/nn-phylogenetics

Novel Symmetry-preserving Neural Network Model for Phylogenetic Inference

Primary LanguagePythonMIT LicenseMIT

Novel Symmetry-preserving Neural Network Model for Phylogenetic Inference

Xudong Tang, Leonardo Zepeda-Nuñez, Shengwen Yang, Zelin Zhao, and Claudia Solis-Lemus.

Citation

@article{tang2023novel,
      title={Novel Symmetry-preserving Neural Network Model for Phylogenetic Inference}, 
      author={Xudong Tang and Leonardo Zepeda-Nunez and Shengwen Yang and Zelin Zhao and Claudia Solis-Lemus},
      year={2023},
      eprint={2201.04663},
      journal={arXiv}
}

Folder structure

  • plots contains the code to generate the plots in the manuscripts
  • scripts has the python scripts for the implementation of the neural network model
  • simulation contains the details on the simulation study
    • simulations-zou2019: scripts to simulate data based on Zou2020. These simulations have 4 taxa (species)
    • simulations-5taxa: scripts to simulate data on 5 taxa. Not tested yet
  • notebook.md has the reproducible log of analyses

License

Our code is licensed under the MIT License © Solis-Lemus lab (2023).