Implementation in WebPPL

WebPPL is a probabilistic programming language for the web developed by Noah Goodman et al. that I used to prototyping the implementation of the QT model as a stable version of TreePPL was not available in 2022. This prototype can be cloned from https://github.com/vsenderov/qtbirds.webppl.

Simulation

Its main usefulness is simulating under Algorithm 1 (qtbirds-sim.wppl)—well tested—and Algorithm 2 (qtbirds-sim2.wppl)—not so well tested. You can simulate directly from the command like (see the comments at the top of the file for details):

 *   webppl qtbirds-sim.wppl --require fasta2json 
 *                           --require . 
 *                           --require webppl-fs
 *                           --require phyjs -- ...

Or, you can invoke it from Python.

Inference

WebPPL can also do sequential Monte-Carlo (SMC) and Markov Chain Monte-Carlo inference, but it is not very performant for our model. For this reason qtbirds-inf* are deprecated as of 2024-09-26.

Version

You should use version sp13.1.0 of qtbirds.webppl (see GitHub tags), as version 14 contains a wrong inference schema. Either way, you should not use qtbirds.webppl for inference.