Probabilistic programming

Probabilistic programming (PP) is a programming paradigm in which probabilistic models are specified and inference for these models is performed automatically.^[1] It represents an attempt to unify probabilistic modeling and traditional general purpose programming in order to make the former easier and more widely applicable.^[2][3] It can be used to create systems that help make decisions in the face of uncertainty.

Programming languages used for probabilistic programming are referred to as "probabilistic programming languages" (PPLs).

Applications

Probabilistic reasoning has been used for a wide variety of tasks such as predicting stock prices, recommending movies, diagnosing computers, detecting cyber intrusions and image detection.^[4] However, until recently (partially due to limited computing power), probabilistic programming was limited in scope, and most inference algorithms had to be written manually for each task.

Nevertheless, in 2015, a 50-line probabilistic computer vision program was used to generate 3D models of human faces based on 2D images of those faces. The program used inverse graphics as the basis of its inference method, and was built using the Picture package in Julia.^[4] This made possible "in 50 lines of code what used to take thousands".^[5][6]

The Gen probabilistic programming library (also written in Julia) has been applied to vision and robotics tasks.^[7]

More recently, the probabilistic programming system Turing.jl has been applied in various pharmaceutical^[8] and economics applications.^[9]

Probabilistic programming in Julia has also been combined with differentiable programming by combining the Julia package Zygote.jl with Turing.jl. ^[10]

Probabilistic programming languages are also commonly used in Bayesian cognitive science to develop and evaluate models of cognition. ^[11]

Probabilistic programming languages

PPLs often extend from a basic language. The choice of underlying basic language depends on the similarity of the model to the basic language's ontology, as well as commercial considerations and personal preference. For instance, Dimple^[12] and Chimple^[13] are based on Java, Infer.NET is based on .NET Framework,^[14] while PRISM extends from Prolog.^[15] However, some PPLs such as WinBUGS offer a self-contained language, that maps closely to the mathematical representation of the statistical models, with no obvious origin in another programming language.^[16][17]

The language for winBUGS was implemented to perform Bayesian computation using Gibbs Sampling (and related algorithms). Although implemented in a relatively unknown programming language (Component Pascal), this language permits Bayesian inference for a wide variety of statistical models using a flexible computational approach. The same BUGS language may be used to specify Bayesian models for inference via different computational choices ("samplers") and conventions or defaults, using a standalone program winBUGS (or related R packages, rbugs and r2winbugs) and JAGS (Just Another Gibbs Sampler, another standalone program with related R packages including rjags, R2jags, and runjags). More recently, other languages to support Bayesian model specification and inference allow different or more efficient choices for the underlying Bayesian computation, and are accessible from the R data analysis and programming environment, e.g.: Stan, NIMBLE and NUTS. The influence of the BUGS language is evident in these later languages, which even use the same syntax for some aspects of model specification.

Several PPLs are in active development, including some in beta test. Two popular tools are Stan and PyMC.^[18]

Relational

A probabilistic relational programming language (PRPL) is a PPL specially designed to describe and infer with probabilistic relational models (PRMs).

A PRM is usually developed with a set of algorithms for reducing, inference about and discovery of concerned distributions, which are embedded into the corresponding PRPL.

Probabilistic logic programming

Main article: Probabilistic logic programming

Probabilistic logic programming is a programming paradigm that extends logic programming with probabilities.

Most approaches to probabilistic logic programming are based on the distribution semantics, which splits a program into a set of probabilistic facts and a logic program. It defines a probability distribution on interpretations of the Herbrand universe of the program.^[19]

List of probabilistic programming languages

This list summarises the variety of PPLs that are currently available, and clarifies their origins.

Name	Extends from	Host language
Analytica^[20]		C++
bayesloop^[21]^[22]	Python	Python
Bean Machine^[23]	PyTorch	Python
CuPPL^[24]	NOVA^[25]
Venture^[26]	Scheme	C++
Probabilistic-C^[27]	C	C
Anglican^[28]	Clojure	Clojure
IBAL^[29]	OCaml
BayesDB^[30]	SQLite, Python
PRISM^[15]	B-Prolog
Infer.NET^[14]	.NET Framework	.NET Framework
dimple^[12]	MATLAB, Java
chimple^[13]	MATLAB, Java
BLOG^[31]	Java
diff-SAT^[32]	Answer set programming, SAT (DIMACS CNF)
PSQL^[33]	SQL
BUGS^[16]		Component Pascal
FACTORIE^[34]	Scala	Scala
PMTK^[35]	MATLAB	MATLAB
Alchemy^[36]	C++
Dyna^[37]	Prolog
Figaro^[38]	Scala	Scala
Church^[39]	Scheme	Various: JavaScript, Scheme
ProbLog^[40]	Prolog	Python
ProBT^[41]	C++, Python
Stan^[17]	BUGS	C++
Hakaru^[42]	Haskell	Haskell
BAli-Phy (software)^[43]	Haskell	C++
ProbCog^[44]		Java, Python
Gamble^[45]		Racket
PWhile^[46]	While	Python
Tuffy^[47]		Java
PyMC^[48]	Python	Python
Rainier^[49]^[50]	Scala	Scala
greta^[51]	TensorFlow	R
pomegranate^[52]	Python	Python
Lea^[53]	Python	Python
WebPPL^[54]	JavaScript	JavaScript
Let's Chance^[55]	Scratch	JavaScript
Picture^[4]	Julia	Julia
Turing.jl^[56]	Julia	Julia
Gen^[57]	Julia	Julia
Low-level First-order PPL^[58]	Python, Clojure, Pytorch	Various: Python, Clojure
Troll^[59]		Moscow ML
Edward^[60]	TensorFlow	Python
TensorFlow Probability^[61]	TensorFlow	Python
Edward2^[62]	TensorFlow Probability	Python
Pyro^[63]	PyTorch	Python
NumPyro^[64]	JAX	Python
Saul^[65]	Scala	Scala
RankPL^[66]		Java
Birch^[67]		C++
PSI^[68]		D
Blang^[69]
MultiVerse^[70]	Python	Python

