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"metadata": {
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"source": [
"# Om Maa"
]
},
{
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"source": [
"!pip install langchain predictionguard lancedb html2text sentence-transformers PyPDF2\n",
"!pip install huggingface_hub\n",
"!pip install transformers\n",
"!pip install sentencepiece\n",
"!pip install streamlit"
],
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"text": [
"Requirement already satisfied: langchain in /usr/local/lib/python3.10/dist-packages (0.1.6)\n",
"Requirement already satisfied: predictionguard in /usr/local/lib/python3.10/dist-packages (1.9.1)\n",
"Requirement already satisfied: lancedb in /usr/local/lib/python3.10/dist-packages (0.5.4)\n",
"Requirement already satisfied: html2text in /usr/local/lib/python3.10/dist-packages (2020.1.16)\n",
"Requirement already satisfied: sentence-transformers in /usr/local/lib/python3.10/dist-packages (2.3.1)\n",
"Requirement already satisfied: PyPDF2 in /usr/local/lib/python3.10/dist-packages (3.0.1)\n",
"Requirement already satisfied: PyYAML>=5.3 in /usr/local/lib/python3.10/dist-packages (from langchain) (6.0.1)\n",
"Requirement already satisfied: SQLAlchemy<3,>=1.4 in /usr/local/lib/python3.10/dist-packages (from langchain) (2.0.25)\n",
"Requirement already satisfied: aiohttp<4.0.0,>=3.8.3 in /usr/local/lib/python3.10/dist-packages (from langchain) (3.9.3)\n",
"Requirement already satisfied: async-timeout<5.0.0,>=4.0.0 in /usr/local/lib/python3.10/dist-packages (from langchain) (4.0.3)\n",
"Requirement already satisfied: dataclasses-json<0.7,>=0.5.7 in /usr/local/lib/python3.10/dist-packages (from langchain) (0.6.4)\n",
"Requirement already satisfied: jsonpatch<2.0,>=1.33 in /usr/local/lib/python3.10/dist-packages (from langchain) (1.33)\n",
"Requirement already satisfied: langchain-community<0.1,>=0.0.18 in /usr/local/lib/python3.10/dist-packages (from langchain) (0.0.19)\n",
"Requirement already satisfied: langchain-core<0.2,>=0.1.22 in /usr/local/lib/python3.10/dist-packages (from langchain) (0.1.22)\n",
"Requirement already satisfied: langsmith<0.1,>=0.0.83 in /usr/local/lib/python3.10/dist-packages (from langchain) (0.0.87)\n",
"Requirement already satisfied: numpy<2,>=1 in /usr/local/lib/python3.10/dist-packages (from langchain) (1.23.5)\n",
"Requirement already satisfied: pydantic<3,>=1 in /usr/local/lib/python3.10/dist-packages (from langchain) (2.6.1)\n",
"Requirement already satisfied: requests<3,>=2 in /usr/local/lib/python3.10/dist-packages (from langchain) (2.31.0)\n",
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"Requirement already satisfied: tabulate>=0.8.10 in /usr/local/lib/python3.10/dist-packages (from predictionguard) (0.9.0)\n",
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]
}
]
},
{
"cell_type": "code",
"source": [
"import os\n",
"import urllib.request\n",
"\n",
"import html2text\n",
"import predictionguard as pg\n",
"from langchain import PromptTemplate, FewShotPromptTemplate\n",
"from langchain.text_splitter import CharacterTextSplitter\n",
"from sentence_transformers import SentenceTransformer\n",
"import numpy as np\n",
"import lancedb\n",
"from lancedb.embeddings import with_embeddings\n",
"import pandas as pd\n",
"\n",
"\n",
"os.environ['PREDICTIONGUARD_TOKEN'] = \"q1VuOjnffJ3NO2oFN8Q9m8vghYc84ld13jaqdF7E\"\n"
],
"metadata": {
"id": "EuSop0GXy2JY"
},
"execution_count": null,
"outputs": []
},
{
"cell_type": "code",
"source": [
"# Streamlit App Initiation\n",
"\n",
"import streamlit as st\n",
"\n",
"# Replace input() with Streamlit's input widgets\n",
"# Sidebar for inputting the name, age, gender, and ethnicity\n",
"name = st.sidebar.text_input('Name')\n",
"age = st.sidebar.number_input('Age', min_value=0, max_value=120, step=1)\n",
"gender = st.sidebar.selectbox('Gender', ['Male', 'Female', 'Other'])\n",
"ethnicity = st.sidebar.text_input('Ethnicity')\n",
"\n",
"\n",
"\n",
"# Main container\n",
"with st.form(key='patient_form'):\n",
" # Text input for procedures\n",
