def test(filename):
p = 5
for i in xrange(10):
num = 10*(i+1)
read = MAR()
read = read.create(filename,partitions = p)
poses = np.where(np.array(read.body['label']) == "yes")[0]
negs = np.where(np.array(read.body['label']) == "no")[0]
pos_sel = np.random.choice(poses, num, replace=False)
neg_sel = np.random.choice(negs, num*10, replace=False)
for id in pos_sel:
read.code_error(id)
for id in neg_sel:
read.code_error(id)
read.get_numbers()
start = time.time()
a,b,c,d = read.train_para()
duration = time.time()-start
print(duration)
read.get_numbers()
start = time.time()
a,b,c,d = read.train()
duration2 = time.time()-start
print(duration2)
def Supervised(filename, old_files = [], stop='', stopat=1, error='none', interval = 100000, starting =1, seed=0,
step =10, learner='svm_linear', boost=None):
print("FILENAME: ", filename, "OLDFILES: ", len(old_files))
stopat = float(stopat)
np.random.seed(seed)
read = MAR()
read = read.create(filename, old_files)
read.step = step
read.interval = interval
read.seed = seed
if boost:
util.vote(read, clf_name=boost, seed=seed, all=False, temp=str(seed) + filename)
return
num2 = read.get_allpos()
target = int(num2 * stopat)
if stop == 'est':
read.enable_est = True
else:
read.enable_est = False
if boost == None:
read.train_supervised(learner, seed)
pos, neg, total = read.get_numbers()
if boost:
read.query_boost()
else:
read.query_supervised()
read.record['est'][0] = read.est_num
while True:
pos, neg, total = read.get_numbers()
# try:
# print("%d, %d, %d" %(pos,pos+neg, read.est_num))
# except:
# print("%d, %d" %(pos,pos+neg))
if pos + neg >= total:
break
# if pos >= target and (pos+neg) >= total * .22 and read.enable_est and read.est_num*stopat<= pos:
# break
if boost:
ids = read.query_boost()[:read.step]
else:
ids = read.query_supervised()[:read.step]
read.code_batch(ids)
return read
def START(filename, cl="linear"):
stop = 1
thres = 40
# thres=10000000000
read = MAR()
read = read.create(filename)
target = int(read.get_allbugs() * stop)
while True:
found, cost, total = read.get_numbers()
try:
print("%d, %d" % (found, cost))
except:
pass
if found >= target:
break
if found == 0 or cost < thres:
for id in read.loc_sort():
read.code(id, read.body["label"][id])
else:
ids, c = read.train(cl=cl)
for id in ids:
read.code(id, read.body["label"][id])
read.plot()
set_trace()
return read
def START_est(filename):
stop = 0.90
thres = 40
flag = True
read = MAR()
read = read.create(filename)
read.restart()
read = MAR()
read = read.create(filename)
target = int(read.get_allpos() * stop)
while True:
pos, neg, total = read.get_numbers()
# print("%d, %d" %(pos,pos+neg))
if pos >= target:
break
if pos == 0 or pos + neg < thres:
for id in read.random():
read.code(id, read.body["label"][id])
else:
a, b, ids, c = read.train(pne=True)
if pos >= 60 and flag:
read.cache_est()
# read.xx=read.simcurve['x']
# read.yy=read.simcurve['pos']
flag = False
for id in ids:
read.code(id, read.body["label"][id])
return read
def START_AUTO(filename):
read = MAR()
read = read.create(filename)
pos_last = 0
full_life = 3
life = full_life
while True:
pos, neg, total = read.get_numbers()
print("%d/ %d" % (pos, pos + neg))
if pos >= 10:
if pos == pos_last:
life = life - 1
if life == 0:
break
else:
life = full_life
if pos == 0:
for id in read.random():
read.code(id, read.body["label"][id])
else:
a, b, ids, c = read.train()
for id in ids:
read.code(id, read.body["label"][id])
pos_last = pos
return read
def Supervised(filename,
old_files=[],
stop='est',
stopat=1,
error='none',
interval=100000,
starting=1,
seed=0,
