def minibatch2input(self, batch, predict=False, topk=None):
if topk == None:
topk = 10000
topk = min(topk, len(batch[0]['selected_cands']['cands']))
n_ments = len(batch)
# only uisng negative samples when the document doesn't have any supervision (i.e. not CoNLL)
tps = [m['selected_cands']['true_pos'] >= 0 for m in batch]
if not predict and (self.args.multi_instance
or self.args.semisup) and not np.any(tps):
n_negs = self.args.n_negs
else:
n_negs = 0
# convert data items to pytorch inputs
token_ids = [
m['context'][0] +
m['context'][1] if len(m['context'][0]) + len(m['context'][1]) > 0
else [self.model.word_voca.unk_id] for m in batch
]
s_ltoken_ids = [m['snd_ctx'][0] for m in batch]
s_rtoken_ids = [m['snd_ctx'][1] for m in batch]
s_mtoken_ids = [m['snd_ment'] for m in batch]
entity_ids = torch.LongTensor(
[m['selected_cands']['cands'][:topk] for m in batch])
p_e_m = torch.FloatTensor(
[m['selected_cands']['p_e_m'][:topk] for m in batch])
entity_mask = torch.FloatTensor(
[m['selected_cands']['mask'][:topk] for m in batch])
true_pos = torch.LongTensor([
m['selected_cands']['true_pos']
if m['selected_cands']['true_pos'] < topk else -1 for m in batch
])
p_e_ent_net = torch.FloatTensor([
m['selected_cands']['p_e_ent_net'][:topk] for m in batch
]) if len(batch) > 1 else torch.zeros(1, entity_ids.shape[1])
if n_negs > 0:
# add n_negs negative samples at the beginning of lists
def ent_neg_sample(neg_cands_p_e_m, exclusive):
sample_ids = np.random.choice(len(neg_cands_p_e_m),
n_negs * 10)
all_samples = list(
zip(
np.array([s[0] for s in neg_cands_p_e_m
])[sample_ids].astype(int),
np.array([s[1] for s in neg_cands_p_e_m])[sample_ids]))
exclusive = set(exclusive)
samples = []
for s in all_samples:
if s[0] not in exclusive:
samples.append(s)
if len(samples) < n_negs:
samples = samples + [(self.model.entity_voca.unk_id, 1e-3)
] * (n_negs - len(samples))
else:
shuffle(samples)
samples = samples[:n_negs]
return np.array([s[0] for s in samples
]), np.array([s[1] for s in samples])
neg_cands_p_e_m = [list(zip(list(m['cands']), list(m['p_e_m']))) + \
(list(zip(list(m['neg_cands'], [1e-3] * len(m['neg_cands'])))) if len(m['cands']) <= topk else [])
for m in batch]
neg_cands_p_e_m = [
ent_neg_sample(si, entity_ids_i) for si, entity_ids_i in zip(
neg_cands_p_e_m, entity_ids.numpy())
]
neg_entity_ids = torch.Tensor(
[si[0].astype(float) for si in neg_cands_p_e_m]).long()
neg_p_e_m = torch.Tensor(
[si[1].astype(float) for si in neg_cands_p_e_m])
neg_entity_mask = torch.ones(n_ments, n_negs)
entity_ids = torch.cat([neg_entity_ids, entity_ids], dim=1)
entity_mask = torch.cat([neg_entity_mask, entity_mask], dim=1)
p_e_m = torch.cat([neg_p_e_m, p_e_m], dim=1)
true_pos = true_pos.add_(n_negs)
entity_ids = Variable(entity_ids.cuda())
true_pos = Variable(true_pos.cuda())
p_e_m = Variable(p_e_m.cuda())
p_e_ent_net = Variable(p_e_ent_net.cuda())
entity_mask = Variable(entity_mask.cuda())
token_ids, token_mask = utils.make_equal_len(
token_ids, self.model.word_voca.unk_id)
s_ltoken_ids, s_ltoken_mask = utils.make_equal_len(
s_ltoken_ids, self.model.snd_word_voca.unk_id, to_right=False)
s_rtoken_ids, s_rtoken_mask = utils.make_equal_len(
s_rtoken_ids, self.model.snd_word_voca.unk_id)
s_rtoken_ids = [l[::-1] for l in s_rtoken_ids]
