Fig. 1

Sample data layout for standard and reference-aided prediction. Each cell in this matrix corresponds to a sample x _i of a subject s _i taken at some time during the viral challenge study. The corresponding infection state label y _i for each target sample x _i is shown in Fig. 2.C for the particular case of the H3N2 challenge study. The standard predictor tries to predict the state using only the target sample. The reference-aided predictor uses both the target sample and the reference sample taken prior to inoculation time, denoted by the white vertical line