diff --git a/src/shogun/lib/tapkee/tapkee_shogun.cpp b/src/shogun/lib/tapkee/tapkee_shogun.cpp
index 10e859ec32e..22bf435e7ec 100644
--- a/src/shogun/lib/tapkee/tapkee_shogun.cpp
+++ b/src/shogun/lib/tapkee/tapkee_shogun.cpp
@@ -20,8 +20,8 @@
 	#define TAPKEE_WITH_ARPACK
 #endif
 #define TAPKEE_USE_LGPL_COVERTREE
-#include <shogun/lib/tapkee/tapkee.hpp>
-#include <shogun/lib/tapkee/callbacks/pimpl_callbacks.hpp>
+#include <tapkee/tapkee.hpp>
+#include <tapkee/callbacks/pimpl_callbacks.hpp>
 
 using namespace shogun;
 
diff --git a/third_party/tapkee/callbacks/neighbor_callbacks.hpp b/third_party/tapkee/callbacks/neighbor_callbacks.hpp
index c73eeac2646..04b849362f8 100644
--- a/third_party/tapkee/callbacks/neighbor_callbacks.hpp
+++ b/third_party/tapkee/callbacks/neighbor_callbacks.hpp
@@ -7,7 +7,7 @@
 #define TAPKEE_NEIGHBOR_CALLBACK_H_
 
 /* Tapkee includes */
-#include <shogun/lib/tapkee/tapkee_defines.hpp>
+#include <tapkee/tapkee_defines.hpp>
 /* End of Tapkee includes */
 
 template<class RandomAccessIterator>
diff --git a/third_party/tapkee/chain_interface.hpp b/third_party/tapkee/chain_interface.hpp
index bc6d3ef7b36..772e5fb2bee 100644
--- a/third_party/tapkee/chain_interface.hpp
+++ b/third_party/tapkee/chain_interface.hpp
@@ -7,9 +7,9 @@
 #define TAPKEE_CHAIN_H_
 
 /* Tapkee includes */
-#include <shogun/lib/tapkee/embed.hpp>
-#include <shogun/lib/tapkee/callbacks/dummy_callbacks.hpp>
-#include <shogun/lib/tapkee/callbacks/eigen_callbacks.hpp>
+#include <tapkee/embed.hpp>
+#include <tapkee/callbacks/dummy_callbacks.hpp>
+#include <tapkee/callbacks/eigen_callbacks.hpp>
 /* End of Tapkee includes */
 
 namespace tapkee
diff --git a/third_party/tapkee/defines.hpp b/third_party/tapkee/defines.hpp
index fd02636bcea..c73b129f21e 100644
--- a/third_party/tapkee/defines.hpp
+++ b/third_party/tapkee/defines.hpp
@@ -7,10 +7,10 @@
 #define TAPKEE_DEFINES_H_
 
 /* Tapkee includes */
-#include <shogun/lib/tapkee/exceptions.hpp>
-#include <shogun/lib/tapkee/parameters/parameters.hpp>
-#include <shogun/lib/tapkee/traits/callbacks_traits.hpp>
-#include <shogun/lib/tapkee/traits/methods_traits.hpp>
+#include <tapkee/exceptions.hpp>
+#include <tapkee/parameters/parameters.hpp>
+#include <tapkee/traits/callbacks_traits.hpp>
+#include <tapkee/traits/methods_traits.hpp>
 /* End of Tapkee includes */
 
 #include <string>
@@ -20,14 +20,14 @@
 #define TAPKEE_MINOR_VERSION 0
 
 /* Tapkee includes */
-#include <shogun/lib/tapkee/defines/eigen3.hpp>
-#include <shogun/lib/tapkee/defines/types.hpp>
-#include <shogun/lib/tapkee/defines/methods.hpp>
-#include <shogun/lib/tapkee/defines/keywords.hpp>
-#include <shogun/lib/tapkee/defines/stdtypes.hpp>
-#include <shogun/lib/tapkee/defines/synonyms.hpp>
-#include <shogun/lib/tapkee/defines/random.hpp>
-#include <shogun/lib/tapkee/projection.hpp>
+#include <tapkee/defines/eigen3.hpp>
+#include <tapkee/defines/types.hpp>
+#include <tapkee/defines/methods.hpp>
+#include <tapkee/defines/keywords.hpp>
+#include <tapkee/defines/stdtypes.hpp>
+#include <tapkee/defines/synonyms.hpp>
+#include <tapkee/defines/random.hpp>
+#include <tapkee/projection.hpp>
 /* End of Tapkee includes */
 
