PhyloGFN: Phylogenetic inference with generative flow networks

• URL: http://arxiv.org/abs/2310.08774v2
• Date: Mon, 25 Mar 2024 00:18:35 GMT
• Title: PhyloGFN: Phylogenetic inference with generative flow networks
• Authors: Mingyang Zhou, Zichao Yan, Elliot Layne, Nikolay Malkin, Dinghuai Zhang, Moksh Jain, Mathieu Blanchette, Yoshua Bengio,
• Abstract summary: We introduce the framework of generative flow networks (GFlowNets) to tackle two core problems in phylogenetics: parsimony-based and phylogenetic inference. Because GFlowNets are well-suited for sampling complex structures, they are a natural choice for exploring and sampling from the multimodal posterior distribution over tree topologies. We demonstrate that our amortized posterior sampler, PhyloGFN, produces diverse and high-quality evolutionary hypotheses on real benchmark datasets.
• Score: 57.104166650526416
• License: http://creativecommons.org/licenses/by/4.0/
• Abstract: Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains challenging: the high complexity of tree space poses a significant obstacle for the current combinatorial and probabilistic techniques. In this paper, we adopt the framework of generative flow networks (GFlowNets) to tackle two core problems in phylogenetics: parsimony-based and Bayesian phylogenetic inference. Because GFlowNets are well-suited for sampling complex combinatorial structures, they are a natural choice for exploring and sampling from the multimodal posterior distribution over tree topologies and evolutionary distances. We demonstrate that our amortized posterior sampler, PhyloGFN, produces diverse and high-quality evolutionary hypotheses on real benchmark datasets. PhyloGFN is competitive with prior works in marginal likelihood estimation and achieves a closer fit to the target distribution than state-of-the-art variational inference methods. Our code is available at https://github.com/zmy1116/phylogfn.

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