" disease = st.text_area('DISEASE', height=100)\n",
"\n",
" # Text input for prescriptions (where you would get drug_names)\n",
" prescriptions = st.text_area('PRESCRIPTIONS', height=100)\n",
"\n",
" # Text input for additional information\n",
" additional_info = st.text_area('ADDITIONAL INFO', height=100)\n",
"\n",
" # Submit button for the form\n",
" submit_button = st.form_submit_button(label='Predict Drug Effects')"
],
"metadata": {
"id": "HY6rtcqwzKvs"
},
"execution_count": null,
"outputs": []
},
{
"cell_type": "code",
"source": [
"from PyPDF2 import PdfReader\n",
"\n",
"# Replace 'path_to_your_pdf_file.pdf' with the path to your PDF file\n",
"pdf_path = '/content/drug_side_effects_summary_cleaned.pdf'\n",
"reader = PdfReader(pdf_path)\n",
"\n",
"# Initialize an empty string to accumulate text\n",
"text = ''\n",
"\n",
"# Iterate over each page in the PDF\n",
"for page in reader.pages:\n",
" # Extract text from the page and append it to the text string\n",
" text += page.extract_text() + \"\\n\"\n",
"\n",
"# Now, `text` contains the text content of the PDF. You can print it or process it further.\n",
"print(text[:500]) # Example: print the first 500 characters to understand the structure"
],
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "_4V02kdgymGD",
"outputId": "6d152fd6-6cc6-459f-ad9c-dada5a9ffda7"
},
"execution_count": null,
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
"Drug Side Effects Summary\n",
"Drug and Disease Interactions with Side Effects\n",
"1. This particular disease, Acne, interacts with the drug doxycycline and has the following side effects:\n",
"- hives, difficult breathing, swelling in your face or throat) or a severe skin reaction (fever, sore\n",
"throat, burning in your eyes, skin pain, red or purple skin rash that spreads and causes blistering\n",
"and peeling). Seek medical treatment if you have a serious drug reaction that can affect many parts\n",
"of your body. Symp\n"
]
}
]
},
{
"cell_type": "code",
"source": [
"import re\n",
"\n",
"# Function to clean the extracted text\n",
"def clean_text(text):\n",
" # Correcting unwanted line breaks and spaces\n",
" text = re.sub(r'-\\n', '', text) # Remove hyphenation\n",
" text = re.sub(r'\\n', ' ', text) # Replace new lines with space\n",
" text = re.sub(r'\\s+', ' ', text) # Replace multiple spaces with single space\n",
" text = text.strip() # Remove leading and trailing spaces\n",
" return text\n",
"\n",
"# Clean the extracted text\n",
"cleaned_text = clean_text(text)\n",
"\n",
"# Return a portion of the cleaned text to verify the cleaning\n",
"cleaned_text[:500]\n",
"\n",
"# Define a function to chunk text with specified size and overlap using standard Python\n",
"def chunk_text(text, chunk_size=700, overlap=50):\n",
" chunks = []\n",
" start = 0\n",
" while start < len(text):\n",
" # If we're not at the beginning, move back 'overlap' characters for context\n",
" if start > 0:\n",
" start -= overlap\n",
" end = start + chunk_size\n",
" chunks.append(text[start:end])\n",
" start += chunk_size\n",
" return chunks\n",
"\n",
"# Chunk the cleaned text into smaller pieces for LLM input\n",
"docs_alternative = chunk_text(cleaned_text, chunk_size=700, overlap=50)\n",
"\n",
"# Prepare to display the first few chunks to verify the result\n",
"chunks_to_display_alt = 3\n",
"chunks_preview_alt = [docs_alternative[i] for i in range(min(len(docs_alternative), chunks_to_display_alt))]\n",
"\n",
"chunks_preview_alt"
],
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "sni4-EqKzaUt",
"outputId": "9f63f715-df5b-41d6-c42b-c27a9388071f"
},
"execution_count": null,
"outputs": [
{
"output_type": "execute_result",
"data": {
"text/plain": [
"['Drug Side Effects Summary Drug and Disease Interactions with Side Effects 1. This particular disease, Acne, interacts with the drug doxycycline and has the following side effects: - hives, difficult breathing, swelling in your face or throat) or a severe skin reaction (fever, sore throat, burning in your eyes, skin pain, red or purple skin rash that spreads and causes blistering and peeling). Seek medical treatment if you have a serious drug reaction that can affect many parts of your body. Symptoms may include: skin rash, fever, swollen glands, flu-like symptoms, muscle aches, severe weakness, unusual bruising, or yellowing of your skin or eyes. This reaction may occur several weeks after y',\n",
