MedicalRag2

Setup

Run the following command

1. Install the requirement

./setup.sh

2. Unzip all the pdf file (optional)
   Note: the zip file must be in the ingestion/pdf directory

./unzip.sh

3. Setup environment key for OpenAI in parent folder .env (optional)

OPENAI_API_KEY=xxx
EMBEDDING_MODEL_NAME="openai/text-embedding-3-small"
# EMBEDDING_MODEL_NAME="huggingface/ls-da3m0ns/bge_large_medical"
# EMBEDDING_MODEL_NAME="ollama/snowflake-arctic-embed"
RERANKING_MODEL_NAME="ncbi/MedCPT-Cross-Encoder"

4. Run this command to ingest the pdf to the chromaDB

python3 ingestion/apply_ingestion.py

4. You should download ollama and pull the required LLM
   This is a few that you can test out:

    ollama pull phi3:latest
    ollama pull llama3:8b
    ollama pull llama3:instruct
    ollama pull gemma:2b
    ollama pull gemma:2b-instruct
    ollama pull gemma:7b-instruct
    ollama pull gemma:latest

5. Run this command to start the application

streamlit run app.py