Journal Article

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

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

2021

Overview

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. The proliferation of molecular biology and bioinformatics tools necessary to generate huge quantities of immune receptor data has not been matched by frameworks that allow easy data analysis. The authors present immuneML, an open-source collaborative ecosystem for machine learning analysis of adaptive immune receptor repertoires.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 631/114/1305 / 631/114/2398 / 631/250/2152 / Antigens / Bioinformatics / Classification / Collaboration / Cytomegalovirus / Data analysis / Deep learning / Documentation / Engineering / Interfaces / Interoperability / Machine learning / Metadata / Molecular biology / Receptors / Reproducibility / Support vector machines / Trouble shooting