EpiVECS: exploring spatiotemporal epidemiological data using cluster embedding and interactive visualization

Lee Mason, Blánaid Hicks, Jonas S. Almeida

Research output: Contribution to journalArticlepeer-review


The analysis of data over space and time is a core part of descriptive epidemiology, but the complexity of spatiotemporal data makes this challenging. There is a need for methods that simplify the exploration of such data for tasks such as surveillance and hypothesis generation. In this paper, we use combined clustering and dimensionality reduction methods (hereafter referred to as ‘cluster embedding’ methods) to spatially visualize patterns in epidemiological time-series data. We compare several cluster embedding techniques to see which performs best along a variety of internal cluster validation metrics. We find that methods based on k-means clustering generally perform better than self-organizing maps on real world epidemiological data, with some minor exceptions. We also introduce EpiVECS, a tool which allows the user to perform cluster embedding and explore the results using interactive visualization. EpiVECS is available as a privacy preserving, in-browser open source web application at https://episphere.github.io/epivecs.

Original languageEnglish
Article number21193
Number of pages13
JournalScientific Reports
Publication statusPublished - 01 Dec 2023

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