ARTree: A Deep Autoregressive Model for Phylogenetic Inference

Published: 21 Sept 2023, Last Modified: 02 Nov 2023NeurIPS 2023 spotlightEveryoneRevisionsBibTeX
Keywords: phylogenetic inference, autoregressive model, graph neural network, density estimation, variational inference
TL;DR: A novel deep autoregressive model for phylogenetic inference
Abstract: Designing flexible probabilistic models over tree topologies is important for developing efficient phylogenetic inference methods. To do that, previous works often leverage the similarity of tree topologies via hand-engineered heuristic features which would require domain expertise and may suffer from limited approximation capability. In this paper, we propose a deep autoregressive model for phylogenetic inference based on graph neural networks (GNNs), called ARTree. By decomposing a tree topology into a sequence of leaf node addition operations and modeling the involved conditional distributions based on learnable topological features via GNNs, ARTree can provide a rich family of distributions over tree topologies that have simple sampling algorithms, without using heuristic features. We demonstrate the effectiveness and efficiency of our method on a benchmark of challenging real data tree topology density estimation and variational Bayesian phylogenetic inference problems.
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Submission Number: 5910