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Volume 3 Issue 11, November 2021

A machine learning platform for the immune system

Deciphering the immune information encoded in adaptive immune receptor repertoires (AIRR) is important for next-generation immunodiagnostics and therapeutics design. However, the proliferation of molecular biology and bioinformatics tools that are necessary to generate large quantities of immune receptor data has not yet been matched by frameworks that allow for routine data analysis by biomedical scientists. Machine learning is a crucial technology for the transformation of AIRR into biomarkers of disease and infection, given its capacity to separate immunological signals from noise. In a paper in this issue, Pavlović et al. present immuneML, an open-source collaborative platform for AIRR machine learning. immuneML implements each step of the AIRR machine learning process using fully specified and shareable workflows and adapted to different user backgrounds.

See Pavlović et al.

Image: Image courtesy of Lonneke Scheffer and Rahmad Akbar. Cover design: Lauren Heslop

Editorial

  • Although the initial inspiration of neural networks came from biology, insights from physics have helped neural networks to become usable. New connections between physics and machine learning produce powerful computational methods.

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Reviews

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Research

  • 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.

    • Milena Pavlović
    • Lonneke Scheffer
    • Geir Kjetil Sandve
    Article
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  • Identifying a chemical substance using mass spectrometry without knowing its structure is challenging. To help detect novel designer drugs from their mass spectra, Skinnider et al. describe a generative model that is biased towards creating potentially psychoactive molecules and thus helps identify potential candidates for a specific sample.

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  • Radiofrequency pulses of different shapes can increase the efficiency of applications such as broadcasting or medical imaging, but finding the optimal shape for a specific use can be computationally costly. Shin and colleagues present a new method based on deep reinforcement learning to design radiofrequency pulses for use in MRI, which is demonstrated to cover different types of optimization goals for each application.

    • Dongmyung Shin
    • Younghoon Kim
    • Jongho Lee
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