classifier_trainer_EC1_random.py

import numpy as np
from sklearn.model_selection import train_test_split
from transformers import DistilBertModel, BertModel, BertTokenizer, BertForMaskedLM, BertForPreTraining, \
    BertForSequenceClassification, AutoModelForSequenceClassification
import torch
from datasets import load_dataset, Dataset
from transformers import DataCollatorWithPadding, DataCollatorForLanguageModeling
from transformers import TrainingArguments
import pandas as pd
from datasets import load_metric
import random
from torch import nn
from transformers import Trainer
import os
from transformers import AutoConfig, EarlyStoppingCallback
from transformers.models.bert import BertPreTrainedModel
from torch.nn import BCEWithLogitsLoss, CrossEntropyLoss, MSELoss
from transformers.modeling_outputs import SequenceClassifierOutput
from transformers.trainer_utils import IntervalStrategy
import shutil
import time
from sklearn import preprocessing
from collections import Counter
from sklearn.metrics import confusion_matrix, mean_squared_error, classification_report
from sklearn.metrics import f1_score, matthews_corrcoef, accuracy_score, roc_auc_score, precision_score, recall_score, average_precision_score

mode = 0
os.environ["CUDA_VISIBLE_DEVICES"] = '1'

########################################################### Data Preparation: ##########################################
# Loading dataset from csv file:
df_train = pd.read_csv('./random_train_df')
df_dev = pd.read_csv('./random_dev_df')
df_test = pd.read_csv('./random_test_df')

# Preprocessing training labels: output-labels_OHE
EC_total1 = list(df_train['EC_num'].values)
seq = list(df_train['sequence'].values)
seq_clean = []
EC_labels = []
EC1_labels = []
EC2_labels = []
EC3_labels = []
EC4_labels = []

sum=0
for i in range(0,len(EC_total1)):
    EC_total_struc = EC_total1[i].replace('[', '').replace(']', '').replace(' ', '').replace('\'', '').split(',')
    EC1_list = []
    if (len(EC_total_struc) > 4):
        for j in range(0,len(EC_total_struc)):
            if EC_total_struc[j].split('.')[0] not in EC1_list:
                EC1_list.append(EC_total_struc[j].split('.')[0])
        print(EC_total_struc)
        print(EC1_list)
        print(i)
        # sum+=1
    if len(EC1_list) > 1:
        sum+=1


for i in range(0,len(EC_total1)):
    EC_labels_temp = []
    if EC_total1[i] != '[]':
        EC_total_struc = EC_total1[i].replace('[', '').replace(']', '').replace(' ', '').replace('\'', '').split(',')
        # Mining first EC value:
        EC1 = EC_total_struc[0].split('.')[0]
        EC1_labels.append(EC1)
        EC_labels_temp.append(EC1)

        # Mining second EC value:
        EC2 = 'x'
        for a in EC_total_struc:
            # EC2 = a.split('.')[1]
            if a.split('.')[1] != '-':
                EC2 = a.split('.')[1]
                break

        EC2_labels.append(EC2)
        EC_labels_temp.append(EC2)

        # Mining third EC value:
        EC3 = 'x'
        for a in EC_total_struc:
            # EC2 = a.split('.')[1]
            if a.split('.')[2] != '-':
                EC3 = a.split('.')[2]
                break

        EC3_labels.append(EC3)
        EC_labels_temp.append(EC3)

        # Mining fourth EC value:
        EC4 = 'x'
        for a in EC_total_struc:
            # EC2 = a.split('.')[1]
            if a.split('.')[3] != '-':
                EC4 = a.split('.')[3]
                break

        EC4_labels.append(EC4)
        EC_labels_temp.append(EC4)

        EC_labels.append(EC_labels_temp)
    else:
        EC1_labels.append('x')
        EC2_labels.append('x')
        EC3_labels.append('x')
        EC4_labels.append('x')
        EC_labels.append([])

le_1 = preprocessing.LabelEncoder()
le_1.fit(EC1_labels)
EC1_labels_encoded = le_1.transform(EC1_labels)
# le_2 = preprocessing.LabelEncoder()
# le_2.fit(EC2_labels)
# EC2_labels_encoded = le_2.transform(EC2_labels)
# le_3 = preprocessing.LabelEncoder()
# le_3.fit(EC3_labels)
# EC3_labels_encoded = le_3.transform(EC3_labels)
# le_2.inverse_transform()


"""
Total samples: 438522
Total blank EC_num: 229699
Blank EC1: 229699
Blank EC2: 231657
Blank EC3: 237544
Blank EC4: 260220
"""

# count=0
# for a in EC4_labels:
#     if a == 'x':
#         count+=1

text = []
labels = []
check = []
for i in range(0,len(EC1_labels_encoded)):
    if EC1_labels[i] != 'x':
        comment = ' '.join(seq[i])
        # comment = str(EC2_labels_encoded[i]) + " " + comment
        text.append(comment)
        labels.append(EC1_labels_encoded[i])


text_3 = text
labels_3 = labels
####################################################

labels_OHE = []
label_num = len(list(set(labels_3)))
for i in range(0, len(labels_3)):
    l_arr = np.zeros((label_num), int)
    l_arr[labels_3[i]] = int(1)
    labels_OHE.append(l_arr)


counts = np.zeros((label_num), int)
for i in range(0, len(labels_3)):
    counts[labels_3[i]] += 1

text_train = text_3
labels_train = labels_OHE



# Preprocessing dev labels: output-labels_OHE
EC_total1 = list(df_dev['EC_num'].values)
seq = list(df_dev['sequence'].values)
seq_clean = []
EC_labels = []
EC1_labels = []
EC2_labels = []
EC3_labels = []
EC4_labels = []
for i in range(0,len(EC_total1)):
    EC_labels_temp = []
    if EC_total1[i] != '[]':
        EC_total_struc = EC_total1[i].replace('[', '').replace(']', '').replace(' ', '').replace('\'', '').split(',')
        # Mining first EC value:
        EC1 = EC_total_struc[0].split('.')[0]
        EC1_labels.append(EC1)
        EC_labels_temp.append(EC1)

