Top 38 Python Libraries for Data Science, Data Visualization & Machine Learning

This article compiles the 38 top Python libraries for data science, data visualization & machine learning, as best determined by KDnuggets staff.

It has been some time since we last performed a Python libraries roundup, and as such we have taken the opportunity to start the month of November with just such a fresh list.


How We Built This List of 38 Python Libraries for Data Science


Last time we at KDnuggets did this, editor and author Dan Clark split up the vast array of Python data science related libraries up into several smaller collections, including data science libraries, machine learning libraries, and deep learning libraries. While splitting libraries into categories is inherently arbitrary, this made sense at the time of previous publication.

This time, however, we have split the collected on open source Python data science libraries in two. This first post (this) covers "data science, data visualization & machine learning," and can be thought of as "traditional" data science tools covering common tasks. The second post, to be published next week, will cover libraries for use in building neural networks, and those for performing natural language processing and computer vision tasks.

Again, this separation and classification is arbitrary, in some instances more than others, but we have done our best to group tools together by intended use case, hoping this is most useful for readers.

We Organized Python Libraries for Data Science Into 6 Categories:

The categories included in this post, which we see as taking into account common data science libraries — those likely to be used by practitioners in the data science space for generalized, non-neural network, non-research work — are:

  • Data - libraries for the management, manipulation, and other processing of data
  • Math - while many libraries perform mathematical tasks, this small collection does so exclusively
  • Machine learning - self explanatory; excludes libraries primarily meant for building neural networks or for automating machine learning processes
  • Automated machine learning - libraries that primarily function to automate processes related to machine learning
  • Data visualization - libraries that primarily serve a function related to visualizing data, as opposed to modeling, preprocessing, etc.
  • Explanation & exploration - libraries primarily for exploring and explaining models or data

Our list is made up of libraries that our team decided together by consensus was representative of common and well-used Python data science libraries. Also, to be included a library must have a Github repository. The categories are in no particular order, and neither are the libraries included within each. We contemplated constructing an ordering arbitrarily by stars or some other metric, but decided against it in order not explicitly stray from placing any perceived value or importance of the libraries within. Their listing here, then, is purely random. Library descriptions are directly from the Github repositories, in some form or another.

Thanks to Ahmed Anis for contributing to the collection of this data, and to the rest of the KDnuggets staff for their inputs, insights, and suggestions.

Note that visualization below, by Gregory Piatetsky, represents each library by type, plots it by stars and contributors, and its symbol size is reflective of the relative number of commits the library has on Github.


Figure 1: Top Python Libraries for Data Science, Data Visualization & Machine Learning
Plotted by number of stars and number of contributors; relative size by number of contributors


And, so without further ado, here are the 38 top Python libraries for data science, data visualization & machine learning, as best determined by KDnuggets staff.


Best Python Libraries for: Data


1. Apache Spark

Stars: 27600, Commits: 28197, Contributors: 1638


Apache Spark - A unified analytics engine for large-scale data processing


2. Pandas

Stars: 26800, Commits: 24300, Contributors: 2126

Pandas is a Python package that provides fast, flexible, and expressive data structures designed to make working with "relational" or "labeled" data both easy and intuitive. It aims to be the fundamental high-level building block for doing practical, real world data analysis in Python.

3. Dask

Stars: 7300, Commits: 6149, Contributors: 393

Parallel computing with task scheduling


Best Python Libraries For: Math


4. Scipy

Stars: 7500, Commits: 24247, Contributors: 914

SciPy (pronounced "Sigh Pie") is open-source software for mathematics, science, and engineering. It includes modules for statistics, optimization, integration, linear algebra, Fourier transforms, signal and image processing, ODE solvers, and more.


5. Numpy

Stars: 1500, Commits: 24266, Contributors: 1010


The fundamental package for scientific computing with Python.


Best Python Libraries For: Machine Learning


6. Scikit-Learn
Stars: 42500, Commits: 26162, Contributors: 1881


Scikit-learn is a Python module for machine learning built on top of SciPy and is distributed under the 3-Clause BSD license.


7. XGBoost

Stars: 19900, Commits: 5015, Contributors: 461

Scalable, Portable and Distributed Gradient Boosting (GBDT, GBRT or GBM) Library, for Python, R, Java, Scala, C++ and more. Runs on single machine, Hadoop, Spark, Flink and DataFlow


8. LightGBM

Stars: 11600, Commits: 2066, Contributors: 172


A fast, distributed, high performance gradient boosting (GBT, GBDT, GBRT, GBM or MART) framework based on decision tree algorithms, used for ranking, classification and many other machine learning tasks.


9. Catboost

Stars: 5400, Commits: 12936, Contributors: 188


A fast, scalable, high performance Gradient Boosting on Decision Trees library, used for ranking, classification, regression and other machine learning tasks for Python, R, Java, C++. Supports computation on CPU and GPU.