step=10):
stopat = float(stopat)
np.random.seed(seed)
read = MAR()
read = read.create(filename, old_files)
read.step = step
read.interval = interval
num2 = read.get_allpos()
target = int(num2 * stopat)
if stop == 'est':
read.enable_est = True
else:
read.enable_est = False
read.train_supervised()
pos, neg, total = read.get_numbers()
read.query_supervised()
read.record['est'][0] = read.est_num
while True:
pos, neg, total = read.get_numbers()
try:
print("%d, %d, %d" % (pos, pos + neg, read.est_num))
except:
print("%d, %d" % (pos, pos + neg))
if pos + neg >= total:
break
if pos >= target and read.est_num * stopat <= pos:
break
for id in read.query_supervised()[:read.step]:
read.code_error(id, error=error)
return read
def test_semi(filename="Hall.csv"):
num = 20
read = MAR()
read = read.create(filename)
poses = np.where(np.array(read.body['label']) == "yes")[0]
negs = np.where(np.array(read.body['label']) == "no")[0]
pos_sel = np.random.choice(poses, num, replace=False)
neg_sel = np.random.choice(negs, num*10, replace=False)
for id in pos_sel:
read.code_error(id)
for id in neg_sel:
read.code_error(id)
read.enable_est = True
read.get_numbers()
a,b,c,d = read.train()
set_trace()
def Codes(filename, code):
stop = 0.95
thres = 0
if "P" in code:
starting = 5
else:
starting = 1
weighting = "W" in code or "M" in code
uncertain = "U" in code
stopping = "S" in code
read = MAR()
read = read.create(filename)
read.restart()
read = MAR()
read = read.create(filename)
if not ("A" in code or "M" in code):
read.enough = 100000
target = int(read.get_allpos() * stop)
while True:
pos, neg, total = read.get_numbers()
# print("%d, %d" %(pos,pos+neg))
if pos >= target:
break
if pos < starting or pos + neg < thres:
for id in read.random():
read.code(id, read.body["label"][id])
else:
a, b, c, d, e = read.train(weighting=weighting)
if pos < 30 and uncertain:
for id in a:
read.code(id, read.body["label"][id])
else:
if stopping:
now = 0
while pos < target:
for id in e[now:now + read.step]:
read.code(id, read.body["label"][id])
pos, neg, total = read.get_numbers()
now = now + read.step
else:
for id in c:
read.code(id, read.body["label"][id])
return read
def LINEAR(filename):
read = MAR()
read = read.create(filename)
while True:
pos, neg, total = read.get_numbers()
if total - (pos + neg) < 10:
break
for id in read.random():
read.code(id, read.body["label"][id])
return read
def Boosting(filename, old_files = [], stop='', stopat=1, error='none', interval = 100000, starting =1, seed=0, step =10):
print("FILENAME: ", filename, "OLDFILES: ", len(old_files))
stopat = float(stopat)
np.random.seed(seed)
read = MAR()
read = read.create(filename,old_files)
read.step = step
read.interval = interval
util.vote(read)
num2 = read.get_allpos()
target = int(num2 * stopat)
if stop == 'est':
read.enable_est = True
else:
read.enable_est = False
pos, neg, total = read.get_numbers()
read.query_boost()
read.record['est'][0]= read.est_num
while True:
pos, neg, total = read.get_numbers()
try:
print("%d, %d, %d" %(pos,pos+neg, read.est_num))
except:
print("%d, %d" %(pos,pos+neg))
if pos + neg >= total:
break
if read.enable_est and read.est_num*stopat<= pos:
break
for id in read.query_boost()[:read.step]:
read.code_error(id, error=error)
return read
def TEST_AL(filename,
old_files=[],
stop='est',
stopat=1,
error='none',
interval=100000,
starting=1,
seed=0,
step=10):
stopat = float(stopat)
thres = 0
counter = 0
pos_last = 0
np.random.seed(seed)
read = MAR()
read = read.create(filename, old_files)
read.step = step
read.interval = interval
num2 = read.get_allpos()
