Study on DNA Storage Encoding Based IAOA under Innovation Constraints
Abstract
1. Introduction
2. Algorithm Description
2.1. Arithmetic Optimization Algorithm
2.2. IAOA
2.2.1. Elementary Function Perturbation
2.2.2. Double Adaptive Weighting Strategy
Algorithm 1. Pseudo-code of the IAOA. |
1: Initialization parameters and population location i (i = 1,2...N) 2: While(t < T) 3: 4: for i = 1 : N 5: for j = 1 : N 6: if r1 > MOA 7: if r2 > 0.5 (exploration phase) 8: 9: else 10: 11: end if 12: if r3 > 0.5 (development phase) 13: 14: else 15: 16: end if 17: end if 18: end for 19: end for 20: end while 21: Return to the optimal solution |
2.3. Benchmark Function Comparison
2.4. Wilcoxon Rank Sum Test
3. Construct DNA Storage Sets
3.1. Double-Matching Constraint
3.2. Error-Pairing Constraint
3.3. Hamming Distance Constraint
3.4. GC Content Constraint
3.5. No-Runlength Constraint
3.6. DNA Storage Sets Constructed Using Traditional Combinatorial Constraints
3.7. Encoding Sets Constructed Using Double-Matching and Error-Pairing Constraints
3.8. Storage Set Quality Comparison
4. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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ID | Metric | IAOA | EAOA | DAOA | pAOA | AOA | SCA | SSA | WOA | GSA | MVO |
---|---|---|---|---|---|---|---|---|---|---|---|
F1 | AVG | 0 | 8.06 × 10−6 | 0 | 7.17 × 10−7 | 8.65 × 10−26 | 7.6776 | 1.58 × 10−7 | 1.41 × 10−30 | 2.53 × 10−16 | 1.34 × 100 |
STD | 0 | 2.88 × 10−5 | 0 | 1.87 × 10−6 | 4.74 × 10−25 | 12.3019 | 1.71 × 10−7 | 4.91 × 10−30 | 9.67 × 10−17 | 5.38 × 10−1 | |
F2 | AVG | 0 | 9.93 × 10−98 | 0 | 7.74 × 10−70 | 0 | 0.01806 | 2.66293 | 1.06 × 10−21 | 0.055655 | 2.20 × 100 |
STD | 0 | 5.44 × 10−97 | 0 | 4.24 × 10−69 | 0 | 0.02457 | 1.66802 | 2.39 × 10−21 | 0.194074 | 7.31 × 100 | |
F3 | AVG | 0 | 0.002257 | 0 | 0.002124 | 0.008014 | 9961.453 | 1709.94 | 5.39 × 10−7 | 896.5347 | 2.04 × 102 |
STD | 0 | 0.002291 | 0 | 0.00177 | 0.01192 | 6699.979 | 11242.3 | 2.93 × 10−6 | 318.9559 | 6.63 × 101 | |
F4 | AVG | 0 | 0.012309 | 0 | 0.008175 | 0.02667 | 36.7941 | 11.6741 | 0.072581 | 7.35487 | 2.16 × 100 |
STD | 0 | 0.004386 | 0 | 0.003422 | 0.02021 | 13.1414 | 4.1792 | 0.39747 | 1.741452 | 8.66 × 10−1 | |
F5 | AVG | 27.7041 | 28.5909 | 28.0863 | 28.5339 | 28.3946 | 27188.68 | 296.125 | 27.86558 | 2.84 × 101 | 7.89 × 102 |
STD | 0.27902 | 0.29615 | 0.34232 | 0.13585 | 0.3301 | 72171.04 | 508.863 | 0.763626 | 2.00 × 10−1 | 8.74 × 102 | |
