Fixing remaining hdbscan bug (rapidsai#4179)

Closes rapidsai#4054

Authors:
  - Corey J. Nolet (https://github.com/cjnolet)

Approvers:
  - Dante Gama Dessavre (https://github.com/dantegd)

URL: rapidsai#4179

cpp/include/cuml/cluster/hdbscan.hpp

@@ -137,7 +137,6 @@ enum CLUSTER_SELECTION_METHOD { EOM = 0, LEAF = 1 };
 
 class RobustSingleLinkageParams {
  public:
-  int k                = 5;
   int min_samples      = 5;
   int min_cluster_size = 5;
   int max_cluster_size = 0;

cpp/src/hdbscan/detail/reachability.cuh

@@ -50,15 +50,14 @@ namespace Reachability {
  * @tparam value_t data type for distance
  * @tparam tpb block size for kernel
  * @param[in] knn_dists knn distance array (size n * k)
- * @param[in] k neighborhood size
  * @param[in] min_samples this neighbor will be selected for core distances
  * @param[in] n number of samples
  * @param[out] out output array (size n)
  * @param[in] stream stream for which to order cuda operations
  */
 template <typename value_idx, typename value_t, int tpb = 256>
 void core_distances(
-  value_t* knn_dists, int k, int min_samples, size_t n, value_t* out, cudaStream_t stream)
+  value_t* knn_dists, int min_samples, size_t n, value_t* out, cudaStream_t stream)
 {
   int blocks = raft::ceildiv(n, (size_t)tpb);
 
@@ -67,7 +66,7 @@ void core_distances(
   auto indices = thrust::make_counting_iterator<value_idx>(0);
 
   thrust::transform(exec_policy, indices, indices + n, out, [=] __device__(value_idx row) {
-    return knn_dists[row * k + (min_samples - 1)];
+    return knn_dists[row * min_samples + (min_samples - 1)];
   });
 }
 
@@ -118,7 +117,6 @@ void mutual_reachability_graph(const raft::handle_t& handle,
                                size_t m,
                                size_t n,
                                raft::distance::DistanceType metric,
-                               int k,
                                int min_samples,
                                value_t alpha,
                                value_idx* indptr,
@@ -139,10 +137,10 @@ void mutual_reachability_graph(const raft::handle_t& handle,
 
   // This is temporary. Once faiss is updated, we should be able to
   // pass value_idx through to knn.
-  rmm::device_uvector<value_idx> coo_rows(k * m, stream);
-  rmm::device_uvector<int64_t> int64_indices(k * m, stream);
-  rmm::device_uvector<value_idx> inds(k * m, stream);
-  rmm::device_uvector<value_t> dists(k * m, stream);
+  rmm::device_uvector<value_idx> coo_rows(min_samples * m, stream);
+  rmm::device_uvector<int64_t> int64_indices(min_samples * m, stream);
+  rmm::device_uvector<value_idx> inds(min_samples * m, stream);
+  rmm::device_uvector<value_t> dists(min_samples * m, stream);
 
   // perform knn
   brute_force_knn(handle,
@@ -153,7 +151,7 @@ void mutual_reachability_graph(const raft::handle_t& handle,
                   m,
                   int64_indices.data(),
                   dists.data(),
-                  k,
+                  min_samples,
                   true,
                   true,
                   metric);
@@ -166,24 +164,24 @@ void mutual_reachability_graph(const raft::handle_t& handle,
                     [] __device__(int64_t in) -> value_idx { return in; });
 
   // Slice core distances (distances to kth nearest neighbor)
-  core_distances<value_idx>(dists.data(), k, min_samples, m, core_dists, stream);
+  core_distances<value_idx>(dists.data(), min_samples, m, core_dists, stream);
 
   /**
    * Compute L2 norm
    */
   mutual_reachability_knn_l2(
-    handle, inds.data(), dists.data(), X, m, n, k, core_dists, (value_t)1.0 / alpha);
+    handle, inds.data(), dists.data(), X, m, n, min_samples, core_dists, (value_t)1.0 / alpha);
 