        # Mining second EC value:
        EC2 = 'x'
        for a in EC_total_struc:
            # EC2 = a.split('.')[1]
            if a.split('.')[1] != '-':
                EC2 = a.split('.')[1]
                break

        EC2_labels.append(EC2)
        EC_labels_temp.append(EC2)

        # Mining third EC value:
        EC3 = 'x'
        for a in EC_total_struc:
            # EC2 = a.split('.')[1]
            if a.split('.')[2] != '-':
                EC3 = a.split('.')[2]
                break

        EC3_labels.append(EC3)
        EC_labels_temp.append(EC3)

        # Mining fourth EC value:
        EC4 = 'x'
        for a in EC_total_struc:
            # EC2 = a.split('.')[1]
            if a.split('.')[3] != '-':
                EC4 = a.split('.')[3]
                break

        EC4_labels.append(EC4)
        EC_labels_temp.append(EC4)

        EC_labels.append(EC_labels_temp)
    else:
        EC1_labels.append('x')
        EC2_labels.append('x')
        EC3_labels.append('x')
        EC4_labels.append('x')
        EC_labels.append([])

# le_1 = preprocessing.LabelEncoder()
# le_1.fit(EC1_labels)
EC1_labels_encoded = le_1.transform(EC1_labels)
# le_2 = preprocessing.LabelEncoder()
# le_2.fit(EC2_labels)

# EC2_labels_encoded = le_2.transform(EC2_labels) ###Fix needed for EC2 classification

# le_3 = preprocessing.LabelEncoder()
# le_3.fit(EC3_labels)
# EC3_labels_encoded = le_3.transform(EC3_labels)
# le_2.inverse_transform()


"""
Total samples: 438522
Total blank EC_num: 229699
Blank EC1: 229699
Blank EC2: 231657
Blank EC3: 237544
Blank EC4: 260220
"""

count=0
for a in EC1_labels:
    if a == 'x':
        count+=1

text = []
labels = []
check = []
for i in range(0,len(EC1_labels_encoded)):
    if EC1_labels[i] != 'x':
        comment = ' '.join(seq[i])
        # comment = str(EC2_labels_encoded[i]) + " " + comment
        text.append(comment)
        labels.append(EC1_labels_encoded[i])


text_3 = text
labels_3 = labels
####################################################

labels_OHE = []
label_num = len(list(set(labels_3)))

for i in range(0, len(labels_3)):
    l_arr = np.zeros((label_num), int)
    l_arr[labels_3[i]] = int(1)
    labels_OHE.append(l_arr)


counts = np.zeros((label_num), int)
for i in range(0, len(labels_3)):
    counts[labels_3[i]] += 1

text_dev = text_3
labels_dev = labels_OHE

# text_train, text_test, labels_train, labels_test = train_test_split(text_3, labels_OHE, stratify=labels_3, test_size=0.1)
# # text_test1, text_test2, labels_test1, labels_test2 = train_test_split(text_test, labels_test, test_size=0.1)

dict_train = {'text':text_train,'labels':labels_train}
dict_test = {'text':text_dev,'labels':labels_dev}
########################################################################################################################


########################################################################################################################
############################################### Building Model: ########################################################

class MyBertForSequenceClassification(BertPreTrainedModel):
    def __init__(self, config):
        super().__init__(config)
        self.num_labels = config.num_labels
        self.config = config

        self.bert = BertModel(config)
        classifier_dropout = (
            config.classifier_dropout if config.classifier_dropout is not None else config.hidden_dropout_prob
        )
        self.dropout = nn.Dropout(classifier_dropout)
        if config.intermediate_hidden_size != 0:
            self.intermediate_classifier = nn.Linear(config.hidden_size, config.intermediate_hidden_size)
            self.classifier = nn.Linear(config.intermediate_hidden_size, config.num_labels)
        else:
            self.classifier = nn.Linear(config.hidden_size, config.num_labels)

        self.init_weights()

    def forward(
        self,
        input_ids=None,
        attention_mask=None,
        token_type_ids=None,
        position_ids=None,
        head_mask=None,
        inputs_embeds=None,
        labels=None,
        output_attentions=None,
        output_hidden_states=None,
        return_dict=None,
    ):
        r"""
        labels (:obj:`torch.LongTensor` of shape :obj:`(batch_size,)`, `optional`):
            Labels for computing the sequence classification/regression loss. Indices should be in :obj:`[0, ...,
            config.num_labels - 1]`. If :obj:`config.num_labels == 1` a regression loss is computed (Mean-Square loss),
            If :obj:`config.num_labels > 1` a classification loss is computed (Cross-Entropy).
        """
        return_dict = return_dict if return_dict is not None else self.config.use_return_dict

        outputs = self.bert(
            input_ids,
            attention_mask=attention_mask,
            token_type_ids=token_type_ids,
            position_ids=position_ids,
            head_mask=head_mask,
            inputs_embeds=inputs_embeds,
            output_attentions=output_attentions,
            output_hidden_states=output_hidden_states,
            return_dict=return_dict,
        )

