changed config

Author: willie3838

config/config_hparam.json

@@ -1,28 +1,27 @@
 {
-	"name": "biomarker_log",
+  "name": "biomarker_log",
 
-	"d_model_name" : "seyonec/PubChem10M_SMILES_BPE_450k",
-	"p_model_name" : "Rostlab/prot_bert_bfd",
-	
-	"gpu_ids" : "4,5,6,7",
-	"model_mode" : "train",
-	"load_checkpoint" : "./checkpoint/bindingDB/epoch=33-step=13463.ckpt",
+  "d_model_name": "seyonec/PubChem10M_SMILES_BPE_450k",
+  "p_model_name": "Rostlab/prot_bert_bfd",
 
-	"prot_maxlength" : 545,
-	"layer_limit" : true,
+  "gpu_ids": "1",
+  "model_mode": "train",
+  "load_checkpoint": "./checkpoint/bindingDB/epoch=33-step=13463.ckpt",
 
-	"max_epoch": 50,
-	"batch_size": 54,
-	"num_workers": 16,
+  "prot_maxlength": 545,
+  "layer_limit": true,
 
-	"task_name" : "davis",
-	"lr": 5e-6,
-	"layer_features" : [768, 32, 1],
-	"dropout" : 0.1,
-	"loss_fn" : "smooth",
+  "max_epoch": 50,
+  "batch_size": 54,
+  "num_workers": 16,
 
-	"traindata_rate" : 1.0,
-	"pretrained": {"chem": true, "prot": true},
-	"num_seed" : 9095
-}
+  "task_name": "davis",
+  "lr": 5e-6,
+  "layer_features": [768, 32, 1],
+  "dropout": 0.1,
+  "loss_fn": "smooth",
 
+  "traindata_rate": 1.0,
+  "pretrained": { "chem": true, "prot": true },
+  "num_seed": 9095
+}

train.py

@@ -21,6 +21,7 @@
 
 from sklearn.metrics import f1_score, roc_curve, precision_score, recall_score, auc
 from sklearn.metrics import roc_auc_score, average_precision_score
+from module.model import deleteEncodingLayers
 
 class BiomarkerDataset(Dataset):
     def __init__(self, list_IDs, labels, df_dti, d_tokenizer, p_tokenizer, prot_maxLength):

train_regression.py

@@ -8,7 +8,7 @@
 from utils.attention_flow import *
 from utils.emetric import regression_score
 
-from module.model import BApredictModel
+from module.model import BApredictModel, deleteEncodingLayers
 from module.datamodule import BAPredictDataModule
 
 import torch