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Learning the structure of a Bayesian network

Creative Commons LicenseaGrUMinteractive online version
# %matplotlib inline
## from pylab import *
import math
import matplotlib.pyplot as plt
import pyagrum as gum
import pyagrum.lib.notebook as gnb
import pyagrum.explain as explain
import pyagrum.lib.bn_vs_bn as bnvsbn
gum.about()
gnb.configuration()
pyAgrum 2.3.0.9
(c) 2015-2024 Pierre-Henri Wuillemin, Christophe Gonzales
This is free software; see the source code for copying conditions.
There is ABSOLUTELY NO WARRANTY; not even for MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE. For details, see 'pyagrum.warranty'.
LibraryVersion
OSposix [darwin]
Python3.14.0 (main, Oct 7 2025, 09:34:52) [Clang 17.0.0 (clang-1700.3.19.1)]
IPython9.6.0
Matplotlib3.10.7
Numpy2.3.4
pyDot4.0.1
pyAgrum2.3.0.9
Wed Oct 29 13:58:45 2025 CET
bn = gum.loadBN("res/asia.bif")
bn
G tuberculos_or_cancer tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea smoking smoking bronchitis bronchitis smoking->bronchitis lung_cancer lung_cancer smoking->lung_cancer tuberculosis tuberculosis tuberculosis->tuberculos_or_cancer bronchitis->dyspnoea lung_cancer->tuberculos_or_cancer visit_to_Asia visit_to_Asia visit_to_Asia->tuberculosis
gum.generateSample(bn, 50000, "out/sample_asia.csv", True);

out/sample_asia.csv: 0%| |

out/sample_asia.csv: 100%|█████████████████████████████████|

Log2-Likelihood : -161108.69919616362
with open("out/sample_asia.csv", "r") as src:
for _ in range(10):
print(src.readline(), end="")
bronchitis,tuberculos_or_cancer,tuberculosis,dyspnoea,positive_XraY,visit_to_Asia,smoking,lung_cancer
1,1,1,1,1,1,0,1
1,1,1,1,1,1,1,1
1,1,1,1,1,1,0,1
1,1,1,1,1,1,1,1
0,1,1,0,1,1,1,1
1,1,1,1,1,1,1,1
1,1,1,1,1,1,1,1
1,1,1,1,1,1,1,1
0,1,1,0,1,1,1,1
learner = gum.BNLearner("out/sample_asia.csv", bn) # using bn as template for variables
print(learner)
Filename : out/sample_asia.csv
Size : (50000,8)
Variables : visit_to_Asia[2], tuberculosis[2], tuberculos_or_cancer[2], positive_XraY[2], lung_cancer[2], smoking[2], bronchitis[2], dyspnoea[2]
Induced types : False
Missing values : False
Algorithm : MIIC
Correction : MDL
Prior : -
print(f"Row of visit_to_Asia : {learner.idFromName('visit_to_Asia')}") # first row is 0
Row of visit_to_Asia : 0
print(f"Variable in row 4 : {learner.nameFromId(4)}")
Variable in row 4 : lung_cancer

The BNLearner is capable of recognizing missing values in databases. For this purpose, just indicate as a last argument the list of the strings that represent missing values.

## it is possible to add as a last argument a list of the symbols that represent missing values:
## whenever a cell of the database is equal to one of these strings, it is considered as a
## missing value
learner = gum.BNLearner("res/asia_missing.csv", bn, ["?", "N/A"])
print(f"Are there missing values in the database ? {learner.state()['Missing values'][0]}")
Are there missing values in the database ? True

When reading a csv file, BNLearner can try to find the correct type for discrete variable. Especially for numeric values.

%%writefile out/testTypeInduction.csv
A,B,C,D
1,2,0,hot
0,3,-2,cold
0,1,2,hot
1,2,2,warm
Overwriting out/testTypeInduction.csv
print("* by default, type induction is on (True) :")
learner = gum.BNLearner("out/testTypeInduction.csv")
bn3 = learner.learnBN()
for v in sorted(bn3.names()):
print(f" - {bn3.variable(v)}")
print("")
print("* but you can disable it :")
learner = gum.BNLearner("out/testTypeInduction.csv", ["?"], False)
bn3 = learner.learnBN()
for v in sorted(bn3.names()):
print(f" - {bn3.variable(v)}")
print("")
print("Note that when a Labelized variable is found, the labesl are alphabetically sorted.")
* by default, type induction is on (True) :
- A:Range([0,1])
- B:Range([1,3])
- C:Integer({-2|0|2})
- D:Labelized({cold|hot|warm})
* but you can disable it :
- A:Labelized({0|1})
- B:Labelized({1|2|3})
- C:Labelized({-2|0|2})
- D:Labelized({cold|hot|warm})
Note that when a Labelized variable is found, the labesl are alphabetically sorted.

We give the bnbn as a parameter for the learner in order to have the variables and the order of the labels for each variables. Please try to remove the argument bnbn in the first line below to see the difference …

learner = gum.BNLearner("out/sample_asia.csv", bn) # using bn as template for variables and labels
bn2 = learner.learnParameters(bn.dag())
gnb.showBN(bn2)

svg

gnb.sideBySide(
"<H3>Original BN</H3>",
"<H3>Learned NB</H3>",
bn.cpt("visit_to_Asia"),
bn2.cpt("visit_to_Asia"),
bn.cpt("tuberculosis"),
bn2.cpt("tuberculosis"),
ncols=2,
)

Original BN

Learned NB

visit_to_Asia
0
1
0.01000.9900
visit_to_Asia
0
1
0.01000.9900
tuberculosis
visit_to_Asia
0
1
0
0.05000.9500
1
0.01000.9900
tuberculosis
visit_to_Asia
0
1
0
0.05790.9421
1
0.00900.9910

Structural learning a BN from the database

Section titled “Structural learning a BN from the database”

Note that, currently, the BNLearner is not yet able to learn in the presence of missing values. This is the reason why, when it discovers that there exist such values, it raises a gum.MissingValueInDatabase exception.

with open("res/asia_missing.csv", "r") as asiafile:
for _ in range(10):
print(asiafile.readline(), end="")
try:
learner = gum.BNLearner("res/asia_missing.csv", bn, ["?", "N/A"])
bn2 = learner.learnBN()
except gum.MissingValueInDatabase:
print("exception raised: there are missing values in the database")
smoking,lung_cancer,bronchitis,visit_to_Asia,tuberculosis,tuberculos_or_cancer,dyspnoea,positive_XraY
0,0,0,1,1,0,0,0
1,1,0,1,1,1,0,1
1,1,1,1,1,1,1,1
1,1,0,1,1,1,0,N/A
0,1,0,1,1,1,1,1
1,1,1,1,1,1,1,1
1,1,1,1,1,1,0,1
1,1,0,1,1,1,0,1
1,1,1,1,1,1,1,1
exception raised: there are missing values in the database

