An Intelligent Optimization Algorithm for Constructing a DNA Storage Code: NOL-HHO
Abstract
:1. Introduction
2. Constraints on DNA Codes
3. Improve the Constrained DNA-Sequence Lower Bound’s Method
3.1. The Original Algorithm (HHO)
3.2. The Improved Algorithm (NOL-HHO)
3.2.1. Nonlinear Control Parameter Strategy
3.2.2. Random Opposition-Based Learning Strategy
3.3. NOL-HHO Algorithm’s Pseudocode and Flow Char
4. Test of the Proposed Algorithm NOL-HHO
4.1. Benchmark Test Functions
4.2. Comparison of Test Results with Other Algorithms
4.3. Wilcoxon Rank-Sum Test
5. Bound DNA Storage Constraint Coding
6. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
- Wang, Y.; Noor-A-Rahim, M.D.; Gunawan, E.; Guan, Y.; Poh, C.L. Construction of bio-constrained code for DNA data storage. IEEE Commun. Lett. 2019, 23, 963–966. [Google Scholar] [CrossRef]
- Li, D.; Wang, Y.; Noor-A-Rahim, M.D.; Guan, Y.; Shi, Z.; Gunawan, E. Optimized code design for constrained DNA data storage with asymmetric errors. IEEE Access 2019, 7, 84107–84121. [Google Scholar]
- Ping, Z.; Ma, D.; Huang, X.; Chen, S.; Liu, L.; Guo, F.; Zhu, S.J.; Shen, Y. Carbon-based archiving: Current progress and future prospects of DNA-based data storage. GigaScience 2019, 8, giz075. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Church, G.M.; Gao, Y.; Kosuri, S. Next-generation digital information storage in DNA. Science 2012, 337, 1628. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Zhang, S.; Huang, B.; Song, X.; Zhang, T.; Wang, H.; Liu, Y. A high storage density strategy for digital information based on synthetic DNA. 3 Biotech 2019, 9, 342. [Google Scholar] [CrossRef] [PubMed]
- Goldman, N.; Bertone, P.; Chen, S.; Dessimoz, C.; Leproust, E.M.; Sipos, B. Towards practical, high-capacity, low-maintenance information storage in synthesized DNA. Nature 2013, 494, 77–80. [Google Scholar] [CrossRef] [PubMed]
- Erlich, Y.; Zielinski, D. DNA Fountain enables a robust and efficient storage architecture. Science 2017, 355, 950–954. [Google Scholar] [CrossRef] [Green Version]
- Palluk, S.; Arlow, D.H.; Rond, T.D.; Barthel, S.; Kang, J.S.; Bector, R. De novo DNA synthesis using polymerase-nucleotide conjugates. Nat. Biotechnol. 2018, 36, 645–650. [Google Scholar] [CrossRef]
- Shendure, J.; Balasubramanian, S.; Church, G.M.; Gilbert, W.; Rogers, J.; Schloss, J.A. DNA sequencing at 40: Past, present and future. Nature 2017, 550, 345–353. [Google Scholar] [CrossRef]
- Baum, E.B. Building an associative memory vastly larger than the brain. Science 1995, 268, 583–585. [Google Scholar] [CrossRef] [Green Version]
- Clelland, C.T.; Risca, V.; Bancroft, C. Hiding messages in DNA microdots. Nature 1999, 399, 533–534. [Google Scholar] [CrossRef]
- Bancroft, C.; Bowler, T.; Bloom, B.; Clelland, C.T. Long-Term Storage of Information in DNA. Science 2001, 293, 1763–1765. [Google Scholar] [CrossRef]
- Kashiwamura, S.; Yamamoto, M.; Kameda, A.; Shiba, T.; Ohuchi, A. Potential for enlarging DNA memory: The validity of experimental operations of scaled-up nested primer molecular memory. BioSystems 2005, 80, 99–112. [Google Scholar] [CrossRef]
