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RAG Series Part 2: How to Evaluate Your RAG Application

Apoorva Joshi20 min read • Published Apr 15, 2024 • Updated May 13, 2024
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If you have ever deployed machine learning models in production, you know that evaluation is an important part of the process. Evaluation is how you pick the right model for your use case, ensure that your model’s performance translates from prototype to production, and catch performance regressions. While evaluating Generative AI applications (also referred to as LLM applications) might look a little different, the same tenets for why we should evaluate these models apply.
In this tutorial, we will break down how to evaluate LLM applications, with the example of a Retrieval Augmented Generation (RAG) application. Specifically, we will cover the following:
  • Challenges with evaluating LLM applications
  • Defining metrics to evaluate LLM applications
  • How to evaluate a RAG application
Before we begin, it is important to distinguish LLM model evaluation from LLM application evaluation. Evaluating LLM models involves measuring the performance of a given model across different tasks, whereas LLM application evaluation is about evaluating different components of an LLM application such as prompts, retrievers, etc., and the system as a whole. In this tutorial, we will focus on evaluating LLM applications.

Challenges with evaluating LLM applications

The reason we don’t hear as much about evaluating LLM applications is that it is currently challenging and time-consuming. Conventional machine learning models such as regression and classification have a mathematically well-defined set of metrics such as mean squared error (MSE), precision, and recall for evaluation. In many cases, ground truth is also readily available for evaluation. However, this is not the case with LLM applications.
LLM applications today are being used for complex tasks such as summarization, long-form question-answering, and code generation. Conventional metrics such as precision and accuracy in their original form don’t apply in these scenarios, since the output from these tasks is not a simple binary prediction or a floating point value to calculate true/false positives or residuals from. Metrics such as faithfulness and relevance that are more applicable to these tasks are emerging but hard to quantify definitively. The probabilistic nature of LLMs also makes evaluation challenging — simple formatting changes at the prompt level, such as adding new lines or bullet points, can have a significant impact on model outputs. And finally, ground truth is hard to come by and is time-consuming to create manually.

How to evaluate LLM applications

While there is no prescribed way to evaluate LLM applications today, some guiding principles are emerging.
Whether it’s choosing embedding models or evaluating LLM applications, focus on your specific task. This is especially applicable while choosing parameters for evaluation. Here are a few examples:
TaskEvaluation parameters
Content moderationRecall and precision on toxicity and bias
Query generationCorrect output syntax and attributes, extracts the right information upon execution
Dialogue (chatbots, summarization, Q&A)Faithfulness, relevance
Tasks like content moderation and query generation are more straightforward since they have definite expected answers. However, for open-ended tasks involving dialogue, the best we can do is to check for factual consistency (faithfulness) and relevance of the answer to the user question. Currently, a common approach for performing such evaluations is using strong LLMs. While this technique may be subject to some of the challenges we face with LLMs today, such as hallucinations and biases, it scales better than human evaluation. When choosing an evaluator LLM, the Chatbot Arena Leaderboard is a good resource since it is a crowdsourced list of the best-performing LLMs ranked by human preference.
Once you have figured out the parameters for evaluation, you need an evaluation dataset. It is worth spending the time and effort to handcraft a small dataset (even 50 samples is a good start!) consisting of the most common questions users might ask your application, some edge (read: complex) cases, as well as questions that help assess the response of your system to malicious and/or inappropriate inputs. You can evaluate the system separately on each of these question sets to get a more granular understanding of the strengths and weaknesses of your system. In addition to curating a dataset of questions, you may also want to write out ground truth answers to the questions. While these are especially important for tasks like query generation that have a definitive right or wrong answer, they can also be useful for grounding LLMs when using them as a judge for evaluation.
As with any software, you will want to evaluate each component separately and the system as a whole. In RAG systems, for example, you will want to evaluate the retrieval and generation to ensure that you are retrieving the right context and generating suitable answers, whereas in tool-calling agents, you will want to validate the intermediate responses from each of the tools. You will also want to evaluate the overall system for correctness, typically done by comparing the final answer to the ground truth answer.
Finally, think about how you will collect feedback from your users, incorporate it into your evaluation pipeline, and track the performance of your application over time.

