1 files changed, 51 insertions, 0 deletions
diff --git a/utils/kernel_string_subseq.h b/utils/kernel_string_subseq.h
new file mode 100644
index 00000000..516e8b89
--- /dev/null
+++ b/utils/kernel_string_subseq.h
@@ -0,0 +1,51 @@
+#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