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.

Phylogenetic trees elucidate evolutionary relationships among species, but phylogenetic inference remains challenging due to the complexity of combining continuous (branch lengths) and discrete parameters (tree topology).

Our implementation is found at https://github.com/m1m0r1/geophy

Designing flexible probabilistic models over tree topologies is important for developing efficient phylogenetic inference methods.

Computational phylogenetics has become an established tool in historical linguistics, with many language families now analyzed using likelihood-based inference. However, standard approaches rely on expert-annotated cognate sets, which are sparse, labor-intensive to produce, and limited to individual language families. This paper explores alternatives by comparing the established method to two fully automated methods that extract phylogenetic signal directly from lexical data. One uses automatic cognate clustering with unigram/concept features; the other applies multiple sequence alignment (MSA) derived from a pair-hidden Markov model. Both are evaluated against expert classifications from Glottolog and typological data from Grambank. Also, the intrinsic strengths of the phylogenetic signal in the characters are compared. Results show that MSA-based inference yields trees more consistent with linguistic classifications, better predicts typological variation, and provides a clearer phylogenetic signal, suggesting it as a promising, scalable alternative to traditional cognate-based methods. This opens new avenues for global-scale language phylogenies beyond expert annotation bottlenecks.