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authormaszhongming <mingz5@illinois.edu>2025-09-16 15:15:29 -0500
committermaszhongming <mingz5@illinois.edu>2025-09-16 15:15:29 -0500
commit73c194f304f827b55081b15524479f82a1b7d94c (patch)
tree5e8660e421915420892c5eca18f1ad680f80a861 /notebooks/disease_retrieval_accuracy.ipynb
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+{
+ "cells": [
+ {
+ "cell_type": "code",
+ "execution_count": 1,
+ "id": "945c420e-bb44-4ffb-b899-e049caf0d918",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "import os\n",
+ "os.chdir('..')"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "id": "f2bdefb3-3e59-409a-81b4-2e9ffbdfdb1a",
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "/root/anaconda3/envs/kg_rag_test_2/lib/python3.10/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n",
+ " from .autonotebook import tqdm as notebook_tqdm\n"
+ ]
+ }
+ ],
+ "source": [
+ "import pandas as pd\n",
+ "from kg_rag.utility import *\n",
+ "from tqdm import tqdm\n",
+ "\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "id": "19fc98b9-64a8-40c0-9e5a-92b4392e6969",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "data = pd.read_csv('data/dataset_for_entity_retrieval_accuracy_analysis.csv')\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 14,
+ "id": "2851be4c-2a76-4f6d-b5f4-118e8122b155",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "VECTOR_DB_PATH = config_data[\"VECTOR_DB_PATH\"]\n",
+ "SENTENCE_EMBEDDING_MODEL_FOR_NODE_RETRIEVAL = config_data[\"SENTENCE_EMBEDDING_MODEL_FOR_NODE_RETRIEVAL\"]\n",
+ "\n",
+ "vectorstore = load_chroma(VECTOR_DB_PATH, SENTENCE_EMBEDDING_MODEL_FOR_NODE_RETRIEVAL)\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 16,
+ "id": "7255fbab-d8b4-43a3-b870-9d67ad79d061",
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "322it [00:05, 56.20it/s]"
+ ]
+ },
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "CPU times: user 4.74 s, sys: 896 ms, total: 5.64 s\n",
+ "Wall time: 5.73 s\n"
+ ]
+ },
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "\n"
+ ]
+ }
+ ],
+ "source": [
+ "%%time\n",
+ "\n",
+ "correct_retrieval = 0\n",
+ "\n",
+ "for index, row in tqdm(data.iterrows()):\n",
+ " question = row['text']\n",
+ " entities = disease_entity_extractor_v2(question) \n",
+ " for entity in entities:\n",
+ " node_search_result = vectorstore.similarity_search_with_score(entity, k=1)\n",
+ " if node_search_result[0][0].page_content == row['node_hits']:\n",
+ " correct_retrieval += 1 \n",
+ " break\n",
+ " \n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 20,
+ "id": "2f997335-bff7-431c-bbd8-608513eddcc7",
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Retrieval accuracy is 99.7%\n"
+ ]
+ }
+ ],
+ "source": [
+ "retrieval_accuracy = 100*correct_retrieval/data.shape[0]\n",
+ "print(f'Retrieval accuracy is {round(retrieval_accuracy,1)}%')\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "afe971ab-b8b9-4c88-9657-c588813b412f",
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 3 (ipykernel)",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.10.9"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}