Issue No. 02 - April-June (2007 vol. 4)
In this paper, we present a novel approach Bio-IEDM (Biomedical Information Extraction and Data Mining) to integrate text mining and predictive modeling to analyze biomolecular network from biomedical literature databases. Our method consists of two phases. In phase 1, we discuss a semisupervised efficient learning approach to automatically extract biological relationships such as protein-protein interaction, protein-gene interaction from the biomedical literature databases to construct the biomolecular network. Our method automatically learns the patterns based on a few user seed tuples and then extracts new tuples from the biomedical literature based on the discovered patterns. The derived biomolecular network forms a large scale-free network graph. In phase 2, we present a novel clustering algorithm to analyze the biomolecular network graph to identify biologically meaningful subnetworks (communities). The clustering algorithm considers the characteristics of the scale-free network graphs and is based on the local density of the vertex and its neighborhood functions that can be used to find more meaningful clusters with different density level. The experimental results indicate our approach is very effective in extracting biological knowledge from a huge collection of biomedical literature. The integration of data mining and information extraction provides a promising direction for analyzing the biomolecular network.
Biomolecular network, semisupervised learning, scale-free network, information extraction, biological complexes (communities).
Daniel D. Wu, Xiaohua Hu, "Data Mining and Predictive Modeling of Biomolecular Network from Biomedical Literature Databases", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 4, no. , pp. 251-263, April-June 2007, doi:10.1109/TCBB.2007.070211