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Preprints, Working Papers, ... Year : 2020

Probabilistic programming: a powerful new approach to statistical phylogenetics

Fredrik Ronquist
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Jan Kudlicka
Viktor Senderov
Johannes Borgström
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Daniel Lundén
Lawrence Murray
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Thomas B Schön
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David Broman
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Abstract

Statistical phylogenetic analysis currently relies on complex, dedicated software packages, making it difficult for evolutionary biologists to explore new models and inference strategies. Recent years have seen more generic solutions based on probabilistic graphical models, but this formalism can only partly express phylogenetic problems. Here we show that universal probabilistic programming languages (PPLs) solve the modeling language expressivity problem, while still supporting automated generation of efficient inference algorithms. To prove the latter point, we develop automated generation of sequential Monte Carlo (SMC) algorithms for PPL descriptions of arbitrary biological diversification (birth-death) models. SMC is a new inference strategy for these problems, supporting both parameter inference and efficient Bayesian model testing. We then automatically generate SMC algorithms for several recent diversification models that have been difficult or impossible to tackle previously. Finally, applying these algorithms to 40 bird phylogenies, we show that models with slowing diversification, constant turnover and many small shifts generally explain the data best. Our work opens up several related problem domains to PPL approaches, and shows that few hurdles remain before these techniques can be effectively applied to the full range of phylogenetic models.
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hal-03033672 , version 1 (01-12-2020)

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Fredrik Ronquist, Jan Kudlicka, Viktor Senderov, Johannes Borgström, Nicolas Lartillot, et al.. Probabilistic programming: a powerful new approach to statistical phylogenetics. 2020. ⟨hal-03033672⟩
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