For now, there are three scored-based algorithms that are wrapped in pyAgrum : LocalSearchWithTabuList, GreedyHillClimbing and K2

learner = gum.BNLearner("out/sample_asia.csv", bn) # using bn as template for variables
learner.useLocalSearchWithTabuList()
print(learner)
bn2 = learner.learnBN()
print("Learned in {0}ms".format(1000 * learner.currentTime()))
gnb.flow.row(bn, bn2, explain.getInformation(bn2), captions=["Original BN", "Learned BN", "information"])
Filename : out/sample_asia.csv
Size : (50000,8)
Variables : visit_to_Asia[2], tuberculosis[2], tuberculos_or_cancer[2], positive_XraY[2], lung_cancer[2], smoking[2], bronchitis[2], dyspnoea[2]
Induced types : False
Missing values : False
Algorithm : Local Search with Tabu List
Tabu list size : 2
Score : BDeu
Prior : -
Learned in 15.564ms
G tuberculos_or_cancer tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea smoking smoking bronchitis bronchitis smoking->bronchitis lung_cancer lung_cancer smoking->lung_cancer tuberculosis tuberculosis tuberculosis->tuberculos_or_cancer bronchitis->dyspnoea lung_cancer->tuberculos_or_cancer visit_to_Asia visit_to_Asia visit_to_Asia->tuberculosis
Original BN
G tuberculos_or_cancer tuberculos_or_cancer tuberculosis tuberculosis tuberculos_or_cancer->tuberculosis lung_cancer lung_cancer tuberculos_or_cancer->lung_cancer dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea smoking smoking bronchitis bronchitis smoking->bronchitis tuberculosis->lung_cancer visit_to_Asia visit_to_Asia tuberculosis->visit_to_Asia tuberculosis->dyspnoea positive_XraY positive_XraY positive_XraY->tuberculos_or_cancer positive_XraY->tuberculosis bronchitis->dyspnoea lung_cancer->smoking
Learned BN
G tuberculos_or_cancer tuberculos_or_cancer tuberculosis tuberculosis tuberculos_or_cancer->tuberculosis lung_cancer lung_cancer tuberculos_or_cancer->lung_cancer dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea smoking smoking bronchitis bronchitis smoking->bronchitis tuberculosis->lung_cancer visit_to_Asia visit_to_Asia tuberculosis->visit_to_Asia tuberculosis->dyspnoea positive_XraY positive_XraY positive_XraY->tuberculos_or_cancer positive_XraY->tuberculosis bronchitis->dyspnoea lung_cancer->smoking
PyAgrum inline image

information

To apprehend the distance between the original and the learned BN, we have several tools :

  • Compute the KL divergence (and other distance) between original and learned joint distribution
kl = gum.ExactBNdistance(bn, bn2)
kl.compute()
{'klPQ': 0.0002454972790806624,
'errorPQ': 0,
'klQP': 0.0002170115306462794,
'errorQP': 128,
'hellinger': 0.009492813820926288,
'bhattacharya': 4.5052130085963663e-05,
'jensen-shannon': 6.276601520482401e-05}
  • Compute some scores on the BNs (as binary classifiers) abd show the graphical diff between the two graphs
gnb.flow.row(bn, bn2, captions=["bn", "bn2"])
gnb.flow.row(
bnvsbn.graphDiff(bn, bn2),
bnvsbn.graphDiff(bn2, bn),
bnvsbn.graphDiffLegend(),
captions=["bn versus bn2", "bn2 versus bn", ""],
)
gcmp = bnvsbn.GraphicalBNComparator(bn, bn2)
gnb.flow.add_html(
"<br/>".join([f"{k} : {v:.2f}" for k, v in gcmp.skeletonScores().items() if k != "count"]), "Skeleton scores"
)
gnb.flow.add_html("<br/>".join([f"{k} : {v:.2f}" for k, v in gcmp.scores().items() if k != "count"]), "Scores")
gnb.flow.display()
G tuberculos_or_cancer tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea smoking smoking bronchitis bronchitis smoking->bronchitis lung_cancer lung_cancer smoking->lung_cancer tuberculosis tuberculosis tuberculosis->tuberculos_or_cancer bronchitis->dyspnoea lung_cancer->tuberculos_or_cancer visit_to_Asia visit_to_Asia visit_to_Asia->tuberculosis
bn
G tuberculos_or_cancer tuberculos_or_cancer tuberculosis tuberculosis tuberculos_or_cancer->tuberculosis lung_cancer lung_cancer tuberculos_or_cancer->lung_cancer dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea smoking smoking bronchitis bronchitis smoking->bronchitis tuberculosis->lung_cancer visit_to_Asia visit_to_Asia tuberculosis->visit_to_Asia tuberculosis->dyspnoea positive_XraY positive_XraY positive_XraY->tuberculos_or_cancer positive_XraY->tuberculosis bronchitis->dyspnoea lung_cancer->smoking
bn2
G visit_to_Asia visit_to_Asia tuberculosis tuberculosis tuberculosis->visit_to_Asia tuberculos_or_cancer tuberculos_or_cancer lung_cancer lung_cancer tuberculosis->lung_cancer dyspnoea dyspnoea tuberculosis->dyspnoea tuberculos_or_cancer->tuberculosis positive_XraY positive_XraY tuberculos_or_cancer->lung_cancer tuberculos_or_cancer->dyspnoea positive_XraY->tuberculosis positive_XraY->tuberculos_or_cancer smoking smoking lung_cancer->smoking bronchitis bronchitis smoking->bronchitis bronchitis->dyspnoea
bn versus bn2
G visit_to_Asia visit_to_Asia tuberculosis tuberculosis visit_to_Asia->tuberculosis tuberculos_or_cancer tuberculos_or_cancer tuberculosis->tuberculos_or_cancer lung_cancer lung_cancer tuberculosis->lung_cancer dyspnoea dyspnoea tuberculosis->dyspnoea positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY tuberculos_or_cancer->dyspnoea positive_XraY->tuberculosis lung_cancer->tuberculos_or_cancer smoking smoking smoking->lung_cancer bronchitis bronchitis smoking->bronchitis bronchitis->dyspnoea
bn2 versus bn
G a->b overflow c->d Missing e->f reversed g->h Correct
recall : 1.00
precision : 0.73
fscore : 0.84
dist2opt : 0.27
Skeleton scores
recall : 0.38
precision : 0.27
fscore : 0.32
dist2opt : 0.96
Scores

A greedy Hill Climbing algorithm (with insert, remove and change arc as atomic operations).

