"""
The Ground Bayes Network (GBN) in ProbReM is the smallest subset of data that is required to answer a specific query. While the PRM uses a first-order representation of the world, the inference process needs a propositional represenation of the data. The :mod:`network.groundBN` module implements an efficient data structure for that purpose.
"""
from analytics.performance import time_analysis
from network.vertices import GBNvertex,ReferenceVertex,computeRefID
[docs]class GBNGraph(dict):
'''
A `GBNGraph` is a dictionary that contains a set of vertices of type :class:`GBNvertex`.
The `GBNGraph` instance itself is a dictionary which is used to store vertices {key=vertex_id : value= :class:`GBNvertex`}. There are also various different dictionaries of all `GBNvertex` objects that allow fast retrieval of sets of GBN vertices.
'''
def __init__(self):
'''
init
'''
self.allByAttribute = {}
"""
A dicitonary that groups all `GBNvertex` instances according to their attribute class, e.g. {key=:class:`Attribute` : value=[ list of :class:`!GBNvertex` ]}
"""
self.samplingVertices = {}
"""
A dicitonary that groups all sampling `GBNvertex` instances (event & latent vertices), e.g. {key=vertex_id : value= :class:`!GBNvertex`}
"""
self.eventVertices = {}
"""
A dicitonary that groups all event `GBNvertex` instances according to their attribute class, e.g. {key=vertex_id : value= :class:`!GBNvertex`}
"""
self.samplingVerticesByAttribute = {}
"""
A dicitonary that groups all sampling `GBNvertex` instances (event & latent vertices) according to their attribute class, e.g. {key=:class:`Attribute` : value=[ list of :class:`!GBNvertex` ]}
"""
[docs] def addEvidenceVertex(self,ID,attr,obj,value):
"""
Instantiates a new evidence :class:`!GBNvertex` and updates the corresponding GBN data structures.
:arg ID: Unique ID
:arg attr: :class:`Attribute`
:arg obj: Primary Key of attribute object
:arg value: Value of vertex
"""
self[ID] = GBNvertex(ID=ID,attr=attr,obj=obj,fixed=True,value=value)
if attr in self.allByAttribute:
self.allByAttribute[attr].append(self[ID])
else:
self.allByAttribute[attr] = []
self.allByAttribute[attr].append(self[ID])
return ID
[docs] def addSamplingVertex(self,ID,attr,obj):
"""
Instantiates a new sampling :class:`!GBNvertex` and updates the corresponding GBN data structures.
:arg ID: Unique ID
:arg attr: :class:`Attribute`
:arg obj: Primary Key of attribute object
"""
self[ID] = GBNvertex(ID=ID,attr=attr,obj=obj,fixed=False)
self.samplingVertices[ID] = self[ID]
if attr in self.samplingVerticesByAttribute:
self.samplingVerticesByAttribute[attr].append(self[ID])
else:
self.samplingVerticesByAttribute[attr] = []
self.samplingVerticesByAttribute[attr].append(self[ID])
if attr in self.allByAttribute:
self.allByAttribute[attr].append(self[ID])
else:
self.allByAttribute[attr] = []
self.allByAttribute[attr].append(self[ID])
return ID
[docs] def addVertex(self,ID,attr,obj, **args):
'''
General method to add a vertex to the graph.
'''
"""
General method to add a vertex to the graph. Note that the node is only instantiated (and added) if `ID` is not in the graph already.
If not, instantiates a new :class:`!GBNvertex` and updates the corresponding GBN data structures.
