This code implements a Fusion Retrieval system that combines vector-based similarity search with keyword-based BM25 retrieval. The approach aims to leverage the strengths of both methods to improve the overall quality and relevance of document retrieval.
Motivation
Traditional retrieval methods often rely on either semantic understanding (vector-based) or keyword matching (BM25). Each approach has its strengths and weaknesses. Fusion retrieval aims to combine these methods to create a more robust and accurate retrieval system that can handle a wider range of queries effectively.
Key Components
- PDF processing and text chunking
- Vector store creation using FAISS and OpenAI embeddings
- BM25 index creation for keyword-based retrieval
- Custom fusion retrieval function that combines both methods
Method Details
Document Preprocessing
- The PDF is loaded and split into chunks using RecursiveCharacterTextSplitter.
- Chunks are cleaned by replacing ‘t’ with spaces (likely addressing a specific formatting issue).
Vector Store Creation
- OpenAI embeddings are used to create vector representations of the text chunks.
- A FAISS vector store is created from these embeddings for efficient similarity search.
BM25 Index Creation
- A BM25 index is created from the same text chunks used for the vector store.
- This allows for keyword-based retrieval alongside the vector-based method.
Fusion Retrieval Function
The fusion_retrieval function is the core of this implementation:
- It takes a query and performs both vector-based and BM25-based retrieval.
- Scores from both methods are normalized to a common scale.
- A weighted combination of these scores is computed (controlled by the
alphaparameter). - Documents are ranked based on the combined scores, and the top-k results are returned.
Benefits of this Approach
- Improved Retrieval Quality: By combining semantic and keyword-based search, the system can capture both conceptual similarity and exact keyword matches.
- Flexibility: The
alphaparameter allows for adjusting the balance between vector and keyword search based on specific use cases or query types. - Robustness: The combined approach can handle a wider range of queries effectively, mitigating weaknesses of individual methods.
- Customizability: The system can be easily adapted to use different vector stores or keyword-based retrieval methods.
Fusion retrieval represents a powerful approach to document search that combines the strengths of semantic understanding and keyword matching. By leveraging both vector-based and BM25 retrieval methods, it offers a more comprehensive and flexible solution for information retrieval tasks. This approach has potential applications in various fields where both conceptual similarity and keyword relevance are important, such as academic research, legal document search, or general-purpose search engines.
Import libraries
import os
import sys
from dotenv import load_dotenv
from langchain.docstore.document import Document
from typing import List
from rank_bm25 import BM25Okapi
import numpy as np
sys.path.append(os.path.abspath(os.path.join(os.getcwd(), '..'))) # Add the parent directory to the path sicnce we work with notebooks
from helper_functions import *
from evaluation.evalute_rag import *
# Load environment variables from a .env file
load_dotenv()
# Set the OpenAI API key environment variable
os.environ["OPENAI_API_KEY"] = os.getenv('OPENAI_API_KEY')
Define document path
path = "../data/Understanding_Climate_Change.pdf"
Encode the pdf to vector store and return split document from the step before to create BM25 instance
def encode_pdf_and_get_split_documents(path, chunk_size=1000, chunk_overlap=200):
"""
Encodes a PDF book into a vector store using OpenAI embeddings.
Args:
path: The path to the PDF file.
chunk_size: The desired size of each text chunk.
chunk_overlap: The amount of overlap between consecutive chunks.
Returns:
A FAISS vector store containing the encoded book content.
"""
# Load PDF documents
loader = PyPDFLoader(path)
documents = loader.load()
# Split documents into chunks
text_splitter = RecursiveCharacterTextSplitter(
chunk_size=chunk_size, chunk_overlap=chunk_overlap, length_function=len
)
texts = text_splitter.split_documents(documents)
cleaned_texts = replace_t_with_space(texts)
# Create embeddings and vector store
embeddings = OpenAIEmbeddings()
vectorstore = FAISS.from_documents(cleaned_texts, embeddings)
return vectorstore, cleaned_texts
Create vectorstore and get the chunked documents
vectorstore, cleaned_texts = encode_pdf_and_get_split_documents(path)
Create a bm25 index for retrieving documents by keywords
def create_bm25_index(documents: List[Document]) -> BM25Okapi:
"""
Create a BM25 index from the given documents.
BM25 (Best Matching 25) is a ranking function used in information retrieval.
It's based on the probabilistic retrieval framework and is an improvement over TF-IDF.
Args:
documents (List[Document]): List of documents to index.
Returns:
BM25Okapi: An index that can be used for BM25 scoring.
"""
# Tokenize each document by splitting on whitespace
# This is a simple approach and could be improved with more sophisticated tokenization
tokenized_docs = [doc.page_content.split() for doc in documents]
return BM25Okapi(tokenized_docs)
bm25 = create_bm25_index(cleaned_texts) # Create BM25 index from the cleaned texts (chunks)
Define a function that retrieves both semantically and by keyword, normalizes the scores and gets the top k documents
def fusion_retrieval(vectorstore, bm25, query: str, k: int = 5, alpha: float = 0.5) -> List[Document]:
"""
Perform fusion retrieval combining keyword-based (BM25) and vector-based search.
Args:
vectorstore (VectorStore): The vectorstore containing the documents.
bm25 (BM25Okapi): Pre-computed BM25 index.
query (str): The query string.
k (int): The number of documents to retrieve.
alpha (float): The weight for vector search scores (1-alpha will be the weight for BM25 scores).
Returns:
List[Document]: The top k documents based on the combined scores.
"""
epsilon = 1e-8
# Step 1: Get all documents from the vectorstore
all_docs = vectorstore.similarity_search("", k=vectorstore.index.ntotal)
# Step 2: Perform BM25 search
bm25_scores = bm25.get_scores(query.split())
# Step 3: Perform vector search
vector_results = vectorstore.similarity_search_with_score(query, k=len(all_docs))
# Step 4: Normalize scores
vector_scores = np.array([score for _, score in vector_results])
vector_scores = 1 - (vector_scores - np.min(vector_scores)) / (np.max(vector_scores) - np.min(vector_scores) + epsilon)
bm25_scores = (bm25_scores - np.min(bm25_scores)) / (np.max(bm25_scores) - np.min(bm25_scores) + epsilon)
# Step 5: Combine scores
combined_scores = alpha * vector_scores + (1 - alpha) * bm25_scores
# Step 6: Rank documents
sorted_indices = np.argsort(combined_scores)[::-1]
# Step 7: Return top k documents
return [all_docs[i] for i in sorted_indices[:k]]
Use Case example
# Query
query = "What are the impacts of climate change on the environment?"
# Perform fusion retrieval
top_docs = fusion_retrieval(vectorstore, bm25, query, k=5, alpha=0.5)
docs_content = [doc.page_content for doc in top_docs]
show_context(docs_content)
Dr. Md. Harun Ar Rashid, MPH, MD, PhD, is a highly respected medical specialist celebrated for his exceptional clinical expertise and unwavering commitment to patient care. With advanced qualifications including MPH, MD, and PhD, he integrates cutting-edge research with a compassionate approach to medicine, ensuring that every patient receives personalized and effective treatment. His extensive training and hands-on experience enable him to diagnose complex conditions accurately and develop innovative treatment strategies tailored to individual needs. In addition to his clinical practice, Dr. Harun Ar Rashid is dedicated to medical education and research, writing and inventory creative thinking, innovative idea, critical care managementing make in his community to outreach, often participating in initiatives that promote health awareness and advance medical knowledge. His career is a testament to the high standards represented by his credentials, and he continues to contribute significantly to his field, driving improvements in both patient outcomes and healthcare practices.