learner = gum.BNLearner("out/sample_asia.csv", bn) # using bn as template for variables
learner.useGreedyHillClimbing()
print(learner)
bn2 = learner.learnBN()
print("Learned in {0}ms".format(1000 * learner.currentTime()))
gnb.sideBySide(
bn,
bn2,
gnb.getBNDiff(bn, bn2),
explain.getInformation(bn2),
captions=["Original BN", "Learned BN", "Graphical diff", "information"],
)
Filename : out/sample_asia.csv
Size : (50000,8)
Variables : visit_to_Asia[2], tuberculosis[2], tuberculos_or_cancer[2], positive_XraY[2], lung_cancer[2], smoking[2], bronchitis[2], dyspnoea[2]
Induced types : False
Missing values : False
Algorithm : Greedy Hill Climbing
Score : BDeu
Prior : -
Learned in 13.482ms
G tuberculos_or_cancer tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea smoking smoking bronchitis bronchitis smoking->bronchitis lung_cancer lung_cancer smoking->lung_cancer tuberculosis tuberculosis tuberculosis->tuberculos_or_cancer bronchitis->dyspnoea lung_cancer->tuberculos_or_cancer visit_to_Asia visit_to_Asia visit_to_Asia->tuberculosis
Original BN
G tuberculos_or_cancer tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea smoking smoking tuberculosis tuberculosis tuberculosis->tuberculos_or_cancer visit_to_Asia visit_to_Asia tuberculosis->visit_to_Asia bronchitis bronchitis bronchitis->smoking lung_cancer lung_cancer bronchitis->lung_cancer bronchitis->dyspnoea lung_cancer->tuberculos_or_cancer lung_cancer->smoking
Learned BN
G visit_to_Asia visit_to_Asia tuberculosis tuberculosis tuberculosis->visit_to_Asia tuberculos_or_cancer tuberculos_or_cancer tuberculosis->tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea lung_cancer lung_cancer lung_cancer->tuberculos_or_cancer smoking smoking lung_cancer->smoking bronchitis bronchitis bronchitis->lung_cancer bronchitis->smoking bronchitis->dyspnoea
Graphical diff
G tuberculos_or_cancer tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea smoking smoking tuberculosis tuberculosis tuberculosis->tuberculos_or_cancer visit_to_Asia visit_to_Asia tuberculosis->visit_to_Asia bronchitis bronchitis bronchitis->smoking lung_cancer lung_cancer bronchitis->lung_cancer bronchitis->dyspnoea lung_cancer->tuberculos_or_cancer lung_cancer->smoking
PyAgrum inline image

information

And a K2 for those who likes it :)

learner = gum.BNLearner("out/sample_asia.csv", bn) # using bn as template for variables
learner.useK2([0, 1, 2, 3, 4, 5, 6, 7])
print(learner)
bn2 = learner.learnBN()
print("Learned in {0}ms".format(1000 * learner.currentTime()))
gnb.sideBySide(
bn,
bn2,
gnb.getBNDiff(bn, bn2),
explain.getInformation(bn2),
captions=["Original BN", "Learned BN", "Graphical diff", "information"],
)
Filename : out/sample_asia.csv
Size : (50000,8)
Variables : visit_to_Asia[2], tuberculosis[2], tuberculos_or_cancer[2], positive_XraY[2], lung_cancer[2], smoking[2], bronchitis[2], dyspnoea[2]
Induced types : False
Missing values : False
Algorithm : K2
K2 order : visit_to_Asia, tuberculosis, tuberculos_or_cancer, positive_XraY, lung_cancer, smoking, bronchitis, dyspnoea
Score : BDeu
Prior : -
Learned in 6.264ms
G tuberculos_or_cancer tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea smoking smoking bronchitis bronchitis smoking->bronchitis lung_cancer lung_cancer smoking->lung_cancer tuberculosis tuberculosis tuberculosis->tuberculos_or_cancer bronchitis->dyspnoea lung_cancer->tuberculos_or_cancer visit_to_Asia visit_to_Asia visit_to_Asia->tuberculosis
Original BN
G tuberculos_or_cancer tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY lung_cancer lung_cancer tuberculos_or_cancer->lung_cancer dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea smoking smoking bronchitis bronchitis smoking->bronchitis tuberculosis tuberculosis tuberculosis->tuberculos_or_cancer tuberculosis->lung_cancer bronchitis->dyspnoea lung_cancer->smoking visit_to_Asia visit_to_Asia visit_to_Asia->tuberculosis
Learned BN
G visit_to_Asia visit_to_Asia tuberculosis tuberculosis visit_to_Asia->tuberculosis tuberculos_or_cancer tuberculos_or_cancer tuberculosis->tuberculos_or_cancer lung_cancer lung_cancer tuberculosis->lung_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY tuberculos_or_cancer->lung_cancer dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea smoking smoking lung_cancer->smoking bronchitis bronchitis smoking->bronchitis bronchitis->dyspnoea
Graphical diff
G tuberculos_or_cancer tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY lung_cancer lung_cancer tuberculos_or_cancer->lung_cancer dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea smoking smoking bronchitis bronchitis smoking->bronchitis tuberculosis tuberculosis tuberculosis->tuberculos_or_cancer tuberculosis->lung_cancer bronchitis->dyspnoea lung_cancer->smoking visit_to_Asia visit_to_Asia visit_to_Asia->tuberculosis
PyAgrum inline image

information

K2 can be very good if the order is the good one (a topological order of nodes in the reference)

learner = gum.BNLearner("out/sample_asia.csv", bn) # using bn as template for variables
learner.useK2([7, 6, 5, 4, 3, 2, 1, 0])
print(learner)
bn2 = learner.learnBN()
print("Learned in {0}s".format(learner.currentTime()))
gnb.sideBySide(
bn,
bn2,
gnb.getBNDiff(bn, bn2),
explain.getInformation(bn2),
captions=["Original BN", "Learned BN", "Graphical diff", "information"],
)
Filename : out/sample_asia.csv
Size : (50000,8)
Variables : visit_to_Asia[2], tuberculosis[2], tuberculos_or_cancer[2], positive_XraY[2], lung_cancer[2], smoking[2], bronchitis[2], dyspnoea[2]
Induced types : False
Missing values : False
Algorithm : K2
K2 order : dyspnoea, bronchitis, smoking, lung_cancer, positive_XraY, tuberculos_or_cancer, tuberculosis, visit_to_Asia
Score : BDeu
Prior : -
Learned in 0.007757s
G tuberculos_or_cancer tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea smoking smoking bronchitis bronchitis smoking->bronchitis lung_cancer lung_cancer smoking->lung_cancer tuberculosis tuberculosis tuberculosis->tuberculos_or_cancer bronchitis->dyspnoea lung_cancer->tuberculos_or_cancer visit_to_Asia visit_to_Asia visit_to_Asia->tuberculosis
Original BN
G tuberculos_or_cancer tuberculos_or_cancer tuberculosis tuberculosis tuberculos_or_cancer->tuberculosis smoking smoking lung_cancer lung_cancer smoking->lung_cancer visit_to_Asia visit_to_Asia tuberculosis->visit_to_Asia positive_XraY positive_XraY positive_XraY->tuberculos_or_cancer bronchitis bronchitis bronchitis->tuberculos_or_cancer bronchitis->smoking bronchitis->positive_XraY bronchitis->lung_cancer lung_cancer->tuberculos_or_cancer lung_cancer->tuberculosis lung_cancer->positive_XraY dyspnoea dyspnoea dyspnoea->tuberculos_or_cancer dyspnoea->smoking dyspnoea->positive_XraY dyspnoea->bronchitis dyspnoea->lung_cancer
Learned BN
G visit_to_Asia visit_to_Asia tuberculosis tuberculosis tuberculosis->visit_to_Asia tuberculos_or_cancer tuberculos_or_cancer tuberculos_or_cancer->tuberculosis positive_XraY positive_XraY dyspnoea dyspnoea positive_XraY->tuberculos_or_cancer lung_cancer lung_cancer lung_cancer->tuberculosis lung_cancer->tuberculos_or_cancer lung_cancer->positive_XraY smoking smoking smoking->lung_cancer bronchitis bronchitis bronchitis->tuberculos_or_cancer bronchitis->positive_XraY bronchitis->lung_cancer bronchitis->smoking dyspnoea->tuberculos_or_cancer dyspnoea->positive_XraY dyspnoea->lung_cancer dyspnoea->smoking dyspnoea->bronchitis
Graphical diff
G tuberculos_or_cancer tuberculos_or_cancer tuberculosis tuberculosis tuberculos_or_cancer->tuberculosis smoking smoking lung_cancer lung_cancer smoking->lung_cancer visit_to_Asia visit_to_Asia tuberculosis->visit_to_Asia positive_XraY positive_XraY positive_XraY->tuberculos_or_cancer bronchitis bronchitis bronchitis->tuberculos_or_cancer bronchitis->smoking bronchitis->positive_XraY bronchitis->lung_cancer lung_cancer->tuberculos_or_cancer lung_cancer->tuberculosis lung_cancer->positive_XraY dyspnoea dyspnoea dyspnoea->tuberculos_or_cancer dyspnoea->smoking dyspnoea->positive_XraY dyspnoea->bronchitis dyspnoea->lung_cancer
PyAgrum inline image

