Abstract
We present a variational autoencoder framework for learning and generating configurations of structured polymer globules from distance matrices. We used coarse-grained molecular dynamics to sample polyethylene structures, which we used as the training set for our deep learning model. By combining convolution and attention layers, the model encodes the structural patterns of distance matrices into an organized and roto-translationally invariant latent space of lower dimensionality. The generative capability of the variational autoencoder, coupled with a post-processing pipeline based on multidimensional scaling and short molecular dynamics, enables the recovery of physically meaningful configurations. The reconstructed and generated samples reproduce key observables, including energy, size, and entanglement, despite minor discrepancies in the raw decoder output.