   // self-loops get max distance
   auto coo_rows_counting_itr = thrust::make_counting_iterator<value_idx>(0);
   thrust::transform(exec_policy,
                     coo_rows_counting_itr,
-                    coo_rows_counting_itr + (m * k),
+                    coo_rows_counting_itr + (m * min_samples),
                     coo_rows.data(),
-                    [k] __device__(value_idx c) -> value_idx { return c / k; });
+                    [min_samples] __device__(value_idx c) -> value_idx { return c / min_samples; });
 
   raft::sparse::linalg::symmetrize(
-    handle, coo_rows.data(), inds.data(), dists.data(), m, m, k * m, out);
+    handle, coo_rows.data(), inds.data(), dists.data(), m, m, min_samples * m, out);
 
   raft::sparse::convert::sorted_coo_to_csr(out.rows(), out.nnz, indptr, m + 1, stream);
 
@@ -205,4 +203,4 @@ void mutual_reachability_graph(const raft::handle_t& handle,
 };  // end namespace Reachability
 };  // end namespace detail
 };  // end namespace HDBSCAN
-};  // end namespace ML
+};  // end namespace ML

cpp/src/hdbscan/detail/reachability_faiss.cuh

@@ -57,7 +57,8 @@ __global__ void l2SelectMinK(faiss::gpu::Tensor<value_t, 2, true> inner_products
                              faiss::gpu::Tensor<value_t, 1, true> core_dists,
                              faiss::gpu::Tensor<value_t, 2, true> out_dists,
                              faiss::gpu::Tensor<int, 2, true> out_inds,
-                             int batch_offset,
+                             int batch_offset_i,
+                             int batch_offset_j,
                              int k,
                              value_t initK,
                              value_t alpha)
@@ -85,19 +86,19 @@ __global__ void l2SelectMinK(faiss::gpu::Tensor<value_t, 2, true> inner_products
 
   for (; i < limit; i += blockDim.x) {
     value_t v = sqrt(faiss::gpu::Math<value_t>::add(
-      sq_norms[row + batch_offset],
-      faiss::gpu::Math<value_t>::add(sq_norms[i], inner_products[row][i])));
+      sq_norms[row + batch_offset_i],
+      faiss::gpu::Math<value_t>::add(sq_norms[i + batch_offset_j], inner_products[row][i])));
 
-    v = max(core_dists[i], max(core_dists[row + batch_offset], alpha * v));
+    v = max(core_dists[i + batch_offset_j], max(core_dists[row + batch_offset_i], alpha * v));
     heap.add(v, i);
   }
 
   if (i < inner_products.getSize(1)) {
     value_t v = sqrt(faiss::gpu::Math<value_t>::add(
-      sq_norms[row + batch_offset],
-      faiss::gpu::Math<value_t>::add(sq_norms[i], inner_products[row][i])));
+      sq_norms[row + batch_offset_i],
+      faiss::gpu::Math<value_t>::add(sq_norms[i + batch_offset_j], inner_products[row][i])));
 
-    v = max(core_dists[i], max(core_dists[row + batch_offset], alpha * v));
+    v = max(core_dists[i + batch_offset_j], max(core_dists[row + batch_offset_i], alpha * v));
     heap.addThreadQ(v, i);
   }
 
@@ -127,7 +128,8 @@ void runL2SelectMin(faiss::gpu::Tensor<value_t, 2, true>& productDistances,
                     faiss::gpu::Tensor<value_t, 1, true>& coreDistances,
                     faiss::gpu::Tensor<value_t, 2, true>& outDistances,
                     faiss::gpu::Tensor<int, 2, true>& outIndices,
-                    int batch_offset,
+                    int batch_offset_i,
+                    int batch_offset_j,
                     int k,
                     value_t alpha,
                     cudaStream_t stream)
@@ -149,7 +151,8 @@ void runL2SelectMin(faiss::gpu::Tensor<value_t, 2, true>& productDistances,
                                    coreDistances,                         \
                                    outDistances,                          \
                                    outIndices,                            \
-                                   batch_offset,                          \
+                                   batch_offset_i,                        \
+                                   batch_offset_j,                        \
                                    k,                                     \
                                    faiss::gpu::Limits<value_t>::getMax(), \
                                    alpha);                                \
@@ -323,7 +326,6 @@ void mutual_reachability_knn_l2(const raft::handle_t& handle,
     auto outIndexView    = out_inds_tensor.narrow(0, i, curQuerySize);
 
