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Pseudo-perplexity in one fell swoop for protein fitness estimation

Pranav Kantroo1,2,*, Günter P. Wagner3,4,5, and Benjamin B. Machta2,6,†

  • 1Computational Biology and Bioinformatics Program, Yale University, New Haven, Connecticut 06520, USA
  • 2Quantitative Biology Institute, Yale University, New Haven, Connecticut 06520, USA
  • 3Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA
  • 4Department of Evolutionary Biology, University of Vienna, Djerassi Platz 1, A-1030 Vienna, Austria
  • 5Hagler Institute for Advanced Studies, Texas A&M, College Station, Texas 77843, USA
  • 6Department of Physics, Yale University, New Haven, Connecticut 06520, USA

  • *Contact author: pranav.kantroo@yale.edu
  • †Contact author: benjamin.machta@yale.edu

RAG-ESM: Improving Pretrained Protein Language Models via Sequence Retrieval

Damiano Sgarbossa and Anne-Florence Bitbol

PRX Life 3 033013 (2025)

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