target = int(num2 * stopat)
if stop == 'est':
read.enable_est = True
else:
read.enable_est = False
while True:
pos, neg, total = read.get_numbers()
try:
print("%d, %d, %d" % (pos, pos + neg, read.est_num))
except:
print("%d, %d" % (pos, pos + neg))
if pos + neg >= total:
break
if pos < starting or pos + neg < thres:
for id in read.random():
read.code_error(id, error=error)
else:
a, b, c, d = read.train(weighting=True, pne=True)
if pos >= target and read.est_num * stopat <= pos:
break
for id in c:
read.code_error(id, error=error)
# read.export()
# results = analyze(read)
# print(results)
# read.plot()
return read
def LOC(filename):
stop = 1
read = MAR()
read = read.create(filename)
target = int(read.get_allpos() * stop)
while True:
pos, neg, total = read.get_numbers()
print("%d, %d" % (pos, pos + neg))
if pos >= target:
break
for id in read.loc_sort():
read.code(id, read.body["label"][id])
return read
def START_ERROR(filename):
read = MAR()
read = read.create(filename)
pos_last = 0
full_life = 3
human_error = 0.2
life = full_life
while True:
pos, neg, total = read.get_numbers()
print("%d/ %d" % (pos, pos + neg))
if pos >= 10:
if pos == pos_last:
life = life - 1
if life == 0:
break
else:
life = full_life
if pos == 0:
for id in read.random():
if read.body["label"][id] == "no":
if random.random() < human_error**2:
hl = "yes"
else:
hl = "no"
elif read.body["label"][id] == "yes":
if random.random() < 2 * (human_error - human_error**2):
hl = "no"
else:
hl = "yes"
read.code(id, hl)
else:
a, b, ids, c = read.train()
for id in ids:
if read.body["label"][id] == "no":
if random.random() < human_error**2:
hl = "yes"
else:
hl = "no"
elif read.body["label"][id] == "yes":
if random.random() < 2 * (human_error - human_error**2):
hl = "no"
else:
hl = "yes"
read.code(id, hl)
pos_last = pos
read.export()
return read
def UPDATE(filename, old, pne=False, cl="RF"):
stop = 1
read = MAR()
read = read.create(filename)
read.create_old(old)
num2 = read.get_allpos()
target = int(num2 * stop)
while True:
pos, neg, total = read.get_numbers()
print("%d/ %d" % (pos, pos + neg))
if pos >= target:
break
a, b, ids, c = read.train(pne=pne, cl=cl)
for id in ids:
read.code(id, read.body["label"][id])
return read
def REUSE_RANDOM(filename, old):
stop = 0.9
read = MAR()
read = read.create(filename)
read.create_old(old)
num2 = read.get_allpos()
target = int(num2 * stop)
while True:
pos, neg, total = read.get_numbers()
# print("%d/ %d" % (pos,pos+neg))
if pos >= target:
break
a, b, ids, c = read.train_reuse_random()
for id in ids:
read.code(id, read.body["label"][id])
return read
def START_LOC(filename, cl="SVM-linear"):
stop = 1
read = MAR()
read = read.create(filename)
target = int(read.get_allpos() * stop)
while True:
pos, neg, total = read.get_numbers()
print("%d, %d" % (pos, pos + neg))
if pos >= target:
break
if pos == 0 or pos + neg < 40:
for id in read.loc_sort():
read.code(id, read.body["label"][id])
else:
a, b, ids, c = read.train(cl=cl)
for id in ids:
read.code(id, read.body["label"][id])
return read
def TIME_START(filename):
stop = 0.9
read = MAR()
read = read.create(filename)
num2 = read.get_allpos()
target = int(num2 * stop)
while True:
pos, neg, total = read.get_numbers()
# print("%d/ %d" % (pos,pos+neg))
if pos >= target:
break
if pos == 0:
for id in read.random():
read.code(id, read.body["label"][id])
else:
a, b, ids, c = read.train_kept()
for id in ids:
read.code(id, read.body["label"][id])
return read
def UPDATE_AUTO(filename, old, pne=True):
read = MAR()
read = read.create(filename)
read.create_old(old)
