vectorized update_r

clustering/affinity_propagation.ipynb

@@ -89,7 +89,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "$ r(i, k) \\leftarrow - \\max\\limits_{k' s.t. k' \\neq k}\\{ a(i, k') + s(i, k') \\}$"
+    "$ r(i, k) \\leftarrow s(i, k) - \\max\\limits_{k' s.t. k' \\neq k}\\{ a(i, k') + s(i, k') \\}$"
    ]
   },
   {
@@ -97,13 +97,36 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "def update_r(lmda=0.9):    \n",
-    "    for i in range(x.shape[0]):\n",
-    "        for k in range(x.shape[0]):\n",
-    "            v = S[i, :] + A[i, :]\n",
-    "            v[k] = -np.inf\n",
-    "            v[i]= -np.inf\n",
-    "            R[i, k] = R[i, k] * lmda + (1 - lmda) * (S[i, k] - np.max(v))"
+    "def update_r(lmda=0.9):\n",
+    "    # For every column k, except for the column with the maximum value the max is the same.\n",
+    "    # So we can subtract the maximum for every row, and only need to do something different for k == argmax\n",
+    "        \n",
+    "    global R\n",
+    "    v = S + A\n",
+    "    rows = np.arange(x.shape[0])\n",
+    "    # We only compare the current point to all other points, so the diagonal can be filled with -infinity\n",
+    "    np.fill_diagonal(v, -np.inf)\n",
+    "    \n",
+    "    # max values\n",
+    "    idx_max = np.argmax(v, axis=1)\n",
+    "    first_max = v[rows, idx_max]\n",
+    "    \n",
+    "    # Second max values. For every column where k is the max value.\n",
+    "    v[rows, idx_max] = -np.inf\n",
+    "    second_max = v[rows, np.argmax(v, axis=1)]\n",
+    "    \n",
+    "    # Broadcast the maximum value per row over all the columns per row.\n",
+    "    max_matrix = np.zeros_like(R) + first_max[:, None]\n",
+    "    max_matrix[rows, idx_max] = second_max\n",
+    "    \n",
+    "    max_matrix = S - max_matrix\n",
+    "    \n",
+    "    R = R * lmda + (1 - lmda) * R_new\n",
+    "\n",
+    "  \n",
+    "A, R, S = create_matrices()\n",
+    "update_r()\n",
+    "R"
    ]
   },
   {
@@ -113,6 +136,30 @@
     "$ a(i, k) \\leftarrow \\min\\{0, r(k,k) + \\sum\\limits_{i' s.t. i' \\notin \\{i, k\\}}{\\max\\{0, r(i', k)\\}}$ "
    ]
   },
+  {
+   "cell_type": "code",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "np.diag(k)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "A, R, S = create_matrices()\n",
+    "preference = np.median(S)\n",
+    "# update_r()\n",
+    "\n",
+    "i, k = np.meshgrid(np.arange(100), np.arange(100))\n",
+    "\n",
+    "v = S + A\n",
+    "\n",
+    "v[i, k] = -np.inf\n"
+   ]
+  },
   {
    "cell_type": "code",
    "metadata": {