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PoonLab / Kaphi

Kernel-embedded ABC-SMC for phylodynamic inference
GNU Affero General Public License v3.0
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Align distance metric cannot be zero for both subsets #111

Closed gtng92 closed 6 years ago

gtng92 commented 6 years ago

Question about the Align metric algorithm: In Nye et al the algorithm picks any pair of edges, but the edge from tree 1 and the edge from tree 2 must have the same subset of of leaf tips.

If I'm comparing two large trees, won't I only be able to compare the trees by using the root as the edge for both trees? Otherwise the edge I pick from tree 1 might not have the same leaf tips as the edge chosen from tree 2. And then there may be zeros in the subsets, giving a distance metric of 0.

ArtPoon commented 6 years ago

When partitioning the tree labels into two subsets, it should not be possible for both checks to be zero -- in other words, if the left partition of tree 1 contains no labels in common with a partition in tree 2, then the right partition of tree 1 should have some overlap.