Phylogenetic Inference

Phylogenetic inference aims to reconstruct evolutionary relationships between entities, such as species or languages, by analyzing shared characteristics. Current research heavily emphasizes developing improved probabilistic models, particularly leveraging deep learning architectures like graph neural networks and normalizing flows, to overcome the computational challenges posed by the vast space of possible tree topologies. These advancements are improving the accuracy and efficiency of phylogenetic inference, leading to more reliable evolutionary hypotheses across diverse fields, from biology to linguistics. The resulting refined inferences have significant implications for understanding evolutionary processes and informing applications in areas such as epidemiology and historical linguistics.

Papers

November 13, 2024

Machine learning approaches to explore important features behind bird flight modes
Yukino Kawai, Tatsuya Hisada, Kozue Shiomi, Momoko Hayamizu
Machine Learning Bird Specie Flight Pattern Phenotypic Data Important Feature Phylogenetic Inference

February 5, 2024

Are Sounds Sound for Phylogenetic Reconstruction?
Luise Häuser, Gerhard Jäger, Taraka Rama, Johann-Mattis List, Alexandros Stamatakis
Language Evolution Phylogenetic Tree Cognate Detection Phylogenetic Inference Language Clustering

February 2, 2024

Automating Sound Change Prediction for Phylogenetic Inference: A Tukanoan Case Study
Kalvin Chang, Nathaniel R. Robinson, Anna Cai, Ting Chen, Annie Zhang, David R. Mortensen
Case Study Phylogenetic Inference Parsimony Learning Typological Database

October 14, 2023

ARTree: A Deep Autoregressive Model for Phylogenetic Inference
Tianyu Xie, Cheng Zhang
Tree Topology Phylogenetic Inference Variational Bayesian Phylogenetic Inference

October 12, 2023

PhyloGFN: Phylogenetic inference with generative flow networks
Mingyang Zhou, Zichao Yan, Elliot Layne, Nikolay Malkin, Dinghuai Zhang, Moksh Jain, Mathieu Blanchette, Yoshua Bengio
Generative Flow Network Scientific Hypothesis Phylogenetic Tree Phylogenetic Inference Bayesian Phylogenetic Inference

October 2, 2023

Improved Variational Bayesian Phylogenetic Inference using Mixtures
Oskar Kviman, Ricky Molén, Jens Lagergren
Mixture Component Posterior Approximation Phylogenetic Inference Posterior Tree Distribution Variational Bayesian Phylogenetic Inference

July 7, 2023

GeoPhy: Differentiable Phylogenetic Inference via Geometric Gradients of Tree Topologies
Takahiro Mimori, Michiaki Hamada
Variational Inference Natural Gradient Phylogenetic Tree Tree Topology Phylogenetic Inference Variational Bayesian Phylogenetic Inference

June 9, 2023

Leaping through tree space: continuous phylogenetic inference for rooted and unrooted trees
Matthew J Penn, Neil Scheidwasser, Joseph Penn, Christl A Donnelly, David A Duchêne, Samir Bhatt
Tree Specie Phylogenetic Tree Collaborative Exploration Phylogenetic Inference Bayesian Phylogenetic Inference

February 17, 2023

Learnable Topological Features for Phylogenetic Inference via Graph Neural Networks
Cheng Zhang
Graph Neural Network Topological Learning Phylogenetic Tree Phylogenetic Inference Tree Topology Variational Bayesian Phylogenetic Inference

April 16, 2022

A Variational Approach to Bayesian Phylogenetic Inference
Cheng Zhang, Frederick A. Matsen
Variational Inference Variational Method Phylogenetic Inference Bayesian Phylogenetic Inference

February 22, 2022

Multiple Importance Sampling ELBO and Deep Ensembles of Variational Approximations
Oskar Kviman, Harald Melin, Hazal Koptagel, Víctor Elvira, Jens Lagergren
Variational Inference Deep Ensemble Marginal Likelihood Variational Approximation Evidence Lower Bound Phylogenetic Inference

Phylogenetic Inference

Papers

Machine learning approaches to explore important features behind bird flight modes

Are Sounds Sound for Phylogenetic Reconstruction?

Automating Sound Change Prediction for Phylogenetic Inference: A Tukanoan Case Study

ARTree: A Deep Autoregressive Model for Phylogenetic Inference

PhyloGFN: Phylogenetic inference with generative flow networks

Improved Variational Bayesian Phylogenetic Inference using Mixtures

GeoPhy: Differentiable Phylogenetic Inference via Geometric Gradients of Tree Topologies

Leaping through tree space: continuous phylogenetic inference for rooted and unrooted trees

Learnable Topological Features for Phylogenetic Inference via Graph Neural Networks

A Variational Approach to Bayesian Phylogenetic Inference

Multiple Importance Sampling ELBO and Deep Ensembles of Variational Approximations