README.md

Penn Machine Learning Benchmarks

This repository contains the code and data for a large, curated set of benchmark datasets for evaluating and comparing supervised machine learning algorithms. These data sets cover a broad range of applications, and include binary/multi-class classification problems and regression problems, as well as combinations of categorical, ordinal, and continuous features.

Please go to our home page to interactively browse the datasets, vignette, and contribution guide!

Breaking changes in PMLB 1.0

This repository has been restructured, and several dataset names have been changed!

If you have an older version of PMLB, we highly recommend you upgrade it to v1.0 for updated URLs and names of datasets:

pip install pmlb --upgrade

Datasets

Datasets are tracked with Git Large File Storage (LFS). If you would like to clone the entire repository, please install and set up Git LFS for your user account. Alternatively, you can download the .zip file from GitHub.

All data sets are stored in a common format:

• First row is the column names
• Each following row corresponds to one row of the data
• The target column is named target
• All columns are tab (\t) separated
• All files are compressed with gzip to conserve space

The complete table of dataset characteristics is also available for download. Please note, in our documentation, a feature is considered:

• "binary" if it is of type integer and has 2 unique values (equivalent to pandas profiling's "boolean")
• "categorical" if it is of type integer and has more than 2 unique values (equivalent to pandas profiling's "categorical")
• "continuous" if it is of type float (equivalent to pandas profiling's "numeric").

Python wrapper

For easy access to the benchmark data sets, we have provided a Python wrapper named pmlb. The wrapper can be installed on Python via pip:

pip install pmlb

and used in Python scripts as follows:

from pmlb import fetch_data

# Returns a pandas DataFrame
adult_data = fetch_data('adult')
print(adult_data.describe())

The fetch_data function has two additional parameters:

• return_X_y (True/False): Whether to return the data in scikit-learn format, with the features and labels stored in separate NumPy arrays.
• local_cache_dir (string): The directory on your local machine to store the data files so you don't have to fetch them over the web again. By default, the wrapper does not use a local cache directory.

For example:

from pmlb import fetch_data

# Returns NumPy arrays
adult_X, adult_y = fetch_data('adult', return_X_y=True, local_cache_dir='./')
print(adult_X)
print(adult_y)

You can also list all of the available data sets as follows:

from pmlb import dataset_names

print(dataset_names)

Or if you only want a list of available classification or regression datasets:

from pmlb import classification_dataset_names, regression_dataset_names

print(classification_dataset_names)
print('')
print(regression_dataset_names)

Example usage: Compare two classification algorithms with PMLB

PMLB is designed to make it easy to benchmark machine learning algorithms against each other. Below is a Python code snippet showing the most basic way to use PMLB to compare two algorithms.

from sklearn.linear_model import LogisticRegression
from sklearn.naive_bayes import GaussianNB
from sklearn.model_selection import train_test_split

import matplotlib.pyplot as plt
import seaborn as sb

from pmlb import fetch_data, classification_dataset_names

logit_test_scores = []
gnb_test_scores = []

for classification_dataset in classification_dataset_names:
    X, y = fetch_data(classification_dataset, return_X_y=True)
    train_X, test_X, train_y, test_y = train_test_split(X, y)

    logit = LogisticRegression()
    gnb = GaussianNB()

    logit.fit(train_X, train_y)
    gnb.fit(train_X, train_y)

    logit_test_scores.append(logit.score(test_X, test_y))
    gnb_test_scores.append(gnb.score(test_X, test_y))

sb.boxplot(data=[logit_test_scores, gnb_test_scores], notch=True)
plt.xticks([0, 1], ['LogisticRegression', 'GaussianNB'])
plt.ylabel('Test Accuracy')

Contributing

See our Contributing Guide. We're looking for help with documentation, and also appreciate new dataset and functionality contributions.

Citing PMLB

If you use PMLB in a scientific publication, please consider citing one of the following papers:

Joseph D. Romano, Le, Trang T., William La Cava, John T. Gregg, Daniel J. Goldberg, Praneel Chakraborty, Natasha L. Ray, Daniel Himmelstein, Weixuan Fu, and Jason H. Moore. PMLB v1.0: an open source dataset collection for benchmarking machine learning methods. arXiv preprint arXiv:2012.00058 (2020).

@article{romano2021pmlb,
  title={PMLB v1.0: an open source dataset collection for benchmarking machine learning methods},
  author={Romano, Joseph D and Le, Trang T and La Cava, William and Gregg, John T and Goldberg, Daniel J and Chakraborty, Praneel and Ray, Natasha L and Himmelstein, Daniel and Fu, Weixuan and Moore, Jason H},
  journal={arXiv preprint arXiv:2012.00058v2},
  year={2021}
}

Randal S. Olson, William La Cava, Patryk Orzechowski, Ryan J. Urbanowicz, and Jason H. Moore (2017). PMLB: a large benchmark suite for machine learning evaluation and comparison. BioData Mining 10, page 36.

BibTeX entry:

@article{Olson2017PMLB,
    author="Olson, Randal S. and La Cava, William and Orzechowski, Patryk and Urbanowicz, Ryan J. and Moore, Jason H.",
    title="PMLB: a large benchmark suite for machine learning evaluation and comparison",
    journal="BioData Mining",
    year="2017",
    month="Dec",
    day="11",
    volume="10",
    number="1",
    pages="36",
    issn="1756-0381",
    doi="10.1186/s13040-017-0154-4",
    url="https://doi.org/10.1186/s13040-017-0154-4"
}

Support for PMLB

PMLB was developed in the Computational Genetics Lab at the University of Pennsylvania with funding from the NIH under grant AI117694, LM010098 and LM012601. We are incredibly grateful for the support of the NIH and the University of Pennsylvania during the development of this project.