String-Based Molecule Generation Via Multi-Decoder VAE

Abstract

In this study, we investigate the problem of string-based molecular generation via variational autoencoders (VAEs) that have served a popular generative approach for various tasks in artificial intelligence. Our main idea is to maintain multiple decoders while sharing a single encoder, i.e., it is a type of ensemble techniques. Here, we first found that training each decoder independently may not be effective as the bias of the ensemble decoder increases severely under its auto-regressive inference. To alleviate this issue, our proposed technique is two-fold: (a) a different latent variable is sampled for each decoder (from estimated mean and variance offered by the shared encoder) to encourage diverse characteristics of decoders and (b) a collaborative loss is used during training to control the aggregated quality of decoders using different latent variables. In our experiments, the proposed VAE model particularly performs well for generating a sample from out-of-domain distribution.