class MutualBootStrapper:
def __init__(self, data, seeds, patterns=None, processing=1):
if processing == 0:
tokenized = self.tokenize(data)
self.pos_tagged_data = self.pos_tag(tokenized)
self.find_patterns = self.find_patterns_tagged
self.find_seeds = self.find_seeds_tagged
elif processing == 1:
self.chunked_data = data
self.find_patterns = self.find_patterns_chunked
self.find_seeds = self.find_seeds_chunked
self.permanent_lexicon = set(seeds)
self.temporary_lexicon = defaultdict(set)
for s in seeds:
self.temporary_lexicon[s] = set()
self.best_extraction_patterns = set()
self.pattern_alphabet = Alphabet()
if patterns is not None:
for p in patterns:
self.pattern_alphabet.add(p)
self.n_counter_sets = None # import for getting candidate seeds
self.f_counter_sets = None
self.n_pattern_array = None
self.f_pattern_array = None
self.first_pattern_words = set()
def tokenize(self, text):
print "tokenizing...",
all_entries = []
for entry in text:
tokenized_entry = self._nested_tokenize(entry)
all_entries.append(tokenized_entry)
print "[DONE]"
return all_entries
def _nested_tokenize(self, untokenized_sentences):
tokenized_sents = nltk.sent_tokenize(untokenized_sentences)
tokenized_words = [nltk.word_tokenize(sent) for sent in tokenized_sents]
self._postprocess_tokenized_text(tokenized_words)
return tokenized_words
def _postprocess_tokenized_text(self, tokenized):
for i,sent in enumerate(tokenized):
for j,word in enumerate(sent):
tokenized[i][j] = word.lower()
if "/" in word:
tokenized[i][j] = re.sub(r"/", r" / ", word)
#mutating the list
def pos_tag(self, tokenized_data):
print "POS tagging... ",
pos_tagged_data = []
for entry in tokenized_data:
new_entry = []
for sentence in entry:
tagged = [("<START>", "<START>")]
tagged.extend(nltk.pos_tag(sentence))
new_entry.append(tagged)
pos_tagged_data.append(new_entry)
print "[DONE]"
return pos_tagged_data
def build_patterns_tagged(self, sentence, index, size):
window_start = index-size
window_end = index+1
sentence_copy = list(sentence)
sentence_copy[index] = "<x>",
while window_start <= index: # this isn't quite right
try:
candidate = zip(*sentence_copy[window_start:window_end])[0]
except IndexError:
candidate = []
if len(candidate) > 1:
self.pattern_alphabet.add(tuple(candidate))
if candidate[0] != "<x>":
self.first_pattern_words.add(candidate[0])
else:
self.first_pattern_words.add(candidate[1])
window_start += 1
window_end += 1
def find_patterns_tagged(self):
for entry in self.pos_tagged_data:
for sentence in entry:
for i,(word,tag) in enumerate(sentence):
if word in self.temporary_lexicon:
self.build_patterns_tagged(sentence, i, 2)
self.build_patterns_tagged(sentence, i, 1)
def find_patterns_chunked(self):
for entry in self.chunked_data:
for sentence in entry:
for i,word in enumerate(sentence):
if isinstance(word, Chunk) and word.head in self.temporary_lexicon:
self.build_patterns_chunked(sentence, i, 2)
self.build_patterns_chunked(sentence, i, 1)
def build_patterns_chunked(self, sentence, index, size):
sentence_copy = list(sentence)
sentence_copy[index] = "<x>",
sentence_copy = self._flatten_chunks(sentence_copy)
index = sentence_copy.index("<x>")
window_start = index-size
window_end = index+1
while window_start <= index:
candidate = sentence_copy[window_start:window_end]
if len(candidate) > 1:
self.pattern_alphabet.add(tuple(candidate))
window_start += 1
window_end += 1
def _flatten_chunks(self, sentence):
flattened_sentence = []
for constituent in sentence:
if isinstance(constituent, Chunk):
flattened_sentence.extend(constituent.tokens)
else:
flattened_sentence.append(constituent[0])
