Protein function prediction through multi-view multi-label latent tensor reconstruction

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Journal Title
Journal ISSN
Volume Title
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
Date
2024-05-02
Major/Subject
Mcode
Degree programme
Language
en
Pages
21
Series
BMC Bioinformatics, Volume 25, issue 1, pp. 1-21
Abstract
Background: In last two decades, the use of high-throughput sequencing technologies has accelerated the pace of discovery of proteins. However, due to the time and resource limitations of rigorous experimental functional characterization, the functions of a vast majority of them remain unknown. As a result, computational methods offering accurate, fast and large-scale assignment of functions to new and previously unannotated proteins are sought after. Leveraging the underlying associations between the multiplicity of features that describe proteins could reveal functional insights into the diverse roles of proteins and improve performance on the automatic function prediction task. Results: We present GO-LTR, a multi-view multi-label prediction model that relies on a high-order tensor approximation of model weights combined with non-linear activation functions. The model is capable of learning high-order relationships between multiple input views representing the proteins and predicting high-dimensional multi-label output consisting of protein functional categories. We demonstrate the competitiveness of our method on various performance measures. Experiments show that GO-LTR learns polynomial combinations between different protein features, resulting in improved performance. Additional investigations establish GO-LTR’s practical potential in assigning functions to proteins under diverse challenging scenarios: very low sequence similarity to previously observed sequences, rarely observed and highly specific terms in the gene ontology. Implementation: The code and data used for training GO-LTR is available at https://github.com/aalto-ics-kepaco/GO-LTR-prediction.
Description
Publisher Copyright: © The Author(s) 2024.
Keywords
CAFA, Gene ontology, Machine learning, Protein function
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Citation
Armah-Sekum, R E, Szedmak, S & Rousu, J 2024, ' Protein function prediction through multi-view multi-label latent tensor reconstruction ', BMC Bioinformatics, vol. 25, no. 1, 174, pp. 1-21 . https://doi.org/10.1186/s12859-024-05789-4