Add Jensen-Shanon kernel This patch adds a CDotKernel based Jensen-Sh…

…annon kernel to shogun-toolbox. Sources of modular interface has been changed so it can be used via the modular interfaces as well.
shogun-toolbox · Feb 10, 2012 · e0a1155 · e0a1155
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diff --git a/src/interfaces/modular/Kernel.i b/src/interfaces/modular/Kernel.i
@@ -86,6 +86,7 @@
 %rename(DotKernel) CDotKernel;
 %rename(RationalQuadraticKernel) CRationalQuadraticKernel;
 %rename(MultiquadricKernel) CMultiquadricKernel;
+%rename(JensenShannonKernel) CJensenShannonKernel;
 
 /* Include Class Headers to make them visible from within the target language */
 %include <shogun/kernel/Kernel.h>
@@ -200,3 +201,4 @@ namespace shogun
 %include <shogun/kernel/ZeroMeanCenterKernelNormalizer.h>
 %include <shogun/kernel/MultiquadricKernel.h>
 %include <shogun/kernel/RationalQuadraticKernel.h>
+%include <shogun/kernel/JensenShannonKernel.h>
diff --git a/src/interfaces/modular/Kernel_includes.i b/src/interfaces/modular/Kernel_includes.i
@@ -74,4 +74,5 @@
 #include <shogun/kernel/ZeroMeanCenterKernelNormalizer.h>
 #include <shogun/kernel/RationalQuadraticKernel.h>
 #include <shogun/kernel/CircularKernel.h>
+#include <shogun/kernel/JensenShannonKernel.h>
 %}
diff --git a/src/shogun/kernel/JensenShannonKernel.cpp b/src/shogun/kernel/JensenShannonKernel.cpp
@@ -0,0 +1,78 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Written (W) 2012 Viktor Gal
+ * Copyright (C) 2012 Viktor Gal
+ */
+
+#include <shogun/lib/common.h>
+#include <shogun/kernel/JensenShannonKernel.h>
+#include <shogun/features/Features.h>
+#include <shogun/features/SimpleFeatures.h>
+#include <shogun/io/SGIO.h>
+
+using namespace shogun;
+
+CJensenShannonKernel::CJensenShannonKernel()
+: CDotKernel(0)
+{
+}
+
+CJensenShannonKernel::CJensenShannonKernel(int32_t size)
+: CDotKernel(size)
+{
+}
+
+CJensenShannonKernel::CJensenShannonKernel(
+	CSimpleFeatures<float64_t>* l, CSimpleFeatures<float64_t>* r, int32_t size)
+: CDotKernel(size)
+{
+	init(l,r);
+}
+
+CJensenShannonKernel::~CJensenShannonKernel()
+{
+	cleanup();
+}
+
+bool CJensenShannonKernel::init(CFeatures* l, CFeatures* r)
+{
+	bool result=CDotKernel::init(l,r);
+	init_normalizer();
+	return result;
+}
+
+float64_t CJensenShannonKernel::compute(int32_t idx_a, int32_t idx_b)
+{
+	int32_t alen, blen;
+	bool afree, bfree;
+
+	float64_t* avec=
+		((CSimpleFeatures<float64_t>*) lhs)->get_feature_vector(idx_a, alen, afree);
+	float64_t* bvec=
+		((CSimpleFeatures<float64_t>*) rhs)->get_feature_vector(idx_b, blen, bfree);
+	ASSERT(alen==blen);
+
+	float64_t result=0;
+
+	/* calcualte Jensen-Shannon kernel */
+	for (int32_t i=0; i<alen; i++) {
+		float64_t a_i = 0, b_i = 0;
+		float64_t ab = avec[i]+bvec[i];
+		if (avec[i] != 0)
+			a_i = avec[i]/2 * log2(ab/avec[i]);
+		if (bvec[i] != 0)
+			b_i = bvec[i]/2 * log2(ab/bvec[i]);
+
+		result += a_i + b_i;
+	}
+
