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