 #ifdef TAPKEE_CUSTOM_PROPERTIES
diff --git a/third_party/tapkee/defines/keywords.hpp b/third_party/tapkee/defines/keywords.hpp
index b818e08e341..0cc6ee648b3 100644
--- a/third_party/tapkee/defines/keywords.hpp
+++ b/third_party/tapkee/defines/keywords.hpp
@@ -7,7 +7,7 @@
 #define TAPKEE_DEFINES_KEYWORDS_H_
 
 /* Tapkee includes */
-#include <shogun/lib/tapkee/defines/types.hpp>
+#include <tapkee/defines/types.hpp>
 /* End of Tapkee includes */
 
 namespace tapkee
diff --git a/third_party/tapkee/defines/synonyms.hpp b/third_party/tapkee/defines/synonyms.hpp
index 9a81a2be4f2..51c7c5ce94a 100644
--- a/third_party/tapkee/defines/synonyms.hpp
+++ b/third_party/tapkee/defines/synonyms.hpp
@@ -7,8 +7,8 @@
 #define TAPKEE_DEFINES_SYNONYMS_H_
 
 /* Tapkee includes */
-#include <shogun/lib/tapkee/defines/types.hpp>
-#include <shogun/lib/tapkee/defines/stdtypes.hpp>
+#include <tapkee/defines/types.hpp>
+#include <tapkee/defines/stdtypes.hpp>
 /* End of Tapkee includes */
 
 namespace tapkee
diff --git a/third_party/tapkee/embed.hpp b/third_party/tapkee/embed.hpp
index 1a50b8c6e9c..ec3deb010d5 100644
--- a/third_party/tapkee/embed.hpp
+++ b/third_party/tapkee/embed.hpp
@@ -7,8 +7,8 @@
 #define TAPKEE_EMBED_H_
 
 /* Tapkee includes */
-#include <shogun/lib/tapkee/defines.hpp>
-#include <shogun/lib/tapkee/methods.hpp>
+#include <tapkee/defines.hpp>
+#include <tapkee/methods.hpp>
 /* End of Tapkee includes */
 
 namespace tapkee
diff --git a/third_party/tapkee/external/barnes_hut_sne/tsne.hpp b/third_party/tapkee/external/barnes_hut_sne/tsne.hpp
index bfc4bcfb454..6d628af1c73 100644
--- a/third_party/tapkee/external/barnes_hut_sne/tsne.hpp
+++ b/third_party/tapkee/external/barnes_hut_sne/tsne.hpp
@@ -33,10 +33,10 @@
 #define TSNE_H
 
 /* Tapkee includes */
-#include <shogun/lib/tapkee/utils/logging.hpp>
-#include <shogun/lib/tapkee/utils/time.hpp>
-#include <shogun/lib/tapkee/external/barnes_hut_sne/quadtree.hpp>
-#include <shogun/lib/tapkee/external/barnes_hut_sne/vptree.hpp>
+#include <tapkee/utils/logging.hpp>
+#include <tapkee/utils/time.hpp>
+#include <tapkee/external/barnes_hut_sne/quadtree.hpp>
+#include <tapkee/external/barnes_hut_sne/vptree.hpp>
 /* End of Tapkee includes */
 
 #include <math.h>
diff --git a/third_party/tapkee/methods.hpp b/third_party/tapkee/methods.hpp
index 363e52015c8..0646916e871 100644
--- a/third_party/tapkee/methods.hpp
+++ b/third_party/tapkee/methods.hpp
@@ -7,28 +7,28 @@
 #define TAPKEE_METHODS_H_
 