+	((CSimpleFeatures<float64_t>*) lhs)->free_feature_vector(avec, idx_a, afree);
+	((CSimpleFeatures<float64_t>*) rhs)->free_feature_vector(bvec, idx_b, bfree);
+
+	return result;
+}
+
diff --git a/src/shogun/kernel/JensenShannonKernel.h b/src/shogun/kernel/JensenShannonKernel.h
@@ -0,0 +1,86 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Written (W) 2012 Viktor Gal
+ * Copyright (C) 2012 Viktor Gal
+ */
+
+#ifndef _JENSENSHANNONKERNEL_H___
+#define _JENSENSHANNONKERNEL_H___
+
+#include <shogun/lib/common.h>
+#include <shogun/kernel/DotKernel.h>
+#include <shogun/features/SimpleFeatures.h>
+
+namespace shogun
+{
+/** @brief The Jensen-Shannon kernel operating on real-valued vectors computes
+ * the Jensen-Shannon distance between the features. Often used in computer vision.
+ *
+ * It is defined as
+ * \f[
+ * k({\bf x},({\bf x'})= \sum_{i=0}^{l} \frac{x_i}{2} \log_2\frac{x_i+x'_i}{x_i} + \frac{x'_i}{2} \log_2\frac{x_i+x'_i}{x'_i}
+ * \f]
+ * */
+class CJensenShannonKernel: public CDotKernel
+{
+	public:
+		/** default constructor  */
+		CJensenShannonKernel();
+
+		/** constructor
+		 *
+		 * @param size cache size
+		 */
+		CJensenShannonKernel(int32_t size);
+
+		/** constructor
+		 *
+		 * @param l features of left-hand side
+		 * @param r features of right-hand side
+		 * @param size cache size
+		 */
+		CJensenShannonKernel(
+			CSimpleFeatures<float64_t>* l, CSimpleFeatures<float64_t>* r,
+			int32_t size=10);
+
+		virtual ~CJensenShannonKernel();
+
+		/** initialize kernel
+		 *
+		 * @param l features of left-hand side
+		 * @param r features of right-hand side
+		 * @return if initializing was successful
+		 */
+		virtual bool init(CFeatures* l, CFeatures* r);
+
+		/** return what type of kernel we are
+		 *
+		 * @return kernel type JENSENSHANNON
+		 */
+		virtual EKernelType get_kernel_type() { return K_JENSENSHANNON; }
+
+		/** return the kernel's name
+		 *
+		 * @return name JensenShannonKernel
+		 */
+		virtual const char* get_name() const { return "JensenShannonKernel"; }
+
+	protected:
+
+		/** compute kernel function for features a and b
+		 * idx_{a,b} denote the index of the feature vectors
+		 * in the corresponding feature object
+		 *
+		 * @param idx_a index a
+		 * @param idx_b index b
+		 * @return computed kernel function at indices a,b
+		 */
+		virtual float64_t compute(int32_t idx_a, int32_t idx_b);
+
+};
+}
+#endif /* _JENSENSHANNONKERNEL_H___ */
diff --git a/src/shogun/kernel/Kernel.cpp b/src/shogun/kernel/Kernel.cpp
@@ -751,6 +751,7 @@ void CKernel::list_kernel()
 		ENUM_CASE(K_SPECTRUMMISMATCHRBF)
 		ENUM_CASE(K_DISTANTSEGMENTS)
 		ENUM_CASE(K_BESSEL)
+		ENUM_CASE(K_JENSENSHANNON)
 	}
 
 	switch (get_feature_class())

diff --git a/src/shogun/kernel/Kernel.h b/src/shogun/kernel/Kernel.h
@@ -107,6 +107,7 @@ enum EKernelType
 	K_INVERSEMULTIQUADRIC = 440,
 	K_DISTANTSEGMENTS = 450,
 	K_BESSEL = 460,
+	K_JENSENSHANNON = 470
 };
 
 /** kernel property */