# PyBBN
PyBBN is Python library for Bayesian Belief Networks (BBNs) exact inference using the [junction tree algorithm](https://en.wikipedia.org/wiki/Junction_tree_algorithm) or Probability Propagation in Trees of Clusters (PPTC). The implementation is taken directly from [C. Huang and A. Darwiche, "Inference in
Belief Networks: A Procedural Guide," in International Journal of Approximate Reasoning, vol. 15,
pp. 225--263, 1999](http://pages.cs.wisc.edu/~dpage/ijar95.pdf). In this API, PPTC is applied to BBNs with all discrete variables. When dealing with a BBN with all Gaussian variables (or a Gaussian Belief Network, GBN), exact inference is conducted through an incremental algorithm manipulating the means and covariance matrix. Additionally, there is the ability to generate singly- and multi-connected graphs, which is taken from [JS Ide and FG Cozman,
"Random Generation of Bayesian Network," in Advances in Artificial Intelligence, Lecture Notes in Computer Science, vol 2507](https://pdfs.semanticscholar.org/5273/2fb57129443592024b0e7e46c2a1ec36639c.pdf). There is also the option to generate sample data from your BBN. This synthetic data may be summarized to generate your posterior marginal probabilities and work as a form of approximate inference. Lastly, we have added Pearl's `do-operator` for causal inference.
# Power Up, Next Level
turing_bbn | pyspark-bbn
:------------------------------------------------------------------------------------:|:---------------------------------------------------------------------------------------:
 |
If you like py-bbn, please inquire about our next-generation products below! info@oneoffcoder.com
* [turing_bbn](https://turing-bbn.oneoffcoder.com/) is a C++17 implementation of py-bbn; take your causal and probabilistic inferences to the next computing level!
* [pyspark-bbn](https://pyspark-bbn.oneoffcoder.com/) is a is a scalable, massively parallel processing MPP framework for learning structures and parameters of Bayesian Belief Networks BBNs using [Apache Spark](https://spark.apache.org/).
# Exact Inference, Discrete Variables
Below is an example code to create a Bayesian Belief Network, transform it into a join tree, and then set observation evidence. The last line prints the marginal probabilities for each node.
```python
from pybbn.graph.dag import Bbn
from pybbn.graph.edge import Edge, EdgeType
from pybbn.graph.jointree import EvidenceBuilder
from pybbn.graph.node import BbnNode
from pybbn.graph.variable import Variable
from pybbn.pptc.inferencecontroller import InferenceController
# create the nodes
a = BbnNode(Variable(0, 'a', ['on', 'off']), [0.5, 0.5])
b = BbnNode(Variable(1, 'b', ['on', 'off']), [0.5, 0.5, 0.4, 0.6])
c = BbnNode(Variable(2, 'c', ['on', 'off']), [0.7, 0.3, 0.2, 0.8])
d = BbnNode(Variable(3, 'd', ['on', 'off']), [0.9, 0.1, 0.5, 0.5])
e = BbnNode(Variable(4, 'e', ['on', 'off']), [0.3, 0.7, 0.6, 0.4])
f = BbnNode(Variable(5, 'f', ['on', 'off']), [0.01, 0.99, 0.01, 0.99, 0.01, 0.99, 0.99, 0.01])
g = BbnNode(Variable(6, 'g', ['on', 'off']), [0.8, 0.2, 0.1, 0.9])
h = BbnNode(Variable(7, 'h', ['on', 'off']), [0.05, 0.95, 0.95, 0.05, 0.95, 0.05, 0.95, 0.05])
# create the network structure
bbn = Bbn() \
.add_node(a) \
.add_node(b) \
.add_node(c) \
.add_node(d) \
.add_node(e) \
.add_node(f) \
.add_node(g) \
.add_node(h) \
.add_edge(Edge(a, b, EdgeType.DIRECTED)) \
.add_edge(Edge(a, c, EdgeType.DIRECTED)) \
.add_edge(Edge(b, d, EdgeType.DIRECTED)) \
.add_edge(Edge(c, e, EdgeType.DIRECTED)) \
.add_edge(Edge(d, f, EdgeType.DIRECTED)) \
.add_edge(Edge(e, f, EdgeType.DIRECTED)) \
.add_edge(Edge(c, g, EdgeType.DIRECTED)) \
.add_edge(Edge(e, h, EdgeType.DIRECTED)) \
.add_edge(Edge(g, h, EdgeType.DIRECTED))
# convert the BBN to a join tree
join_tree = InferenceController.apply(bbn)
# insert an observation evidence
ev = EvidenceBuilder() \
.with_node(join_tree.get_bbn_node_by_name('a')) \
.with_evidence('on', 1.0) \
.build()
join_tree.set_observation(ev)
# print the marginal probabilities
for node in join_tree.get_bbn_nodes():
potential = join_tree.get_bbn_potential(node)
print(node)
print(potential)
```
# Exact Inference, Gaussian Variables
The example belows shows how to perform inference on multivariate Gaussian variables.
