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Commit 5f26cfb2 authored by Menezes, Luke J (PG/T - Comp Sci & Elec Eng)'s avatar Menezes, Luke J (PG/T - Comp Sci & Elec Eng)
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%% Cell type:code id:3f7f7977-2d7f-45d9-a5ce-860e9f12b167 tags:
``` python
from flask import Flask, jsonify, request, render_template
import json
import os
import logging
import pandas as pd
import datasets, evaluate
from transformers import pipeline
import torch
from datetime import datetime
from functools import partial
import numpy as np
import seaborn as sns
import string
import nltk
import re
import time
from transformers import AutoTokenizer, AutoModelForTokenClassification, DataCollatorForTokenClassification, TrainingArguments, Trainer, EarlyStoppingCallback
```
%% Output
/Users/meenusathyanarayanan/anaconda3/lib/python3.11/site-packages/transformers/utils/generic.py:260: UserWarning: torch.utils._pytree._register_pytree_node is deprecated. Please use torch.utils._pytree.register_pytree_node instead.
torch.utils._pytree._register_pytree_node(
/Users/meenusathyanarayanan/anaconda3/lib/python3.11/site-packages/transformers/utils/generic.py:260: UserWarning: torch.utils._pytree._register_pytree_node is deprecated. Please use torch.utils._pytree.register_pytree_node instead.
torch.utils._pytree._register_pytree_node(
%% Cell type:code id:59de7380-6213-4d2c-9c21-d2e51a242c98 tags:
``` python
from datasets import load_dataset
dataset = load_dataset("surrey-nlp/PLOD-filtered")
dataset=dataset['train']
```
%% Cell type:code id:e381b9eb-06ea-4333-adea-3aae055d6a56 tags:
``` python
max(len(example['tokens']) for example in dataset)
```
%% Output
1247
%% Cell type:code id:c9fccb03-9080-4d79-9323-2a7e29e31c47 tags:
``` python
def filter_long(data):
return len(data['tokens']) <= 500
dataset = dataset.filter(filter_long)
```
%% Cell type:code id:39c416a9-bdde-44c5-a88e-962ec39e6c51 tags:
``` python
from datasets import load_dataset
import random
def print_random_tokens(dataset):
# Get the total number of rows in the dataset
num_rows = len(dataset)
# Generate 1000 random unique indices from the dataset
random_indices = random.sample(range(num_rows), 1000)
# Retrieve the 'tokens' from these random indices
random_tokens = dataset.select(random_indices)['tokens']
# Print each list of tokens
for tokens in random_tokens:
print(tokens)
# Load the dataset
# dataset = load_dataset("surrey-nlp/PLOD-unfiltered")
# train_dataset = dataset["train"]
# # Example usage of the function
# print_random_tokens(train_dataset)
```
%% Cell type:code id:15fb65b5-33dd-43d4-92a7-de043b4334a9 tags:
``` python
app = Flask(__name__)
```
%% Cell type:code id:64969fe0-4820-457a-ac94-b737ee928727 tags:
``` python
@app.route('/use-pretrained', methods=['GET'])
def use_pretrained():
"""Endpoint to load and use a pre-trained model."""
try:
# Load the pre-trained model and tokenizer
global loaded_tokenizer, loaded_model
loaded_tokenizer = AutoTokenizer.from_pretrained("SciBERT-finetuned-NER")
loaded_model = AutoModelForTokenClassification.from_pretrained("SciBERT-finetuned-NER")
return jsonify(success="Pre-trained model loaded successfully")
except Exception as e:
return jsonify(error=str(e)), 500
```
%% Cell type:code id:3358edd7-ced6-4a2e-b838-ac354c9c0809 tags:
``` python
@app.route('/predict', methods=['POST'])
## Train must be run before this
## run from command line with: curl -s -H "Content-Type: application/json" -X POST -d '{"input": }' localhost:8080/predict
## examples:
## curl -s -H "Content-Type: application/json" -X POST -d '{"input": "For this purpose the Gothenburg Young Persons Empowerment Scale (GYPES) was developed."}' localhost:8080/predict
## curl -s -H "Content-Type: application/json" -X POST -d '{"input": "Recent work by us and others suggest that the host’s heat shock protein 90 (Hsp90) chaperone can modulate the evolutionary paths traversed by viruses [18, 19]."}' localhost:8080/predict
def predict():
inputs = request.get_json().get('input')
converted_inputs = split_string(inputs)
predictions = predict_tags(converted_inputs, loaded_tokenizer, loaded_model, label_encoding)
ner_tags = [i[1] for i in predictions]
save_results(converted_inputs, ner_tags)
return jsonify(predictions = str(predictions))
```
%% Cell type:code id:92347951-af52-4c1f-b81f-f89cd3272c3a tags:
``` python
@app.route('/test-model', methods=['GET'])
def test_model():
start_time = time.time()
"""Endpoint to test the pre-trained model on 1000 random dataset samples."""
