Skip to content

B
BiTransDPI
提交 5294c72d 作者: 朱学凯
操作

add save check point

上级 bd182dde
正在显示 包含 41 行增加 和 20 行删除
.idea/CPI.iml
...@@ -2,7 +2,7 @@ ...@@ -2,7 +2,7 @@
<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 (code)" 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/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 (code)" 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/workspace.xml
...@@ -2,8 +2,16 @@ ...@@ -2,8 +2,16 @@
<project version="4"> <project version="4">
<component name="ChangeListManager"> <component name="ChangeListManager">
<list default="true" id="f877ac68-9cea-46d8-9125-207eebe5b5d6" name="Default Changelist" comment=""> <list default="true" id="f877ac68-9cea-46d8-9125-207eebe5b5d6" name="Default Changelist" comment="">
<change beforePath="$PROJECT_DIR$/.idea/CPI.iml" beforeDir="false" afterPath="$PROJECT_DIR$/.idea/CPI.iml" afterDir="false" />
<change beforePath="$PROJECT_DIR$/.idea/misc.xml" beforeDir="false" afterPath="$PROJECT_DIR$/.idea/misc.xml" afterDir="false" />
<change beforePath="$PROJECT_DIR$/.idea/workspace.xml" beforeDir="false" afterPath="$PROJECT_DIR$/.idea/workspace.xml" afterDir="false" /> <change beforePath="$PROJECT_DIR$/.idea/workspace.xml" beforeDir="false" afterPath="$PROJECT_DIR$/.idea/workspace.xml" afterDir="false" />
<change beforePath="$PROJECT_DIR$/config/config.json" beforeDir="false" afterPath="$PROJECT_DIR$/config/config.json" afterDir="false" />
<change beforePath="$PROJECT_DIR$/config/config_layer_3.json" beforeDir="false" afterPath="$PROJECT_DIR$/config/config_layer_3.json" afterDir="false" />
<change beforePath="$PROJECT_DIR$/config/config_layer_6.json" beforeDir="false" afterPath="$PROJECT_DIR$/config/config_layer_6.json" afterDir="false" />
<change beforePath="$PROJECT_DIR$/config/config_layer_9.json" beforeDir="false" afterPath="$PROJECT_DIR$/config/config_layer_9.json" afterDir="false" />
<change beforePath="$PROJECT_DIR$/eval.py" beforeDir="false" afterPath="$PROJECT_DIR$/eval.py" afterDir="false" /> <change beforePath="$PROJECT_DIR$/eval.py" beforeDir="false" afterPath="$PROJECT_DIR$/eval.py" afterDir="false" />
<change beforePath="$PROJECT_DIR$/experment_result/loss.svg" beforeDir="false" />
<change beforePath="$PROJECT_DIR$/run_interaction.py" beforeDir="false" afterPath="$PROJECT_DIR$/run_interaction.py" afterDir="false" />
</list> </list>
<option name="SHOW_DIALOG" value="false" /> <option name="SHOW_DIALOG" value="false" />
<option name="HIGHLIGHT_CONFLICTS" value="true" /> <option name="HIGHLIGHT_CONFLICTS" value="true" />
...@@ -29,7 +37,12 @@ ...@@ -29,7 +37,12 @@
<property name="WebServerToolWindowFactoryState" value="false" /> <property name="WebServerToolWindowFactoryState" value="false" />
<property name="restartRequiresConfirmation" value="false" /> <property name="restartRequiresConfirmation" value="false" />
</component> </component>
<component name="RunManager" selected="Python.eval"> <component name="RecentsManager">
<key name="MoveFile.RECENT_KEYS">
<recent name="E:\CPI\project\CPI\predict\lr-1e-6-batch-64-layer3-0413-4-17677" />
</key>
</component>
<component name="RunManager" selected="Python.run_interaction">
<configuration name="eval" type="PythonConfigurationType" factoryName="Python" temporary="true" nameIsGenerated="true"> <configuration name="eval" type="PythonConfigurationType" factoryName="Python" temporary="true" nameIsGenerated="true">
<module name="CPI" /> <module name="CPI" />
<option name="INTERPRETER_OPTIONS" value="" /> <option name="INTERPRETER_OPTIONS" value="" />
...@@ -76,8 +89,8 @@ ...@@ -76,8 +89,8 @@
</configuration> </configuration>
<recent_temporary> <recent_temporary>
<list> <list>
<item itemvalue="Python.eval" />
<item itemvalue="Python.run_interaction" /> <item itemvalue="Python.run_interaction" />