 /* Tapkee includes */
-#include <shogun/lib/tapkee/defines.hpp>
-#include <shogun/lib/tapkee/utils/naming.hpp>
-#include <shogun/lib/tapkee/utils/time.hpp>
-#include <shogun/lib/tapkee/utils/logging.hpp>
-#include <shogun/lib/tapkee/utils/conditional_select.hpp>
-#include <shogun/lib/tapkee/utils/features.hpp>
-#include <shogun/lib/tapkee/parameters/defaults.hpp>
-#include <shogun/lib/tapkee/parameters/context.hpp>
-#include <shogun/lib/tapkee/routines/locally_linear.hpp>
-#include <shogun/lib/tapkee/routines/eigendecomposition.hpp>
-#include <shogun/lib/tapkee/routines/generalized_eigendecomposition.hpp>
-#include <shogun/lib/tapkee/routines/multidimensional_scaling.hpp>
-#include <shogun/lib/tapkee/routines/diffusion_maps.hpp>
-#include <shogun/lib/tapkee/routines/laplacian_eigenmaps.hpp>
-#include <shogun/lib/tapkee/routines/isomap.hpp>
-#include <shogun/lib/tapkee/routines/pca.hpp>
-#include <shogun/lib/tapkee/routines/random_projection.hpp>
-#include <shogun/lib/tapkee/routines/spe.hpp>
-#include <shogun/lib/tapkee/routines/fa.hpp>
-#include <shogun/lib/tapkee/routines/manifold_sculpting.hpp>
-#include <shogun/lib/tapkee/neighbors/neighbors.hpp>
-#include <shogun/lib/tapkee/external/barnes_hut_sne/tsne.hpp>
+#include <tapkee/defines.hpp>
+#include <tapkee/utils/naming.hpp>
+#include <tapkee/utils/time.hpp>
+#include <tapkee/utils/logging.hpp>
+#include <tapkee/utils/conditional_select.hpp>
+#include <tapkee/utils/features.hpp>
+#include <tapkee/parameters/defaults.hpp>
+#include <tapkee/parameters/context.hpp>
+#include <tapkee/routines/locally_linear.hpp>
+#include <tapkee/routines/eigendecomposition.hpp>
+#include <tapkee/routines/generalized_eigendecomposition.hpp>
+#include <tapkee/routines/multidimensional_scaling.hpp>
+#include <tapkee/routines/diffusion_maps.hpp>
+#include <tapkee/routines/laplacian_eigenmaps.hpp>
+#include <tapkee/routines/isomap.hpp>
+#include <tapkee/routines/pca.hpp>
+#include <tapkee/routines/random_projection.hpp>
+#include <tapkee/routines/spe.hpp>
+#include <tapkee/routines/fa.hpp>
+#include <tapkee/routines/manifold_sculpting.hpp>
+#include <tapkee/neighbors/neighbors.hpp>
+#include <tapkee/external/barnes_hut_sne/tsne.hpp>
 /* End of Tapkee includes */
 
 namespace tapkee
diff --git a/third_party/tapkee/neighbors/covertree.hpp b/third_party/tapkee/neighbors/covertree.hpp
index d6b9f628da0..df3c5dc3102 100644
--- a/third_party/tapkee/neighbors/covertree.hpp
+++ b/third_party/tapkee/neighbors/covertree.hpp
@@ -11,7 +11,7 @@
 #define COVERTREE_H_
 
 /* Tapkee includes */
-#include <shogun/lib/tapkee/neighbors/covertree_point.hpp>
+#include <tapkee/neighbors/covertree_point.hpp>
 /* End of Tapkee includes */
 
 #include <cmath>
diff --git a/third_party/tapkee/neighbors/covertree_point.hpp b/third_party/tapkee/neighbors/covertree_point.hpp
index 7113894dd1e..3443e127198 100644
--- a/third_party/tapkee/neighbors/covertree_point.hpp
+++ b/third_party/tapkee/neighbors/covertree_point.hpp
@@ -12,7 +12,7 @@
 #define _JL_COVERTREE_POINT_H_
 
 /* Tapkee includes */
-#include <shogun/lib/tapkee/defines.hpp>
+#include <tapkee/defines.hpp>
 /* End of Tapkee includes */
 
