Merge branch 'main' of github.com:Xuekai-Zhu/CPI into main

# Conflicts:
#	.idea/workspace.xml
#	eval.py

.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

.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

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

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,

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,

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,

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

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)
 
-