An Ontology-Driven Clustering Method for Supporting Gene Expression Analysis
CBMS '05 Proceedings of the 18th IEEE Symposium on Computer-Based Medical Systems
Correlation between Gene Expression and GO Semantic Similarity
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Incorporating Gene Ontology in Clustering Gene Expression Data
CBMS '06 Proceedings of the 19th IEEE Symposium on Computer-Based Medical Systems
Feature Extraction: Foundations and Applications (Studies in Fuzziness and Soft Computing)
Feature Extraction: Foundations and Applications (Studies in Fuzziness and Soft Computing)
Proceedings of the 2007 ACM symposium on Applied computing
A review of feature selection techniques in bioinformatics
Bioinformatics
Using Gene Ontology to Enhance Effectiveness of Similarity Measures for Microarray Data
BIBM '08 Proceedings of the 2008 IEEE International Conference on Bioinformatics and Biomedicine
Using information content to evaluate semantic similarity in a taxonomy
IJCAI'95 Proceedings of the 14th international joint conference on Artificial intelligence - Volume 1
The WEKA data mining software: an update
ACM SIGKDD Explorations Newsletter
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine
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To emphasize gene interactions in the classification algorithms, a new representation is proposed, comprising gene-pairs and not single genes. Each pair is represented by L1 difference in the corresponding expression values. The novel representation is evaluated on benchmark datasets and is shown to often increase classification accuracy for genetic datasets. Exploiting the gene-pair representation and the Gene Ontology (GO), the semantic similarity of gene pairs can be incorporated to pre-select pairs with a high similarity value. The GO-based feature selection approach is compared to the plain data driven selection and is shown to often increase classification accuracy.