s_rtoken_mask = [l[::-1] for l in s_rtoken_mask]
s_mtoken_ids, s_mtoken_mask = utils.make_equal_len(
s_mtoken_ids, self.model.snd_word_voca.unk_id)
token_ids = Variable(torch.LongTensor(token_ids).cuda())
token_mask = Variable(torch.FloatTensor(token_mask).cuda())
s_ltoken_ids = Variable(torch.LongTensor(s_ltoken_ids).cuda())
s_ltoken_mask = Variable(torch.FloatTensor(s_ltoken_mask).cuda())
s_rtoken_ids = Variable(torch.LongTensor(s_rtoken_ids).cuda())
s_rtoken_mask = Variable(torch.FloatTensor(s_rtoken_mask).cuda())
s_mtoken_ids = Variable(torch.LongTensor(s_mtoken_ids).cuda())
s_mtoken_mask = Variable(torch.FloatTensor(s_mtoken_mask).cuda())
ret = {
'token_ids': token_ids,
'token_mask': token_mask,
'entity_ids': entity_ids,
'entity_mask': entity_mask,
'p_e_m': p_e_m,
'p_e_ent_net': p_e_ent_net,
'true_pos': true_pos,
's_ltoken_ids': s_ltoken_ids,
's_ltoken_mask': s_ltoken_mask,
's_rtoken_ids': s_rtoken_ids,
's_rtoken_mask': s_rtoken_mask,
's_mtoken_ids': s_mtoken_ids,
's_mtoken_mask': s_mtoken_mask,
'n_negs': n_negs
}
return ret
def predict(self, data):
predictions = {items[0]['doc_name']: [] for items in data}
self.model.eval()
for batch in data: # each document is a minibatch
token_ids = [
m['context'][0] + m['context'][1] if len(m['context'][0]) +
len(m['context'][1]) > 0 else [self.model.word_voca.unk_id]
for m in batch
]
s_ltoken_ids = [m['snd_ctx'][0] for m in batch]
s_rtoken_ids = [m['snd_ctx'][1] for m in batch]
s_mtoken_ids = [m['snd_ment'] for m in batch]
lctx_ids = s_ltoken_ids
rctx_ids = s_rtoken_ids
m_ids = s_mtoken_ids
entity_ids = Variable(
torch.LongTensor([m['selected_cands']['cands']
for m in batch]).cuda())
p_e_m = Variable(
torch.FloatTensor(
[m['selected_cands']['p_e_m'] for m in batch]).cuda())
entity_mask = Variable(
torch.FloatTensor([m['selected_cands']['mask']
for m in batch]).cuda())
true_pos = Variable(
torch.LongTensor(
[m['selected_cands']['true_pos'] for m in batch]).cuda())
token_ids, token_mask = utils.make_equal_len(
token_ids, self.model.word_voca.unk_id)
s_ltoken_ids, s_ltoken_mask = utils.make_equal_len(
s_ltoken_ids, self.model.snd_word_voca.unk_id, to_right=False)
s_rtoken_ids, s_rtoken_mask = utils.make_equal_len(
s_rtoken_ids, self.model.snd_word_voca.unk_id)
s_rtoken_ids = [l[::-1] for l in s_rtoken_ids]
s_rtoken_mask = [l[::-1] for l in s_rtoken_mask]
s_mtoken_ids, s_mtoken_mask = utils.make_equal_len(
s_mtoken_ids, self.model.snd_word_voca.unk_id)
token_ids = Variable(torch.LongTensor(token_ids).cuda())
token_mask = Variable(torch.FloatTensor(token_mask).cuda())
# too ugly, but too lazy to fix it
self.model.s_ltoken_ids = Variable(
torch.LongTensor(s_ltoken_ids).cuda())
self.model.s_ltoken_mask = Variable(
torch.FloatTensor(s_ltoken_mask).cuda())
self.model.s_rtoken_ids = Variable(
torch.LongTensor(s_rtoken_ids).cuda())
self.model.s_rtoken_mask = Variable(
torch.FloatTensor(s_rtoken_mask).cuda())
self.model.s_mtoken_ids = Variable(
torch.LongTensor(s_mtoken_ids).cuda())
self.model.s_mtoken_mask = Variable(
torch.FloatTensor(s_mtoken_mask).cuda())
scores = self.model.forward(token_ids,
token_mask,
entity_ids,
entity_mask,
p_e_m,
gold=true_pos.view(-1, 1))
scores = scores.cpu().data.numpy()
# print out relation weights
if self.args.mode == 'eval' and self.args.print_rel:
print('================================')