information
import numpy as np
%matplotlib inline
learner = gum.BNLearner("out/sample_asia.csv", bn) # using bn as template for variables
learner.useLocalSearchWithTabuList()
## we could prefere a log2likelihood score
## learner.useScoreLog2Likelihood()
learner.setMaxTime(10)
## representation of the error as a pseudo log (negative values really represents negative epsilon
@np.vectorize
def pseudolog(x):
res = np.log(x) # np.log(y)
return res if x > 0 else -res
## in order to control the complexity, we limit the number of parents
learner.setMaxIndegree(7) # no more than 3 parent by node
learner.setEpsilon(1e-10)
gnb.animApproximationScheme(learner, scale=pseudolog) # scale by default is np.log10
bn2 = learner.learnBN()

svg

learner = gum.BNLearner("out/sample_asia.csv", bn) # using bn as template for variables
learner.useGreedyHillClimbing()
learner.setMaxIndegree(1) # no more than 1 parent by node
print(learner)
bntree = learner.learnBN()
gnb.sideBySide(
bn,
bntree,
gnb.getBNDiff(bn, bntree),
explain.getInformation(bntree),
captions=["Original BN", "Learned BN", "Graphical diff", "information"],
)
Filename : out/sample_asia.csv
Size : (50000,8)
Variables : visit_to_Asia[2], tuberculosis[2], tuberculos_or_cancer[2], positive_XraY[2], lung_cancer[2], smoking[2], bronchitis[2], dyspnoea[2]
Induced types : False
Missing values : False
Algorithm : Greedy Hill Climbing
Score : BDeu
Prior : -
Constraint Max InDegree : 1
G tuberculos_or_cancer tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea smoking smoking bronchitis bronchitis smoking->bronchitis lung_cancer lung_cancer smoking->lung_cancer tuberculosis tuberculosis tuberculosis->tuberculos_or_cancer bronchitis->dyspnoea lung_cancer->tuberculos_or_cancer visit_to_Asia visit_to_Asia visit_to_Asia->tuberculosis
Original BN
G tuberculos_or_cancer tuberculos_or_cancer tuberculosis tuberculosis tuberculos_or_cancer->tuberculosis positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY smoking smoking visit_to_Asia visit_to_Asia tuberculosis->visit_to_Asia bronchitis bronchitis bronchitis->smoking lung_cancer lung_cancer bronchitis->lung_cancer dyspnoea dyspnoea bronchitis->dyspnoea lung_cancer->tuberculos_or_cancer
Learned BN
G visit_to_Asia visit_to_Asia tuberculosis tuberculosis tuberculosis->visit_to_Asia tuberculos_or_cancer tuberculos_or_cancer tuberculos_or_cancer->tuberculosis positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea lung_cancer lung_cancer lung_cancer->tuberculos_or_cancer smoking smoking smoking->lung_cancer bronchitis bronchitis bronchitis->lung_cancer bronchitis->smoking bronchitis->dyspnoea
Graphical diff
G tuberculos_or_cancer tuberculos_or_cancer tuberculosis tuberculosis tuberculos_or_cancer->tuberculosis positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY smoking smoking visit_to_Asia visit_to_Asia tuberculosis->visit_to_Asia bronchitis bronchitis bronchitis->smoking lung_cancer lung_cancer bronchitis->lung_cancer dyspnoea dyspnoea bronchitis->dyspnoea lung_cancer->tuberculos_or_cancer
PyAgrum inline image

information
learner = gum.BNLearner("out/sample_asia.csv", bn) # using bn as template for variables
learner.useGreedyHillClimbing()
## I know that smoking causes cancer
learner.addMandatoryArc("smoking", "lung_cancer") # smoking->lung_cancer
## I know that visit to Asia may change the risk of tuberculosis
learner.addMandatoryArc("visit_to_Asia", "tuberculosis") # visit_to_Asia->tuberculosis
print(learner)
bn2 = learner.learnBN()
gnb.sideBySide(
bn,
bn2,
gnb.getBNDiff(bn, bn2),
explain.getInformation(bn2),
captions=["Original BN", "Learned BN", "Graphical diff", "information"],
)
Filename : out/sample_asia.csv
Size : (50000,8)
Variables : visit_to_Asia[2], tuberculosis[2], tuberculos_or_cancer[2], positive_XraY[2], lung_cancer[2], smoking[2], bronchitis[2], dyspnoea[2]
Induced types : False
Missing values : False
Algorithm : Greedy Hill Climbing
Score : BDeu
Prior : -
Constraint Mandatory Arcs : {visit_to_Asia->tuberculosis, smoking->lung_cancer}
G tuberculos_or_cancer tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea smoking smoking bronchitis bronchitis smoking->bronchitis lung_cancer lung_cancer smoking->lung_cancer tuberculosis tuberculosis tuberculosis->tuberculos_or_cancer bronchitis->dyspnoea lung_cancer->tuberculos_or_cancer visit_to_Asia visit_to_Asia visit_to_Asia->tuberculosis
Original BN
G tuberculos_or_cancer tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY smoking smoking lung_cancer lung_cancer smoking->lung_cancer tuberculosis tuberculosis tuberculosis->tuberculos_or_cancer dyspnoea dyspnoea tuberculosis->dyspnoea bronchitis bronchitis bronchitis->smoking bronchitis->lung_cancer bronchitis->dyspnoea lung_cancer->tuberculos_or_cancer visit_to_Asia visit_to_Asia visit_to_Asia->tuberculosis dyspnoea->smoking dyspnoea->lung_cancer
Learned BN
G visit_to_Asia visit_to_Asia tuberculosis tuberculosis visit_to_Asia->tuberculosis tuberculos_or_cancer tuberculos_or_cancer tuberculosis->tuberculos_or_cancer dyspnoea dyspnoea tuberculosis->dyspnoea positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY tuberculos_or_cancer->dyspnoea lung_cancer lung_cancer lung_cancer->tuberculos_or_cancer smoking smoking smoking->lung_cancer bronchitis bronchitis bronchitis->lung_cancer bronchitis->smoking bronchitis->dyspnoea dyspnoea->lung_cancer dyspnoea->smoking
Graphical diff
G tuberculos_or_cancer tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY smoking smoking lung_cancer lung_cancer smoking->lung_cancer tuberculosis tuberculosis tuberculosis->tuberculos_or_cancer dyspnoea dyspnoea tuberculosis->dyspnoea bronchitis bronchitis bronchitis->smoking bronchitis->lung_cancer bronchitis->dyspnoea lung_cancer->tuberculos_or_cancer visit_to_Asia visit_to_Asia visit_to_Asia->tuberculosis dyspnoea->smoking dyspnoea->lung_cancer
PyAgrum inline image

information

By default, a BDEU score is used. But it can be changed.

