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提交 d5064e86 作者: 朱学凯
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add token type ids

上级 e92d1555
正在显示 包含 177 行增加 和 188 行删除
.idea/CPI.iml
<?xml version="1.0" encoding="UTF-8"?> <?xml version="1.0" encoding="UTF-8"?>
<module type="PYTHON_MODULE" version="4"> <module type="PYTHON_MODULE" version="4">
<component name="NewModuleRootManager"> <component name="NewModuleRootManager">
<content url="file://$MODULE_DIR$" /> <content url="file://$MODULE_DIR$" />
<orderEntry type="jdk" jdkName="Python 3.6 (py3.6)" jdkType="Python SDK" /> <orderEntry type="jdk" jdkName="Python 3.6 (py3.6)" jdkType="Python SDK" />
<orderEntry type="sourceFolder" forTests="false" /> <orderEntry type="sourceFolder" forTests="false" />
</component> </component>
</module> </module>
\ No newline at end of file
.idea/inspectionProfiles/Project_Default.xml 0 → 100644
<component name="InspectionProjectProfileManager">
<profile version="1.0">
<option name="myName" value="Project Default" />
<inspection_tool class="PyPackageRequirementsInspection" enabled="true" level="WARNING" enabled_by_default="true">
<option name="ignoredPackages">
<value>
<list size="1">
<item index="0" class="java.lang.String" itemvalue="subword-nmt" />
</list>
</value>
</option>
</inspection_tool>
</profile>
</component>
\ No newline at end of file
.idea/misc.xml
<?xml version="1.0" encoding="UTF-8"?> <?xml version="1.0" encoding="UTF-8"?>
<project version="4"> <project version="4">
<component name="ProjectRootManager" version="2" project-jdk-name="Python 3.6 (py3.6)" project-jdk-type="Python SDK" /> <component name="ProjectRootManager" version="2" project-jdk-name="Python 3.6 (py3.6)" project-jdk-type="Python SDK" />
</project> </project>
\ No newline at end of file
.idea/modules.xml
<?xml version="1.0" encoding="UTF-8"?> <?xml version="1.0" encoding="UTF-8"?>
<project version="4"> <project version="4">
<component name="ProjectModuleManager"> <component name="ProjectModuleManager">
<modules> <modules>
<module fileurl="file://$PROJECT_DIR$/.idea/CPI.iml" filepath="$PROJECT_DIR$/.idea/CPI.iml" /> <module fileurl="file://$PROJECT_DIR$/.idea/CPI.iml" filepath="$PROJECT_DIR$/.idea/CPI.iml" />
</modules> </modules>
</component> </component>
</project> </project>
\ No newline at end of file
.idea/shelf/Uncommitted_changes_before_Update_at_2021_4_11,_11_03_上午_[Default_Changelist]/shelved.patch deleted 100644 → 0
Index: .idea/workspace.xml ++ /dev/null
Index: .idea/workspace.xml
IDEA additional info:
Subsystem: com.intellij.openapi.diff.impl.patch.BaseRevisionTextPatchEP
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Subsystem: com.intellij.openapi.diff.impl.patch.CharsetEP
<+>UTF-8
===================================================================
diff --git a/.idea/workspace.xml b/.idea/workspace.xml
--- a/.idea/workspace.xml (revision d2a304581cb05de7f85d60774094ec940d9ff199)
+++ b/.idea/workspace.xml (date 1618051977139)
@@ -3,7 +3,6 @@
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<option name="SHOW_DIALOG" value="false" />
<option name="HIGHLIGHT_CONFLICTS" value="true" />
@@ -65,7 +64,7 @@
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<option name="presentableId" value="Default" />
<updated>1617788646167</updated>
- <workItem from="1617788647548" duration="5550000" />
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<servers />
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.idea/shelf/Uncommitted_changes_before_Update_at_2021_4_11__11_03___Default_Changelist_.xml deleted 100644 → 0
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\ No newline at end of file
.idea/vcs.xml
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<project version="4"> <project version="4">
<component name="VcsDirectoryMappings"> <component name="VcsDirectoryMappings">
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\ No newline at end of file
.idea/workspace.xml
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\ No newline at end of file
dataset.py
...@@ -136,12 +136,13 @@ class Data_Encoder(data.Dataset): ...@@ -136,12 +136,13 @@ class Data_Encoder(data.Dataset):
# tokenization # tokenization
d = self.dbpe.process_line(self.smile[index].strip()).split() d = self.dbpe.process_line(self.smile[index].strip()).split()
p = self.sps[index].strip().split(',') p = self.sps[index].strip().split(',')
y = np.float32(self.affinity[index].strip()) y = np.float64(self.affinity[index].strip())
input_seq = [self.begin_id] + d + [self.sep_id] + p + [self.sep_id] input_seq = [self.begin_id] + d + [self.sep_id] + p + [self.sep_id]
token_type_ids = np.concatenate((np.zeros((len(d) + 2), dtype=np.int), np.ones((len(p) + 1), dtype=np.int)))
token_type_ids = np.pad(token_type_ids, (0, self.max_len-len(input_seq)), 'constant', constant_values=0)
input, input_mask = seq2emb_encoder(input_seq, self.max_len, self.vocab) input, input_mask = seq2emb_encoder(input_seq, self.max_len, self.vocab)
return torch.from_numpy(input).long(), torch.from_numpy(token_type_ids).long(), y
return input, y
if __name__ == "__main__": if __name__ == "__main__":
......