<item itemvalue="Python.eval" />
</list> </list>
</recent_temporary> </recent_temporary>
</component> </component>
...@@ -108,7 +121,8 @@ ...@@ -108,7 +121,8 @@
</option> </option>
</component> </component>
<component name="com.intellij.coverage.CoverageDataManagerImpl"> <component name="com.intellij.coverage.CoverageDataManagerImpl">
<SUITE FILE_PATH="coverage/CPI$eval.coverage" NAME="eval Coverage Results" MODIFIED="1618307776551" SOURCE_PROVIDER="com.intellij.coverage.DefaultCoverageFileProvider" RUNNER="coverage.py" COVERAGE_BY_TEST_ENABLED="true" COVERAGE_TRACING_ENABLED="false" WORKING_DIRECTORY="$PROJECT_DIR$" /> <SUITE FILE_PATH="coverage/CPI$run_interaction.coverage" NAME="run_interaction Coverage Results" MODIFIED="1618474485850" SOURCE_PROVIDER="com.intellij.coverage.DefaultCoverageFileProvider" RUNNER="coverage.py" COVERAGE_BY_TEST_ENABLED="true" COVERAGE_TRACING_ENABLED="false" WORKING_DIRECTORY="$PROJECT_DIR$" />
<SUITE FILE_PATH="coverage/CPI$run_interaction.coverage" NAME="run_interaction Coverage Results" MODIFIED="1618133791228" SOURCE_PROVIDER="com.intellij.coverage.DefaultCoverageFileProvider" RUNNER="coverage.py" COVERAGE_BY_TEST_ENABLED="true" COVERAGE_TRACING_ENABLED="false" WORKING_DIRECTORY="$PROJECT_DIR$" /> <SUITE FILE_PATH="coverage/CPI$eval.coverage" NAME="eval Coverage Results" MODIFIED="1618326256952" SOURCE_PROVIDER="com.intellij.coverage.DefaultCoverageFileProvider" RUNNER="coverage.py" COVERAGE_BY_TEST_ENABLED="true" COVERAGE_TRACING_ENABLED="false" WORKING_DIRECTORY="$PROJECT_DIR$" />
<SUITE FILE_PATH="coverage/CPI$draft.coverage" NAME="draft Coverage Results" MODIFIED="1617456765793" SOURCE_PROVIDER="com.intellij.coverage.DefaultCoverageFileProvider" RUNNER="coverage.py" COVERAGE_BY_TEST_ENABLED="true" COVERAGE_TRACING_ENABLED="false" WORKING_DIRECTORY="$PROJECT_DIR$" />
</component> </component>
</project> </project>
\ No newline at end of file
config/config.json
...@@ -5,14 +5,14 @@ ...@@ -5,14 +5,14 @@
"attention_probs_dropout_prob": 0.1, "attention_probs_dropout_prob": 0.1,
"hidden_act": "gelu", "hidden_act": "gelu",
"hidden_dropout_prob": 0.1, "hidden_dropout_prob": 0.1,
"hidden_size": 768, "hidden_size": 384,
"initializer_range": 0.02, "initializer_range": 0.02,
"intermediate_size": 1536, "intermediate_size": 1536,
"layer_norm_eps": 1e-12, "layer_norm_eps": 1e-12,
"max_position_embeddings": 512, "max_position_embeddings": 384,
"model_type": "bert", "model_type": "bert",
"num_attention_heads": 12, "num_attention_heads": 12,
"num_hidden_layers": 3, "num_hidden_layers": 12,
"pad_token_id": 0, "pad_token_id": 0,
"type_vocab_size": 2, "type_vocab_size": 2,
"vocab_size": 23615 "vocab_size": 23615
......
config/config_layer_3.json
...@@ -9,7 +9,7 @@ ...@@ -9,7 +9,7 @@
"initializer_range": 0.02, "initializer_range": 0.02,
"intermediate_size": 1536, "intermediate_size": 1536,
"layer_norm_eps": 1e-12, "layer_norm_eps": 1e-12,
"max_position_embeddings": 512, "max_position_embeddings": 384,
"model_type": "bert", "model_type": "bert",
"num_attention_heads": 12, "num_attention_heads": 12,
"num_hidden_layers": 3, "num_hidden_layers": 3,
......
config/config_layer_6.json
...@@ -5,11 +5,11 @@ ...@@ -5,11 +5,11 @@
"attention_probs_dropout_prob": 0.1, "attention_probs_dropout_prob": 0.1,
"hidden_act": "gelu", "hidden_act": "gelu",
"hidden_dropout_prob": 0.1, "hidden_dropout_prob": 0.1,
"hidden_size": 768, "hidden_size": 384,
"initializer_range": 0.02, "initializer_range": 0.02,
"intermediate_size": 3072, "intermediate_size": 1536,
"layer_norm_eps": 1e-12, "layer_norm_eps": 1e-12,
"max_position_embeddings": 512, "max_position_embeddings": 384,
"model_type": "bert", "model_type": "bert",
"num_attention_heads": 12, "num_attention_heads": 12,
"num_hidden_layers": 6, "num_hidden_layers": 6,
......
