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lutteropp / NetRAX

Phylogenetic Network Inference without ILS
GNU General Public License v3.0
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Idea for a fast, CLV-based network pseudolikelihood #60

Open lutteropp opened 3 years ago

lutteropp commented 3 years ago

CLV of a node ->Weighted average of CLVs from different cases. See picture. Unbenanntes Notizbuch (22)-5

lutteropp commented 3 years ago

I can implement that thing in an hour. It is super straight-forward.

lutteropp commented 3 years ago

I implemented it (took about 1.5 hours to code). Turns out it works pretty well! :-)

lutteropp commented 3 years ago

Here I printed the pseudologlikelihood and pseudo-BIC after each accepted move, to show how well this estimation performs: example-run.txt

Cool thing is that computing this pseudologlikelihood doesn't take much more than computing the loglikelihood of a single phylogenetic tree.

lutteropp commented 3 years ago

My idea is to use pseudologlikelihood during initial prefiltering phase, and then move the top 10% of prefiltered candidates to the normal candidate ranking which uses real loglikelihood for scoring (the scoring involves brlenopt).

stamatak commented 3 years ago

that sounds like a reasonable approach

On 30.04.21 14:29, Sarah Lutteropp wrote:

My idea is to use pseudologlikelihood during initial prefiltering phase, and then move the top 10% of prefiltered candidates to the normal candidate ranking which uses real loglikelihood for scoring (the scoring involves brlenopt).

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-- Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology

www.exelixis-lab.org