def test_binary_blocks():
X, Y = generate_blocks(n_samples=10)
crf = GridCRF()
clf = StructuredPerceptron(model=crf, max_iter=40)
clf.fit(X, Y)
Y_pred = clf.predict(X)
assert_array_equal(Y, Y_pred)
def test_multinomial_blocks():
X, Y = generate_blocks_multinomial(n_samples=10, noise=0.3, seed=0)
crf = GridCRF(n_states=X.shape[-1])
clf = StructuredPerceptron(model=crf, max_iter=10)
clf.fit(X, Y)
Y_pred = clf.predict(X)
assert_array_equal(Y, Y_pred)
def test_overflow_averaged():
X = np.array([[np.finfo('d').max]])
Y = np.array([-1])
pcp = StructuredPerceptron(model=BinaryClf(n_features=1),
max_iter=2, average=True)
pcp.fit(X, Y)
assert_true(np.isfinite(pcp.w[0]))
def test_multinomial_blocks():
X, Y = toy.generate_blocks_multinomial(n_samples=10, noise=0.3, seed=0)
crf = GridCRF(n_states=X.shape[-1])
clf = StructuredPerceptron(problem=crf, max_iter=10)
clf.fit(X, Y)
Y_pred = clf.predict(X)
assert_array_equal(Y, Y_pred)
def test_binary_blocks():
X, Y = toy.generate_blocks(n_samples=10)
crf = GridCRF()
clf = StructuredPerceptron(problem=crf, max_iter=40)
clf.fit(X, Y)
Y_pred = clf.predict(X)
assert_array_equal(Y, Y_pred)
def test_overflow_averaged():
X = np.array([[np.finfo('d').max]])
Y = np.array([-1])
pcp = StructuredPerceptron(model=BinaryClf(n_features=1),
max_iter=2, average=True)
pcp.fit(X, Y)
assert_true(np.isfinite(pcp.w[0]))
def test_binary_blocks_perceptron_online():
#testing subgradient ssvm on easy binary dataset
X, Y = toy.generate_blocks(n_samples=10)
crf = GridCRF()
clf = StructuredPerceptron(model=crf, max_iter=20)
clf.fit(X, Y)
Y_pred = clf.predict(X)
assert_array_equal(Y, Y_pred)
def test_binary_blocks_perceptron_online():
#testing subgradient ssvm on easy binary dataset
X, Y = generate_blocks(n_samples=10)
inference_method = get_installed(['qpbo', 'ad3', 'lp'])[0]
crf = GridCRF(inference_method=inference_method)
clf = StructuredPerceptron(model=crf, max_iter=20)
clf.fit(X, Y)
Y_pred = clf.predict(X)
assert_array_equal(Y, Y_pred)
def createModel(data, labels, num_classes=2):
weight_class=np.ones(2)
model = chain_crf.ChainCRF(directed=True)
clf = StructuredPerceptron(model=model,max_iter=1000,batch=False,average=True)
print("Structured Perceptron + Chain CRF")
train_start = time()
clf.fit(X=data, Y=labels)
train_end = time()
print("Training took " + str((train_end - train_start) / 60) + " minutes to complete\n")
return clf
def main():
from pystruct.learners import StructuredPerceptron
import warnings
with warnings.catch_warnings():
warnings.simplefilter("ignore")
data = "notebooks/data/wsj_sec_2_21_gold_dependencies"
X, Y = read_parse(data, limit=10000, length=20)
model = FirstOrderModel(feature_hash=1000000,
joint_feature_format="fast")
sp = StructuredPerceptron(model, verbose=1, max_iter=10, average=False)
sp.fit(X, Y)
np.save("/tmp/w", sp.w)
def main():
from pystruct.learners import StructuredPerceptron
import warnings
with warnings.catch_warnings():
warnings.simplefilter("ignore")
data = "notebooks/data/wsj_sec_2_21_gold_dependencies"
X, Y = read_parse(data, limit=10000, length=20)
model = FirstOrderModel(feature_hash=1000000,
joint_feature_format="fast")
sp = StructuredPerceptron(model, verbose=1, max_iter=10, average=False)
sp.fit(X, Y)
np.save("/tmp/w", sp.w)
def test_averaged():
