Reconstructing Network Outbreaks under Group Surveillance

TL;DR

This paper addresses the complex problem of reconstructing disease outbreaks from pooled testing data on networks, introducing NP-hardness results and approximation algorithms that improve outbreak detection accuracy.

Contribution

It formulates the POOLCASCADEMLE problem for network outbreak reconstruction with pooled tests, proves its NP-hardness, and proposes approximation and LP-based methods for solutions.

Findings

Our algorithms outperform baselines in outbreak recovery.

The problem is NP-hard under the IC model.

Effective methods are developed for both full and one-hop cascade scenarios.

Abstract

A key public health problem during an outbreak is to reconstruct the disease cascade from a partial set of confirmed infections. This has been studied extensively under the Maximum Likelihood Estimation (MLE) formulation, which reduces the problem to finding some type of Steiner subgraph on a network. Group surveillance like wastewater or aerosol monitoring is a form of mass/pooled testing where samples from multiple individuals are pooled together and tested once for all. While a single negative test clears multiple individuals, a positive test does not reveal the infected individuals in the test pool. We introduce the POOLCASCADEMLE problem in the setting of a network propagation process, where the goal is to find a MLE cascade subgraph which is consistent with the pooled test outcomes. Previous work on reconstruction assumes that the test results are of individuals, i.e., pools of size one, and requires a consistent cascade to connect the positive testing nodes. In POOLCASCADEMLE, a consistent cascade must choose at least one node in each positive pool, adding another combinatorial layer. We show that, under the Independent Cascade (IC) model, POOLCASCADEMLE is NP-hard, and present an approximation algorithm based on a reduction to the Group Steiner Tree problem. We also consider a one-hop version of this problem, in which the disease can spread for one time step after being seeded. We show that even this restricted version is NP-hard, and develop a method using linear programming relaxation and rounding. We evaluate the performance of our methods on real and synthetic contact networks, in terms of missing infection recovery and prevalence estimation. We find that our approach outperforms meaningful baselines which correspond to pools of size one and use state-of-the-art methods.