- Ailenberg, M.; Rotstein, O. An improved Huffman coding method for archiving text, images, and music characters in DNA. BioTechniques 2009, 47, 747–754. [Google Scholar] [CrossRef]
- Yazdi, S.M.H.T.; Yuan, Y.; Ma, J.; Zhao, H.; Milenkovic, O. A rewritable, random-access DNA-based storage system. Sci. Rep. 2015, 5, 14138. [Google Scholar] [CrossRef]
- Bornholt, J.; Lopez, R.; Carmean, D.M.; Ceze, L.; Seelig, G.; Strauss, K. A DNA-based archival storage system. Archit. Support Program. Lang. Oper. Syst. 2016, 44, 637–649. [Google Scholar]
- Blawat, M.; Gaedke, K.; Hütter, I.; Chen, X.; Turczyk, B.; Inverso, S. Forward error correction for DNA data storage. Int. Conf. Concept. Struct. 2016, 80, 1011–1022. [Google Scholar] [CrossRef] [Green Version]
- Yazdi, S.M.H.T.; Gabrys, R.; Milenkovic, O. Portable and Error-Free DNA-Based Data Storage. Sci. Rep. 2017, 7, 5011. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Gabrys, R.; Kiah, H.M.; Milenkovic, O. Asymmetric Lee distance codes for DNA-based storage. IEEE Trans. Inf. Theory 2017, 63, 4982–4995. [Google Scholar] [CrossRef]
- Immink, K.A.S.; Cai, K. Design of capacity-approaching constrained codes for DNA-based storage systems. IEEE Commun. Lett. 2018, 22, 224–227. [Google Scholar] [CrossRef]
- Organick, L.; Ang, S.D.; Chen, Y.J.; Lopez, R.; Yekhanin, S.; Makarychev, K. Random access in large-scale DNA data storage. Nat. Biotechnol. 2018, 36, 242–248. [Google Scholar] [CrossRef] [PubMed]
- Yazdi, S.M.H.T.; Kiah, H.M.; Gabrys, R.; Milenkovic, O. Mutually uncorrelated primers for DNA-based data storage. IEEE Trans. Inf. Theory. 2018, 64, 6283–6296. [Google Scholar] [CrossRef] [Green Version]
- Song, W.; Cai, K.; Zhang, M.; Yuen, C. Codes with run-length and GC-content constraints for DNA-based data storage. IEEE Commun. Lett. 2018, 22, 2004–2007. [Google Scholar] [CrossRef]
- Carmean, D.; Ceze, L.; Seelig, G.; Stewart, K.; Strauss, K.; Willsey, M. DNA data storage and hybrid molecular –electronic computing. Proc. IEEE 2018, 107, 63–72. [Google Scholar] [CrossRef]
- Heckel, R.; Mikutis, G.; Grass, R.N. A Characterization of the DNA Data storage Channel. Sci. Rep. 2019, 9, 1–12. [Google Scholar] [CrossRef] [Green Version]
- Limbachiya, D.; Gupta, M.K.; Aggarwal, V. Family of constrained codes for archival DNA data storage. IEEE Commun. Lett. 2018, 22, 1972–1975. [Google Scholar] [CrossRef]
- Takahashi, C.N.; Nguyen, B.H.; Strauss, K.; Ceze, L. Demonstration of end-to-end automation of DNA data storage. Sci. Rep. 2019, 9, 4998. [Google Scholar] [CrossRef] [Green Version]
- Sun, J.; Wang, Q.; Diao, W.; Zhou, C.; Wang, B.; Rao, L. Digital information storage on DNA in living organisms. Med Res. Arch. 2019, 7. [Google Scholar] [CrossRef]
- Ceze, L.; Nivala, J.; Strauss, K. Molecular digital data storage using DNA. Nat. Rev. Genet. 2019, 20, 456–466. [Google Scholar] [CrossRef]
- Wang, Y.; Keith, M.; Leyme, A.; Bergelson, S.; Feschenko, M. Monitoring long-term DNA storage via absolute copy number quantification by ddPCR. Anal. Biochem. 2019, 583. [Google Scholar] [CrossRef]
