def _run():
"""Run experiment"""
parser = argparse.ArgumentParser(description='Job runner for ActiveTM '
'experiments')
parser.add_argument('settings', help=\
'''the path to a file containing settings, as described in \
README.md in the root ActiveTM directory''')
parser.add_argument('outputdir', help='directory for output')
parser.add_argument('label', help='identifying label')
parser.add_argument('seed', default=-1, type=int, nargs='?')
args = parser.parse_args()
# print('Parsed arguments')
settings = utils.parse_settings(args.settings)
# print('Parsed settings')
trueoutputdir = os.path.join(args.outputdir, settings['group'])
if not os.path.exists(trueoutputdir):
try:
os.makedirs(trueoutputdir)
except OSError:
pass
# print('Ensured true output directory exists')
filename = socket.gethostname()+'.'+str(os.getpid())
runningfile = os.path.join(args.outputdir, 'running',
filename)
try:
with open(runningfile, 'w') as outputfh:
outputfh.write('running')
# print('Created running mark')
start = time.time()
input_pickle = os.path.join(args.outputdir, utils.get_pickle_name(args.settings))
with open(input_pickle, 'rb') as ifh:
dataset = pickle.load(ifh)
# print('Got pickle')
if args.seed == -1:
rng = random.Random(int(settings['seed']))
else:
rng = random.Random(args.seed)
# print('Set random seed: ', args.seed)
model = models.build(rng, settings)
# print('Built model')
test_doc_ids, labeled_doc_ids, unlabeled_doc_ids =\
partition_data_ids(dataset.num_docs, rng, settings)
test_labels = []
test_words = []
for t in test_doc_ids:
test_labels.append(dataset.labels[dataset.titles[t]])
test_words.append(dataset.doc_tokens(t))
test_labels_mean = np.mean(test_labels)
known_labels = []
for t in labeled_doc_ids:
known_labels.append(dataset.labels[dataset.titles[t]])
# print('Set up initial sets')
SELECT_METHOD = select.factory[settings['select']]
END_LABELED = int(settings['endlabeled'])
LABEL_INCREMENT = int(settings['increment'])
CAND_SIZE = int(settings['candsize'])
results = []
end = time.time()
init_time = datetime.timedelta(seconds=end-start)
start = time.time()
# sandt = select_and_train
sandt_start = time.time()
model.train(dataset, labeled_doc_ids, known_labels)
# print('Trained model')
sandt_end = time.time()
count = 0
predictions = evaluate.get_predictions(model, test_words)
pr2 = evaluate.pR2(predictions,
test_labels,
test_labels_mean)
maes = evaluate.mean_absolute_errors(predictions, test_labels)
np.savetxt(utils.get_mae_out_name(trueoutputdir, args.label, count),
maes)
results.append([len(labeled_doc_ids),
datetime.timedelta(seconds=time.time()-start).total_seconds(),
datetime.timedelta(seconds=sandt_end-sandt_start).total_seconds(),
pr2])
while len(labeled_doc_ids) < END_LABELED and len(unlabeled_doc_ids) > 0:
count += 1
sandt_start = time.time()
# must make unlabeled_doc_ids (which is a set) into a list
candidates = select.reservoir(list(unlabeled_doc_ids), rng, CAND_SIZE)
chosen = SELECT_METHOD(dataset, labeled_doc_ids, candidates, model,
rng, LABEL_INCREMENT)
for c in chosen:
known_labels.append(dataset.labels[dataset.titles[c]])
labeled_doc_ids.append(c)
unlabeled_doc_ids.remove(c)
model.train(dataset, labeled_doc_ids, known_labels, True)
sandt_end = time.time()
predictions = evaluate.get_predictions(model, test_words)
pr2 = evaluate.pR2(predictions, test_labels, test_labels_mean)
maes = evaluate.mean_absolute_errors(predictions, test_labels)
np.savetxt(utils.get_mae_out_name(trueoutputdir, args.label, count),
maes)
results.append([len(labeled_doc_ids),
datetime.timedelta(seconds=time.time()-start).total_seconds(),
datetime.timedelta(seconds=sandt_end-sandt_start).total_seconds(),
pr2])
model.cleanup()
output = []
output.append('# init time: {:s}'.format(str(init_time)))
for result in results:
output.append('\t'.join([str(r) for r in result]))
output.append('')
with open(os.path.join(trueoutputdir, args.label), 'w') as ofh:
ofh.write('\n'.join(output))
finally:
os.remove(runningfile)
def demo(C_SEED):
"""Runs a demo of active learning simulation with sLDA via sampling"""
start = time.time()
rng = random.Random(SEED)
slda.set_seed(C_SEED)
dataset = ankura.run_pipeline(PIPELINE)
pre_labels = {}
with open(SOTU_LABELS) as ifh:
for line in ifh:
data = line.strip().split()
pre_labels[data[0]] = float(data[1])
labels = []
for doc_id in range(dataset.num_docs):
labels.append(pre_labels[dataset.titles[doc_id]])
end = time.time()
print('Import took:', datetime.timedelta(seconds=end-start))
print()
start = time.time()
# initialize sets
shuffled_doc_ids = list(range(dataset.num_docs))
rng.shuffle(shuffled_doc_ids)
test_doc_ids = shuffled_doc_ids[:TEST_SIZE]
test_labels = []
test_words = []
for t in test_doc_ids:
test_labels.append(labels[t])
