search

PoonLab / Kaphi

Kernel-embedded ABC-SMC for phylodynamic inference
GNU Affero General Public License v3.0
4 stars 2 forks source link

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

Open ArtPoon opened 7 years ago

ArtPoon commented 7 years ago

Pending minimal repro case.

ArtPoon commented 6 years ago

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.

ArtPoon commented 6 years ago

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.

ArtPoon commented 6 years ago

Could be related to #134

ArtPoon commented 6 years ago

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.