        if self.config.use_pooler == 1:
            pooled_output = outputs[1]
        elif self.config.use_mean == 1:
            # print(attention_mask.shape)
            # token_embeddings.sum(axis=1) / attention_mask.sum(axis=-1).unsqueeze(-1)
            pooled_output = torch.sum(outputs[0] * attention_mask.unsqueeze(-1), dim=1) / torch.sum(attention_mask, dim=1).unsqueeze(-1)
            # print(pooled_output.shape)
            # pooled_output = torch.mean(outputs[0], dim=1)
        else:
            pooled_output = outputs[0][:, 0]

        pooled_output = self.dropout(pooled_output)
        if config.intermediate_hidden_size != 0:
            intermediate_output = self.intermediate_classifier(pooled_output)
            logits = self.classifier(intermediate_output)
        else:
            logits = self.classifier(pooled_output)

        loss = None
        if labels is not None:
            if self.config.problem_type is None:
                if self.num_labels == 1:
                    self.config.problem_type = "regression"
                elif self.num_labels > 1 and (labels.dtype == torch.long or labels.dtype == torch.int):
                    self.config.problem_type = "single_label_classification"
                else:
                    self.config.problem_type = "multi_label_classification"

            if self.config.problem_type == "regression":
                loss_fct = MSELoss()
                if self.num_labels == 1:
                    loss = loss_fct(logits.squeeze(), labels.squeeze())
                else:
                    loss = loss_fct(logits, labels)
            elif self.config.problem_type == "single_label_classification":
                loss_fct = CrossEntropyLoss()
                loss = loss_fct(logits.view(-1, self.num_labels), labels.view(-1))
            elif self.config.problem_type == "multi_label_classification":
                # loss_fct = BCEWithLogitsLoss()
                loss_fct = CrossEntropyLoss()
                # print(list(logits.size()))
                # print(list(labels.size()))
                # print(logits.dtype)
                # print(labels.dtype)
                labels = labels.type(torch.float32)
                loss = loss_fct(logits, labels)
        if not return_dict:
            output = (logits,) + outputs[2:]
            return ((loss,) + output) if loss is not None else output

        return SequenceClassifierOutput(
            loss=loss,
            logits=logits,
            hidden_states=outputs.hidden_states,
            attentions=outputs.attentions,
        )


def tokenize_function(example):

    return tokenizer(example["text"], add_special_tokens=True, truncation=True, max_length=1024)



def compute_metrics(eval_preds):
    # print("PROBLEM!!!")
    metric = load_metric("accuracy")
    # sdfdf
    # metric = load_metric("accuracy")
    logits, labels = eval_preds
    predictions = np.argmax(logits, axis=-1)
    labels_real = np.argmax(labels, axis=1)
    return metric.compute(predictions=predictions, references=labels_real)

model_type = "Rostlab/prot_bert_bfd"
# model_type = "Rostlab/prot_bert"
# model_type = "bert-base-cased"
# model_type = "bert-base-uncased"
# model_type = "distilbert-base-uncased"

# do_lower_case = True
do_lower_case = False
tokenizer = BertTokenizer.from_pretrained(model_type, do_lower_case=do_lower_case)
# elif (a==str(0) or a==str(1) or a==str(2) or a==str(3) or a==str(4) or a==str(5) or a==str(6)):
# tokenizer.add_tokens(["0","1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16","17","18","19","20","21","22","23","24"])



##########################################################################################################################
# import torch
# from transformers import BertTokenizer, BertModel
#
# tokenizer = BertTokenizer.from_pretrained("bert-base-cased")
# model = BertModel.from_pretrained("bert-base-cased")
#
# print(len(tokenizer))  # 28996
# tokenizer.add_tokens(["NEW_TOKEN1"])
# print(len(tokenizer))  # 28997
#
# model.resize_token_embeddings(len(tokenizer))
# # The new vector is added at the end of the embedding matrix
#
# print(len(model.embeddings.word_embeddings.weight[-1, :]))
# # Randomly generated matrix
#
# model.embeddings.word_embeddings.weight[-1, :] = torch.zeros([model.config.hidden_size])
#
# print(len(model.embeddings.word_embeddings.weight[-1, :]))
# # outputs a vector of zeros of shape [768]

########################################################################################################################

# model = BertForSequenceClassification.from_pretrained("Rostlab/prot_bert_bfd")
config = AutoConfig.from_pretrained(model_type)
# subject = 'secreted'
# subject = 'iamppred'
# subject = 'ampscanner'
# subject = 'iamp2l'
# subject = 'ampep'
# subject = 'secproct'
# subject = 'hemolythic'
# subject = 'hlppredfuse'
# subject = 'rnnamp'
subject = 'EC_num'

config.classifier_dropout = 0
config.hidden_dropout_prob = 0
# config.hidden_size = 1024

mode_hidden_map = {0:0, 1:32, 2:128, 3:1024}
# config.intermediate_hidden_size = 1024
# config.intermediate_hidden_size = 128
# config.intermediate_hidden_size = 32
# config.intermediate_hidden_size = 0
config.intermediate_hidden_size = mode_hidden_map[mode]


########################################################################################################################
##################################################### Training: ##########################################################
# num_epochs = 1
# num_epochs = 10
num_epochs = 15
# num_epochs = 100

config.use_pooler = 0
config.use_mean = 1


# Enabling multilabel classification:
config.num_labels = label_num
config.problem_type = "multi_label_classification"

# freeze_positional = 0
# freeze_non_positional = 0
# freeze_attention = 0
# freeze_layer_norm = 0
# freeze_pooler = 0

# freeze_positional = 1
# freeze_non_positional = 1
# freeze_attention = 1
# freeze_layer_norm = 1
# freeze_pooler = 1

freeze_positional = 0
freeze_non_positional = 1
freeze_attention = 1
freeze_layer_norm = 0
freeze_pooler = 0

transfer = 0
random_init = 0
if random_init:
    transfer = 0
if subject == 'secreted':
    transfer = 0

early_stopping = 1
patience = 10
if early_stopping:
    create_validation_split = 1
else:
    create_validation_split = 0
ten_fold = 0

