lutteropp / NetRAX

Phylogenetic Network Inference without ILS
GNU General Public License v3.0
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Speed up ranking of candidates #53

Open lutteropp opened 3 years ago

lutteropp commented 3 years ago

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:

lutteropp commented 3 years ago

There is also still this open idea to speed up brlen optimization even more: https://github.com/lutteropp/NetRAX/issues/43#issuecomment-798883538

lutteropp commented 3 years ago

For pre-filtering arc insertion moves, there still is the ancestral-states-idea from https://github.com/lutteropp/NetRAX/issues/41