Mean squared error (MSE) and earthmoving distance for VAE’s ability to reconstruct Cell Painting and L1000 profiles.

We compare these values with results derived from shuffled models. Earthmoving distance is calculated by taking the mean of the earthmoving distance of each sample. We add the 95% percentile range of earthmoving distance in parenthesis (0.05 lowest, 0.95 highest). Note that since our models required that we normalize Cell Painting and L1000 input data differently (see Methods), the metrics cannot be compared across data modalities.