CRISP: A Probabilistic Model for Individual-Level COVID-19 Infection Risk Estimation Based on Contact Data

TL;DR

CRISP is a probabilistic graphical model that uses individual contact data and test outcomes to accurately estimate COVID-19 infection risks at the micro-level, enabling targeted mitigation strategies.

Contribution

This paper introduces the first efficient inference model for COVID-19 spread based on individual contact data, extending traditional macro-level epidemic models.

Findings

CRISP can be parametrized by R0 and mimics classical SEIR population dynamics.

The model supports fine-grained control and inference for mitigation policies.

Efficient block-Gibbs sampling enables practical testing and contact tracing.

Abstract

We present CRISP (COVID-19 Risk Score Prediction), a probabilistic graphical model for COVID-19 infection spread through a population based on the SEIR model where we assume access to (1) mutual contacts between pairs of individuals across time across various channels (e.g., Bluetooth contact traces), as well as (2) test outcomes at given times for infection, exposure and immunity tests. Our micro-level model keeps track of the infection state for each individual at every point in time, ranging from susceptible, exposed, infectious to recovered. We develop both a Monte Carlo EM as well as a message passing algorithm to infer contact-channel specific infection transmission probabilities. Our Monte Carlo algorithm uses Gibbs sampling to draw samples of the latent infection status of each individual over the entire time period of analysis, given the latent infection status of all contacts and test outcome data. Experimental results with simulated data demonstrate our CRISP model can be parametrized by the reproduction factor $R_0$ and exhibits population-level infectiousness and recovery time series similar to those of the classical SEIR model. However, due to the individual contact data, this model allows fine grained control and inference for a wide range of COVID-19 mitigation and suppression policy measures. Moreover, the block-Gibbs sampling algorithm is able to support efficient testing in a test-trace-isolate approach to contain COVID-19 infection spread. To the best of our knowledge, this is the first model with efficient inference for COVID-19 infection spread based on individual-level contact data; most epidemic models are macro-level models that reason over entire populations. The implementation of CRISP is available in Python and C++ at https://github.com/zalandoresearch/CRISP.