Transformer-based tool recommendation system in Galaxy.

Journal: BMC bioinformatics
PMID: 38012574

Abstract

BACKGROUND: Galaxy is a web-based open-source platform for scientific analyses. Researchers use thousands of high-quality tools and workflows for their respective analyses in Galaxy. Tool recommender system predicts a collection of tools that can be used to extend an analysis. In this work, a tool recommender system is developed by training a transformer on workflows available on Galaxy Europe and its performance is compared to other neural networks such as recurrent, convolutional and dense neural networks.

Authors

  • Anup Kumar
    Department of Urology, University of Central Florida College of Medicine and Global Robotics Institute, Florida Hospital-Celebration Health, Celebration, FL, USA.
  • Björn Grüning
    Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany.
  • Rolf Backofen
    Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee 106, Freiburg, 79110, Germany.

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