Automated development of latent representations for optimization of sequences using autoencoders

In this paper, we propose an automated method for the development of new representations of sequences. For this purpose, we introduce a two-way mapping from variable length sequence representations to a latent representation modelled as the bottleneck of an LSTM (long short-term memory) autoencoder. Desirable properties of such mappings include smooth fitness landscapes for optimization problems and better evolvability. This work explores the capabilities of such latent encodings in the context of optimization of 3D structures. Various improvements are adopted that include manipulating the autoencoder architecture and its training procedure. The results of evolutionary algorithms that use different variants of automatically developed encodings are compared.