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Tensor_exp.py
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Tensor_exp.py
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#! /usr/bin/python
from model import *
# Utils ----------------------------------------------------------------------
def load_file(path):
return scipy.sparse.csr_matrix(cPickle.load(open(path)),
dtype=theano.config.floatX)
def compute_prauc(pred, lab):
pred = np.asarray(pred)
lab = np.asarray(lab)
order = np.argsort(pred)
lab_ordered = lab[order]
pred_ordered = pred[order]
precision = {}
recall = {}
# All examples are classified 1
precision[np.min(pred_ordered) - 1.0] = (np.sum(lab_ordered) /
float(len(lab)))
recall[np.min(pred_ordered) - 1.0] = 1.
for i in range(len(lab)):
if len(lab) - i - 1 == 0:
# No examples are classified 1
precision[pred_ordered[i]] = 1
else:
precision[pred_ordered[i]] = (np.sum(lab_ordered[i + 1:]) /
float(len(lab) - i - 1))
recall[pred_ordered[i]] = (np.sum(lab_ordered[i + 1:]) /
float(np.sum(lab_ordered)))
# Precision-Recall curve points
points = []
for i in np.sort(precision.keys())[::-1]:
points += [(float(recall[i]), float(precision[i]))]
# Compute area
auc = sum((y0 + y1) / 2. * (x1 - x0) for (x0, y0), (x1, y1) in
zip(points[:-1], points[1:]))
return auc
class DD(dict):
"""This class is only used to replace a state variable of Jobman"""
def __getattr__(self, attr):
if attr == '__getstate__':
return super(DD, self).__getstate__
elif attr == '__setstate__':
return super(DD, self).__setstate__
elif attr == '__slots__':
return super(DD, self).__slots__
return self[attr]
def __setattr__(self, attr, value):
assert attr not in ('__getstate__', '__setstate__', '__slots__')
self[attr] = value
def __str__(self):
return 'DD%s' % dict(self)
def __repr__(self):
return str(self)
def __deepcopy__(self, memo):
z = DD()
for k, kv in self.iteritems():
z[k] = copy.deepcopy(kv, memo)
return z
# ----------------------------------------------------------------------------
# Experiment function --------------------------------------------------------
def Tensorexp(state, channel):
# Show experiment parameters
print >> sys.stderr, state
np.random.seed(state.seed)
# Experiment folder
if hasattr(channel, 'remote_path'):
state.savepath = channel.remote_path + '/'
elif hasattr(channel, 'path'):
state.savepath = channel.path + '/'
else:
if not os.path.isdir(state.savepath):
os.mkdir(state.savepath)
# Positives
trainl = load_file(state.datapath + state.dataset +
'-train-pos-lhs-fold%s.pkl' % state.fold)
trainr = load_file(state.datapath + state.dataset +
'-train-pos-rhs-fold%s.pkl' % state.fold)
traino = load_file(state.datapath + state.dataset +
'-train-pos-rel-fold%s.pkl' % state.fold)
if state.op == 'SE':
traino = traino[-state.Nrel:, :]
# Negatives
trainln = load_file(state.datapath + state.dataset +
'-train-neg-lhs-fold%s.pkl' % state.fold)
trainrn = load_file(state.datapath + state.dataset +
'-train-neg-rhs-fold%s.pkl' % state.fold)
trainon = load_file(state.datapath + state.dataset +
'-train-neg-rel-fold%s.pkl' % state.fold)
if state.op == 'SE':
trainon = trainon[-state.Nrel:, :]
# Valid set
validl = load_file(state.datapath + state.dataset +
'-valid-lhs-fold%s.pkl' % state.fold)
validr = load_file(state.datapath + state.dataset +
'-valid-rhs-fold%s.pkl' % state.fold)
valido = load_file(state.datapath + state.dataset +
'-valid-rel-fold%s.pkl' % state.fold)
if state.op == 'SE':
valido = valido[-state.Nrel:, :]
outvalid = cPickle.load(open(state.datapath +
'%s-valid-targets-fold%s.pkl' % (state.dataset, state.fold)))
# Test set
testl = load_file(state.datapath + state.dataset +
'-test-lhs-fold%s.pkl' % state.fold)
testr = load_file(state.datapath + state.dataset +
'-test-rhs-fold%s.pkl' % state.fold)
testo = load_file(state.datapath + state.dataset +
'-test-rel-fold%s.pkl' % state.fold)
if state.op == 'SE':
testo = testo[-state.Nrel:, :]
outtest = cPickle.load(open(state.datapath +
'%s-test-targets-fold%s.pkl' % (state.dataset, state.fold)))
# Model declaration
if not state.loadmodel:
# operators
if state.op == 'Unstructured':
leftop = Unstructured()
rightop = Unstructured()
elif state.op == 'SME_lin':
leftop = LayerLinear(np.random, 'lin', state.ndim, state.ndim,
state.nhid, 'left')
rightop = LayerLinear(np.random, 'lin', state.ndim, state.ndim,
state.nhid, 'right')
elif state.op == 'SME_bil':
leftop = LayerBilinear(np.random, 'lin', state.ndim, state.ndim,
state.nhid, 'left')
rightop = LayerBilinear(np.random, 'lin', state.ndim, state.ndim,
state.nhid, 'right')
elif state.op == 'SE':
