Again, it's the Iris dataset (I promise I will unleash some 'real' datasets at some point). I've done a lot of bivariate cluster plots, so I wanted to put together a 1d probability distribution based upon a custom query.
In this instance, it's purely plotting the joint probability distribution of each of the variables given the class, e.g. P(sepal_length|iris_class), P(petal_length|iris_class) ... and so on.
In [1]:
%matplotlib inline
import pandas as pd
import sys
sys.path.append("../../../bayesianpy")
import bayesianpy
from bayesianpy.network import Builder as builder
import logging
import os
import math
import numpy as np
import scipy.stats as ss
import matplotlib.pyplot as plt
import seaborn as sns
logger = logging.getLogger()
logger.addHandler(logging.StreamHandler())
logger.setLevel(logging.INFO)
bayesianpy.jni.attach(logger)
db_folder = bayesianpy.utils.get_path_to_parent_dir("")
iris = pd.read_csv(os.path.join(db_folder, "data/iris.csv"), index_col=False)
Create the network, specifying a latent variable.
In [2]:
network = bayesianpy.network.create_network()
cluster = builder.create_cluster_variable(network, 4)
node = builder.create_multivariate_continuous_node(network, iris.drop('iris_class',axis=1).columns.tolist(), "joint")
builder.create_link(network, cluster, node)
class_variable = builder.create_discrete_variable(network, iris, 'iris_class', iris['iris_class'].unique())
builder.create_link(network, cluster, class_variable)
And finally, query the model, specifying each variable in a separate query (otherwise the query will return a covariance matrix)
In [3]:
head_variables = ['sepal_length', 'sepal_width', 'petal_length', 'petal_width']
with bayesianpy.data.DataSet(iris, db_folder, logger) as dataset:
model = bayesianpy.model.NetworkModel(network, logger)
model.train(dataset)
queries = [bayesianpy.model.QueryConditionalJointProbability(
head_variables=[v],
tail_variables=['iris_class']) for v in head_variables]
(engine, _, _) = bayesianpy.model.InferenceEngine(network).create()
query = bayesianpy.model.SingleQuery(network, engine, logger)
results = query.query(queries)
jd = bayesianpy.visual.JointDistribution()
fig = plt.figure(figsize=(10,10))
for i, r in enumerate(list(results)):
ax = fig.add_subplot(2, 2, i+1)
jd.plot_distribution_with_variance(ax, iris, queries[i].get_head_variables(), r)
plt.show()