pos_last = -1
full_life = 5
life = full_life
while True:
pos, neg, total = read.get_numbers()
print("%d/ %d" % (pos, pos + neg))
if pos == pos_last:
life = life - 1
if life == 0:
break
else:
life = full_life
a, b, ids, c = read.train(pne)
for id in ids:
read.code(id, read.body["label"][id])
pos_last = pos
return read
def REUSE(filename, old, pne=True):
stop = 0.9
thres = 5
read = MAR()
read = read.create(filename)
read.create_old(old)
num2 = read.get_allpos()
target = int(num2 * stop)
while True:
pos, neg, total = read.get_numbers()
print("%d/ %d" % (pos, pos + neg))
if pos >= target:
break
if pos < thres:
a, b, ids, c = read.train(pne)
for id in ids:
read.code(id, read.body["label"][id])
else:
a, b, ids, c = read.train_reuse(pne)
for id in ids:
read.code(id, read.body["label"][id])
return read
def START_DOC2VEC(filename):
stop = 0.95
thres = 40
read = MAR()
read = read.create(filename)
read.restart()
read = MAR()
read = read.create(filename)
target = int(read.get_allpos() * stop)
while True:
pos, neg, total = read.get_numbers()
print("%d, %d" % (pos, pos + neg))
if pos >= target:
break
if pos == 0 or pos + neg < thres:
for id in read.random():
read.code(id, read.body["label"][id])
else:
a, b, c, d, e = read.train(weighting=True)
for id in c:
read.code(id, read.body["label"][id])
return read
def UPDATE_REUSE(filename, old):
stop = 0.9
lifes = 2
life = lifes
last_pos = 0
thres = 5
read = MAR()
read = read.create(filename)
read.create_old(old)
num2 = read.get_allpos()
target = int(num2 * stop)
while True:
pos, neg, total = read.get_numbers()
# print("%d/ %d" % (pos, pos + neg))
if pos - last_pos:
life = lifes
else:
life = life - 1
last_pos = pos
if pos >= target:
break
# if (pos >= thres or pos==0) and life<1:
if (pos >= thres) and life < 1:
# print("reuse")
lifes = 0
a, b, ids, c = read.train_reuse()
for id in ids:
read.code(id, read.body["label"][id])
else:
# print("update")
a, b, ids, c = read.train()
for id in ids:
read.code(id, read.body["label"][id])
return read
sys.path.append(root)
from mar import MAR
from pdb import set_trace
if __name__ == "__main__":
data_path = "Hall.csv"
target_recall = 0.95
thres = 10
query = "defect prediction"
read = MAR()
read = read.create(data_path)
read.enable_est = True
if query:
read.BM25(query.split())
while True:
pos, neg, total = read.get_numbers()
try:
print("%d, %d, %d" % (pos, pos + neg, read.est_num))
except:
print("%d, %d" % (pos, pos + neg))
if pos + neg >= total:
break
if pos < 1:
if query:
ids, scores = read.BM25_get()
for id in ids:
read.code(id, read.body["label"][id])
else:
for id in read.random():
def active_learning(filename,
query='',
stop='true',
stopat=0.95,
error='none',
interval=100000,
seed=0):
stopat = float(stopat)
thres = 0
starting = 1
counter = 0
pos_last = 0
np.random.seed(seed)
read = MAR()
read = read.create(filename)
read.interval = interval
read.BM25(query.strip().split('_'))
num2 = read.get_allpos()
target = int(num2 * stopat)
print("number of target, true/close here:", target)
if stop == 'est':
read.enable_est = True
else:
read.enable_est = False
while True:
pos, neg, total = read.get_numbers()
try:
print("%d, %d, %d" % (pos, pos + neg, read.est_num))
except:
print("%d, %d" % (pos, pos + neg))
if pos + neg >= total:
if stop == 'knee' and error == 'random':
coded = np.where(
np.array(read.body['code']) != "undetermined")[0]
seq = coded[np.argsort(read.body['time'][coded])]
part1 = set(seq[:read.kneepoint * read.step]) & set(
np.where(np.array(read.body['code']) == "no")[0])
part2 = set(seq[read.kneepoint * read.step:]) & set(
