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# Copyright 2000 by Jeffrey Chang. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""This provides code for a general Naive Bayes learner.
Naive Bayes is a supervised classification algorithm that uses Bayes
rule to compute the fit between a new observation and some previously
observed data. The observations are discrete feature vectors, with
the Bayes assumption that the features are independent. Although this
is hardly ever true, the classifier works well enough in practice.
observation A feature vector of discrete data.
class A possible classification for an observation.
NaiveBayes Holds information for a naive Bayes classifier.
train Train a new naive Bayes classifier.
calculate Calculate the probabilities of each class, given an observation.
classify Classify an observation into a class.
import numpy
def _contents(items):
term = 1.0/len(items)
counts = {}
for item in items:
counts[item] = counts.get(item,0) + term
return counts
class NaiveBayes(object):
"""Holds information for a NaiveBayes classifier.
classes List of the possible classes of data.
p_conditional CLASS x DIM array of dicts of value -> P(value|class,dim)
p_prior List of the prior probabilities for every class.
dimensionality Dimensionality of the data.
def __init__(self):
self.classes = []
self.p_conditional = None
self.p_prior = []
self.dimensionality = None
def calculate(nb, observation, scale=0):
"""calculate(nb, observation[, scale]) -> probability dict
Calculate log P(class|observation) for each class. nb is a NaiveBayes
classifier that has been trained. observation is a list representing
the observed data. scale is whether the probability should be
scaled by P(observation). By default, no scaling is done. The return
value is a dictionary where the keys is the class and the value is the
log probability of the class.
# P(class|observation) = P(observation|class)*P(class)/P(observation)
# Taking the log:
# lP(class|observation) = lP(observation|class)+lP(class)-lP(observation)
# Make sure the observation has the right dimensionality.
if len(observation) != nb.dimensionality:
raise ValueError("observation in %d dimension, but classifier in %d" \
% (len(observation), nb.dimensionality))
# Calculate log P(observation|class) for every class.
n = len(nb.classes)
lp_observation_class = numpy.zeros(n) # array of log P(observation|class)
for i in range(n):
# log P(observation|class) = SUM_i log P(observation_i|class)
probs = [None] * len(observation)
for j in range(len(observation)):
probs[j] = nb.p_conditional[i][j].get(observation[j], 0)
lprobs = numpy.log(numpy.clip(probs, 1.e-300, 1.e+300))
lp_observation_class[i] = sum(lprobs)
# Calculate log P(class).
lp_prior = numpy.log(nb.p_prior)
# Calculate log P(observation).
lp_observation = 0.0 # P(observation)
if scale: # Only calculate this if requested.
# log P(observation) = log SUM_i P(observation|class_i)P(class_i)
obs = numpy.exp(numpy.clip(lp_prior+lp_observation_class,-700,+700))
lp_observation = numpy.log(sum(obs))
# Calculate log P(class|observation).
lp_class_observation = {} # Dict of class : log P(class|observation)
for i in range(len(nb.classes)):
lp_class_observation[nb.classes[i]] = \
lp_observation_class[i] + lp_prior[i] - lp_observation
return lp_class_observation
def classify(nb, observation):
"""classify(nb, observation) -> class
Classify an observation into a class.
# The class is the one with the highest probability.
probs = calculate(nb, observation, scale=0)
max_prob = max_class = None
for klass in nb.classes:
if max_prob is None or probs[klass] > max_prob:
max_prob, max_class = probs[klass], klass
return max_class
def train(training_set, results, priors=None, typecode=None):
"""train(training_set, results[, priors]) -> NaiveBayes
Train a naive bayes classifier on a training set. training_set is a
list of observations. results is a list of the class assignments
for each observation. Thus, training_set and results must be the same
length. priors is an optional dictionary specifying the prior
probabilities for each type of result. If not specified, the priors
will be estimated from the training results.
if not len(training_set):
raise ValueError("No data in the training set.")
if len(training_set) != len(results):
raise ValueError("training_set and results should be parallel lists.")
# If no typecode is specified, try to pick a reasonable one. If
# training_set is a Numeric array, then use that typecode.
# Otherwise, choose a reasonable default.
# Check to make sure each vector in the training set has the same
# dimensionality.
dimensions = [len(x) for x in training_set]
if min(dimensions) != max(dimensions):
raise ValueError("observations have different dimensionality")
nb = NaiveBayes()
nb.dimensionality = dimensions[0]
# Get a list of all the classes, and
# estimate the prior probabilities for the classes.
if priors is not None:
percs = priors
nb.classes = list(set(results))
class_freq = _contents(results)
nb.classes = class_freq.keys()
percs = class_freq
nb.classes.sort() # keep it tidy
nb.p_prior = numpy.zeros(len(nb.classes))
for i in range(len(nb.classes)):
nb.p_prior[i] = percs[nb.classes[i]]
# Collect all the observations in class. For each class, make a
# matrix of training instances versus dimensions. I might be able
# to optimize this with Numeric, if the training_set parameter
# were guaranteed to be a matrix. However, this may not be the
# case, because the client may be hacking up a sparse matrix or
# something.
c2i = {} # class to index of class
for index, key in enumerate(nb.classes):
c2i[key] = index
observations = [[] for c in nb.classes] # separate observations by class
for i in range(len(results)):
klass, obs = results[i], training_set[i]
# Now make the observations Numeric matrics.
for i in range(len(observations)):
# XXX typecode must be specified!
observations[i] = numpy.asarray(observations[i], typecode)
# Calculate P(value|class,dim) for every class.
# This is a good loop to optimize.
nb.p_conditional = []
for i in range(len(nb.classes)):
class_observations = observations[i] # observations for this class
nb.p_conditional.append([None] * nb.dimensionality)
for j in range(nb.dimensionality):
# Collect all the values in this dimension.
values = class_observations[:, j]
# Add pseudocounts here. This needs to be parameterized.
#values = list(values) + range(len(nb.classes)) # XXX add 1
# Estimate P(value|class,dim)
nb.p_conditional[i][j] = _contents(values)
return nb
if __name__ == "__main__":
# Car data from example 'Naive Bayes Classifier example' by Eric Meisner November 22, 2003
['Red', 'Sports', 'Domestic'],
['Red', 'Sports', 'Domestic'],
['Red', 'Sports', 'Domestic'],
['Yellow', 'Sports', 'Domestic'],
['Yellow', 'Sports', 'Imported'],
['Yellow', 'SUV', 'Imported'],
['Yellow', 'SUV', 'Imported'],
['Yellow', 'SUV', 'Domestic'],
['Red', 'SUV', 'Imported'],
['Red', 'Sports', 'Imported']
carmodel = train(xcar, ycar)
carresult = classify(carmodel, ['Red', 'Sports', 'Domestic'])
print 'Is Yes?', carresult
carresult = classify(carmodel, ['Red', 'SUV', 'Domestic'])
print 'Is No?', carresult
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