XDSL

class pgmpy.readwrite.XDSL.XDSLReader(path=None, string=None)

Initializes the reader object for XDSL file formats[1] created through GeNIe[2].

Parameters:

• path (file or str) – Path to the XDSL file.

• string (str) – A string containing the XDSL file content.

Examples

>>> # AsiaDiagnosis.xdsl is an example file downloadable from
>>> # https://repo.bayesfusion.com/bayesbox.html
>>> # The file has been modified slightly to adhere to XDSLReader requirements
>>> from pgmpy.readwrite import XDSLReader
>>> reader = XDSLReader("AsiaDiagnosis.xdsl")
>>> model = reader.get_model()

Reference

[1] https://support.bayesfusion.com/docs/GeNIe/saving_xdslfileformat.html [2] https://www.bayesfusion.com/genie/

get_edges()

Returns the edges of the network

Examples

>>> reader = XDSLReader("AsiaDiagnosis.xdsl")
>>> reader.get_edges()
[['asia', 'tub'],
['smoke', 'lung'],
['tub', 'either'],
['lung', 'either'],
['either', 'xray'],
['smoke', 'bronc'],
['either', 'dysp'],
['bronc', 'dysp']]

get_model(state_name_type=<class 'str'>)

Returns a Bayesian Network instance from the file/string.

Parameters:

state_name_type (int, str, or bool (default: str)) – The data type to which to convert the state names of the variables.

Returns:

DiscreteBayesianNetwork instance

Return type:

The read model.

Examples

>>> from pgmpy.readwrite import XDSLReader
>>> reader = XDSLReader("AsiaDiagnosis.xdsl")
>>> model = reader.get_model()

get_parents()

Returns the parents of the variables present in the network

Examples

>>> reader = XDSLReader("AsiaDiagnosis.xdsl")
>>> reader.get_parents()
{'asia': [],
'tub': ['asia'],
'smoke': [],
'lung': ['smoke'],
'either': ['tub', 'lung'],
'xray': ['either'],
'bronc': ['smoke'],
'dysp': ['either', 'bronc']
}

get_states()

Returns the states of variables present in the network

Examples

>>> reader = XDSLReader("AsiaDiagnosis.xdsl")
>>> reader.get_states()
{'asia': ['no', 'yes'],
'tub': ['no', 'yes'],
'smoke': ['no', 'yes'],
'lung': ['no', 'yes'],
'either': ['Nothing',
'CancerORTuberculosis'],
'xray': ['Normal', 'Abnormal'],
'bronc': ['Absent', 'Present'], '
dysp': ['Absent', 'Present']
}

get_values()

Returns the CPD of the variables present in the network

Examples

>>> reader = XDSLReader("AsiaDiagnosis.xdsl")
>>> reader.get_values()
{'asia': [[0.99], [0.01]],
'tub': [[0.99, 0.95], [0.01, 0.05]],
'smoke': [[0.5], [0.5]],
'lung': [[0.99, 0.9], [0.01, 0.1]],
'either': [[1.0, 1.0, 1.0, 0.0], [0.0, 0.0, 0.0, 1.0]],
'xray': [[0.95, 0.02], [0.05, 0.98]],
'bronc': [[0.7, 0.4], [0.3, 0.6]],
'dysp': [[0.9, 0.2, 0.3, 0.1], [0.1, 0.8, 0.7, 0.9]]
}

get_variables()

Returns list of variables of the network

Examples

>>> reader = XDSLReader("AsiaDiagnosis.xdsl")
>>> reader.get_variables()
['asia', 'tub', 'smoke', 'lung', 'either', 'xray', 'bronc', 'dysp']

class pgmpy.readwrite.XDSL.XDSLWriter(model, network_id='MyNetwork', num_samples='0', disc_samples='0', encoding='utf-8')

Initialise a XDSL writer object to export pgmpy models to XDSL file format[1] used by GeNIe[2].

Parameters:

• model (pgmpy.models.DiscreteBayesianNetwork instance.) – The model to write to the file.

• network_id (str (default: "MyNetwork")) – Name/id of the network

• num_samples (int (default: 0)) – Number of samples used for continuous variables

• disc_samples (int (default: 0)) – Number of samples used for discrete variables

• encoding (str (optional, default='utf-8')) – Encoding for text data

Examples

>>> from pgmpy.readwrite import XDSLWriter
>>> from pgmpy.utils import get_example_model
>>> asia = get_example_model('asia')
>>> writer = XDSLWriter(asia)
>>> writer.write_xdsl('asia.xdsl')

Reference

[1] https://support.bayesfusion.com/docs/GeNIe/saving_xdslfileformat.html [2] https://www.bayesfusion.com/genie/

get_cpds()

Add the complete CPT element (with states and probabilities) to XDSL.

Returns:

dict

Return type:

dict of type {variable: table tag}

Examples

>>> writer = XMLBIFWriter(model)
>>> writer.get_values()
{'asia': <TabularCPD representing P(asia:2) at 0x1885817c830>,
'tub': <TabularCPD representing P(tub:2 | asia:2) at 0x1885a7e57c0>,
'smoke': <TabularCPD representing P(smoke:2) at 0x18858327950>,
'lung': <TabularCPD representing P(lung:2 | smoke:2) at 0x188583278f0>,
'bronc': <TabularCPD representing P(bronc:2 | smoke:2) at 0x18855e05610>,
'either': <TabularCPD representing P(either:2 | lung:2, tub:2) at 0x188582792e0>,
'xray': <TabularCPD representing P(xray:2 | either:2) at 0x1885a7e5910>,
'dysp': <TabularCPD representing P(dysp:2 | bronc:2, either:2) at 0x18858278b90>}

get_variables()

Add variables and their XML elements/representation to XDSL

Returns:

dict

Return type:

dict of type {variable: variable tags}

Examples

>>> writer = XMLBIFWriter(model)
>>> writer.get_variables()
{'asia': <Element 'cpt' at 0x000001DC6BFA1350>,
'tub': <Element 'cpt' at 0x000001DC6BFA35B0>,
'smoke': <Element 'cpt' at 0x000001DC6BFA3560>,
'lung': <Element 'cpt' at 0x000001DC6BFA12B0>,
'bronc': <Element 'cpt' at 0x000001DC6BFA1260>,
'either': <Element 'cpt' at 0x000001DC6BFA3510>,
'xray': <Element 'cpt' at 0x000001DC6BFA34C0>,
'dysp': <Element 'cpt' at 0x000001DC6BFA1210>}

write_xdsl(filename=None)

Write the xdsl data into the file.

Parameters:

filename (Name (path) of the file.)

Examples

>>> from pgmpy.readwrite import XDSLWriter
>>> from pgmpy.utils import get_example_model
>>> model = get_example_model('asia')
>>> writer = XDSLWriter(model)
>>> writer.write_xdsl('asia.xdsl')