A1 Refereed original research article in a scientific journal
Convolutional Neural Network-Based Artificial Intelligence for Classification of Protein Localization Patterns
Authors: Liimatainen Kaisa, Huttunen Riku, Latonen Leena, Ruusuvuori Pekka
Publisher: MDPI
Publication year: 2021
Journal: Biomolecules
Journal name in source: BIOMOLECULES
Journal acronym: BIOMOLECULES
Article number: ARTN 264
Volume: 11
Issue: 2
Number of pages: 15
DOI: https://doi.org/10.3390/biom11020264
Web address : https://doi.org/10.3390/biom11020264
Self-archived copy’s web address: https://research.utu.fi/converis/portal/detail/Publication/53644135
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.
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