10. Dlib

Stars: 9500, Commits: 7868, Contributors: 146


Dlib is a modern C++ toolkit containing machine learning algorithms and tools for creating complex software in C++ to solve real world problems. Can be used with Python via dlib API


11. Annoy

Stars: 7700, Commits: 778, Contributors: 53


Approximate Nearest Neighbors in C++/Python optimized for memory usage and loading/saving to disk


12. H20ai
Stars: 500, Commits: 27894, Contributors: 137

Open Source Fast Scalable Machine Learning Platform For Smarter Applications: Deep Learning, Gradient Boosting & XGBoost, Random Forest, Generalized Linear Modeling (Logistic Regression, Elastic Net), K-Means, PCA, Stacked Ensembles, Automatic Machine Learning (AutoML), etc.


13. StatsModels

Stars: 5600, Commits: 13446, Contributors: 247


Statsmodels: statistical modeling and econometrics in Python


14. mlpack

Stars: 3400, Commits: 24575, Contributors: 190

mlpack is an intuitive, fast, and flexible C++ machine learning library with bindings to other languages


15. Pattern

Stars: 7600, Commits: 1434, Contributors: 20

Web mining module for Python, with tools for scraping, natural language processing, machine learning, network analysis and visualization.


16. Prophet

Stars: 11500, Commits: 595, Contributors: 106


Tool for producing high quality forecasts for time series data that has multiple seasonality with linear or non-linear growth.


Best Python Libraries For: Automated Machine Learning


17. TPOT

Stars: 7500, Commits: 2282, Contributors: 66


A Python Automated Machine Learning tool that optimizes machine learning pipelines using genetic programming.


18. auto-sklearn

Stars: 4100, Commits: 2343, Contributors: 52


auto-sklearn is an automated machine learning toolkit and a drop-in replacement for a scikit-learn estimator.


19. Hyperopt-sklearn
Stars: 1100, Commits: 188, Contributors: 18

Hyperopt-sklearn is Hyperopt-based model selection among machine learning algorithms in scikit-learn.

20. SMAC-3
Stars: 529, Commits: 1882, Contributors: 29

Sequential Model-based Algorithm Configuration

21. scikit-optimize
Stars: 1900, Commits: 1540, Contributors: 59

Scikit-Optimize, or skopt, is a simple and efficient library to minimize (very) expensive and noisy black-box functions. It implements several methods for sequential model-based optimization.

22. Nevergrad
Stars: 2700, Commits: 663, Contributors: 38

A Python toolbox for performing gradient-free optimization

23. Optuna
Stars: 3500, Commits: 7749, Contributors: 97

Optuna is an automatic hyperparameter optimization software framework, particularly designed for machine learning.


Best Python Libraries For: Data Visualization


24. Apache Superset

Stars: 30300, Commits: 5833, Contributors: 492


Apache Superset is a Data Visualization and Data Exploration Platform


25. Matplotlib

Stars: 12300, Commits: 36716, Contributors: 1002

Matplotlib is a comprehensive library for creating static, animated, and interactive visualizations in Python.


26. Plotly

Stars: 7900, Commits: 4604, Contributors: 137 is an interactive, open-source, and browser-based graphing library for Python


27. Seaborn

Stars: 7700, Commits: 2702, Contributors: 126


Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics.


28. folium

Stars: 4900, Commits: 1443, Contributors: 109

Folium builds on the data wrangling strengths of the Python ecosystem and the mapping strengths of the Leaflet.js library. Manipulate your data in Python, then visualize it in a Leaflet map via folium.


29. Bqplot

Stars: 2900, Commits: 3178, Contributors: 45


Bqplot is a 2-D visualization system for Jupyter, based on the constructs of the Grammar of Graphics.


30. VisPy

Stars: 2500, Commits: 6352, Contributors: 117


VisPy is a high-performance interactive 2D/3D data visualization library. VisPy leverages the computational power of modern Graphics Processing Units (GPUs) through the OpenGL library to display very large datasets. Applications of VisPy include:


31. PyQtgraph

Stars: 2200, Commits: 2200, Contributors: 142

Fast data visualization and GUI tools for scientific / engineering applications

32. Bokeh

Stars: 1400, Commits: 18726, Contributors: 467


Bokeh is an interactive visualization library for modern web browsers. It provides elegant, concise construction of versatile graphics, and affords high-performance interactivity over large or streaming datasets.


33. Altair

Stars: 600, Commits: 3031, Contributors: 106


Altair is a declarative statistical visualization library for Python. With Altair, you can spend more time understanding your data and its meaning.


Best Python Libraries For: Explanation & Exploration


34. eli5

Stars: 2200, Commits: 1198, Contributors: 15


A library for debugging/inspecting machine learning classifiers and explaining their predictions


35. LIME

Stars: 800, Commits: 501, Contributors: 41


Lime: Explaining the predictions of any machine learning classifier


36. SHAP

Stars: 10400, Commits: 1376, Contributors: 96


A game theoretic approach to explain the output of any machine learning model.


37. YellowBrick

Stars: 300, Commits: 825, Contributors: 92

Visual analysis and diagnostic tools to facilitate machine learning model selection.

38. pandas-profiling

Stars: 6200, Commits: 704, Contributors: 47

Create HTML profiling reports from pandas DataFrame objects