RAG — a very quick refresher

For the rest of the tutorial, we will take RAG as an example to demonstrate how to evaluate an LLM application. But before that, here’s a very quick refresher on RAG.
This is what a RAG application might look like:
RAG Architecture
In a RAG application, the goal is to enhance the quality of responses generated by an LLM by supplementing its parametric knowledge with context retrieved from an external knowledge base. To build the knowledge base, large reference documents are broken up into smaller chunks, and each chunk is stored in a database along with its vector embedding generated using an embedding model.
Given a user query, it is first embedded using the same embedding model, and the most relevant chunks are retrieved based on the similarity between the query and chunk vectors. An LLM then uses the user’s question, prompt, and the retrieved documents to generate an answer to the question.

How to evaluate a RAG application

The main elements to evaluate in a RAG application are as follows:
  • Retrieval: This involves experimenting with different data processing strategies, embedding models, etc., and evaluating how they impact retrieval.
  • Generation: Once you decide on the best settings for the retriever, this step involves experimenting with different LLMs to find the best completion model for the task.
In this tutorial, we will evaluate different embedding models for retrieval, different completion models for generation, and the system as a whole with the best-performing models.

Before we begin


We will use the following metrics for evaluation:
  • Context precision: Evaluates the ability of the retriever to rank retrieved items in order of relevance to the ground truth answer
  • Context recall: Measures the extent to which the retrieved context aligns with the ground truth answer
  • Faithfulness: Measures the factual consistency of the generated answer against the retrieved context
  • Answer relevance: Measures how relevant the generated answer is to the given prompt (question + retrieved context)
  • Answer semantic similarity: Measures the semantic similarity between the generated answer and the ground truth
  • Answer correctness: Measures the accuracy of the generated answer compared to the ground truth
You can read more about how these metrics are calculated.


We will use LangChain to create a sample RAG application and the RAGAS framework for evaluation. RAGAS is open-source, has out-of-the-box support for all the above metrics, supports custom evaluation prompts, and has integrations with frameworks such as LangChain, LlamaIndex, and observability tools such as LangSmith and Arize Phoenix.


We will use the ragas-wikiqa dataset available on Hugging Face. The dataset consists of ~230 general knowledge questions, including the ground truth answers for these questions. Your evaluation dataset, however, should be a good representation of how users will interact with your application.

Where’s the code?

The Jupyter Notebook for this tutorial can be found on GitHub.

Step 1: Install the required libraries

We will require the following libraries for this tutorial:
  • datasets: Python library to get access to datasets available on Hugging Face Hub
  • ragas: Python library for the RAGAS framework
  • langchain: Python library to develop LLM applications using LangChain
  • langchain-mongodb: Python package to use MongoDB Atlas as a vector store with LangChain
  • langchain-openai: Python package to use OpenAI models in LangChain
  • pymongo: Python driver for interacting with MongoDB
  • pandas: Python library for data analysis, exploration, and manipulation
  • tdqm: Python module to show a progress meter for loops
  • matplotlib, seaborn: Python libraries for data visualization

Step 2: Setup pre-requisites

In this tutorial, we will use MongoDB Atlas Vector Search as a vector store and retriever. But first, you will need a MongoDB Atlas account with a database cluster and get the connection string to connect to your cluster. Follow these steps to get set up:
Don’t forget to add the IP of your host machine to the IP Access list for your cluster.
Once you have the connection string, set it in your code:
We will be using OpenAI’s embedding and chat completion models, so you’ll also need to obtain an OpenAI API key and set it as an environment variable for the OpenAI client to use:

Step 3: Download the evaluation dataset

As mentioned previously, we will use the ragas-wikiqa dataset available on Hugging Face. We will download it using the datasets library and convert it into a pandas dataframe:
The dataset has the following columns that are important to us:
  • question: User questions
  • correct_answer: Ground truth answers to the user questions
  • context: List of reference texts to answer the user questions

