|
| 1 | +""" |
| 2 | +Use a genetic algorithm to solve the travelling salesman problem (TSP) |
| 3 | +which asks the following question: |
| 4 | +"Given a list of cities and the distances between each pair of cities, what is the |
| 5 | + shortest possible route that visits each city exactly once and returns to the origin |
| 6 | + city?" |
| 7 | +
|
| 8 | +https://en.wikipedia.org/wiki/Genetic_algorithm |
| 9 | +https://en.wikipedia.org/wiki/Travelling_salesman_problem |
| 10 | +
|
| 11 | +Author: Clark |
| 12 | +""" |
| 13 | + |
| 14 | +import copy |
| 15 | +import random |
| 16 | + |
| 17 | +cities = { |
| 18 | + 0: [0, 0], |
| 19 | + 1: [0, 5], |
| 20 | + 2: [3, 8], |
| 21 | + 3: [8, 10], |
| 22 | + 4: [12, 8], |
| 23 | + 5: [12, 4], |
| 24 | + 6: [8, 0], |
| 25 | + 7: [6, 2], |
| 26 | +} |
| 27 | + |
| 28 | + |
| 29 | +def main( |
| 30 | + cities: dict[int, list[int]], |
| 31 | + population_size: int, |
| 32 | + iterations_num: int, |
| 33 | + crossover_probability: float, |
| 34 | + mutation_probability: float, |
| 35 | +) -> tuple[list[int], float]: |
| 36 | + """ |
| 37 | + Genetic algorithm main function |
| 38 | +
|
| 39 | + The algorithm is stochastic, so seed ``random`` and assert invariants of the |
| 40 | + returned tour rather than one exact ordering (not reproducible across |
| 41 | + platforms / Python versions). |
| 42 | +
|
| 43 | + >>> import random |
| 44 | + >>> random.seed(0) |
| 45 | + >>> path, best = main(cities=cities, population_size=100, iterations_num=100, |
| 46 | + ... crossover_probability=0.6, mutation_probability=0.2) |
| 47 | + >>> path[0] == 0 and path[-1] == 0 # starts and ends at the origin city |
| 48 | + True |
| 49 | + >>> sorted(path[:-1]) == sorted(cities) # every city visited exactly once |
| 50 | + True |
| 51 | + >>> 37 <= best < 45 # converges close to the optimal round-trip (~37.9) |
| 52 | + True |
| 53 | + >>> main(cities={0: [0, 0], 1: [2, 2]}, population_size=10, iterations_num=10, |
| 54 | + ... crossover_probability=0.6, mutation_probability=0.2) |
| 55 | + ([0, 1, 0], 5.656854249492381) |
| 56 | + >>> main(cities={},population_size=10,iterations_num=10, |
| 57 | + ... crossover_probability=0.6,mutation_probability=0.2) |
| 58 | + Traceback (most recent call last): |
| 59 | + ... |
| 60 | + IndexError: list assignment index out of range |
| 61 | + """ |
| 62 | + best_path: list[int] = [] |
| 63 | + best_distance = float("inf") |
| 64 | + |
| 65 | + chromosomes, cities_list = init(cities, population_size) |
| 66 | + fitness_matrix, best_path, best_distance = fitness( |
| 67 | + cities, chromosomes, best_path, best_distance |
| 68 | + ) |
| 69 | + for _ in range(iterations_num): |
| 70 | + """ |
| 71 | + Uncomment to choose another selection operator |
| 72 | + Only one of the two selection operators can be uncommented at the same time. |
| 73 | + """ |
| 74 | + # chromosomes = chose_ts(fitness_matrix, chromosomes, population_size) |
| 75 | + chromosomes = chose_rws(fitness_matrix, chromosomes, population_size) |
| 76 | + for x in range(int(population_size / 2)): # Population crossover |
| 77 | + chromosomes[x], chromosomes[x + int(population_size / 2)] = crossing( |
| 78 | + chromosomes[x], |
| 79 | + chromosomes[x + int(population_size / 2)], |
| 80 | + crossover_probability, |
| 81 | + cities_list, |
| 82 | + ) |
| 83 | + for x in range(population_size): # Population variation |
| 84 | + chromosomes[x] = mutate(chromosomes[x], mutation_probability) |
| 85 | + |
| 86 | + fitness_matrix, best_path, best_distance = fitness( |
| 87 | + cities, chromosomes, best_path, best_distance |
| 88 | + ) |
| 89 | + |
| 90 | + return best_path, best_distance |
| 91 | + |
| 92 | + |
| 93 | +def distance(city1: list[int], city2: list[int]) -> float: |
| 94 | + """ |
