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 very high performance. 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...
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| Format: | Article |
| Language: | English |
| Published: |
IEEE
2018
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| Online Access: | http://ir.unimas.my/id/eprint/19014/ http://ir.unimas.my/id/eprint/19014/1/encoding1.pdf |
| _version_ | 1848838630850691072 |
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| author | Choong, Allen Chieng Hoon Lee, Nung Kion |
| author_facet | Choong, Allen Chieng Hoon Lee, Nung Kion |
| author_sort | Choong, Allen Chieng Hoon |
| building | UNIMAS Institutional Repository |
| collection | Online Access |
| description | Convolutionary neural network (CNN) is a popular choice for supervised DNA motif prediction due to its very high performance. 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 | 2025-11-15T06:58:37Z |
| format | Article |
| id | unimas-19014 |
| institution | Universiti Malaysia Sarawak |
| institution_category | Local University |
| language | English |
| last_indexed | 2025-11-15T06:58:37Z |
| publishDate | 2018 |
| publisher | IEEE |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | unimas-190142021-11-03T02:26:34Z http://ir.unimas.my/id/eprint/19014/ Evaluation of Convolutionary Neural Networks Modeling of DNA Sequences using Ordinal versus one-hot Encoding Method Choong, Allen Chieng Hoon Lee, Nung Kion Q Science (General) QA75 Electronic computers. Computer science T Technology (General) Convolutionary neural network (CNN) is a popular choice for supervised DNA motif prediction due to its very high performance. 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 2018-01-29 Article PeerReviewed text en http://ir.unimas.my/id/eprint/19014/1/encoding1.pdf Choong, Allen Chieng Hoon and Lee, Nung Kion (2018) Evaluation of Convolutionary Neural Networks Modeling of DNA Sequences using Ordinal versus one-hot Encoding Method. IEEE Xplore, 1 (2018). pp. 1-6. https://ieeexplore.ieee.org/abstract/document/8270400 10.1109/ICONDA.2017.8270400 |
| spellingShingle | Q Science (General) QA75 Electronic computers. Computer science T Technology (General) Choong, Allen Chieng Hoon 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) QA75 Electronic computers. Computer science T Technology (General) |
| url | http://ir.unimas.my/id/eprint/19014/ http://ir.unimas.my/id/eprint/19014/ http://ir.unimas.my/id/eprint/19014/ http://ir.unimas.my/id/eprint/19014/1/encoding1.pdf |