- Anavy, L.; Vaknin, I.; Atar, O.; Amit, R.; Yakhini, Z. Data storage in DNA with fewer synthesis cycles using composite DNA letters. Nat. Biotechnol. 2019, 37, 1229–1236. [Google Scholar] [CrossRef] [PubMed]
- Li, X.; Wang, B.; Lv, H.; Yin, Q.; Zhang, Q.; Wei, X. Constraining DNA sequences with a triplet-bases unpaired. IEEE Trans. NanoBiosci. 2020. [Google Scholar] [CrossRef] [PubMed]
- Wang, B.; Zhang, Q.; Wei, X. Tabu Variable Neighborhood Search for Designing DNA Barcodes. IEEE Trans. NanoBiosci. 2020, 19, 127–131. [Google Scholar] [CrossRef] [PubMed]
- Heidari, A.A.; Mirjalili, S.; Faris, H.; Aljarah, I.; Mafarja, M.; Chen, H. Harris hawks optimization: Algorithm and applications. Future Gener. Comput. Syst. 2019, 97, 849–872. [Google Scholar] [CrossRef]
- Bui, D.T.; Moayedi, H.; Kalantar, B.; Osouli, A.; Pradhan, B.; Nguyen, H. A novel swarm intelligence—Harris hawks optimization for spatial assessment of landslide susceptibility. Sensors 2019, 19, 3590. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Jia, H.; Lang, C.; Oliva, D.; Song, W.; Peng, X. Dynamic Harris Hawks Optimization with Mutation Mechanism for Satellite Image Segmentation. Remote Sens. 2019, 11, 1421. [Google Scholar] [CrossRef] [Green Version]
- Bao, X.; Jia, H.; Lang, C. A Novel Hybrid Harris Hawks Optimization for Color Image Multilevel Thresholding Segmentation. IEEE Access 2019, 7, 76529–76546. [Google Scholar] [CrossRef]
- Teng, Z.; Lv, J.; Guo, L. An improved hybrid grey wolf optimization algorithm. Soft Comput. 2019, 23, 6617–6631. [Google Scholar] [CrossRef]
- Tizhoosh, H.R. Opposition-Based Learning: A New Scheme for Machine Intelligence. In Proceedings of the International Conference on Computational Intelligence for Modelling, Control and Automation and International Conference on Intelligent Agents, Web Technologies and Internet Commerce (CIMCA-IAWTIC’06), Vienna, Austria, 28–30 November 2005; pp. 695–701. [Google Scholar]
- Banerjee, A.; Herjee, V.M.; Ghoshal, S.P. An opposition-based harmony search algorithm for engineering optimization problems. Ain Shams Eng. J. 2014, 5, 85–101. [Google Scholar] [CrossRef] [Green Version]
- Dong, W.; Kang, L.; Zhang, W. Opposition-based particle swarm optimization with adaptive mutation strategy. Soft Comput. 2017, 21, 5081–5090. [Google Scholar] [CrossRef]
- Ibrahim, R.A.; Elaziz, M.A.; Oliva, D.; Cuevas, E.; Lu, S. An opposition-based social spider optimization for feature selection. Soft Comput. 2019, 23, 13547–13567. [Google Scholar] [CrossRef]
- Digalakis, J.G.; Margaritis, K.G. On benchmarking functions for genetic algorithms. Int. J. Comput. Math. 2000, 77, 481–506. [Google Scholar] [CrossRef]
- Yao, X.; Liu, Y.; Lin, G. Evolutionary programming made faster. IEEE Trans. Evol. Comput. 1999, 3, 82–102z. [Google Scholar]
- Simon, D. Biogeography-Based Optimization. IEEE Trans. Evol. Comput. 2008, 12, 702–713. [Google Scholar] [CrossRef] [Green Version]
- Yang, X.; Karamanoglu, M.; He, X. Flower pollination algorithm: A novel approach for multiobjective optimization. Eng. Optim. 2013, 46, 1222–1237. [Google Scholar] [CrossRef] [Green Version]
- Mirjalili, S.; Mirjalili, S.M.; Lewis, A. Grey Wolf Optimizer. Adv. Eng. Softw. 2014, 69, 46–61. [Google Scholar] [CrossRef] [Green Version]