# Under a lot of noise, averaging helps. This fails with less noise.
X, Y = generate_blocks_multinomial(n_samples=15, noise=3, seed=0)
X_train, Y_train = X[:10], Y[:10]
X_test, Y_test = X[10:], Y[10:]
crf = GridCRF()
clf = StructuredPerceptron(model=crf, max_iter=3)
clf.fit(X_train, Y_train)
no_avg_test = clf.score(X_test, Y_test)
clf.set_params(average=True)
clf.fit(X_train, Y_train)
avg_test = clf.score(X_test, Y_test)
assert_greater(avg_test, no_avg_test)
def test_partial_averaging():
"""Use XOR weight cycling to test partial averaging"""
X = np.array([[a, b, 1] for a in (-1, 1) for b in (-1, 1)], dtype=np.float)
Y = np.array([-1, 1, 1, -1])
pcp = StructuredPerceptron(model=BinarySVMModel(n_features=3), max_iter=5, decay_exponent=1, decay_t0=1)
weight = {}
for average in (0, 1, 4, -1):
pcp.set_params(average=average)
pcp.fit(X, Y)
weight[average] = pcp.w
assert_array_equal(weight[4], weight[-1])
assert_array_almost_equal(weight[0], [1.5, 3, 0])
assert_array_almost_equal(weight[1], [1.75, 3.5, 0])
assert_array_almost_equal(weight[4], [2.5, 5, 0])
def createModel(data, labels, num_classes=2):
model = ChainCRF(n_states=num_classes,
n_features=int(len(columns) - 5),
directed=True)
clf = StructuredPerceptron(model=model,
max_iter=200,
verbose=False,
batch=False,
average=True)
print("Structured Perceptron + Chain CRF")
train_start = time()
clf.fit(X=data, Y=labels)
train_end = time()
print("Training took " + str((train_end - train_start) / 60) +
" minutes to complete\n")
return clf
def test_averaged():
# Under a lot of noise, averaging helps. This fails with less noise.
X, Y = generate_blocks_multinomial(n_samples=15, noise=3, seed=0)
X_train, Y_train = X[:10], Y[:10]
X_test, Y_test = X[10:], Y[10:]
crf = GridCRF()
clf = StructuredPerceptron(model=crf, max_iter=3)
clf.fit(X_train, Y_train)
no_avg_test = clf.score(X_test, Y_test)
clf.set_params(average=True)
clf.fit(X_train, Y_train)
avg_test = clf.score(X_test, Y_test)
assert_greater(avg_test, no_avg_test)
def createModel(data, labels):
model = GraphCRF(n_states=3,
n_features=int(len(columns) - 4),
directed=True,
inference_method='max-product')
clf = StructuredPerceptron(model=model,
max_iter=100,
verbose=False,
batch=False,
average=True)
print("Structured Perceptron + Graph CRF")
train_start = time()
clf.fit(X=data, Y=labels)
train_end = time()
print("Training took " + str((train_end - train_start) / 60) +
" minutes to complete\n")
return clf
def test_averaging_early_stopping():
"""Test averaging over final epoch when early stopping"""
# we use logical OR, an easy problem solved after the second epoch
X = np.array([[a, b, 1] for a in (-1, 1) for b in (-1, 1)], dtype=np.float)
Y = np.array([-1, 1, 1, 1])
pcp = StructuredPerceptron(model=BinaryClf(n_features=3), max_iter=3,
average=-1)
pcp.fit(X, Y)
# The exact weight is used without the influence of the early iterations
assert_array_equal(pcp.w, [1, 1, 1])
# If we were expecting 3 iterations, we would end up with a zero vector
pcp.set_params(average=2)
pcp.fit(X, Y)
assert_array_equal(pcp.w, [0, 0, 0])
class PerceptronTrainer:
def __init__(self, max_iter=25, verbose=False):
self.dsm = DiscourseSequenceModel(True)
self.sp = StructuredPerceptron(self.dsm,
verbose=(1 if verbose else 0),
max_iter=max_iter,
