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{
"cells": [
{
"cell_type": "markdown",
"id": "cb1537e6",
"metadata": {},
"source": [
"# Using Pinecone for Embeddings Search\n",
"\n",
"This notebook takes you through a simple flow to download some data, embed it, and then index and search it using a selection of vector databases. This is a common requirement for customers who want to store and search our embeddings with their own data in a secure environment to support production use cases such as chatbots, topic modelling and more.\n",
"\n",
"### What is a Vector Database\n",
"\n",
"A vector database is a database made to store, manage and search embedding vectors. The use of embeddings to encode unstructured data (text, audio, video and more) as vectors for consumption by machine-learning models has exploded in recent years, due to the increasing effectiveness of AI in solving use cases involving natural language, image recognition and other unstructured forms of data. Vector databases have emerged as an effective solution for enterprises to deliver and scale these use cases.\n",
"\n",
"### Why use a Vector Database\n",
"\n",
"Vector databases enable enterprises to take many of the embeddings use cases we've shared in this repo (question and answering, chatbot and recommendation services, for example), and make use of them in a secure, scalable environment. Many of our customers make embeddings solve their problems at small scale but performance and security hold them back from going into production - we see vector databases as a key component in solving that, and in this guide we'll walk through the basics of embedding text data, storing it in a vector database and using it for semantic search.\n",
"\n",
"\n",
"### Demo Flow\n",
"The demo flow is:\n",
"- **Setup**: Import packages and set any required variables\n",
"- **Load data**: Load a dataset and embed it using OpenAI embeddings\n",
"- **Pinecone**\n",
" - *Setup*: Here we'll set up the Python client for Pinecone. For more details go [here](https://docs.pinecone.io/docs/quickstart)\n",
" - *Index Data*: We'll create an index with namespaces for __titles__ and __content__\n",
" - *Search Data*: We'll test out both namespaces with search queries to confirm it works\n",
"\n",
"Once you've run through this notebook you should have a basic understanding of how to setup and use vector databases, and can move on to more complex use cases making use of our embeddings."
]
},
{
"cell_type": "markdown",
"id": "e2b59250",
"metadata": {},
"source": [
"## Setup\n",
"\n",
"Import the required libraries and set the embedding model that we'd like to use."
]
},
{
"cell_type": "code",
"execution_count": 16,
"id": "8d8810f9",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Requirement already satisfied: pinecone-client in /Users/colin.jarvis/Documents/dev/cookbook/openai-cookbook/vector_db/lib/python3.10/site-packages (2.2.2)\n",
"Requirement already satisfied: requests>=2.19.0 in /Users/colin.jarvis/Documents/dev/cookbook/openai-cookbook/vector_db/lib/python3.10/site-packages (from pinecone-client) (2.31.0)\n",
"Requirement already satisfied: pyyaml>=5.4 in /Users/colin.jarvis/Documents/dev/cookbook/openai-cookbook/vector_db/lib/python3.10/site-packages (from pinecone-client) (6.0)\n",
"Requirement already satisfied: loguru>=0.5.0 in /Users/colin.jarvis/Documents/dev/cookbook/openai-cookbook/vector_db/lib/python3.10/site-packages (from pinecone-client) (0.7.0)\n",