| 95 | + Calculate the distance between two coordinate points |
| 96 | + >>> distance([0, 0], [3, 4] ) |
| 97 | + 5.0 |
| 98 | + >>> distance([0, 0], [-3, 4] ) |
| 99 | + 5.0 |
| 100 | + >>> distance([0, 0], [-3, -4] ) |
| 101 | + 5.0 |
| 102 | + """ |
| 103 | + return (((city1[0] - city2[0]) ** 2) + ((city1[1] - city2[1]) ** 2)) ** 0.5 |
| 104 | + |
| 105 | + |
| 106 | +def init( |
| 107 | + cities: dict[int, list[int]], population_size: int |
| 108 | +) -> tuple[list[list[int]], list[int]]: |
| 109 | + """ |
| 110 | + Initialization generates initial population |
| 111 | + >>> init(cities={0: [0, 0], 1: [2, 2]}, population_size=2) |
| 112 | + ([[0, 1, 0], [0, 1, 0]], [1]) |
| 113 | + >>> init(cities={0: [0, 0], 1: [2, 2]}, population_size=0) |
| 114 | + ([], [1]) |
| 115 | + >>> init(cities={},population_size=2) |
| 116 | + Traceback (most recent call last): |
| 117 | + ... |
| 118 | + IndexError: list assignment index out of range |
| 119 | + """ |
| 120 | + chromosomes = [] |
| 121 | + cities_list = list(cities.keys()) |
| 122 | + del cities_list[0] |
| 123 | + for _ in range(population_size): |
| 124 | + chromosome = [] |
| 125 | + chromosome.append(0) # Add starting point |
| 126 | + chromosome.extend(random.sample(cities_list, len(cities_list))) |
| 127 | + chromosome.append(0) # Add end point |
| 128 | + chromosomes.append(chromosome) |
| 129 | + return chromosomes, cities_list |
| 130 | + |
| 131 | + |
| 132 | +def fitness( |
| 133 | + cities: dict[int, list[int]], |
| 134 | + chromosomes: list[list[int]], |
| 135 | + best_path: list[int], |
| 136 | + best_distance: float, |
| 137 | +) -> tuple[list[float], list[int], float]: |
| 138 | + """ |
| 139 | + Calculate population fitness |
| 140 | + Generate a fitness matrix and obtain the optimal value in the current population |
| 141 | + >>> fitness(cities={0: [0, 0], 1: [2, 2]},chromosomes=[[0,1,0]], |
| 142 | + ... best_path=[], best_distance=float("inf")) |
| 143 | + ([0.17677669529663687], [0, 1, 0], 5.656854249492381) |
| 144 | + >>> fitness(cities={0: [0, 0], 1: [2, 2]},chromosomes=[[0,1,0],[0,1,0]], |
| 145 | + ... best_path=[], best_distance=float("inf")) |
| 146 | + ([0.17677669529663687, 0.17677669529663687], [0, 1, 0], 5.656854249492381) |
| 147 | + >>> fitness(cities={}, chromosomes=[[0,1,0]], |
| 148 | + ... best_path=[], best_distance=float("inf")) |
| 149 | + Traceback (most recent call last): |
| 150 | + ... |
| 151 | + KeyError: 0 |
| 152 | + >>> fitness(cities={0: [0, 0], 1: [2, 2]},chromosomes=[], |
| 153 | + ... best_path=[], best_distance=float("inf")) |
| 154 | + ([], [], inf) |
| 155 | + """ |
| 156 | + fitness_matrix = [] |
| 157 | + new_best_path = best_path |
| 158 | + new_best_distance = best_distance |
| 159 | + for chromosome in chromosomes: |
| 160 | + total_distance = 0.0 |
| 161 | + for i in range(len(chromosome) - 1): # Calculate total distance |
| 162 | + total_distance += distance(cities[chromosome[i]], cities[chromosome[i + 1]]) |
| 163 | + fitness_matrix.append(1 / total_distance) |
| 164 | + if total_distance < new_best_distance: |
| 165 | + new_best_path = chromosome |
| 166 | + new_best_distance = total_distance |
| 167 | + |
| 168 | + return fitness_matrix, new_best_path, new_best_distance |
| 169 | + |
| 170 | + |
| 171 | +def chose_ts( |
| 172 | + fitness_matrix: list[float], chromosomes: list[list[int]], population_size: int |
| 173 | +) -> list[list[int]]: |
| 174 | + """ |
| 175 | + A type of selection operator |
| 176 | + Tournament Selection |
| 177 | + >>> chose_ts(fitness_matrix=[1], chromosomes=[[0,1,0]], population_size=1) |
| 178 | + [[0, 1, 0]] |
| 179 | + >>> chose_ts(fitness_matrix=[1], chromosomes=[0,1,0], population_size=0) |
| 180 | + [] |