```python
import numpy as np
from pybbn.gaussian.inference import GaussianInference
def get_cowell_data():
"""
Gets Cowell data.
:return: Data and headers.
"""
n = 10000
Y = np.random.normal(0, 1, n)
X = np.random.normal(Y, 1, n)
Z = np.random.normal(X, 1, n)
D = np.vstack([Y, X, Z]).T
return D, ['Y', 'X', 'Z']
# assume we have data and headers (variable names per column)
# X is the data (rows are observations, columns are variables)
# H is just a list of variable names
X, H = get_cowell_data()
# then we can compute the means and covariance matrix easily
M = X.mean(axis=0)
E = np.cov(X.T)
# the means and covariance matrix are all we need for gaussian inference
# notice how we keep `g` around?
# we'll use `g` over and over to do inference with evidence/observations
g = GaussianInference(H, M, E)
# {'Y': (0.00967, 0.98414), 'X': (0.01836, 2.02482), 'Z': (0.02373, 3.00646)}
print(g.P)
# we can make a single observation with do_inference()
g1 = g.do_inference('X', 1.5)
# {'X': (1.5, 0), 'Y': (0.76331, 0.49519), 'Z': (1.51893, 1.00406)}
print(g1.P)
# we can make multiple observations with do_inferences()
g2 = g.do_inferences([('Z', 1.5), ('X', 2.0)])
# {'Z': (1.5, 0), 'X': (2.0, 0), 'Y': (1.97926, 0.49509)}
print(g2.P)
```
# Building
To build, you will need 3.7. Managing environments through [Anaconda](https://www.anaconda.com/download/#linux) is highly recommended to be able to build this project (though not absolutely required if you know what you are doing). Assuming you have installed Anaconda, you may create an environment as follows (make sure you `cd` into the root of this project's location).
To create the environment, use the following commands.
```bash
conda env create -f environment.yml
```
If you want to use the environments with Jupyter, install the kernel.
```bash
conda activate pybbn37
python -m ipykernel install --user --name pybbn37 --display-name "pybbn37"
```
Then you may build the project as follows. (Note that in Python 3.6 you will get some warnings).
```bash
make build
```
To build the documents, go into the docs sub-directory and type in the following.
```bash
make html
```
## Testing
You can do a fresh test with Docker as follows.
```bash
docker build -t pybbn-test:local -f Dockerfile.test .
```
# Installing
## From PyPi
Use pip to install the package as it has been published to [PyPi](https://pypi.python.org/pypi/pybbn).
```bash
pip install pybbn
```
## From Source
If you check out the source do the following.
```bash
pip list | grep pybbn
pip uninstall pybbn
python setup.py install
pip list | grep pybbn
```
## GraphViz issue
Make sure you [install GraphViz](https://graphviz.gitlab.io/download/) on your system.
* CentOS: `yum install graphviz*`
* Ubuntu: `sudo apt-get install graphviz libgraphviz-dev`
* Mac OSX: `brew install graphviz` and when you install pygraphviz `pip install pygraphviz --install-option="--include-path=/usr/local/lib/graphviz/" --install-option="--library-path=/usr/local/lib/graphviz/"`
* Windows: use the [msi installer](https://graphviz.gitlab.io/_pages/Download/windows/graphviz-2.38.msi)
* For Anaconda + Windows, install pygraphviz from this [channel](https://anaconda.org/alubbock/pygraphviz) `conda install -c alubbock pygraphviz`
## testpypi issue
You should **NOT** be doing this operation, but if you do want to install from `testpypi`, then add the `--extra-index-url` as follows.
```bash
pip install -i https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ pybbn
```
# Other Python Bayesian Belief Network Inference Libraries
Here is a list of other Python libraries for inference in Bayesian Belief Networks.
| Library | Algorithm | Algorithm Type | License |
| -------:| ---------:| -------------: | -------:|
| [BayesPy](https://github.com/bayespy/bayespy)| variational message passing | approximate | MIT |
| [pomegranate](https://github.com/jmschrei/pomegranate) | loopy belief | approximate | MIT |
| [pgmpy](https://github.com/pgmpy/pgmpy) | multiple | approximate/exact | MIT |
| [libpgm](https://github.com/CyberPoint/libpgm) | likelihood sampling | approximate | Proprietary |
| [bayesnetinference](https://github.com/sonph/bayesnetinference) | variable elimination | exact | None |
I found other [packages](https://pypi.python.org/pypi?%3Aaction=search&term=bayesian+network&submit=search) in PyPI too.