learner = gum.BNLearner("out/sample_asia.csv", bn) # using bn as template for variables
learner.useGreedyHillClimbing()
## I know that smoking causes cancer
learner.addMandatoryArc(0, 1)
## we prefere a log2likelihood score
learner.useScoreLog2Likelihood()
## in order to control the complexity, we limit the number of parents
learner.setMaxIndegree(1) # no more than 1 parent by node
print(learner)
bn2 = learner.learnBN()
kl = gum.ExactBNdistance(bn, bn2)
gnb.sideBySide(
bn,
bn2,
gnb.getBNDiff(bn, bn2),
"<br/>".join(["<b>" + k + "</b> :" + str(v) for k, v in kl.compute().items()]),
captions=["original", "learned BN", "diff", "distances"],
)
Filename : out/sample_asia.csv
Size : (50000,8)
Variables : visit_to_Asia[2], tuberculosis[2], tuberculos_or_cancer[2], positive_XraY[2], lung_cancer[2], smoking[2], bronchitis[2], dyspnoea[2]
Induced types : False
Missing values : False
Algorithm : Greedy Hill Climbing
Score : Log2Likelihood
Prior : -
Constraint Max InDegree : 1
Constraint Mandatory Arcs : {visit_to_Asia->tuberculosis}
G tuberculos_or_cancer tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea smoking smoking bronchitis bronchitis smoking->bronchitis lung_cancer lung_cancer smoking->lung_cancer tuberculosis tuberculosis tuberculosis->tuberculos_or_cancer bronchitis->dyspnoea lung_cancer->tuberculos_or_cancer visit_to_Asia visit_to_Asia visit_to_Asia->tuberculosis
original
G tuberculos_or_cancer tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY lung_cancer lung_cancer tuberculos_or_cancer->lung_cancer visit_to_Asia visit_to_Asia tuberculos_or_cancer->visit_to_Asia dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea smoking smoking tuberculosis tuberculosis bronchitis bronchitis bronchitis->smoking visit_to_Asia->tuberculosis dyspnoea->bronchitis
learned BN
G visit_to_Asia visit_to_Asia tuberculosis tuberculosis visit_to_Asia->tuberculosis tuberculos_or_cancer tuberculos_or_cancer tuberculosis->tuberculos_or_cancer tuberculos_or_cancer->visit_to_Asia positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY lung_cancer lung_cancer tuberculos_or_cancer->lung_cancer dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea smoking smoking smoking->lung_cancer bronchitis bronchitis bronchitis->smoking dyspnoea->bronchitis
diff
klPQ :0.122659583144537
errorPQ :0
klQP :0.035362312624309146
errorQP :64
hellinger :0.2008652891479617
bhattacharya :0.020379688845562502
jensen-shannon :0.0233148500701501
distances

There are multiple ways to compare Bayes net…

help(gnb.getBNDiff)
Help on function getBNDiff in module pyagrum.lib.notebook:
getBNDiff(bn1, bn2, size=None, noStyle=False)
get a HTML string representation of a graphical diff between the arcs of _bn1 (reference) with those of _bn2.
if `noStyle` is False use 4 styles (fixed in pyagrum.config) :
- the arc is common for both
- the arc is common but inverted in `bn2`
- the arc is added in `bn2`
- the arc is removed in `bn2`
Parameters
----------
bn1: pyagrum.BayesNet
the reference
bn2: pyagrum.BayesNet
the compared one
size: float|str
size (for graphviz) of the rendered graph
noStyle: bool
with style or not.
Returns
-------
str
the HTML representation of the comparison
gnb.showBNDiff(bn, bn2)

svg

import pyagrum.lib.bn_vs_bn as gbnbn
help(gbnbn.graphDiff)
Help on function graphDiff in module pyagrum.lib.bn_vs_bn:
graphDiff(bnref, bncmp, noStyle=False)
Return a pydot graph that compares the arcs of bnref to bncmp.
graphDiff allows bncmp to have less nodes than bnref. (this is not the case in GraphicalBNComparator.dotDiff())
if noStyle is False use 4 styles (fixed in pyagrum.config) :
- the arc is common for both
- the arc is common but inverted in _bn2
- the arc is added in _bn2
- the arc is removed in _bn2
See graphDiffLegend() to add a legend to the graph.
Warning
-------
if pydot is not installed, this function just returns None
Returns
-------
pydot.Dot
the result dot graph or None if pydot can not be imported
gbnbn.GraphicalBNComparator?
gcmp = gbnbn.GraphicalBNComparator(bn, bn2)
gnb.sideBySide(
bn, bn2, gcmp.dotDiff(), gbnbn.graphDiffLegend(), bn2, bn, gbnbn.graphDiff(bn2, bn), gbnbn.graphDiffLegend(), ncols=4
)
G tuberculos_or_cancer tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea smoking smoking bronchitis bronchitis smoking->bronchitis lung_cancer lung_cancer smoking->lung_cancer tuberculosis tuberculosis tuberculosis->tuberculos_or_cancer bronchitis->dyspnoea lung_cancer->tuberculos_or_cancer visit_to_Asia visit_to_Asia visit_to_Asia->tuberculosis
G tuberculos_or_cancer tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY lung_cancer lung_cancer tuberculos_or_cancer->lung_cancer visit_to_Asia visit_to_Asia tuberculos_or_cancer->visit_to_Asia dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea smoking smoking tuberculosis tuberculosis bronchitis bronchitis bronchitis->smoking visit_to_Asia->tuberculosis dyspnoea->bronchitis
G visit_to_Asia visit_to_Asia tuberculosis tuberculosis visit_to_Asia->tuberculosis tuberculos_or_cancer tuberculos_or_cancer tuberculosis->tuberculos_or_cancer tuberculos_or_cancer->visit_to_Asia positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY lung_cancer lung_cancer tuberculos_or_cancer->lung_cancer dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea smoking smoking smoking->lung_cancer bronchitis bronchitis bronchitis->smoking dyspnoea->bronchitis
G a->b overflow c->d Missing e->f reversed g->h Correct
G tuberculos_or_cancer tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY lung_cancer lung_cancer tuberculos_or_cancer->lung_cancer visit_to_Asia visit_to_Asia tuberculos_or_cancer->visit_to_Asia dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea smoking smoking tuberculosis tuberculosis bronchitis bronchitis bronchitis->smoking visit_to_Asia->tuberculosis dyspnoea->bronchitis
G tuberculos_or_cancer tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea smoking smoking bronchitis bronchitis smoking->bronchitis lung_cancer lung_cancer smoking->lung_cancer tuberculosis tuberculosis tuberculosis->tuberculos_or_cancer bronchitis->dyspnoea lung_cancer->tuberculos_or_cancer visit_to_Asia visit_to_Asia visit_to_Asia->tuberculosis
G visit_to_Asia visit_to_Asia tuberculosis tuberculosis visit_to_Asia->tuberculosis tuberculos_or_cancer tuberculos_or_cancer tuberculosis->tuberculos_or_cancer tuberculos_or_cancer->visit_to_Asia positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY lung_cancer lung_cancer dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea lung_cancer->tuberculos_or_cancer smoking smoking smoking->lung_cancer bronchitis bronchitis smoking->bronchitis bronchitis->dyspnoea
G a->b overflow c->d Missing e->f reversed g->h Correct
print("But also gives access to different scores :")
print(gcmp.scores())
print(gcmp.skeletonScores())
print(gcmp.hamming())
But also gives access to different scores :
{'count': {'tp': 3, 'tn': 44, 'fp': 4, 'fn': 5}, 'recall': 0.375, 'precision': 0.42857142857142855, 'fscore': 0.39999999999999997, 'dist2opt': 0.8468504072413839}
{'count': {'tp': 6, 'tn': 19, 'fp': 1, 'fn': 2}, 'recall': 0.75, 'precision': 0.8571428571428571, 'fscore': 0.7999999999999999, 'dist2opt': 0.2879377767249482}
{'hamming': 3, 'structural hamming': 7}
print("KL divergence can be computed")
kl = gum.ExactBNdistance(bn, bn2)
kl.compute()
KL divergence can be computed
{'klPQ': 0.122659583144537,
'errorPQ': 0,
'klQP': 0.035362312624309146,
'errorQP': 64,
'hellinger': 0.2008652891479617,
'bhattacharya': 0.020379688845562502,
'jensen-shannon': 0.0233148500701501}