Step 4: Create reference document chunks

We noticed that the reference texts in the context column are quite long. Typically for RAG, large texts are broken down into smaller chunks at ingest time. Given a user query, only the most relevant chunks are retrieved, to pass on as context to the LLM. So as a next step, we will chunk up our reference texts before embedding and ingesting them into MongoDB:
The above code does the following:
  • Defines how to split the text into chunks: We use the from_tiktoken_encoder method of the RecursiveCharacterTextSplitter class in LangChain. This way, the texts are split by character and recursively merged into tokens by the tokenizer as long as the chunk size (in terms of number of tokens) is less than the specified chunk size (chunk_size). Some overlap between chunks has been shown to improve retrieval, so we set an overlap of 30 characters in the chunk_overlap parameter. The keep_separator parameter indicates whether or not to keep the default separators such as \n\n, \n, etc. in the chunked text, and the encoding_name indicates the model to use to generate tokens.
  • Defines a split_texts function: This function takes a list of reference texts (texts) as input, splits them using the text splitter, and returns the list of chunked texts.
  • Applies the split_texts function to the context column of our dataset
  • Creates a list of chunked texts for the entire dataset
In practice, you may want to experiment with different chunking strategies as well while evaluating retrieval, but for this tutorial, we are only focusing on evaluating different embedding models.

Step 5: Create embeddings and ingest them into MongoDB

Now that we have chunked up our reference documents, let’s embed and ingest them into MongoDB Atlas to build a knowledge base (vector store) for our RAG application. Since we want to evaluate two embedding models for the retriever, we will create separate vector stores (collections) using each model.
We will be evaluating the text-embedding-ada-002 and text-embedding-3-small (we will call them ada-002 and 3-small in the rest of the tutorial) embedding models from OpenAI, so first, let’s define a function to generate embeddings using OpenAI’s Embeddings API:
The embedding function above takes a list of texts (docs) and a model name (model) as arguments and returns a list of embeddings generated using the specified model. The OpenAI API returns a list of embedding objects, which need to be parsed to get the final list of embeddings. A sample response from the API looks like the following:
Now, let’s use each model to embed the chunked texts and ingest them along with their embeddings into a MongoDB collection:
The above code does the following:
  • Creates a PyMongo client (client) to connect to a MongoDB Atlas cluster
  • Specifies the database (DB_NAME) to connect to — we are calling the database ragas_evals; if the database doesn’t exist, it will be created at ingest time
  • Specifies the batch size (batch_size) for generating embeddings in bulk
  • Specifies the embedding models (EVAL_EMBEDDING_MODELS) to use for generating embeddings
  • For each embedding model, generates embeddings for the entire evaluation set and creates the documents to be ingested into MongoDB — an example document looks like the following:
  • Deletes any existing documents in the collection named after the model, and bulk inserts the documents into it using the insert_many() method
To verify that the above code ran as expected, navigate to the Atlas UI and ensure that you see two collections, namely text-embedding-ada-002 and text-embedding-3-small, in the ragas_evals database:
Viewing collections in MongoDB Atlas UI
While you are in the Atlas UI, create vector indexes for both collections. The vector index definition specifies the path to the embedding field, dimensions, and the similarity metric to use while retrieving documents using vector search. Ensure that the index name is vector_index for each collection and that the index definition looks as follows:
The number of embedding dimensions in both index definitions is 1536 since ada-002 and 3-small have the same number of dimensions.

