Vector similarity search using Neon Postgres

Sep 28, 2023
Open in Github

This notebook guides you through using Neon Serverless Postgres as a vector database for OpenAI embeddings. It demonstrates how to:

  1. Use embeddings created by OpenAI API.
  2. Store embeddings in a Neon Serverless Postgres database.
  3. Convert a raw text query to an embedding with OpenAI API.
  4. Use Neon with the pgvector extension to perform vector similarity search.


Before you begin, ensure that you have the following:

  1. A Neon Postgres database. You can create an account and set up a project with a ready-to-use neondb database in a few simple steps. For instructions, see Sign up and Create your first project.
  2. A connection string for your Neon database. You can copy it from the Connection Details widget on the Neon Dashboard. See Connect from any application.
  3. The pgvector extension. Install the extension in Neon by running CREATE EXTENSION vector;. For instructions, see Enable the pgvector extension.
  4. Your OpenAI API key.
  5. Python and pip.

Install required modules

This notebook requires the openai, psycopg2, pandas, wget, and python-dotenv packages. You can install them with pip:

! pip install openai psycopg2 pandas wget python-dotenv

Prepare your OpenAI API key

An OpenAI API key is required to generate vectors for documents and queries.

If you do not have an OpenAI API key, obtain one from

Add the OpenAI API key as an operating system environment variable or provide it for the session when prompted. If you define an environment variable, name the variable OPENAI_API_KEY.

For information about configuring your OpenAI API key as an environment variable, refer to Best Practices for API Key Safety.

# Test to ensure that your OpenAI API key is defined as an environment variable or provide it when prompted
# If you run this notebook locally, you may have to reload the terminal and the notebook to make the environment available

import os
from getpass import getpass

# Check if OPENAI_API_KEY is set as an environment variable
if os.getenv("OPENAI_API_KEY") is not None:
    print("Your OPENAI_API_KEY is ready")
    # If not, prompt for it
    api_key = getpass("Enter your OPENAI_API_KEY: ")
    if api_key:
        print("Your OPENAI_API_KEY is now available for this session")
        # Optionally, you can set it as an environment variable for the current session
        os.environ["OPENAI_API_KEY"] = api_key
        print("You did not enter your OPENAI_API_KEY")
Your OPENAI_API_KEY is ready
import os
import psycopg2
from dotenv import load_dotenv

# Load environment variables from .env file

# The connection string can be provided directly here.
# Replace the next line with Your Neon connection string.
connection_string = "postgres://<user>:<password>@<hostname>/<dbname>"

# If connection_string is not directly provided above, 
# then check if DATABASE_URL is set in the environment or .env.
if not connection_string:
    connection_string = os.environ.get("DATABASE_URL")

    # If neither method provides a connection string, raise an error.
    if not connection_string:
        raise ValueError("Please provide a valid connection string either in the code or in the .env file as DATABASE_URL.")

# Connect using the connection string
connection = psycopg2.connect(connection_string)

# Create a new cursor object
cursor = connection.cursor()

Test the connection to your database:

# Execute this query to test the database connection
cursor.execute("SELECT 1;")
result = cursor.fetchone()

# Check the query result
if result == (1,):
    print("Your database connection was successful!")
    print("Your connection failed.")
Your database connection was successful!

This guide uses pre-computed Wikipedia article embeddings available in the OpenAI Cookbook examples directory so that you do not have to compute embeddings with your own OpenAI credits.

Import the pre-computed embeddings zip file:

import wget

embeddings_url = ""

# The file is ~700 MB. Importing it will take several minutes.

Extract the downloaded zip file:

import zipfile
import os
import re
import tempfile

current_directory = os.getcwd()
zip_file_path = os.path.join(current_directory, "")
output_directory = os.path.join(current_directory, "../../data")

with zipfile.ZipFile(zip_file_path, "r") as zip_ref:

# Check to see if the csv file was extracted
file_name = "vector_database_wikipedia_articles_embedded.csv"
data_directory = os.path.join(current_directory, "../../data")
file_path = os.path.join(data_directory, file_name)

if os.path.exists(file_path):
    print(f"The csv file {file_name} exists in the data directory.")
    print(f"The csv file {file_name} does not exist in the data directory.")
The file vector_database_wikipedia_articles_embedded.csv exists in the data directory.
create_table_sql = '''
CREATE TABLE IF NOT EXISTS public.articles (
    url TEXT,
    title TEXT,
    content TEXT,
    title_vector vector(1536),
    content_vector vector(1536),
    vector_id INTEGER

ALTER TABLE public.articles ADD PRIMARY KEY (id);

# SQL statement for creating indexes
create_indexes_sql = '''
CREATE INDEX ON public.articles USING ivfflat (content_vector) WITH (lists = 1000);