return flattened_sentence
def set_counter_arrays(self):
tmp_lst = [[]] * self.pattern_alphabet.size() # must be careful about pointers here
self.n_counter_sets = map(set, tmp_lst)
self.f_counter_sets = map(set, tmp_lst)
def find_seeds_chunked(self):
for entry in self.chunked_data:
for sentence in entry:
for i in range(len(sentence)):
if isinstance(sentence[i], Chunk):
self.match_pattern_chunked(sentence, i, 2)
self.match_pattern_chunked(sentence, i, 1)
def match_pattern_chunked(self, sentence, index, size):
candidate_seed = sentence[index].head
sentence_copy = list(sentence)
sentence_copy[index] = "<x>",
sentence_copy = self._flatten_chunks(sentence_copy)
index = sentence_copy.index("<x>")
window_start = index-size
window_end = index+1
while window_start <= index:
window = sentence_copy[window_start:window_end]
pattern = tuple(window)
if len(pattern) > 1 and \
self.pattern_alphabet.has_label(pattern) and \
len(candidate_seed) > 2:
pattern_index = self.pattern_alphabet.get_index(pattern)
# increment our counters
self.n_counter_sets[pattern_index].add(candidate_seed)
if candidate_seed not in self.temporary_lexicon:
self.f_counter_sets[pattern_index].add(candidate_seed)
window_start += 1
window_end += 1
def find_seeds_tagged(self):
for entry in self.pos_tagged_data:
for sentence in entry:
for i in range(len(sentence)):
if sentence[i][0] in self.first_pattern_words:
self.match_pattern_tagged(sentence, i, 3)
self.match_pattern_tagged(sentence, i, 2)
def match_pattern_tagged(self, sentence, index, size):
window_start = index-1
window_end = index+size-1
window = sentence[window_start:window_end]
for seed_candidate_index in range(len(window)):
window_copy = list(window)
_,pos = window_copy[seed_candidate_index]
window_copy[seed_candidate_index] = ("<x>", pos)
pattern = tuple(zip(*window_copy)[0])
if len(pattern) > 1 and \
self.pattern_alphabet.has_label(pattern) and \
window[seed_candidate_index][1].startswith("NN") and \
len(window[seed_candidate_index][0]) > 2:
candidate_seed = window[seed_candidate_index][0]
pattern_index = self.pattern_alphabet.get_index(pattern)
# increment our counters
self.n_counter_sets[pattern_index].add(candidate_seed)
if candidate_seed not in self.temporary_lexicon:
self.f_counter_sets[pattern_index].add(candidate_seed)
def calculate_pattern_scores(self):
self.n_pattern_array = numpy.array(map(len, self.n_counter_sets), dtype=float) + 1.
self.f_pattern_array = numpy.array(map(len, self.f_counter_sets), dtype=float) + 1.
self.pattern_scores = numpy.nan_to_num((self.f_pattern_array/self.n_pattern_array)*numpy.log2(self.f_pattern_array))
def calculate_seed_scores(self):
self.candidate_seed_scores = {}
for candidate_seed,matched_patterns_set in self.temporary_lexicon.iteritems():
matched_patterns = list(matched_patterns_set)
score = numpy.sum((self.pattern_scores[matched_patterns] * 0.01) + 1)
#print score
self.candidate_seed_scores[candidate_seed] = score
def cull_candidates(self):
self.calculate_pattern_scores()
self.calculate_seed_scores()
sorted_candidates = sorted([(v,k) for k,v in self.candidate_seed_scores.iteritems()], reverse=True)
#print sorted_candidates
try:
return zip(*sorted_candidates)[1][:5]
except IndexError:
return []
def run_mutual_bootstrapping(self):
added_patterns = 0
best_score = 5
while added_patterns < 10 or best_score > 1.8:
self.find_patterns()
self.set_counter_arrays()
self.find_seeds()
self.calculate_pattern_scores()
best_pattern_index = numpy.nanargmax(self.pattern_scores)
while best_pattern_index in self.best_extraction_patterns:
self.pattern_scores[best_pattern_index] = -10000000.
