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Hey, there is several way to optimize the FloydWashall algorithm:
-maybe this one is a good option https://www.ijarse.com/images/fullpdf/1371224241_SHORTEST_PATH_USING_NEURAL_NETWORK.pdf
-this other repository seems to be good start, just need to optimize it for this specific case issue and win a x2 ratio.
https://github.com/mosco/floyd-warshall-cython
Unfortunately, I never had the time to test and implement those kind of option for now.
If you need fast result, I'm always run boost hic by centromeric arm on human dataset, for compartment result seems to be nice like this. It's depending of what you need.
If you want to run boost hic only once, I advise you an alpha close to 0.2 by default
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