Use single-precision floats for UMAP, for speed.

js/runUmap.js

@@ -132,7 +132,7 @@ export function initializeUmap(x, options = {}) {
             nnres = x;
         }
 
-        raw_coords = utils.createFloat64WasmArray(2 * nnres.numberOfCells());
+        raw_coords = utils.createFloat32WasmArray(2 * nnres.numberOfCells());
         output = gc.call(
             module => module.initialize_umap(nnres.results, epochs, minDist, raw_coords.offset, nthreads),
             UmapStatus,

js/utils.js

@@ -34,6 +34,17 @@ export function createBigUint64WasmArray (length) {
     return wa.createBigUint64WasmArray(wasmArraySpace(), length);
 }
 
+/**
+ * Helper function to create a Float32WasmArray from the **wasmarrays.js** package.
+ *
+ * @param {number} length - Length of the array.
+ *
+ * @return {Float32WasmArray} Float32WasmArray on the **scran.js** Wasm heap.
+ */
+export function createFloat32WasmArray(length) {
+    return wa.createFloat32WasmArray(wasmArraySpace(), length);
+}
+
 /**
  * Helper function to create a Float64WasmArray from the **wasmarrays.js** package.
  *

src/run_umap.cpp

@@ -9,7 +9,7 @@
 #include <chrono>
 
 struct UmapStatus {
-    typedef umappp::Status<int32_t, double> Status;
+    typedef umappp::Status<int32_t, float> Status;
 
     Status status;
 
@@ -27,7 +27,7 @@ struct UmapStatus {
 
     UmapStatus deepcopy(uintptr_t Y) const {
         auto copy = status;
-        copy.set_embedding(reinterpret_cast<double*>(Y), false);
+        copy.set_embedding(reinterpret_cast<float*>(Y), false);
         return UmapStatus(std::move(copy));
     }
 
@@ -41,8 +41,20 @@ UmapStatus initialize_umap(const NeighborResults& neighbors, int32_t num_epochs,
     opt.min_dist = min_dist;
     opt.num_epochs = num_epochs;
     opt.num_threads = nthreads;
-    double* embedding = reinterpret_cast<double*>(Y);
-    auto stat = umappp::initialize(neighbors.neighbors, 2, embedding, opt);
+
+    std::vector<std::vector<std::pair<int32_t, float> > > copy(neighbors.neighbors.size());
+    for (size_t i = 0, end = copy.size(); i < end; ++i) {
+        auto& output = copy[i];
+        const auto& src = neighbors.neighbors[i];
+        size_t n = src.size();
+        output.reserve(n);
+        for (size_t j = 0; j < n; ++j) {
+            output.emplace_back(src[j].first, src[j].second);
+        }
+    }
+
+    float* embedding = reinterpret_cast<float*>(Y);
+    auto stat = umappp::initialize(std::move(copy), 2, embedding, opt);
     return UmapStatus(std::move(stat));
 }