SEPIA: simulation-based evaluation of prioritization algorithms

Published in BMC Medical Informatics and Decision Making, 2021

Recommended citation: Almaraz K, Jang T, Lewis M, Ngo T, Song M, Moshiri N (2021). "SEPIA: simulation-based evaluation of prioritization algorithms." BMC Medical Informatics and Decision Making. 21:177. doi:10.1186/s12911-021-01536-4


The ability to prioritize people living with HIV (PLWH) by risk of future transmissions could aid public health officials in optimizing epidemiological intervention. While methods exist to perform such prioritization based on molecular data, their effectiveness and accuracy are poorly understood, and it is unclear how one can directly compare the accuracy of different methods. We introduce SEPIA (Simulation-based Evaluation of PrIoritization Algorithms), a novel simulation-based framework for determining the effectiveness of prioritization algorithms. SEPIA expands upon prior related work by defining novel metrics of effectiveness with which to compare prioritization techniques, as well as by creating a simulation-based tool with which to perform such effectiveness comparisons. Under several metrics of effectiveness that we propose, we compare two existing prioritization approaches: one phylogenetic (ProACT) and one distance-based (growth of HIV-TRACE transmission clusters).


Using all proposed metrics, ProACT consistently slightly outperformed the transmission cluster growth approach. However, both methods consistently performed just marginally better than random, suggesting that there is significant room for improvement in prioritization tools.


We hope that, by providing ways to quantify the effectiveness of prioritization methods in simulation, SEPIA will aid researchers in developing novel risk prioritization tools for PLWH.