F6 | AVG | 1.937 | 2.4126 | 4.8677 | 1.5769 | 3.2316 | 21.998 | 1.80 × 10−7 | 3.116266 | 2.50 × 10−16 | 1.34 × 100 |
STD | 0.38153 | 0.44494 | 0.50584 | 0.2591 | 0.2455 | 27.8352 | 3.00 × 10−7 | 0.532429 | 1.74 × 10−16 | 3.43 × 10−1 | |
F7 | AVG | 5.42 × 10−5 | 6.25 × 10−5 | 7.40 × 10−5 | 4.51 × 10−5 | 5.45 × 10−5 | 0.08458 | 0.1757 | 0.001425 | 0.089441 | 3.21 × 10−2 |
STD | 7.85 × 10−5 | 8.45 × 10−5 | 8.20 × 10−5 | 3.70 × 10−5 | 5.15 × 10−5 | 0.09798 | 0.0629 | 0.001149 | 0.04339 | 1.32 × 10−2 |
ID | Metric | IAOA | EAOA | DAOA | pAOA | AOA | SCA | SSA | WOA | GSA | MVO |
---|---|---|---|---|---|---|---|---|---|---|---|
F8 | AVG | −6717.1783 | −6021.7325 | −4156.4559 | −6953.88 | −5395.427 | −3771.665 | −7455.8 | −5080.76 | −2821.07 | −7550 |
STD | 580.0765 | 698.8845 | 599.9788 | 424.3747 | 436.8011 | 293.4553 | 772.811 | 695.7968 | 493.0375 | 6.27 × 102 | |
F9 | AVG | 0 | 0 | 0 | 0 | 0 | 41.6519 | 58.3708 | 0 | 25.96841 | 1.20 × 102 |
STD | 0 | 0 | 0 | 0 | 0 | 44.3312 | 20.016 | 0 | 7.470068 | 3.29 × 101 | |
F10 | AVG | 8.88 × 10−16 | 8.88 × 10−16 | 8.88 × 10−16 | 8.88 × 10−16 | 8.88 × 10−16 | 14.2857 | 2.6796 | 7.4043 | 0.062087 | 2.03 × 100 |
STD | 0 | 0 | 0 | 0 | 0 | 8.5929 | 0.8275 | 9.897572 | 0.23628 | 5.47 × 10−1 | |
F11 | AVG | 0 | 0.004063 | 0 | 1.31 × 10−5 | 0.1689 | 0.8665 | 0.016 | 0.000289 | 27.70154 | 8.60 × 10−1 |
STD | 0 | 0.009628 | 0 | 8.60 × 10−6 | 0.1347 | 0.3957 | 0.0112 | 0.001586 | 5.040343 | 8.21 × 10−2 | |
F12 | AVG | 0.20433 | 0.5004 | 0.70028 | 0.2241 | 0.5195 | 183961.2 | 6.9915 | 0.339676 | 1.799617 | 2.43 × 100 |
STD | 0.034199 | 0.043832 | 0.066711 | 0.0416 | 0.04741 | 841708.7 | 4.4175 | 0.214864 | 0.95114 | 1.39 × 100 | |
F13 | AVG | 2.2663 | 2.7269 | 2.7643 | 2.7669 | 2.8475 | 109173.3 | 15.8757 | 1.889015 | 8.899084 | 1.96 × 10−1 |
STD | 0.24611 | 0.30181 | 0.298724 | 0.1274 | 0.07852 | 266184.2 | 16.1462 | 0.266088 | 7.126241 | 1.26 × 10−1 |
Comparison | p-Value |
---|---|
IAOA-AOA | 0.005847 |
IAOA-pAOA | 0.028056 |
IAOA-SCA | 0.001474 |
IAOA-SSA | 0.039243 |
IAOA-WOA | 0.026231 |
IAOA-GSA | 0.009633 |
IAOA-MVO | 0.008775 |
n\d | 3 | 4 | 5 | 6 | 7 | 8 | 9 | |
---|---|---|---|---|---|---|---|---|
Altruistic | 11 | |||||||
4 | NOL-HHO | 12 | ||||||
IAOA | 12 | |||||||
Altruistic | 17 | 7 | ||||||
5 | NOL-HHO | 20 | 8 | |||||
IAOA | 20 | 8 | ||||||
Altruistic | 44 | 16 | 6 | |||||
6 | NOL-HHO | 55 | 23 | 8 | ||||
IAOA | 61 | 24 | 8 | |||||