" 'yes. This reaction may occur several weeks after you began using doxycycline. Doxycycline may cause serious side effects. Call your doctor at once if you have: severe stomach pain, diarrhea that is watery or bloody - throat irritation, trouble swallowing - chest pain, irregular heart rhythm, feeling short of breath - little or no urination - low white blood cell counts - fever, chills, swollen glands, body aches, weakness, pale skin, easy bruising or bleeding - severe headaches, ringing in your ears, dizziness, nausea, vision problems, pain behind your eyes - loss of appetite, upper stomach pain (that may spread to your back), tiredness, nausea or vomiting, fast heart rate, dark urine, jaund',\n",
" 'ea or vomiting, fast heart rate, dark urine, jaundice (yellowing of the skin or eyes). Common side effects of doxycycline may include: nausea and vomiting - upset stomach - loss of appetite - mild diarrhea - skin rash or itching - darkened skin color - vaginal itching or discharge. Drug Side Effects Summary 2. This particular disease, Acne, interacts with the drug spironolactone and has the following side effects: - hives - difficulty breathing - swelling of your face, lips, tongue, or throat. Call your doctor at once if you have: a light-headed feeling, like you might pass out - little or no urination - high potassium level - nausea , weakness, tingly feeling, chest pain, irregular heartbea']"
]
},
"metadata": {},
"execution_count": 15
}
]
},
{
"cell_type": "code",
"source": [
"# Format the chunks to avoid prompt template conflicts\n",
"chunks_preview_alt = [x.replace('#', '-') for x in chunks_preview_alt]\n",
"\n",
"# Embeddings setup\n",
"name = \"all-MiniLM-L12-v2\"\n",
"model = SentenceTransformer(name)\n",
"\n",
"# Embedding functions\n",
"def embed_batch(batch):\n",
" return [model.encode(sentence, show_progress_bar=True) for sentence in batch]\n",
"\n",
"def embed(sentence):\n",
" return model.encode(sentence)\n",
"\n",
"# Ensure the LanceDB directory does not exist already to avoid errors\n",
"lancedb_dir = \".lancedb\"\n",
"if not os.path.exists(lancedb_dir):\n",
" os.mkdir(lancedb_dir)\n",
"uri = lancedb_dir\n",
"db = lancedb.connect(uri)\n",
"\n",
"# Prepare metadata for embedding\n",
"metadata = [[i, chunks_preview_alt] for i, chunks_preview_alt in enumerate(chunks_preview_alt)]\n",
"doc_df = pd.DataFrame(metadata, columns=[\"chunk\", \"text\"])\n",
"\n",
"# Embed the documents\n",
"data = with_embeddings(embed_batch, doc_df)\n",
"\n",
"# LanceDB operations\n",
"# if not db.has_table(\"pdf_data\"):\n",
"db.create_table(\"pdf_data\", data=data)\n",
"table = db.open_table(\"pdf_data\")\n",
"table.add(data=data)\n",
"\n",
"# Note: Adjust the 'create_table' and 'open_table' to match your dataset/table names\n"
],
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/",
"height": 587,
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},
"id": "F8Ga5Vq0zdXL",
"outputId": "ca2e1acd-4f9f-4982-84ea-305a02f6d3b9"
},
"execution_count": null,
"outputs": [
{
"output_type": "stream",
"name": "stderr",
"text": [
"/usr/local/lib/python3.10/dist-packages/huggingface_hub/utils/_token.py:88: UserWarning: \n",
"The secret `HF_TOKEN` does not exist in your Colab secrets.\n",
"To authenticate with the Hugging Face Hub, create a token in your settings tab (https://huggingface.co/settings/tokens), set it as secret in your Google Colab and restart your session.\n",
"You will be able to reuse this secret in all of your notebooks.\n",
"Please note that authentication is recommended but still optional to access public models or datasets.\n",
" warnings.warn(\n"
]
},
{
"output_type": "display_data",
"data": {
"text/plain": [
"modules.json: 0%| | 0.00/349 [00:00