Using Chroma for Embeddings Search

Colin Jarvis, Anton Troynikov

Jun 28, 2023

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.

What is a Vector Database

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.

Why use a Vector Database

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.

Demo Flow

The demo flow is:

Setup: Import packages and set any required variables
Load data: Load a dataset and embed it using OpenAI embeddings
Chroma:
- Setup: Here we'll set up the Python client for Chroma. For more details go here
- Index Data: We'll create collections with vectors for titles and content
- Search Data: We'll run a few searches to confirm it works

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.

Setup

Import the required libraries and set the embedding model that we'd like to use.

# Make sure the OpenAI library is installed
%pip install openai

# We'll need to install the Chroma client
%pip install chromadb

# Install wget to pull zip file
%pip install wget

# Install numpy for data manipulation
%pip install numpy

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import openai
import pandas as pd
import os
import wget
from ast import literal_eval

# Chroma's client library for Python
import chromadb

# I've set this to our new embeddings model, this can be changed to the embedding model of your choice
EMBEDDING_MODEL = "text-embedding-ada-002"

# Ignore unclosed SSL socket warnings - optional in case you get these errors
import warnings

warnings.filterwarnings(action="ignore", message="unclosed", category=ResourceWarning)
warnings.filterwarnings("ignore", category=DeprecationWarning)

Load data

In this section we'll load embedded data that we've prepared previous to this session.

embeddings_url = 'https://cdn.openai.com/API/examples/data/vector_database_wikipedia_articles_embedded.zip'

# The file is ~700 MB so this will take some time
wget.download(embeddings_url)

'vector_database_wikipedia_articles_embedded.zip'

import zipfile
with zipfile.ZipFile("vector_database_wikipedia_articles_embedded.zip","r") as zip_ref:
    zip_ref.extractall("../data")

article_df = pd.read_csv('../data/vector_database_wikipedia_articles_embedded.csv')

article_df.head()

	id	url	title	text	title_vector	content_vector	vector_id
0	1	https://simple.wikipedia.org/wiki/April	April	April is the fourth month of the year in the J...	[0.001009464613161981, -0.020700545981526375, ...	[-0.011253940872848034, -0.013491976074874401,...	0
1	2	https://simple.wikipedia.org/wiki/August	August	August (Aug.) is the eighth month of the year ...	[0.0009286514250561595, 0.000820168002974242, ...	[0.0003609954728744924, 0.007262262050062418, ...	1
2	6	https://simple.wikipedia.org/wiki/Art	Art	Art is a creative activity that expresses imag...	[0.003393713850528002, 0.0061537534929811954, ...	[-0.004959689453244209, 0.015772193670272827, ...	2
3	8	https://simple.wikipedia.org/wiki/A	A	A or a is the first letter of the English alph...	[0.0153952119871974, -0.013759135268628597, 0....	[0.024894846603274345, -0.022186409682035446, ...	3
4	9	https://simple.wikipedia.org/wiki/Air	Air	Air refers to the Earth's atmosphere. Air is a...	[0.02224554680287838, -0.02044147066771984, -0...	[0.021524671465158463, 0.018522677943110466, -...	4

# Read vectors from strings back into a list
article_df['title_vector'] = article_df.title_vector.apply(literal_eval)
article_df['content_vector'] = article_df.content_vector.apply(literal_eval)

# Set vector_id to be a string
article_df['vector_id'] = article_df['vector_id'].apply(str)

article_df.info(show_counts=True)

<class 'pandas.core.frame.DataFrame'>
RangeIndex: 25000 entries, 0 to 24999
Data columns (total 7 columns):
 #   Column          Non-Null Count  Dtype 
---  ------          --------------  ----- 
 0   id              25000 non-null  int64 
 1   url             25000 non-null  object
 2   title           25000 non-null  object
 3   text            25000 non-null  object
 4   title_vector    25000 non-null  object
 5   content_vector  25000 non-null  object
 6   vector_id       25000 non-null  object
dtypes: int64(1), object(6)
memory usage: 1.3+ MB

Chroma

We'll index these embedded documents in a vector database and search them. The first option we'll look at is Chroma, an easy to use open-source self-hosted in-memory vector database, designed for working with embeddings together with LLMs.