- Yang, X.; Gandomi, A.H. Bat algorithm: A novel approach for global engineering optimization. Eng. Comput. 2012, 29, 464–483. [Google Scholar] [CrossRef] [Green Version]
- Gandomi, A.H.; Yang, X.; Alavi, A.H. Mixed variable structural optimization using Firefly Algorithm. Comput. Struct. 2011, 89, 23–24. [Google Scholar] [CrossRef]
- Mirjalili, S. Moth-flame optimization algorithm. Knowl. -Based Syst. 2015, 89, 228–249. [Google Scholar] [CrossRef]
- Cao, B.; Zhao, S.; Li, X.; Wang, B. K-means Multi-Verse Optimizer (KMVO) Algorithm to Construct DNA Storage Codes. IEEE Access 2020, 8, 29547–29556. [Google Scholar] [CrossRef]
- Derrac, J.; García, S.; Molina, D.; Herrera, F. A practical tutorial on the use of nonparametric statistical tests as a methodology for comparing evolutionary and swarm intelligence algorithms. Swarm Evol. Comput. 2011, 1, 3–18. [Google Scholar] [CrossRef]
- Mirjalili, S. Dragonfly algorithm: A new meta-heuristic optimization technique for solving single-objective, discrete, and multi-objective problems. Neural Comput. Appl. 2016, 27, 1053–1073. [Google Scholar] [CrossRef]
- Limbachiya, D.; Dhameliya, V.; Khakhar, M.; Gupta, M.K. On optimal family of codes for archival DNA storage. In 2015 Seventh International Workshop on Signal Design and Its Applications in Communications (IWSDA); IEEE: Bengaluru, India, 2015; pp. 123–127. [Google Scholar] [CrossRef] [Green Version]
- Dong, Y.; Sun, F.; Ping, Z.; Ouyang, Q.; Qian, L. DNA storage: Research landscape and future prospects. Natl. Sci. Rev. 2020, nwaa007. [Google Scholar] [CrossRef] [Green Version]
- Song, T.; Rodriguez-Paton, A.; Zheng, P.; Zeng, X. Spiking neural P systems with colored spikes. IEEE Trans. Cogn. Dev. Syst. 2018, 10, 1106–1115. [Google Scholar] [CrossRef]
- Wang, B.; Xie, Y.; Zhou, S.; Zheng, X.; Zhou, C. Correcting errors in image encryption based on DNA coding. Molecules 2018, 23, 1878. [Google Scholar] [CrossRef] [Green Version]
- Song, T.; Pang, S.; Hao, S.; Rodríguez-Patón, A.; Zheng, P. A parallel image skeletonizing method using spiking neural P systems with weights. Neural Process. Lett. 2019, 50, 1485–1502. [Google Scholar] [CrossRef]
- Song, T.; Pan, L.; Wu, T.; Zheng, P.; Wong, M.L.D.; Rodriguez-Paton, A. Spiking neural P systems with learning functions. IEEE Trans. NanoBiosci. 2019, 18, 176–190. [Google Scholar] [CrossRef]
- Koch, J.; Gantenbein, S.; Masania, K.; Stark, W.J.; Erlich, Y.; Grass, R.N. A DNA-of-things storage architecture to create materials with embedded memory. Nat. Biotechnol. 2020, 38, 39–43. [Google Scholar] [CrossRef]
- Lopez, R.; Chen, Y.J.; Ang, S.D.; Yekhanin, S.; Makarychev, K.; Racz, M.Z.; Seelig, G.; Strauss, K.; Ceze, L. DNA assembly for nanopore data storage readout. Nat. Commun. 2019, 10, 1–9. [Google Scholar] [CrossRef] [Green Version]
ID | Metric | NOL-HHO | HHO | GA | PSO | BBO | FPA | GWO | BAT | FA | MFO | DE |
---|---|---|---|---|---|---|---|---|---|---|---|---|
F1 | AVG | 0.00 × 10+00 | 3.95 × 10−97 | 1.03 × 10+03 | 1.83 × 10+04 | 7.59 × 10+01 | 2.01 × 10+03 | 1.18 × 10−27 | 6.59 × 10+04 | 7.11 × 10−03 | 1.01 × 10+03 | 1.33 × 10−03 |