best_pattern_index = numpy.nanargmax(self.pattern_scores)
if self.pattern_scores[best_pattern_index] < 0.7:
return
best_score = self.pattern_scores[best_pattern_index]
#print best_score, self.pattern_alphabet.get_label(best_pattern_index)
self.best_extraction_patterns.add(best_pattern_index)
for seed in self.n_counter_sets[best_pattern_index]:
self.temporary_lexicon[seed].add(best_pattern_index)
added_patterns += 1
def run_meta_bootstrapping(self):
best_five = self.cull_candidates()
self.permanent_lexicon.update(best_five)
self.temporary_lexicon = defaultdict(set)
for s in self.permanent_lexicon:
self.temporary_lexicon[s] = set()
def run(self, num_iterations=50):
for i in range(num_iterations):
print "Iteration: {:d}".format(i+1)
print "running mutual bootstrapping..."
self.run_mutual_bootstrapping()
print "[DONE]"
print "running meta bootstrapping...",
self.run_meta_bootstrapping()
print "[DONE]"
print "number of seed terms: {:d}".format(len(self.permanent_lexicon))
print "number of total patterns: {:d}".format(self.pattern_alphabet.size())
print "\n"
def save_seeds(self, outfile):
with open(outfile, "w") as f_out:
f_out.write("\n".join(s.encode("utf-8") for s in self.permanent_lexicon))
def save_patterns(self, outfile):
with open(outfile, "w") as f_out:
patterns = []
for pattern_index in self.best_extraction_patterns:
patterns.append(" ".join(self.pattern_alphabet.get_label(pattern_index)))
f_out.write("\n".join(s.encode("utf-8") for s in patterns))
class Parser:
def __init__(self, feature_generator_list, decay = False):
self.feature_generator_list = feature_generator_list
self.feature_alphabet = Alphabet()
self.label_alphabet = Alphabet() #you will need this if you use labeled arc
self.weights = None
self.learning_rate = 0.0001
self.num_iterations = 10
self.caches = {}
self.decay = decay
def featurize(self, src, dst, sentence, grow_alphabets=True):
"""Generate feature indices for an arc from src->dst
Arg:
Arc from src(index)->dst(index)
sentence is a dictionary in which you can put whatever in.
"""
feature_list = []
for feature_generator in self.feature_generator_list:
feature_list.extend(feature_generator(src, dst, sentence))
if grow_alphabets: #set to false when running this function on dev/test set
for feature, bias in feature_list:
self.feature_alphabet.add(feature)
for src,dst,label in sentence['arcs']:
self.label_alphabet.add(label)
feature_vector = [(self.feature_alphabet.get_index(x), feature_value)
for x, feature_value in feature_list \
if self.feature_alphabet.has_label(x)]
return ([x for x,y in feature_vector], numpy.array([y for x,y in feature_vector]))
def make_fully_connected_graph(self, sentence):
"""Make a graph to make an MST from
If G is such graph, then the weight for an arc from token i to token j is
G[i][j] i.e. G is a diction and G[i] is also a dictionary.
If arc i->j does not exist, then j not in G[i].
You will need to use self.featurize for all possible edges
Arg:
sentence is a dictionary in which you can put whatever in.
Add your implementation
"""
G = {}
#get a list of indices
indices = range(len(sentence['tokens']))
#make an arc for each pair
for i in indices:
G[i] = {}
for j in indices:
if i != j:
G[i][j] = self.featurize(int(i), int(j), sentence, False)
return G
###########################
#Actual training function!#
###########################
def train(self, training_sentences, dev_sentences=None, prealloc=False):
"""Perceptron algorithm for learning edge weights
If a dev set is provided, then we can evaluate the parser at every k iterations
just so we know the progress of the training process and see if we need more iterations.