In this section, we will:

Instantiate the Chroma client
Create collections for each class of embedding
Query each collection

Instantiate the Chroma client

Create the Chroma client. By default, Chroma is ephemeral and runs in memory. However, you can easily set up a persistent configuration which writes to disk.

chroma_client = chromadb.EphemeralClient() # Equivalent to chromadb.Client(), ephemeral.
# Uncomment for persistent client
# chroma_client = chromadb.PersistentClient()

Create collections

Chroma collections allow you to store and filter with arbitrary metadata, making it easy to query subsets of the embedded data.

Chroma is already integrated with OpenAI's embedding functions. The best way to use them is on construction of a collection, as follows. Alternatively, you can 'bring your own embeddings'. More information can be found here

from chromadb.utils.embedding_functions import OpenAIEmbeddingFunction

# Test that your OpenAI API key is correctly set as an environment variable
# Note. if you run this notebook locally, you will need to reload your terminal and the notebook for the env variables to be live.

# Note. alternatively you can set a temporary env variable like this:
# os.environ["OPENAI_API_KEY"] = 'sk-xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx'

if os.getenv("OPENAI_API_KEY") is not None:
    openai.api_key = os.getenv("OPENAI_API_KEY")
    print ("OPENAI_API_KEY is ready")
else:
    print ("OPENAI_API_KEY environment variable not found")


embedding_function = OpenAIEmbeddingFunction(api_key=os.environ.get('OPENAI_API_KEY'), model_name=EMBEDDING_MODEL)

wikipedia_content_collection = chroma_client.create_collection(name='wikipedia_content', embedding_function=embedding_function)
wikipedia_title_collection = chroma_client.create_collection(name='wikipedia_titles', embedding_function=embedding_function)

OPENAI_API_KEY is ready

Populate the collections

Chroma collections allow you to populate, and filter on, whatever metadata you like. Chroma can also store the text alongside the vectors, and return everything in a single query call, when this is more convenient.

For this use-case, we'll just store the embeddings and IDs, and use these to index the original dataframe.

# Add the content vectors
wikipedia_content_collection.add(
    ids=article_df.vector_id.tolist(),
    embeddings=article_df.content_vector.tolist(),
)

# Add the title vectors
wikipedia_title_collection.add(
    ids=article_df.vector_id.tolist(),
    embeddings=article_df.title_vector.tolist(),
)

Search the collections

Chroma handles embedding queries for you if an embedding function is set, like in this example.

def query_collection(collection, query, max_results, dataframe):
    results = collection.query(query_texts=query, n_results=max_results, include=['distances']) 
    df = pd.DataFrame({
                'id':results['ids'][0], 
                'score':results['distances'][0],
                'title': dataframe[dataframe.vector_id.isin(results['ids'][0])]['title'],
                'content': dataframe[dataframe.vector_id.isin(results['ids'][0])]['text'],
                })
    
    return df

title_query_result = query_collection(
    collection=wikipedia_title_collection,
    query="modern art in Europe",
    max_results=10,
    dataframe=article_df
)
title_query_result.head()

	id	score	title	content
2	23266	0.249646	Art	Art is a creative activity that expresses imag...
11777	15436	0.271688	Hellenistic art	The art of the Hellenistic time (from 400 B.C....
12178	23265	0.279306	Byzantine art	Byzantine art is a form of Christian Greek art...
13215	11777	0.294415	Art film	Art films are a type of movie that is very dif...
15436	22108	0.305937	Renaissance art	Many of the most famous and best-loved works o...

content_query_result = query_collection(
    collection=wikipedia_content_collection,
    query="Famous battles in Scottish history",
    max_results=10,
    dataframe=article_df
)
content_query_result.head()

	id	score	title	content
2923	13135	0.261328	1651	\n\nEvents \n January 1 – Charles II crowned K...
3694	13571	0.277058	Stirling	Stirling () is a city in the middle of Scotlan...
6248	2923	0.294823	841	\n\nEvents \n June 25: Battle of Fontenay – Lo...
6297	13568	0.300756	1746	\n\nEvents \n January 8 – Bonnie Prince Charli...
11702	11708	0.307572	William Wallace	William Wallace was a Scottish knight who foug...

Now that you've got a basic embeddings search running, you can hop over to the Chroma docs to learn more about how to add filters to your query, update/delete data in your collections, and deploy Chroma.