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Kernel may not be positive semi-definite for labelled subtrees #104

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ArtPoon opened this issue Sep 8, 2017 · 4 comments
Open

Kernel may not be positive semi-definite for labelled subtrees #104

ArtPoon opened this issue Sep 8, 2017 · 4 comments
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@ArtPoon
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ArtPoon commented Sep 8, 2017

Pending minimal repro case.

@ArtPoon ArtPoon added this to the Near future milestone Sep 8, 2017
@ArtPoon ArtPoon added the bug label Sep 11, 2017
@ArtPoon ArtPoon self-assigned this Sep 11, 2017
@ArtPoon ArtPoon modified the milestones: Near future, version 0.2 Sep 25, 2017
@ArtPoon ArtPoon modified the milestones: version 0.2, Near future Nov 20, 2017
@ArtPoon ArtPoon modified the milestones: Near future, version 0.3 Jan 29, 2018
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ArtPoon commented Jan 29, 2018

When matching subtrees, we currently ladderize the trees so that branching skews to the same side, and rotate cherries so that branch lengths are the most concordant (but do we still do this?).

When comparing subtrees with labels, it is no longer clear how to handle the case where branches are discordant with respect to BOTH lengths and labels.

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ArtPoon commented Jan 29, 2018

A consequence of this is that the diagonal entries --- k(t1,t1) --- are not 1 when we normalize all entries by sqrt(k(t1,t1) * k(t2,t2)), where t2 = t1.
Again, I haven't gotten around to building a minimal repro case for this issue yet.

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ArtPoon commented Feb 26, 2018

Could be related to #134

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ArtPoon commented Mar 19, 2018

This should be addressed in our present refactoring of the kernel, where labels are evaluated as productions at internal nodes instead of at the tips.

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