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immuneML: an ecosystem for machine learning analysis of adaptive immune receptor repertoires

View ORCID ProfileMilena Pavlović, View ORCID ProfileLonneke Scheffer, View ORCID ProfileKeshav Motwani, View ORCID ProfileChakravarthi Kanduri, Radmila Kompova, Nikolay Vazov, Knut Waagan, View ORCID ProfileFabian L. M. Bernal, Alexandre Almeida Costa, View ORCID ProfileBrian Corrie, View ORCID ProfileRahmad Akbar, View ORCID ProfileGhadi S. Al Hajj, View ORCID ProfileGabriel Balaban, View ORCID ProfileTodd M. Brusko, View ORCID ProfileMaria Chernigovskaya, Scott Christley, Lindsay G. Cowell, View ORCID ProfileRobert Frank, View ORCID ProfileIvar Grytten, View ORCID ProfileSveinung Gundersen, Ingrid Hobæk Haff, View ORCID ProfileSepp Hochreiter, View ORCID ProfileEivind Hovig, View ORCID ProfilePing-Han Hsieh, View ORCID ProfileGünter Klambauer, View ORCID ProfileMarieke L. Kuijjer, View ORCID ProfileChristin Lund-Andersen, Antonio Martini, Thomas Minotto, View ORCID ProfileJohan Pensar, View ORCID ProfileKnut Rand, View ORCID ProfileEnrico Riccardi, View ORCID ProfilePhilippe A. Robert, Artur Rocha, View ORCID ProfileAndrei Slabodkin, View ORCID ProfileIgor Snapkov, View ORCID ProfileLudvig M. Sollid, Dmytro Titov, View ORCID ProfileCédric R. Weber, Michael Widrich, View ORCID ProfileGur Yaari, View ORCID ProfileVictor Greiff, View ORCID ProfileGeir Kjetil Sandve
doi: https://doi.org/10.1101/2021.03.08.433891
Milena Pavlović
1Department of Informatics, University of Oslo, Norway
2Centre for Bioinformatics, University of Oslo, Norway
3K.G. Jebsen Centre for Coeliac Disease Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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  • ORCID record for Milena Pavlović
Lonneke Scheffer
1Department of Informatics, University of Oslo, Norway
2Centre for Bioinformatics, University of Oslo, Norway
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  • ORCID record for Lonneke Scheffer
Keshav Motwani
4Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida Diabetes Institute, USA
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Chakravarthi Kanduri
2Centre for Bioinformatics, University of Oslo, Norway
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Radmila Kompova
2Centre for Bioinformatics, University of Oslo, Norway
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Nikolay Vazov
6University Center for Information Technology, University of Oslo, Norway
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Knut Waagan
6University Center for Information Technology, University of Oslo, Norway
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Fabian L. M. Bernal
6University Center for Information Technology, University of Oslo, Norway
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Alexandre Almeida Costa
7Institute for Systems and Computer Engineering, Technology and Science, Portugal
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Brian Corrie
8Biological Sciences, Simon Fraser University, Canada
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Rahmad Akbar
9Department of Immunology, University of Oslo, Norway
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Ghadi S. Al Hajj
1Department of Informatics, University of Oslo, Norway
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Gabriel Balaban
1Department of Informatics, University of Oslo, Norway
2Centre for Bioinformatics, University of Oslo, Norway
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Todd M. Brusko
4Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida Diabetes Institute, USA
5Department of Pediatrics, College of Medicine, University of Florida Diabetes Institute, USA
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Maria Chernigovskaya
9Department of Immunology, University of Oslo, Norway
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Scott Christley
10Department of Population and Data Sciences, UT Southwestern Medical Center, USA
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Lindsay G. Cowell
11Department of Mathematics, University of Oslo, Norway
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Robert Frank
9Department of Immunology, University of Oslo, Norway
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Ivar Grytten
1Department of Informatics, University of Oslo, Norway
2Centre for Bioinformatics, University of Oslo, Norway
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Sveinung Gundersen
2Centre for Bioinformatics, University of Oslo, Norway
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Ingrid Hobæk Haff
11Department of Mathematics, University of Oslo, Norway
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Sepp Hochreiter
12ELLIS Unit Linz and LIT AI Lab, Institute for Machine Learning, Johannes Kepler University Linz, Austria
13Institute of Advanced Research in Artificial Intelligence (IARAI)
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Eivind Hovig
1Department of Informatics, University of Oslo, Norway
2Centre for Bioinformatics, University of Oslo, Norway
14Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Norway
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Ping-Han Hsieh
15Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Norway
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Günter Klambauer
12ELLIS Unit Linz and LIT AI Lab, Institute for Machine Learning, Johannes Kepler University Linz, Austria
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Marieke L. Kuijjer
15Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Norway
16Department of Pathology, Leiden University Medical Center, the Netherlands
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Christin Lund-Andersen
14Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Norway
17Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Norway
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Antonio Martini
1Department of Informatics, University of Oslo, Norway
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Thomas Minotto
11Department of Mathematics, University of Oslo, Norway
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Johan Pensar
11Department of Mathematics, University of Oslo, Norway
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Knut Rand
1Department of Informatics, University of Oslo, Norway
2Centre for Bioinformatics, University of Oslo, Norway
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Enrico Riccardi
1Department of Informatics, University of Oslo, Norway
2Centre for Bioinformatics, University of Oslo, Norway
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Philippe A. Robert
9Department of Immunology, University of Oslo, Norway
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Artur Rocha
7Institute for Systems and Computer Engineering, Technology and Science, Portugal
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Andrei Slabodkin
9Department of Immunology, University of Oslo, Norway
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Igor Snapkov
9Department of Immunology, University of Oslo, Norway
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Ludvig M. Sollid
3K.G. Jebsen Centre for Coeliac Disease Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
9Department of Immunology, University of Oslo, Norway
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Dmytro Titov
2Centre for Bioinformatics, University of Oslo, Norway
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Cédric R. Weber
18Department of Biosystems Science and Engineering, ETH Zürich, Switzerland
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Michael Widrich
12ELLIS Unit Linz and LIT AI Lab, Institute for Machine Learning, Johannes Kepler University Linz, Austria
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Gur Yaari
19Faculty of Engineering, Bar Ilan University, Israel
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Victor Greiff
9Department of Immunology, University of Oslo, Norway
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Geir Kjetil Sandve
1Department of Informatics, University of Oslo, Norway
2Centre for Bioinformatics, University of Oslo, Norway
3K.G. Jebsen Centre for Coeliac Disease Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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  • For correspondence: geirksa@ifi.uio.no
  • Abstract
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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. To date, 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 (i) reproducing a large-scale study on immune state prediction, (ii) developing, integrating, and applying a novel method for antigen specificity prediction, and (iii) showcasing streamlined interpretability-focused benchmarking of AIRR ML.

Competing Interest Statement

VG declares advisory board positions in aiNET GmbH and Enpicom B.V.

Footnotes

  • ↵☯ Joint supervision

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted March 15, 2021.
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immuneML: an 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 Gundersen, Ingrid Hobæk Haff, Sepp Hochreiter, 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
bioRxiv 2021.03.08.433891; doi: https://doi.org/10.1101/2021.03.08.433891
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immuneML: an 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 Gundersen, Ingrid Hobæk Haff, Sepp Hochreiter, 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
bioRxiv 2021.03.08.433891; doi: https://doi.org/10.1101/2021.03.08.433891

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