonstrate the effectiveness of the proposed approach as compared to conventional methods.

Original languageEnglish (US)
Pages (from-to)1528-1537
Number of pages10
JournalIEEE Journal of Biomedical and Health Informatics
Issue number4
StatePublished - Apr 1 2022


  • Gaussian processes
  • Neural processes
  • data interpolation
  • deep learning
  • medical data

ASJC Scopus subject areas

  • Health Information Management
  • Health Informatics
  • Electrical and Electronic Engineering
  • Computer Science Applications


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