weights = self.model._rel_ctx_ctx_weights.cpu().data.numpy()
voca = self.model.snd_word_voca
for i in range(len(batch)):
print(
' '.join([voca.id2word[id] for id in lctx_ids[i]]),
utils.tokgreen(' '.join(
[voca.id2word[id] for id in m_ids[i]])),
' '.join([voca.id2word[id] for id in rctx_ids[i]]))
for j in range(len(batch)):
if i == j:
continue
np.set_printoptions(precision=2)
print(
'\t', weights[:, i, j], '\t',
' '.join([voca.id2word[id] for id in lctx_ids[j]]),
utils.tokgreen(' '.join(
[voca.id2word[id] for id in m_ids[j]])),
' '.join([voca.id2word[id] for id in rctx_ids[j]]))
pred_ids = np.argmax(scores, axis=1)
pred_entities = [
m['selected_cands']['named_cands'][i]
if m['selected_cands']['mask'][i] == 1 else
(m['selected_cands']['named_cands'][0]
if m['selected_cands']['mask'][0] == 1 else 'NI')
for (i, m) in zip(pred_ids, batch)
]
# print(pred_entities)
doc_names = [m['doc_name'] for m in batch]
if self.args.mode == 'eval' and self.args.print_incorrect:
gold = [
item['selected_cands']['named_cands'][
item['selected_cands']['true_pos']]
if item['selected_cands']['true_pos'] >= 0 else 'UNKNOWN'
for item in batch
]
pred = pred_entities
for i in range(len(gold)):
if gold[i] != pred[i]:
print('--------------------------------------------')
# pprint(batch[i]['raw'])
print(gold[i], pred[i])
print(pred_ids[i], scores[i])
for dname, entity in zip(doc_names, pred_entities):
predictions[dname].append({'pred': (entity, 0.)})
return predictions
def predict(self, data):
predictions = {items[0]['doc_name']: [] for items in data}
self.model.eval()
for batch in data: # each document is a minibatch
token_ids = [
m['context'][0] + m['context'][1] if len(m['context'][0]) +
len(m['context'][1]) > 0 else [self.model.word_voca.unk_id]
for m in batch
]
s_ltoken_ids = [m['snd_ctx'][0] for m in batch]
s_rtoken_ids = [m['snd_ctx'][1] for m in batch]
s_mtoken_ids = [m['snd_ment'] for m in batch]
lctx_ids = s_ltoken_ids
rctx_ids = s_rtoken_ids
m_ids = s_mtoken_ids
entity_ids = Variable(
torch.LongTensor([m['selected_cands']['cands']
for m in batch]).to(device))
p_e_m = Variable(
torch.FloatTensor(
[m['selected_cands']['p_e_m'] for m in batch]).to(device))
entity_mask = Variable(
torch.FloatTensor([m['selected_cands']['mask']
for m in batch]).to(device))
true_pos = Variable(
torch.LongTensor([
m['selected_cands']['true_pos'] for m in batch
]).to(device))
token_ids, token_mask = utils.make_equal_len(
token_ids, self.model.word_voca.unk_id)
s_ltoken_ids, s_ltoken_mask = utils.make_equal_len(
s_ltoken_ids, self.model.snd_word_voca.unk_id, to_right=False)
s_rtoken_ids, s_rtoken_mask = utils.make_equal_len(
s_rtoken_ids, self.model.snd_word_voca.unk_id)
s_rtoken_ids = [l[::-1] for l in s_rtoken_ids]
s_rtoken_mask = [l[::-1] for l in s_rtoken_mask]
s_mtoken_ids, s_mtoken_mask = utils.make_equal_len(
s_mtoken_ids, self.model.snd_word_voca.unk_id)
token_ids = Variable(torch.LongTensor(token_ids).to(device))
token_mask = Variable(torch.FloatTensor(token_mask).to(device))
# too ugly, but too lazy to fix it
self.model.s_ltoken_ids = Variable(
torch.LongTensor(s_ltoken_ids).to(device))
self.model.s_ltoken_mask = Variable(
torch.FloatTensor(s_ltoken_mask).to(device))
self.model.s_rtoken_ids = Variable(
torch.LongTensor(s_rtoken_ids).to(device))
