Commit b82572c0 authored by Almouhannad's avatar Almouhannad

Add classifier

parent f1c1b376
test.ipynb
clf-test.ipynb
{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# ***Setup***"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"import nltk\n",
"from nltk.stem import PorterStemmer\n",
"from nltk.tokenize import word_tokenize\n",
"from nltk.corpus import stopwords\n",
"\n",
"from sklearn.feature_extraction.text import TfidfVectorizer\n",
"from sklearn.naive_bayes import MultinomialNB\n",
"from sklearn.metrics import accuracy_score, classification_report\n",
"\n",
"from tabulate import tabulate\n",
"\n",
"import pandas as pd\n",
"TRAIN_SET_PATH = 'data/Preprocessed_Symptom2Disease_Train.csv'\n",
"TEST_SET_PATH = 'data/Preprocessed_Symptom2Disease_Test.csv'"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"##### Now, we have to download `Punkt Tokenizer Model`, try running following cell, if it didn't work successfully then try to download model manually from following links: [Manual installation](https://www.nltk.org/data.html), and [Model link](https://raw.githubusercontent.com/nltk/nltk_data/gh-pages/packages/tokenizers/punkt.zip).\n"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"[nltk_data] Downloading package punkt to\n",
"[nltk_data] C:\\Users\\TOSHIBA\\AppData\\Roaming\\nltk_data...\n",
"[nltk_data] Package punkt is already up-to-date!\n"
]
},
{
"data": {
"text/plain": [
"True"
]
},
"execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"nltk.download('punkt')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"##### You must see an output similar to the following output:\n",
"> `[nltk_data] Downloading package punkt to` \n",
"> `[nltk_data] C:\\Users\\TOSHIBA\\AppData\\Roaming\\nltk_data...` \n",
"> `[nltk_data] Package punkt is already up-to-date!` \n"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"[nltk_data] Downloading package stopwords to\n",
"[nltk_data] C:\\Users\\TOSHIBA\\AppData\\Roaming\\nltk_data...\n",
"[nltk_data] Package stopwords is already up-to-date!\n"
]
},
{
"data": {
"text/plain": [
"True"
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"nltk.download('stopwords')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"***Some helper functions***"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
"stemmer = PorterStemmer()\n",
"\n",
"def stem_text(text):\n",
" tokens = word_tokenize(text) # Tokenize the text\n",
" stemmed_tokens = [stemmer.stem(token) for token in tokens] # Apply stemming\n",
" return ' '.join(stemmed_tokens)"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [],
"source": [
"stop_words = set(stopwords.words('english'))\n",
"\n",
"def remove_stopwords(text):\n",
" tokens = word_tokenize(text) # Tokenize the text\n",
" filtered_tokens = [word for word in tokens if word not in stop_words] # Remove stop words\n",
" return ' '.join(filtered_tokens)"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [],
"source": [
"def print_clf_report_as_table(report):\n",
" data = []\n",
" for key, value in report.items():\n",
" if key != 'accuracy' and key != 'macro avg' and key != 'weighted avg':\n",
" data.append([key, value['precision'], value['recall'], value['f1-score'], value['support']])\n",
"\n",
" data.append(['accuracy', '', '', report['accuracy'], ''])\n",
"\n",
" data.append(['macro avg', report['macro avg']['precision'], report['macro avg']['recall'], report['macro avg']['f1-score'], ''])\n",
"\n",
" data.append(['weighted avg', report['weighted avg']['precision'], report['weighted avg']['recall'], report['weighted avg']['f1-score'], ''])\n",
"\n",
" print(tabulate(data, headers=['Class', 'Precision', 'Recall', 'F1-score', 'Support'], tablefmt='psql'))"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# ***0- Read train and test sets***"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [],
"source": [
"train_set = pd.read_csv(TRAIN_SET_PATH)\n",
"X_train = train_set['text']\n",
"y_train = train_set['label']"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [],
"source": [
"test_set = pd.read_csv(TEST_SET_PATH)\n",
"X_test = test_set['text']\n",
"y_test = test_set['label']"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# ***1- Apply stemming to all symptoms(texts)***\n"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [],
"source": [
"X_train = X_train.apply(stem_text)\n",
"X_test = X_test.apply(stem_text)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# ***2- Remove stopping words***"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [],
"source": [
"X_train = X_train.apply(remove_stopwords)\n",
"X_test = X_test.apply(remove_stopwords)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# ***3-Feature Vectorization using `TF-IDF`***"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"##### `TF-IDF` stands for `Term Frequency-Inverse Document Frequency` which measure how important the word is in a document\n",
"- ##### ***Why?*** Text needs to be transformed into numerical form to be used in machine learning models."