:arg ID: Unique ID
:arg attr: :class:`Attribute`
:arg obj: Primary Key of attribute object
:arg **args: Dictionary of other parameters
"""
if ID not in self:
self[ID] = GBNvertex(ID=ID,attr=attr,obj=obj,**args)
#print 'Added %s(E=%s) to GBN'%(ID,self[ID].fixed)
#also add references to the helper data structures
if not self[ID].fixed:
self.samplingVertices[ID] = self[ID]
if attr in self.samplingVerticesByAttribute:
self.samplingVerticesByAttribute[attr].append(self[ID])
else:
self.samplingVerticesByAttribute[attr] = []
self.samplingVerticesByAttribute[attr].append(self[ID])
if attr in self.allByAttribute:
self.allByAttribute[attr].append(self[ID])
else:
self.allByAttribute[attr] = []
self.allByAttribute[attr].append(self[ID])
return ID
return False
'''
else:
?Gather statistics about how many nodes were added reduntantly
'''
[docs] def addReferenceVertex(self,gbnV,dependency):
'''Adds a :class:`.ReferenceVertex` to the ground Bayesian network.
For now, the reference attribute (all exist attributes) are assumed to be sampling nodes (i.e. not in the evidence nor in the event variables)
'''
ID = computeRefID(gbnV)
if ID not in self:
self[ID] = ReferenceVertex(ID=ID, gbnV=gbnV,dep=dependency)
attr = self[ID].attr
#also add references to the helper data structures
if not self[ID].fixed:
self.samplingVertices[ID] = self[ID]
if attr in self.samplingVerticesByAttribute:
self.samplingVerticesByAttribute[attr].append(self[ID])
else:
self.samplingVerticesByAttribute[attr] = []
self.samplingVerticesByAttribute[attr].append(self[ID])
if attr in self.allByAttribute:
self.allByAttribute[attr].append(self[ID])
else:
self.allByAttribute[attr] = []
self.allByAttribute[attr].append(self[ID])
# initialize reference
# add initial edges
return ID
#nothing added
return False
def __missing__(self,key):
'''
Called if we try to access a vertex that isn't in the graph.
'''
return None
[docs] def logLikelihood(self):
'''
Returns the loglikelihood of the `GBNGraph`
'''
loglik = 0
for gbnV in self.values():
loglik += gbnV.logLikelihood()
return loglik
def __repr__(self):
'''
String representation of the statistics of the current Graph
'''
rep = '-- Ground Bayesian Network --\n'
def prettyStat(gbndict):
'''Returns a string representation of the `gbndict` dictionary
'''
s = ''
for attr,gbnvs in gbndict.items():
s += '%s (%s),'%(attr.fullname,len(gbnvs))
return s[:-1]
rep += 'All : %s vertices\n\t%s\n'%(len(self),prettyStat(self.allByAttribute))
rep += 'Sampling : %s vertices\n\t%s\n'%(len(self.samplingVertices),prettyStat(self.samplingVerticesByAttribute))
return rep[:-1] #don't return last '\n'
[docs]class GBNqueue(dict):
'''
A queue that keeps track of vertices that need to be processed when
constructing the Ground Bayesian network.
This class is also a dictionary as the information is stored in groups
that correspond to sets of vertices that share the same local distribution
(= the same attribute).
{ key=:class:`Attribute` : value=[ list of :class:`!GBNvertex` ] }
'''
def __init__(self):
'''
Init
'''
def isEmpty(self):
if len(self)==0:
return True
else:
return False
[docs] def pop(self):
'''
Return a set of GBNvertex instances of the same attribute :math:`A \in A(X)`.
This allows us to retrieve the required data in one call to the data interface.
We choose an attribute, remove the
key from the dictionary and return the associated list.
:returns: List of :class:`!GBNvertex`
'''
return self.popitem()
[docs] def push(self, gbnVertex):
'''
If another :class:`!GBNvertex` is pushed onto the stack, it is added to the list
associated with the `gbnVertex.attr`
:arg gbnVertex: :class:`GBNvertex`
'''
#print 'Adding %s to Queue'%(gbnVertex.ID)
self[gbnVertex.attr].append(gbnVertex)
def __missing__(self,key):
'''
In case the key - an attribute instance - is not in the dictionary we add it
with an empty list of vertices.
'''
self[key] = []
return self[key]