test_words.append(dataset.doc_tokens(t))
test_labels_mean = numpy.mean(test_labels)
labeled_doc_ids = shuffled_doc_ids[TEST_SIZE:TEST_SIZE+START_LABELED]
known_labels = []
for t in labeled_doc_ids:
known_labels.append(labels[t])
unlabeled_doc_ids = set(shuffled_doc_ids[TEST_SIZE+START_LABELED:])
model = slda.SamplingSLDA(rng, NUM_TOPICS, ALPHA, BETA, VAR,
NUM_TRAIN, NUM_SAMPLES_TRAIN, TRAIN_BURN, TRAIN_LAG,
NUM_SAMPLES_PREDICT, PREDICT_BURN, PREDICT_LAG)
# learning loop
model.train(dataset, labeled_doc_ids, known_labels)
metric = evaluate.pR2(model, test_words, test_labels, test_labels_mean)
print(len(labeled_doc_ids), metric,
datetime.timedelta(seconds=time.time()-start))
while len(labeled_doc_ids) < END_LABELED and len(unlabeled_doc_ids) > 0:
candidates = select.reservoir(list(unlabeled_doc_ids),
rng, CAND_SIZE)
chosen = SELECT_METHOD(dataset, labeled_doc_ids, candidates, model, rng, LABEL_INCREMENT)
for c in chosen:
known_labels.append(labels[c])
labeled_doc_ids.append(c)
unlabeled_doc_ids.remove(c)
model.train(dataset, labeled_doc_ids, known_labels, True)
metric = evaluate.pR2(model, test_words, test_labels, test_labels_mean)
print(len(labeled_doc_ids), metric,
datetime.timedelta(seconds=time.time()-start))
model.cleanup()
end = time.time()
print()
print('Total simulation time:', datetime.timedelta(seconds=end-start))
print()
def demo(C_SEED):
"""Runs a demo of active learning simulation with sLDA via sampling"""
start = time.time()
rng = random.Random(SEED)
slda.set_seed(C_SEED)
dataset = ankura.run_pipeline(PIPELINE)
pre_labels = {}
with open(SOTU_LABELS) as ifh:
for line in ifh:
data = line.strip().split()
pre_labels[data[0]] = float(data[1])
labels = []
for doc_id in range(dataset.num_docs):
labels.append(pre_labels[dataset.titles[doc_id]])
end = time.time()
print("Import took:", datetime.timedelta(seconds=end - start))
print()
start = time.time()
# initialize sets
shuffled_doc_ids = list(range(dataset.num_docs))
rng.shuffle(shuffled_doc_ids)
test_doc_ids = shuffled_doc_ids[:TEST_SIZE]
test_labels = []
test_words = []
for t in test_doc_ids:
test_labels.append(labels[t])
test_words.append(dataset.doc_tokens(t))
test_labels_mean = numpy.mean(test_labels)
labeled_doc_ids = shuffled_doc_ids[TEST_SIZE : TEST_SIZE + START_LABELED]
known_labels = []
for t in labeled_doc_ids:
known_labels.append(labels[t])
unlabeled_doc_ids = set(shuffled_doc_ids[TEST_SIZE + START_LABELED :])
model = slda.SamplingSLDA(
rng,
NUM_TOPICS,
ALPHA,
BETA,
VAR,
NUM_TRAIN,
NUM_SAMPLES_TRAIN,
TRAIN_BURN,
TRAIN_LAG,
NUM_SAMPLES_PREDICT,
PREDICT_BURN,
PREDICT_LAG,
)
# learning loop
model.train(dataset, labeled_doc_ids, known_labels)
metric = evaluate.pR2(model, test_words, test_labels, test_labels_mean)
print(len(labeled_doc_ids), metric, datetime.timedelta(seconds=time.time() - start))
while len(labeled_doc_ids) < END_LABELED and len(unlabeled_doc_ids) > 0:
candidates = select.reservoir(list(unlabeled_doc_ids), rng, CAND_SIZE)
chosen = SELECT_METHOD(dataset, labeled_doc_ids, candidates, model, rng, LABEL_INCREMENT)
for c in chosen:
known_labels.append(labels[c])
labeled_doc_ids.append(c)
unlabeled_doc_ids.remove(c)
model.train(dataset, labeled_doc_ids, known_labels, True)
metric = evaluate.pR2(model, test_words, test_labels, test_labels_mean)
print(len(labeled_doc_ids), metric, datetime.timedelta(seconds=time.time() - start))
model.cleanup()
end = time.time()
print()
print("Total simulation time:", datetime.timedelta(seconds=end - start))
print()
for t in labeled_doc_ids:
known_labels.append(dataset.labels[dataset.titles[t]])
SELECT_METHOD = select.factory[settings['select']]
END_LABELED = int(settings['endlabeled'])
LABEL_INCREMENT = int(settings['increment'])
CAND_SIZE = int(settings['candsize'])
results = []
end = time.time()
init_time = datetime.timedelta(seconds=end-start)
start = time.time()
select_and_train_start = time.time()
model.train(dataset, labeled_doc_ids, known_labels)
select_and_train_end = time.time()
metric = evaluate.pR2(model, test_words, test_labels,
test_labels_mean)
results.append([len(labeled_doc_ids),
datetime.timedelta(seconds=time.time()-start).total_seconds(),
datetime.timedelta(seconds=select_and_train_end-select_and_train_start).total_seconds(),
metric])
while len(labeled_doc_ids) < END_LABELED and len(unlabeled_doc_ids) > 0:
select_and_train_start = time.time()
# must make unlabeled_doc_ids (which is a set) into a list
candidates = select.reservoir(list(unlabeled_doc_ids), rng, CAND_SIZE)
chosen = SELECT_METHOD(dataset, labeled_doc_ids, candidates, model,
rng, LABEL_INCREMENT)
for c in chosen:
known_labels.append(dataset.labels[dataset.titles[c]])
labeled_doc_ids.append(c)
unlabeled_doc_ids.remove(c)
model.train(dataset, labeled_doc_ids, known_labels, True)