"Requirement already satisfied: typing-extensions>=3.7.4 in /Users/colin.jarvis/Documents/dev/cookbook/openai-cookbook/vector_db/lib/python3.10/site-packages (from pinecone-client) (4.5.0)\n",
"Requirement already satisfied: dnspython>=2.0.0 in /Users/colin.jarvis/Documents/dev/cookbook/openai-cookbook/vector_db/lib/python3.10/site-packages (from pinecone-client) (2.3.0)\n",
"Requirement already satisfied: python-dateutil>=2.5.3 in /Users/colin.jarvis/Documents/dev/cookbook/openai-cookbook/vector_db/lib/python3.10/site-packages (from pinecone-client) (2.8.2)\n",
"Requirement already satisfied: urllib3>=1.21.1 in /Users/colin.jarvis/Documents/dev/cookbook/openai-cookbook/vector_db/lib/python3.10/site-packages (from pinecone-client) (1.26.16)\n",
"Requirement already satisfied: tqdm>=4.64.1 in /Users/colin.jarvis/Documents/dev/cookbook/openai-cookbook/vector_db/lib/python3.10/site-packages (from pinecone-client) (4.65.0)\n",
"Requirement already satisfied: numpy>=1.22.0 in /Users/colin.jarvis/Documents/dev/cookbook/openai-cookbook/vector_db/lib/python3.10/site-packages (from pinecone-client) (1.25.0)\n",
"Requirement already satisfied: six>=1.5 in /Users/colin.jarvis/Documents/dev/cookbook/openai-cookbook/vector_db/lib/python3.10/site-packages (from python-dateutil>=2.5.3->pinecone-client) (1.16.0)\n",
"Requirement already satisfied: charset-normalizer<4,>=2 in /Users/colin.jarvis/Documents/dev/cookbook/openai-cookbook/vector_db/lib/python3.10/site-packages (from requests>=2.19.0->pinecone-client) (3.1.0)\n",
"Requirement already satisfied: idna<4,>=2.5 in /Users/colin.jarvis/Documents/dev/cookbook/openai-cookbook/vector_db/lib/python3.10/site-packages (from requests>=2.19.0->pinecone-client) (3.4)\n",
"Requirement already satisfied: certifi>=2017.4.17 in /Users/colin.jarvis/Documents/dev/cookbook/openai-cookbook/vector_db/lib/python3.10/site-packages (from requests>=2.19.0->pinecone-client) (2023.5.7)\n",
"Requirement already satisfied: wget in /Users/colin.jarvis/Documents/dev/cookbook/openai-cookbook/vector_db/lib/python3.10/site-packages (3.2)\n"
]
}
],
"source": [
"# We'll need to install the Pinecone client\n",
"!pip install pinecone-client\n",
"\n",
"#Install wget to pull zip file\n",
"!pip install wget"
]
},
{
"cell_type": "code",
"execution_count": 1,
"id": "5be94df6",
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/Users/colin.jarvis/Documents/dev/cookbook/openai-cookbook/vector_db/lib/python3.10/site-packages/pinecone/index.py:4: TqdmExperimentalWarning: Using `tqdm.autonotebook.tqdm` in notebook mode. Use `tqdm.tqdm` instead to force console mode (e.g. in jupyter console)\n",
" from tqdm.autonotebook import tqdm\n"
]
}
],
"source": [
"import openai\n",
"\n",
"from typing import List, Iterator\n",
"import pandas as pd\n",
"import numpy as np\n",
"import os\n",
"import wget\n",
"from ast import literal_eval\n",
"\n",
"# Pinecone's client library for Python\n",
"import pinecone\n",
"\n",
"# I've set this to our new embeddings model, this can be changed to the embedding model of your choice\n",
"EMBEDDING_MODEL = \"text-embedding-3-small\"\n",
"\n",
"# Ignore unclosed SSL socket warnings - optional in case you get these errors\n",
"import warnings\n",
"\n",
"warnings.filterwarnings(action=\"ignore\", message=\"unclosed\", category=ResourceWarning)\n",
"warnings.filterwarnings(\"ignore\", category=DeprecationWarning) "
]
},
{
"cell_type": "markdown",
"id": "e5d9d2e1",
"metadata": {},
"source": [
"## Load data\n",
"\n",
"In this section we'll load embedded data that we've prepared [in this article](../../Embedding_Wikipedia_articles_for_search.ipynb)."