First we learn a structure with HillClimbing (faster ?)

learner = gum.BNLearner("out/sample_asia.csv", bn) # using bn as template for variables
learner.useGreedyHillClimbing()
learner.addMandatoryArc(0, 1)
bn2 = learner.learnBN()
kl = gum.ExactBNdistance(bn, bn2)
gnb.sideBySide(
bn,
bn2,
gnb.getBNDiff(bn, bn2),
"<br/>".join(["<b>" + k + "</b> :" + str(v) for k, v in kl.compute().items()]),
captions=["original", "learned BN", "diff", "distances"],
)
G tuberculos_or_cancer tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea smoking smoking bronchitis bronchitis smoking->bronchitis lung_cancer lung_cancer smoking->lung_cancer tuberculosis tuberculosis tuberculosis->tuberculos_or_cancer bronchitis->dyspnoea lung_cancer->tuberculos_or_cancer visit_to_Asia visit_to_Asia visit_to_Asia->tuberculosis
original
G tuberculos_or_cancer tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea smoking smoking tuberculosis tuberculosis tuberculosis->tuberculos_or_cancer bronchitis bronchitis bronchitis->smoking lung_cancer lung_cancer bronchitis->lung_cancer bronchitis->dyspnoea lung_cancer->tuberculos_or_cancer lung_cancer->smoking visit_to_Asia visit_to_Asia visit_to_Asia->tuberculosis
learned BN
G visit_to_Asia visit_to_Asia tuberculosis tuberculosis visit_to_Asia->tuberculosis tuberculos_or_cancer tuberculos_or_cancer tuberculosis->tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea lung_cancer lung_cancer lung_cancer->tuberculos_or_cancer smoking smoking lung_cancer->smoking bronchitis bronchitis bronchitis->lung_cancer bronchitis->smoking bronchitis->dyspnoea
diff
klPQ :0.00024105451496356508
errorPQ :0
klQP :0.00021087593292772806
errorQP :128
hellinger :0.009400672333381922
bhattacharya :4.4181654289395046e-05
jensen-shannon :6.150358231389019e-05
distances

And then we refine with tabuList

learner = gum.BNLearner("out/sample_asia.csv", bn) # using bn as template for variables
learner.useLocalSearchWithTabuList()
learner.setInitialDAG(bn2.dag())
print(learner)
bn3 = learner.learnBN()
kl = gum.ExactBNdistance(bn, bn3)
gnb.sideBySide(
bn,
bn2,
gnb.getBNDiff(bn, bn2),
"<br/>".join(["<b>" + k + "</b> :" + str(v) for k, v in kl.compute().items()]),
captions=["original", "learned BN", "diff", "distances"],
)
Filename : out/sample_asia.csv
Size : (50000,8)
Variables : visit_to_Asia[2], tuberculosis[2], tuberculos_or_cancer[2], positive_XraY[2], lung_cancer[2], smoking[2], bronchitis[2], dyspnoea[2]
Induced types : False
Missing values : False
Algorithm : Local Search with Tabu List
Tabu list size : 2
Score : BDeu
Prior : -
Initial DAG : True (digraph {
0;
1;
2;
3;
4;
5;
6;
7;
0 -> 1;
6 -> 7;
2 -> 3;
6 -> 5;
2 -> 7;
4 -> 5;
4 -> 2;
1 -> 2;
6 -> 4;
}
)
G tuberculos_or_cancer tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea smoking smoking bronchitis bronchitis smoking->bronchitis lung_cancer lung_cancer smoking->lung_cancer tuberculosis tuberculosis tuberculosis->tuberculos_or_cancer bronchitis->dyspnoea lung_cancer->tuberculos_or_cancer visit_to_Asia visit_to_Asia visit_to_Asia->tuberculosis
original
G tuberculos_or_cancer tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea smoking smoking tuberculosis tuberculosis tuberculosis->tuberculos_or_cancer bronchitis bronchitis bronchitis->smoking lung_cancer lung_cancer bronchitis->lung_cancer bronchitis->dyspnoea lung_cancer->tuberculos_or_cancer lung_cancer->smoking visit_to_Asia visit_to_Asia visit_to_Asia->tuberculosis
learned BN
G visit_to_Asia visit_to_Asia tuberculosis tuberculosis visit_to_Asia->tuberculosis tuberculos_or_cancer tuberculos_or_cancer tuberculosis->tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea lung_cancer lung_cancer lung_cancer->tuberculos_or_cancer smoking smoking lung_cancer->smoking bronchitis bronchitis bronchitis->lung_cancer bronchitis->smoking bronchitis->dyspnoea
diff
klPQ :0.00024105451496356508
errorPQ :0
klQP :0.00021087593292772806
errorQP :128
hellinger :0.009400672333381922
bhattacharya :4.4181654289395046e-05
jensen-shannon :6.150358231389019e-05
distances

