Upload 3 files

.env

@@ -0,0 +1,9 @@
+VECTARA_INDEX_API_KEY = "zwt_ni_bLu6MRQXzWKPIU__Uubvy_0Xz_FEr-2sfUg"
+VECTARA_QUERY_API_KEY = "zwt_ni_bLu6MRQXzWKPIU__Uubvy_0Xz_FEr-2sfUg"
+VECTARA_API_KEY = "zut_ni_bLoa0I3AeNSjxeZ-UfECnm_9Xv5d4RVBAqw"
+VECTARA_CORPUS_ID = "2"
+VECTARA_CUSTOMER_ID = "2653936430"
+TOGETHER_API = "7e6c200b7b36924bc1b4a5973859a20d2efa7180e9b5c977301173a6c099136b"
+GOOGLE_SEARCH_API_KEY = "AIzaSyD-1OMuZ0CxGAek0PaXrzHOmcDWFvZQtm8"
+UNSTRUCTURED_API_KEY = "eBqsGxYYIfTdPRH7PEveZGVIH6ZHny"
+PINECONE_API_KEY = "4523c180-39fd-4c48-99e8-88164df85b0a"

medmind.py

@@ -0,0 +1,288 @@
+from llama_index.indices.managed.vectara import VectaraIndex
+from dotenv import load_dotenv
+import os
+from docx import Document
+from llama_index.llms.together import TogetherLLM
+from llama_index.core.llms import ChatMessage, MessageRole
+from Bio import Entrez 
+import ssl
+from transformers import AutoModelForSequenceClassification, AutoTokenizer
+import streamlit as st
+from googleapiclient.discovery import build
+from typing import List, Optional
+
+load_dotenv()
+
+os.environ["VECTARA_INDEX_API_KEY"] = os.getenv("VECTARA_INDEX_API_KEY", "zwt_ni_bLu6MRQXzWKPIU__Uubvy_0Xz_FEr-2sfUg")
+os.environ["VECTARA_QUERY_API_KEY"] = os.getenv("VECTARA_QUERY_API_KEY", "zwt_ni_bLu6MRQXzWKPIU__Uubvy_0Xz_FEr-2sfUg")
+os.environ["VECTARA_API_KEY"] = os.getenv("VECTARA_API_KEY", "zut_ni_bLoa0I3AeNSjxeZ-UfECnm_9Xv5d4RVBAqw")
+os.environ["VECTARA_CORPUS_ID"] = os.getenv("VECTARA_CORPUS_ID", "2")
+os.environ["VECTARA_CUSTOMER_ID"] = os.getenv("VECTARA_CUSTOMER_ID", "2653936430")
+os.environ["TOGETHER_API"] = os.getenv("TOGETHER_API", "7e6c200b7b36924bc1b4a5973859a20d2efa7180e9b5c977301173a6c099136b")
+os.environ["GOOGLE_SEARCH_API_KEY"] = os.getenv("GOOGLE_SEARCH_API_KEY", "AIzaSyBnQwS5kPZGKuWj6sH1aBx5F5bZq0Q5jJk")
+
+# Initialize the Vectara index
+index = VectaraIndex()
+
+endpoint = 'https://api.together.xyz/inference'
+
+# Load the hallucination evaluation model
+model_name = "vectara/hallucination_evaluation_model"
+model = AutoModelForSequenceClassification.from_pretrained(model_name)
+tokenizer = AutoTokenizer.from_pretrained(model_name)
+
+def search_pubmed(query: str) -> Optional[List[str]]:
+    """
+    Searches PubMed for a given query and returns a list of formatted results 
+    (or None if no results are found).
+    """
+    Entrez.email = "[email protected]"  # Replace with your email
+
+    try:
+        ssl._create_default_https_context = ssl._create_unverified_context
+
+        handle = Entrez.esearch(db="pubmed", term=query, retmax=3)
+        record = Entrez.read(handle)
+        id_list = record["IdList"]
+
+        if not id_list:
+            return None
+
+        handle = Entrez.efetch(db="pubmed", id=id_list, retmode="xml")
+        articles = Entrez.read(handle)
+
+        results = []
+        for article in articles['PubmedArticle']:
+            try:
+                medline_citation = article['MedlineCitation']
+                article_data = medline_citation['Article']
+                title = article_data['ArticleTitle']
+                abstract = article_data.get('Abstract', {}).get('AbstractText', [""])[0]
+
+                result = f"**Title:** {title}\n**Abstract:** {abstract}\n"
+                result += f"**Link:** https://pubmed.ncbi.nlm.gov/{medline_citation['PMID']}\n\n"
+                results.append(result)
+            except KeyError as e:
+                print(f"Error parsing article: {article}, Error: {e}")
+
+        return results
+
+    except Exception as e:
+        print(f"Error accessing PubMed: {e}")
+        return None
+
+def chat_with_pubmed(article_text, article_link):
+    """
+    Engages in a chat-like interaction with a PubMed article using TogetherLLM.
+    """
+    try:
+        llm = TogetherLLM(model="QWEN/QWEN1.5-14B-CHAT", api_key=os.environ['TOGETHER_API'])
+        messages = [
+            ChatMessage(role=MessageRole.SYSTEM, content="You are a helpful AI assistant summarizing and answering questions about the following medical research article: " + article_link),
+            ChatMessage(role=MessageRole.USER, content=article_text)
+        ]
+        response = llm.chat(messages)
+        return str(response) if response else "I'm sorry, I couldn't generate a summary for this article."
+    except Exception as e:
+        print(f"Error in chat_with_pubmed: {e}")
+        return "An error occurred while generating a summary."
+
+def search_web(query: str, num_results: int = 3) -> Optional[List[str]]:
+    """
