An improved binary particle swarm optimization algorithm for DNA encoding enhancement
The accuracy of DNA computing highly depends on the DNA strands used in solving complex computations. As such, many approaches are proposed to design DNA oligonucleotides that are stable and unique. In this paper, an improved binary particle swarm optimization (IBPSO) algorithm is proposed and imple...
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| Format: | Article |
| Language: | English |
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IEEE
2011
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| Online Access: | http://ir.unimas.my/id/eprint/16643/ http://ir.unimas.my/id/eprint/16643/1/An%20Improved%20Binary%20Particle%20Swarm%20Optimization%20%28abstract%29.pdf |
| _version_ | 1848838104772771840 |
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| author | Mohd Saufee, Muhammad Krishna Veni, Selvan Sharifah Masniah, Wan Masra |
| author_facet | Mohd Saufee, Muhammad Krishna Veni, Selvan Sharifah Masniah, Wan Masra |
| author_sort | Mohd Saufee, Muhammad |
| building | UNIMAS Institutional Repository |
| collection | Online Access |
| description | The accuracy of DNA computing highly depends on the DNA strands used in solving complex computations. As such, many approaches are proposed to design DNA oligonucleotides that are stable and unique. In this paper, an improved binary particle swarm optimization (IBPSO) algorithm is proposed and implemented. Four objective functions which are H-measure, similarity, hairpin and continuity are employed to define the uniqueness of designed sequences. The DNA words are constrained within a predefined range of GC-content and melting temperature. The performances and the ability of the algorithm to enhance the characteristics of generated DNA code words are analyzed. The results obtained show that this algorithm executes better sequences and did perform better compared to other optimization techniques. Moreover, it converges faster than the previously suggested binary particle swarm optimization algorithm. |
| first_indexed | 2025-11-15T06:50:15Z |
| format | Article |
| id | unimas-16643 |
| institution | Universiti Malaysia Sarawak |
| institution_category | Local University |
| language | English |
| last_indexed | 2025-11-15T06:50:15Z |
| publishDate | 2011 |
| publisher | IEEE |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | unimas-166432017-06-14T06:45:51Z http://ir.unimas.my/id/eprint/16643/ An improved binary particle swarm optimization algorithm for DNA encoding enhancement Mohd Saufee, Muhammad Krishna Veni, Selvan Sharifah Masniah, Wan Masra TK Electrical engineering. Electronics Nuclear engineering The accuracy of DNA computing highly depends on the DNA strands used in solving complex computations. As such, many approaches are proposed to design DNA oligonucleotides that are stable and unique. In this paper, an improved binary particle swarm optimization (IBPSO) algorithm is proposed and implemented. Four objective functions which are H-measure, similarity, hairpin and continuity are employed to define the uniqueness of designed sequences. The DNA words are constrained within a predefined range of GC-content and melting temperature. The performances and the ability of the algorithm to enhance the characteristics of generated DNA code words are analyzed. The results obtained show that this algorithm executes better sequences and did perform better compared to other optimization techniques. Moreover, it converges faster than the previously suggested binary particle swarm optimization algorithm. IEEE 2011 Article PeerReviewed text en http://ir.unimas.my/id/eprint/16643/1/An%20Improved%20Binary%20Particle%20Swarm%20Optimization%20%28abstract%29.pdf Mohd Saufee, Muhammad and Krishna Veni, Selvan and Sharifah Masniah, Wan Masra (2011) An improved binary particle swarm optimization algorithm for DNA encoding enhancement. IEEE Symposium on Swarm Intelligence (SIS), 2011. ISSN ISBN: 978-1-61284-052-9 http://ieeexplore.ieee.org/document/5952579/ DOI: 10.1109/SIS.2011.5952579 |
| spellingShingle | TK Electrical engineering. Electronics Nuclear engineering Mohd Saufee, Muhammad Krishna Veni, Selvan Sharifah Masniah, Wan Masra An improved binary particle swarm optimization algorithm for DNA encoding enhancement |
| title | An improved binary particle swarm optimization algorithm for DNA encoding enhancement |
| title_full | An improved binary particle swarm optimization algorithm for DNA encoding enhancement |
| title_fullStr | An improved binary particle swarm optimization algorithm for DNA encoding enhancement |
| title_full_unstemmed | An improved binary particle swarm optimization algorithm for DNA encoding enhancement |
| title_short | An improved binary particle swarm optimization algorithm for DNA encoding enhancement |
| title_sort | improved binary particle swarm optimization algorithm for dna encoding enhancement |
| topic | TK Electrical engineering. Electronics Nuclear engineering |
| url | http://ir.unimas.my/id/eprint/16643/ http://ir.unimas.my/id/eprint/16643/ http://ir.unimas.my/id/eprint/16643/ http://ir.unimas.my/id/eprint/16643/1/An%20Improved%20Binary%20Particle%20Swarm%20Optimization%20%28abstract%29.pdf |