ARTree: A Deep Autoregressive Model for Phylogenetic Inference

Tianyu Xie, Cheng Zhang

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.

Submission Number: 5910