clean up cosine distance

cuda/knn_kernel.cu

@@ -4,26 +4,24 @@
 
 #define THREADS 1024
 
-// Code from https://github.com/adamantmc/CudaCosineSimilarity/blob/master/src/CudaCosineSimilarity.cu
-template <typename scalar_t>
-__global__ void
-dot(double *a, double *b, size_t size) {
-    double result = 0;
-
-    for(int i = 0; i < size; i++) {
-        result += a[i] * b[i];
+template <typename scalar_t> struct Cosine {
+  static inline __device__ scalar_t dot(const scalar_t *a, const scalar_t *b,
+                                        size_t size) {
+    scalar_t result = 0;
+    for (ptrdiff_t i = 0; i < size; i++) {
+      result += a[i] * b[i];
     }
-
     return result;
-}
+  }
 
-template <typename scalar_t>
-__global__ void
-norm(double *a, size_t size) {
-      double result = dot(a,a,size);
-      result = sqrt(result);
-      return result;
-}
+  static inline __device__ scalar_t norm(const scalar_t *a, size_t size) {
+    scalar_t result = 0;
+    for (ptrdiff_t i = 0; i < size; i++) {
+      result += a[i] * a[i];
+    }
+    return sqrt(result);
+  }
+};
 
 template <typename scalar_t>
 __global__ void
@@ -52,16 +50,16 @@ knn_kernel(const scalar_t *__restrict__ x, const scalar_t *__restrict__ y,
 
       scalar_t tmp_dist = 0;
       if (cosine) {
-        tmp_dist = norm(x,dim)*norm(y,dim)-dot(x,y,dim)
-      }
-      else {
+        tmp_dist =
+            Cosine<scalar_t>::norm(x, dim) * Cosine<scalar_t>::norm(y, dim) -
+            Cosine<scalar_t>::dot(x, y, dim);
+      } else {
         for (ptrdiff_t d = 0; d < dim; d++) {
           tmp_dist += (x[n_x * dim + d] - y[n_y * dim + d]) *
                       (x[n_x * dim + d] - y[n_y * dim + d]);
         }
       }
 
-
       for (ptrdiff_t k_idx_1 = 0; k_idx_1 < k; k_idx_1++) {
         if (dist[n_y * k + k_idx_1] > tmp_dist) {
           for (ptrdiff_t k_idx_2 = k - 1; k_idx_2 > k_idx_1; k_idx_2--) {

setup.py

@@ -31,7 +31,7 @@ if CUDA_HOME is not None:
 __version__ = '1.4.3a1'
 url = 'https://github.com/rusty1s/pytorch_cluster'
 
-install_requires = ['scipy', 'scikit-learn']
+install_requires = ['scipy']
 setup_requires = ['pytest-runner']
 tests_require = ['pytest', 'pytest-cov']
 

test/test_knn.py

@@ -33,6 +33,11 @@ def test_knn(dtype, device):
     assert row.tolist() == [0, 0, 1, 1]
     assert col.tolist() == [2, 3, 4, 5]
 
+    if x.is_cuda:
+        row, col = knn(x, y, 2, batch_x, batch_y, cosine=True)
+        assert row.tolist() == [0, 0, 1, 1]
+        assert col.tolist() == [0, 1, 4, 5]
+
 
 @pytest.mark.parametrize('dtype,device', product(grad_dtypes, devices))
 def test_knn_graph(dtype, device):

torch_cluster/knn.py

 import torch
 import scipy.spatial
-import sklearn.neighbors
 
 if torch.cuda.is_available():
     import torch_cluster.knn_cuda
@@ -22,6 +21,9 @@ def knn(x, y, k, batch_x=None, batch_y=None, cosine=False):
         batch_y (LongTensor, optional): Batch vector
             :math:`\mathbf{b} \in {\{ 0, \ldots, B-1\}}^M`, which assigns each
             node to a specific example. (default: :obj:`None`)
+        cosine (boolean, optional): If :obj:`True`, will use the cosine
+            distance instead of euclidean distance to find nearest neighbors.
+            (default: :obj:`False`)
 
     :rtype: :class:`LongTensor`
 
@@ -57,6 +59,9 @@ def knn(x, y, k, batch_x=None, batch_y=None, cosine=False):
     if x.is_cuda:
         return torch_cluster.knn_cuda.knn(x, y, k, batch_x, batch_y, cosine)
 
+    if cosine:
+        raise NotImplementedError('Cosine distance not implemented for CPU')
+
     # Rescale x and y.
     min_xy = min(x.min().item(), y.min().item())
     x, y = x - min_xy, y - min_xy
@@ -68,14 +73,9 @@ def knn(x, y, k, batch_x=None, batch_y=None, cosine=False):
     x = torch.cat([x, 2 * x.size(1) * batch_x.view(-1, 1).to(x.dtype)], dim=-1)
     y = torch.cat([y, 2 * y.size(1) * batch_y.view(-1, 1).to(y.dtype)], dim=-1)
 
-    query_opts=dict(k=k)
-    if cosine:
-        tree = sklearn.neighbors.KDTree(x.detach().numpy(), metric='cosine')
-    else:
-        tree = scipy.spatial.cKDTree(x.detach().numpy())
-        query_opts['distance_upper_bound']=x.size(1)
-    dist, col = tree.query(
-        y.detach().cpu(), **query_opts)
+    tree = scipy.spatial.cKDTree(x.detach().numpy())
+    dist, col = tree.query(y.detach().cpu(), k=k,
+                           distance_upper_bound=x.size(1))
     dist = torch.from_numpy(dist).to(x.dtype)
     col = torch.from_numpy(col).to(torch.long)
     row = torch.arange(col.size(0), dtype=torch.long).view(-1, 1).repeat(1, k)
@@ -85,7 +85,8 @@ def knn(x, y, k, batch_x=None, batch_y=None, cosine=False):
     return torch.stack([row, col], dim=0)
 
 
-def knn_graph(x, k, batch=None, loop=False, flow='source_to_target', cosine=False):
+def knn_graph(x, k, batch=None, loop=False, flow='source_to_target',
+              cosine=False):
     r"""Computes graph edges to the nearest :obj:`k` points.
 
     Args:
@@ -100,6 +101,9 @@ def knn_graph(x, k, batch=None, loop=False, flow='source_to_target', cosine=Fals
         flow (string, optional): The flow direction when using in combination
             with message passing (:obj:`"source_to_target"` or
             :obj:`"target_to_source"`). (default: :obj:`"source_to_target"`)
+        cosine (boolean, optional): If :obj:`True`, will use the cosine
+            distance instead of euclidean distance to find nearest neighbors.
+            (default: :obj:`False`)
 
     :rtype: :class:`LongTensor`