算法导论 — 思考题15-5 编辑距离

题目：


分析：
a：

• 字符串x的下标范围[0, 1, 2, ..., m]，y的下标范围[0, 1, 2, ..., n]；
• 二维数组d[i, j]为距离矩阵，用于计算两点之间的编辑距离，我们的目标是求x和y的编辑距离，即d[m, n]；
• 二维数组option[i, j]用于存储每一步的操作；
• dict_cost为每种操作的代价，字典格式；

分析不同操作的条件和代价：

• 如果1 <= i <= m 且 1 <= j <= n:

1. copy

	 if x[i - 1] == y[j - 1]:
	 	dis[0] = dict_cost['copy'] + d[i-1][j-1]

2. replace：
   个人认为这里x和y对应位置的字符不一样时，也是可以进行替换的

	dis[1] = dict_cost['replace'] + d[i-1][j-1]

3. delete

	dis[2] = dict_cost['delete'] + d[i-1][j]

4. insert

 	dis[3] = dict_cost['insert'] + d[i][j-1]

5. twiddle

	 if i >= 2 and j >= 2 and x[i-1] == y[j-2] and x[i-2] == y[j-1]:
	 	dis[4] = dict_cost['twiddle'] + d[i-2][j-2]

6. kill
   只能在j = n时，才会执行kill操作；kill操作需要最后单独执行；

	# kill的情况单独处理
    kill_index = -1
    for i in range(1, m):
        temp = d[i][n] + dict_cost['kill']
        if temp < d[m][n]:
            kill_index = i
            d[m][n] = temp
            option[m][n] = 5

在上述几种操作（除kill以外）中取代价最小的操作，并记录这一步的操作：

	d[i][j] = min(dis)
	option[i][j] = dis.index(min(dis))

• 边界情况：

1. i = 0 且 j = 0

	d[0][0] = 0
    option[0][0] = -1

2. i = 0 且 j != 0，此时x为空，只能执行插入操作

    for j in range(1, n + 1):
        d[0][j] = j * dict_cost['insert']
        option[0][j] = 3

3. j = 0 且 i != 0，此时y为空，只能执行删除操作

    for i in range(1, m + 1):
        d[i][0] = i * dict_cost['delete']
        option[i][0] = 2

完整的代码如下：

"""
    算法导论（第三版） P232，15-5 编辑距离
"""

import numpy as np


def print_result(i, j, kill_index, option):
    if option[i][j] == -1:
        return
    if option[i][j] == 0:
        print_result(i-1, j-1, kill_index, option)
        print('copy')
    elif option[i][j] == 1:
        print_result(i-1, j-1, kill_index, option)
        print('replace')
    elif option[i][j] == 2:
        print_result(i-1, j, kill_index, option)
        print('delete')
    elif option[i][j] == 3:
        print_result(i, j-1, kill_index, option)
        print('insert')
    elif option[i][j] == 4:
        print_result(i-2, j-2, kill_index, option)
        print('twiddle')
    else:
        print_result(kill_index, j, kill_index, option)
        print('kill')


def function(x, y, dict_cost):
    m, n = len(x), len(y)
    d = np.full((m + 1, n + 1), np.inf, dtype=float)    # 距离矩阵
    columns = ['copy', 'replace', 'delete', 'insert', 'twiddle', 'kill']
    option = np.full((m + 1, n + 1), -1, dtype=int)   # 记录每一步的选择，与columns对应
    d[0][0] = 0
    option[0][0] = -1
    for j in range(1, n + 1):
        d[0][j] = j * dict_cost['insert']
        option[0][j] = 3
    for i in range(1, m + 1):
        d[i][0] = i * dict_cost['delete']
        option[i][0] = 2

    for i in range(1, m + 1):
        for j in range(1, n + 1):
            dis = [np.inf] * 5  # 分别对应：'copy'，'replace'，'delete'，'insert'，'twiddle'

            if x[i - 1] == y[j - 1]:
                dis[0] = dict_cost['copy'] + d[i-1][j-1]
            dis[1] = dict_cost['replace'] + d[i-1][j-1]
            dis[2] = dict_cost['delete'] + d[i-1][j]
            dis[3] = dict_cost['insert'] + d[i][j-1]
            if i >= 2 and j >= 2 and x[i-1] == y[j-2] and x[i-2] == y[j-1]:
                dis[4] = dict_cost['twiddle'] + d[i-2][j-2]

            d[i][j] = min(dis)
            option[i][j] = dis.index(min(dis))