leftop = LayerMat('lin', state.ndim, state.nhid)
rightop = LayerMat('lin', state.ndim, state.nhid)
# embeddings
if not state.loademb:
embeddings = Embeddings(np.random, state.Nent, state.ndim, 'emb')
else:
f = open(state.loademb)
embeddings = cPickle.load(f)
f.close()
if state.op == 'SE' and type(embeddings) is not list:
relationl = Embeddings(np.random, state.Nrel,
state.ndim * state.nhid, 'rell')
relationr = Embeddings(np.random, state.Nrel,
state.ndim * state.nhid, 'relr')
embeddings = [embeddings, relationl, relationr]
simfn = eval(state.simfn + 'sim')
else:
f = open(state.loadmodel)
embeddings = cPickle.load(f)
leftop = cPickle.load(f)
rightop = cPickle.load(f)
simfn = cPickle.load(f)
f.close()
# Functions compilation
trainfunc = TrainFn(simfn, embeddings, leftop, rightop, marge=state.marge)
testfunc = SimFn(simfn, embeddings, leftop, rightop)
out = []
outb = []
state.bestvalid = -1
batchsize = trainl.shape[1] / state.nbatches
print >> sys.stderr, "BEGIN TRAINING"
timeref = time.time()
for epoch_count in xrange(1, state.totepochs + 1):
# Shuffling
order = np.random.permutation(trainl.shape[1])
trainl = trainl[:, order]
trainr = trainr[:, order]
traino = traino[:, order]
order = np.random.permutation(trainln.shape[1])
trainln = trainln[:, order]
trainrn = trainrn[:, order]
trainon = trainon[:, order]
for i in range(state.nbatches):
tmpl = trainl[:, i * batchsize:(i + 1) * batchsize]
tmpr = trainr[:, i * batchsize:(i + 1) * batchsize]
tmpo = traino[:, i * batchsize:(i + 1) * batchsize]
tmpln = trainln[:, i * batchsize:(i + 1) * batchsize]
tmprn = trainrn[:, i * batchsize:(i + 1) * batchsize]
tmpon = trainon[:, i * batchsize:(i + 1) * batchsize]
# training iteration
outtmp = trainfunc(state.lremb, state.lrparam / float(batchsize),
tmpl, tmpr, tmpo, tmpln, tmprn, tmpon)
out += [outtmp[0] / float(batchsize)]
outb += [outtmp[1]]
# embeddings normalization
if type(embeddings) is list:
embeddings[0].normalize()
else:
embeddings.normalize()
if (epoch_count % state.test_all) == 0:
# model evaluation
print >> sys.stderr, "-- EPOCH %s (%s seconds per epoch):" % (
epoch_count,
round(time.time() - timeref, 3) / float(state.test_all))
timeref = time.time()
print >> sys.stderr, "COST >> %s +/- %s, %% updates: %s%%" % (
round(np.mean(out), 4), round(np.std(out), 4),
round(np.mean(outb) * 100, 3))
out = []
outb = []
valsim = testfunc(validl, validr, valido)[0]
state.valid = compute_prauc(valsim, outvalid)
print >> sys.stderr, "\tPR AUC >> valid: %s" % (state.valid)
if state.bestvalid == -1 or state.valid > state.bestvalid:
testsim = testfunc(testl, testr, testo)[0]
state.besttest = compute_prauc(testsim, outtest)
state.bestvalid = state.valid
state.bestepoch = epoch_count
# Save model best valid model
f = open(state.savepath + '/best_valid_model.pkl', 'w')
cPickle.dump(embeddings, f, -1)
cPickle.dump(leftop, f, -1)
cPickle.dump(rightop, f, -1)
cPickle.dump(simfn, f, -1)
f.close()
print >> sys.stderr, "\t\t##### NEW BEST VALID >> test: %s" % (
state.besttest)
# Save current model
f = open(state.savepath + '/current_model.pkl', 'w')
cPickle.dump(embeddings, f, -1)
cPickle.dump(leftop, f, -1)
cPickle.dump(rightop, f, -1)
cPickle.dump(simfn, f, -1)
f.close()
state.nbepochs = epoch_count
print >> sys.stderr, "\t(the evaluation took %s seconds)" % (
round(time.time() - timeref, 3))
timeref = time.time()
channel.save()
return channel.COMPLETE
def launch(datapath='data/', dataset='umls', fold=0, Nent=184,
Nrel=49, loadmodel=False, loademb=False, op='Unstructured',
simfn='Dot', ndim=50, nhid=50, marge=1., lremb=0.1, lrparam=1.,
nbatches=100, totepochs=2000, test_all=1, seed=666, savepath='.'):
# Argument of the experiment script
state = DD()
state.datapath = datapath
state.dataset = dataset
state.fold = fold
state.Nent = Nent
state.Nrel = Nrel
state.loadmodel = loadmodel
state.loademb = loademb
state.op = op
state.simfn = simfn
state.ndim = ndim
state.nhid = nhid
state.marge = marge
state.lremb = lremb
state.lrparam = lrparam
state.nbatches = nbatches
state.totepochs = totepochs
state.test_all = test_all
state.seed = seed
state.savepath = savepath
if not os.path.isdir(state.savepath):
os.mkdir(state.savepath)
# Jobman channel remplacement
class Channel(object):
def __init__(self, state):
self.state = state
f = open(self.state.savepath + '/orig_state.pkl', 'w')
cPickle.dump(self.state, f, -1)
f.close()
self.COMPLETE = 1
def save(self):
f = open(self.state.savepath + '/current_state.pkl', 'w')
cPickle.dump(self.state, f, -1)
f.close()
channel = Channel(state)
Tensorexp(state, channel)
if __name__ == '__main__':
launch()