Evaluation of Convolutionary Neural Networks Modeling of DNA Sequences using Ordinal versus one-hot Encoding Method
Convolutionary neural network (CNN) is a popular choice for supervised DNA motif prediction due to its excellent performances. To employ CNN, the input DNA sequences are required to be encoded as numerical values and represented as either vectors or multi-dimensional matrices. This paper evaluates...
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| Format: | Article |
| Language: | English |
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IEEE
2017
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| Online Access: | http://ir.unimas.my/id/eprint/18960/ http://ir.unimas.my/id/eprint/18960/7/Evaluation%20of%20Convolutionary%20Neural%20Networks%20%28abstract%29.pdf |
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| author | Chieng, Allen Hoon Choong Lee, Nung Kion |
| author_facet | Chieng, Allen Hoon Choong Lee, Nung Kion |
| author_sort | Chieng, Allen Hoon Choong |
| building | UNIMAS Institutional Repository |
| collection | Online Access |
| description | Convolutionary neural network (CNN) is a popular
choice for supervised DNA motif prediction due to its excellent performances. To employ CNN, the input DNA sequences are required to be encoded as numerical values and represented as either vectors or multi-dimensional matrices. This paper evaluates a simple and more compact ordinal encoding method versus the popular one-hot encoding for DNA sequences. We compare the performances of both encoding methods using three sets of datasets enriched with DNA motifs. We found that the ordinal encoding performs comparable to the one-hot method
but with significant reduction in training time. In addition, the one-hot encoding performances are rather consistent across various datasets but would require suitable CNN configuration to perform well. The ordinal encoding with matrix representation performs best in some of the evaluated datasets. This study implies that the performances of CNN for DNA motif discovery depends on the suitable design of the sequence encoding and
representation. The good performances of the ordinal encoding method demonstrates that there are still rooms for improvement for the one-hot encoding method. |
| first_indexed | 2025-11-15T06:58:24Z |
| format | Article |
| id | unimas-18960 |
| institution | Universiti Malaysia Sarawak |
| institution_category | Local University |
| language | English |
| last_indexed | 2025-11-15T06:58:24Z |
| publishDate | 2017 |
| publisher | IEEE |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | unimas-189602019-08-01T02:35:28Z http://ir.unimas.my/id/eprint/18960/ Evaluation of Convolutionary Neural Networks Modeling of DNA Sequences using Ordinal versus one-hot Encoding Method Chieng, Allen Hoon Choong Lee, Nung Kion Q Science (General) Convolutionary neural network (CNN) is a popular choice for supervised DNA motif prediction due to its excellent performances. To employ CNN, the input DNA sequences are required to be encoded as numerical values and represented as either vectors or multi-dimensional matrices. This paper evaluates a simple and more compact ordinal encoding method versus the popular one-hot encoding for DNA sequences. We compare the performances of both encoding methods using three sets of datasets enriched with DNA motifs. We found that the ordinal encoding performs comparable to the one-hot method but with significant reduction in training time. In addition, the one-hot encoding performances are rather consistent across various datasets but would require suitable CNN configuration to perform well. The ordinal encoding with matrix representation performs best in some of the evaluated datasets. This study implies that the performances of CNN for DNA motif discovery depends on the suitable design of the sequence encoding and representation. The good performances of the ordinal encoding method demonstrates that there are still rooms for improvement for the one-hot encoding method. IEEE 2017 Article PeerReviewed text en http://ir.unimas.my/id/eprint/18960/7/Evaluation%20of%20Convolutionary%20Neural%20Networks%20%28abstract%29.pdf Chieng, Allen Hoon Choong and Lee, Nung Kion (2017) Evaluation of Convolutionary Neural Networks Modeling of DNA Sequences using Ordinal versus one-hot Encoding Method. International Conference On Computer And Drone Applications (ICONDA) 2017. ISSN 978-1-5386-0765-7 (ISBN) (In Press) https://www.biorxiv.org/content/early/2017/10/25/186965 DOI: 10.1101/186965 |
| spellingShingle | Q Science (General) Chieng, Allen Hoon Choong Lee, Nung Kion Evaluation of Convolutionary Neural Networks Modeling of DNA Sequences using Ordinal versus one-hot Encoding Method |
| title | Evaluation of Convolutionary Neural Networks Modeling of DNA Sequences using Ordinal versus one-hot Encoding Method |
| title_full | Evaluation of Convolutionary Neural Networks Modeling of DNA Sequences using Ordinal versus one-hot Encoding Method |
| title_fullStr | Evaluation of Convolutionary Neural Networks Modeling of DNA Sequences using Ordinal versus one-hot Encoding Method |
| title_full_unstemmed | Evaluation of Convolutionary Neural Networks Modeling of DNA Sequences using Ordinal versus one-hot Encoding Method |
| title_short | Evaluation of Convolutionary Neural Networks Modeling of DNA Sequences using Ordinal versus one-hot Encoding Method |
| title_sort | evaluation of convolutionary neural networks modeling of dna sequences using ordinal versus one-hot encoding method |
| topic | Q Science (General) |
| url | http://ir.unimas.my/id/eprint/18960/ http://ir.unimas.my/id/eprint/18960/ http://ir.unimas.my/id/eprint/18960/ http://ir.unimas.my/id/eprint/18960/7/Evaluation%20of%20Convolutionary%20Neural%20Networks%20%28abstract%29.pdf |