3 papers
q-bio.PE2025
ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference
Tianyu Xie, Yicong Mao, Cheng Zhang
Probabilistic modeling over the combinatorially large space of tree topologies remains a central challenge in phylogenetic inference. Previous approaches often necessitate pre-samp…
q-bio.PE2025
Vector encoding of phylogenetic trees by ordered leaf attachment
Harry Richman, Cheng Zhang, Frederick A. Matsen
As part of work to connect phylogenetics with machine learning, there has been considerable recent interest in vector encodings of phylogenetic trees. We present a simple new "orde…
q-bio.PE2024
Finding high posterior density phylogenies by systematically extending a directed acyclic graph
Chris Jennings-Shaffer, David H Rich, Matthew Macaulay +7
Bayesian phylogenetics typically estimates a posterior distribution, or aspects thereof, using Markov chain Monte Carlo methods. These methods integrate over tree space by applying…