Idea for a fast, CLV-based network pseudolikelihood

Question

Idea for a fast, CLV-based network pseudolikelihood

Opened this issue 4 years ago · 5 comments

lutteropp commented 4 years ago

CLV of a node ->Weighted average of CLVs from different cases. See picture.

Answer 1 · 2021-04-29T19:34:37.000Z

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

Answer 2 · 2021-04-30T01:33:34.000Z

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

Answer 3 · 2021-04-30T11:24:13.000Z

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.

Answer 4 · 2021-04-30T11:28:53.000Z

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).

Answer 5 · 2021-04-30T11:32:48.000Z

that sounds like a reasonable approach

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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). — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#60 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAGXB6XGFDCZ34MQVB5ZHYLTLKIAPANCNFSM432RQ5ZA>.

-- Alexandros (Alexis) Stamatakis Research Group Leader, Heidelberg Institute for Theoretical Studies Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology www.exelixis-lab.org