Arg:
a list of dictionaries in which you can put whatever in.
Add your implementation
"""
#this is where you should populate the feature alphabet and the weight vector
#cache training sentences; populate alphabets
print "Populating features and caching training sentences ..."
self._add_to_caches(training_sentences, 'training', not prealloc)
print "Done!"
#cache dev sentences
if dev_sentences:
print "Caching dev sentences ... "
self._add_to_caches(dev_sentences, 'dev', False)
print "Done!"
#initialize weight vector
if not prealloc: #don't touch this business if it's preallocated
print "Initializing weight vector ..."
self.weights = numpy.zeros(len(self.feature_alphabet))
#self.weights = numpy.zeros((len(self.feature_alphabet) + 1) * len(self.label_alphabet))
random.seed()
for i, weight in enumerate(self.weights):
self.weights[i] += .00001
print "Done!"
#okay, start training, bro
for i in xrange(self.num_iterations):
print "Pass %d:\n" % (i + 1)
if dev_sentences is not None and i % 2 == 0: # tracking progress
print "Current UAS: %f" % self.evaluate(dev_sentences, 'dev')
for j, sentence in enumerate(training_sentences):
if not j % 1000:
print "Training on sentences %d to %d of %d ..." % \
(j, min(j+999, len(training_sentences)), len(training_sentences))
#graph = self.make_fully_connected_graph(sentence)
fcg = self.caches['training']['fcgs'][j]
graph = self._featurized_to_weighted(fcg)
max_spanning_tree = mst(0, graph)
#Add training function here
gold = self.caches['training']['counts'][j]
hypo = self._get_counts(self._fcg_to_featurized(\
fcg, max_spanning_tree))
self._mutate_weights(gold, hypo)
if self.decay:
self.learning_rate *= 0.9
def evaluate(self, sentences, key):
"""Compute evaluation metrics
Compute Unlabeled Arc Score (UAS) and optionally other metrics
Add your implementation
"""
good = 0
total = 0
for j, sent in enumerate(sentences):
fcg = self.caches[key]['fcgs'][j]
graph = self._featurized_to_weighted(fcg)
try:
hypo = self._arcset(mst(0, graph))
except: #debug
print '.',
continue
gold = set([(int(i), int(j)) for i,j,lab in sent['arcs']])
good += len(hypo.intersection(gold))
total += len(gold)
return float(good)/ total
def serialize(self, fname):
"""Convert to dictionary representation and serialize."""
d = {}
d['weights'] = self.weights
d['feat_alph'] = self.feature_alphabet.to_dict()
d['label_alph'] = self.label_alphabet.to_dict()
d['features'] = self.feature_generator_list
d['decay'] = self.decay
with open(fname, 'wb') as outf:
cPickle.dump(d, outf)
def deserialize(self, fname):
"""Retrieve from serialization; keep defaults where possible."""
with open(fname, 'rb') as inf:
d = cPickle.load(inf)
self.weights = d['weights']
self.feature_alphabet = Alphabet.from_dict(d['feat_alph'])
self.label_alphabet = Alphabet.from_dict(d['label_alph'])
self.feature_generator_list = d['features']
self.decay = d['decay']
def try_parse(self, inp):
"""Determine whether provided input is a file or a string."""
import nltk
#was it a text file?
try:
inp = open(inp, 'rb').read()
#nope!
except IOError:
pass
paragraph = nltk.sent_tokenize(inp)
for sentence in paragraph:
self.parse(sentence)
def parse(self, sentence_string):
"""Extra credit : parse an arbitrary string
This is actually what we want at the end.
Given an arbitrary string
0) split it into sentences (if you want to accept multiple sentences.)
1) tokenize
2) POS-tag and other pre-processing technique
3) parse it!
