(a) NMI scores of each donor between the MuDCoD inferred modules on day-30 and on day-52 against the differentiation efficiency. For each cell type (DA, Sert, Epen1), each donor’s modules from day-30 and day-52 were compared with NMI and plotted against donor’s differentiation efficiency. (b) Comparison of the mean NMI scores within and between the low and high differentiation efficiency groups of Epen1 cells. Donor labels for differentiation efficiency were obtained from HipSci Consortium et al. (2021). NMI scores between pairs of donors are calculated based on their MuDCoD inferred modules. Differentiation efficiency groups were generated based on the percentiles of differentiation efficiency values across the donors, i.e. 50-th percentile (inclusive) corresponds to the low differentiation efficiency group.