domain_mapping/biomedical_train/bc5cdr-disease/prediction/predict.py

# %%

# from datasets import load_from_disk
import os
import glob

os.environ['NCCL_P2P_DISABLE'] = '1'
os.environ['NCCL_IB_DISABLE'] = '1'
os.environ["CUDA_DEVICE_ORDER"] = "PCI_BUS_ID"
os.environ["CUDA_VISIBLE_DEVICES"] = "0,1,2,3"

import re
import torch
from torch.utils.data import DataLoader

from transformers import (
    AutoTokenizer,
    AutoModelForSequenceClassification,
    DataCollatorWithPadding,
)
import evaluate
import numpy as np
import pandas as pd
# import matplotlib.pyplot as plt
from datasets import Dataset, DatasetDict

from tqdm import tqdm

torch.set_float32_matmul_precision('high')


BATCH_SIZE = 256

# %%
# construct the target id list
data_path = '../../../biomedical_data_import/bc2gm_train.csv'
train_df = pd.read_csv(data_path, skipinitialspace=True)
entity_ids = train_df['entity_id'].to_list()
target_id_list = sorted(list(set(entity_ids)))
# target_id_list = [id for id in target_id_list]


# %%
id2label = {}
label2id = {}
for idx, val in enumerate(target_id_list):
    id2label[idx] = val
    label2id[val] = idx


# introduce pre-processing functions
def preprocess_text(text):
    # 1. Make all uppercase
    text = text.lower()

    # Substitute digits with '#'
    # text = re.sub(r'\d+', '#', text)

    # standardize spacing
    text = re.sub(r'\s+', ' ', text).strip()

    return text




# outputs a list of dictionaries
# processes dataframe into lists of dictionaries
# each element maps input to output
# input: tag_description
# output: class label
def process_df_to_dict(df):
    output_list = []
    for _, row in df.iterrows():
        desc = row['mention']
        desc = preprocess_text(desc)
        row_id = row['entity_id']
        element = {
            'text' : desc,
            'labels': label2id[row_id], # ensure labels starts from 0
        }
        output_list.append(element)

    return output_list


def create_dataset():
    # train 
    data_path = '../../../biomedical_data_import/bc2gm_test.csv'
    test_df = pd.read_csv(data_path, skipinitialspace=True)


    combined_data = DatasetDict({
        'test': Dataset.from_list(process_df_to_dict(test_df)),
    })
    return combined_data




# %%

def test():

    test_dataset = create_dataset()

    # prepare tokenizer

    checkpoint_directory = f'../checkpoint'
    # Use glob to find matching paths
    # path is usually checkpoint_fold_1/checkpoint-<step number>
    # we are guaranteed to save only 1 checkpoint from training
    pattern = 'checkpoint-*'
    model_checkpoint = glob.glob(os.path.join(checkpoint_directory, pattern))[0]

    tokenizer = AutoTokenizer.from_pretrained(model_checkpoint, return_tensors="pt", clean_up_tokenization_spaces=True)


    # %%

    # given a dataset entry, run it through the tokenizer
    def preprocess_function(example):
        input = example['text']
        # text_target sets the corresponding label to inputs
        # there is no need to create a separate 'labels'
        model_inputs = tokenizer(
            input,
            truncation=True,
        )
        return model_inputs

    # map maps function to each "row" in the dataset
    # aka the data in the immediate nesting
    datasets = test_dataset.map(
        preprocess_function,
        batched=True,
        num_proc=8,
        remove_columns="text",
    )


    datasets.set_format(type='torch', columns=['input_ids', 'attention_mask', 'labels'])

    # print datasets['test'] columns
    column_info = datasets['test'].features
    for column, dtype in column_info.items():
        print(f"Column: {column}, Type: {dtype}")

    model = AutoModelForSequenceClassification.from_pretrained(
        model_checkpoint,
        num_labels=len(target_id_list),
        id2label=id2label,
        label2id=label2id)
    # important! after extending tokens vocab
    model.resize_token_embeddings(len(tokenizer))

    model = model.eval()

    device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
    model.to(device)

    pred_labels = []
    actual_labels = []

    data_collator = DataCollatorWithPadding(tokenizer=tokenizer)

    dataloader = DataLoader(
        datasets['test'],
        batch_size=BATCH_SIZE, 
        shuffle=False,
        collate_fn=data_collator)

    for batch in tqdm(dataloader):
            # Inference in batches
            input_ids = batch['input_ids']
            attention_mask = batch['attention_mask']
            # save labels too
            actual_labels.extend(batch['labels'])
            

            # Move to GPU if available
            input_ids = input_ids.to(device)
            attention_mask = attention_mask.to(device)

            # Perform inference
            with torch.no_grad():
                logits = model(
                    input_ids,
                    attention_mask).logits
                predicted_class_ids = logits.argmax(dim=1).to("cpu")
                pred_labels.extend(predicted_class_ids)

    pred_labels = [tensor.item() for tensor in pred_labels]


    # %%
    from sklearn.metrics import accuracy_score, f1_score, precision_score, recall_score, confusion_matrix
    y_true = actual_labels
    y_pred = pred_labels

    # Compute metrics
    accuracy = accuracy_score(y_true, y_pred)
    average_parameter = 'weighted'
    zero_division_parameter = 0
    f1 = f1_score(y_true, y_pred, average=average_parameter, zero_division=zero_division_parameter)
    precision = precision_score(y_true, y_pred, average=average_parameter, zero_division=zero_division_parameter)
    recall = recall_score(y_true, y_pred, average=average_parameter, zero_division=zero_division_parameter)

    with open("output.txt", "a") as f:

        print('*' * 80, file=f)
        # Print the results
        print(f'Accuracy: {accuracy:.5f}', file=f)
        print(f'F1 Score: {f1:.5f}', file=f)
        print(f'Precision: {precision:.5f}', file=f)
        print(f'Recall: {recall:.5f}', file=f)

    # export result
    label_list = [id2label[id] for id in pred_labels]
    df = pd.DataFrame({
        'class_prediction': pd.Series(label_list) 
    })

    # we can save the t5 generation output here
    df.to_csv(f"exports/result.csv", index=False)






# %%
# reset file before writing to it
with open("output.txt", "w") as f:
    print('', file=f)
    test()