4) draw it using nltk draw_trees like in the example
it does not support labeled arc though :(
"""
#draw a tree
from nltk.draw.tree import draw_trees
from nltk.tree import Tree
import nltk
words = nltk.pos_tag(nltk.word_tokenize(sentence_string))
sentence = {'tokens': ['ROOT'], 'arcs': [], 'pos':['ROOT']}
for word, pos in words:
sentence['tokens'].append(word)
sentence['pos'].append(pos)
indices = range(len(sentence['tokens']))
fcg = self.make_fully_connected_graph(sentence)
weighted = self._featurized_to_weighted(fcg)
max_spanning_tree = mst(0, weighted)
wlist = sentence['tokens']
#print the dependencies
for i in max_spanning_tree.keys():
for j in max_spanning_tree[i].keys():
print "%s->%s" % (i, j)
t = self._build_tree(max_spanning_tree, 0, wlist)
draw_trees(Tree(t))
###################################
#A whole bunch of helper functions#
###################################
def _build_tree(self, G, root, wlist):
if root in G.keys():
return '(' + str(wlist[root]) + ' '.join([self._build_tree(\
G, ind, wlist) for ind in G[root]]) + ')'
else:
return '(%s)' % str(wlist[root])
def _featurized_to_weighted(self, graph):
"""Converts a fully-connected graph to one with arc weights"""
wG = {}
for i in graph.keys():
#for j in graph[i].keys():
for j in graph.keys():
if i != j:
arclength = -(numpy.sum(self.weights[graph[i][j][0]] \
* graph[i][j][1]))
if not arclength:
arclength = 1
if i in wG.keys():
wG[i][j] = arclength
else:
wG[i] = {j: arclength}
return wG
def _add_to_caches(self, sentence_set, key, grow_alph):
"""Add to the stored caches under a given key"""
self.caches[key] = {'fcgs': [], 'counts': []}
for sentence in sentence_set:
self.caches[key]['counts'].append(\
self._get_counts(self._sentence_to_featurized(\
sentence, grow_alph)))
for sentence in sentence_set:
self.caches[key]['fcgs'].append(\
self.make_fully_connected_graph(sentence))
def _get_counts(self, graph):
"""Convert a graph into a dictionary of arc counts"""
counts = {}
for i in graph.keys():
for j in graph[i].keys():
for feat, weight in zip(*graph[i][j]):
if feat in counts.keys():
counts[feat] += weight
else:
counts[feat] = weight
return counts
def _fcg_to_featurized(self, fully_connected, spanning_tree):
""" Given a maximum spanning tree, retrieve the appropriate features
from the fcg.
"""
feat_tree = {}
for head in spanning_tree.keys():
for dep, weight in spanning_tree[head].iteritems():
if head in feat_tree.keys():
feat_tree[head][dep] = fully_connected[head][dep]
else:
feat_tree[head] = {dep: fully_connected[head][dep]}
return feat_tree
def _sentence_to_featurized(self, sentence, grow = True):
"""
Create a graph dictionary with feature vectors.
"""
#declare a graph (it's an empty dictionary)
G = {}
#featurize all arcs
for src, dst, label in sentence['arcs']:
features = self.featurize(int(src), int(dst), sentence, grow)
try:
G[int(src)][int(dst)] = features
except:
G[int(src)] = {int(dst): features}
return G
def _mutate_weights(self, gold, hypo):
"""
Change the weights by comparing a hypothesis with the gold standard.
"""
counts = {}
#get set of all features involved; aggregate counts
for elem in set(gold.keys()).union(set(hypo.keys())):
counts[elem] = gold.get(elem, 0) - hypo.get(elem, 0)
#adjust weights
self.weights[counts.keys()] += \
numpy.array(counts.values()) * self.learning_rate
def _arcset(self, G):
return set([(i, j) for i in G.keys() for j in G[i].keys()])
class Naive_Bayes(object):
""""""
def __init__(self, data, feature_function):
"""
Takes a dictionary mapping labels to lists of strings with that label, and a function which
produces a list of feature values from a string.
