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Merged
KMCzajkowski merged 1 commit into from
Jun 23, 2025
Merged

Add speed related improvements #3

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92 changes: 51 additions & 41 deletions editdistance/_edit_distance_osa.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -4,58 +4,67 @@

std::vector<std::vector<double>> compute_dp_table(
const std::string& a,
const std::string& b,
const std::map<CppEditopName, double>& cost_map
const std::string& b,
double replace_weight,
double insert_weight,
double delete_weight,
double swap_weight
) {
int len_a = a.length();
int len_b = b.length();
std::vector<std::vector<double>> dp(len_a + 1, std::vector<double>(len_b + 1, 0.0));

for (int i = 0; i <= len_a; ++i) {
dp[i][0] = i * cost_map.at(DELETE);
dp[i][0] = i * delete_weight;
}
for (int j = 0; j <= len_b; ++j) {
dp[0][j] = j * cost_map.at(INSERT);
dp[0][j] = j * insert_weight;
}

for (int i = 1; i <= len_a; ++i) {
for (int j = 1; j <= len_b; ++j) {
double deletion = dp[i-1][j] + cost_map.at(DELETE);
double insertion = dp[i][j-1] + cost_map.at(INSERT);
double substitution_cost = (a[i-1] == b[j-1]) ? 0.0 : cost_map.at(REPLACE);
double substitution = dp[i-1][j-1] + substitution_cost;

if (a[i-1] == b[j-1]) {
dp[i][j] = dp[i-1][j-1]; // match, no cost
continue; // skip swap and other ops, match is optimal
}
double deletion = dp[i-1][j] + delete_weight;
double insertion = dp[i][j-1] + insert_weight;
double substitution = dp[i-1][j-1] + replace_weight;
dp[i][j] = std::min({deletion, insertion, substitution});

if (i > 1 && j > 1 &&
a[i-1] == b[j-2] && a[i-2] == b[j-1]) {
dp[i][j] = std::min(dp[i][j],
dp[i-2][j-2] + cost_map.at(SWAP));
dp[i-2][j-2] + swap_weight);
}
}
}

return dp;
}


double cpp_compute_distance(
const std::string& a,
const std::string& b,
const std::map<CppEditopName, double>& cost_map
const std::string& b,
double replace_weight,
double insert_weight,
double delete_weight,
double swap_weight
) {
auto dp = compute_dp_table(a, b, cost_map);
auto dp = compute_dp_table(a, b, replace_weight, insert_weight, delete_weight, swap_weight);
return dp[a.length()][b.length()];
}

std::vector<std::vector<CppEditop>> backtrack_all_paths(
const std::string& a,
const std::string& b,
const std::map<CppEditopName, double>& cost_map,
const std::vector<std::vector<double>>& dp,
int i,
int j,
std::vector<CppEditop>& current_path
std::vector<CppEditop>& current_path,
double replace_weight,
double insert_weight,
double delete_weight,
double swap_weight
) {
if (i == 0 && j == 0) {
std::vector<CppEditop> reversed_path = current_path;
Expand All @@ -67,70 +76,71 @@ std::vector<std::vector<CppEditop>> backtrack_all_paths(
double current_cost = dp[i][j];
const double tol = 1e-6;


if (i > 0 && std::abs((dp[i-1][j] + cost_map.at(DELETE)) - current_cost) < tol) {
CppEditop op(DELETE, i-1, i-1, cost_map.at(DELETE), std::string(1, a[i-1]));
if (i > 0 && std::abs((dp[i-1][j] + delete_weight) - current_cost) < tol) {
CppEditop op(DELETE, i-1, i-1, delete_weight, std::string(1, a[i-1]));
current_path.push_back(op);
auto paths = backtrack_all_paths(a, b, cost_map, dp, i-1, j, current_path);
auto paths = backtrack_all_paths(a, b, dp, i-1, j, current_path, replace_weight, insert_weight, delete_weight, swap_weight);
all_paths.insert(all_paths.end(), paths.begin(), paths.end());
current_path.pop_back();
}

if (j > 0 && std::abs((dp[i][j-1] + cost_map.at(INSERT)) - current_cost) < tol) {
CppEditop op(INSERT, i, i, cost_map.at(INSERT), std::string(1, b[j-1]));
if (j > 0 && std::abs((dp[i][j-1] + insert_weight) - current_cost) < tol) {
CppEditop op(INSERT, i, i, insert_weight, std::string(1, b[j-1]));
current_path.push_back(op);
auto paths = backtrack_all_paths(a, b, cost_map, dp, i, j-1, current_path);
auto paths = backtrack_all_paths(a, b, dp, i, j-1, current_path, replace_weight, insert_weight, delete_weight, swap_weight);
all_paths.insert(all_paths.end(), paths.begin(), paths.end());
current_path.pop_back();
}


