4.7 Article

Logistic tensor decomposition with sparse subspace learning for prediction of multiple disease types of human-virus protein-protein interactions

Journal

BRIEFINGS IN BIOINFORMATICS
Volume 24, Issue 1, Pages -

Publisher

OXFORD UNIV PRESS
DOI: 10.1093/bib/bbac604

Keywords

human proteins; virus proteins; disease types; logical tensor decomposition; sparse subspace learning

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Viral infection involves a large number of protein-protein interactions (PPIs) between the virus and the host, and the identification of these PPIs plays an important role in revealing viral infection and pathogenesis. We propose a novel computational framework, LTDSSL, to determine human-virus PPIs under different disease types. Experimental results show that LTDSSL has better predictive performance for both new disease types and new triples than the state-of-the-art methods.
Viral infection involves a large number of protein-protein interactions (PPIs) between the virus and the host, and the identification of these PPIs plays an important role in revealing viral infection and pathogenesis. Existing computational models focus on predicting whether human proteins and viral proteins interact, and rarely take into account the types of diseases associated with these interactions. Although there are computational models based on a matrix and tensor decomposition for predicting multi-type biological interaction relationships, these methods cannot effectively model high-order nonlinear relationships of biological entities and are not suitable for integrating multiple features. To this end, we propose a novel computational framework, LTDSSL, to determine human-virus PPIs under different disease types. LTDSSL utilizes logistic functions to model nonlinear associations, sets importance levels to emphasize the importance of observed interactions and utilizes sparse subspace learning of multiple features to improve model performance. Experimental results show that LTDSSL has better predictive performance for both new disease types and new triples than the state-of-the-art methods. In addition, the case study further demonstrates that LTDSSL can effectively predict human-viral PPIs under various disease types.

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