 #include <iostream>
diff --git a/third_party/tapkee/neighbors/neighbors.hpp b/third_party/tapkee/neighbors/neighbors.hpp
index 40d7828d27b..94663b7cd8b 100644
--- a/third_party/tapkee/neighbors/neighbors.hpp
+++ b/third_party/tapkee/neighbors/neighbors.hpp
@@ -7,12 +7,12 @@
 #define TAPKEE_NEIGHBORS_H_
 
 /* Tapkee includes */
-#include <shogun/lib/tapkee/defines.hpp>
+#include <tapkee/defines.hpp>
 #ifdef TAPKEE_USE_LGPL_COVERTREE
-	#include <shogun/lib/tapkee/neighbors/covertree.hpp>
+	#include <tapkee/neighbors/covertree.hpp>
 #endif
-#include <shogun/lib/tapkee/neighbors/connected.hpp>
-#include <shogun/lib/tapkee/neighbors/vptree.hpp>
+#include <tapkee/neighbors/connected.hpp>
+#include <tapkee/neighbors/vptree.hpp>
 /* End of Tapkee includes */
 
 #include <vector>
diff --git a/third_party/tapkee/neighbors/vptree.hpp b/third_party/tapkee/neighbors/vptree.hpp
index 00b92c3a266..fd146cd2835 100644
--- a/third_party/tapkee/neighbors/vptree.hpp
+++ b/third_party/tapkee/neighbors/vptree.hpp
@@ -7,7 +7,7 @@
 #define TAPKEE_VPTREE_H_
 
 /* Tapkee includes */
-#include <shogun/lib/tapkee/defines.hpp>
+#include <tapkee/defines.hpp>
 /* End of Tapkee includes */
 
 #include <vector>
diff --git a/third_party/tapkee/parameters/parameters.hpp b/third_party/tapkee/parameters/parameters.hpp
index 9af5c0a830d..eb339abff8f 100644
--- a/third_party/tapkee/parameters/parameters.hpp
+++ b/third_party/tapkee/parameters/parameters.hpp
@@ -7,7 +7,7 @@
 #define TAPKEE_PARAMETERS_H_
 
 /* Tapkee includes */
-#include <shogun/lib/tapkee/parameters/value_keeper.hpp>
+#include <tapkee/parameters/value_keeper.hpp>
 /* End of Tapkee includes */
 
 #include <sstream>
diff --git a/third_party/tapkee/parameters/value_keeper.hpp b/third_party/tapkee/parameters/value_keeper.hpp
index 8dee4a3eb25..56d76d58673 100644
--- a/third_party/tapkee/parameters/value_keeper.hpp
+++ b/third_party/tapkee/parameters/value_keeper.hpp
@@ -7,7 +7,7 @@
 #define TAPKEE_VALUE_KEEPER_H_
 
 /* Tapkee includes */
-#include <shogun/lib/tapkee/parameters/policy.hpp>
+#include <tapkee/parameters/policy.hpp>
 /* End of Tapkee includes */
 
 namespace tapkee
diff --git a/third_party/tapkee/routines/diffusion_maps.hpp b/third_party/tapkee/routines/diffusion_maps.hpp
index d06a425aed5..8e2a0ed58a4 100644
--- a/third_party/tapkee/routines/diffusion_maps.hpp
+++ b/third_party/tapkee/routines/diffusion_maps.hpp
@@ -7,8 +7,8 @@
 #define TAPKEE_DiffusionMapS_H_
 
 /* Tapkee includes */
-#include <shogun/lib/tapkee/defines.hpp>
-#include <shogun/lib/tapkee/utils/time.hpp>
+#include <tapkee/defines.hpp>
+#include <tapkee/utils/time.hpp>
 /* End of Tapke includes */
 
 namespace tapkee
diff --git a/third_party/tapkee/routines/eigendecomposition.hpp b/third_party/tapkee/routines/eigendecomposition.hpp
index dceb06f4d3e..0eee20b39c3 100644
--- a/third_party/tapkee/routines/eigendecomposition.hpp
+++ b/third_party/tapkee/routines/eigendecomposition.hpp
@@ -14,10 +14,10 @@
 