Impact of the size of the database for the learning

Section titled “Impact of the size of the database for the learning”
rows = 3
sizes = [400, 500, 700, 1000, 2000, 5000, 10000, 50000, 75000, 100000, 150000, 175000, 200000, 300000, 500000]
def extract_asia(n):
"""
extract n line from asia.csv to extract.csv
"""
with open("out/sample_asia.csv", "r") as src:
with open("out/extract_asia.csv", "w") as dst:
for _ in range(n + 1):
print(src.readline(), end="", file=dst)
gnb.flow.clear()
nbr = 0
l = []
for i in sizes:
extract_asia(i)
learner = gum.BNLearner("out/extract_asia.csv", bn) # using bn as template for variables
learner.useGreedyHillClimbing()
print(learner.state()["Size"][0])
bn2 = learner.learnBN()
kl = gum.ExactBNdistance(bn, bn2)
r = kl.compute()
l.append(math.log(r["klPQ"]))
gnb.flow.add(gnb.getBNDiff(bn, bn2, size="3!"), f"size={i}")
gnb.flow.display()
plt.plot(sizes, l)
print(f"final value computed : {l[-1]}")
(400,8)
(500,8)
(700,8)
(1000,8)
(2000,8)
(5000,8)
(10000,8)
(50000,8)
(50000,8)
(50000,8)
(50000,8)
(50000,8)
(50000,8)
(50000,8)
(50000,8)
G visit_to_Asia visit_to_Asia tuberculosis tuberculosis visit_to_Asia->tuberculosis tuberculos_or_cancer tuberculos_or_cancer tuberculosis->tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY smoking smoking tuberculos_or_cancer->smoking dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea lung_cancer lung_cancer lung_cancer->tuberculos_or_cancer lung_cancer->dyspnoea smoking->lung_cancer bronchitis bronchitis bronchitis->smoking dyspnoea->bronchitis
size=400
G visit_to_Asia visit_to_Asia tuberculosis tuberculosis visit_to_Asia->tuberculosis tuberculos_or_cancer tuberculos_or_cancer tuberculosis->tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY smoking smoking tuberculos_or_cancer->smoking dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea lung_cancer lung_cancer lung_cancer->tuberculos_or_cancer smoking->visit_to_Asia smoking->lung_cancer bronchitis bronchitis bronchitis->smoking dyspnoea->bronchitis
size=500
G visit_to_Asia visit_to_Asia tuberculosis tuberculosis visit_to_Asia->tuberculosis tuberculos_or_cancer tuberculos_or_cancer tuberculosis->tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea lung_cancer lung_cancer lung_cancer->tuberculos_or_cancer smoking smoking lung_cancer->smoking bronchitis bronchitis smoking->bronchitis bronchitis->tuberculos_or_cancer bronchitis->dyspnoea
size=700
G visit_to_Asia visit_to_Asia tuberculosis tuberculosis visit_to_Asia->tuberculosis tuberculos_or_cancer tuberculos_or_cancer tuberculosis->tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea lung_cancer lung_cancer lung_cancer->tuberculos_or_cancer smoking smoking lung_cancer->smoking bronchitis bronchitis bronchitis->smoking dyspnoea->bronchitis
size=1000
G visit_to_Asia visit_to_Asia tuberculosis tuberculosis visit_to_Asia->tuberculosis positive_XraY positive_XraY visit_to_Asia->positive_XraY tuberculos_or_cancer tuberculos_or_cancer tuberculos_or_cancer->tuberculosis tuberculos_or_cancer->positive_XraY lung_cancer lung_cancer tuberculos_or_cancer->lung_cancer bronchitis bronchitis tuberculos_or_cancer->bronchitis dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea lung_cancer->tuberculosis smoking smoking lung_cancer->smoking smoking->bronchitis bronchitis->dyspnoea
size=2000
G visit_to_Asia visit_to_Asia tuberculosis tuberculosis visit_to_Asia->tuberculosis positive_XraY positive_XraY visit_to_Asia->positive_XraY tuberculos_or_cancer tuberculos_or_cancer tuberculosis->tuberculos_or_cancer tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea lung_cancer lung_cancer lung_cancer->tuberculos_or_cancer smoking smoking lung_cancer->smoking bronchitis bronchitis lung_cancer->bronchitis bronchitis->smoking dyspnoea->bronchitis
size=5000
G visit_to_Asia visit_to_Asia tuberculosis tuberculosis tuberculosis->visit_to_Asia tuberculos_or_cancer tuberculos_or_cancer tuberculosis->tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea lung_cancer lung_cancer lung_cancer->tuberculos_or_cancer smoking smoking smoking->lung_cancer bronchitis bronchitis bronchitis->lung_cancer bronchitis->smoking bronchitis->dyspnoea
size=10000
G visit_to_Asia visit_to_Asia tuberculosis tuberculosis tuberculosis->visit_to_Asia tuberculos_or_cancer tuberculos_or_cancer tuberculosis->tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea lung_cancer lung_cancer lung_cancer->tuberculos_or_cancer smoking smoking lung_cancer->smoking bronchitis bronchitis bronchitis->lung_cancer bronchitis->smoking bronchitis->dyspnoea
size=50000
G visit_to_Asia visit_to_Asia tuberculosis tuberculosis tuberculosis->visit_to_Asia tuberculos_or_cancer tuberculos_or_cancer tuberculosis->tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea lung_cancer lung_cancer lung_cancer->tuberculos_or_cancer smoking smoking lung_cancer->smoking bronchitis bronchitis bronchitis->lung_cancer bronchitis->smoking bronchitis->dyspnoea
size=75000
G visit_to_Asia visit_to_Asia tuberculosis tuberculosis tuberculosis->visit_to_Asia tuberculos_or_cancer tuberculos_or_cancer tuberculosis->tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea lung_cancer lung_cancer lung_cancer->tuberculos_or_cancer smoking smoking lung_cancer->smoking bronchitis bronchitis bronchitis->lung_cancer bronchitis->smoking bronchitis->dyspnoea
size=100000
G visit_to_Asia visit_to_Asia tuberculosis tuberculosis tuberculosis->visit_to_Asia tuberculos_or_cancer tuberculos_or_cancer tuberculosis->tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea lung_cancer lung_cancer lung_cancer->tuberculos_or_cancer smoking smoking lung_cancer->smoking bronchitis bronchitis bronchitis->lung_cancer bronchitis->smoking bronchitis->dyspnoea
size=150000
G visit_to_Asia visit_to_Asia tuberculosis tuberculosis tuberculosis->visit_to_Asia tuberculos_or_cancer tuberculos_or_cancer tuberculosis->tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea lung_cancer lung_cancer lung_cancer->tuberculos_or_cancer smoking smoking lung_cancer->smoking bronchitis bronchitis bronchitis->lung_cancer bronchitis->smoking bronchitis->dyspnoea
size=175000
G visit_to_Asia visit_to_Asia tuberculosis tuberculosis tuberculosis->visit_to_Asia tuberculos_or_cancer tuberculos_or_cancer tuberculosis->tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea lung_cancer lung_cancer lung_cancer->tuberculos_or_cancer smoking smoking lung_cancer->smoking bronchitis bronchitis bronchitis->lung_cancer bronchitis->smoking bronchitis->dyspnoea
size=200000
G visit_to_Asia visit_to_Asia tuberculosis tuberculosis tuberculosis->visit_to_Asia tuberculos_or_cancer tuberculos_or_cancer tuberculosis->tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea lung_cancer lung_cancer lung_cancer->tuberculos_or_cancer smoking smoking lung_cancer->smoking bronchitis bronchitis bronchitis->lung_cancer bronchitis->smoking bronchitis->dyspnoea
size=300000
G visit_to_Asia visit_to_Asia tuberculosis tuberculosis tuberculosis->visit_to_Asia tuberculos_or_cancer tuberculos_or_cancer tuberculosis->tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea lung_cancer lung_cancer lung_cancer->tuberculos_or_cancer smoking smoking lung_cancer->smoking bronchitis bronchitis bronchitis->lung_cancer bronchitis->smoking bronchitis->dyspnoea
size=500000
final value computed : -8.33048744688638

