def __call__(self, doc, **kwargs):
output_set_name = kwargs.get("outputASName", "GATEML")
doc_text = doc.text
current_gate_file_name = doc.features['gate.SourceURL']
current_gate_file_base_name = os.path.basename(current_gate_file_name)
#print(doc._name)
workingSet = doc.annset(self.workingSet)
config = {'TARGET': {'labels': self.mm.target_labels}}
test_dataIter = GateReader(postProcessor=self.readerPostProcessor,
config=config)
outputType = 'MLpred'
if self.instanceType:
outputType = self.instanceType
instanceSet = workingSet.with_type([self.instanceType])
for instanceAnno in instanceSet:
current_instance_text = doc_text[instanceAnno.
start:instanceAnno.end]
if self.targetFeature:
current_instance_target_feature = instanceAnno.features[
self.targetFeature]
else:
### add a dummy target
current_instance_target_feature = self.mm.target_labels[0]
test_dataIter.addSample(current_instance_text,
current_instance_target_feature,
anno_start=instanceAnno.start,
anno_end=instanceAnno.end)
else:
current_instance_text = doc_text
current_instance_target_feature = self.mm.target_labels[0]
if self.targetFile:
if current_gate_file_base_name in self.target_dict:
current_instance_target_feature = self.target_dict[
current_gate_file_base_name]
test_dataIter.addSample(current_instance_text,
current_instance_target_feature,
anno_start=0,
anno_end=len(current_instance_text))
test_dataIter._reset_iter()
apply_output_dict = self.mm.apply(test_dataIter)
output_set = doc.annset(output_set_name)
output_set.clear()
#print(apply_output_dict['all_cls_att'])
test_dataIter.postProcessor.postProcessMethod = 'postProcess4GATEapply'
for each_sample_id, dataIterItem in enumerate(test_dataIter):
each_sample = dataIterItem[0]
bert_tokenized = dataIterItem[1]
pred_score = apply_output_dict['all_prediction'][each_sample_id]
pred_label_string = apply_output_dict['all_pred_label_string'][
each_sample_id]
cls_att = apply_output_dict['all_cls_att'][each_sample_id]
anno_start = each_sample['anno_start']
anno_end = each_sample['anno_end']
output_feature_map = {
'pred_score': pred_score,
self.targetFeature: pred_label_string
}
output_set.add(anno_start, anno_end, outputType,
output_feature_map)
#recon_token_list, topn_indices, topn_values = single_att_reconstruction(bert_tokenized, cls_att)
#off_set_dict = construct_offset_id(doc_text, recon_token_list)
#print(len(recon_token_list), len(token_offset_list))
if self.resultsExportFile:
result_export_line = current_gate_file_base_name + '\t' + str(
anno_start) + '\t' + str(
anno_end) + '\t' + pred_label_string + '\t' + doc_text[
anno_start:anno_end] + '\n'
self.f_results_export.write(result_export_line)
if not self.instanceType and self.targetFile and self.target2GateType:
output_feature_map = {
self.targetFeature: each_sample['target']
}
output_set.add(anno_start, anno_end, self.target2GateType,
output_feature_map)
###export attention
#for att_id, att_word_index in enumerate(topn_indices):
# att_score = topn_values[att_id]
# if att_word_index in off_set_dict:
# att_feature_map = {'score':str(att_score)}
# print(off_set_dict[att_word_index][0], off_set_dict[att_word_index][1], len(doc_text))
# output_set.add(off_set_dict[att_word_index][0], off_set_dict[att_word_index][1], 'attentions', att_feature_map)
test_dataIter.postProcessor.postProcessMethod = 'postProcess4Model'
class GateMLTrain:
def __init__(self):
self.script_path = os.path.abspath(__file__)
self.processorLoger = getLogger('processorLoger')
def start(self, **kwargs):
#print(kwargs)
#self.all_doc = []
readerPostProcessor = BertPostProcessor(x_fields=['text'], y_field='target')
self.train_dataIter = GateReader(postProcessor=readerPostProcessor, shuffle=True)
self.workingSet = kwargs.get('workingSet', '')
self.instanceType = kwargs.get('instanceType', None)
self.targetType = kwargs.get('targetType', None)
self.targetFeature = kwargs.get('targetFeature', None)
self.targetFile = kwargs.get('targetFile', None)
self.gpu = str_to_bool(kwargs.get('gpu', 'False'))
self.model_path = kwargs.get('model_path')
if self.targetFile:
self.target_dict = {}
with open(self.targetFile, 'r') as ft:
for each_line_id, each_line in enumerate(ft):