Difficulty

Reasoning about variables as probability distributions causes difficulties for novice programmers, but these difficulties can be addressed through use of Bayesian network visualisations and graphs of variable distributions embedded within the source code editor.^[71]

See also

• Statistical relational learning
• Inductive programming
• Bayesian programming
• Plate notation

Notes

1. "Probabilistic programming does in 50 lines of code what used to take thousands". phys.org. April 13, 2015. Retrieved April 13, 2015.
2. . probabilistic-programming.org. Archived from the original on January 10, 2016. Retrieved December 24, 2013.
3. Pfeffer, Avrom (2014), Practical Probabilistic Programming, Manning Publications. p.28. ISBN 978-1 6172-9233-0
4. "Short probabilistic programming machine-learning code replaces complex programs for computer-vision tasks". KurzweilAI. April 13, 2015. Retrieved November 27, 2017.
5. Hardesty, Larry (April 13, 2015). "Graphics in reverse".
6. "MIT shows off machine-learning script to make CREEPY HEADS". The Register.
7. "MIT's Gen programming system flattens the learning curve for AI projects". VentureBeat. June 27, 2019. Retrieved June 27, 2019.
8. Semenova, Elizaveta; Williams, Dominic P.; Afzal, Avid M.; Lazic, Stanley E. (November 1, 2020). "A Bayesian neural network for toxicity prediction". Computational Toxicology. 16: 100133. doi:10.1016/j.comtox.2020.100133. ISSN 2468-1113. S2CID 225362130.
9. Williams, Dominic P.; Lazic, Stanley E.; Foster, Alison J.; Semenova, Elizaveta; Morgan, Paul (2020), "Predicting Drug-Induced Liver Injury with Bayesian Machine Learning", Chemical Research in Toxicology, 33 (1): 239–248, doi:10.1021/acs.chemrestox.9b00264, PMID 31535850, S2CID 202689667
10. Innes, Mike; Edelman, Alan; Fischer, Keno; Rackauckas, Chris; Saba, Elliot; Viral B Shah; Tebbutt, Will (2019). "∂P: A Differentiable Programming System to Bridge Machine Learning and Scientific Computing". arXiv:1907.07587 [cs.PL].
11. Goodman, Noah D; Tenenbaum, Joshua B; Buchsbaum, Daphna; Hartshorne, Joshua; Hawkins, Robert; O'Donnell, Timothy J; Tessler, Michael Henry. "Probabilistic Models of Cognition". Probabilistic Models of Cognition - 2nd Edition. Retrieved May 27, 2023.
12. "Dimple Home Page". analog.com. July 2, 2021.
13. "Chimple Home Page". analog.com. April 16, 2021.
14. "Infer.NET". microsoft.com. Microsoft.
15. . rjida.meijo-u.ac.jp. Archived from the original on March 1, 2015. Retrieved July 8, 2015.
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20. "Analytica-- A Probabilistic Modeling Language". lumina.com.
21. "bayesloop - Probabilistic programming framework". bayesloop.com.
22. "GitHub -- bayesloop". GitHub. December 7, 2021.
23. "Bean Machine - A universal probabilistic programming language to enable fast and accurate Bayesian analysis". beanmachine.org.
24. "Probabilistic Programming with CuPPL". popl19.sigplan.org.
25. Collins, Alexander; Grewe, Dominik; Grover, Vinod; Lee, Sean; Susnea, Adriana (June 9, 2014). "NOVA: A Functional Language for Data Parallelism". Proceedings of ACM SIGPLAN International Workshop on Libraries, Languages, and Compilers for Array Programming. Array'14. pp. 8–13. doi:10.1145/2627373.2627375. ISBN 9781450329378. S2CID 6748967. {{cite book}}: |work= ignored (help)
26. . mit.edu. Archived from the original on January 25, 2016. Retrieved September 20, 2014.
27. . ox.ac.uk. Archived from the original on January 4, 2016. Retrieved March 24, 2015.
28. "The Anglican Probabilistic Programming System". ox.ac.uk. January 6, 2021.
29. . Archived from the original on December 26, 2010.
30. "BayesDB on SQLite. A Bayesian database table for querying the probable implications of data as easily as SQL databases query the data itself". GitHub. December 26, 2021.
31. . mit.edu. Archived from the original on June 16, 2011.
