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The most effective method currently seems to be to enumerate the different permutations at each level and calculate the total number of line intersections after different permutations to find the situation with the least number of intersections.
https://codesandbox.io/s/pedantic-rui-jr492w?file=/nodes-edges.js
In this example here, see how node F->I crosses C->J, even though it looks like it can be avoided if J and I were swapped
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