PyMC: a modern, and comprehensive probabilistic programming framework in Python

Author:

Abril-Pla Oriol1ORCID,Andreani Virgile23ORCID,Carroll Colin4,Dong Larry56,Fonnesbeck Christopher J.7,Kochurov Maxim8,Kumar Ravin9,Lao Junpeng10ORCID,Luhmann Christian C.1112,Martin Osvaldo A.13ORCID,Osthege Michael14,Vieira Ricardo8,Wiecki Thomas8,Zinkov Robert15ORCID

Affiliation:

1. ArviZ-Devs, Barcelona, Spain

2. Biomedical Engineering Department, Boston University, Boston, United States of America

3. Biological Design Center, Boston University, Boston, United States of America

4. Google, Cambridge, MA, United States of America

5. Dalla Lana School of Public Health, University of Toronto, Toronto, Canada

6. Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, Canada

7. Baseball Operations Research and Development, Philadelphia Phillies, Philadelphia, United States of America

8. PyMC Labs, Berlin, Germany

9. Google, Mountain View, CA, United States of America

10. Google, Zürich, Switzerland

11. Department of Psychology, Stony Brook University, Stony Brook, United States of America

12. Institute for Advanced Computational Science, Stony Brook University, Stony Brook NY, United States of America

13. IMASL-CONICET, Universidad Nacional de San Luis, San Luis, Argentina

14. Forschungszentrum Jülich GmbH, Jülich, Germany

15. Oxford University, Oxford, United Kingdom

Abstract

PyMC is a probabilistic programming library for Python that provides tools for constructing and fitting Bayesian models. It offers an intuitive, readable syntax that is close to the natural syntax statisticians use to describe models. PyMC leverages the symbolic computation library PyTensor, allowing it to be compiled into a variety of computational backends, such as C, JAX, and Numba, which in turn offer access to different computational architectures including CPU, GPU, and TPU. Being a general modeling framework, PyMC supports a variety of models including generalized hierarchical linear regression and classification, time series, ordinary differential equations (ODEs), and non-parametric models such as Gaussian processes (GPs). We demonstrate PyMC’s versatility and ease of use with examples spanning a range of common statistical models. Additionally, we discuss the positive role of PyMC in the development of the open-source ecosystem for probabilistic programming.

Funder

NumFOCUS

PyMC Labs

National Agency of Scientific and Technological Promotion ANPCyT

National Scientific and Technical Research Council CONICET

Publisher

PeerJ

Subject

General Computer Science

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