svg

gnb.flow.clear()
nbr = 0
l = []
for i in sizes:
extract_asia(i)
learner = gum.BNLearner("out/extract_asia.csv", bn) # using bn as template for variables
learner.useMIIC()
print(learner.state()["Size"][0])
bn2 = learner.learnBN()
kl = gum.ExactBNdistance(bn, bn2)
r = kl.compute()
l.append(math.log(r["klPQ"]))
gnb.flow.add(gnb.getBNDiff(bn, bn2, size="3!"), f"size={i}")
gnb.flow.display()
plt.plot(sizes, l)
print(l[-1])
(400,8)
(500,8)
(700,8)
(1000,8)
(2000,8)
(5000,8)
(10000,8)
(50000,8)
(50000,8)
(50000,8)
(50000,8)
(50000,8)
(50000,8)
(50000,8)
(50000,8)
G visit_to_Asia visit_to_Asia tuberculosis tuberculosis visit_to_Asia->tuberculosis tuberculos_or_cancer tuberculos_or_cancer tuberculosis->tuberculos_or_cancer positive_XraY positive_XraY lung_cancer lung_cancer tuberculos_or_cancer->lung_cancer dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea positive_XraY->tuberculos_or_cancer lung_cancer->dyspnoea smoking smoking smoking->lung_cancer bronchitis bronchitis bronchitis->smoking dyspnoea->bronchitis
size=400
G visit_to_Asia visit_to_Asia tuberculosis tuberculosis visit_to_Asia->tuberculosis tuberculos_or_cancer tuberculos_or_cancer tuberculosis->tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea lung_cancer lung_cancer lung_cancer->tuberculos_or_cancer smoking smoking smoking->lung_cancer bronchitis bronchitis bronchitis->smoking dyspnoea->bronchitis
size=500
G visit_to_Asia visit_to_Asia tuberculosis tuberculosis visit_to_Asia->tuberculosis tuberculos_or_cancer tuberculos_or_cancer tuberculosis->tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea lung_cancer lung_cancer lung_cancer->tuberculos_or_cancer smoking smoking smoking->lung_cancer bronchitis bronchitis smoking->bronchitis bronchitis->dyspnoea
size=700
G visit_to_Asia visit_to_Asia tuberculosis tuberculosis visit_to_Asia->tuberculosis tuberculos_or_cancer tuberculos_or_cancer tuberculosis->tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea lung_cancer lung_cancer lung_cancer->tuberculos_or_cancer smoking smoking lung_cancer->smoking bronchitis bronchitis bronchitis->smoking dyspnoea->bronchitis
size=1000
G visit_to_Asia visit_to_Asia tuberculosis tuberculosis visit_to_Asia->tuberculosis tuberculos_or_cancer tuberculos_or_cancer tuberculosis->tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea lung_cancer lung_cancer lung_cancer->tuberculos_or_cancer smoking smoking smoking->lung_cancer bronchitis bronchitis bronchitis->smoking bronchitis->dyspnoea
size=2000
G visit_to_Asia visit_to_Asia tuberculosis tuberculosis visit_to_Asia->tuberculosis tuberculos_or_cancer tuberculos_or_cancer tuberculosis->tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea lung_cancer lung_cancer lung_cancer->tuberculos_or_cancer smoking smoking smoking->lung_cancer bronchitis bronchitis bronchitis->smoking bronchitis->dyspnoea
size=5000
G visit_to_Asia visit_to_Asia tuberculosis tuberculosis visit_to_Asia->tuberculosis tuberculos_or_cancer tuberculos_or_cancer tuberculosis->tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea lung_cancer lung_cancer lung_cancer->tuberculos_or_cancer smoking smoking smoking->lung_cancer bronchitis bronchitis bronchitis->smoking bronchitis->dyspnoea
size=10000
G visit_to_Asia visit_to_Asia tuberculosis tuberculosis visit_to_Asia->tuberculosis tuberculos_or_cancer tuberculos_or_cancer tuberculosis->tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea lung_cancer lung_cancer lung_cancer->tuberculos_or_cancer smoking smoking smoking->lung_cancer bronchitis bronchitis bronchitis->smoking bronchitis->dyspnoea
size=50000
G visit_to_Asia visit_to_Asia tuberculosis tuberculosis visit_to_Asia->tuberculosis tuberculos_or_cancer tuberculos_or_cancer tuberculosis->tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea lung_cancer lung_cancer lung_cancer->tuberculos_or_cancer smoking smoking smoking->lung_cancer bronchitis bronchitis bronchitis->smoking bronchitis->dyspnoea
size=75000
G visit_to_Asia visit_to_Asia tuberculosis tuberculosis visit_to_Asia->tuberculosis tuberculos_or_cancer tuberculos_or_cancer tuberculosis->tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea lung_cancer lung_cancer lung_cancer->tuberculos_or_cancer smoking smoking smoking->lung_cancer bronchitis bronchitis bronchitis->smoking bronchitis->dyspnoea
size=100000
G visit_to_Asia visit_to_Asia tuberculosis tuberculosis visit_to_Asia->tuberculosis tuberculos_or_cancer tuberculos_or_cancer tuberculosis->tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea lung_cancer lung_cancer lung_cancer->tuberculos_or_cancer smoking smoking smoking->lung_cancer bronchitis bronchitis bronchitis->smoking bronchitis->dyspnoea
size=150000
G visit_to_Asia visit_to_Asia tuberculosis tuberculosis visit_to_Asia->tuberculosis tuberculos_or_cancer tuberculos_or_cancer tuberculosis->tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea lung_cancer lung_cancer lung_cancer->tuberculos_or_cancer smoking smoking smoking->lung_cancer bronchitis bronchitis bronchitis->smoking bronchitis->dyspnoea
size=175000
G visit_to_Asia visit_to_Asia tuberculosis tuberculosis visit_to_Asia->tuberculosis tuberculos_or_cancer tuberculos_or_cancer tuberculosis->tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea lung_cancer lung_cancer lung_cancer->tuberculos_or_cancer smoking smoking smoking->lung_cancer bronchitis bronchitis bronchitis->smoking bronchitis->dyspnoea
size=200000
G visit_to_Asia visit_to_Asia tuberculosis tuberculosis visit_to_Asia->tuberculosis tuberculos_or_cancer tuberculos_or_cancer tuberculosis->tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea lung_cancer lung_cancer lung_cancer->tuberculos_or_cancer smoking smoking smoking->lung_cancer bronchitis bronchitis bronchitis->smoking bronchitis->dyspnoea
size=300000
G visit_to_Asia visit_to_Asia tuberculosis tuberculosis visit_to_Asia->tuberculosis tuberculos_or_cancer tuberculos_or_cancer tuberculosis->tuberculos_or_cancer positive_XraY positive_XraY tuberculos_or_cancer->positive_XraY dyspnoea dyspnoea tuberculos_or_cancer->dyspnoea lung_cancer lung_cancer lung_cancer->tuberculos_or_cancer smoking smoking smoking->lung_cancer bronchitis bronchitis bronchitis->smoking bronchitis->dyspnoea
size=500000
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