BERT Language Model and Gene Sequences - How Do I Relate Clusters of Sequences?
The UMAP results look very pretty :)

If I were to try to make sense of this blob, I'd try to do the following.


Pull out Gene Ontology (GO) terms for a list of candidate genes (you can try to subset Uniprot / Swissprot for some examples). Then I feed through some genes through your fragmented BERT kmer approach to see where they land. I'd be particularly interested in seeing where transmembrane proteins and enzymes land here.
I'd try to color this by introns vs exons (you should be able to extract this sort of information from your genome files). There is a good chance that the difference between introns / exons could explain some of these differences.
It maybe worth looking into genes that only encode RNAs vs genes that encode proteins.