Using Chou's amphiphilic Pseudo-Amino Acid Composition and Extreme Learning Machine for prediction of Protein-protein interactions

Qiao Ying Huang, Zhu Hong You, Shuai Li, Zexuan Zhu

Research output: Chapter in book / Conference proceedingConference article published in proceeding or bookAcademic researchpeer-review

5 Citations (Scopus)


Protein-protein interactions (PPIs) play crucial roles in the execution of various cellular processes. Almost every cellular process relies on transient or permanent physical bindings of proteins. Unfortunately, the experimental methods for identifying PPIs are both time-consuming and expensive. Therefore, it is important to develop computational approaches for predicting PPIs. In this study, a novel approach is presented to predict PPIs using only the information of protein sequences. This method is developed based on learning algorithm-Extreme Learning Machine (ELM) combined with the concept of Chous Pseudo-Amino Acid Composition (PseAAC) composition. PseAAC is a combination of a set of discrete sequence correlation factors and the 20 components of the conventional amino acid composition, so this method can observe a remarkable improvement in prediction quality. ELM classifier is selected as prediction engine, which is a kind of accurate and fast-learning innovative classification method based on the random generation of the input-to-hidden-units weights followed by the resolution of the linear equations to obtain the hidden-to-output weights. When performed on the PPIs data of Saccharomyces cerevisiae, the proposed method achieved 79.66% prediction accuracy with 79.16% sensitivity at the precision of 79.96%. Extensive experiments are performed to compare our method with state-of-the-art techniques Support Vector Machine (SVM). Achieved results show that the proposed approach is very promising for predicting PPIs, and it can be a helpful supplement for PPIs prediction.
Original languageEnglish
Title of host publicationProceedings of the International Joint Conference on Neural Networks
Number of pages5
ISBN (Electronic)9781479914845
Publication statusPublished - 1 Jan 2014
Event2014 International Joint Conference on Neural Networks, IJCNN 2014 - Beijing, China
Duration: 6 Jul 201411 Jul 2014


Conference2014 International Joint Conference on Neural Networks, IJCNN 2014


  • Extreme Learning Machine(ELM)
  • Protein-protein Interactions
  • Pseudo-amino Acid Composition
  • Support Vector Machine (SVM)

ASJC Scopus subject areas

  • Software
  • Artificial Intelligence

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