     auto queryView = x_tensor.narrow(0, i, curQuerySize);
-    norms_tensor.narrow(0, i, curQuerySize);
 
     auto outDistanceBufRowView = outDistanceBufs[curStream]->narrow(0, 0, curQuerySize);
     auto outIndexBufRowView    = outIndexBufs[curStream]->narrow(0, 0, curQuerySize);
@@ -365,19 +367,19 @@ void mutual_reachability_knn_l2(const raft::handle_t& handle,
                                 outDistanceView,
                                 outIndexView,
                                 i,
+                                j,
                                 k,
                                 alpha,
                                 streams[curStream]);
       } else {
-        norms_tensor.narrow(0, j, curCentroidSize);
-
         // Write into our intermediate output
         runL2SelectMin<value_t>(distanceBufView,
                                 norms_tensor,
                                 core_dists_tensor,
                                 outDistanceBufColView,
                                 outIndexBufColView,
                                 i,
+                                j,
                                 k,
                                 alpha,
                                 streams[curStream]);

cpp/src/hdbscan/runner.h

@@ -125,21 +125,18 @@ void build_linkage(const raft::handle_t& handle,
 {
   auto stream = handle.get_stream();
 
-  int k = params.k + 1;
-
   /**
    * Mutual reachability graph
    */
   rmm::device_uvector<value_idx> mutual_reachability_indptr(m + 1, stream);
-  raft::sparse::COO<value_t, value_idx> mutual_reachability_coo(stream, k * m * 2);
+  raft::sparse::COO<value_t, value_idx> mutual_reachability_coo(stream, params.min_samples * m * 2);
   rmm::device_uvector<value_t> core_dists(m, stream);
 
   detail::Reachability::mutual_reachability_graph(handle,
                                                   X,
                                                   (size_t)m,
                                                   (size_t)n,
                                                   metric,
-                                                  k,
                                                   params.min_samples,
                                                   params.alpha,
                                                   mutual_reachability_indptr.data(),

cpp/test/sg/hdbscan_test.cu

@@ -94,7 +94,6 @@ class HDBSCANTest : public ::testing::TestWithParam<HDBSCANInputs<T, IdxT>> {
                                                  mst_weights.data());
 
     HDBSCAN::Common::HDBSCANParams hdbscan_params;
-    hdbscan_params.k                = params.k;
     hdbscan_params.min_cluster_size = params.min_cluster_size;
     hdbscan_params.min_samples      = params.min_pts;
 
@@ -116,6 +115,7 @@ class HDBSCANTest : public ::testing::TestWithParam<HDBSCANInputs<T, IdxT>> {
 
  protected:
   HDBSCANInputs<T, IdxT> params;
+  IdxT* labels_ref;
   int k;
 
   double score;
@@ -218,7 +218,6 @@ class ClusterCondensingTest : public ::testing::TestWithParam<ClusterCondensingI
 
  protected:
   ClusterCondensingInputs<T, IdxT> params;
-  int k;
 
   double score;
 };

docs/source/api.rst

@@ -347,6 +347,14 @@ Agglomerative Clustering
 .. autoclass:: cuml.AgglomerativeClustering
     :members:
 
+
+HDBSCAN
+-------
+
+.. autoclass:: cuml.cluster.HDBSCAN
+   :members:
+
+
 Dimensionality Reduction and Manifold Learning
 ==============================================
 