CREATE INDEX ON public.articles USING ivfflat (title_vector) WITH (lists = 1000);

# Execute the SQL statements

# Commit the changes

Load the data

Load the pre-computed vector data into your articles table from the .csv file. There are 25000 records, so expect the operation to take several minutes.

import io

# Path to your local CSV file
csv_file_path = '../../data/vector_database_wikipedia_articles_embedded.csv'

# Define a generator function to process the csv file
def process_file(file_path):
    with open(file_path, 'r', encoding='utf-8') as file:
        for line in file:
            yield line

# Create a StringIO object to store the modified lines
modified_lines = io.StringIO(''.join(list(process_file(csv_file_path))))

# Create the COPY command for copy_expert
copy_command = '''
COPY public.articles (id, url, title, content, title_vector, content_vector, vector_id)

# Execute the COPY command using copy_expert
cursor.copy_expert(copy_command, modified_lines)

# Commit the changes

Check the number of records to ensure the data has been been loaded. There should be 25000 records.

# Check the size of the data
count_sql = """select count(*) from public.articles;"""
result = cursor.fetchone()

Search your data

After the data is stored in your Neon database, you can query the data for nearest neighbors.

Start by defining the query_neon function, which is executed when you run the vector similarity search. The function creates an embedding based on the user's query, prepares the SQL query, and runs the SQL query with the embedding. The pre-computed embeddings that you loaded into your database were created with text-embedding-3-small OpenAI model, so you must use the same model to create an embedding for the similarity search.

A vector_name parameter is provided that allows you to search based on "title" or "content".

def query_neon(query, collection_name, vector_name="title_vector", top_k=20):

    # Create an embedding vector from the user query
    embedded_query = openai.Embedding.create(

    # Convert the embedded_query to PostgreSQL compatible format
    embedded_query_pg = "[" + ",".join(map(str, embedded_query)) + "]"

    # Create the SQL query
    query_sql = f"""
    SELECT id, url, title, l2_distance({vector_name},'{embedded_query_pg}'::VECTOR(1536)) AS similarity
    FROM {collection_name}
    ORDER BY {vector_name} <-> '{embedded_query_pg}'::VECTOR(1536)
    LIMIT {top_k};
    # Execute the query
    results = cursor.fetchall()

    return results

Run a similarity search based on title_vector embeddings:

# Query based on `title_vector` embeddings
import openai

query_results = query_neon("Greek mythology", "Articles")
for i, result in enumerate(query_results):
    print(f"{i + 1}. {result[2]} (Score: {round(1 - result[3], 3)})")
1. Greek mythology (Score: 0.998)
2. Roman mythology (Score: 0.7)
3. Greek underworld (Score: 0.637)
4. Mythology (Score: 0.635)
5. Classical mythology (Score: 0.629)
6. Japanese mythology (Score: 0.615)
7. Norse mythology (Score: 0.569)
8. Greek language (Score: 0.566)
9. Zeus (Score: 0.534)
10. List of mythologies (Score: 0.531)
11. Jupiter (mythology) (Score: 0.53)
12. Greek (Score: 0.53)
13. Gaia (mythology) (Score: 0.526)
14. Titan (mythology) (Score: 0.522)
15. Mercury (mythology) (Score: 0.521)
16. Ancient Greece (Score: 0.52)
17. Greek alphabet (Score: 0.52)
18. Venus (mythology) (Score: 0.515)
19. Pluto (mythology) (Score: 0.515)
20. Athena (Score: 0.514)

Run a similarity search based on content_vector embeddings:

# Query based on `content_vector` embeddings
query_results = query_neon("Famous battles in Greek history", "Articles", "content_vector")
for i, result in enumerate(query_results):
    print(f"{i + 1}. {result[2]} (Score: {round(1 - result[3], 3)})")
1. 222 BC (Score: 0.489)
2. Trojan War (Score: 0.458)
3. Peloponnesian War (Score: 0.456)
4. History of the Peloponnesian War (Score: 0.449)
5. 430 BC (Score: 0.441)
6. 168 BC (Score: 0.436)
7. Ancient Greece (Score: 0.429)
8. Classical Athens (Score: 0.428)
9. 499 BC (Score: 0.427)
10. Leonidas I (Score: 0.426)
11. Battle (Score: 0.421)
12. Greek War of Independence (Score: 0.421)
13. Menelaus (Score: 0.419)
14. Thebes, Greece (Score: 0.417)
15. Patroclus (Score: 0.417)
16. 427 BC (Score: 0.416)
17. 429 BC (Score: 0.413)
18. August 2 (Score: 0.412)
19. Ionia (Score: 0.411)
20. 323 (Score: 0.409)