 /* Tapkee includes */
 #ifdef TAPKEE_WITH_ARPACK
-	#include <shogun/lib/tapkee/utils/arpack_wrapper.hpp>
+	#include <tapkee/utils/arpack_wrapper.hpp>
 #endif
-#include <shogun/lib/tapkee/routines/matrix_operations.hpp>
-#include <shogun/lib/tapkee/defines.hpp>
+#include <tapkee/routines/matrix_operations.hpp>
+#include <tapkee/defines.hpp>
 /* End of Tapkee includes */
 
 namespace tapkee
diff --git a/third_party/tapkee/routines/generalized_eigendecomposition.hpp b/third_party/tapkee/routines/generalized_eigendecomposition.hpp
index 0569b04515a..b3feb066601 100644
--- a/third_party/tapkee/routines/generalized_eigendecomposition.hpp
+++ b/third_party/tapkee/routines/generalized_eigendecomposition.hpp
@@ -8,9 +8,9 @@
 
 /* Tapkee includes */
 #ifdef TAPKEE_WITH_ARPACK
-	#include <shogun/lib/tapkee/utils/arpack_wrapper.hpp>
+	#include <tapkee/utils/arpack_wrapper.hpp>
 #endif
-#include <shogun/lib/tapkee/routines/matrix_operations.hpp>
+#include <tapkee/routines/matrix_operations.hpp>
 /* End of Tapkee includes */
 
 namespace tapkee
diff --git a/third_party/tapkee/routines/isomap.hpp b/third_party/tapkee/routines/isomap.hpp
index e30e83a235f..216550148a0 100644
--- a/third_party/tapkee/routines/isomap.hpp
+++ b/third_party/tapkee/routines/isomap.hpp
@@ -7,10 +7,10 @@
 #define TAPKEE_Isomap_H_
 
 /* Tapkee includes */
-#include <shogun/lib/tapkee/defines.hpp>
-#include <shogun/lib/tapkee/utils/fibonacci_heap.hpp>
-#include <shogun/lib/tapkee/utils/reservable_priority_queue.hpp>
-#include <shogun/lib/tapkee/utils/time.hpp>
+#include <tapkee/defines.hpp>
+#include <tapkee/utils/fibonacci_heap.hpp>
+#include <tapkee/utils/reservable_priority_queue.hpp>
+#include <tapkee/utils/time.hpp>
 /* End of Tapkee includes */
 
 #include <limits>
diff --git a/third_party/tapkee/routines/laplacian_eigenmaps.hpp b/third_party/tapkee/routines/laplacian_eigenmaps.hpp
index 298035e58fa..41d915b9023 100644
--- a/third_party/tapkee/routines/laplacian_eigenmaps.hpp
+++ b/third_party/tapkee/routines/laplacian_eigenmaps.hpp
@@ -7,8 +7,8 @@
 #define TAPKEE_LaplacianEigenmaps_H_
 
 /* Tapkee includes */
-#include <shogun/lib/tapkee/defines.hpp>
-#include <shogun/lib/tapkee/utils/time.hpp>
+#include <tapkee/defines.hpp>
+#include <tapkee/utils/time.hpp>
 /* End of Tapkee includes */
 
 namespace tapkee
diff --git a/third_party/tapkee/routines/locally_linear.hpp b/third_party/tapkee/routines/locally_linear.hpp
index 2b6fe842c51..3227676d2d4 100644
--- a/third_party/tapkee/routines/locally_linear.hpp
+++ b/third_party/tapkee/routines/locally_linear.hpp
@@ -7,11 +7,11 @@
 #define TAPKEE_LOCALLY_LINEAR_H_
 
