Error margin analysis for feature gene extraction
<p>Abstract</p> <p>Background</p> <p>Feature gene extraction is a fundamental issue in microarray-based biomarker discovery. It is normally treated as an optimization problem of finding the best predictive feature genes that can effectively and stably discriminate disti...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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BMC
2010-05-01
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| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/11/241 |
| _version_ | 1818642311333019648 |
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| author | Lacy Jessica Zhu Hai Long Chow Chi Kin Kuo Winston P |
| author_facet | Lacy Jessica Zhu Hai Long Chow Chi Kin Kuo Winston P |
| author_sort | Lacy Jessica |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Feature gene extraction is a fundamental issue in microarray-based biomarker discovery. It is normally treated as an optimization problem of finding the best predictive feature genes that can effectively and stably discriminate distinct types of disease conditions, e.g. tumors and normals. Since gene microarray data normally involves thousands of genes at, tens or hundreds of samples, the gene extraction process may fall into local optimums if the gene set is optimized according to the maximization of classification accuracy of the classifier built from it.</p> <p>Results</p> <p>In this paper, we propose a novel gene extraction method of error margin analysis to optimize the feature genes. The proposed algorithm has been tested upon one synthetic dataset and two real microarray datasets. Meanwhile, it has been compared with five existing gene extraction algorithms on each dataset. On the synthetic dataset, the results show that the feature set extracted by our algorithm is the closest to the actual gene set. For the two real datasets, our algorithm is superior in terms of balancing the size and the validation accuracy of the resultant gene set when comparing to other algorithms.</p> <p>Conclusion</p> <p>Because of its distinct features, error margin analysis method can stably extract the relevant feature genes from microarray data for high-performance classification.</p> |
| first_indexed | 2024-12-16T23:41:03Z |
| format | Article |
| id | doaj.art-dd9348375770400fadce9b292b7aee78 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-16T23:41:03Z |
| publishDate | 2010-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-dd9348375770400fadce9b292b7aee782022-12-21T22:11:36ZengBMCBMC Bioinformatics1471-21052010-05-0111124110.1186/1471-2105-11-241Error margin analysis for feature gene extractionLacy JessicaZhu Hai LongChow Chi KinKuo Winston P<p>Abstract</p> <p>Background</p> <p>Feature gene extraction is a fundamental issue in microarray-based biomarker discovery. It is normally treated as an optimization problem of finding the best predictive feature genes that can effectively and stably discriminate distinct types of disease conditions, e.g. tumors and normals. Since gene microarray data normally involves thousands of genes at, tens or hundreds of samples, the gene extraction process may fall into local optimums if the gene set is optimized according to the maximization of classification accuracy of the classifier built from it.</p> <p>Results</p> <p>In this paper, we propose a novel gene extraction method of error margin analysis to optimize the feature genes. The proposed algorithm has been tested upon one synthetic dataset and two real microarray datasets. Meanwhile, it has been compared with five existing gene extraction algorithms on each dataset. On the synthetic dataset, the results show that the feature set extracted by our algorithm is the closest to the actual gene set. For the two real datasets, our algorithm is superior in terms of balancing the size and the validation accuracy of the resultant gene set when comparing to other algorithms.</p> <p>Conclusion</p> <p>Because of its distinct features, error margin analysis method can stably extract the relevant feature genes from microarray data for high-performance classification.</p>http://www.biomedcentral.com/1471-2105/11/241 |
| spellingShingle | Lacy Jessica Zhu Hai Long Chow Chi Kin Kuo Winston P Error margin analysis for feature gene extraction BMC Bioinformatics |
| title | Error margin analysis for feature gene extraction |
| title_full | Error margin analysis for feature gene extraction |
| title_fullStr | Error margin analysis for feature gene extraction |
| title_full_unstemmed | Error margin analysis for feature gene extraction |
| title_short | Error margin analysis for feature gene extraction |
| title_sort | error margin analysis for feature gene extraction |
| url | http://www.biomedcentral.com/1471-2105/11/241 |
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