"""
# your code here!
self.data = data
self.feature_codebook = Alphabet()
# self.word_dict = Alphabet()
self.label_codebook = Alphabet()
self.feature_function = feature_function
# def _build_instance_list(self):
# """"""
# instance_list = {}
# for label, documents in self.data.items():
# instance_list[label] = []
# for doc in documents:
# vector = self.extract_feature(self.data, doc, s)
# instance_list[label].append(vector)
# self.instance_list = instance_list
#
# def _populate_codebook(self):
# """"""
# for label in self.instance_list:
# self.label_codebook.add(label)
# #here we use all the word set as features
# self.feature_codebook = copy.deepcopy(self.word_dict)
def extract_feature(self, string):
""""""
vector = np.zeros(self.feature_codebook.size())
tokens = set(nltk.regexp_tokenize(string, pattern="\w+"))
indice = 0
for word in tokens:
if self.feature_codebook.has_label(word):
indice = self.feature_codebook.get_index(word)
vector[indice] = 1.0
return vector
def _collect_counts(self):
""""""
self.count_table = np.zeros((self.feature_codebook.size(), self.label_codebook.size()))
self.count_y_table = np.zeros(self.label_codebook.size())
for label, docs in self.instance_list.items():
Y_index = self.label_codebook.get_index(label)
for vector in docs:
self.count_y_table[Y_index] += 1.0
self.count_table[:, Y_index] += vector
# for sparse vector we use different counting method
# for x in vector:
# self.count_table[x,Y_index] += 1.0
def train(self, theta):
""""""
self.instance_list = self.feature_function(self.data, self.label_codebook, self.feature_codebook, theta)
# self._populate_codebook_withSelectFeature()
# self.instance_list = self.feature_function(self.data, self.label_codebook, self.feature_codebook, select_feature)
self._collect_counts()
self.p_x_given_y_table = np.zeros((self.feature_codebook.size(), self.label_codebook.size()))
self.p_y_table = np.zeros(self.label_codebook.size())
self.p_x_given_y_table = (self.count_table + 0.2) / (self.count_y_table + self.feature_codebook.size() * 0.2)
self.p_y_table = self.count_y_table / self.count_y_table.sum()
def compute_log_unnormalized_score(self, feature_vector):
"""Compute log P(X|Y) + log P(Y) for all values of Y
Returns a vector of loglikelihood.
loglikelihood_vector[0] = log P(X|Y=0) + log P(Y=0)
"""
loglikelihood_vector = np.zeros(self.label_codebook.size())
for label in range(0, self.label_codebook.size()):
logpro = math.log(self.p_y_table[label])
for feature_index in range(0, self.feature_codebook.size()):
logpro += feature_vector[feature_index] * math.log(self.p_x_given_y_table[feature_index, label]) + (1 - feature_vector[feature_index]) * math.log(1 - self.p_x_given_y_table[feature_index, label])
loglikelihood_vector[label] = logpro
return loglikelihood_vector
def classify(self, string):
"""
Classifies a string according to the feature function and training data
provided at initialization.
Predict the label of the given instance
return the predict label for the input document
"""
# your code here!
feature_vector = self.extract_feature(string)
logvector = self.compute_log_unnormalized_score(feature_vector)
# print vector
pre_label_index = np.argmax(logvector)
return self.label_codebook.get_label(pre_label_index)
class MaxEnt(BaseClassifier):
def __init__(self):
"""Initialize the model
label_codebook, feature_codebook, parameters must be
assigned properly in order for the model to work.
parameters and codebooks will be handled in the train function
"""
super(MaxEnt, self).__init__()
self.label_codebook = Alphabet()
self.feature_codebook = Alphabet()
#self.gaussian_prior_variance = 1
self.parameters = []
self.gaussian_prior_variance = 1.0
def compute_observed_counts(self, instance_list):
"""Compute observed feature counts
It should only be done once because it's parameter-independent.
The observed feature counts are then stored internally.