average=True)
def fit(self, trainX, trainY):
import warnings
with warnings.catch_warnings():
warnings.simplefilter('ignore')
self.sp.fit(trainX, trainY)
def predict(self, testX):
predY = self.sp.predict(testX)
return predY
def score(self, testX, testY):
return self.sp.score(testX, testY)
def weights(self):
return self.dsm._vec.inverse_transform(self.sp.w)
def test_averaging_early_stopping():
"""Test averaging over final epoch when early stopping"""
# we use logical OR, an easy problem solved after the second epoch
X = np.array([[a, b, 1] for a in (-1, 1) for b in (-1, 1)], dtype=np.float)
Y = np.array([-1, 1, 1, 1])
pcp = StructuredPerceptron(model=BinarySVMModel(n_features=3), max_iter=3, average=-1)
pcp.fit(X, Y)
# The exact weight is used without the influence of the early iterations
assert_array_equal(pcp.w, [1, 1, 1])
# If we were expecting 3 iterations, we would end up with a zero vector
pcp.set_params(average=2)
pcp.fit(X, Y)
assert_array_equal(pcp.w, [0, 0, 0])
def test_partial_averaging():
"""Use XOR weight cycling to test partial averaging"""
X = np.array([[a, b, 1] for a in (-1, 1) for b in (-1, 1)], dtype=np.float)
Y = np.array([-1, 1, 1, -1])
pcp = StructuredPerceptron(model=BinaryClf(n_features=3), max_iter=5,
decay_exponent=1, decay_t0=1)
weight = {}
for average in (0, 1, 4, -1):
pcp.set_params(average=average)
pcp.fit(X, Y)
weight[average] = pcp.w
assert_array_equal(weight[4], weight[-1])
assert_array_almost_equal(weight[0], [1.5, 3, 0])
assert_array_almost_equal(weight[1], [1.75, 3.5, 0])
assert_array_almost_equal(weight[4], [2.5, 5, 0])
def test_xor():
"""Test perceptron behaviour against hand-computed values for XOR"""
X = np.array([[a, b, 1] for a in (-1, 1) for b in (-1, 1)], dtype=np.float)
Y = np.array([-1, 1, 1, -1])
# Should cycle weight vectors (1, 1, -1), (0, 2, 0), (1, 1, 1), (0, 0, 0)
# but this depends on how ties are settled. Maybe the test can be
# made robust to this
# Batch version should cycle (0, 0, -2), (0, 0, 0)
expected_predictions = [
np.array([1, 1, 1, 1]), # online, no average, w = (0, 0, 0, 0)
np.array([-1, 1, -1, 1]), # online, average, w ~= (0.5, 1, 0)
np.array([1, 1, 1, 1]), # batch, no average, w = (0, 0, 0)
np.array([-1, -1, -1, -1]) # batch, average, w ~= (0, 0, -2)
]
pcp = StructuredPerceptron(model=BinaryClf(n_features=3), max_iter=2)
for pred, (batch, average) in zip(expected_predictions,
product((False, True), (False, True))):
pcp.set_params(batch=batch, average=average)
pcp.fit(X, Y)
# We don't compare w explicitly but its prediction. As the perceptron
# is invariant to the scaling of w, this will allow the optimization of
# the underlying implementation
assert_array_equal(pcp.predict(X), pred)
def test_xor():
"""Test perceptron behaviour against hand-computed values for XOR"""
X = np.array([[a, b, 1] for a in (-1, 1) for b in (-1, 1)], dtype=np.float)
Y = np.array([-1, 1, 1, -1])
# Should cycle weight vectors (1, 1, -1), (0, 2, 0), (1, 1, 1), (0, 0, 0)
# but this depends on how ties are settled. Maybe the test can be
# made robust to this
# Batch version should cycle (0, 0, -2), (0, 0, 0)
expected_predictions = [
np.array([1, 1, 1, 1]), # online, no average, w = (0, 0, 0, 0)
np.array([-1, 1, -1, 1]), # online, average, w ~= (0.5, 1, 0)
