GNNs enable phylogenetic diversification parameter inference

Association·arcadia

Claim that GNNs may be helpful for inference of diversification dynamics (e.g., speciation/extinction parameters) using phylogenetic trees.

Confidence

70%

active

Evidence Quote

“GNNs may also be helpful for the inference of diversification dynamics using phylogenetic trees”

Relationship

Graph Neural Networks (GNNs) enables Diversification parameters

Arguments

Graph Neural Networks (GNNs)subject

Diversification parametersobject

Connections (3)

GNNs as flexible models for evolutionary inference tasksInferenceChain

Petabase-scale sequence alignment increases viral discoveryAssociation

Advances in phylogenetic-informed graph deep learning for dynamic evolutionary inferenceInferenceChain

Evidence

“Reference to Morlon H. (2014)”

(2014). Phylogenetic approaches for studying diversification doi:10.1111/ele.12251 ↗

“Reference to Morlon H, Andréoletti J, Barido-Sottani J, Lambert S, Perez-Lamarque B, Quintero I, Senderov V, Veron P. (2024)”

(2024). Phylogenetic Insights into Diversification doi:10.1146/annurev-ecolsys-102722-020508 ↗

“Reference to Featherstone LA, Zhang JM, Vaughan TG, Duchene S. (2022)”

(2022). Epidemiological inference from pathogen genomes: A review of phylodynamic models and applications doi:10.1093/ve/veac045 ↗

“Reference to Fountain-Jones NM, Appaw RC, Carver S, Didelot X, Volz E, Charleston M. (2020)”

(2020). Emerging phylogenetic structure of the SARS-CoV-2 pandemic doi:10.1093/ve/veaa082 ↗

“Reference to Lai A, Bergna A, Acciarri C, Galli M, Zehender G. (2020)”

(2020). Early phylogenetic estimate of the effective reproduction number of SARS‐CoV‐2 doi:10.1002/jmv.25723 ↗

“Reference to Vaughan TG, Sciré J, Nadeau SA, Stadler T. (2020)”

(2020). Estimates of outbreak-specific SARS-CoV-2 epidemiological parameters from genomic data doi:10.1101/2020.09.12.20193284 ↗

“Reference to Attwood SW, Hill SC, Aanensen DM, Connor TR, Pybus OG. (2022)”

(2022). Phylogenetic and phylodynamic approaches to understanding and combating the early SARS-CoV-2 pandemic doi:10.1038/s41576-022-00483-8 ↗

“Reference to Rife BD, Mavian C, Chen X, Ciccozzi M, Salemi M, Min J, Prosperi MC. (2017)”

(2017). Phylodynamic applications in 21st century global infectious disease research doi:10.1186/s41256-017-0034-y ↗

“Reference to Lajaaiti I et al. (2023), comparing deep learning architectures for parameter inference from phylogenies.”

Lajaaiti I et al. (2023). A Comparison of Deep Learning Architectures for Inferring Parameters of Diversification Models from Extant Phylogenies doi:10.1101/2023.03.03.530992 ↗

“Reference to Pennell MW et al. (2014)”

Pennell MW et al. (2014). geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees doi:10.1093/bioinformatics/btu181 ↗

“Reference to Morlon H et al. (2016)”

Morlon H et al. (2016). RPANDA: an R package for macroevolutionary analyses on phylogenetic trees doi:10.1111/2041-210x.12526 ↗