add save check point

5294c72d · 朱学凯 · bd182dde · 5294c72d · 5294c72d · 5294c72d
--- a/.idea/CPI.iml
+++ b/.idea/CPI.iml
@@ -2,7 +2,7 @@
 <module type="PYTHON_MODULE" version="4">
  <component name="NewModuleRootManager">
    <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" />
  </component>
 </module>
\ No newline at end of file
--- a/.idea/misc.xml
+++ b/.idea/misc.xml
 <?xml version="1.0" encoding="UTF-8"?>
 <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>
\ No newline at end of file
--- a/.idea/workspace.xml
+++ b/.idea/workspace.xml
@@ -2,8 +2,16 @@
 <project version="4">
  <component name="ChangeListManager">
    <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="$PROJECT_DIR$/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="$PROJECT_DIR$/experment_result/loss.svg" beforeDir="false" />
+      <change beforePath="$PROJECT_DIR$/run_interaction.py" beforeDir="false" afterPath="$PROJECT_DIR$/run_interaction.py" afterDir="false" />
    </list>
    <option name="SHOW_DIALOG" value="false" />
    <option name="HIGHLIGHT_CONFLICTS" value="true" />
@@ -29,7 +37,12 @@
    <property name="WebServerToolWindowFactoryState" value="false" />
    <property name="restartRequiresConfirmation" value="false" />
  </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">
      <module name="CPI" />
      <option name="INTERPRETER_OPTIONS" value="" />
@@ -76,8 +89,8 @@
    </configuration>
    <recent_temporary>
      <list>
-        <item itemvalue="Python.eval" />
        <item itemvalue="Python.run_interaction" />
+        <item itemvalue="Python.eval" />
      </list>
    </recent_temporary>
  </component>
@@ -108,7 +121,8 @@
    </option>
  </component>
  <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="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$run_interaction.coverage" NAME="run_interaction Coverage Results" MODIFIED="1618474485850" SOURCE_PROVIDER="com.intellij.coverage.DefaultCoverageFileProvider" RUNNER="coverage.py" COVERAGE_BY_TEST_ENABLED="true" COVERAGE_TRACING_ENABLED="false" WORKING_DIRECTORY="$PROJECT_DIR$" />
+    <SUITE FILE_PATH="coverage/CPI$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>
 </project>
\ No newline at end of file
--- a/__pycache__/configuration_bert.cpython-36.pyc
+++ b/__pycache__/configuration_bert.cpython-36.pyc
--- a/__pycache__/dataset.cpython-36.pyc
+++ b/__pycache__/dataset.cpython-36.pyc
--- a/__pycache__/modeling_bert.cpython-36.pyc
+++ b/__pycache__/modeling_bert.cpython-36.pyc
--- a/config/config.json
+++ b/config/config.json
@@ -5,14 +5,14 @@
  "attention_probs_dropout_prob": 0.1,
  "hidden_act": "gelu",
  "hidden_dropout_prob": 0.1,
-  "hidden_size": 768,
+  "hidden_size": 384,
  "initializer_range": 0.02,
  "intermediate_size": 1536,
  "layer_norm_eps": 1e-12,
-  "max_position_embeddings": 512,
+  "max_position_embeddings": 384,
  "model_type": "bert",
  "num_attention_heads": 12,
-  "num_hidden_layers": 3,
+  "num_hidden_layers": 12,
  "pad_token_id": 0,
  "type_vocab_size": 2,
  "vocab_size": 23615

--- a/config/config_layer_3.json
+++ b/config/config_layer_3.json
@@ -9,7 +9,7 @@
  "initializer_range": 0.02,
  "intermediate_size": 1536,
  "layer_norm_eps": 1e-12,
-  "max_position_embeddings": 512,
+  "max_position_embeddings": 384,
  "model_type": "bert",
  "num_attention_heads": 12,
  "num_hidden_layers": 3,

--- a/config/config_layer_6.json
+++ b/config/config_layer_6.json
@@ -5,11 +5,11 @@
  "attention_probs_dropout_prob": 0.1,
  "hidden_act": "gelu",
  "hidden_dropout_prob": 0.1,
-  "hidden_size": 768,
+  "hidden_size": 384,
  "initializer_range": 0.02,
-  "intermediate_size": 3072,
+  "intermediate_size": 1536,
  "layer_norm_eps": 1e-12,
-  "max_position_embeddings": 512,
+  "max_position_embeddings": 384,
  "model_type": "bert",
  "num_attention_heads": 12,
  "num_hidden_layers": 6,

--- a/config/config_layer_9.json
+++ b/config/config_layer_9.json
@@ -5,11 +5,11 @@
  "attention_probs_dropout_prob": 0.1,
  "hidden_act": "gelu",
  "hidden_dropout_prob": 0.1,
-  "hidden_size": 768,
+  "hidden_size": 384,
  "initializer_range": 0.02,
-  "intermediate_size": 3072,
+  "intermediate_size": 1536,
  "layer_norm_eps": 1e-12,
-  "max_position_embeddings": 512,
+  "max_position_embeddings": 384,
  "model_type": "bert",
  "num_attention_heads": 12,
  "num_hidden_layers": 9,

--- a/eval.py
+++ b/eval.py
@@ -29,6 +29,6 @@ def eval(pred_path, label_path):


 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'
    eval(pred_result, test_label_path)
--- a/experment_result/loss.svg
+++ b/experment_result/loss.svg
--- a/predict/lr-1e-6-batch-64-layer3-0413-4-17677/eval_results
+++ b/predict/lr-1e-6-batch-64-layer3-0413-4-17677/eval_results
+RMSE : 1.4722575781012768 ; Pearson Correlation Coefficient : 0.2622760899895615
\ No newline at end of file
--- a/predict/lr-1e-6-batch-64-layer3-0413-4-17677/test.txt
+++ b/predict/lr-1e-6-batch-64-layer3-0413-4-17677/test.txt
--- a/run_interaction.py
+++ b/run_interaction.py
@@ -50,6 +50,7 @@ def train(args, model, dataset):
    writer = SummaryWriter('./log/' + args.savedir)
    num_step = args.epochs * len(data_generator)
    step = 0
+    save_step = num_step // 5
    # detect GPU
    if torch.cuda.is_available():
        model.cuda()
@@ -57,7 +58,9 @@ def train(args, model, dataset):
    print('epoch num : {}'.format(args.epochs))
    print('step num : {}'.format(num_step))
    print('batch size : {}'.format(args.batch_size))
+    print('learning rate : {}'.format(args.lr))
    print('begin training')
+    # training
    for epoch in range(args.epochs):
        for i, (input, affinity) in enumerate(data_generator):
            # use cuda
@@ -79,7 +82,7 @@ def train(args, model, dataset):
            print('Training at Epoch ' + str(epoch + 1) + ' step ' + str(step) + ' with loss ' + str(
                loss.cpu().detach().numpy()))
            # 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 + '/'
                if not os.path.exists(save_path):
                    os.mkdir(save_path)
@@ -153,7 +156,7 @@ if __name__ == '__main__':
    parser.add_argument('--task', choices=['train', 'test', 'channel', 'ER', 'GPCR', 'kinase'],
                        default='train', type=str, metavar='TASK',
                        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')
    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')
@@ -184,4 +187,3 @@ if __name__ == '__main__':
    # assert args.shuffle == False
    main(args)

-