np.where(np.array(read.body['code']) == "yes")[0])
for id in part1 | part2:
read.code_error(id, error=error)
break
if pos < starting or pos + neg < thres:
for id in read.BM25_get():
read.code_error(id, error=error)
else:
a, b, c, d = read.train(weighting=True, pne=True)
if stop == 'est':
if stopat * read.est_num <= pos:
break
elif stop == 'soft':
if pos >= 10 and pos_last == pos:
counter = counter + 1
else:
counter = 0
pos_last = pos
if counter >= 5:
break
elif stop == 'knee':
if pos >= 10:
if read.knee():
if error == 'random':
coded = np.where(
np.array(read.body['code']) != "undetermined"
)[0]
seq = coded[np.argsort(
np.array(read.body['time'])[coded])]
part1 = set(
seq[:read.kneepoint * read.step]) & set(
np.where(
np.array(read.body['code']) == "no")
[0])
part2 = set(
seq[read.kneepoint * read.step:]) & set(
np.where(
np.array(read.body['code']) == "yes")
[0])
for id in part1 | part2:
read.code_error(id, error=error)
break
else:
if pos >= target:
break
if pos < 10:
for id in a:
read.code_error(id, error=error)
else:
for id in c:
read.code_error(id, error=error)
set_trace()
return read
def active_learning(filename,
query='',
stop='true',
stopat=1.00,
error='none',
interval=100000,
seed=0):
stopat = float(stopat)
thres = 0
starting = 1
counter = 0
pos_last = 0
np.random.seed(seed)
read = MAR()
read = read.create(filename)
# random sampling or by querying similar documents
# self.bm is provided with a list or a view of a dict's value which is not sorted
read.BM25(query.strip().split('_'))
# get the rest #pos documents
num2 = read.get_allpos()
target = int(
num2 * stopat
) # stopat is 1. Is it the minum num of pos to activate svm training ?
if stop == 'est': # stop = 'true'
read.enable_est = True
else:
read.enable_est = False # will excute this line
while True:
pos, neg, total = read.get_numbers()
try:
print("%d, %d, %d" %
(pos, pos + neg, read.est_num)) # what is est_num ?
except:
print("%d, %d" % (pos, pos + neg)) # execute this line
if pos + neg >= total: # do not go inside
if stop == 'knee' and error == 'random':
coded = np.where(
np.array(read.body['code']) != "undetermined")[0]
seq = coded[np.argsort(read.body['time'][coded])]
part1 = set(seq[:read.kneepoint * read.step]) & set(
np.where(np.array(read.body['code']) == "no")[0])
part2 = set(seq[read.kneepoint * read.step:]) & set(
np.where(np.array(read.body['code']) == "yes")[0])
for id in part1 | part2:
read.code_error(id, error=error)
break
if pos < starting or pos + neg < thres: # the second condition doesn't work
for id in read.BM25_get(
): # select a set of candidates from self.pool
read.code_error(
id, error=error
) # simulate human labeling error, default is no error
else:
a, b, c, d = read.train(weighting=True, pne=True)
if stop == 'est':
if stopat * read.est_num <= pos:
break
elif stop == 'soft':
if pos >= 10 and pos_last == pos:
counter = counter + 1
else:
counter = 0
pos_last = pos
if counter >= 5:
break
elif stop == 'knee':
if pos >= 10:
if read.knee():
if error == 'random':
coded = np.where(
np.array(read.body['code']) != "undetermined"
)[0]
seq = coded[np.argsort(
np.array(read.body['time'])[coded])]
part1 = set(
seq[:read.kneepoint * read.step]) & set(
np.where(
np.array(read.body['code']) == "no")
[0])
part2 = set(
seq[read.kneepoint * read.step:]) & set(
np.where(
np.array(read.body['code']) == "yes")
[0])
for id in part1 | part2:
read.code_error(id, error=error)
break
else:
if pos >= target:
break
if pos < 10:
for id in a:
read.code_error(id, error=error)
else:
for id in c:
read.code_error(id, error=error)
return read