DeConPPI: Deep Consensus-Based Prediction of Protein-Protein Interactions

Halsana, Aanzil Akram; Chakroborty, Tapas; Basu, Subhadip

doi:10.1007/978-981-99-2680-0_42

Lecture Notes in Networks and Systems

2023

DOI: 10.1007/978-981-99-2680-0_42

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DeConPPI: Deep Consensus-Based Prediction of Protein-Protein Interactions

Aanzil Akram Halsana

Tapas Chakroborty

Subhadip Basu

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2024

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Protein features fusion using attributed network embedding for predicting protein-protein interaction

Cao,

Zainudin,

Daud

2024

BMC Genomics

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Background Protein-protein interactions (PPIs) hold significant importance in biology, with precise PPI prediction as a pivotal factor in comprehending cellular processes and facilitating drug design. However, experimental determination of PPIs is laborious, time-consuming, and often constrained by technical limitations. Methods We introduce a new node representation method based on initial information fusion, called FFANE, which amalgamates PPI networks and protein sequence data to enhance the precision of PPIs’ prediction. A Gaussian kernel similarity matrix is initially established by leveraging protein structural resemblances. Concurrently, protein sequence similarities are gauged using the Levenshtein distance, enabling the capture of diverse protein attributes. Subsequently, to construct an initial information matrix, these two feature matrices are merged by employing weighted fusion to achieve an organic amalgamation of structural and sequence details. To gain a more profound understanding of the amalgamated features, a Stacked Autoencoder (SAE) is employed for encoding learning, thereby yielding more representative feature representations. Ultimately, classification models are trained to predict PPIs by using the well-learned fusion feature. Results When employing 5-fold cross-validation experiments on SVM, our proposed method achieved average accuracies of 94.28%, 97.69%, and 84.05% in terms of Saccharomyces cerevisiae, Homo sapiens, and Helicobacter pylori datasets, respectively. Conclusion Experimental findings across various authentic datasets validate the efficacy and superiority of this fusion feature representation approach, underscoring its potential value in bioinformatics.

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Protein features fusion using attributed network embedding for predicting protein-protein interaction

Cao,

Zainudin,

Daud

2024

BMC Genomics

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show abstract

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DeConPPI: Deep Consensus-Based Prediction of Protein-Protein Interactions

Cited by 1 publication

References 12 publications

Protein features fusion using attributed network embedding for predicting protein-protein interaction

Protein features fusion using attributed network embedding for predicting protein-protein interaction

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