config/config_layer_9.json
...@@ -5,11 +5,11 @@ ...@@ -5,11 +5,11 @@
"attention_probs_dropout_prob": 0.1, "attention_probs_dropout_prob": 0.1,
"hidden_act": "gelu", "hidden_act": "gelu",
"hidden_dropout_prob": 0.1, "hidden_dropout_prob": 0.1,
"hidden_size": 768, "hidden_size": 384,
"initializer_range": 0.02, "initializer_range": 0.02,
"intermediate_size": 3072, "intermediate_size": 1536,
"layer_norm_eps": 1e-12, "layer_norm_eps": 1e-12,
"max_position_embeddings": 512, "max_position_embeddings": 384,
"model_type": "bert", "model_type": "bert",
"num_attention_heads": 12, "num_attention_heads": 12,
"num_hidden_layers": 9, "num_hidden_layers": 9,
......
eval.py
...@@ -29,6 +29,6 @@ def eval(pred_path, label_path): ...@@ -29,6 +29,6 @@ def eval(pred_path, label_path):
if __name__ == '__main__': if __name__ == '__main__':
pred_result = './predict/lr-1e-6-batch-64-layer3-0411-2-9439/test.txt' pred_result = './predict/lr-1e-6-batch-64-layer3-0413-4-17677/test.txt'
test_label_path = './data/test_ic50' test_label_path = './data/test_ic50'
eval(pred_result, test_label_path) eval(pred_result, test_label_path)
experment_result/loss.svg deleted 100644 → 0
This source diff could not be displayed because it is too large. You can view the blob instead.
predict/lr-1e-6-batch-64-layer3-0413-4-17677/eval_results 0 → 100644
RMSE : 1.4722575781012768 ; Pearson Correlation Coefficient : 0.2622760899895615
\ No newline at end of file
predict/lr-1e-6-batch-64-layer3-0413-4-17677/test.txt 0 → 100644
This source diff could not be displayed because it is too large. You can view the blob instead.
run_interaction.py
...@@ -50,6 +50,7 @@ def train(args, model, dataset): ...@@ -50,6 +50,7 @@ def train(args, model, dataset):
writer = SummaryWriter('./log/' + args.savedir) writer = SummaryWriter('./log/' + args.savedir)
num_step = args.epochs * len(data_generator) num_step = args.epochs * len(data_generator)
step = 0 step = 0
save_step = num_step // 5
# detect GPU # detect GPU
if torch.cuda.is_available(): if torch.cuda.is_available():
model.cuda() model.cuda()
...@@ -57,7 +58,9 @@ def train(args, model, dataset): ...@@ -57,7 +58,9 @@ def train(args, model, dataset):
print('epoch num : {}'.format(args.epochs)) print('epoch num : {}'.format(args.epochs))
print('step num : {}'.format(num_step)) print('step num : {}'.format(num_step))
print('batch size : {}'.format(args.batch_size)) print('batch size : {}'.format(args.batch_size))
print('learning rate : {}'.format(args.lr))
print('begin training') print('begin 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, affinity) in enumerate(data_generator):
# use cuda # use cuda
...@@ -79,7 +82,7 @@ def train(args, model, dataset): ...@@ -79,7 +82,7 @@ def train(args, model, dataset):
print('Training at Epoch ' + str(epoch + 1) + ' step ' + str(step) + ' with loss ' + str( print('Training at Epoch ' + str(epoch + 1) + ' step ' + str(step) + ' with loss ' + str(
loss.cpu().detach().numpy())) loss.cpu().detach().numpy()))
# save # save
if epoch > 1 and epoch % 2 == 0 and i % 1200 == 0: if epoch >= 1 and step % save_step == 0:
save_path = './model/' + args.savedir + '/' save_path = './model/' + args.savedir + '/'
if not os.path.exists(save_path): if not os.path.exists(save_path):
os.mkdir(save_path) os.mkdir(save_path)
...@@ -153,7 +156,7 @@ if __name__ == '__main__': ...@@ -153,7 +156,7 @@ if __name__ == '__main__':
parser.add_argument('--task', choices=['train', 'test', 'channel', 'ER', 'GPCR', 'kinase'], parser.add_argument('--task', choices=['train', 'test', 'channel', 'ER', 'GPCR', 'kinase'],
default='train', type=str, metavar='TASK', default='train', type=str, metavar='TASK',
help='Task name. Could be train, test, channel, ER, GPCR, kinase.') help='Task name. Could be train, test, channel, ER, GPCR, kinase.')
parser.add_argument('--lr', '--learning-rate', default=1e-4, type=float, parser.add_argument('--lr', '--learning-rate', default=1e-5, type=float,
metavar='LR', help='initial learning rate', dest='lr') metavar='LR', help='initial learning rate', dest='lr')
parser.add_argument('--config', default='./config/config.json', type=str, help='model config file path') parser.add_argument('--config', default='./config/config.json', type=str, help='model config file path')
# parser.add_argument('--log', default='training_log', type=str, help='training log') # parser.add_argument('--log', default='training_log', type=str, help='training log')
...@@ -184,4 +187,3 @@ if __name__ == '__main__': ...@@ -184,4 +187,3 @@ if __name__ == '__main__':
# assert args.shuffle == False # assert args.shuffle == False
main(args) main(args)
Markdown 格式
0% 或
您添加了 0 人 到此讨论。请谨慎行事。
请先完成此评论的编辑！
请 注册 或者 后发表评论