np.array([1, 1, 1, 1]), # batch, no average, w = (0, 0, 0)
np.array([-1, -1, -1, -1]), # batch, average, w ~= (0, 0, -2)
]
pcp = StructuredPerceptron(model=BinarySVMModel(n_features=3), max_iter=2)
for pred, (batch, average) in zip(expected_predictions, product((False, True), (False, True))):
pcp.set_params(batch=batch, average=average)
pcp.fit(X, Y)
# We don't compare w explicitly but its prediction. As the perceptron
# is invariant to the scaling of w, this will allow the optimization of
# the underlying implementation
assert_array_equal(pcp.predict(X), pred)
import matplotlib.pyplot as plt
G = nx.DiGraph()
np.seterr(divide='ignore', invalid='ignore')
trainArticles = open('data/singleShort.txt',
'r').readlines() #=importArticles.getData('train')
testArticles = open('data/singleShortTest.txt',
'r').readlines() #= importArticles.getData('test')
print len(trainArticles)
print len(testArticles)
listOfYears = []
#X, Y = generate_blocks(n_samples=10)
#inference_method = get_installed(['qpbo', 'ad3', 'lp'])[0]
#crf = GridCRF(inference_method=inference_method)
clf = StructuredPerceptron(model=GridCRF, max_iter=120)
probs = []
titles = []
#A
def getArticle(article):
singleSets = []
try:
chunks = gc.getChunks(article[1])
tags = tag.getTags(article[1], chunks)
#if tags == []:
# continue # check this is right. go to next itteration
"""The Stanford Open IE tags"""
subject = tags['subject']
relation = tags['relation']
def main():
parser = argparse.ArgumentParser(description='Run parsing experiments.')
parser.add_argument('--original_rules', type=str, help='Original rule file')
parser.add_argument('--binarized_rules', type=str, help='Binarized rule file')
parser.add_argument('--training_ps', type=str,
help='Lexicalized phrase structure file.')
parser.add_argument('--training_dep', type=str,
help='Dependency parse file.')
parser.add_argument('--store_hypergraph_dir', type=str,
help='Directory to store/load hypergraphs.')
parser.add_argument('--save_hypergraph', type=bool,
help='Construct and save hypergraphs.')
parser.add_argument('--limit', type=int, help='Number of sentences to use.')
parser.add_argument('--test_file', type=str, help='Test file.')
parser.add_argument('--gold_file', type=str, help='Gold file.')
parser.add_argument('--model', type=str, help='Weight model.')
parser.add_argument('--test_limit', type=int, help='Number of sentences to test on.')
parser.add_argument('--run_eval', default=False, type=bool, help='')
parser.add_argument('--test_load', default=False, type=bool, help='')
parser.add_argument('--debugger', default=False, type=bool, help='')
parser.add_argument('--oracle', default=False, type=bool, help='Run oracle experiments')
parser.add_argument('config', type=str)
parser.add_argument('label', type=str)
print >>sys.stderr, open(sys.argv[1]).read()
argparse_config.read_config_file(parser, sys.argv[1])
args = parser.parse_args()
print args
if args.debugger:
from IPython.core import ultratb
sys.excepthook = ultratb.FormattedTB(color_scheme='Linux', call_pdb=1)
output_dir = os.path.join("Data", args.label)
data_out = os.path.join(output_dir, "mydata.txt")
print >>sys.stderr, data_out
# Set up logging.
logger.setLevel(logging.DEBUG)
handler = logging.StreamHandler(open(data_out, 'w'))
logger.addHandler(handler)