+    Searches the web using the Google Search API and returns a list of formatted results
+    (or None if no results are found).
+    """
+    try:
+        service = build("customsearch", "v1", developerKey=os.environ["GOOGLE_SEARCH_API_KEY"])
+
+        # Execute the search request
+        res = service.cse().list(q=query, cx="877170db56f5c4629", num=num_results).execute()
+
+        if "items" not in res:
+            return None
+
+        results = []
+        for item in res["items"]:
+            title = item["title"]
+            link = item["link"]
+            snippet = item["snippet"]
+            result = f"**Title:** {title}\n**Link:** {link}\n**Snippet:** {snippet}\n\n"
+            results.append(result)
+
+        return results
+
+    except Exception as e:
+        print(f"Error performing web search: {e}")
+        return None
+
+def medmind_chatbot(user_input, chat_history=None):
+    """
+    Processes user input, interacts with various resources, and generates a response. 
+    Handles potential errors, maintains chat history, and evaluates hallucination risk.
+    """
+
+    if chat_history is None:
+        chat_history = []
+
+    response_parts = []  # Collect responses from different sources
+
+    try:
+        # Vectara Search
+        try:
+            query_str = user_input
+            response = index.as_query_engine().query(query_str)
+            response_parts.append(f"**MedMind Vectara Knowledge Base Response:**\n{response.response}")
+        except Exception as e:
+            print(f"Error in Vectara search: {e}")
+            response_parts.append("Vectara knowledge base is currently unavailable.")
+
+        # PubMed Search and Chat
+        pubmed_results = search_pubmed(user_input)
+        if pubmed_results:
+            response_parts.append("**PubMed Articles (Chat & Summarize):**")
+            for article_text in pubmed_results:
+                title, abstract, link = article_text.split("\n")[:3]
+                chat_summary = chat_with_pubmed(abstract, link)
+                response_parts.append(f"{title}\n{chat_summary}\n{link}\n")
+        else:
+            response_parts.append("No relevant PubMed articles found.")
+
+        # Web Search
+        web_results = search_web(user_input)
+        if web_results:
+            response_parts.append("**Web Search Results:**")
+            response_parts.extend(web_results)
+        else:
+            response_parts.append("No relevant web search results found.")
+
+        # Combine response parts into a single string
+        response_text = "\n\n".join(response_parts)
+
+        # Hallucination Evaluation
+        def vectara_hallucination_evaluation_model(text):
+            inputs = tokenizer(text, return_tensors="pt")
+            outputs = model(**inputs)
+            hallucination_probability = outputs.logits[0][0].item()  
+            return hallucination_probability
+
+        hallucination_score = vectara_hallucination_evaluation_model(response_text)
+        HIGH_HALLUCINATION_THRESHOLD = 0.9
+        if hallucination_score > HIGH_HALLUCINATION_THRESHOLD:
+            response_text = "I'm still under development and learning. I cannot confidently answer this question yet."
+
+    except Exception as e:
+        print(f"Error in chatbot: {e}")
+        response_text = "An error occurred. Please try again later."
+
+    chat_history.append((user_input, response_text))
+    return response_text, chat_history
+
+def show_info_popup():
+    with st.expander("How to use MedMind"):
+        st.write("""
+        **MedMind is an AI-powered chatbot designed to assist with medical information.**
+
+        **Capabilities:**
+
+        *   **Answers general medical questions:** MedMind utilizes a curated medical knowledge base to provide answers to a wide range of health-related inquiries.
+        *   **Summarizes relevant research articles from PubMed:** The chatbot can retrieve and summarize research articles from the PubMed database, making complex scientific information more accessible.
+        *   **Provides insights from a curated medical knowledge base:** Beyond simple answers, MedMind offers additional insights and context from its knowledge base to enhance understanding. 
+        *   **Perform safe web searches related to your query:** The chatbot can perform web searches using the Google Search API, ensuring the safety and relevance of the results.
+
+        **Limitations:**
+