| 181 | + >>> chose_ts(fitness_matrix=[], chromosomes=[[0,1,0]], population_size=1) |
| 182 | + Traceback (most recent call last): |
| 183 | + ... |
| 184 | + IndexError: list index out of range |
| 185 | + >>> chose_ts(fitness_matrix=[1], chromosomes=[], population_size=1) |
| 186 | + Traceback (most recent call last): |
| 187 | + ... |
| 188 | + IndexError: list index out of range |
| 189 | + >>> import random |
| 190 | + >>> random.seed(0) |
| 191 | + >>> chose_ts(fitness_matrix=[1], chromosomes=[0, 1, 0], population_size=2) |
| 192 | + Traceback (most recent call last): |
| 193 | + ... |
| 194 | + IndexError: list index out of range |
| 195 | + """ |
| 196 | + chromosomes_new = [] |
| 197 | + for _ in range(population_size): |
| 198 | + x1 = random.randint(0, population_size - 1) |
| 199 | + x2 = random.randint(0, population_size - 1) |
| 200 | + if fitness_matrix[x1] >= fitness_matrix[x2]: |
| 201 | + chromosomes_new.append(chromosomes[x1]) |
| 202 | + else: |
| 203 | + chromosomes_new.append(chromosomes[x2]) |
| 204 | + return chromosomes_new |
| 205 | + |
| 206 | + |
| 207 | +def chose_rws( |
| 208 | + fitness_matrix: list[float], chromosomes: list[list[int]], population_size: int |
| 209 | +) -> list[list[int]]: |
| 210 | + """ |
| 211 | + A type of selection operator |
| 212 | + Roulette Wheel Selection |
| 213 | + >>> chose_rws(fitness_matrix=[1], chromosomes=[[0,1,0]], population_size=1) |
| 214 | + [[0, 1, 0]] |
| 215 | + >>> chose_rws(fitness_matrix=[1], chromosomes=[0,1,0], population_size=0) |
| 216 | + [0, 1, 0] |
| 217 | + >>> chose_rws(fitness_matrix=[], chromosomes=[[0,1,0]], population_size=1) |
| 218 | + Traceback (most recent call last): |
| 219 | + ... |
| 220 | + IndexError: list index out of range |
| 221 | + >>> chose_rws(fitness_matrix=[1], chromosomes=[], population_size=1) |
| 222 | + Traceback (most recent call last): |
| 223 | + ... |
| 224 | + IndexError: list index out of range |
| 225 | + >>> chose_rws(fitness_matrix=[1], chromosomes=[0,1,0], population_size=2) |
| 226 | + [0, 0, 0] |
| 227 | + """ |
| 228 | + probabilitys = [0.0] * len(fitness_matrix) |
| 229 | + total_probability = 0.0 |
| 230 | + for i in fitness_matrix: |
| 231 | + total_probability += i |
| 232 | + for i in range(len(fitness_matrix)): |
| 233 | + probabilitys[i] = fitness_matrix[i] / total_probability |
| 234 | + |
| 235 | + chromosomes_new = copy.deepcopy(chromosomes) |
| 236 | + for i in range(population_size): |
| 237 | + k = 0.0 |
| 238 | + r = random.uniform(0, 1) |
| 239 | + for j in range(population_size): |
| 240 | + k = k + probabilitys[j] |
| 241 | + if r <= k: |
| 242 | + chromosomes_new[i] = chromosomes[j] |
| 243 | + break |
| 244 | + return chromosomes_new |
| 245 | + |
| 246 | + |
| 247 | +def crossing( |
| 248 | + chromosome_a: list[int], |
| 249 | + chromosome_b: list[int], |
| 250 | + crossover_probability: float, |
| 251 | + cities_list: list[int], |
| 252 | +) -> tuple[list[int], list[int]]: |
| 253 | + """ |
| 254 | + Population crossover |
| 255 | + >>> crossing(chromosome_a=[0,1,0], chromosome_b=[0,1,0], |
| 256 | + ... crossover_probability=0,cities_list=[1]) |
| 257 | + ([0, 1, 0], [0, 1, 0]) |
| 258 | + >>> crossing(chromosome_a=[0,1,0], chromosome_b=[0,1,0], |
| 259 | + ... crossover_probability=1,cities_list=[1]) |
| 260 | + ([0, 1, 0], [0, 1, 0]) |
| 261 | + >>> crossing(chromosome_a=[0,1,0], chromosome_b=[], |
| 262 | + ... crossover_probability=1,cities_list=[1]) |
| 263 | + Traceback (most recent call last): |
| 264 | + ... |
| 265 | + IndexError: list index out of range |
| 266 | + >>> crossing(chromosome_a=[0,1,0], chromosome_b=[0,1,0], |
| 267 | + ... crossover_probability=1,cities_list=[]) |
| 268 | + ([0, 1, 0], [0, 1, 0]) |
| 269 | + """ |
| 270 | + new_chromosome_a = copy.deepcopy(chromosome_a) |