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "5dff8b55",
"metadata": {},
"outputs": [],
"source": [
"embeddings_url = 'https://cdn.openai.com/API/examples/data/vector_database_wikipedia_articles_embedded.zip'\n",
"\n",
"# The file is ~700 MB so this will take some time\n",
"wget.download(embeddings_url)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "21097972",
"metadata": {},
"outputs": [],
"source": [
"import zipfile\n",
"with zipfile.ZipFile(\"vector_database_wikipedia_articles_embedded.zip\",\"r\") as zip_ref:\n",
" zip_ref.extractall(\"../data\")"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "70bbd8ba",
"metadata": {},
"outputs": [],
"source": [
"article_df = pd.read_csv('../data/vector_database_wikipedia_articles_embedded.csv')"
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "1721e45d",
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
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"<style scoped>\n",
" .dataframe tbody tr th:only-of-type {\n",
" vertical-align: middle;\n",
" }\n",
"\n",
" .dataframe tbody tr th {\n",
" vertical-align: top;\n",
" }\n",
"\n",
" .dataframe thead th {\n",
" text-align: right;\n",
" }\n",
"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>id</th>\n",
" <th>url</th>\n",
" <th>title</th>\n",
" <th>text</th>\n",
" <th>title_vector</th>\n",
" <th>content_vector</th>\n",
" <th>vector_id</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>1</td>\n",
" <td>https://simple.wikipedia.org/wiki/April</td>\n",
" <td>April</td>\n",
" <td>April is the fourth month of the year in the J...</td>\n",
" <td>[0.001009464613161981, -0.020700545981526375, ...</td>\n",
" <td>[-0.011253940872848034, -0.013491976074874401,...</td>\n",
" <td>0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>2</td>\n",
" <td>https://simple.wikipedia.org/wiki/August</td>\n",
" <td>August</td>\n",
" <td>August (Aug.) is the eighth month of the year ...</td>\n",
" <td>[0.0009286514250561595, 0.000820168002974242, ...</td>\n",
" <td>[0.0003609954728744924, 0.007262262050062418, ...</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>6</td>\n",
" <td>https://simple.wikipedia.org/wiki/Art</td>\n",
" <td>Art</td>\n",
" <td>Art is a creative activity that expresses imag...</td>\n",
" <td>[0.003393713850528002, 0.0061537534929811954, ...</td>\n",
" <td>[-0.004959689453244209, 0.015772193670272827, ...</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>8</td>\n",
" <td>https://simple.wikipedia.org/wiki/A</td>\n",
" <td>A</td>\n",
" <td>A or a is the first letter of the English alph...</td>\n",
" <td>[0.0153952119871974, -0.013759135268628597, 0....</td>\n",
" <td>[0.024894846603274345, -0.022186409682035446, ...</td>\n",
" <td>3</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>9</td>\n",
" <td>https://simple.wikipedia.org/wiki/Air</td>\n",
" <td>Air</td>\n",
" <td>Air refers to the Earth's atmosphere. Air is a...</td>\n",
" <td>[0.02224554680287838, -0.02044147066771984, -0...</td>\n",
" <td>[0.021524671465158463, 0.018522677943110466, -...</td>\n",
" <td>4</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" id url title \\\n",
"0 1 https://simple.wikipedia.org/wiki/April April \n",
"1 2 https://simple.wikipedia.org/wiki/August August \n",
"2 6 https://simple.wikipedia.org/wiki/Art Art \n",
"3 8 https://simple.wikipedia.org/wiki/A A \n",
"4 9 https://simple.wikipedia.org/wiki/Air Air \n",
"\n",
" text \\\n",
"0 April is the fourth month of the year in the J... \n",
"1 August (Aug.) is the eighth month of the year ... \n",
"2 Art is a creative activity that expresses imag... \n",
"3 A or a is the first letter of the English alph... \n",
"4 Air refers to the Earth's atmosphere. Air is a... \n",
"\n",
" title_vector \\\n",
"0 [0.001009464613161981, -0.020700545981526375, ... \n",
"1 [0.0009286514250561595, 0.000820168002974242, ... \n",
"2 [0.003393713850528002, 0.0061537534929811954, ... \n",
"3 [0.0153952119871974, -0.013759135268628597, 0.... \n",
"4 [0.02224554680287838, -0.02044147066771984, -0... \n",
"\n",
" content_vector vector_id \n",
"0 [-0.011253940872848034, -0.013491976074874401,... 0 \n",
"1 [0.0003609954728744924, 0.007262262050062418, ... 1 \n",
"2 [-0.004959689453244209, 0.015772193670272827, ... 2 \n",
"3 [0.024894846603274345, -0.022186409682035446, ... 3 \n",
"4 [0.021524671465158463, 0.018522677943110466, -... 4 "
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"article_df.head()"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "960b82af",
"metadata": {},
