Conference proceeding
Aligning Multiple PPI Networks with Representation Learning on Networks
The Institute of Electrical and Electronics Engineers, Inc. (IEEE) Conference Proceedings
01 Jan 2018
Abstract
Conference Title: 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Conference Start Date: 2018, Dec. 3 Conference End Date: 2018, Dec. 6 Conference Location: Madrid, Spain Protein-protein interaction (PPI) network alignment has been motivating researches for the comprehension of the underlying crucial biological knowledge, such as conserved evolutionary pathways and functionally conserved proteins throughout different species. Existing PPI network alignment methods have tried to improve the coverage ratio by aligning all proteins from different species. However, there is a fundamental biological justification needed to be acknowledged, that not every protein in a species can, nor should, find homologous proteins in other species. In this paper, we propose a novel approach for multiple PPI network alignment that tries to align only those proteins with the most similarities. To provide more comprehensive supports in computing the similarity, we integrate structural features of the networks together with biological characteristics during the alignment. For the structural features, we apply on PPI networks a representation learning method, which creates a low-dimensional vector embedding with the surrounding topologies of each protein in the network. This approach quantifies the structural features, and provides a new way to determine the topological similarity of the networks by transferring which as calculations in vector similarities. We also propose a new metric for the topological evaluation which can better assess the topological quality of the alignment results across different networks. Both biological and topological evaluations demonstrate our approach is promising and preferable against previous multiple alignment methods.
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Details
- Title
- Aligning Multiple PPI Networks with Representation Learning on Networks
- Creators
- Bo SongJianliang GaoHongliang DuZheng ChenXiaohua Hu
- Publication Details
- The Institute of Electrical and Electronics Engineers, Inc. (IEEE) Conference Proceedings
- Publisher
- The Institute of Electrical and Electronics Engineers, Inc. (IEEE)
- Resource Type
- Conference proceeding
- Language
- English
- Academic Unit
- Information Science (Informatics)
- Identifiers
- 991019170353504721