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mattapow / dodonaphy

hyperbolic embeddings for variational approximation of phylogenetic posteriors
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Exact embedding #22

Closed mattapow closed 2 years ago

mattapow commented 2 years ago

Exactly embed initial trees, rather than using hydra's approximation.

A. Cvetkovski and M. Crovella, "Hyperbolic Embedding and Routing for Dynamic Graphs," IEEE INFOCOM 2009, 2009, pp. 1647-1655, doi: 10.1109/INFCOM.2009.5062083.

Sarkar, Rik. "Low distortion delaunay embedding of trees in hyperbolic plane." International Symposium on Graph Drawing. Springer, Berlin, Heidelberg, 2011.

mattapow commented 2 years ago

Cvetjovski gives exact tree embeddings in 2D Poincaré, but the geodesic distance between taxa doesn't correspond to the tree distance. Here's their example.

Screen Shot 2022-01-17 at 4 55 26 pm
mattapow commented 2 years ago

Tip-tip distances are not preserved in the embedding process with these techniques.