The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires

Milena Pavlović, Lonneke Scheffer, Keshav Motwani, Chakravarthi Kanduri, Radmila Kompova, Nikolay Vazov, Knut Waagan, Fabian L.M. Bernal, Alexandre Almeida Costa, Brian Corrie, Rahmad Akbar, Ghadi S. Al Hajj, Gabriel Balaban, Todd M. Brusko, Maria Chernigovskaya, Scott Christley, Lindsay G. Cowell, Robert Frank, Ivar Grytten, Sveinung GundersenIngrid Hobæk Haff, Eivind Hovig, Ping Han Hsieh, Günter Klambauer, Marieke L. Kuijjer, Christin Lund-Andersen, Antonio Martini, Thomas Minotto, Johan Pensar, Knut Rand, Enrico Riccardi, Philippe A. Robert, Artur Rocha, Andrei Slabodkin, Igor Snapkov, Ludvig M. Sollid, Dmytro Titov, Cédric R. Weber, Michael Widrich, Gur Yaari, Victor Greiff, Geir Kjetil Sandve

Research output: Contribution to journalArticlepeer-review

2 Scopus citations

Abstract

Adaptive immune receptor repertoires (AIRR) are key targets for biomedical research as they record past and ongoing adaptive immune responses. The capacity of machine learning (ML) to identify complex discriminative sequence patterns renders it an ideal approach for AIRR-based diagnostic and therapeutic discovery. So far, widespread adoption of AIRR ML has been inhibited by a lack of reproducibility, transparency and interoperability. immuneML (immuneml.uio.no) addresses these concerns by implementing each step of the AIRR ML process in an extensible, open-source software ecosystem that is based on fully specified and shareable workflows. To facilitate widespread user adoption, immuneML is available as a command-line tool and through an intuitive Galaxy web interface, and extensive documentation of workflows is provided. We demonstrate the broad applicability of immuneML by (1) reproducing a large-scale study on immune state prediction, (2) developing, integrating and applying a novel deep learning method for antigen specificity prediction and (3) showcasing streamlined interpretability-focused benchmarking of AIRR ML.

Original languageEnglish (US)
Pages (from-to)936-944
Number of pages9
JournalNature Machine Intelligence
Volume3
Issue number11
DOIs
StatePublished - Nov 2021
Externally publishedYes

ASJC Scopus subject areas

  • Software
  • Human-Computer Interaction
  • Computer Vision and Pattern Recognition
  • Computer Networks and Communications
  • Artificial Intelligence

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