HoloClean: A Machine Learning System for Data Enrichment
HoloClean is built on top of PyTorch and PostgreSQL.
HoloClean is a statistical inference engine to impute, clean, and enrich data. As a weakly supervised machine learning system, HoloClean leverages available quality rules, value correlations, reference data, and multiple other signals to build a probabilistic model that accurately captures the data generation process, and uses the model in a variety of data curation tasks. HoloClean allows data practitioners and scientists to save the enormous time they spend in building piecemeal cleaning solutions, and instead, effectively communicate their domain knowledge in a declarative way to enable accurate analytics, predictions, and insights form noisy, incomplete, and erroneous data.
HoloClean was tested on Python versions 2.7, 3.6, and 3.7. It requires PostgreSQL version 9.4 or higher.
1. Install and configure PostgreSQL
We describe how to install PostgreSQL and configure it for HoloClean (creating a database, a user, and setting the required permissions).
Option 1: Native installation of PostgreSQL
A native installation of PostgreSQL runs faster than docker containers. We explain how to install PostgreSQL then how to configure it for HoloClean use.
a. Installing PostgreSQL
On Ubuntu, install PostgreSQL by running
$ apt-get install postgresql postgresql-contrib
For macOS, you can find the installation instructions on https://www.postgresql.org/download/macosx/
b. Setting up PostgreSQL for HoloClean
By default, HoloClean needs a database
holo and a user
holocleanuser with permissions on it.
Start the PostgreSQL
psqlconsole from the terminal using
$ psql --user <username>. You can omit
--user <username>to use current user.
Create a database
CREATE DATABASE holo; CREATE USER holocleanuser; ALTER USER holocleanuser WITH PASSWORD 'abcd1234'; GRANT ALL PRIVILEGES ON DATABASE holo TO holocleanuser; \c holo ALTER SCHEMA public OWNER TO holocleanuser;
You can connect to the
holo database from the PostgreSQL
psql console by running
psql -U holocleanuser -W holo.
HoloClean currently populates the database
holo with auxiliary and meta tables.
To clear the database simply connect as a
root user or as
holocleanuser and run
DROP DATABASE holo; CREATE DATABASE holo;
Option 2: Using Docker
If you are familiar with docker, an easy way to start using HoloClean is to start a PostgreSQL docker container.
To start a PostgreSQL docker container, run the following command:
docker run --name pghc \ -e POSTGRES_DB=holo -e POSTGRES_USER=holocleanuser -e POSTGRES_PASSWORD=abcd1234 \ -p 5432:5432 \ -d postgres:11
which starts a backend server and creates a database with the required permissions.
You can then use
docker start pghc and
docker stop pghc to start/stop the container.
Note the port number which may conflict with existing PostgreSQL servers. Read more about this docker image here.
2. Setting up HoloClean
HoloClean runs on Python 2.7 or 3.6+. We recommend running it from within a virtual environment.
Creating a virtual environment for HoloClean
Option 1: Conda Virtual Environment
First, download Anaconda (not miniconda) from this link. Follow the steps for your OS and framework.
Second, create a conda environment (python 2.7 or 3.6+). For example, to create a Python 3.6 conda environment, run:
$ conda create -n hc36 python=3.6
Upon starting/restarting your terminal session, you will need to activate your conda environment by running
$ conda activate hc36
Option 2: Set up a virtual environment using pip and Virtualenv
If you are familiar with
virtualenv, you can use it to create
a virtual environment.
For Python 3.6, create a new environment with your preferred virtualenv wrapper, for example:
Either follow instructions here or install via
$ pip install virtualenv
Then, create a
virtualenv environment by creating a new directory for a Python 3.6 virtualenv environment
$ mkdir -p hc36 $ virtualenv --python=python3.6 hc36
python3.6 is a valid reference to a Python 3.6 executable.
Activate the environment
$ source hc36/bin/activate
Install the required python packages
Note: make sure that the environment is activated throughout the installation process.
When you are done, deactivate it using
source deactivate, or
depending on your version.
In the project root directory, run the following to install the required packages. Note that this commands installs the packages within the activated virtual environment.
$ pip install -r requirements.txt
Note for macOS Users:
you may need to install XCode developer tools using
See the code in
examples/holoclean_repair_example.py for a documented usage of HoloClean.
In order to run the example script, run the following:
$ cd examples $ ./start_example.sh
Notice that the script sets up the Python path environment to run HoloClean.