| 271 | + new_chromosome_b = copy.deepcopy(chromosome_b) |
| 272 | + |
| 273 | + if random.random() <= crossover_probability: |
| 274 | + crossover_segment = sorted( |
| 275 | + [ |
| 276 | + random.randint(0, len(new_chromosome_a) - 1), |
| 277 | + random.randint(0, len(new_chromosome_a) - 1), |
| 278 | + ] |
| 279 | + ) |
| 280 | + |
| 281 | + for k in range((crossover_segment[1] - crossover_segment[0]) + 1): |
| 282 | + ( |
| 283 | + new_chromosome_a[crossover_segment[0] + k], |
| 284 | + new_chromosome_b[crossover_segment[0] + k], |
| 285 | + ) = ( |
| 286 | + new_chromosome_b[crossover_segment[0] + k], |
| 287 | + new_chromosome_a[crossover_segment[0] + k], |
| 288 | + ) |
| 289 | + |
| 290 | + for chromosome in [new_chromosome_a, new_chromosome_b]: |
| 291 | + unique_elements_set = set(chromosome) |
| 292 | + if len(unique_elements_set) != len( |
| 293 | + chromosome |
| 294 | + ): # Determine whether the chromosome segment has duplication |
| 295 | + for segment_index in range( |
| 296 | + (crossover_segment[1] - crossover_segment[0]) + 1 |
| 297 | + ): |
| 298 | + target_index = 0 |
| 299 | + for chrom_index in range( |
| 300 | + 1, len(chromosome) - 1 |
| 301 | + ): # Exclude start and end points 0 when searching |
| 302 | + if chrom_index == (crossover_segment[0] + segment_index): |
| 303 | + continue |
| 304 | + if ( |
| 305 | + chromosome[chrom_index] |
| 306 | + == chromosome[crossover_segment[0] + segment_index] |
| 307 | + ): |
| 308 | + target_index = chrom_index |
| 309 | + break |
| 310 | + if target_index != 0: |
| 311 | + cities_list_copy = copy.deepcopy(cities_list) |
| 312 | + for t in chromosome: |
| 313 | + try: |
| 314 | + cities_list_copy.remove(t) |
| 315 | + except ValueError: |
| 316 | + continue |
| 317 | + chromosome[target_index] = random.sample(cities_list_copy, 1)[0] |
| 318 | + |
| 319 | + return new_chromosome_a, new_chromosome_b |
| 320 | + |
| 321 | + |
| 322 | +def mutate(chromosome: list[int], mutation_probability: float) -> list[int]: |
| 323 | + """ |
| 324 | + Population variation: swap two interior cities (endpoints stay at 0). |
| 325 | +
|
| 326 | + >>> mutate([0, 1, 0], mutation_probability=0) # no mutation -> unchanged |
| 327 | + [0, 1, 0] |
| 328 | + >>> import random |
| 329 | + >>> random.seed(1) |
| 330 | + >>> mutate([0, 1, 2, 3, 0], mutation_probability=1) # swaps two interior cities |
| 331 | + [0, 2, 1, 3, 0] |
| 332 | +
|
| 333 | + An empty chromosome has no interior cities to swap; match only the exception |
| 334 | + type since the exact stdlib message changes across Python versions. |
| 335 | +
|
| 336 | + >>> mutate([], mutation_probability=1) # doctest: +IGNORE_EXCEPTION_DETAIL |
| 337 | + Traceback (most recent call last): |
| 338 | + ... |
| 339 | + ValueError |
| 340 | + """ |
| 341 | + new_chromosome = copy.deepcopy(chromosome) |
| 342 | + if random.random() <= mutation_probability: |
| 343 | + mutate_location = [ |
| 344 | + random.randint(1, len(new_chromosome) - 2), |
| 345 | + random.randint(1, len(new_chromosome) - 2), |
| 346 | + ] # Exclude start and end points 0 |
| 347 | + new_chromosome[mutate_location[0]], new_chromosome[mutate_location[1]] = ( |
| 348 | + new_chromosome[mutate_location[1]], |
| 349 | + new_chromosome[mutate_location[0]], |
| 350 | + ) |
| 351 | + return new_chromosome |
| 352 | + |
| 353 | + |
| 354 | +if __name__ == "__main__": |
| 355 | + best_path, best_distance = main( |
| 356 | + cities=cities, |
| 357 | + population_size=100, |
| 358 | + iterations_num=100, |
| 359 | + crossover_probability=0.6, |
| 360 | + mutation_probability=0.2, |
| 361 | + ) |
| 362 | + |
| 363 | + print(f"{best_path = }") |
| 364 | + print(f"{best_distance = }") |
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