STD | 0.00 × 10+00 | 1.72 × 10−96 | 5.79 × 10+02 | 3.01 × 10+03 | 2.75 × 10+01 | 5.60 × 10+02 | 1.47 × 10−27 | 7.51 × 10+03 | 3.21 × 10−03 | 3.05 × 10+03 | 5.92 × 10−04 | |
F2 | AVG | 0.00 × 10+00 | 1.56 × 10−51 | 2.47 × 10+01 | 3.58 × 10+02 | 1.36 × 10−03 | 3.22 × 10+01 | 9.71 × 10−17 | 2.71 × 10+08 | 4.34 × 10−01 | 3.19 × 10+01 | 6.83 × 10−03 |
STD | 0.00 × 10+00 | 6.98 × 10−51 | 5.68 × 10+00 | 1.35 × 10+03 | 7.45 × 10−03 | 5.55 × 10+00 | 5.60 × 10−17 | 1.30 × 10+09 | 1.84 × 10−01 | 2.06 × 10+01 | 2.06 × 10−03 | |
F3 | AVG | 0.00 × 10+00 | 1.92 × 10−63 | 2.65 × 10+04 | 4.05 × 10+04 | 1.21 × 10+04 | 1.41 × 10+03 | 5.12 × 10−05 | 1.38 × 10+05 | 1.66 × 10+03 | 2.43 × 10+04 | 3.97 × 10+04 |
STD | 0.00 × 10+00 | 1.05 × 10−62 | 3.44 × 10+03 | 8.21 × 10+03 | 2.69 × 10+03 | 5.59 × 10+02 | 2.03 × 10−04 | 4.72 × 10+04 | 6.72 × 10+02 | 1.41 × 10+04 | 5.37 × 10+03 | |
F4 | AVG | 0.00 × 10+00 | 1.02 × 10−47 | 5.17 × 10+01 | 4.39 × 10+01 | 3.02 × 10+01 | 2.38 × 10+01 | 1.24 × 10−06 | 8.51 × 10+01 | 1.11 × 10−01 | 7.00 × 10+01 | 1.15 × 10+01 |
STD | 0.00 × 10+00 | 5.01 × 10−47 | 1.05 × 10+01 | 3.64 × 10+00 | 4.39 × 10+00 | 2.77 × 10+00 | 1.94 × 10−06 | 2.95 × 10+00 | 4.75 × 10−02 | 7.06 × 10+00 | 2.37 × 10+00 | |
F5 | AVG | 1.90 × 10−03 | 1.32 × 10−02 | 1.95 × 10+04 | 1.96 × 10+07 | 1.82 × 10+03 | 3.17 × 10+05 | 2.70 × 10+01 | 2.10 × 10+08 | 7.97 × 10+01 | 7.35 × 10+03 | 1.06 × 10+02 |
STD | 4.25 × 10−03 | 1.87 × 10−02 | 1.31 × 10+04 | 6.25 × 10+06 | 9.40 × 10+02 | 1.75 × 10+05 | 7.78 × 10−01 | 4.17 × 10+07 | 7.39 × 10+01 | 2.26 × 10+04 | 1.01 × 10+02 | |
F6 | AVG | 6.73 × 10−09 | 1.15 × 10−04 | 9.01 × 10+02 | 1.87 × 10+04 | 6.71 × 10+01 | 1.70 × 10+03 | 8.44 × 10−01 | 6.69 × 10+04 | 6.94 × 10−03 | 2.68 × 10+03 | 1.44 × 10−03 |
STD | 2.95 × 10−05 | 1.56 × 10−04 | 2.84 × 10+02 | 2.92 × 10+03 | 2.20 × 10+01 | 3.13 × 10+02 | 3.18 × 10−01 | 5.87 × 10+03 | 3.61 × 10−03 | 5.84 × 10+03 | 5.38 × 10−04 | |
F7 | AVG | 7.91 × 10−05 | 1.40 × 10−04 | 1.91 × 10−01 | 1.07 × 10+01 | 2.91 × 10−03 | 3.41 × 10−01 | 1.70 × 10−03 | 4.57 × 10+01 | 6.62 × 10−02 | 4.50 × 10+00 | 5.24 × 10−02 |
STD | 4.02 × 10−05 | 1.07 × 10−04 | 1.50 × 10−01 | 3.05 × 10+00 | 1.83 × 10−03 | 1.10 × 10−01 | 1.06 × 10−03 | 7.82 × 10+00 | 4.23 × 10−02 | 9.21 × 10+00 | 1.37 × 10−02 | |
F8 | AVG | −1.26 × 10+04 | −1.25 × 10+04 | −1.26 × 10+04 | −3.86× 10+03 | −1.24 × 10+04 | −6.45 × 10+03 | −5.97 × 10+03 | −2.33 × 10+03 | −5.85 × 10+03 | −8.48 × 10+03 | −6.82× 10+03 |
STD | 2.17 × 10−01 | 1.47 × 10+02 | 4.51 × 10+00 | 2.49 × 10+02 | 3.50 × 10+01 | 3.03 × 10+02 | 7.10 × 10+02 | 2.96 × 10+02 | 1.16 × 10+03 | 7.98 × 10+02 | 3.94 × 10+02 | |
F9 | AVG | 0.00 × 10+00 | 0.00 × 10+00 | 9.04 × 10+00 | 2.87 × 10+02 | 0.00 × 10+00 | 1.82 × 10+02 | 2.19 × 10+00 | 1.92 × 10+02 | 3.82 × 10+01 | 1.59 × 10+02 | 1.58 × 10+02 |
STD | 0.00 × 10+00 | 0.00 × 10+00 | 4.58 × 10+00 | 1.95 × 10+01 | 0.00 × 10+00 | 1.24 × 10+01 | 3.69 × 10+00 | 3.56 × 10+01 | 1.12 × 10+01 | 3.21 × 10+01 | 1.17 × 10+01 | |
F10 | AVG | 8.88 × 10−16 | 8.88 × 10−16 | 1.36 × 10+01 | 1.75 × 10+01 | 2.13 × 10+00 | 7.14 × 10+00 | 1.03 × 10−13 | 1.92 × 10+01 | 4.58 × 10−02 | 1.74 × 10+01 | 1.21 × 10−02 |