"outputs": [],
"source": [
"# Read vectors from strings back into a list\n",
"article_df['title_vector'] = article_df.title_vector.apply(literal_eval)\n",
"article_df['content_vector'] = article_df.content_vector.apply(literal_eval)\n",
"\n",
"# Set vector_id to be a string\n",
"article_df['vector_id'] = article_df['vector_id'].apply(str)"
]
},
{
"cell_type": "code",
"execution_count": 5,
"id": "a334ab8b",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"<class 'pandas.core.frame.DataFrame'>\n",
"RangeIndex: 25000 entries, 0 to 24999\n",
"Data columns (total 7 columns):\n",
" # Column Non-Null Count Dtype \n",
"--- ------ -------------- ----- \n",
" 0 id 25000 non-null int64 \n",
" 1 url 25000 non-null object\n",
" 2 title 25000 non-null object\n",
" 3 text 25000 non-null object\n",
" 4 title_vector 25000 non-null object\n",
" 5 content_vector 25000 non-null object\n",
" 6 vector_id 25000 non-null object\n",
"dtypes: int64(1), object(6)\n",
"memory usage: 1.3+ MB\n"
]
}
],
"source": [
"article_df.info(show_counts=True)"
]
},
{
"cell_type": "markdown",
"id": "ed32fc87",
"metadata": {},
"source": [
"## Pinecone\n",
"\n",
"The next option we'll look at is **Pinecone**, a managed vector database which offers a cloud-native option.\n",
"\n",
"Before you proceed with this step you'll need to navigate to [Pinecone](pinecone.io), sign up and then save your API key as an environment variable titled ```PINECONE_API_KEY```.\n",
"\n",
"For section we will:\n",
"- Create an index with multiple namespaces for article titles and content\n",
"- Store our data in the index with separate searchable \"namespaces\" for article **titles** and **content**\n",
"- Fire some similarity search queries to verify our setup is working"
]
},
{
"cell_type": "code",
"execution_count": 6,
"id": "92e6152a",
"metadata": {},
"outputs": [],
"source": [
"api_key = os.getenv(\"PINECONE_API_KEY\")\n",
"pinecone.init(api_key=api_key)"
]
},
{
"cell_type": "markdown",
"id": "63b28543",
"metadata": {},
"source": [
"### Create Index\n",
"\n",
"First we will need to create an index, which we'll call `wikipedia-articles`. Once we have an index, we can create multiple namespaces, which can make a single index searchable for various use cases. For more details, consult [Pinecone documentation](https://docs.pinecone.io/docs/namespaces#:~:text=Pinecone%20allows%20you%20to%20partition,different%20subsets%20of%20your%20index.).\n",
"\n",
"If you want to batch insert to your index in parallel to increase insertion speed then there is a great guide in the Pinecone documentation on [batch inserts in parallel](https://docs.pinecone.io/docs/insert-data#sending-upserts-in-parallel)."
]
},
{
"cell_type": "code",
"execution_count": 7,
"id": "0a71c575",
"metadata": {},
"outputs": [],
"source": [
"# Models a simple batch generator that make chunks out of an input DataFrame\n",
"class BatchGenerator:\n",
" \n",
" \n",
" def __init__(self, batch_size: int = 10) -> None:\n",
" self.batch_size = batch_size\n",
" \n",
" # Makes chunks out of an input DataFrame\n",
" def to_batches(self, df: pd.DataFrame) -> Iterator[pd.DataFrame]:\n",
" splits = self.splits_num(df.shape[0])\n",
" if splits <= 1:\n",
" yield df\n",
" else:\n",
" for chunk in np.array_split(df, splits):\n",
" yield chunk\n",
"\n",
" # Determines how many chunks DataFrame contains\n",
" def splits_num(self, elements: int) -> int:\n",
" return round(elements / self.batch_size)\n",
" \n",
" __call__ = to_batches\n",
"\n",
"df_batcher = BatchGenerator(300)"
]
},
{
"cell_type": "code",
"execution_count": 8,
"id": "7ea9ad46",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"['podcasts', 'wikipedia-articles']"
]
},
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# Pick a name for the new index\n",
"index_name = 'wikipedia-articles'\n",
"\n",
"# Check whether the index with the same name already exists - if so, delete it\n",
"if index_name in pinecone.list_indexes():\n",
" pinecone.delete_index(index_name)\n",
" \n",
"# Creates new index\n",
"pinecone.create_index(name=index_name, dimension=len(article_df['content_vector'][0]))\n",
"index = pinecone.Index(index_name=index_name)\n",
"\n",
"# Confirm our index was created\n",
"pinecone.list_indexes()"
]
},
{
"cell_type": "code",
"execution_count": 9,
"id": "5daeba00",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Uploading vectors to content namespace..\n"
]
}
],
"source": [
"# Upsert content vectors in content namespace - this can take a few minutes\n",