Altruistic | 110 | 36 | 11 | 4 | ||||
7 | NOL-HHO | 121 | 42 | 14 | 7 | |||
IAOA | 136 | 46 | 16 | 7 | ||||
Altruistic | 289 | 86 | 29 | 9 | 4 | |||
8 | NOL-HHO | 339 | 108 | 35 | 13 | 5 | ||
IAOA | 373 | 114 | 39 | 16 | 5 | |||
Altruistic | 662 | 199 | 59 | 15 | 8 | 4 | ||
9 | NOL-HHO | 705 | 216 | 69 | 22 | 11 | 4 | |
IAOA | 789 | 231 | 71 | 27 | 11 | 5 | ||
Altruistic | 1810 | 525 | 141 | 43 | 7 | 5 | 4 | |
10 | NOL-HHO | 1796 | 546 | 148 | 51 | 20 | 9 | 4 |
IAOA | 1945 | 549 | 156 | 56 | 22 | 10 | 5 |
n\d | 3 | 4 | 5 | 6 | 7 | 8 | 9 |
---|---|---|---|---|---|---|---|
4 | 12 | ||||||
5 | 20 | 8 | |||||
6 | 58 | 22 | 8 | ||||
7 | 125 | 42 | 17 | 6 | |||
8 | 322 | 96 | 29 | 13 | 5 | ||
9 | 587 | 194 | 50 | 18 | 9 | 6 | |
10 | 1206 | 398 | 117 | 46 | 16 | 8 | 4 |
n\d | 3 | 4 | 5 | 6 | 7 | 8 | 9 |
---|---|---|---|---|---|---|---|
4 | 12 | ||||||
5 | 20 | 8 | |||||
6 | 60 | 23 | 8 | ||||
7 | 126 | 43 | 18 | 6 | |||
8 | 338 | 119 | 33 | 14 | 5 | ||
9 | 598 | 201 | 58 | 21 | 11 | 7 | |
10 | 1391 | 408 | 126 | 49 | 18 | 8 | 4 |
n\d | 3 | 4 | 5 | 6 | 7 | 8 | 9 |
---|---|---|---|---|---|---|---|
4 | 12 | ||||||
5 | 20 | 8 | |||||
6 | 45 | 17 | 7 | ||||
7 | 124 | 42 | 15 | 6 | |||
8 | 245 | 79 | 28 | 11 | 5 | ||
9 | 577 | 178 | 54 | 19 | 9 | 4 | |
10 | 1073 | 374 | 110 | 39 | 15 | 8 | 4 |
n\d | 3 | 4 | 5 | 6 | 7 | 8 | 9 | |
---|---|---|---|---|---|---|---|---|
8 | 3.5538 | 4.0477 | 6.0929 | 5.4760 | 4.6825 | |||
3.0968 | 3.3164 | 5.3873 | 5.1429 | 4.3069 | ||||
9 | 3.3585 | 2.6020 | 5.6688 | 4.6172 | 4.5196 | 4.8333 | ||
2.7969 | 2.5061 | 4.3512 | 4.1070 | 4.2980 | 4.7471 | |||
10 | 6.8984 | 2.9266 | 3.3843 | 3.2426 | 4.3286 | 2.6257 | 3.0167 | |
5.9291 | 2.7699 | 2.7484 | 2.8492 | 3.2602 | 2.5596 | 2.8941 |
n\d | 3 | 4 | 5 | 6 | 7 | 8 | 9 | |
---|---|---|---|---|---|---|---|---|
8 | 3.5538 | 4.0477 | 6.0929 | 5.4760 | 4.6825 | |||
3.0775 | 3.2602 | 5.1959 | 4.7633 | 3.9234 | ||||
9 | 3.3585 | 2.6020 | 5.6688 | 4.6172 | 4.5196 | 4.8333 | ||
2.7502 | 1.9650 | 4.0618 | 3.6314 | 3.9391 | 4.0712 | |||
10 | 6.8984 | 2.9266 | 3.3843 | 3.2426 | 4.3286 | 2.6257 | 3.0167 | |
5.1916 | 2.7484 | 2.4791 | 2.7502 | 3.3756 | 2.3892 | 2.8166 |
n\d | 3 | 4 | 5 | 6 | 7 | 8 | 9 | |
---|---|---|---|---|---|---|---|---|
8 | 3.5538 | 4.0477 | 6.0929 | 5.4760 | 4.6825 | |||
2.6499 | 3.4963 | 4.7498 | 4.4845 | 3.2870 | ||||
9 | 3.3585 | 2.6020 | 5.6688 | 4.6172 | 4.5196 | 4.8333 | ||
2.5067 | 1.4909 | 3.9142 | 3.1942 | 3.5079 | 3.8270 | |||