Note that we are fitting the model with the intercept terms
so the count of intercept term is the count of that class.
fill the feature_counts table with observed counts
"""
#the data and label in instance both use sparse vector
self.feature_counts = numpy.zeros((self.feature_codebook.size() + 1) * self.label_codebook.size())
for instance in instance_list:
Y_index = (self.feature_codebook.size()+1)*instance.label
self.feature_counts[Y_index] +=1
#instance.data is numpy array
indices = Y_index + instance.data +1
self.feature_counts[indices] +=1
#print self.feature_counts[:self.feature_codebook.size()+1]
#print self.feature_counts[self.feature_codebook.size()+1:]
def compute_expected_feature_counts(self,instance_list):
"""Compute expected feature counts
E(feature|X) = sum over i,y E(feature(Xi,yi)|Xi)
= sum over i,y feature(Xi,yi) P(Y=yi|Xi)
We take advantage of inference function in this class to compute
expected feature counts, which is only needed for training.
computing the expected feature counts by adding up all the expectation counts of all feature.
return expected feature counts table
"""
expected_feature_counts = numpy.zeros(len(self.parameters))
for instance in instance_list:
posterior = self.compute_label_unnormalized_loglikelihood_vector(instance.data)
posterior = numpy.exp(posterior-logsumexp(posterior))
for label in range(0,self.label_codebook.size()):
Y_index = label*(self.feature_codebook.size() + 1)
expected_feature_counts[Y_index] += posterior[label]
indices = Y_index + instance.data + 1
expected_feature_counts[indices] += posterior[label]
return expected_feature_counts
def classify_instance(self, instance):
"""Applying the model to a new instance
Returns:
label with the maximum probability
"""
vector = self.compute_posterior_distribution(instance)
#print vector
pre_label_index = numpy.argmax(vector)
return pre_label_index
def compute_posterior_distribution(self, instance):
"""Compute P(Y|X)
Return a vector of the same size as the label_codebook
the vector contains the unnormalized likelihood vector since we only use them for finding the most probable label, so we don't have
to normalized it.
"""
sparse_vector = numpy.array([self.feature_codebook.get_index(i) for i in instance.data if self.feature_codebook.has_label(i)])
posterior_distribution = numpy.zeros(self.label_codebook.size())
posterior_distribution = numpy.exp(self.compute_label_unnormalized_loglikelihood_vector(sparse_vector))
return posterior_distribution
def compute_label_unnormalized_loglikelihood_vector(self,sparse_feature_vector):
"""Compute unnormalized log score from log-linear model
log P(Y|X) is proportional to feature vector * parameter vector
But we use a sparse vector representation, so we need to use
index tricks that numpy allows us to do.
for each label compute the unnormalized loglikelihood (sum of lambdas) given the sparse_feature_vector
Returns:
a vector of scores according to different y(label)
"""
loglikelihood_score_vector = numpy.zeros(self.label_codebook.size())
for label in range(0,self.label_codebook.size()):
Y_index = label*(self.feature_codebook.size() + 1)
indices = Y_index + sparse_feature_vector + 1
if len(indices)!=0:
loglikelihood_score_vector[label] = self.parameters[Y_index] + sum(self.parameters[indices])
else:
loglikelihood_score_vector[label] = self.parameters[Y_index]
return loglikelihood_score_vector
def objective_function(self, parameters):
"""Compute negative (log P(Y|X,lambdas) + log P(lambdas))
The function that we want to optimize over. Here I use Gaussian distribution(mean=0.0 sigma=1.0) prior to model P(lambda)
Args:
parameters updated by the training procedure
Returns:
negtive total likelihood
"""
total_loglikelihood = 0.0
numerator = 0.0
denominator = 0.0
#prior = 0.0
#self.gaussian_prior_variance = 1.0
prior = sum([i**2/(2*self.gaussian_prior_variance**2) for i in parameters])
self.parameters=numpy.array(parameters)
# Compute the loglikelihood here
loglikelihood_score_vector = numpy.zeros(self.label_codebook.size())
for instance in self.training_data:
Y_index = instance.label*(self.feature_codebook.size() + 1)
indices = Y_index + instance.data + 1
numerator += (parameters[Y_index]+sum(parameters[indices]))
score_vector = self.compute_label_unnormalized_loglikelihood_vector(instance.data)
#print score_vector
denominator += logsumexp(score_vector)
#print numerator
#print denominator
total_loglikelihood = numerator - denominator - prior
print - total_loglikelihood
return - total_loglikelihood
def gradient_function(self, parameters):
"""Compute gradient of negative (log P(Y|X,lambdas) + log P(lambdas)) wrt lambdas
With some algebra, we have that
gradient wrt lambda i = observed_count of feature i - expected_count of feature i - lambda i / gaussian_prior_variance^2
The first term is computed before running the optimization function and is a constant.
