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Speed up ranking of candidates #53

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lutteropp opened this issue Apr 5, 2021 · 2 comments
Open

Speed up ranking of candidates #53

lutteropp opened this issue Apr 5, 2021 · 2 comments

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@lutteropp
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lutteropp commented Apr 5, 2021

Nearly all of the runtime (> 90%) now gets spent in ranking move candidates. This is because we currently rank move candidates based on the BIC score we get after performing the move and optimizing the 1-neighborhood of the branches affected by the move. This can be seen in this call graph:
callgraph

We are only interested in the best-ranking move candidate, as this is the one we will apply.

This focuses all optimization efforts on the candidate ranking. Ideas:

  • Filter the candidates to rank by doing a fast pre-ranking before the actual ranking (-> optimize even less branches? use some pseudo-likelihood function?).
  • Parallelize the ranking of move candidates.
@lutteropp
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lutteropp commented Apr 5, 2021

There is also still this open idea to speed up brlen optimization even more:
#43 (comment)

@lutteropp
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For pre-filtering arc insertion moves, there still is the ancestral-states-idea from #41

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