Tested CI with typechecking

iuliivasilev · Aug 4, 2024 · 630acff · 630acff
1 parent 7f143e4
commit 630acff
Showing 1 changed file with 66 additions and 21 deletions.
diff --git a/demonstration/Articles/Refactoring.ipynb b/demonstration/Articles/Refactoring.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": 78,
-   "id": "374b961a",
+   "id": "49b2156d",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -14,7 +14,7 @@
   {
    "cell_type": "code",
    "execution_count": 3,
-   "id": "9a9f032a",
+   "id": "2a46605a",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -110,7 +110,7 @@
   {
    "cell_type": "code",
    "execution_count": 22,
-   "id": "17768980",
+   "id": "75e8e27c",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -158,8 +158,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 79,
-   "id": "eb902005",
+   "execution_count": 98,
+   "id": "9847863b",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -199,8 +199,53 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 80,
-   "id": "3e4acf25",
+   "execution_count": null,
+   "id": "8ad4da3a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "@njit\n",
+    "def get_pairs(T, P, E):\n",
+    "    n = len(T)\n",
+    "    concordant_pairs = 0\n",
+    "    total_pairs = 0\n",
+    "    for i in range(n):\n",
+    "        for j in range(i + 1, n):\n",
+    "            if E[i] == 1 and T[i] <= T[j]:\n",
+    "                total_pairs += 1\n",
+    "                if P[i] < P[j]:\n",
+    "                    concordant_pairs += 1\n",
+    "                elif P[i] == P[j]:\n",
+    "                    concordant_pairs += 0.5\n",
+    "    return concordant_pairs, total_pairs\n",
+    "\n",
+    "def concordance_index_self(T, P, E):\n",
+    "    \"\"\"\n",
+    "    Calculates the concordance index (C-index) for survival analysis.\n",
+    "\n",
+    "    Args:\n",
+    "    T: Array of true event times.\n",
+    "    P: Array of predicted event times.\n",
+    "    E: Array of event indicators (1 if event occurred, 0 if censored).\n",
+    "\n",
+    "    Returns:\n",
+    "    The concordance index.\n",
+    "    \"\"\"\n",
+    "    order = np.argsort(T)\n",
+    "    P = np.array(P)[order]\n",
+    "    T = np.array(T)[order]\n",
+    "    E = np.array(E)[order]\n",
+    "    concordant_pairs, total_pairs = get_pairs(T, P, E)\n",
+    "    \n",
+    "    if total_pairs == 0:\n",
+    "        return 0\n",
+    "    return concordant_pairs / total_pairs\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 93,
+   "id": "051083de",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -212,12 +257,12 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 71,
-   "id": "7ab1c5b3",
+   "execution_count": 99,
+   "id": "7f5b0643",
    "metadata": {},
    "outputs": [],
    "source": [
-    "for i in range(1000):\n",
+    "for i in range(10000):\n",
     "    a = np.random.rand(100)*100\n",
     "    b = np.random.rand(100)*100\n",
     "    e = np.round(np.random.rand(100))\n",
@@ -227,8 +272,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 81,
-   "id": "6995ee3e",
+   "execution_count": 95,
+   "id": "d6fdf195",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -244,15 +289,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 82,
-   "id": "64fde2e0",
+   "execution_count": 89,
+   "id": "d7ba9fdc",
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "672 ms ± 2.16 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)\n"
+      "667 ms ± 2.49 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)\n"
      ]
     }
    ],
@@ -262,15 +307,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 83,
-   "id": "85e2e7b0",
+   "execution_count": 100,
+   "id": "3efaefab",
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "22.9 ms ± 197 µs per loop (mean ± std. dev. of 7 runs, 1 loop each)\n"
+      "22.9 ms ± 84.8 µs per loop (mean ± std. dev. of 7 runs, 10 loops each)\n"
      ]
     }
    ],
@@ -281,7 +326,7 @@
   {
    "cell_type": "code",
    "execution_count": 84,
-   "id": "91add654",
+   "id": "2da0a02b",
    "metadata": {},
    "outputs": [
     {
@@ -302,7 +347,7 @@
   {
    "cell_type": "code",
    "execution_count": 52,
-   "id": "08d95f7f",
+   "id": "623deba5",
    "metadata": {},
    "outputs": [
     {
@@ -325,7 +370,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "69e4e1bf",
+   "id": "0defdd05",
    "metadata": {},
    "outputs": [],
    "source": []