"print(\"Uploading vectors to content namespace..\")\n",
"for batch_df in df_batcher(article_df):\n",
" index.upsert(vectors=zip(batch_df.vector_id, batch_df.content_vector), namespace='content')"
]
},
{
"cell_type": "code",
"execution_count": 10,
"id": "5fc1b083",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Uploading vectors to title namespace..\n"
]
}
],
"source": [
"# Upsert title vectors in title namespace - this can also take a few minutes\n",
"print(\"Uploading vectors to title namespace..\")\n",
"for batch_df in df_batcher(article_df):\n",
" index.upsert(vectors=zip(batch_df.vector_id, batch_df.title_vector), namespace='title')"
]
},
{
"cell_type": "code",
"execution_count": 11,
"id": "f90c7fba",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"{'dimension': 1536,\n",
" 'index_fullness': 0.1,\n",
" 'namespaces': {'content': {'vector_count': 25000},\n",
" 'title': {'vector_count': 25000}},\n",
" 'total_vector_count': 50000}"
]
},
"execution_count": 11,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# Check index size for each namespace to confirm all of our docs have loaded\n",
"index.describe_index_stats()"
]
},
{
"cell_type": "markdown",
"id": "2da40a69",
"metadata": {},
"source": [
"### Search data\n",
"\n",
"Now we'll enter some dummy searches and check we get decent results back"
]
},
{
"cell_type": "code",
"execution_count": 12,
"id": "c8280363",
"metadata": {},
"outputs": [],
"source": [
"# First we'll create dictionaries mapping vector IDs to their outputs so we can retrieve the text for our search results\n",
"titles_mapped = dict(zip(article_df.vector_id,article_df.title))\n",
"content_mapped = dict(zip(article_df.vector_id,article_df.text))"
]
},
{
"cell_type": "code",
"execution_count": 13,
"id": "3c8c2aa1",
"metadata": {},
"outputs": [],
"source": [
"def query_article(query, namespace, top_k=5):\n",
" '''Queries an article using its title in the specified\n",
" namespace and prints results.'''\n",
"\n",
" # Create vector embeddings based on the title column\n",
" embedded_query = openai.Embedding.create(\n",
" input=query,\n",
" model=EMBEDDING_MODEL,\n",
" )[\"data\"][0]['embedding']\n",
"\n",
" # Query namespace passed as parameter using title vector\n",
" query_result = index.query(embedded_query, \n",
" namespace=namespace, \n",
" top_k=top_k)\n",
"\n",
" # Print query results \n",
" print(f'\\nMost similar results to {query} in \"{namespace}\" namespace:\\n')\n",
" if not query_result.matches:\n",
" print('no query result')\n",
" \n",
" matches = query_result.matches\n",
" ids = [res.id for res in matches]\n",
" scores = [res.score for res in matches]\n",
" df = pd.DataFrame({'id':ids, \n",
" 'score':scores,\n",
" 'title': [titles_mapped[_id] for _id in ids],\n",
" 'content': [content_mapped[_id] for _id in ids],\n",
" })\n",
" \n",
" counter = 0\n",
" for k,v in df.iterrows():\n",
" counter += 1\n",
" print(f'{v.title} (score = {v.score})')\n",
" \n",
" print('\\n')\n",
"\n",
" return df"
]
},
{
"cell_type": "code",
"execution_count": 14,
"id": "3402b1b1",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
"Most similar results to modern art in Europe in \"title\" namespace:\n",
"\n",
"Museum of Modern Art (score = 0.875177085)\n",
"Western Europe (score = 0.867441177)\n",
"Renaissance art (score = 0.864156306)\n",
"Pop art (score = 0.860346854)\n",
"Northern Europe (score = 0.854658186)\n",
"\n",
"\n"
]
}
],
"source": [
"query_output = query_article('modern art in Europe','title')"
]
},
{
"cell_type": "code",
"execution_count": 15,
"id": "64a3f90a",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
"Most similar results to Famous battles in Scottish history in \"content\" namespace:\n",
"\n",
"Battle of Bannockburn (score = 0.869336188)\n",
"Wars of Scottish Independence (score = 0.861470938)\n",
"1651 (score = 0.852588475)\n",
"First War of Scottish Independence (score = 0.84962213)\n",
"Robert I of Scotland (score = 0.846214116)\n",
"\n",
"\n"
]
}
],
"source": [
"content_query_output = query_article(\"Famous battles in Scottish history\",'content')"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "0119d87a",
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "vector_db_split",
"language": "python",
"name": "vector_db_split"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.11"
},
"vscode": {
"interpreter": {
"hash": "fd16a328ca3d68029457069b79cb0b38eb39a0f5ccc4fe4473d3047707df8207"
}
}
},
"nbformat": 4,
"nbformat_minor": 5
}
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