# Java
But I am coming from the Java mothership and I want to use Bayesian Belief Networks in Java. How do I perform probabilistic inference in Java?
This Python code base is a port of the [original Java code](https://github.com/vangj/jbayes).
# Help
- [Documentation](https://py-bbn.readthedocs.io/)
- [Chat Room](https://gitter.im/dataflava/py-bbn)
# Citation
```
@misc{vang_2017,
title={PyBBN},
url={https://github.com/vangj/py-bbn/},
journal={GitHub},
author={Vang, Jee},
year={2017},
month={Jan}}
```
## Online Articles
I found these online articles using PyBBN.
- [BBN: Bayesian Belief Networks — How to Build Them Effectively in Python](https://towardsdatascience.com/bbn-bayesian-belief-networks-how-to-build-them-effectively-in-python-6b7f93435bba)
- [Introduction to Bayesian Belief Networks](https://towardsdatascience.com/introduction-to-bayesian-belief-networks-c012e3f59f1b)
# Copyright Stuff
## Software
```
Copyright 2017 -- 2023 Jee Vang
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
```
## Art Copyright
Copyright 2020 Daytchia Vang
# Sponsor, Love
- [Patreon](https://www.patreon.com/vangj)
- [GitHub](https://github.com/sponsors/vangj)
Raw data
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"description": "\n\n# PyBBN\n\nPyBBN is Python library for Bayesian Belief Networks (BBNs) exact inference using the [junction tree algorithm](https://en.wikipedia.org/wiki/Junction_tree_algorithm) or Probability Propagation in Trees of Clusters (PPTC). The implementation is taken directly from [C. Huang and A. Darwiche, \"Inference in\nBelief Networks: A Procedural Guide,\" in International Journal of Approximate Reasoning, vol. 15,\npp. 225--263, 1999](http://pages.cs.wisc.edu/~dpage/ijar95.pdf). In this API, PPTC is applied to BBNs with all discrete variables. When dealing with a BBN with all Gaussian variables (or a Gaussian Belief Network, GBN), exact inference is conducted through an incremental algorithm manipulating the means and covariance matrix. Additionally, there is the ability to generate singly- and multi-connected graphs, which is taken from [JS Ide and FG Cozman, \n\"Random Generation of Bayesian Network,\" in Advances in Artificial Intelligence, Lecture Notes in Computer Science, vol 2507](https://pdfs.semanticscholar.org/5273/2fb57129443592024b0e7e46c2a1ec36639c.pdf). There is also the option to generate sample data from your BBN. This synthetic data may be summarized to generate your posterior marginal probabilities and work as a form of approximate inference. Lastly, we have added Pearl's `do-operator` for causal inference.\n\n# Power Up, Next Level\n\nturing_bbn | pyspark-bbn\n:------------------------------------------------------------------------------------:|:---------------------------------------------------------------------------------------:\n |\n\nIf you like py-bbn, please inquire about our next-generation products below! info@oneoffcoder.com\n\n* [turing_bbn](https://turing-bbn.oneoffcoder.com/) is a C++17 implementation of py-bbn; take your causal and probabilistic inferences to the next computing level!\n* [pyspark-bbn](https://pyspark-bbn.oneoffcoder.com/) is a is a scalable, massively parallel processing MPP framework for learning structures and parameters of Bayesian Belief Networks BBNs using [Apache Spark](https://spark.apache.org/).\n\n# Exact Inference, Discrete Variables\n\nBelow is an example code to create a Bayesian Belief Network, transform it into a join tree, and then set observation evidence. The last line prints the marginal probabilities for each node.