A Highly Efficient Approach to Protein Interactome Mapping Based on Collaborative Filtering Framework

Xin Luo, Zhuhong You, Mengchu Zhou, Shuai Li, Hareton Leung, Yunni Xia, Qingsheng Zhu

Research output: Contribution to journalArticlepeer-review

62 Scopus citations


The comprehensive mapping of protein-protein interactions (PPIs) is highly desired for one to gain deep insights into both fundamental cell biology processes and the pathology of diseases. Finely-set small-scale experiments are not only very expensive but also inefficient to identify numerous interactomes despite their high accuracy. High-throughput screening techniques enable efficient identification of PPIs; yet the desire to further extract useful knowledge from these data leads to the problem of binary interactome mapping. Network topology-based approaches prove to be highly efficient in addressing this problem; however, their performance deteriorates significantly on sparse putative PPI networks. Motivated by the success of collaborative filtering (CF)-based approaches to the problem of personalized-recommendation on large, sparse rating matrices, this work aims at implementing a highly efficient CF-based approach to binary interactome mapping. To achieve this, we first propose a CF framework for it. Under this framework, we model the given data into an interactome weight matrix, where the feature-vectors of involved proteins are extracted. With them, we design the rescaled cosine coefficient to model the inter-neighborhood similarity among involved proteins, for taking the mapping process. Experimental results on three large, sparse datasets demonstrate that the proposed approach outperforms several sophisticated topology-based approaches significantly.

Original languageEnglish (US)
Article number7702
JournalScientific reports
StatePublished - Jan 9 2015

All Science Journal Classification (ASJC) codes

  • General


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