# Load data.
print args.training_dep
print args.training_ps
if args.training_dep:
X, Y = train.read_data_set(args.training_dep,
args.training_ps,
args.limit)
orules = tree.read_original_rules(open(args.original_rules))
grammar = read_rule_set(open(args.binarized_rules))
# for rule in grammar.unary_rules:
# print rule
X, Y = zip(*[(x, y) for x, y in zip(X, Y)
if len(x.words) >= 5])
binarized_Y = [tree.binarize(orules, make_bounds(x.deps), y)[0] for x, y in zip(X, Y)]
model = train.ReconstructionModel(feature_hash=int(1e7),
joint_feature_format="fast",
joint_feature_cache=False,
part_feature_cache=False)
model.set_grammar(grammar)
model.initialize(X, binarized_Y)
if args.test_load:
print "LOAD"
graphs = []
start = memory()
for i in range(1000 -1):
if len(X[i].words) < 5:
continue
x = X[i]
path = "%s/graphs%s.graph"%(args.store_hypergraph_dir, i)
encoder = LexicalizedCFGEncoder(x.words, x.tags, grammar)
pre = memory()
graph = pydecode.load(path)
print i, memory() - pre, len(graph.edges), len(X[i].words), memory() - start
pre = memory()
encoder.load("%s/encoder%s.pickle"%(
args.store_hypergraph_dir, i), graph)
print i, memory() - pre
graphs.append((graph, encoder))
elif args.save_hypergraph:
print "SAVING"
import time
model.set_from_disk(None)
for i in range(40000):
if len(X[i].words) < 5:
continue
# if len(X[i].words) > 15: continue
graph, encoder = model.dynamic_program(X[i])
# Sanity Check
# print binarized_Y[i]
# print encoder.structure_path(graph, binarized_Y[i])
if i % 100 == 0:
print i
pydecode.save("%s/graphs%s.graph"%(
args.store_hypergraph_dir, X[i].index),
graph)
encoder.save("%s/encoder%s.pickle"%(
args.store_hypergraph_dir, X[i].index), graph)
del graph
del encoder
elif args.oracle:
print "ORACLE"
trees_out = open(os.path.join(output_dir, "oracle.txt"), 'w')
model = train.ReconstructionModel(feature_hash=int(1e7), part_feature_cache=False,
joint_feature_cache=False,
joint_feature_format="sparse")
model.set_grammar(grammar)
model.initialize(X, binarized_Y)
model.set_from_disk(None)
X_test, Y_test = train.read_data_set(
args.test_file, args.gold_file, args.test_limit)
w = np.load(args.model)
# GOLD TREES
binarized_Y_test = []
for x, orig_y in zip(X_test, Y_test):
y = tree.binarize(orules, orig_y)
try:
graph, encoder = model.dynamic_program(x)
label_values = np.zeros(np.max(graph.labeling) + 1)
label_values.fill(-1)
possible = 0
brackets = set()
for part in encoder.transform_structure(y):
X = grammar.rule_nonterms(part[5])[0]
brackets.add((part[0], part[2], X))
#print part
if tuple(part) in encoder.encoder:
label = encoder.encoder[tuple(part)]
label_values[label] = 10.0
possible += 1
print "transform"
label_weights = np.zeros(len(graph.labeling))
graph_labels = graph.labeling[graph.labeling != -1]
parts = encoder.transform_labels(graph_labels)
weights = []
for part in parts:
X = grammar.rule_nonterms(part[5])[0]
if part[1] != part[2] and X[0] != "Z":
if (part[0], part[2], X) in brackets:
weights.append(2.0)
else:
weights.append(-2.0)
else:
weights.append(0.0)
label_weights = np.zeros(len(graph.labeling))
label_weights[graph.labeling != -1] = np.array(weights)