\n\n```python\nfrom pybbn.graph.dag import Bbn\nfrom pybbn.graph.edge import Edge, EdgeType\nfrom pybbn.graph.jointree import EvidenceBuilder\nfrom pybbn.graph.node import BbnNode\nfrom pybbn.graph.variable import Variable\nfrom pybbn.pptc.inferencecontroller import InferenceController\n\n# create the nodes\na = BbnNode(Variable(0, 'a', ['on', 'off']), [0.5, 0.5])\nb = BbnNode(Variable(1, 'b', ['on', 'off']), [0.5, 0.5, 0.4, 0.6])\nc = BbnNode(Variable(2, 'c', ['on', 'off']), [0.7, 0.3, 0.2, 0.8])\nd = BbnNode(Variable(3, 'd', ['on', 'off']), [0.9, 0.1, 0.5, 0.5])\ne = BbnNode(Variable(4, 'e', ['on', 'off']), [0.3, 0.7, 0.6, 0.4])\nf = BbnNode(Variable(5, 'f', ['on', 'off']), [0.01, 0.99, 0.01, 0.99, 0.01, 0.99, 0.99, 0.01])\ng = BbnNode(Variable(6, 'g', ['on', 'off']), [0.8, 0.2, 0.1, 0.9])\nh = BbnNode(Variable(7, 'h', ['on', 'off']), [0.05, 0.95, 0.95, 0.05, 0.95, 0.05, 0.95, 0.05])\n\n# create the network structure\nbbn = Bbn() \\\n .add_node(a) \\\n .add_node(b) \\\n .add_node(c) \\\n .add_node(d) \\\n .add_node(e) \\\n .add_node(f) \\\n .add_node(g) \\\n .add_node(h) \\\n .add_edge(Edge(a, b, EdgeType.DIRECTED)) \\\n .add_edge(Edge(a, c, EdgeType.DIRECTED)) \\\n .add_edge(Edge(b, d, EdgeType.DIRECTED)) \\\n .add_edge(Edge(c, e, EdgeType.DIRECTED)) \\\n .add_edge(Edge(d, f, EdgeType.DIRECTED)) \\\n .add_edge(Edge(e, f, EdgeType.DIRECTED)) \\\n .add_edge(Edge(c, g, EdgeType.DIRECTED)) \\\n .add_edge(Edge(e, h, EdgeType.DIRECTED)) \\\n .add_edge(Edge(g, h, EdgeType.DIRECTED))\n\n# convert the BBN to a join tree\njoin_tree = InferenceController.apply(bbn)\n\n# insert an observation evidence\nev = EvidenceBuilder() \\\n .with_node(join_tree.get_bbn_node_by_name('a')) \\\n .with_evidence('on', 1.0) \\\n .build()\njoin_tree.set_observation(ev)\n\n# print the marginal probabilities\nfor node in join_tree.get_bbn_nodes():\n potential = join_tree.get_bbn_potential(node)\n print(node)\n print(potential)\n```\n\n# Exact Inference, Gaussian Variables\n\nThe example belows shows how to perform inference on multivariate Gaussian variables.\n\n```python\nimport numpy as np\n\nfrom pybbn.gaussian.inference import GaussianInference\n\n\ndef get_cowell_data():\n \"\"\"\n Gets Cowell data.\n\n :return: Data and headers.\n \"\"\"\n n = 10000\n Y = np.random.normal(0, 1, n)\n X = np.random.normal(Y, 1, n)\n Z = np.random.normal(X, 1, n)\n\n D = np.vstack([Y, X, Z]).T\n return D, ['Y', 'X', 'Z']\n\n\n# assume we have data and headers (variable names per column)\n# X is the data (rows are observations, columns are variables)\n# H is just a list of variable names\nX, H = get_cowell_data()\n\n# then we can compute the means and covariance matrix easily\nM = X.mean(axis=0)\nE = np.cov(X.T)\n\n# the means and covariance matrix are all we need for gaussian inference\n# notice how we keep `g` around?\n# we'll use `g` over and over to do inference with evidence/observations\ng = GaussianInference(H, M, E)\n# {'Y': (0.00967, 0.98414), 'X': (0.01836, 2.02482), 'Z': (0.02373, 3.00646)}\nprint(g.P)\n\n# we can make a single observation with do_inference()\ng1 = g.do_inference('X', 1.5)\n# {'X': (1.5, 0), 'Y': (0.76331, 0.49519), 'Z': (1.51893, 1.00406)}\nprint(g1.P)\n\n# we can make multiple observations with do_inferences()\ng2 = g.do_inferences([('Z', 1.5), ('X', 2.0)])\n# {'Z': (1.5, 0), 'X': (2.0, 0), 'Y': (1.97926, 0.49509)}\nprint(g2.P)\n```\n\n# Building\n\nTo build, you will need 3.7. Managing environments through [Anaconda](https://www.anaconda.com/download/#linux) is highly recommended to be able to build this project (though not absolutely required if you know what you are doing). Assuming you have installed Anaconda, you may create an environment as follows (make sure you `cd` into the root of this project's location).\n\nTo create the environment, use the following commands.\n\n```bash\nconda env create -f environment.yml\n```\n\nIf you want to use the environments with Jupyter, install the kernel.\n\n```bash\nconda activate pybbn37\npython -m ipykernel install --user --name pybbn37 --display-name \"pybbn37\"\n```\n\nThen you may build the project as follows. (Note that in Python 3.6 you will get some warnings).\n\n```bash\nmake build\n```\n\nTo build the documents, go into the docs sub-directory and type in the following.\n\n```bash\nmake html\n```\n\n## Testing\n\nYou can do a fresh test with Docker as follows.