self.model.s_rtoken_mask = Variable(
torch.FloatTensor(s_rtoken_mask).to(device))
self.model.s_mtoken_ids = Variable(
torch.LongTensor(s_mtoken_ids).to(device))
self.model.s_mtoken_mask = Variable(
torch.FloatTensor(s_mtoken_mask).to(device))
scores = self.model.forward(token_ids,
token_mask,
entity_ids,
entity_mask,
p_e_m,
gold=true_pos.view(-1, 1))
scores = scores.cpu().data.numpy()
# print out relation weights
if self.args.mode == 'eval' and self.args.print_rel:
print('================================')
weights = self.model._rel_ctx_ctx_weights.cpu().data.numpy()
voca = self.model.snd_word_voca
for i in range(len(batch)):
print(
' '.join([voca.id2word[id] for id in lctx_ids[i]]),
utils.tokgreen(' '.join(
[voca.id2word[id] for id in m_ids[i]])),
' '.join([voca.id2word[id] for id in rctx_ids[i]]))
for j in range(len(batch)):
if i == j:
continue
np.set_printoptions(precision=2)
print(
'\t', weights[:, i, j], '\t',
' '.join([voca.id2word[id] for id in lctx_ids[j]]),
utils.tokgreen(' '.join(
[voca.id2word[id] for id in m_ids[j]])),
' '.join([voca.id2word[id] for id in rctx_ids[j]]))
pred_ids = np.argmax(scores, axis=1)
processed_scores = []
for i, score in enumerate(scores):
min_score = np.min(score)
if all(list(map(lambda x: x == min_score, score))):
processed_scores.append(scores[i].tolist())
continue
count = 0
for j, s in enumerate(score):
if s == min_score:
scores[i][j] = np.NINF
count += 1
non_inf_list = list(
filter(lambda x: x != float('-inf'), scores[i]))
mean = np.mean(non_inf_list)
processed_scores.append(
((scores[i] - mean) * len(non_inf_list) * 10).tolist())
e_x = np.exp(processed_scores -
np.amax(processed_scores, axis=1, keepdims=True))
softmax_scores = e_x / e_x.sum(axis=1, keepdims=True)
pred_scores = np.amax(np.array(processed_scores), axis=1)
pred_confidences = np.amax(softmax_scores, axis=1)
pred_entities = [
m['selected_cands']['named_cands'][i]
if m['selected_cands']['mask'][i] == 1 else
(m['selected_cands']['named_cands'][0]
if m['selected_cands']['mask'][0] == 1 else 'NIL')
for (i, m) in zip(pred_ids, batch)
]
doc_names = [m['doc_name'] for m in batch]
if self.args.mode == 'eval' and self.args.print_incorrect:
gold = [
item['selected_cands']['named_cands'][
item['selected_cands']['true_pos']]
if item['selected_cands']['true_pos'] >= 0 else 'UNKNOWN'
for item in batch
]
pred = pred_entities
for i in range(len(gold)):
if gold[i] != pred[i]:
print('--------------------------------------------')
pprint(batch[i]['raw'])
print(gold[i], pred[i])
for dname, entity, pred_score, pred_confidence in zip(
doc_names, pred_entities, pred_scores, pred_confidences):
predictions[dname].append({
'pred': (entity, 0.),
'score': pred_score,
'confidence': pred_confidence
})
return predictions
def train(self, org_train_dataset, org_dev_datasets, config):
print('extracting training data')
train_dataset = self.get_data_items(org_train_dataset, predict=False)
print('#train docs', len(train_dataset))
dev_datasets = []
for dname, data in org_dev_datasets:
dev_datasets.append((dname, self.get_data_items(data,
predict=True)))
print(dname, '#dev docs', len(dev_datasets[-1][1]))
print('creating optimizer')
optimizer = optim.Adam(
[p for p in self.model.parameters() if p.requires_grad],
lr=config['lr'])
best_f1 = -1