# graph_labels = graph.labeling[graph.labeling != -1]
# parts = encoder.transform_labels(graph_labels)
# parts_features = model.parts_features(x, parts)
# feature_indices = pydecode.model.sparse_feature_indices(parts_features,
# model.temp_shape,
# model.offsets,
# model.feature_hash)
# # Sum the feature weights for the features in each label row.
# label_weights = np.zeros(len(graph.labeling))
# label_weights[graph.labeling != -1] = \
# np.sum(np.take(w, feature_indices, mode="clip"), axis=1)
oracle_weights = pydecode.transform(graph, label_values)
path = pydecode.best_path(graph, oracle_weights + label_weights)
print "Match", oracle_weights.T * path.v, possible
y_hat = encoder.transform_path(path)
print >>trees_out, tree.remove_head(tree.unbinarize(y_hat)) \
.pprint(100000)
except:
print >>trees_out, ""
print "error"
continue
elif args.test_file:
print "TESTING"
trees_out = open(os.path.join(output_dir, "trees.txt"), 'w')
model = train.ReconstructionModel(feature_hash=int(1e7), part_feature_cache=False,
joint_feature_cache=False,
joint_feature_format="sparse")
model.set_grammar(grammar)
model.initialize(X, binarized_Y)
model.set_from_disk(None)
X_test, Y_test = train.read_data_set(
args.test_file, args.gold_file, args.test_limit)
w = np.load(args.model)
# binarized_Y_test = []
# for i, y in enumerate(Y_test):
# print i
# binarized_Y_test.append(tree.binarize(orules, y))
# for x, y in zip(X_test, binarized_Y_test):
for x in X_test:
try:
graph, encoder = model.dynamic_program(x)
y_hat = model.inference(x, w)
for part in encoder.transform_structure(y_hat):
print part, grammar.rule_nonterms(part[-1]), model.score_part(x, w, part)
a = w.T * model.joint_feature(x, y_hat)
# b = w.T * model.joint_feature(x, y)
# print a, b
# if b > a: print "FAIL"
print
print tree.remove_head(y_hat)
print
print tree.remove_head(tree.unbinarize(y_hat))\
.pprint()
# print tree.remove_head(tree.unbinarize(y))\
# .pprint()
# print
#)\tree.remove_head(
print >>trees_out, tree.remove_head(tree.unbinarize(y_hat)) \
.pprint(100000)
except:
print "error"
print >>trees_out, ""
elif args.run_eval:
test_file = os.path.join(output_dir, "oracle.txt")
gold_file = args.gold_file
print "Evaling", test_file, gold_file
os.system("../evalb/EVALB/evalb -p ../evalb/EVALB/COLLINS.prm %s %s"%(gold_file, test_file))
else:
print "TRAINING"
model.set_from_disk(args.store_hypergraph_dir)
sp = StructuredPerceptron(model, verbose=1, max_iter=5,
average=False)
import warnings
with warnings.catch_warnings():
warnings.simplefilter("ignore")
sp.fit(X, binarized_Y)
np.save(os.path.join(output_dir, "params"), sp.w)
w = sp.w
def fit(self, X, Y):
model = (self.model if isinstance(self.model, type)
else self.model.__class__)
self.model = model(n_states=34, n_features=X[0].shape[1])
StructuredPerceptron.fit(self, X, Y)
# -*- coding: utf-8 -*- """ Spyder Editor This is a temporary script file. """ import pystruct from pystruct.datasets import load_letters import numpy as np from pystruct.models import ChainCRF from pystruct.learners import StructuredPerceptron letters = load_letters() X, y, folds = letters['data'], letters['labels'], letters['folds'] X, y = np.array(X), np.array(y) X_train, X_test = X[folds == 1], X[folds != 1] y_train, y_test = y[folds == 1], y[folds != 1] model = ChainCRF() ssvm = StructuredPerceptron(model = model, max_iter = 10) ssvm.fit(X_train, y_train)
def __init__(self, max_iter=25, verbose=False):
self.dsm = DiscourseSequenceModel(True)
self.sp = StructuredPerceptron(self.dsm,
verbose=(1 if verbose else 0),
max_iter=max_iter,
average=True)
# -*- coding: utf-8 -*- """ Spyder Editor This is a temporary script file. """ import pystruct from pystruct.datasets import load_letters import numpy as np from pystruct.models import ChainCRF from pystruct.learners import StructuredPerceptron letters = load_letters() X, y, folds = letters['data'], letters['labels'], letters['folds'] X, y = np.array(X), np.array(y) X_train, X_test = X[folds == 1], X[folds != 1] y_train, y_test = y[folds == 1], y[folds != 1] model = ChainCRF() ssvm = StructuredPerceptron(model=model, max_iter=10) ssvm.fit(X_train, y_train)