\n\n```bash\ndocker build -t pybbn-test:local -f Dockerfile.test .\n```\n\n# Installing\n\n## From PyPi\nUse pip to install the package as it has been published to [PyPi](https://pypi.python.org/pypi/pybbn).\n\n```bash\npip install pybbn\n```\n\n## From Source\n\nIf you check out the source do the following.\n\n```bash\npip list | grep pybbn\npip uninstall pybbn\npython setup.py install\npip list | grep pybbn\n```\n\n## GraphViz issue\n\nMake sure you [install GraphViz](https://graphviz.gitlab.io/download/) on your system.\n\n* CentOS: `yum install graphviz*`\n* Ubuntu: `sudo apt-get install graphviz libgraphviz-dev`\n* Mac OSX: `brew install graphviz` and when you install pygraphviz `pip install pygraphviz --install-option=\"--include-path=/usr/local/lib/graphviz/\" --install-option=\"--library-path=/usr/local/lib/graphviz/\"`\n* Windows: use the [msi installer](https://graphviz.gitlab.io/_pages/Download/windows/graphviz-2.38.msi)\n * For Anaconda + Windows, install pygraphviz from this [channel](https://anaconda.org/alubbock/pygraphviz) `conda install -c alubbock pygraphviz`\n\n## testpypi issue\n\nYou should **NOT** be doing this operation, but if you do want to install from `testpypi`, then add the `--extra-index-url` as follows.\n\n```bash\npip install -i https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ pybbn\n```\n\n# Other Python Bayesian Belief Network Inference Libraries\n\nHere is a list of other Python libraries for inference in Bayesian Belief Networks. \n\n| Library | Algorithm | Algorithm Type | License |\n| -------:| ---------:| -------------: | -------:|\n| [BayesPy](https://github.com/bayespy/bayespy)| variational message passing | approximate | MIT |\n| [pomegranate](https://github.com/jmschrei/pomegranate) | loopy belief | approximate | MIT |\n| [pgmpy](https://github.com/pgmpy/pgmpy) | multiple | approximate/exact | MIT |\n| [libpgm](https://github.com/CyberPoint/libpgm) | likelihood sampling | approximate | Proprietary |\n| [bayesnetinference](https://github.com/sonph/bayesnetinference) | variable elimination | exact | None |\n\nI found other [packages](https://pypi.python.org/pypi?%3Aaction=search&term=bayesian+network&submit=search) in PyPI too.\n\n# Java\n\nBut I am coming from the Java mothership and I want to use Bayesian Belief Networks in Java. How do I perform probabilistic inference in Java?\n\nThis Python code base is a port of the [original Java code](https://github.com/vangj/jbayes).\n\n# Help\n\n- [Documentation](https://py-bbn.readthedocs.io/)\n- [Chat Room](https://gitter.im/dataflava/py-bbn)\n\n# Citation\n\n```\n@misc{vang_2017, \ntitle={PyBBN}, \nurl={https://github.com/vangj/py-bbn/}, \njournal={GitHub},\nauthor={Vang, Jee}, \nyear={2017}, \nmonth={Jan}}\n```\n\n## Online Articles\nI found these online articles using PyBBN.\n\n- [BBN: Bayesian Belief Networks \u2014 How to Build Them Effectively in Python](https://towardsdatascience.com/bbn-bayesian-belief-networks-how-to-build-them-effectively-in-python-6b7f93435bba)\n- [Introduction to Bayesian Belief Networks](https://towardsdatascience.com/introduction-to-bayesian-belief-networks-c012e3f59f1b)\n\n# Copyright Stuff\n\n## Software\n\n```\nCopyright 2017 -- 2023 Jee Vang\n\nLicensed under the Apache License, Version 2.0 (the \"License\");\nyou may not use this file except in compliance with the License.\nYou may obtain a copy of the License at\n\n http://www.apache.org/licenses/LICENSE-2.0\n\nUnless required by applicable law or agreed to in writing, software\ndistributed under the License is distributed on an \"AS IS\" BASIS,\nWITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\nSee the License for the specific language governing permissions and\nlimitations under the License.\n```\n\n## Art Copyright\n\nCopyright 2020 Daytchia Vang\n\n# Sponsor, Love\n\n- [Patreon](https://www.patreon.com/vangj)\n- [GitHub](https://github.com/sponsors/vangj)",
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