@@ -563,12 +571,6 @@ Preprocessing
       add_dummy_feature, binarize, minmax_scale, normalize,
       PolynomialFeatures, robust_scale, scale
 
-Clustering
-----------
-
-.. autoclass:: cuml.experimental.cluster.HDBSCAN
-   :members:
-
 Linear Models
 -------------
 .. autoclass:: cuml.experimental.linear_model.Lars

python/cuml/__init__.py

@@ -21,6 +21,7 @@
 from cuml.cluster.dbscan import DBSCAN
 from cuml.cluster.kmeans import KMeans
 from cuml.cluster.agglomerative import AgglomerativeClustering
+from cuml.cluster.hdbscan import HDBSCAN
 
 from cuml.datasets.arima import make_arima
 from cuml.datasets.blobs import make_blobs

python/cuml/cluster/__init__.py

@@ -17,3 +17,5 @@
 from cuml.cluster.dbscan import DBSCAN
 from cuml.cluster.kmeans import KMeans
 from cuml.cluster.agglomerative import AgglomerativeClustering
+from cuml.cluster.hdbscan import HDBSCAN
+from cuml.cluster.hdbscan import condense_hierarchy

python/cuml/experimental/cluster/hdbscan.pyx → python/cuml/cluster/hdbscan.pyx

@@ -72,7 +72,6 @@ cdef extern from "cuml/cluster/hdbscan.hpp" namespace "ML::HDBSCAN::Common":
         CondensedHierarchy[int, float] &get_condensed_tree()
 
     cdef cppclass HDBSCANParams:
-        int k
         int min_samples
         int min_cluster_size
         int max_cluster_size,
@@ -435,12 +434,11 @@ class HDBSCAN(Base, ClusterMixin, CMajorInputTagMixin):
                  handle=None,
                  verbose=False,
                  connectivity='knn',
-                 n_neighbors=10,
                  output_type=None):
 
-        super().__init__(handle,
-                         verbose,
-                         output_type)
+        super().__init__(handle=handle,
+                         verbose=verbose,
+                         output_type=output_type)
 
         if min_samples is None:
             min_samples = min_cluster_size
@@ -449,8 +447,8 @@ class HDBSCAN(Base, ClusterMixin, CMajorInputTagMixin):
             raise ValueError("'connectivity' can only be one of "
                              "{'knn', 'pairwise'}")
 
-        if n_neighbors > 1023 or n_neighbors < 2:
-            raise ValueError("'n_neighbors' must be a positive number "
+        if 2 < min_samples and min_samples > 1023:
+            raise ValueError("'min_samples' must be a positive number "
                              "between 2 and 1023")
 
         self.min_cluster_size = min_cluster_size
@@ -462,7 +460,6 @@ class HDBSCAN(Base, ClusterMixin, CMajorInputTagMixin):
         self.alpha = alpha
         self.cluster_selection_method = cluster_selection_method
         self.allow_single_cluster = allow_single_cluster
-        self.n_neighbors = n_neighbors
         self.connectivity = connectivity
 
         self.fit_called_ = False
@@ -619,7 +616,6 @@ class HDBSCAN(Base, ClusterMixin, CMajorInputTagMixin):
         self.hdbscan_output_ = <size_t>linkage_output
 
         cdef HDBSCANParams params
-        params.k = self.n_neighbors
         params.min_samples = self.min_samples
         # params.alpha = self.alpha
         params.min_cluster_size = self.min_cluster_size
@@ -730,7 +726,6 @@ class HDBSCAN(Base, ClusterMixin, CMajorInputTagMixin):
 
     def get_param_names(self):
         return super().get_param_names() + [
-            "n_neighbors",
             "metric",
             "min_cluster_size",
             "max_cluster_size",
@@ -740,7 +735,6 @@ class HDBSCAN(Base, ClusterMixin, CMajorInputTagMixin):
             "p",
             "allow_single_cluster",
             "connectivity",
-            "n_neighbors",
             "alpha",
             "gen_min_span_tree",
         ]