Alice Doucet Beaupré

Alice Doucet Beaupré

PhD candidate in Ecology and Evolution

University of Illinois at Urbana-Champaign


I’m a PhD Candidate and past CompGen Fellow in the O’Dwyer Lab. I spend most of my time doing research in theoretical ecology, stochastic processes, microbial ecology, and unsupervised machine learning. These days I am interested in developping unsupervised learning algorithms by taking inspiration from state of the art methods used in computational linguistics and topic modelling—I tweak, modify, and adapt them to make them usable in the context of microbial ecology. The goal is to automate the discovery of microbial units which help better document and analyze the immense diversity and complexity of microbial communities beyond the customary use of operational taxonomic units (OTUs). I am also interested in characterizing the diversification and tempo of evolution of microbial communities using novel non-equilibrium phenomenological models developped in collaboration with James O’Dwyer.


  • Phylodynamics
  • Microbial ecology
  • Computational ecology
  • Stochastic processes
  • Unsupervised learning
  • Nonparametric statistics
  • Renormalization group


  • Program in Ecology, Evolution, and Conservation Biology (PEEC), 2014, 2014

    University of Illinois at Urbana-Champaign

  • MSc in Theoretical Physics, 2009, 2009

    ETH Zürich

  • BSc in Physics, 2006

    Université de Sherbrooke


Unsupervised learning of microbial units

Unsupervised learning approach uncovers contextually important microbial units

Microbial phylodynamics

Coarse-graining of microbial phylogenies characterizes bursty dynamics