if (i > 0 && j > 0) {
double sub_cost = (a[i-1] == b[j-1]) ? 0.0 : cost_map.at(REPLACE);
double sub_cost = (a[i-1] == b[j-1]) ? 0.0 : replace_weight;
if (std::abs((dp[i-1][j-1] + sub_cost) - current_cost) < tol) {
std::string out_char = (sub_cost == 0.0) ? std::string(1, a[i-1]) : std::string(1, b[j-1]);
CppEditop op(REPLACE, i-1, j-1, sub_cost, out_char);
current_path.push_back(op);
auto paths = backtrack_all_paths(a, b, cost_map, dp, i-1, j-1, current_path);
auto paths = backtrack_all_paths(a, b, dp, i-1, j-1, current_path, replace_weight, insert_weight, delete_weight, swap_weight);
all_paths.insert(all_paths.end(), paths.begin(), paths.end());
current_path.pop_back();
}
}


if (i > 1 && j > 1 &&
a[i-1] == b[j-2] && a[i-2] == b[j-1] &&
std::abs((dp[i-2][j-2] + cost_map.at(SWAP)) - current_cost) < tol) {
std::abs((dp[i-2][j-2] + swap_weight) - current_cost) < tol) {
std::string swap_str = std::string(1, b[j-2]) + std::string(1, b[j-1]);
CppEditop op(SWAP, i-2, j-2, cost_map.at(SWAP), swap_str);
CppEditop op(SWAP, i-2, j-2, swap_weight, swap_str);
current_path.push_back(op);
auto paths = backtrack_all_paths(a, b, cost_map, dp, i-2, j-2, current_path);
auto paths = backtrack_all_paths(a, b, dp, i-2, j-2, current_path, replace_weight, insert_weight, delete_weight, swap_weight);
all_paths.insert(all_paths.end(), paths.begin(), paths.end());
current_path.pop_back();
}

return all_paths;
}


std::vector<std::vector<CppEditop>> cpp_compute_all_paths(
const std::string& a,
const std::string& b,
const std::map<CppEditopName, double>& cost_map
const std::string& b,
double replace_weight,
double insert_weight,
double delete_weight,
double swap_weight
) {
auto dp = compute_dp_table(a, b, cost_map);
auto dp = compute_dp_table(a, b, replace_weight, insert_weight, delete_weight, swap_weight);
std::vector<CppEditop> current_path;
return backtrack_all_paths(a, b, cost_map, dp, a.length(), b.length(), current_path);
return backtrack_all_paths(a, b, dp, a.length(), b.length(), current_path, replace_weight, insert_weight, delete_weight, swap_weight);
}


void cpp_print_all_paths(
const std::string& a,
const std::string& b,
const std::map<CppEditopName, double>& cost_map
const std::string& b,
double replace_weight,
double insert_weight,
double delete_weight,
double swap_weight
) {
auto paths = cpp_compute_all_paths(a, b, cost_map);
double distance = cpp_compute_distance(a, b, cost_map);
auto paths = cpp_compute_all_paths(a, b, replace_weight, insert_weight, delete_weight, swap_weight);
double distance = cpp_compute_distance(a, b, replace_weight, insert_weight, delete_weight, swap_weight);

std::cout << "OSA Distance from '" << a << "' to '" << b << "': " << distance << std::endl;
std::cout << "Number of optimal edit sequences: " << paths.size() << std::endl;
Expand Down
35 changes: 25 additions & 10 deletions editdistance/_edit_distance_osa.hpp
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -29,40 +29,55 @@ struct CppEditop {

std::vector<std::vector<double>> compute_dp_table(
const std::string& a,
const std::string& b,
const std::map<CppEditopName, double>& cost_map
const std::string& b,
double replace_weight,
double insert_weight,
double delete_weight,
double swap_weight
);


double cpp_compute_distance(
const std::string& a,
const std::string& b,
const std::map<CppEditopName, double>& cost_map
const std::string& b,
double replace_weight,
double insert_weight,
double delete_weight,
double swap_weight
);


std::vector<std::vector<CppEditop>> backtrack_all_paths(
const std::string& a,
const std::string& b,
const std::map<CppEditopName, double>& cost_map,
const std::vector<std::vector<double>>& dp,
int i,
int j,
std::vector<CppEditop>& current_path
std::vector<CppEditop>& current_path,
double replace_weight,
double insert_weight,
double delete_weight,
double swap_weight
);


std::vector<std::vector<CppEditop>> cpp_compute_all_paths(
const std::string& a,
const std::string& b,
const std::map<CppEditopName, double>& cost_map
const std::string& b,
double replace_weight,
double insert_weight,
double delete_weight,
double swap_weight
);


void cpp_print_all_paths(
const std::string& a,
const std::string& b,
const std::map<CppEditopName, double>& cost_map
const std::string& b,
double replace_weight,
double insert_weight,
double delete_weight,
double swap_weight
);


