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Investigate replacing `Set` with François Pottier's sets from the `baby` library
It supposedly offers several performance advantages over the normal Set.
https://discuss.ocaml.org/t/ann-first-release-of-baby/14840
More broadly, it might be worth experimenting with alternatives to various data structures like Maps (although the baby library doesn't yet have them) or Hashtbls.
This includes both libraries that may already be in the OCaml ecosystem or something else. I recall an Astree paper claiming how a choice of data structure was crucial for their performance.