mlsanityData to 14 Oct 2026

Learnable Topological Features for Phylogenetic Inference via Graph Neural Networks

arXiv 2302.08840 ↗First posted 17 Feb 2023stat.ML cs.LG q-bio.PEcited by 14

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Abstract (arXiv)

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.

Key facts. Cited by 14 papers in the map (data through 14 Oct 2026). Builds on 16 of its 51 references that are in the map. First posted on arXiv 17 Feb 2023.

Builds on

16 of 51 references.

References · 16

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4 more
  1. 2021On the Unreasonable Effectiveness of Feature propagation in Learning on Graphs with Missing Node Featurescited by 63
  2. 2020Improved Variational Bayesian Phylogenetic Inference with Normalizing Flowscited by 17
  3. 2022A Variational Approach to Bayesian Phylogenetic Inferencecited by 9
  4. 2017Phylogenetic Convolutional Neural Networks in Metagenomicscited by 2

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Cited by year (2026 to 14 Oct)

Citing papers per year: 2023: 5; 2024: 4; 2025: 3; 2026: 2.

14 papers.

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  1. 2023PhyloGFN: Phylogenetic inference with generative flow networkscited by 22
  2. 2023GeoPhy: Differentiable Phylogenetic Inference via Geometric Gradients of Tree Topologiescited by 10
  3. 2023ARTree: A Deep Autoregressive Model for Phylogenetic Inferencecited by 5
  4. 2023Improved Variational Bayesian Phylogenetic Inference using Mixturescited by 4
  5. 2024Efficient Mixture Learning in Black-Box Variational Inferencecited by 3
  6. 2025Variational Combinatorial Sequential Monte Carlo for Bayesian Phylogenetics in Hyperbolic Spacecited by 3
  7. 2025Incomplete Graph Learning: A Comprehensive Surveycited by 3
  8. 2024PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generationcited by 2
  9. 2024Variational Bayesian Phylogenetic Inference with Semi-implicit Branch Length Distributionscited by 1
  10. 2023The tree reconstruction game: phylogenetic reconstruction using reinforcement learningcited by 0
  11. 2024Solving the Tree Containment Problem Using Graph Neural Networkscited by 0
  12. 2025Variational phylogenetic inference with products over bipartitionscited by 0
2 more
  1. 2026FSD-CAP: Fractional Subgraph Diffusion with Class-Aware Propagation for Graph Feature Imputationcited by 0
  2. 2026Deep Generative Models for Phylogenetic Inference with Complex Evolutionary Processescited by 0