# monitor_value = ''
# initial_lr = 5e-6
# initial_lr = 5e-5
initial_lr = 5e-4
if subject == 'iamp2l' or subject == 'iamppred':
    batch_size = 32
if subject == 'secreted' or subject == 'ampscanner' or subject == 'hemolythic' or subject == 'hemolythic_2021' or subject == 'hlppredfuse' or subject == 'rnnamp':
    batch_size = 16
if subject == 'ampep' or subject == 'secproct':
    batch_size = 8
if subject == 'secproct':
    batch_size = 4
if subject == 'EC_num':
    batch_size = 1
balanced_loss = 0

# batch_size = 4
losses_all = []
fold_range = [0]
if ten_fold:
    fold_range = range(10)

for fold in fold_range:
    model = None
    dataset = None
    if transfer == 0:
        if random_init:
            model = MyBertForSequenceClassification(config=config)
        else:
            model = MyBertForSequenceClassification.from_pretrained(model_type, config=config)
    if transfer == 1:
        results_df = pd.read_csv('results/training_results.csv')
        results_df = results_df[results_df['subject'] == 'secreted']
        results_df = results_df[results_df['hidden_layer_size'] == config.intermediate_hidden_size]
        results_df = results_df[results_df['usemean'] == config.use_mean]
        results_df = results_df[results_df['usepooler'] == config.use_pooler]
        secreted_model_dir = results_df.iloc[0]['save_dir']
        model = MyBertForSequenceClassification.from_pretrained(secreted_model_dir, config=config)

    # Loading Checkpoint:
    # model = MyBertForSequenceClassification.from_pretrained("./models/0706-172025/checkpoint-4350")

    # device = torch.device("cuda") if torch.cuda.is_available() else torch.device("cpu")
    # model.to(device)
    # dataset = load_dataset('text', data_files={'train': 'data/uniparc_peptides_spaced.txt'}, cache_dir='data/processed_datasets')
    # dataset = load_dataset('csv', data_files={'train': 'old/input/amp.csv'},
    #                        # cache_dir='data/processed_datasets',
    #                        delimiter=',',
    #                        # task="text-classification"
    #                        )

    # CSV file loader, 2 columns, 'text' and 'labels'. Text is spaced capital sequences.
    if subject == 'iamp2l':
        dataset = load_dataset('csv', data_files={'train': 'data/iamp2l/iamp2l_raw.csv', 'test': 'data/iamp2l/independent/independent.csv'},
                               cache_dir='data/processed_datasets',
                               delimiter=',',
                               # task="text-classification"
                               )
    elif subject == 'iamppred':
        dataset = load_dataset('csv', data_files={'train': 'data/iamppred/old/train.csv', 'test': 'data/iamppred/old/test.csv'},
                               cache_dir='data/processed_datasets',
                               delimiter='\t',
                               # task="text-classification"
                               )
    elif subject == 'secreted':
        dataset = load_dataset('csv', data_files={'train': 'data/swissprot/secreted_all_cleaned_all_train.csv', 'test': 'data/swissprot/secreted_all_cleaned_all_test.csv'},
                               cache_dir='data/processed_datasets',
                               delimiter=',',
                               # task="text-classification"
                               )

    elif subject == 'ampscanner':
        dataset = load_dataset('csv', data_files={'train': 'data/ampscanner/ampscanner_train.csv',
                                                  'test': 'data/ampscanner/ampscanner_test.csv'},
                               cache_dir='data/processed_datasets',
                               delimiter=',',
                               # task="text-classification"
                               )

    elif subject == 'ampep':
        dataset = load_dataset('csv', data_files={'train': 'data/ampep/ampep.csv'},
                               cache_dir='data/processed_datasets',
                               delimiter=',',
                               )

    elif subject == 'secproct':
        dataset = load_dataset('csv', data_files={'train': 'data/secproct/blood_train.csv',
                                                  'test': 'data/secproct/blood_test.csv'},
                               cache_dir='data/processed_datasets',
                               delimiter=',',
                               # task="text-classification"
                               )
    elif subject == 'hemolythic':
        dataset = load_dataset('csv', data_files={'train': 'data/hemolythic/hemolythic_train.csv',
                                                  'test': 'data/hemolythic/hemolythic_test.csv'},
                               cache_dir='data/processed_datasets',
                               delimiter=',',
                               # task="text-classification"
                               )
    elif subject == 'hemolythic_2021':
        dataset = load_dataset('csv', data_files={'train': 'data/hemolythic_2021/hemolythic_2021_train.csv',
                                                  'test': 'data/hemolythic_2021/hemolythic_2021_test.csv'},
                               cache_dir='data/processed_datasets',
                               delimiter=',',
                               # task="text-classification"
                               )
    elif subject == 'hlppredfuse':
        dataset = load_dataset('csv', data_files={'train': 'data/hlppredfuse/hlppredfuse_train.csv',
                                                  'test': 'data/hlppredfuse/hlppredfuse_test.csv'},
                               cache_dir='data/processed_datasets',
                               delimiter=',',
                               # task="text-classification"
                               )
    elif subject == 'rnnamp':
        dataset = load_dataset('csv', data_files={'train': 'data/rnnamp/rnnamp_train.csv',
                                                  'test': 'data/rnnamp/rnnamp_test.csv'},
                               cache_dir='data/processed_datasets',
                               delimiter=',',
                               # task="text-classification"
                               )

    elif subject == 'EC_num':
        # dataset = Dataset.from_pandas(df)
        dataset_train = Dataset.from_dict(dict_train, split='train')
        dataset_test = Dataset.from_dict(dict_test, split='test')