STD | 0.00 × 10+00 | 4.01 × 10−31 | 1.51 × 10+00 | 3.67 × 10−01 | 3.53 × 10−01 | 1.08 × 10+00 | 1.70 × 10−14 | 2.43 × 10−01 | 1.20 × 10−02 | 4.95 × 10+00 | 3.30 × 10−03 | |
F11 | AVG | 0.00 × 10+00 | 0.00 × 10+00 | 1.01 × 10+01 | 1.70 × 10+02 | 1.46 × 10+00 | 1.73 × 10+01 | 4.76 × 10−03 | 6.01 × 10+02 | 4.23 × 10−03 | 3.10 × 10+01 | 3.52 × 10−02 |
STD | 0.00 × 10+00 | 0.00 × 10+00 | 2.43 × 10+00 | 3.17 × 10+01 | 1.69 × 10−01 | 3.63 × 10+00 | 8.57 × 10−03 | 5.50 × 10+01 | 1.29 × 10−03 | 5.94 × 10+01 | 7.20 × 10−02 | |
F12 | AVG | 3.17 × 10−07 | 2.08 × 10−06 | 4.77 × 10+00 | 1.51 × 10+07 | 6.68 × 10−01 | 3.05 × 10+02 | 4.83 × 10−02 | 4.71 × 10+08 | 3.13 × 10−04 | 2.46 × 10+02 | 2.25 × 10−03 |
STD | 5.24 × 10-07 | 1.19 × 10−05 | 1.56 × 10+00 | 9.88 × 10+06 | 2.62 × 10−01 | 1.04 × 10+03 | 2.12 × 10−02 | 1.54 × 10+08 | 1.76 × 10−04 | 1.21 × 10+03 | 1.70 × 10−03 | |
F13 | AVG | 2.27 × 10−06 | 1.57 × 10−04 | 1.52 × 10+01 | 5.73 × 10+07 | 1.82 × 10+00 | 9.59 × 10+04 | 5.96 × 10−01 | 9.40 × 10+08 | 2.08 × 10−03 | 2.73 × 10+07 | 9.12 × 10−03 |
STD | 1.42 × 10−05 | 2.15 × 10−04 | 4.52 × 10+00 | 2.68 × 10+07 | 3.41 × 10−01 | 1.46 × 10+05 | 2.23 × 10−01 | 1.67 × 10+08 | 9.62 × 10−04 | 1.04 × 10+08 | 1.16 × 10−02 |
ID | Metric | NOL-HHO | HHO | GA | PSO | BBO | FPA | GWO | BAT | FA | MFO | DE |
---|---|---|---|---|---|---|---|---|---|---|---|---|
F14 | AVG | 9.98 × 10−01 | 9.98 × 10−01 | 9.98 × 10−01 | 1.39 × 10+00 | 9.98 × 10−01 | 9.98 × 10−01 | 4.17 × 10+00 | 1.27 × 10+01 | 3.51 × 10+00 | 2.74 × 10+00 | 1.23 × 10+00 |
STD | 4.77 × 10−01 | 9.23 × 10−01 | 4.52 × 10−16 | 4.60 × 10−01 | 4.52 × 10−16 | 2.00 × 10−04 | 3.61 × 10+00 | 6.96 × 10+00 | 2.16 × 10+00 | 1.82 × 10+00 | 9.23 × 10−01 | |
F15 | AVG | 3.08 × 10−04 | 3.10 × 10−04 | 3.33 × 10−02 | 1.61 × 10−03 | 1.66 × 10−02 | 6.88 × 10−04 | 6.24 × 10−03 | 3.00 × 10−02 | 1.01 × 10−03 | 2.35 × 10−03 | 5.63 × 10−04 |
STD | 4.23 × 10−05 | 1.97 × 10−04 | 2.70 × 10−02 | 4.60 × 10−04 | 8.60 × 10−03 | 1.55 × 10−04 | 1.25 × 10−02 | 3.33 × 10−02 | 4.01 × 10−04 | 4.92 × 10−03 | 2.81 × 10−04 | |
F16 | AVG | −1.03 × 10+00 | −1.03 × 10+00 | −3.78 × 10−01 | −1.03 × 10+00 | −8.30 × 10−01 | −1.03 × 10+00 | −1.03 × 10+00 | −6.87 × 10−01 | −1.03 × 10+00 | −1.03 × 10+00 | −1.03 × 10+00 |
STD | 1.42 × 10−08 | 6.78 × 10−16 | 3.42 × 10−01 | 2.95 × 10−03 | 3.16 × 10−01 | 6.78 × 10−16 | 6.78 × 10−16 | 8.18 × 10−01 | 6.78 × 10−16 | 6.78 × 10−16 | 6.78 × 10−16 | |
F17 | AVG | 3.98 × 10−01 | 3.98 × 10−01 | 5.24 × 10−01 | 4.00 × 10−01 | 5.49 × 10−01 | 3.98 × 10−01 | 3.98 × 10−01 | 3.98 × 10−01 | 3.98 × 10−01 | 3.98 × 10−01 | 3.98 × 10−01 |
STD | 4.92 × 10−06 | 2.54 × 10−06 | 6.06 × 10−02 | 1.39 × 10−03 | 6.05 × 10−02 | 1.69 × 10−16 | 1.69 × 10−16 | 1.58 × 10−03 | 1.69 × 10−16 | 1.69 × 10−16 | 1.69 × 10−16 | |
F18 | AVG | 3.00 × 10+00 | 3.00 × 10+00 | 3.00 × 10+00 | 3.10 × 10+00 | 3.00 × 10+00 | 3.00 × 10+00 | 3.00 × 10+00 | 1.47 × 10+01 | 3.00 × 10+00 | 3.00 × 10+00 | 3.00 × 10+00 |
STD | 7.69 × 10−07 | 0.00 × 10+00 | 0.00 × 10+00 | 7.60 × 10−02 | 0.00 × 10+00 | 0.00 × 10+00 | 4.07 × 10−05 | 2.21 × 10+01 | 0.00 × 10+00 | 0.00 × 10+00 | 0.00 × 10+00 | |