modeling_bert.py
...@@ -202,7 +202,6 @@ class BertEmbeddings(nn.Module): ...@@ -202,7 +202,6 @@ class BertEmbeddings(nn.Module):
if inputs_embeds is None: if inputs_embeds is None:
inputs_embeds = self.word_embeddings(input_ids) inputs_embeds = self.word_embeddings(input_ids)
token_type_embeddings = self.token_type_embeddings(token_type_ids) token_type_embeddings = self.token_type_embeddings(token_type_ids)
embeddings = inputs_embeds + token_type_embeddings embeddings = inputs_embeds + token_type_embeddings
if self.position_embedding_type == "absolute": if self.position_embedding_type == "absolute":
position_embeddings = self.position_embeddings(position_ids) position_embeddings = self.position_embeddings(position_ids)
......
run_interaction.py
...@@ -7,7 +7,7 @@ from modeling_bert import BertAffinityModel ...@@ -7,7 +7,7 @@ from modeling_bert import BertAffinityModel
from torch.utils.tensorboard import SummaryWriter from torch.utils.tensorboard import SummaryWriter
import os import os
from tqdm import tqdm from tqdm import tqdm
torch.set_default_tensor_type(torch.DoubleTensor)
def get_task(task_name): def get_task(task_name):
if task_name.lower() == 'train': if task_name.lower() == 'train':
...@@ -63,14 +63,14 @@ def train(args, model, dataset): ...@@ -63,14 +63,14 @@ def train(args, model, dataset):
print('begin training') print('begin training')
# training # training
for epoch in range(args.epochs): for epoch in range(args.epochs):
for i, (input, affinity) in enumerate(data_generator): for i, (input, token_type_ids, affinity) in enumerate(data_generator):
# use cuda # use cuda
# input model # input model
if torch.cuda.is_available(): if torch.cuda.is_available():
pred_affinity = model(input.cuda().long()) pred_affinity = model(input_ids=input.cuda(), token_type_ids=token_type_ids.cuda())
loss = loss_fct(pred_affinity, affinity.cuda().unsqueeze(-1)) loss = loss_fct(pred_affinity, affinity.cuda().unsqueeze(-1))
else: else:
pred_affinity = model(input.long()) pred_affinity = model(input_ids=input, token_type_ids=token_type_ids)
loss = loss_fct(pred_affinity, affinity.unsqueeze(-1)) loss = loss_fct(pred_affinity, affinity.unsqueeze(-1))
step += 1 step += 1
writer.add_scalar('loss', loss, global_step=step) writer.add_scalar('loss', loss, global_step=step)
...@@ -175,12 +175,11 @@ if __name__ == '__main__': ...@@ -175,12 +175,11 @@ if __name__ == '__main__':
# local test # local test
# args.task = 'train' args.task = 'train'
# args.savedir='local_test_train' args.savedir='local_test_train'
# args.epochs = 10 args.epochs = 10
# args.lr = 1e-7 args.lr = 1e-5
# args.config = './config/config_layer_3.json' args.config = './config/config_layer_3.json'
# args.shuffle = True
......
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