Learnable Topological Features for Phylogenetic Inference via Graph Neural Networks

Structural information of phylogenetic tree topologies plays an important role in phylogenetic inference. However, finding appropriate topological structures for specific phylogenetic inference tasks often requires significant design effort and domain expertise. In this paper, we propose a novel structural representation method for phylogenetic inference based on learnable topological features. By combining the raw node features that minimize the Dirichlet energy with modern graph representation learning techniques, our learnable topological features can provide efficient structural information of phylogenetic trees that automatically adapts to different downstream tasks without requiring domain expertise. We demonstrate the effectiveness and efficiency of our method on a simulated data tree probability estimation task and a benchmark of challenging real data variational Bayesian phylogenetic inference problems. Phylogenetics is an important discipline of computational biology where the goal is to identify the evolutionary history and relationships among individuals or groups of biological entities. In statistical approaches to phylogenetics, this has been formulated as an inference problem on hypotheses of shared history, i.e., phylogenetic trees, based on observed sequence data (e.g., DNA, RNA, or protein sequences) under a model of evolution.