F19 | AVG | −3.86 × 10+00 | −3.86 × 10+00 | −3.42 × 10+00 | −3.86 × 10+00 | −3.78 × 10+00 | −3.86 × 10+00 | −3.86 × 10+00 | −3.84 × 10+00 | −3.86 × 10+00 | −3.86 × 10+00 | −3.86 × 10+00 |
STD | 1.43 × 10−03 | 2.44 × 10−03 | 3.03 × 10−01 | 1.24 × 10−03 | 1.26 × 10−01 | 3.16 × 10−15 | 3.14 × 10−03 | 1.41 × 10−01 | 3.16 × 10−15 | 1.44 × 10−03 | 3.16 × 10−15 | |
F20 | AVG | −3.260 | −3.322 | −1.61351 | −3.11088 | −2.70774 | −3.2951 | −3.25866 | −3.2546 | −3.28105 | −3.23509 | −3.27048 |
STD | 0.115550 | 0.137406 | 0.46049 | 0.029126 | 0.357832 | 0.019514 | 0.064305 | 0.058943 | 0.063635 | 0.064223 | 0.058919 | |
F21 | AVG | −10.1532 | −10.1451 | −6.66177 | −4.14764 | −8.31508 | −5.21514 | −8.64121 | −4.2661 | −7.67362 | −6.8859 | −9.64796 |
STD | 0.001000 | 0.885673 | 3.732521 | 0.919578 | 2.883867 | 0.008154 | 2.563356 | 2.554009 | 3.50697 | 3.18186 | 1.51572 | |
F22 | AVG | −10.4028 | −10.4015 | −5.58399 | −6.01045 | −9.38408 | −5.34373 | −10.4014 | −5.60638 | −9.63827 | −8.26492 | −9.74807 |
STD | 0.000850 | 1.352375 | 2.605837 | 1.962628 | 2.597238 | 0.053685 | 0.000678 | 3.022612 | 2.293901 | 3.076809 | 1.987703 | |
F23 | AVG | −10.5364 | −10.5364 | −4.69882 | −4.72192 | −6.2351 | −5.29437 | −10.0836 | −3.97284 | −9.75489 | −7.65923 | −10.5364 |
STD | 0.000940 | 0.927655 | 3.256702 | 1.742618 | 3.78462 | 0.356377 | 1.721889 | 3.008279 | 2.345487 | 3.576927 | 8.88 × 10−15 |
ID | Metric | NOL-HHO (100dim) | HHO (100 dim) | NOL-HHO (500 dim) | HHO (500 dim) | NOL-HHO (1000 dim) | HHO (1000 dim) |
---|---|---|---|---|---|---|---|
F1 | AVG | 0.00 × 10+00 | 1.91 × 10−94 | 0.00 × 10+00 | 1.46 × 10−92 | 0.00 × 10+00 | 1.06 × 10−94 |
STD | 0.00 × 10+00 | 8.66 × 10−94 | 0.00 × 10+00 | 8.01 × 10−92 | 0.00 × 10+00 | 4.97 × 10−94 | |
F2 | AVG | 0.00 × 10+00 | 9.98 × 10−52 | 0.00 × 10+00 | 7.87 × 10−49 | 0.00 × 10+00 | 2.52 × 10−50 |
STD | 0.00 × 10+00 | 2.66 × 10−51 | 0.00 × 10+00 | 3.11 × 10−48 | 0.00 × 10+00 | 5.02 × 10−50 | |
F3 | AVG | 0.00 × 10+00 | 1.84 × 10−59 | 0.00 × 10+00 | 6.54 × 10−37 | 0.00 × 10+00 | 1.79 × 10−17 |
STD | 0.00 × 10+00 | 1.01 × 10−58 | 0.00 × 10+00 | 3.58 × 10−36 | 0.00 × 10+00 | 9.81 × 10−17 | |
F4 | AVG | 0.00 × 10+00 | 8.76 × 10−47 | 0.00 × 10+00 | 1.29 × 10−47 | 0.00 × 10+00 | 1.43 × 10−46 |
STD | 0.00 × 10+00 | 4.79 × 10−46 | 0.00 × 10+00 | 4.11 × 10−47 | 0.00 × 10+00 | 7.74 × 10−46 | |
F5 | AVG | 1.22 × 10−04 | 2.36 × 10−02 | 6.66 × 10−02 | 3.10 × 10−01 | 2.29 × 10−02 | 5.73 × 10−01 |
STD | 5.95 × 10−03 | 2.99 × 10−02 | 4.79 × 10−02 | 3.73 × 10−01 | 1.01 × 10−01 | 1.40 × 10+00 | |
F6 | AVG | 7.71 × 10−06 | 5.12 × 10−04 | 6.85 × 10−06 | 2.94 × 10−03 | 1.81 × 10−04 | 3.61 × 10−03 |
STD | 6.62 × 10−05 | 6.77 × 10−04 | 8.04 × 10−04 | 3.98 × 10−01 | 1.02 × 10−03 | 5.38 × 10−03 | |
F7 | AVG | 6.59 × 10−05 | 1.85 × 10−04 | 2.24 × 10−05 | 2.51 × 10−04 | 3.81 × 10−06 | 1.41 × 10−04 |
STD | 3.63 × 10−05 | 4.06 × 10−04 | 2.87 × 10−05 | 2.43 × 10−04 | 5.79 × 10−05 | 1.63 × 10−04 | |
F8 | AVG | −4.19 × 10+04 | −4.19 × 10+04 | −2.09 × 10+05 | −2.09 × 10+05 | −4.19 × 10+05 | −4.19 × 10+05 |
STD | 1.35 × 10+00 | 2.82 × 10+00 | 8.13 × 10+00 | 2.84 × 10+01 | 1.01 × 10+01 | 1.03 × 10+02 | |