 /* Tapkee includes */
-#include <shogun/lib/tapkee/routines/eigendecomposition.hpp>
-#include <shogun/lib/tapkee/defines.hpp>
-#include <shogun/lib/tapkee/utils/matrix.hpp>
-#include <shogun/lib/tapkee/utils/time.hpp>
-#include <shogun/lib/tapkee/utils/sparse.hpp>
+#include <tapkee/routines/eigendecomposition.hpp>
+#include <tapkee/defines.hpp>
+#include <tapkee/utils/matrix.hpp>
+#include <tapkee/utils/time.hpp>
+#include <tapkee/utils/sparse.hpp>
 /* End of Tapkee includes */
 
 namespace tapkee
diff --git a/third_party/tapkee/routines/manifold_sculpting.hpp b/third_party/tapkee/routines/manifold_sculpting.hpp
index efafff2eef1..e3619f4e70f 100644
--- a/third_party/tapkee/routines/manifold_sculpting.hpp
+++ b/third_party/tapkee/routines/manifold_sculpting.hpp
@@ -7,8 +7,8 @@
 #define TAPKEE_MANIFOLD_SCULPTING_H_
 
 /* Tapkee includes */
-#include <shogun/lib/tapkee/defines.hpp>
-#include <shogun/lib/tapkee/utils/sparse.hpp>
+#include <tapkee/defines.hpp>
+#include <tapkee/utils/sparse.hpp>
 /* End of Tapkee includes */
 
 #include <math.h>
diff --git a/third_party/tapkee/routines/matrix_operations.hpp b/third_party/tapkee/routines/matrix_operations.hpp
index 2e6cffc3f8c..781be278bd5 100644
--- a/third_party/tapkee/routines/matrix_operations.hpp
+++ b/third_party/tapkee/routines/matrix_operations.hpp
@@ -8,7 +8,7 @@
 #define TAPKEE_MATRIX_OPS_H_
 
 /* Tapkee includes */
-#include <shogun/lib/tapkee/defines.hpp>
+#include <tapkee/defines.hpp>
 /* End of Tapkee includes */
 
 namespace tapkee
diff --git a/third_party/tapkee/routines/multidimensional_scaling.hpp b/third_party/tapkee/routines/multidimensional_scaling.hpp
index 02e3fc00f75..369fc455c2a 100644
--- a/third_party/tapkee/routines/multidimensional_scaling.hpp
+++ b/third_party/tapkee/routines/multidimensional_scaling.hpp
@@ -7,8 +7,8 @@
 #define TAPKEE_MDS_H_
 
 /* Tapkee includes */
-#include <shogun/lib/tapkee/defines.hpp>
-#include <shogun/lib/tapkee/utils/time.hpp>
+#include <tapkee/defines.hpp>
+#include <tapkee/utils/time.hpp>
 /* End of Tapkee includes */
 
 namespace tapkee
diff --git a/third_party/tapkee/routines/pca.hpp b/third_party/tapkee/routines/pca.hpp
index c33c81b785c..f36ab1b7230 100644
--- a/third_party/tapkee/routines/pca.hpp
+++ b/third_party/tapkee/routines/pca.hpp
@@ -7,8 +7,8 @@
 #define TAPKEE_PCA_H_
 
 /* Tapkee includes */
-#include <shogun/lib/tapkee/defines.hpp>
-#include <shogun/lib/tapkee/utils/time.hpp>
+#include <tapkee/defines.hpp>
+#include <tapkee/utils/time.hpp>
 /* End of Tapkee includes */
 
 namespace tapkee
diff --git a/third_party/tapkee/routines/random_projection.hpp b/third_party/tapkee/routines/random_projection.hpp
index 4aae35c9e4e..2e99ab52b2d 100644
--- a/third_party/tapkee/routines/random_projection.hpp
+++ b/third_party/tapkee/routines/random_projection.hpp
@@ -7,8 +7,8 @@
 #define TAPKEE_RandomProjection_H_
 
 /* Tapkee includes */
-#include <shogun/lib/tapkee/defines.hpp>
-#include <shogun/lib/tapkee/utils/time.hpp>
+#include <tapkee/defines.hpp>
+#include <tapkee/utils/time.hpp>
 /* End of Tapkee includes */
 
 namespace tapkee
diff --git a/third_party/tapkee/routines/spe.hpp b/third_party/tapkee/routines/spe.hpp
index 58868982191..439cb148931 100644
--- a/third_party/tapkee/routines/spe.hpp
+++ b/third_party/tapkee/routines/spe.hpp
@@ -7,8 +7,8 @@
 #define TAPKEE_SPE_H_
 
