PEMS: Pre-trained Epidemic Time-series Models

Providing accurate and reliable predictions about the future of an epidemic is an important problem for enabling informed public health decisions. Recent works have shown that leveraging data-driven solutions that utilize advances in deep learning methods to learn from past data of an epidemic often outperform traditional mechanistic models. However, in many cases, the past data is sparse and may not sufficiently capture the underlying dynamics. While there exists a large amount of data from past epidemics, leveraging prior knowledge from time-series data of other diseases is a non-trivial challenge. Motivated by the success of pre-trained models in language and vision tasks, we tackle the problem of pre-training epidemic time-series models to learn from multiple datasets from different diseases and epidemics. We introduce Pre-trained Epidemic Time-Series Models (PEMS) that learn from diverse time-series datasets of a variety of diseases by formulating pre-training as a set of self-supervised learning (SSL) tasks. We tackle various important challenges specific to pre-training for epidemic time-series such as dealing with heterogeneous dynamics and efficiently capturing useful patterns from multiple epidemic datasets by carefully designing the SSL tasks to learn important priors about the epidemic dynamics that can be leveraged for fine-tuning to multiple downstream tasks. The resultant PEM outperforms previous state-of-the-art methods in various downstream time-series tasks across datasets of varying seasonal patterns, geography, and mechanism of contagion including the novel Covid-19 pandemic unseen in pre-trained data with better efficiency using smaller fraction of datasets.