Statistical analysis of model performances (balanced accuracy) for different descriptors is given in Figure . One can see the model trained on HyFactor latent vectors demonstrated the worst results due to the atoms order dependence in the latent space. Other models showed similar performances, especially model trained on latent vectors of VQGAE showed the same performance as those trained on fragmentbased descriptors. The high performance of the model based on VQGAE latent vectors can be explained by good "local" neighbourhood behaviour as shown in the similarity search benchmark. Indeed, biological measurements are often made for analogues of a structure within the same scaffold; therefore, it can be assumed that local effects are more important than long-range effects in the current QSAR benchmark.