F9 | AVG | 0.00 × 10+00 | 0.00 × 10+00 | 0.00 × 10+00 | 0.00 × 10+00 | 0.00 × 10+00 | 0.00 × 10+00 |
STD | 0.00 × 10+00 | 0.00 × 10+00 | 0.00 × 10+00 | 0.00 × 10+00 | 0.00 × 10+00 | 0.00 × 10+00 | |
F10 | AVG | 8.88 × 10−16 | 8.88 × 10−16 | 8.88 × 10−16 | 8.88 × 10−16 | 8.88 × 10−16 | 8.88 × 10−16 |
STD | 0.00 × 10+00 | 4.01 × 10−31 | 0.00 × 10+00 | 4.01 × 10−31 | 0.00 × 10+00 | 4.01 × 10−31 | |
F11 | AVG | 0.00 × 10+00 | 0.00 × 10+00 | 0.00 × 10+00 | 0.00 × 10+00 | 0.00 × 10+00 | 0.00 × 10+00 |
STD | 0.00 × 10+00 | 0.00 × 10+00 | 0.00 × 10+00 | 0.00 × 10+00 | 0.00 × 10+00 | 0.00 × 10+00 | |
F12 | AVG | 2.62 × 10−09 | 4.23 × 10−06 | 1.17 × 10−10 | 1.41 × 10−06 | 1.18 × 10−08 | 1.02 × 10−06 |
STD | 4.18 × 10−07 | 5.25× 10−06 | 1.02 × 10−07 | 1.48 × 10−06 | 1.94 × 10−07 | 1.16 × 10−06 | |
F13 | AVG | 6.46 × 10−06 | 9.13 × 10−05 | 6.47 × 10−05 | 3.44 × 10−04 | 2.63 × 10−04 | 8.41 × 10−04 |
STD | 1.45 × 10−05 | 1.26 × 10−04 | 1.09 × 10−04 | 4.75 × 10−04 | 1.92 × 10−04 | 1.18 × 10−03 |
F | NOL-HHO | DA | GA | PSO |
---|---|---|---|---|
F1 | 0.086927 | N/A | 0.000183 | 0.045155 |
F2 | N/A | N/A | 0.000183 | 0.121225 |
F3 | 0.198360 | N/A | 0.000183 | 0.003611 |
F4 | N/A | N/A | 0.000183 | 0.307489 |
F5 | 0.540770 | N/A | 0.000183 | 0.10411 |
F6 | 0.470240 | 0.344704 | 0.000183 | N/A |
F7 | 0.000393 | 0.021134 | 0.000183 | N/A |
F8 | 0.156580 | 0.000183 | 0.000183 | N/A |
F9 | 0.091461 | 0.364166 | 0.002202 | N/A |
F10 | 0.076666 | N/A | 0.000183 | 0.472676 |
F11 | 0.060926 | 0.001008 | 0.000183 | N/A |
F12 | 0.26758 | 0.140465 | 0.000183 | N/A |
F13 | 0.111660 | N/A | 0.000183 | 0.79126 |
n\d | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 |
---|---|---|---|---|---|---|---|---|---|
4 | 32 a | 11 a | |||||||
32 K | 12 K | 4 K | |||||||
5 | 68 a | 17 a | 7 a | 2 a | |||||
68 K | 20 K | 8 K | 3 K | ||||||
6 | 216 a | 44 a | 16 a | 6 a | 4 a | ||||
216 K | 55 K | 23 K | 8 K | 4 K | |||||
7 | 528 a | 110 a | 36 a | 11 a | 4 a | 2 a | |||
528 K | 121 K | 42 K | 14 K | 7 K | 3 K | ||||
8 | 1704 a | 289 a | 86 a | 29 a | 9 a | 4 a | 4 a | ||
1694 K | 339 K | 108 K | 35 K | 13 K | 5 K | 4 K | |||
9 | 4336 a | 662 a | 199 a | 59 a | 15 a | 8 a | 4 a | 4 a | |
4310 K | 705 K | 216 K | 69 K | 22 K | 11 K | 4 K | 3 K | ||
10 | 13,688 a | 1810 a | 525 a | 141 a | 43 a | 7 a | 5 a | 4 a | 4 a |
13,410 K | 1796 K | 546 K | 148 K | 51 K | 20 K | 9 K | 4 K | 4 K |
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Yin, Q.; Cao, B.; Li, X.; Wang, B.; Zhang, Q.; Wei, X. An Intelligent Optimization Algorithm for Constructing a DNA Storage Code: NOL-HHO. Int. J. Mol. Sci. 2020, 21, 2191. https://doi.org/10.3390/ijms21062191
Yin Q, Cao B, Li X, Wang B, Zhang Q, Wei X. An Intelligent Optimization Algorithm for Constructing a DNA Storage Code: NOL-HHO. International Journal of Molecular Sciences. 2020; 21(6):2191. https://doi.org/10.3390/ijms21062191
Chicago/Turabian StyleYin, Qiang, Ben Cao, Xue Li, Bin Wang, Qiang Zhang, and Xiaopeng Wei. 2020. "An Intelligent Optimization Algorithm for Constructing a DNA Storage Code: NOL-HHO" International Journal of Molecular Sciences 21, no. 6: 2191. https://doi.org/10.3390/ijms21062191