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Hash Subgraph Pairwise Kernel for Protein-Protein Interaction Extraction
July-Aug. 2012 (vol. 9 no. 4)
pp. 1190-1202
ASCII Text
x 
 
Yanpeng Li, Jian Wang, Zhihao Yang, Hongfei Lin, Yijia Zhang, "Hash Subgraph Pairwise Kernel for Protein-Protein Interaction Extraction," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 9, no. 4, pp. 1190-1202, July-Aug., 2012.
 
 
BibTex
x
 
@article{ 10.1109/TCBB.2012.50,
author = { Yanpeng Li and Jian Wang and Zhihao Yang and Hongfei Lin and Yijia Zhang},
title = {Hash Subgraph Pairwise Kernel for Protein-Protein Interaction Extraction},
journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics},
volume = {9},
number = {4},
issn = {1545-5963},
year = {2012},
pages = {1190-1202},
doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2012.50},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
}
 
 
RefWorks Procite/RefMan/Endnote
x 
 
TY - JOUR
JO - IEEE/ACM Transactions on Computational Biology and Bioinformatics
TI - Hash Subgraph Pairwise Kernel for Protein-Protein Interaction Extraction
IS - 4
SN - 1545-5963
SP1190
EP1202
EPD - 1190-1202
A1 - Yanpeng Li,
A1 - Jian Wang,
A1 - Zhihao Yang,
A1 - Hongfei Lin,
A1 - Yijia Zhang,
PY - 2012
KW - proteins
KW - data mining
KW - graph theory
KW - medical information systems
KW - PPI corpora
KW - hash subgraph pairwise kernel
KW - protein-protein interaction extraction
KW - biomedical literature
KW - biomedical text mining
KW - graph kernel
KW - dependency graphs
KW - sentence structure
KW - Kernel
KW - Syntactics
KW - Proteins
KW - Protein engineering
KW - Feature extraction
KW - Bioinformatics
KW - Arrays
KW - graph kernel.
KW - Biomedical text mining
KW - hash
KW - interaction extraction
VL - 9
JA - IEEE/ACM Transactions on Computational Biology and Bioinformatics
ER -
 
Yanpeng Li, Coll. of Comput. Sci., Dalian Univ. of Technol., Dalian, China
Jian Wang, Coll. of Comput. Sci., Dalian Univ. of Technol., Dalian, China
Zhihao Yang, Coll. of Comput. Sci., Dalian Univ. of Technol., Dalian, China
Hongfei Lin, Coll. of Comput. Sci., Dalian Univ. of Technol., Dalian, China
Yijia Zhang, Coll. of Comput. Sci., Dalian Univ. of Technol., Dalian, China
Extracting protein-protein interaction (PPI) from biomedical literature is an important task in biomedical text mining (BioTM). In this paper, we propose a hash subgraph pairwise (HSP) kernel-based approach for this task. The key to the novel kernel is to use the hierarchical hash labels to express the structural information of subgraphs in a linear time. We apply the graph kernel to compute dependency graphs representing the sentence structure for protein-protein interaction extraction task, which can efficiently make use of full graph structural information, and particularly capture the contiguous topological and label information ignored before. We evaluate the proposed approach on five publicly available PPI corpora. The experimental results show that our approach significantly outperforms all-path kernel approach on all five corpora and achieves state-of-the-art performance.

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Index Terms:
proteins,data mining,graph theory,medical information systems,PPI corpora,hash subgraph pairwise kernel,protein-protein interaction extraction,biomedical literature,biomedical text mining,graph kernel,dependency graphs,sentence structure,Kernel,Syntactics,Proteins,Protein engineering,Feature extraction,Bioinformatics,Arrays,graph kernel.,Biomedical text mining,hash,interaction extraction
Citation:
Yanpeng Li, Jian Wang, Zhihao Yang, Hongfei Lin, Yijia Zhang, "Hash Subgraph Pairwise Kernel for Protein-Protein Interaction Extraction," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 9, no. 4, pp. 1190-1202, July-Aug. 2012, doi:10.1109/TCBB.2012.50
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