if each_line_id == 0:
self.file_suffix = each_line.strip()
else:
line_tok = each_line.split('\t')
self.target_dict[line_tok[0]] = line_tok[1].strip()
def finish(self, **kwargs):
self.train_dataIter.finaliseReader()
print(len(self.train_dataIter))
val_dataIter = None
print(self.train_dataIter.target_labels)
dummy_config = {'MODEL':{'n_classes':len(self.train_dataIter.target_labels)}}
self.mm = ModelManager(gpu=self.gpu, config=dummy_config)
self.mm.genPreBuildModel()
if 'splitValidation' in kwargs:
self.train_dataIter, val_dataIter = self.mm.splitValidation(self.train_dataIter, val_split=float(kwargs.get('splitValidation')))
self.mm.train(self.train_dataIter, save_path=self.model_path, valDataIter=val_dataIter, earlyStopping=True, patience=5)
def __call__(self, doc, **kwargs):
doc_text = doc.text
#print(doc._name)
#print(doc.features)
current_gate_file_name = doc.features['gate.SourceURL']
current_gate_file_base_name = os.path.basename(current_gate_file_name)
#print(current_gate_file_base_name)
workingSet = doc.annset(self.workingSet)
if self.instanceType:
instanceSet = workingSet.with_type([self.instanceType])
for instanceAnno in instanceSet:
#print(instanceAnno)
#print(instanceAnno.start)
#print(instanceAnno.end)
current_instance_text = doc_text[instanceAnno.start:instanceAnno.end]
current_instance_target_feature = instanceAnno.features[self.targetFeature]
#print(current_instance_text, current_instance_target_feature)
self.train_dataIter.addSample(current_instance_text, current_instance_target_feature)
elif self.targetFile:
current_instance_text = doc_text
if current_gate_file_base_name in self.target_dict:
current_instance_target_feature = self.target_dict[current_gate_file_base_name]
self.train_dataIter.addSample(current_instance_text, current_instance_target_feature)
else:
infomessage = 'no target found discard '+current_gate_file_name
self.processorLoger.info(infomessage)
def __call__(self, doc, **kwargs):
output_set_name = kwargs.get("outputASName", "GATEML")
doc_text = doc.text
current_gate_file_name = doc.features['gate.SourceURL']
current_gate_file_base_name = os.path.basename(current_gate_file_name)
#print(doc._name)
workingSet = doc.annset(self.workingSet)
config = {'TARGET': {'labels': self.mm.target_labels}}
test_dataIter = GateReader(postProcessor=self.readerPostProcessor,
config=config)
outputType = 'MLpred'
if self.instanceType:
outputType = self.instanceType
instanceSet = workingSet.with_type([self.instanceType])
for instanceAnno in instanceSet:
current_instance_text = doc_text[instanceAnno.
start:instanceAnno.end]
if self.targetFeature:
current_instance_target_feature = instanceAnno.features[
self.targetFeature]
else:
### add a dummy target
current_instance_target_feature = self.mm.target_labels[0]
test_dataIter.addSample(current_instance_text,
current_instance_target_feature,
anno_start=instanceAnno.start,
anno_end=instanceAnno.end)
else:
current_instance_text = doc_text
current_instance_target_feature = self.mm.target_labels[0]
if self.targetFile:
if current_gate_file_base_name in self.target_dict:
current_instance_target_feature = self.target_dict[
current_gate_file_base_name]
test_dataIter.addSample(current_instance_text,
current_instance_target_feature,
anno_start=0,
anno_end=len(current_instance_text))
test_dataIter._reset_iter()
apply_output_dict = self.mm.apply(test_dataIter)
output_set = doc.annset(output_set_name)
output_set.clear()
test_dataIter.goPoseprocessor = False
for each_sample_id, each_sample in enumerate(test_dataIter):
pred_score = apply_output_dict['all_prediction'][each_sample_id]
pred_label_string = apply_output_dict['all_pred_label_string'][
each_sample_id]
anno_start = each_sample['anno_start']
anno_end = each_sample['anno_end']
output_feature_map = {
'pred_score': pred_score,
self.targetFeature: pred_label_string
}
output_set.add(anno_start, anno_end, outputType,
output_feature_map)
if self.resultsExportFile:
result_export_line = current_gate_file_base_name + '\t' + str(
anno_start) + '\t' + str(
anno_end) + '\t' + pred_label_string + '\t' + doc_text[
anno_start:anno_end] + '\n'
self.f_results_export.write(result_export_line)