+        *   **Not a substitute for professional medical advice:** MedMind is not intended to replace professional medical diagnosis and treatment. Always consult a qualified healthcare provider for personalized medical advice.
+        *   **General knowledge and educational purposes:** The information provided by MedMind is for general knowledge and educational purposes only and may not be exhaustive or specific to individual situations.
+        *   **Under development:** MedMind is still under development and may occasionally provide inaccurate or incomplete information. It's important to critically evaluate responses and cross-reference with reliable sources.
+        *   **Hallucination potential:** While MedMind employs a hallucination evaluation model to minimize the risk of generating fabricated information, there remains a possibility of encountering inaccurate responses, especially for complex or niche queries.
+
+        **How to use:**
+
+        1.  **Type your medical question in the text box.**
+        2.  **MedMind will provide a comprehensive response combining information from various sources.** This may include insights from its knowledge base, summaries of relevant research articles, and safe web search results.
+        3.  **You can continue the conversation by asking follow-up questions or providing additional context.** This helps MedMind refine its search and offer more tailored information.
+        4.  **in case the Medmind doesn't show the output please check your internet connection or rerun the same command**
+        5.  **user can either chat with the documents or with generate resposne from vectara + pubmed + web search**
+        5.  **chat with document feature is still under development so it would be better to avoid using it for now**
+        """)
+
+# Initialize session state
+if 'chat_history' not in st.session_state:
+    st.session_state.chat_history = []
+
+# Define function to display chat history with highlighted user input and chatbot response
+def display_chat_history():
+    for user_msg, bot_msg in st.session_state.chat_history:
+        st.info(f"**You:** {user_msg}")
+        st.success(f"**MedMind:** {bot_msg}")
+
+# Define function to clear chat history
+def clear_chat():
+    st.session_state.chat_history = []
+
+def main():
+    # Streamlit Page Configuration
+    st.set_page_config(page_title="MedMind Chatbot", layout="wide")
+
+    # Custom Styles
+    st.markdown(
+        """
+        <style>
+        .css-18e3th9 {
+            padding-top: 2rem;
+            padding-right: 1rem;
+            padding-bottom: 2rem;
+            padding-left: 1rem;
+        }
+        .stButton>button {
+            background-color: #4CAF50;
+            color: white;
+        }
+        body {
+            background-color: #F0FDF4;
+            color: #333333;
+        }
+        .stMarkdown h1, .stMarkdown h2, .stMarkdown h3, .stMarkdown h4, .stMarkdown h5, .stMarkdown h6 {
+            color: #388E3C;
+        }
+        </style>
+        """,
+        unsafe_allow_html=True,
+    )
+
+    # Title and Introduction
+    st.title("MedMind Chatbot")
+    st.write("Ask your medical questions and get reliable information!")
+
+    # Example Questions (Sidebar)
+    example_questions = [
+        "What are the symptoms of COVID-19?",
+        "How can I manage my diabetes?",
+        "What are the potential side effects of ibuprofen?",
+        "What lifestyle changes can help prevent heart disease?"
+    ]
+    st.sidebar.header("Example Questions")
+    for question in example_questions:
+        st.sidebar.write(question)
+
+    # Output Container
+    output_container = st.container()
+
+    # User Input and Chat History
+    input_container = st.container()
+    with input_container:
+        user_input = st.text_input("You: ", key="input_placeholder", placeholder="Type your medical question here...")
+        new_chat_button = st.button("Start New Chat")
+        if new_chat_button:
+            st.session_state.chat_history = []  # Clear chat history
+
+    if user_input:
+        response, st.session_state.chat_history = medmind_chatbot(user_input, st.session_state.chat_history)
+        with output_container:
+            display_chat_history()
+
+    # Information Popup
+    show_info_popup()
+
+if __name__ == "__main__":
+    main()

requirements.txt

@@ -0,0 +1,14 @@
+llama-index
+python-dotenv
+PyPDF2
+python-docx
+sentence-transformers
+biopython
+langchain
+transformers
+streamlit
+google-api-python-client
+langchain-community
+llama-index-embeddings-huggingface
+llama-index-llms-together
+llama-index-indices-managed-vectara