not_better_count = 0
is_counting = False
eval_after_n_epochs = self.args.eval_after_n_epochs
for e in range(config['n_epochs']):
shuffle(train_dataset)
total_loss = 0
for dc, batch in enumerate(
train_dataset): # each document is a minibatch
self.model.train()
optimizer.zero_grad()
# convert data items to pytorch inputs
token_ids = [
m['context'][0] + m['context'][1]
if len(m['context'][0]) + len(m['context'][1]) > 0 else
[self.model.word_voca.unk_id] for m in batch
]
s_ltoken_ids = [m['snd_ctx'][0] for m in batch]
s_rtoken_ids = [m['snd_ctx'][1] for m in batch]
s_mtoken_ids = [m['snd_ment'] for m in batch]
entity_ids = Variable(
torch.LongTensor(
[m['selected_cands']['cands'] for m in batch]).cuda())
true_pos = Variable(
torch.LongTensor([
m['selected_cands']['true_pos'] for m in batch
]).cuda())
p_e_m = Variable(
torch.FloatTensor(
[m['selected_cands']['p_e_m'] for m in batch]).cuda())
entity_mask = Variable(
torch.FloatTensor(
[m['selected_cands']['mask'] for m in batch]).cuda())
token_ids, token_mask = utils.make_equal_len(
token_ids, self.model.word_voca.unk_id)
s_ltoken_ids, s_ltoken_mask = utils.make_equal_len(
s_ltoken_ids,
self.model.snd_word_voca.unk_id,
to_right=False)
s_rtoken_ids, s_rtoken_mask = utils.make_equal_len(
s_rtoken_ids, self.model.snd_word_voca.unk_id)
s_rtoken_ids = [l[::-1] for l in s_rtoken_ids]
s_rtoken_mask = [l[::-1] for l in s_rtoken_mask]
s_mtoken_ids, s_mtoken_mask = utils.make_equal_len(
s_mtoken_ids, self.model.snd_word_voca.unk_id)
token_ids = Variable(torch.LongTensor(token_ids).cuda())
token_mask = Variable(torch.FloatTensor(token_mask).cuda())
# too ugly but too lazy to fix it
self.model.s_ltoken_ids = Variable(
torch.LongTensor(s_ltoken_ids).cuda())
self.model.s_ltoken_mask = Variable(
torch.FloatTensor(s_ltoken_mask).cuda())
self.model.s_rtoken_ids = Variable(
torch.LongTensor(s_rtoken_ids).cuda())
self.model.s_rtoken_mask = Variable(
torch.FloatTensor(s_rtoken_mask).cuda())
self.model.s_mtoken_ids = Variable(
torch.LongTensor(s_mtoken_ids).cuda())
self.model.s_mtoken_mask = Variable(
torch.FloatTensor(s_mtoken_mask).cuda())
scores = self.model.forward(token_ids,
token_mask,
entity_ids,
entity_mask,
p_e_m,
gold=true_pos.view(-1, 1))
loss = self.model.loss(scores, true_pos)
loss.backward()
optimizer.step()
# self.model.regularize(max_norm=100)
loss = loss.cpu().data.numpy()
total_loss += loss
print('epoch',
e,
"%0.2f%%" % (dc / len(train_dataset) * 100),
loss,
end='\r')
print('epoch', e, 'total loss', total_loss,
total_loss / len(train_dataset))
if (e + 1) % eval_after_n_epochs == 0:
dev_f1 = 0
for di, (dname, data) in enumerate(dev_datasets):
predictions = self.predict(data)
f1 = D.eval(org_dev_datasets[di][1], predictions)
print(dname, utils.tokgreen('micro F1: ' + str(f1)))
if dname == 'aida-A':
dev_f1 = f1
if config[
'lr'] == 1e-4 and dev_f1 >= self.args.dev_f1_change_lr:
eval_after_n_epochs = 2
is_counting = True
best_f1 = dev_f1
not_better_count = 0
config['lr'] = 1e-5
print('change learning rate to', config['lr'])
if self.args.mulrel_type == 'rel-norm':
optimizer = optim.Adam([
p
for p in self.model.parameters() if p.requires_grad
],
lr=config['lr'])
elif self.args.mulrel_type == 'ment-norm':
for param_group in optimizer.param_groups:
param_group['lr'] = config['lr']
if is_counting:
