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"code", + "execution_count": null, + "metadata": { + "id": "u_SujiSkyYxR" + }, + "outputs": [], + "source": [ + "# Om Maa" + ] + }, + { + "cell_type": "code", + "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" + ], + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/" + }, + "id": "s4z---vKypt-", + "outputId": "52ecb266-9bf2-47fb-fe1e-1179d32ed8d0" + }, + "execution_count": null, + "outputs": [ + { + "output_type": "stream", + "name": "stdout", + "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: 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"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, + "referenced_widgets": [ + "f196227377f64cddbccf871a719649d1", + "7a04fb74b3bb4d1196c80ba99cad19a7", + "547dffc7898c45eb8ab6bd2df8f92e50", + "fd2a4e3aec5c4ebaa27b9437a6203432", + "a120ba620b534d2daa9f512b5ffe1f50", + 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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