34,607 research outputs found
Link Mining for Kernel-based Compound-Protein Interaction Predictions Using a Chemogenomics Approach
Virtual screening (VS) is widely used during computational drug discovery to
reduce costs. Chemogenomics-based virtual screening (CGBVS) can be used to
predict new compound-protein interactions (CPIs) from known CPI network data
using several methods, including machine learning and data mining. Although
CGBVS facilitates highly efficient and accurate CPI prediction, it has poor
performance for prediction of new compounds for which CPIs are unknown. The
pairwise kernel method (PKM) is a state-of-the-art CGBVS method and shows high
accuracy for prediction of new compounds. In this study, on the basis of link
mining, we improved the PKM by combining link indicator kernel (LIK) and
chemical similarity and evaluated the accuracy of these methods. The proposed
method obtained an average area under the precision-recall curve (AUPR) value
of 0.562, which was higher than that achieved by the conventional Gaussian
interaction profile (GIP) method (0.425), and the calculation time was only
increased by a few percent
Dynamic Discovery of Type Classes and Relations in Semantic Web Data
The continuing development of Semantic Web technologies and the increasing
user adoption in the recent years have accelerated the progress incorporating
explicit semantics with data on the Web. With the rapidly growing RDF (Resource
Description Framework) data on the Semantic Web, processing large semantic
graph data have become more challenging. Constructing a summary graph structure
from the raw RDF can help obtain semantic type relations and reduce the
computational complexity for graph processing purposes. In this paper, we
addressed the problem of graph summarization in RDF graphs, and we proposed an
approach for building summary graph structures automatically from RDF graph
data. Moreover, we introduced a measure to help discover optimum class
dissimilarity thresholds and an effective method to discover the type classes
automatically. In future work, we plan to investigate further improvement
options on the scalability of the proposed method
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