if dev_f1 < best_f1:
not_better_count += 1
else:
not_better_count = 0
best_f1 = dev_f1
print('save model to', self.args.model_path)
self.model.save(self.args.model_path)
if not_better_count == self.args.n_not_inc:
break
self.model.print_weight_norm()
def predict(self, data, topk=1):
predictions = {items[0]['doc_name']: [] for items in data}
self.model.eval()
for batch in data: # each document is a minibatch
token_ids = [m['context'][0] + m['context'][1]
if len(m['context'][0]) + len(m['context'][1]) > 0
else [self.model.word_voca.unk_id]
for m in batch]
s_ltoken_ids = [m['snd_ctx'][0] for m in batch]
s_rtoken_ids = [m['snd_ctx'][1] for m in batch]
s_mtoken_ids = [m['snd_ment'] for m in batch]
lctx_ids = s_ltoken_ids
rctx_ids = s_rtoken_ids
m_ids = s_mtoken_ids
entity_ids = Variable(torch.LongTensor([m['selected_cands']['cands'] for m in batch]).cuda())
p_e_m = Variable(torch.FloatTensor([m['selected_cands']['p_e_m'] for m in batch]).cuda())
entity_mask = Variable(torch.FloatTensor([m['selected_cands']['mask'] for m in batch]).cuda())
true_pos = Variable(torch.LongTensor([m['selected_cands']['true_pos'] for m in batch]).cuda())
token_ids, token_mask = utils.make_equal_len(token_ids, self.model.word_voca.unk_id)
s_ltoken_ids, s_ltoken_mask = utils.make_equal_len(s_ltoken_ids, self.model.snd_word_voca.unk_id,
to_right=False)
s_rtoken_ids, s_rtoken_mask = utils.make_equal_len(s_rtoken_ids, self.model.snd_word_voca.unk_id)
s_rtoken_ids = [l[::-1] for l in s_rtoken_ids]
s_rtoken_mask = [l[::-1] for l in s_rtoken_mask]
s_mtoken_ids, s_mtoken_mask = utils.make_equal_len(s_mtoken_ids, self.model.snd_word_voca.unk_id)
token_ids = Variable(torch.LongTensor(token_ids).cuda())
token_mask = Variable(torch.FloatTensor(token_mask).cuda())
# too ugly, but too lazy to fix it
self.model.s_ltoken_ids = Variable(torch.LongTensor(s_ltoken_ids).cuda())
self.model.s_ltoken_mask = Variable(torch.FloatTensor(s_ltoken_mask).cuda())
self.model.s_rtoken_ids = Variable(torch.LongTensor(s_rtoken_ids).cuda())
self.model.s_rtoken_mask = Variable(torch.FloatTensor(s_rtoken_mask).cuda())
self.model.s_mtoken_ids = Variable(torch.LongTensor(s_mtoken_ids).cuda())
self.model.s_mtoken_mask = Variable(torch.FloatTensor(s_mtoken_mask).cuda())
scores = self.model.forward(token_ids, token_mask, entity_ids, entity_mask, p_e_m,
gold=true_pos.view(-1, 1))
scores = scores.cpu().data.numpy()
if (topk == 1):
pred_ids = np.argmax(scores, axis=1)
pred_entities = [m['selected_cands']['named_cands'][i] if m['selected_cands']['mask'][i] == 1
else (m['selected_cands']['named_cands'][0] if m['selected_cands']['mask'][0] == 1 else 'NIL')
for (i, m) in zip(pred_ids, batch)]
doc_names = [m['doc_name'] for m in batch]
for dname, entity in zip(doc_names, pred_entities):
predictions[dname].append({'pred': (entity, 0.)})
else:
pred_ids = np.argsort(scores, axis=1)[:,::-1]
pred_entities = [[m['selected_cands']['named_cands'][i] if m['selected_cands']['mask'][i] == 1
else 'NIL' for i in ids]
for (ids, m) in zip(pred_ids, batch)]
doc_names = [m['doc_name'] for m in batch]
for dname, entities in zip(doc_names, pred_entities):
while len(entities)>=2 and entities[-1]=='NIL' and entities[-2]=='NIL':
del entities[-1]
predictions[dname].append({'pred': (entities, 0.)})
return predictions
