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#ifndef KERNEL_STRING_SUBSEQ_H_
#define KERNEL_STRING_SUBSEQ_H_
#include <vector>
#include <cmath>
#include <boost/multi_array.hpp>
template <unsigned N, typename T>
float ssk(const T* s, const size_t s_size, const T* t, const size_t t_size, const float lambda) {
assert(N > 0);
boost::multi_array<float, 3> kp(boost::extents[N + 1][s_size + 1][t_size + 1]);
const float l2 = lambda * lambda;
for (unsigned j = 0; j < s_size; ++j)
for (unsigned k = 0; k < t_size; ++k)
kp[0][j][k] = 1.0f;
for (unsigned i = 0; i < N; ++i) {
for (unsigned j = 0; j < s_size; ++j) {
float kpp = 0.0f;
for (unsigned k = 0; k < t_size; ++k) {
kpp = lambda * (kpp + lambda * (s[j]==t[k]) * kp[i][j][k]);
kp[i + 1][j + 1][k + 1] = lambda * kp[i + 1][j][k + 1] + kpp;
}
}
}
float kn = 0.0f;
for (int i = 0; i < N; ++i)
for (int j = 0; j < s_size; ++j)
for (int k = 0; k < t_size; ++k)
kn += l2 * (s[j] == t[k]) * kp[i][j][k];
return kn;
}
template <unsigned N, typename T>
float ssk(const std::vector<T>& s, const std::vector<T>& t, const float lambda) {
float kst = ssk<N, T>(&s[0], s.size(), &t[0], t.size(), lambda);
if (!kst) return 0.0f;
float kss = ssk<N, T>(&s[0], s.size(), &s[0], s.size(), lambda);
float ktt = ssk<N, T>(&t[0], t.size(), &t[0], t.size(), lambda);
return kst / std::sqrt(kss * ktt);
}
template <unsigned N>
float ssk(const std::string& s, const std::string& t, const float lambda) {
float kst = ssk<N, char>(&s[0], s.size(), &t[0], t.size(), lambda);
if (!kst) return 0.0f;
float kss = ssk<N, char>(&s[0], s.size(), &s[0], s.size(), lambda);
float ktt = ssk<N, char>(&t[0], t.size(), &t[0], t.size(), lambda);
return kst / std::sqrt(kss * ktt);
}
#endif
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