Expand Down
55 changes: 15 additions & 40 deletions editdistance/edit_distance_osa.pyx
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -22,9 +22,15 @@ cdef extern from "_edit_distance_osa.hpp":
double cost
string output_string

vector[vector[CppEditop]] cpp_compute_all_paths(const string& a, const string& b, const map[CppEditopName, double]& cost_map)
void cpp_print_all_paths(const string& a, const string& b, const map[CppEditopName, double]& cost_map)
double cpp_compute_distance(const string& a, const string& b, const map[CppEditopName, double]& cost_map)
vector[vector[CppEditop]] cpp_compute_all_paths(
const string& a, const string& b,
double replace_weight, double insert_weight, double delete_weight, double swap_weight)
void cpp_print_all_paths(
const string& a, const string& b,
double replace_weight, double insert_weight, double delete_weight, double swap_weight)
double cpp_compute_distance(
const string& a, const string& b,
double replace_weight, double insert_weight, double delete_weight, double swap_weight)


class EditopName(Enum):
Expand Down Expand Up @@ -52,19 +58,6 @@ cdef class Editop:
return f"Editop(name={self.name}, src_idx={self.src_idx}, dst_idx={self.dst_idx}, cost={self.cost}, output_string='{self.output_string}')"


cdef map[CppEditopName, double] _convert_cost_map(dict cost_map):
cdef map[CppEditopName, double] cpp_cost_map
if EditopName.INSERT in cost_map:
cpp_cost_map[INSERT] = cost_map[EditopName.INSERT]
if EditopName.DELETE in cost_map:
cpp_cost_map[DELETE] = cost_map[EditopName.DELETE]
if EditopName.REPLACE in cost_map:
cpp_cost_map[REPLACE] = cost_map[EditopName.REPLACE]
if EditopName.SWAP in cost_map:
cpp_cost_map[SWAP] = cost_map[EditopName.SWAP]
return cpp_cost_map


def get_all_paths(
str a,
str b,
Expand All @@ -73,16 +66,10 @@ def get_all_paths(
double delete_weight=1.0,
double swap_weight=1.0
):
cdef dict cost_map = {
EditopName.REPLACE: replace_weight,
EditopName.INSERT: insert_weight,
EditopName.DELETE: delete_weight,
EditopName.SWAP: swap_weight
}
cdef string cpp_a = a.encode("utf-8")
cdef string cpp_b = b.encode("utf-8")
cdef map[CppEditopName, double] cpp_cost_map = _convert_cost_map(cost_map)
cdef vector[vector[CppEditop]] cpp_paths = cpp_compute_all_paths(cpp_a, cpp_b, cpp_cost_map)
cdef vector[vector[CppEditop]] cpp_paths = cpp_compute_all_paths(
cpp_a, cpp_b, replace_weight, insert_weight, delete_weight, swap_weight)
python_paths = []
cdef vector[CppEditop] cpp_path
cdef CppEditop cpp_op
Expand Down Expand Up @@ -120,16 +107,10 @@ def print_all_paths(
double delete_weight=1.0,
double swap_weight=1.0
):
cdef dict cost_map = {
EditopName.REPLACE: replace_weight,
EditopName.INSERT: insert_weight,
EditopName.DELETE: delete_weight,
EditopName.SWAP: swap_weight
}
cdef string cpp_a = a.encode("utf-8")
cdef string cpp_b = b.encode("utf-8")
cdef map[CppEditopName, double] cpp_cost_map = _convert_cost_map(cost_map)
cpp_print_all_paths(cpp_a, cpp_b, cpp_cost_map)
cpp_print_all_paths(
cpp_a, cpp_b, replace_weight, insert_weight, delete_weight, swap_weight)


def compute_distance(
Expand All @@ -140,13 +121,7 @@ def compute_distance(
double delete_weight=1.0,
double swap_weight=1.0
):
cdef dict cost_map = {
EditopName.REPLACE: replace_weight,
EditopName.INSERT: insert_weight,
EditopName.DELETE: delete_weight,
EditopName.SWAP: swap_weight
}
cdef string cpp_a = a.encode("utf-8")
cdef string cpp_b = b.encode("utf-8")
cdef map[CppEditopName, double] cpp_cost_map = _convert_cost_map(cost_map)
return cpp_compute_distance(cpp_a, cpp_b, cpp_cost_map)
return cpp_compute_distance(
cpp_a, cpp_b, replace_weight, insert_weight, delete_weight, swap_weight)
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