        # dataset_test2 = Dataset.from_dict(dict_test2, split='test')
        # dataset = load_dataset('dict')
        # dataset  = load_dataset('csv', data_files={'train': 'df_test_temp.csv',
        #                                           'test': 'df_test_temp.csv'},
        #                        cache_dir='data/processed_datasets',
        #                        delimiter=',',
        #                        # task="text-classification"
        #                        )

    # reload = False
    # if not reload:
    #     # Find the indices for train, validation, and test splits
    #     random.seed(42)
    #     data_len = len(dataset['train'])
    #     randomlist = list(range(data_len))
    #     random.shuffle(randomlist)
    #     valid_begin = int(fold * 0.1 * data_len)
    #     valid_end = int((fold + 1) * 0.1 * data_len)
    #     test_begin = valid_end
    #     test_end = int((fold + 2) * 0.1 * data_len)
    #     if fold == 9:
    #         test_begin = 0
    #         test_end = int(0.1 * data_len)
    #     test_indices = randomlist[test_begin:test_end]
    #     valid_indices = randomlist[valid_begin:valid_end]
    #
    #     # Create the validation split
    #     dataset['validation'] = dataset['train'].select(valid_indices)
    #     if ten_fold:
    #         # In ten fold cross validation, isolate the test split
    #         dataset['test'] = dataset['train'].select(test_indices)
    #         if create_validation_split:
    #             train_indices = [ind for ind in randomlist if ind not in test_indices + valid_indices]
    #             dataset['train'] = dataset['train'].select(train_indices)
    #         else:
    #             # If no validation split is needed (for no early stopping), do not isolate it from the train split
    #             train_indices = [ind for ind in randomlist if ind not in test_indices]
    #             dataset['train'] = dataset['train'].select(train_indices)
    #     else:
    #         if create_validation_split:
    #             train_indices = [ind for ind in randomlist if ind not in valid_indices]
    #             dataset['train'] = dataset['train'].select(train_indices)
    #     del randomlist


    tokenized_datasets_train = dataset_train.map(tokenize_function, batched=True)
    tokenized_datasets_test = dataset_test.map(tokenize_function, batched=True)
    # all_data = tokenize_function(dataset_test)
    # tokenized_datasets_test = copy.deepcopy(dataset_test)
    # tokenized_datasets_test = tokenized_datasets_test.add_column('input_ids', all_data[0])
    # tokenized_datasets_test = tokenized_datasets_test.add_column('token_type_ids', all_data[2])
    # tokenized_datasets_test = tokenized_datasets_test.add_column('attention_mask', all_data[1])

    # all_data = tokenize_function(dataset_train)
    # tokenized_datasets_train = copy.deepcopy(dataset_train)
    # tokenized_datasets_train = tokenized_datasets_train.add_column('input_ids', all_data[0])
    # tokenized_datasets_train = tokenized_datasets_train.add_column('token_type_ids', all_data[2])
    # tokenized_datasets_train = tokenized_datasets_train.add_column('attention_mask', all_data[1])

    # tokenized_datasets_test2 = dataset_test2.map(tokenize_function, batched=True)
    # tokenized_datasets_protein = dataset_protein.map(tokenize_function, batched=True)
    tokenized_datasets_train.set_format("torch", columns=['input_ids'])
    tokenized_datasets_test.set_format("torch", columns=['input_ids'])
    # tokenized_datasets_test2.set_format("torch", columns=['input_ids'])
    # tokenized_datasets.save_to_disk('data/processed_datasets/peptides')
    # tokenized_datasets.save_to_disk('data/processed_datasets/'+subject+str(fold))
    # tokenized_datasets.save_to_disk('data/processed_datasets/'+ subject)

    # else:
    #     # tokenized_datasets = load_from_disk('data/processed_datasets/peptides')
    #     tokenized_datasets = load_from_disk('data/processed_datasets/'+subject+str(fold))
    #     # tokenized_datasets = load_from_disk('data/processed_datasets/secreted')

    tokenized_datasets_train = tokenized_datasets_train.remove_columns('text')
    tokenized_datasets_test = tokenized_datasets_test.remove_columns('text')
    # tokenized_datasets_test2 = tokenized_datasets_test2.remove_columns('text')
    # for c in tokenized_datasets.column_names['train']:
    #     if c in ['keyword', 'length']:
    #         tokenized_datasets = tokenized_datasets.remove_columns(c)

    tokenized_datasets_train.set_format("torch")
    tokenized_datasets_test.set_format("torch")
    # tokenized_datasets_test2.set_format("torch")
    # tokenized_datasets_protein.set_format("torch", columns=['input_ids'])
    # print(tokenized_datasets['train'][1])
    # tokenized_datasets = s.map(tokenize_function, batched=True)
    data_collator = DataCollatorWithPadding(tokenizer=tokenizer)
    # data_collator = DataCollatorForLanguageModeling(tokenizer=tokenizer)

    timestr = time.strftime("%m%d-%H%M%S")
    save_dir = 'models/' + timestr + '/'
    while os.path.isdir(save_dir):
        timestr = timestr.split('-')[0] + '-' + timestr.split('-')[1][:4] + str(int(timestr.split('-')[1][4:] + random.randint(1,60)))
        save_dir = 'models/' + timestr + '/'

    os.makedirs(save_dir, exist_ok=True)

    model.resize_token_embeddings(len(tokenizer))
    training_args = TrainingArguments(num_train_epochs=num_epochs,output_dir=save_dir,
                                      per_device_train_batch_size=batch_size,
                                      learning_rate=initial_lr,
                                      load_best_model_at_end=True,
                                      evaluation_strategy=IntervalStrategy.EPOCH,
                                      metric_for_best_model='eval_accuracy',
                                      save_total_limit=patience+1,
                                      save_strategy = IntervalStrategy.EPOCH,
                                      # # prediction_loss_only=True,
                                      gradient_accumulation_steps=int(32/batch_size), eval_accumulation_steps=int(32/batch_size),
                                      # fp16=True, fp16_full_eval=True,
                                      per_device_eval_batch_size=batch_size,
                                      # # debug="underflow_overflow"
                                      )

    param_names = []
    for name, param in model.named_parameters():
        param_names.append(name)

