Learning genetic perturbation effects with variational causal inference
Table 2
SCCVAE with a learned graph (SCCVAE) consistently achieves superior MSE and MMD values Both the conditional model and the pre-specified graph-based model (Causal-GSP) still outperform the GEARS baselines from Table 1, and the pre-specified graph-based model outperforms the conditional model, but both are more restrictive than SCCVAE with a learned graph. The models with random causal graphs achieve high error, as is expected, but outperform all other models on the fraction same/changed metrics. This is likely due to the shifts being tuned to extreme values during the training/shift selection process to account for the poor distributional match from the random graph.