mlsanityData to 14 Oct 2026

PhyloGFN: Phylogenetic inference with generative flow networks

arXiv 2310.08774 ↗First posted 12 Oct 2023q-bio.PE cs.LG stat.MLcited by 22

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Abstract (arXiv)

Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains challenging: the high complexity of tree space poses a significant obstacle for the current combinatorial and probabilistic techniques. In this paper, we adopt the framework of generative flow networks (GFlowNets) to tackle two core problems in phylogenetics: parsimony-based and Bayesian phylogenetic inference. Because GFlowNets are well-suited for sampling complex combinatorial structures, they are a natural choice for exploring and sampling from the multimodal posterior distribution over tree topologies and evolutionary distances. We demonstrate that our amortized posterior sampler, PhyloGFN, produces diverse and high-quality evolutionary hypotheses on real benchmark datasets. PhyloGFN is competitive with prior works in marginal likelihood estimation and achieves a closer fit to the target distribution than state-of-the-art variational inference methods. Our code is available at https://github.com/zmy1116/phylogfn.

Key facts. Cited by 22 papers in the map (data through 14 Oct 2026). Builds on 18 of its 56 references that are in the map. First posted on arXiv 12 Oct 2023.

Builds on

18 of 56 references.

References · 18

  1. 2017Attention Is All You Needcited by 60,361
  2. 2015Importance Weighted Autoencoderscited by 456
  3. 2021Flow Network based Generative Models for Non-Iterative Diverse Candidate Generationcited by 392
  4. 2021GFlowNet Foundationscited by 290
  5. 2022Trajectory balance: Improved credit assignment in GFlowNetscited by 251
  6. 2022Biological Sequence Design with GFlowNetscited by 174
  7. 2022Bayesian Structure Learning with Generative Flow Networkscited by 153
  8. 2022Generative Flow Networks for Discrete Probabilistic Modelingcited by 114
  9. 2022GFlowNets and variational inferencecited by 106
  10. 2023A theory of continuous generative flow networkscited by 101
  11. 2023Robust Scheduling with GFlowNetscited by 69
  12. 2023Joint Bayesian Inference of Graphical Structure and Parameters with a Single Generative Flow Networkcited by 50
6 more
  1. 2023GFlowNet-EM for learning compositional latent variable modelscited by 40
  2. 2022A Variational Perspective on Generative Flow Networkscited by 39
  3. 2023Learnable Topological Features for Phylogenetic Inference via Graph Neural Networkscited by 14
  4. 2021Variational Combinatorial Sequential Monte Carlo Methods for Bayesian Phylogenetic Inferencecited by 11
  5. 2023GeoPhy: Differentiable Phylogenetic Inference via Geometric Gradients of Tree Topologiescited by 10
  6. 2022VaiPhy: a Variational Inference Based Algorithm for Phylogenycited by 9

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Cited by year (2026 to 14 Oct)

Citing papers per year: 2024: 9; 2025: 6; 2026: 7.

22 papers.

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  1. 2024Discrete Probabilistic Inference as Control in Multi-path Environmentscited by 44
  2. 2024Efficient Diversity-Preserving Diffusion Alignment via Gradient-Informed GFlowNetscited by 32
  3. 2024Generative Flows on Synthetic Pathway for Drug Designcited by 20
  4. 2024Can a Bayesian Oracle Prevent Harm from an Agent?cited by 13
  5. 2024On Divergence Measures for Training GFlowNetscited by 6
  6. 2025Adaptive Destruction Processes for Diffusion Samplerscited by 6
  7. 2024Streaming Bayes GFlowNetscited by 4
  8. 2025FlowQ-Net: A Generative Framework for Automated Quantum Circuit Designcited by 4
  9. 2026Avoid What You Know: Divergent Trajectory Balance for GFlowNetscited by 4
  10. 2024Efficient Mixture Learning in Black-Box Variational Inferencecited by 3
  11. 2024PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generationcited by 2
  12. 2025Learning Decision Trees as Amortized Structure Inferencecited by 2
10 more
  1. 2025A Generative Neural Annealer for Black-Box Combinatorial Optimizationcited by 2
  2. 2025Discrete Compositional Generation via General Soft Operators and Robust Reinforcement Learningcited by 2
  3. 2024Variational Bayesian Phylogenetic Inference with Semi-implicit Branch Length Distributionscited by 1
  4. 2025Variational phylogenetic inference with products over bipartitionscited by 0
  5. 2026Controlling Exploration-Exploitation in GFlowNets via Markov Chain Perspectivescited by 0
  6. 2026Path-dependent Discrete Amortized Inferencecited by 0
  7. 2026Bayesian Symbolic Regression with Entropic Reinforcement Learningcited by 0
  8. 2026Particle GFlowNets: Rethinking Generative Marginalization Modelscited by 0
  9. 2026Deep Generative Models for Phylogenetic Inference with Complex Evolutionary Processescited by 0
  10. 2026MIPS: Mitigating Mode Collapse in Reinforcement Learning for Large Outcome Spacescited by 0