    # positional_embedding_params = ['bert.embeddings.word_embeddings.weight', 'bert.embeddings.position_embeddings.weight',
    #      'bert.embeddings.token_type_embeddings.weight', 'bert.embeddings.LayerNorm.weight',
    #      'bert.embeddings.LayerNorm.bias']
    positional_embedding_params = ['bert.embeddings.position_embeddings.weight']
    non_positional_embedding_params = ['bert.embeddings.word_embeddings.weight', 'bert.embeddings.token_type_embeddings.weight']
    pooler_params = ['bert.pooler.dense.weight', 'bert.pooler.dense.bias']
    classifier_params = ['intermediate_classifier.weight', 'intermediate_classifier.bias', 'classifier.weight', 'classifier.bias']
    layer_norm_params = []
    attention_params = []
    for l in param_names:
        if 'LayerNorm' in l:
            layer_norm_params.append(l)
        elif l not in positional_embedding_params+non_positional_embedding_params+pooler_params+classifier_params:
            attention_params.append(l)
    print(len(positional_embedding_params+non_positional_embedding_params+layer_norm_params+attention_params+pooler_params+classifier_params), len(param_names))
    unfrozen_params = []
    unfrozen_params += classifier_params
    if freeze_positional == 0:
        unfrozen_params += positional_embedding_params
    if freeze_non_positional == 0:
        unfrozen_params += non_positional_embedding_params
    if freeze_layer_norm == 0:
        unfrozen_params += layer_norm_params
    if freeze_pooler == 0:
        unfrozen_params += pooler_params
    if freeze_attention == 0:
        unfrozen_params += attention_params

    frozen_counter = 0
    grad_counter = 0
    for name, param in model.named_parameters():
        if name in unfrozen_params:
            param.requires_grad = True
            grad_counter += len(param.flatten())
        else:
            param.requires_grad = False
            frozen_counter += len(param.flatten())

    print('Frozen parameters:', frozen_counter, grad_counter, grad_counter+frozen_counter, grad_counter*100/(grad_counter+frozen_counter))
    callbacks = []
    if early_stopping == 1:
        callbacks = [EarlyStoppingCallback(early_stopping_patience=patience)]

    # config = AutoConfig.from_pretrained("./models_random_EC1_EX/0805-135007")
    # model = MyBertForSequenceClassification.from_pretrained("./models_random_EC1_EX/0805-135007", config=config)

    trainer = None
    trainer = Trainer(
        model,
        training_args,
        train_dataset=tokenized_datasets_train,
        eval_dataset=tokenized_datasets_test,
        compute_metrics=compute_metrics,
        callbacks=callbacks,
        data_collator=data_collator,
        tokenizer = tokenizer
    )

    # Load checkpoint model:
    # checkpoint = torch.load("./models/0706-172025/checkpoint-4350/")


    trainer.train()

    dirs = [x[0] for x in os.walk(save_dir)]
    for d in dirs:
        if 'checkpoint' in d:
            shutil.rmtree(d, ignore_errors='True')
    trainer.save_model()

    print(trainer.evaluate())
    # Loading saved model:
    # config = AutoConfig.from_pretrained("./models_main/0504-052935")
    # model = MyBertForSequenceClassification.from_pretrained("./models_main/0504-052935", config=config)

    all_predictions_train = trainer.predict(test_dataset=tokenized_datasets_train)
    all_labels_train = np.argmax(np.array(all_predictions_train[1]), axis=-1)
    all_logits_train = all_predictions_train[0]
    all_predictions_train = np.argmax(np.array(all_predictions_train[0]), axis=-1)
    accuracy_train = (np.sum(all_predictions_train == all_labels_train))/len(all_labels_train)

    all_predictions_eval = trainer.predict(test_dataset=tokenized_datasets_test)
    all_labels_eval = np.argmax(np.array(all_predictions_eval[1]), axis=-1)
    all_logits_eval = all_predictions_eval[0]
    all_predictions_eval = np.argmax(np.array(all_predictions_eval[0]), axis=-1)
    accuracy_eval = (np.sum(all_predictions_eval == all_labels_eval)) / len(all_labels_eval)

    # all_predictions_eval2 = trainer.predict(test_dataset=tokenized_datasets_test2)
    # all_labels_eval2 = np.array(all_predictions_eval2[1])
    # all_logits_eval2 = all_predictions_eval2[0]
    # all_predictions_eval2 = np.argmax(np.array(all_predictions_eval2[0]), axis=-1)

