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changed config #3

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41 changes: 20 additions & 21 deletions config/config_hparam.json
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Original file line number Diff line number Diff line change
@@ -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
}
1 change: 1 addition & 0 deletions train.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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):
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2 changes: 1 addition & 1 deletion train_regression.py
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Expand Up @@ -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
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