10 | 6.8984 | 2.9266 | 3.3843 | 3.2426 | 4.3286 | 2.6257 | 3.0167 | |
4.0036 | 2.2510 | 1.8384 | 2.5098 | 3.0063 | 2.2795 | 2.7492 |
n\d | 3 | 4 | 5 | 6 | 7 | 8 | 9 | |
---|---|---|---|---|---|---|---|---|
8 | 134 | 38 | 14 | 5 | 2 | |||
141 | 48 | 16 | 6 | 2 | ||||
9 | 751 | 251 | 68 | 25 | 13 | 7 | ||
776 | 258 | 81 | 29 | 16 | 8 | |||
10 | 3352 | 1064 | 335 | 128 | 46 | 19 | 18 | |
3832 | 1089 | 367 | 137 | 57 | 20 | 8 |
n\d | 3 | 4 | 5 | 6 | 7 | 8 | 9 | |
---|---|---|---|---|---|---|---|---|
8 | 0.4162 | 0.3958 | 0.4828 | 0.3846 | 0.4 | |||
0.4172 | 0.4034 | 0.4848 | 0.4286 | 0.4 | ||||
9 | 1.2794 | 1.2938 | 1.36 | 1.3889 | 1.4444 | 1.1667 | ||
1.2977 | 1.2835 | 1.3966 | 1.3810 | 1.4545 | 1.1429 | |||
10 | 2.7794 | 2.6734 | 2.8632 | 2.7826 | 2.875 | 2.375 | 2.25 | |
2.7549 | 2.6691 | 2.9127 | 2.7959 | 3.1667 | 2.5 | 2.75 |
n\d | 3 | 4 | 5 | 6 | 7 | 8 | 9 | |
---|---|---|---|---|---|---|---|---|
8 | 156 | 47 | 19 | 8 | 3 | |||
127 | 37 | 15 | 4 | 2 | ||||
9 | 1024 | 308 | 100 | 38 | 17 | 6 | ||
683 | 222 | 73 | 24 | 12 | 4 | |||
10 | 5412 | 1482 | 460 | 158 | 76 | 25 | 18 | |
2815 | 1033 | 327 | 125 | 40 | 17 | 8 |
n\d | 3 | 4 | 5 | 6 | 7 | 8 | 9 | |
---|---|---|---|---|---|---|---|---|
8 | 0.4182 | 0.4123 | 0.4872 | 0.5 | 0.6 | |||
0.4097 | 0.3895 | 0.4688 | 0.3636 | 0.4 | ||||
9 | 1.2978 | 1.3333 | 1.4085 | 1.4074 | 1.5455 | 1.2 | ||
1.1837 | 1.2472 | 1.3519 | 1.1429 | 1.3333 | 1 | |||
10 | 2.7825 | 2.6995 | 2.9487 | 2.8214 | 3.4545 | 2.5 | 3.6 | |
2.3576 | 2.4654 | 2.7712 | 2.7778 | 2.5 | 2.125 | 2 |
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Du, H.; Zhou, S.; Yan, W.; Wang, S. Study on DNA Storage Encoding Based IAOA under Innovation Constraints. Curr. Issues Mol. Biol. 2023, 45, 3573-3590. https://doi.org/10.3390/cimb45040233
Du H, Zhou S, Yan W, Wang S. Study on DNA Storage Encoding Based IAOA under Innovation Constraints. Current Issues in Molecular Biology. 2023; 45(4):3573-3590. https://doi.org/10.3390/cimb45040233
Chicago/Turabian StyleDu, Haigui, Shihua Zhou, WeiQi Yan, and Sijie Wang. 2023. "Study on DNA Storage Encoding Based IAOA under Innovation Constraints" Current Issues in Molecular Biology 45, no. 4: 3573-3590. https://doi.org/10.3390/cimb45040233
APA StyleDu, H., Zhou, S., Yan, W., & Wang, S. (2023). Study on DNA Storage Encoding Based IAOA under Innovation Constraints. Current Issues in Molecular Biology, 45(4), 3573-3590. https://doi.org/10.3390/cimb45040233