    # all_predictions_test = trainer.predict(test_dataset=tokenized_datasets['test'])
    # all_labels_test = np.array(all_predictions_test[1])
    # all_logits_test = all_predictions_test[0]
    # all_predictions_test = np.argmax(np.array(all_predictions_test[0]), axis=-1)
    # prediction_df = pd.DataFrame(data=[[all_labels_train, all_predictions_train, all_logits_train,
    #                                    all_labels_eval, all_predictions_eval, all_logits_eval,
    #                                    all_labels_test, all_predictions_test, all_logits_test]], columns=[
    #     'train_labels', 'train_predictions', 'train_logits',
    #     'eval_labels', 'eval_predictions', 'eval_logits',
    #     'test_labels', 'test_predictions', 'test_logits',
    # ])
    # prediction_df.to_csv(save_dir+'predictions.csv', index=False)
    # print(save_dir)
    # print("Eval Accuracies:  \n")
    # print('Acc:', accuracy_score(all_labels_eval, all_predictions_eval),
    #       ', Recall:', recall_score(all_labels_eval, all_predictions_eval, average="weighted"), ', Precision:', precision_score(all_labels_eval, all_predictions_eval, average="weighted"),
    #       ', ROC:', roc_auc_score(all_labels_eval, all_logits_eval[:,1]), ', MCC:', matthews_corrcoef(all_labels_eval, all_predictions_eval),
    #        ', AP:', average_precision_score(all_labels_eval, all_logits_eval[:,1]),
    #       ', F1:', f1_score(all_labels_eval, all_predictions_eval, average="weighted"))
    #
    # print("Training Accuracies:   \n")
    # print('Acc:', accuracy_score(all_labels_train, all_predictions_train),
    #       ', Recall:', recall_score(all_labels_train, all_predictions_train), ', Precision:', precision_score(all_labels_train, all_predictions_train),
    #       ', ROC:', roc_auc_score(all_labels_train, all_logits_train[:,1]), ', MCC:', matthews_corrcoef(all_labels_train, all_predictions_train),
    #        ', AP:', average_precision_score(all_labels_train, all_logits_train[:,1]),
    #       ', F1:', f1_score(all_labels_train, all_predictions_train, average='weighted'))

    # print('Acc:', accuracy_score(all_labels_test, all_predictions_test),
    #       ', Recall:', recall_score(all_labels_test, all_predictions_test), ', Precision:', precision_score(all_labels_test, all_predictions_test),
    #       ', ROC:', roc_auc_score(all_labels_test, all_logits_test[:,1]), ', MCC:', matthews_corrcoef(all_labels_test, all_predictions_test),
    #        ', AP:', average_precision_score(all_labels_test, all_logits_test[:,1]),
    #       ', F1:', f1_score(all_labels_test, all_predictions_test))
    #
    # print(round(accuracy_score(all_labels_test, all_predictions_test), 4),
    #      round(recall_score(all_labels_test, all_predictions_test), 4), round(precision_score(all_labels_test, all_predictions_test), 4),
    #       round(roc_auc_score(all_labels_test, all_logits_test[:,1]), 4), round(matthews_corrcoef(all_labels_test, all_predictions_test), 4))

    # print('F1:', f1_score(all_labels_test, all_predictions_test), ', Acc:', accuracy_score(all_labels_test, all_predictions_test), ', MCC:',
    #       matthews_corrcoef(all_labels_test, all_predictions_test), ', ROC:', roc_auc_score(all_labels_test, all_logits_test[:,1]),
    #       ', Precision:', precision_score(all_labels_test, all_predictions_test), ', Recall:',
    #       recall_score(all_labels_test, all_predictions_test), ', AP:', average_precision_score(all_labels_test, all_logits_test[:,1]))

    # df = pd.DataFrame(data=[[f1_score(all_labels_eval, all_predictions_eval), accuracy_score(all_labels_eval, all_predictions_eval),
    #                    matthews_corrcoef(all_labels_eval, all_predictions_eval), roc_auc_score(all_labels_eval, all_logits_eval[:,1]),
    #                    precision_score(all_labels_eval, all_predictions_eval),
    #                    recall_score(all_labels_eval, all_predictions_eval), average_precision_score(all_labels_eval, all_logits_eval[:,1]),
    #                    f1_score(all_labels_test, all_predictions_test), accuracy_score(all_labels_test, all_predictions_test),
    #                    matthews_corrcoef(all_labels_test, all_predictions_test), roc_auc_score(all_labels_test, all_logits_test[:,1]),
    #                    precision_score(all_labels_test, all_predictions_test),
    #                    recall_score(all_labels_test, all_predictions_test), average_precision_score(all_labels_test, all_logits_test[:,1]),
    #                    subject, config.use_pooler, config.use_mean, config.intermediate_hidden_size, batch_size,
    #                    freeze_positional, patience, freeze_non_positional, freeze_attention,
    #                    freeze_layer_norm, freeze_pooler, initial_lr, transfer, num_epochs, save_dir, early_stopping, create_validation_split, fold, ten_fold]], columns=[
    #                    'f1_eval', 'accuracy_eval', 'mcc_eval', 'roc_auc_eval', 'precision_eval', 'recall_eval', 'average_precision_score_eval',
    #                    'f1_test', 'accuracy_test', 'mcc_test', 'roc_auc_test', 'precision_test', 'recall_test', 'average_precision_score_test',
    #                    'subject', 'usepooler', 'usemean', 'hidden_layer_size', 'batchsize', 'frozenpositional', 'patience',
    #                    'frozennonpositional', 'frozenattention', 'frozenlayernorm', 'frozenpooler', 'lr', 'transfer', 'num_epochs', 'save_dir',
    #                    'early_stopping', 'create_validation_split', 'fold', 'ten_fold'])
    # if not os.path.isfile('results/training_results.csv'):
    #    df.to_csv('results/training_results.csv', index=False)
    # else: # else it exists so append without writing the header
    #    df.to_csv('results/training_results.csv', index=False, mode='a', header=False)