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [],
"source": [
"# Initialize TF-IDF Vectorizer\n",
"vectorizer = TfidfVectorizer()\n",
"\n",
"# Fit the vectorizer on the training data and transform the training and test data\n",
"X_train = vectorizer.fit_transform(X_train)\n",
"X_test = vectorizer.transform(X_test)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# ***4- Train a Classifier (Naive Bayes)***"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [
{
"data": {
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],
"text/plain": [
"MultinomialNB()"
]
},
"execution_count": 12,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"classifier = MultinomialNB()\n",
"classifier.fit(X_train, y_train)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# ***5- Evaluate the Model***"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Accuracy: 0.961038961038961\n"
]
}
],
"source": [
"y_pred = classifier.predict(X_test)\n",
"accuracy = accuracy_score(y_test, y_pred)\n",
"print(f'Accuracy: {accuracy}')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"##### Classification report for each class (each class is a disease)"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"+---------------------------------+--------------------+--------------------+------------+-----------+\n",
"| Class | Precision | Recall | F1-score | Support |\n",
"|---------------------------------+--------------------+--------------------+------------+-----------|\n",
"| acne | 1.0 | 1.0 | 1 | 9 |\n",
"| allergy | 0.875 | 1.0 | 0.933333 | 7 |\n",
"| arthritis | 1.0 | 1.0 | 1 | 7 |\n",
"| bronchial asthma | 1.0 | 1.0 | 1 | 8 |\n",
"| cervical spondylosis | 1.0 | 1.0 | 1 | 9 |\n",
"| chicken pox | 1.0 | 0.875 | 0.933333 | 8 |\n",
"| common cold | 0.8888888888888888 | 1.0 | 0.941176 | 8 |\n",
"| dengue | 0.8888888888888888 | 1.0 | 0.941176 | 8 |\n",
"| diabetes | 1.0 | 0.8 | 0.888889 | 10 |\n",
"| dimorphic hemorrhoids | 1.0 | 1.0 | 1 | 7 |\n",
"| drug reaction | 0.8571428571428571 | 0.8571428571428571 | 0.857143 | 7 |\n",
"| fungal infection | 0.9090909090909091 | 1.0 | 0.952381 | 10 |\n",
"| gastroesophageal reflux disease | 0.8461538461538461 | 1.0 | 0.916667 | 11 |\n",
"| hypertension | 1.0 | 1.0 | 1 | 7 |\n",
"| impetigo | 1.0 | 1.0 | 1 | 11 |\n",
"| jaundice | 1.0 | 1.0 | 1 | 9 |\n",
"| malaria | 1.0 | 1.0 | 1 | 15 |\n",
"| migraine | 1.0 | 0.9090909090909091 | 0.952381 | 11 |\n",
"| peptic ulcer disease | 1.0 | 0.8333333333333334 | 0.909091 | 12 |\n",
"| pneumonia | 0.9166666666666666 | 1.0 | 0.956522 | 11 |\n",
"| psoriasis | 1.0 | 0.9285714285714286 | 0.962963 | 14 |\n",
"| typhoid | 1.0 | 0.9230769230769231 | 0.96 | 13 |\n",
"| urinary tract infection | 0.9230769230769231 | 1.0 | 0.96 | 12 |\n",
"| varicose veins | 1.0 | 1.0 | 1 | 7 |\n",
"| accuracy | | | 0.961039 | |\n",
"| macro avg | 0.9627045408295407 | 0.9635923104673104 | 0.961044 | |\n",
"| weighted avg | 0.9649613854159308 | 0.961038961038961 | 0.960794 | |\n",
"+---------------------------------+--------------------+--------------------+------------+-----------+\n"
]
}
],
"source": [
"report = classification_report(y_test, y_pred, output_dict=True)\n",
"print_clf_report_as_table(report)"
]
}
],
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