Convolutional neural network-based artificial intelligence for classification of protein localization patterns

Kaisa Liimatainen, Riku Huttunen, Leena Latonen, Pekka Ruusuvuori

    Research output: Contribution to journalArticleScientificpeer-review

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    Identifying localization of proteins and their specific subpopulations associated with certain cellular compartments is crucial for understanding protein function and interactions with other macromolecules. Fluorescence microscopy is a powerful method to assess protein localizations, with increasing demand of automated high throughput analysis methods to supplement the technical advancements in high throughput imaging. Here, we study the applicability of deep neural network-based artificial intelligence in classification of protein localization in 13 cellular subcompartments. We use deep learning-based on convolutional neural network and fully convolutional network with similar architectures for the classification task, aiming at achieving accurate classification, but importantly, also comparison of the networks. Our results show that both types of convolutional neural networks perform well in protein localization classification tasks for major cellular organelles. Yet, in this study, the fully convolutional network outperforms the convolutional neural network in classification of images with multiple simultaneous protein localizations. We find that the fully convolutional network, using output visualizing the identified localizations, is a very useful tool for systematic protein localization assessment.

    Original languageEnglish
    Article number264
    Pages (from-to)114
    Number of pages1
    Issue number2
    Publication statusPublished - Feb 2021
    Publication typeA1 Journal article-refereed


    • Artificial intelligence
    • Cellular organelles
    • Classification
    • Convolutional neural networks
    • Deep learning
    • Fluorescence microscopy
    • Phenotyping
    • Protein localization

    Publication forum classification

    • Publication forum level 1

    ASJC Scopus subject areas

    • Biochemistry
    • Molecular Biology


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