# fresh_model = MyBertForSequenceClassification.from_pretrained("Rostlab/prot_bert_bfd", config=config)
# new_model = trainer.model
# new_model.to(device='cpu')
# new_model_state_dict = new_model.state_dict()
# for name, param in fresh_model.named_parameters():
#     # if 'attn' in name or 'mlp' in name:
#     new_param = new_model_state_dict[name]
#     if torch.abs(param.data - new_param.data).sum() > 1e-8:
#         print(f'{name} was modified')
#     else:
#         print(f'{name} is unchanged')


# results_df = pd.read_csv('results/training_results.csv')
# results_df = results_df[results_df['subject'] == 'ampep']
# results_df = results_df[results_df['hidden_layer_size'] == 1024]
#
# all_predictions_test = []
# all_logits_test = []
# all_labels_test = []
# for dir in results_df['save_dir']:
#     pred_df = pd.read_csv(dir+'predictions.csv')
#     all_predictions_test.extend(np.array(pred_df['test_predictions']))
#     all_logits_test.extend(np.array(pred_df['test_logits']))
#     all_labels_test.extend(np.array(pred_df['test_labels']))
#
# print(matthews_corrcoef(all_labels_test, all_predictions_test))
#
# print('F1:', f1_score(all_labels_test, all_predictions_test), ', Acc:', accuracy_score(all_labels_test, all_predictions_test), ', MCC:',
#       matthews_corrcoef(all_labels_test, all_predictions_test), ', ROC:', roc_auc_score(all_labels_test, all_logits_test[:,1]),
#       ', Precision:', precision_score(all_labels_test, all_predictions_test), ', Recall:',
#       recall_score(all_labels_test, all_predictions_test), ', AP:', average_precision_score(all_labels_test, all_logits_test[:,1]))
# print(np.mean(np.array(results_df['mcc_test'])))
#
# alpha = dataset_train['text']
# alpha_all = []
# for a in alpha:
#     for b in a:
#         if b not in alpha_all:
#             alpha_all.append(b)
#
#
# data = tokenized_datasets_test['input_ids']
# seq_data = []
# for proteins in data:
#     seq_data.append(proteins.numpy())
#
# # animo_acids = []
# for a in seq_data:
#     for b in a:
#         if int(b) not in animo_acids:
#             animo_acids.append(int(b))
#
#
# data_temp = tokenized_datasets_temp['input_ids']
# seq_data_temp = []
# for proteins in data_temp:
#     seq_data_temp.append(proteins.numpy())
#
# animo_acids_temp = []
# for a in seq_data_temp:
#     for b in a:
#         if int(b) not in animo_acids_temp:
#             animo_acids_temp.append(int(b))
#
# # 22,26
# print(tokenizer.convert_ids_to_tokens(data_temp[0]))
# y = '3 ' + 'A B C '*512
# text_temp = ['1 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z', '2 L Z A F', y]
# dict_temp = {'text':text_temp,'labels':labels_test[0:3]}
# dataset_temp = Dataset.from_dict(dict_temp, split='train')
# all_data = tokenize_function(dataset_test)
# tokenized_datasets_test = copy.deepcopy(dataset_test)
# tokenized_datasets_test = tokenized_datasets_test.add_column('input_ids', all_data[0])
# tokenized_datasets_test = tokenized_datasets_test.add_column('token_type_ids', all_data[2])
# tokenized_datasets_test = tokenized_datasets_test.add_column('attention_mask', all_data[1])
#
# all_data = tokenize_function(dataset_train)
# tokenized_datasets_train = copy.deepcopy(dataset_train)
# tokenized_datasets_train = tokenized_datasets_train.add_column('input_ids', all_data[0])
# tokenized_datasets_train = tokenized_datasets_train.add_column('token_type_ids', all_data[2])
# tokenized_datasets_train = tokenized_datasets_train.add_column('attention_mask', all_data[1])
#
#
# # tokenized_datasets_temp = dataset_temp.map(tokenize_function, batched=True)
#
# tokenized_datasets_train.set_format("torch", columns=['input_ids'])
# tokenized_datasets_train = tokenized_datasets_train.remove_columns('text')
# tokenized_datasets_train.set_format("torch")
#
# print(tokenizer.convert_ids_to_tokens(tokenized_datasets_temp['input_ids'][0]))
# # ds = load_dataset("cosmos_qa", split="train")
#
# new_column = ["foo"] * len(tokenized_datasets_temp)
# tokenized_datasets_temp = tokenized_datasets_temp.add_column("new_column", new_column)


# import pickle
#
# # Open the file in binary mode
# with open('features.pkl', 'rb') as file:
#     # Call load method to deserialze
#     features_temp = pickle.load(file)
#
# # Open the file in binary mode
# with open('batch.pkl', 'rb') as file:
#     # Call load method to deserialze
#     batch_temp = pickle.load(file)
#
# x = batch_temp['labels']
# x1 = batch_temp['input_ids']
# x2 = batch_temp['token_type_ids']
# x3 = batch_temp['attention_mask']
#
# for i in range(0,len(x2[1])):
#     if x3[2][i] == 0:
#         break
# # Precsion and recall:
# print("\n\nENSEMBLE MODEL:  ")
# print(classification_report(test_pred_flat, test_pred_label_flat,digits=4))
# # Confusion Matrix:
# y_true = test_pred_label_flat
# y_pred = test_pred_flat
# data = confusion_matrix(y_true, y_pred)
# df_cm = pd.DataFrame(data, columns=np.unique(y_true), index = np.unique(y_true))
# df_cm.index.name = 'Actual'
# df_cm.columns.name = 'Predicted'
# plt.figure(figsize = (10,7))
# sn.set(font_scale=1.4)#for label size
# sn.heatmap(df_cm, cmap="Blues", annot=True,annot_kws={"size": 16}, fmt='d')# font size
# plt.title("Confusion matrix for Ensemble model")
# plt.show()