    # kill的情况单独处理
    kill_index = -1
    for i in range(1, m):
        temp = d[i][n] + dict_cost['kill']
        if temp < d[m][n]:
            kill_index = i
            d[m][n] = temp
            option[m][n] = 5

    # 打印结果
    print('Total cost:', d[m][n])
    # print(option)
    print('Process:')
    print_result(m, n, kill_index, option)


if __name__ == '__main__':
    x = 'algorithm'
    y = 'altruistic'
    dict_cost = {'copy':1, 'replace':2, 'delete':3, 'insert':4, 'twiddle':5, 'kill':6}
    function(x, y, dict_cost)

运行结果：该算法的时间复杂度和空间复杂度均为O（mn）

b：
可以将DNA对齐问题转化为编辑问题，对应的操作为：复制、替换、插入、删除，此时求两个字符串的最大编辑距离：

• 复制：x[j] = y[j]，且都不是空格，代价为+1；
• 替换：x[j] != y[j]，且都不是空格，代价为-1；
• 插入：在x中插入空格，代价为-2；
• 删除：在y中插入空格，代价为-2；

递归打印结果：

def get_results(x, y, i, j, option):
    if option[i][j] == -1:
        return [], []
    if option[i][j] == 0 or option[i][j] == 1:   # copy/replace
        xx, yy = get_results(x, y, i-1, j-1, option)
        return xx + [x[i-1]], yy + [y[j-1]]
    elif option[i][j] == 2:     # delete
        xx, yy = get_results(x, y, i-1, j, option)
        return xx + [x[i-1]], yy + [' ']
    else:       # insert
        xx, yy = get_results(x, y, i, j-1, option)
        return xx + [' '], yy + [y[j-1]]

运行结果：

完整代码：

"""
    算法导论（第三版） P232，15-5 编辑距离
"""

import numpy as np


def get_results(x, y, i, j, option):
    if option[i][j] == -1:
        return [], []
    if option[i][j] == 0 or option[i][j] == 1:   # copy/replace
        xx, yy = get_results(x, y, i-1, j-1, option)
        return xx + [x[i-1]], yy + [y[j-1]]
    elif option[i][j] == 2:     # delete
        xx, yy = get_results(x, y, i-1, j, option)
        return xx + [x[i-1]], yy + [' ']
    else:       # insert
        xx, yy = get_results(x, y, i, j-1, option)
        return xx + [' '], yy + [y[j-1]]


def function(x, y, dict_cost):
    m, n = len(x), len(y)
    d = np.full((m + 1, n + 1), -np.inf, dtype=float)    # 距离矩阵
    columns = ['copy', 'replace', 'delete', 'insert']
    option = np.full((m + 1, n + 1), -1, dtype=int)   # 记录每一步的选择，与columns对应
    d[0][0] = 0
    option[0][0] = -1
    for j in range(1, n + 1):
        d[0][j] = j * dict_cost['insert']
        option[0][j] = 3
    for i in range(1, m + 1):
        d[i][0] = i * dict_cost['delete']
        option[i][0] = 2

    for i in range(1, m + 1):
        for j in range(1, n + 1):
            dis = [-np.inf] * 4  # 分别对应：'copy'，'replace'，'delete'，'insert'

            if x[i - 1] == y[j - 1]:
                dis[0] = dict_cost['copy'] + d[i-1][j-1]
            dis[1] = dict_cost['replace'] + d[i-1][j-1]
            dis[2] = dict_cost['delete'] + d[i-1][j]
            dis[3] = dict_cost['insert'] + d[i][j-1]

            d[i][j] = max(dis)
            option[i][j] = dis.index(max(dis))

    # 打印结果
    print('Total cost:', d[m][n])
    # print(option)
    print('Process:')
    xx, yy = get_results(x, y, m, n, option)
    print(xx)
    print(yy)


if __name__ == '__main__':
    x = 'GATCGGCAT'
    y = 'CAATGTGAATC'
    dict_cost = {'copy':1, 'replace':-1, 'delete':-2, 'insert':-2}
    function(x, y, dict_cost)