app.py

from utils import *

import torch
import torch.nn as nn
from torch.utils.data import Dataset, DataLoader
import unicodedata
import re

# Undesirable patterns within texts
patterns = {
    'CONCLUSIONS AND IMPLICATIONS':'',
    'BACKGROUND AND PURPOSE':'',
    'EXPERIMENTAL APPROACH':'',
    'KEY RESULTS AEA':'',
    '©':'',
    '®':'',
    'μ':'',
    '(C)':'',
    'OBJECTIVE:':'',
    'MATERIALS AND METHODS:':'',
    'SIGNIFICANCE:':'',
    'BACKGROUND:':'',
    'RESULTS:':'',
    'METHODS:':'',
    'CONCLUSIONS:':'',
    'AIM:':'',
    'STUDY DESIGN:':'',
    'CLINICAL RELEVANCE:':'',
    'CONCLUSION:':'',
    'HYPOTHESIS:':'',
    'CLINICAL RELEVANCE:':'',
    'Questions/Purposes:':'',
    'Introduction:':'',
    'PURPOSE:':'',
    'PATIENTS AND METHODS:':'',
    'FINDINGS:':'',
    'INTERPRETATIONS:':'',
    'FUNDING:':'',
    'PROGRESS:':'',
    'CONTEXT:':'',
    'MEASURES:':'',
    'DESIGN:':'',
    'BACKGROUND AND OBJECTIVES:':'',
    '<p>':'',
    '</p>':'',
    '<<ETX>>':'',
    '+/-':'',
    }
 
patterns = {x.lower():y for x,y in patterns.items()}

class treat_text:
  def __init__(self, patterns):
    self.patterns = patterns

  def __call__(self,text):
    text = unicodedata.normalize("NFKD",str(text))
    text = multiple_replace(self.patterns,text.lower())
    text = re.sub('(\(.+\))|(\[.+\])|( \d )|(<)|(>)|(- )','', text)
    text = re.sub('( +)',' ', text)
    text = re.sub('(, ,)|(,,)',',', text)
    text = re.sub('(%)|(per cent)',' percent', text)
    return text

# Regex multiple replace function
def multiple_replace(dict, text):

  # Building regex from dict keys
  regex = re.compile("(%s)" % "|".join(map(re.escape, dict.keys())))

  # Substitution
  return regex.sub(lambda mo: dict[mo.string[mo.start():mo.end()]], text) 

treat_text_fun = treat_text(patterns)

import sys
sys.path.append('ML-SLRC/')

path = 'ML-SLRC/'

model_path = path + 'model.pt'
info_path = path + 'Info.json'

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

# # carrega o modelo
model = torch.load(model_path)


# # carrega as meta informações do modelo treinado
with open(info_path, 'r') as f:
  Info = json.load(f)

import random
from datetime import datetime


rand_seed = 2003

# datetime object containing current date and time
now = datetime.now()

time_stamp = now.strftime("%d_%m_%Y_HR_%H_%M_%S")


config = {
    "shots_per_class":8,
    "batch_size":4,
    "epochs":8,
    "learning_rate":5e-05,
    "weight_decay": 0.85,
    "rand_seed":rand_seed,
    'pos_weight':3.5,
    'p_incld': 0.2,
    'p_excld': 0.01,
}


NAME = str(config['shots_per_class'])+'-shots-Learner' +'_'+ time_stamp
num_workers = 0
val_batch = 100

p_included = 0.7
p_notincluded = 0.3
sample_valid = 300




gen_seed = torch.Generator().manual_seed(rand_seed)
np.random.seed(rand_seed)
torch.manual_seed(rand_seed)
random.seed(rand_seed)




def treat_data_input(data, etailment_txt):

  data_train = data.groupby('test').sample(frac=1)
  dataload_all = data.copy()

  dataload_all.test = dataload_all.test.replace({np.nan: 'NANN'})


  dataset_train = SLR_DataSet(data=data_train,
                input= 'text',
                output='test',
                tokenizer= initializer_model_scibert.tokenizer,
                LABEL_MAP=LABEL_MAP,
                treat_text=treat_text_fun,
                etailment_txt=etailment_txt)

  dataset_remain = SLR_DataSet(data=dataload_all,
                input= 'text',
                output='test',
                tokenizer= initializer_model_scibert.tokenizer,
                LABEL_MAP=LABEL_MAP,
                treat_text=treat_text_fun,
                etailment_txt=etailment_txt)



  dataload_train = DataLoader(dataset_train,
              batch_size=config['batch_size'],drop_last=False,
              num_workers=num_workers)

  dataload_remain = DataLoader(dataset_remain,
              batch_size=200,drop_last=False,
              num_workers=num_workers)
  
  return dataload_train, dataload_remain


import gc
from torch.optim import Adam

def treat_train_evaluate(dataload_train, dataload_remain):
  device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')

  gc.collect()
  torch.cuda.empty_cache()


  model_few = deepcopy(model)
  model_few.loss_fn = nn.BCEWithLogitsLoss(reduction = 'mean',
                                          pos_weight=torch.FloatTensor([config['pos_weight']]))


  optimizer = Adam(model_few.parameters(), lr = config['learning_rate'],
                  weight_decay = config['weight_decay'])


  model_few.to('cuda')
  model_few.train()


  trainlog = model_few.fit(optimizer=optimizer, 
                          scheduler = None,
                          data_train_loader=dataload_train,
                        epochs = config['epochs'], print_info = 1, metrics= False,
                        log = None, metrics_print = False)



  (loss, features_out, (logits, outputs)) = model_few.evaluate(dataload_remain)
  return logits

def treat_sort(dataload_all,logits):
  dataload_all['prediction'] = torch.sigmoid(logits)
  dataload_all = dataload_all.sort_values(by=['prediction'], ascending=False).reset_index(drop=True)
  dataload_all.to_excel("output.xlsx") 

def pipeline(data):
  # data = pd.read_csv(fil.name)
  data = pd.read_excel(data)
  dataload_train, dataload_remain = treat_data_input(data,"its a great text")
  logits = treat_train_evaluate(dataload_train, dataload_remain)
  treat_sort(dataload_all,logits)
  return "output.xlsx"


import gradio as gr


with gr.Blocks() as demo:
    fil = gr.File(label="input data")
    output = gr.File(label="output data")
    greet_btn = gr.Button("Greet")
    greet_btn.click(fn=pipeline, inputs=fil, outputs=output)

demo.launch()