 /* Tapkee includes */
-#include <shogun/lib/tapkee/defines.hpp>
-#include <shogun/lib/tapkee/utils/time.hpp>
+#include <tapkee/defines.hpp>
+#include <tapkee/utils/time.hpp>
 /* End of Tapkee includes */
 
 namespace tapkee
diff --git a/third_party/tapkee/tapkee.hpp b/third_party/tapkee/tapkee.hpp
index dfb6c1e8f45..3e0dd8e3a70 100644
--- a/third_party/tapkee/tapkee.hpp
+++ b/third_party/tapkee/tapkee.hpp
@@ -7,8 +7,8 @@
 #define TAPKEE_MAIN_H_
 
 /* Tapkee includes */
-#include <shogun/lib/tapkee/embed.hpp>
-#include <shogun/lib/tapkee/chain_interface.hpp>
+#include <tapkee/embed.hpp>
+#include <tapkee/chain_interface.hpp>
 /* End of Tapkee includes */
 
 #endif
diff --git a/third_party/tapkee/utils/arpack_wrapper.hpp b/third_party/tapkee/utils/arpack_wrapper.hpp
index f24f509d05d..93ec67f8925 100644
--- a/third_party/tapkee/utils/arpack_wrapper.hpp
+++ b/third_party/tapkee/utils/arpack_wrapper.hpp
@@ -11,7 +11,7 @@
 #define EIGEN_ARPACKGENERALIZEDSELFADJOINTEIGENSOLVER_H
 
 /* Tapkee includes */
-#include <shogun/lib/tapkee/defines.hpp>
+#include <tapkee/defines.hpp>
 /* End of Tapkee includes */
 
 using Eigen::Matrix;
diff --git a/third_party/tapkee/utils/features.hpp b/third_party/tapkee/utils/features.hpp
index e2591895f95..4a854e09340 100644
--- a/third_party/tapkee/utils/features.hpp
+++ b/third_party/tapkee/utils/features.hpp
@@ -7,7 +7,7 @@
 #define TAPKEE_FEATURES_H_
 
 /* Tapkee includes */
-#include <shogun/lib/tapkee/defines.hpp>
+#include <tapkee/defines.hpp>
  /* End of Tapkee includes */
 
 namespace tapkee
diff --git a/third_party/tapkee/utils/fibonacci_heap.hpp b/third_party/tapkee/utils/fibonacci_heap.hpp
index 78eb5c262fe..3e05965c9f4 100644
--- a/third_party/tapkee/utils/fibonacci_heap.hpp
+++ b/third_party/tapkee/utils/fibonacci_heap.hpp
@@ -7,7 +7,7 @@
 #define TAPKEE_FIBONACCI_H_
 
 /* Tapkee includes */
-#include <shogun/lib/tapkee/defines.hpp>
+#include <tapkee/defines.hpp>
 /* End of Tapkee includes */
 
 #include <cmath>
diff --git a/third_party/tapkee/utils/sparse.hpp b/third_party/tapkee/utils/sparse.hpp
index fd73f0b0634..a89a32a31f5 100644
--- a/third_party/tapkee/utils/sparse.hpp
+++ b/third_party/tapkee/utils/sparse.hpp
@@ -7,7 +7,7 @@
 #define TAPKEE_SPARSE_H_
 
 /* Tapkee includes */
-#include <shogun/lib/tapkee/defines.hpp>
+#include <tapkee/defines.hpp>
  /* End of Tapkee includes */
 
 namespace tapkee
diff --git a/third_party/tapkee/utils/time.hpp b/third_party/tapkee/utils/time.hpp
index 57852761237..63fb5f2f37d 100644
--- a/third_party/tapkee/utils/time.hpp
+++ b/third_party/tapkee/utils/time.hpp
@@ -7,7 +7,7 @@
 #define TAPKEE_TIME_H_
 
 /* Tapkee includes */
-#include <shogun/lib/tapkee/utils/logging.hpp>
+#include <tapkee/utils/logging.hpp>
 /* End of Tapkee includes */
 
 #include <ctime>