If don’t think that the Autoencoder output will care about the structure of the data you can try to have an UMAP pass like in:

  
      

      Minimatech – 9 Feb 21
  

  
    

Autoencoder with Manifold Learning for Clustering in Python - Minimatech 5

  Using autoencoder and manifold learning to achieve better clustering in Python with Keras

  
    Est. reading time: 10 minutes