dataset = load_dataset("surrey-nlp/PLOD-unfiltered", split='train')
def filter_long(data):
return len(data['tokens']) <= 400
dataset = dataset.filter(filter_long)
sample_indices = random.sample(range(len(dataset)), 20000)
sampled_data = dataset.select(sample_indices)
results = []
print("in test_model")
for item in sampled_data:
# Join tokens to form a single string as the model expects a sequence
input_text = " ".join(item['tokens'])
# Tokenize the text
inputs = loaded_tokenizer(input_text, return_tensors="pt")
# Get model predictions
with torch.no_grad():
outputs = loaded_model(**inputs)
predictions = torch.argmax(outputs.logits, dim=-1)
tokens = loaded_tokenizer.convert_ids_to_tokens(inputs['input_ids'].squeeze())
predicted_tags = [dataset.features['ner_tags'].feature.int2str(p) for p in predictions.squeeze().tolist()]
# Combine tokens and their predicted tags
token_predictions = list(zip(tokens, predicted_tags))
results.append({'text': input_text, 'predictions': token_predictions})
total_time = time.time() - start_time
print("Total time taken: " + str(total_time))
return jsonify(results)
```
%% Cell type:code id:e00a3561-f701-4482-866e-68d26cc8d3d8 tags:
``` python
if __name__ == '__main__':
# Entry point for running on the local machine
# host is localhost; port is 8080; this file is index (.py)
app.run(host='127.0.0.1', port=8080, debug=False)
```
%% Output
* Serving Flask app '__main__'
* Debug mode: off
WARNING: This is a development server. Do not use it in a production deployment. Use a production WSGI server instead.
* Running on http://127.0.0.1:8080
Press CTRL+C to quit
/Users/meenusathyanarayanan/anaconda3/lib/python3.11/site-packages/transformers/utils/generic.py:260: UserWarning: torch.utils._pytree._register_pytree_node is deprecated. Please use torch.utils._pytree.register_pytree_node instead.
torch.utils._pytree._register_pytree_node(
127.0.0.1 - - [24/May/2024 11:21:35] "GET /use-pretrained HTTP/1.1" 200 -
in test_model
[2024-05-24 11:28:18,175] ERROR in app: Exception on /test-model [GET]
Traceback (most recent call last):
File "/Users/meenusathyanarayanan/.local/lib/python3.11/site-packages/flask/app.py", line 1455, in wsgi_app
response = self.full_dispatch_request()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/meenusathyanarayanan/.local/lib/python3.11/site-packages/flask/app.py", line 869, in full_dispatch_request
rv = self.handle_user_exception(e)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/meenusathyanarayanan/.local/lib/python3.11/site-packages/flask/app.py", line 867, in full_dispatch_request
rv = self.dispatch_request()
^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/meenusathyanarayanan/.local/lib/python3.11/site-packages/flask/app.py", line 852, in dispatch_request
return self.ensure_sync(self.view_functions[rule.endpoint])(**view_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/var/folders/3c/_rc81dfd35755sd95j1m_6zc0000gn/T/ipykernel_50926/1002882848.py", line 23, in test_model
outputs = loaded_model(**inputs)
^^^^^^^^^^^^^^^^^^^^^^
File "/Users/meenusathyanarayanan/anaconda3/lib/python3.11/site-packages/torch/nn/modules/module.py", line 1511, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/meenusathyanarayanan/anaconda3/lib/python3.11/site-packages/torch/nn/modules/module.py", line 1520, in _call_impl
return forward_call(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/meenusathyanarayanan/anaconda3/lib/python3.11/site-packages/transformers/models/bert/modeling_bert.py", line 1756, in forward
outputs = self.bert(
^^^^^^^^^^
File "/Users/meenusathyanarayanan/anaconda3/lib/python3.11/site-packages/torch/nn/modules/module.py", line 1511, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/meenusathyanarayanan/anaconda3/lib/python3.11/site-packages/torch/nn/modules/module.py", line 1520, in _call_impl
return forward_call(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/meenusathyanarayanan/anaconda3/lib/python3.11/site-packages/transformers/models/bert/modeling_bert.py", line 1015, in forward
embedding_output = self.embeddings(
^^^^^^^^^^^^^^^^
File "/Users/meenusathyanarayanan/anaconda3/lib/python3.11/site-packages/torch/nn/modules/module.py", line 1511, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/meenusathyanarayanan/anaconda3/lib/python3.11/site-packages/torch/nn/modules/module.py", line 1520, in _call_impl
return forward_call(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/meenusathyanarayanan/anaconda3/lib/python3.11/site-packages/transformers/models/bert/modeling_bert.py", line 238, in forward
embeddings += position_embeddings
RuntimeError: The size of tensor a (534) must match the size of tensor b (512) at non-singleton dimension 1
127.0.0.1 - - [24/May/2024 11:28:18] "GET /test-model HTTP/1.1" 500 -
%% Cell type:code id:c24f86ed-2e75-4cb2-a66a-0db6a18aeb05 tags:
``` python
```
%% Cell type:code id:05340c7e-9ba7-464e-9853-e6011581cee7 tags:
``` python
```
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