Tested performance of refactored CI (increased by 30 times)

iuliivasilev · Aug 3, 2024 · 7f143e4 · 7f143e4
1 parent aafccaf
commit 7f143e4
Showing 1 changed file with 72 additions and 27 deletions.
diff --git a/demonstration/Articles/Refactoring.ipynb b/demonstration/Articles/Refactoring.ipynb
@@ -2,18 +2,19 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 27,
-   "id": "7ca4db35",
+   "execution_count": 78,
+   "id": "374b961a",
    "metadata": {},
    "outputs": [],
    "source": [
-    "from lifelines.utils import concordance_index"
+    "from lifelines.utils import concordance_index\n",
+    "from numba import njit, jit"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 3,
-   "id": "fc02d133",
+   "id": "9a9f032a",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -109,7 +110,7 @@
   {
    "cell_type": "code",
    "execution_count": 22,
-   "id": "fb905b58",
+   "id": "17768980",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -157,11 +158,12 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 66,
-   "id": "47b7fb0d",
+   "execution_count": 79,
+   "id": "eb902005",
    "metadata": {},
    "outputs": [],
    "source": [
+    "@njit\n",
     "def concordance_index_self(T, P, E):\n",
     "    \"\"\"\n",
     "    Calculates the concordance index (C-index) for survival analysis.\n",
@@ -197,8 +199,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 67,
-   "id": "0547a83f",
+   "execution_count": 80,
+   "id": "3e4acf25",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -211,7 +213,7 @@
   {
    "cell_type": "code",
    "execution_count": 71,
-   "id": "b529d42e",
+   "id": "7ab1c5b3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -225,39 +227,82 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 72,
-   "id": "314a5f66",
+   "execution_count": 81,
+   "id": "6995ee3e",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def test_f(f):\n",
+    "    a = 0\n",
+    "    for i in range(1000):\n",
+    "        a = np.random.rand(100)*100\n",
+    "        b = np.random.rand(100)*100\n",
+    "        e = np.round(np.random.rand(100))\n",
+    "        a += f(a, b, e)\n",
+    "    return a"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 82,
+   "id": "64fde2e0",
    "metadata": {},
    "outputs": [
     {
-     "data": {
-      "text/plain": [
-       "(0.5041072200605274, 0.5041072200605274)"
-      ]
-     },
-     "execution_count": 72,
-     "metadata": {},
-     "output_type": "execute_result"
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "672 ms ± 2.16 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)\n"
+     ]
     }
    ],
    "source": [
-    "concordance_index(a, b, e)"
+    "%timeit test_f(concordance_index)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
-   "id": "2e6df15a",
+   "execution_count": 83,
+   "id": "85e2e7b0",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "22.9 ms ± 197 µs per loop (mean ± std. dev. of 7 runs, 1 loop each)\n"
+     ]
+    }
+   ],
+   "source": [
+    "%timeit test_f(concordance_index_self)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 84,
+   "id": "91add654",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "29.344978165938866"
+      ]
+     },
+     "execution_count": 84,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
-    "concordance_index_self(a, b, e)"
+    "672/22.9"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 52,
-   "id": "7af657dc",
+   "id": "08d95f7f",
    "metadata": {},
    "outputs": [
     {
@@ -280,7 +325,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "a4d58b6d",
+   "id": "69e4e1bf",
    "metadata": {},
    "outputs": [],
    "source": []