4 papers
An adaptive time-tree transition kernel for Bayesian phylogenetic inference
Marius Brusselmans, Guy Baele, Samuel L. Hong +4
Bayesian phylogenetic and phylodynamic analyses can be very time-consuming, owing to the combination of complex models that are used to estimate key parameters from increasingly la…
Assessing the Validity of the Fixed Tree Topology Assumption in Phylodynamic Inference
Mathieu Fourment, Jiansi Gao, Marc A Suchard +1
Fixed tree topologies are widely used in phylodynamic analyses to reduce computational burden, yet the consequences of this assumption remain insufficiently understood. Here, we sy…
PhyloVAE: Unsupervised Learning of Phylogenetic Trees via Variational Autoencoders
Tianyu Xie, Harry Richman, Jiansi Gao +2
Learning informative representations of phylogenetic tree structures is essential for analyzing evolutionary relationships. Classical distance-based methods have been widely used t…
On the importance of assessing topological convergence in Bayesian phylogenetic inference
Marius Brusselmans, Luiz Max Carvalho, Samuel L. Hong +7
Modern phylogenetics research is often performed within a Bayesian framework, using sampling algorithms such as Markov chain Monte Carlo (MCMC) to approximate the posterior distrib…