The second term needs inference to get P(Y|X, lambdas) and is a bit expensive.
The third term is from taking the derivative of log gaussian prior
Returns:
a vector of gradient
"""
self.parameters = numpy.array(parameters)
#print self.parameters
#print parameters
gradient_vector = numpy.zeros(len(parameters))
observed_count_vector = self.feature_counts
expected_count_vector = self.compute_expected_feature_counts(self.training_data)
dprior = numpy.array([i/self.gaussian_prior_variance**2 for i in parameters])
# compute gradient here
gradient_vector = observed_count_vector - expected_count_vector - dprior
return - gradient_vector
def train(self, instance_list):
"""Find the optimal parameters for maximum entropy classifier
We setup an instance of MaxEnt to use as an inference engine
necessary for parameter fitting. MaxEnt instance and training set
are stored internally in the trainer just so we can avoid putting in
extra arguments into the optimization function.
We leave the actual number crunching and search to fmin_bfgs function.
There are a few tunable parameters for the optimization function but
the default is usually well-tuned and sufficient for most purposes.
Arg:
instance_list: each instance.data should be a string feature vectors
This function will create a sparse feature vector representation
based on the alphabet.
Returns:
Maximum entropy classifier with the parameters (MAP estimate from the data
and Gaussian prior)
"""
assert(len(instance_list) > 0)
######################################
# Do any further processing right here e.g populate codebook
# making sparse vectors, etc.
self.label_codebook.add('neg')
self.label_codebook.add('pos')
for index,instance in enumerate(instance_list):
sparse_vector = numpy.zeros(0,dtype=numpy.int)
for feature in instance.data:
if not self.feature_codebook.has_label(feature):
self.feature_codebook.add(feature)
sparse_vector = numpy.append(sparse_vector,self.feature_codebook.get_index(feature))
else:
sparse_vector = numpy.append(sparse_vector,self.feature_codebook.get_index(feature))
instance_list[index].data = sparse_vector
##################
self.parameters = numpy.zeros((self.feature_codebook.size() + 1) * self.label_codebook.size())
self.training_data = instance_list
self.compute_observed_counts(instance_list)
num_labels = self.label_codebook.size()
num_features = self.feature_codebook.size()
init_point = numpy.zeros(num_labels * (num_features + 1))
optimal_parameters, _, _ = fmin_l_bfgs_b(self.objective_function, init_point, fprime=self.gradient_function)
print optimal_parameters
self.parameters = optimal_parameters
def to_dict(self):
model_dict = {
'label_alphabet': self.label_codebook.to_dict(),
'feature_alphabet': self.feature_codebook.to_dict(),
'parameters': self.parameters.tolist(),
}
return model_dict
@classmethod
def from_dict(cls, model_dictionary):
model_instance = MaxEnt()
model_instance.label_codebook = Alphabet.from_dict(model_dict['label_alphabet'])
model_instance.feature_codebook = Alphabet.from_dict(model_dict['feature_alphabet'])
model_instance.p_x_given_y_table = numpy.array(model_dict['parameters'])
return model_instance