32. "diff-SAT (probabilistic SAT/ASP)". GitHub. October 8, 2021.
33. Dey, Debabrata; Sarkar, Sumit (1998). "PSQL: A query language for probabilistic relational data". Data & Knowledge Engineering. 28: 107–120. doi:10.1016/S0169-023X(98)00015-9.
34. "Factorie - Probabilistic programming with imperatively-defined factor graphs - Google Project Hosting". google.com.
35. "PMTK3 - probabilistic modeling toolkit for Matlab/Octave, version 3 - Google Project Hosting". google.com.
36. "Alchemy - Open Source AI". washington.edu.
37. . www.dyna.org. Archived from the original on January 17, 2016. Retrieved January 12, 2011.
38. "Charles River Analytics - Probabilistic Modeling Services". cra.com. February 9, 2017.
39. . mit.edu. Archived from the original on January 14, 2016. Retrieved April 8, 2013.
40. "ProbLog: Probabilistic Programming". dtai.cs.kuleuven.be.
41. ProbaYes. . probayes.com. Archived from the original on March 5, 2016. Retrieved November 26, 2013.
42. "Hakaru Home Page". hakaru-dev.github.io/.
43. "BAli-Phy Home Page". bali-phy.org.
44. "ProbCog". GitHub.
45. Culpepper, Ryan (January 17, 2017). "gamble: Probabilistic Programming" – via GitHub.
46. "PWhile Compiler". GitHub. May 25, 2020.
47. "Tuffy: A Scalable Markov Logic Inference Engine". stanford.edu.
48. PyMC devs. "PyMC". pymc-devs.github.io.
49. stripe/rainier, Stripe, August 19, 2020, retrieved August 26, 2020
50. "Rainier · Bayesian inference for Scala". samplerainier.com. Retrieved August 26, 2020.
51. "greta: simple and scalable statistical modelling in R". GitHub. Retrieved October 2, 2018.
52. "Home — pomegranate 0.10.0 documentation". pomegranate.readthedocs.io. Retrieved October 2, 2018.
53. "Lea Home Page". bitbucket.org.
54. "WebPPL Home Page". github.com/probmods/webppl.
55. Let's Chance: Playful Probabilistic Programming for Children | Extended Abstracts of the 2020 CHI Conference on Human Factors in Computing Systems. Chi Ea '20. April 25, 2020. pp. 1–7. doi:10.1145/3334480.3383071. ISBN 9781450368193. S2CID 216079395. Retrieved August 1, 2020. {{cite book}}: |website= ignored (help)
56. "The Turing language for probabilistic programming". GitHub. December 28, 2021.
57. "Gen: A General Purpose Probabilistic Programming Language with Programmable Inference". Retrieved June 17, 2019.
58. "LF-PPL: A Low-Level First Order Probabilistic Programming Language for Non-Differentiable Models". ox.ac.uk. November 2, 2019.
59. "Troll dice roller and probability calculator". topps.diku.dk.
60. "Edward – Home". edwardlib.org. Retrieved January 17, 2017.
61. TensorFlow (April 11, 2018). "Introducing TensorFlow Probability". TensorFlow. Retrieved October 2, 2018.
62. "'Edward2' TensorFlow Probability module". GitHub. Retrieved October 2, 2018.
63. "Pyro". pyro.ai. Retrieved February 9, 2018.
64. "NumPyro". pyro.ai. Retrieved July 23, 2021.
65. "CogComp - Home".
66. Rienstra, Tjitze (January 18, 2018), RankPL: A qualitative probabilistic programming language based on ranking theory, retrieved January 18, 2018
67. "Probabilistic Programming in Birch". birch-lang.org. Retrieved April 20, 2018.
68. "PSI Solver - Exact inference for probabilistic programs". psisolver.org. Retrieved August 18, 2019.
69. "Home". www.stat.ubc.ca.
70. Perov, Yura; Graham, Logan; Gourgoulias, Kostis; Richens, Jonathan G.; Lee, Ciarán M.; Baker, Adam; Johri, Saurabh (January 28, 2020), MultiVerse: Causal Reasoning using Importance Sampling in Probabilistic Programming, arXiv:1910.08091
71. Gorinova, Maria I.; Sarkar, Advait; Blackwell, Alan F.; Syme, Don (January 1, 2016). "A Live, Multiple-Representation Probabilistic Programming Environment for Novices". Proceedings of the 2016 CHI Conference on Human Factors in Computing Systems. CHI '16. New York, NY, USA: ACM. pp. 2533–2537. doi:10.1145/2858036.2858221. ISBN 9781450333627. S2CID 3201542.

External links

• List of Probabilistic Model Mini Language Toolkits