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During an epidemic, it can be difficult to get an estimate of the actual number of people infected at any given time. This is due to multiple reasons, including some cases being asymptomatic and sick people not seeking healthcare for mild symptoms, among others. Large scale random sampling of the population for testing can be expensive, especially in the early stages of an epidemic, when tests are scarce. Here we show how an adaptive prevalence testing method can be developed to obtain a good estimate of the disease burden by learning to intelligently allocate a small number of tests for random testing of the population. Our approach uses a combination of an agent-based simulation and deep learning in an active sensing paradigm. We show that it is possible to get a good state estimate with relatively minimal prevalence testing, and that the trained system adapts quickly and performs well even if the disease parameters change.