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1. Protein2Vec: Aligning Multiple PPI Networks with Representation Learning

   Jianliang Gao, Ling Tian ( October 2019 , IEEE/ACM transactions on computational biology and bioinformatics)

   Research of Protein-Protein Interaction (PPI) Network Alignment is playing an important role in understanding the crucial underlying biological knowledge such as functionally homologous proteins and conserved evolutionary pathways across different species. Existing methods of PPI network alignment often try to improve the coverage ratio of the alignment result by aligning all proteins from different species. However, there is a fundamental biological premise that needs to be considered carefully: not every protein in a species can, nor should, find its homologous proteins in other species. In this work, we propose a novel alignment method to map only those proteins with the most similarity throughout the PPI networks of multiple species. For the similarity features of the protein in the networks, we integrate both topological features with biological characteristics to provide enhanced supports for the alignment procedures. For topological features, we apply a representation learning method on the networks that can generate a low dimensional vector embedding with its surrounding structural features for each protein. The topological similarity of proteins from different PPI networks can thus be transferred as the similarity of their corresponding vector representations, which provides a new way to comprehensively quantify the topological similarities between proteins. We also proposemore »a new measure for the topological evaluation of the alignment results which better uncover the structural quality of the alignment across multiple networks. Both biological and topological evaluations on the alignment results of real datasets demonstrate our approach is promising and preferable against previous multiple alignment methods« less
2. Aligning Multiple PPI Networks with Representation Learning on Networks

   Bo Song, Jianliang Gao ( December 2018 , 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM))

   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 resultsmore »across different networks. Both biological and topological evaluations demonstrate our approach is promising and preferable against previous multiple alignment methods.« less
3. Aligning Multiple PPI Networks with Representation Learning on Networks

   Bo Song, Jianliang Gao ( October 2018 , 2018 IEEE International Conference on Bioinformatics and Biomedicine)

   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 resultsmore »across different networks. Both biological and topological evaluations demonstrate our approach is promising and preferable against previous multiple alignment methods.« less
4. Aligning Multiple PPI Networks with Representation Learning on Networks

   Bo Song, Jianliang Gao ( December 2018 , 2018 IEEE BIBM Conference Proceeding)

   Abstract—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 resultsmore »across different networks. Both biological and topological evaluations demonstrate our approach is promising and preferable against previous multiple alignment methods.« less
5. Aligning Multiple PPI Networks with Representation Learning on Networks

   Bo Song, Jianliang Gao ( December 2018 , 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM))

   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 resultsmore »across different networks. Both biological and topological evaluations demonstrate our approach is promising and preferable against previous multiple alignment methods.« less