Step 6: Compare embedding models for retrieval

As a first step in the evaluation process, we want to ensure that we are retrieving the right context for the LLM. While there are several factors (chunking, re-ranking, etc.) that can impact retrieval, in this tutorial, we will only experiment with different embedding models. We will use the same models that we used in Step 5. We will use LangChain to create a vector store using MongoDB Atlas and use it as a retriever in our RAG application.
The above code defines a get_retriever function that takes an embedding model (model) and the number of documents to retrieve (k) as arguments and returns a retriever object as the output. The function creates a MongoDB Atlas vector store using the MongoDBAtlasVectorSearch class from the langchain-mongodb integration. Specifically, it uses the from_connection_string method of the class to create the vector store from the MongoDB connection string which we obtained in Step 2 above. It also takes additional arguments such as:
  • namespace: The (database, collection) combination to use as the vector store
  • embedding: Embedding model to use to generate the query embedding for retrieval
  • index_name: The MongoDB Atlas vector search index name (as set in Step 5)
  • text_key: The field in the reference documents that contains the text
Finally, it uses the as_retriever method in LangChain to use the vector store as a retriever. as_retriever can take arguments such as search_type which specifies the metric to use to retrieve documents. Here, we choose similarity since we want to retrieve the most similar documents to a given query. We can also specify additional search arguments such as k which is the number of documents to retrieve.
To evaluate the retriever, we will use the context_precision and context_recall metrics from the ragas library. These metrics use the retrieved context, ground truth answers, and the questions. So let’s first gather the list of ground truth answers and questions:
The above code snippet simply converts the question and correct_answer columns from the dataframe we created in Step 3 to lists. We will reuse these lists in the steps that follow.
Finally, here’s the code to evaluate the retriever:
The above code does the following for each of the models that we are evaluating:
  • Creates a dictionary (data) with question, ground_truth, and contexts as keys, corresponding to the questions in the evaluation dataset, their ground truth answers, and retrieved contexts
  • Creates a retriever that retrieves the top two most similar documents to a given query
  • Uses the get_relevant_documents method to obtain the most relevant documents for each question in the evaluation dataset and add them to the contexts list in the data dictionary
  • Converts the data dictionary to a Dataset object
  • Creates a runtime config for RAGAS to override its default concurrency and retry settings — we had to do this to avoid running into OpenAI’s rate limits, but this might be a non-issue depending on your usage tier, or if you are not using OpenAI models
  • Uses the evaluate method from the ragas library to get the overall evaluation metrics for the evaluation dataset
The evaluation results for embedding models we compared look as follows on our dataset:
ModelContext precisionContext recall
Based on the above numbers, ada-002 is better at retrieving the most relevant results at the top but 3-small is better at retrieving contexts that are more aligned with the ground truth answers. So we conclude that 3-small is the better embedding model for retrieval.

Step 7: Compare completion models for generation

Now that we’ve found the best model for our retriever, let’s find the best completion model for the generator component in our RAG application.
But first, let’s build out our RAG “application.” In LangChain, we do this using chains. Chains in LangChain are a sequence of calls either to an LLM, a tool, or a data processing step. Each component in a chain is referred to as a Runnable, and the recommended way to compose chains is using the LangChain Expression Language (LCEL).
In the above code, we define a get_rag_chain function that takes a retriever object and a chat completion model name (model) as arguments and returns a RAG chain as the output. The function creates the following components that together make up the RAG chain:
  • retrieve: Takes the user input (a question) and sends it to the retriever to obtain similar documents; it also formats the output to match the input format expected by the next runnable, which in this case is a dictionary with context and question as keys; the RunnablePassthrough() call for the question key indicates that the user input is simply passed through to the next stage under the question key
  • prompt: Crafts a prompt by populating a prompt template with the context and question from the retrieve stage
  • llm: Specifies the chat model to use for completion
  • parse_output: A simple output parser that parses the result from the LLM into a string
Finally, it creates a RAG chain (rag_chain) using LCEL pipe ( | ) notation to chain together the above components.
For completion models, we will be evaluating the latest updated version of gpt-3.5-turbo and an older version of GPT-3.5 Turbo, i.e., gpt-3.5-turbo-1106. The evaluation code for the generator looks largely similar to what we had in Step 6 except it has additional steps to initialize the RAG chain and invoke it for each question in our evaluation dataset in order to generate answers:
A few changes to note in the above code:
  • The data dictionary has an additional answer key to accumulate answers to the questions in our evaluation dataset.
  • We use the text-embedding-3-small for the retriever since we determined this to be the better embedding model in Step 6.
  • We are using the metrics faithfulness and answer_relevancy to evaluate the generator.
The evaluation results for the completion models we compared look as follows on our dataset:
ModelFaithfulnessAnswer relevance
Based on the above numbers, the latest version of gpt-3.5-turbo produces more factually consistent results than its predecessor, while the older version produces answers that are more pertinent to the given prompt. Let’s say we want to go with the more “faithful” model.
If you don’t want to choose between metrics, consider creating consolidated metrics using a weighted summation after the fact, or customize the prompts used for evaluation.

Step 8: Measure the overall performance of the RAG application

Finally, let’s evaluate the overall performance of the system using the best-performing models:
In the above code, we use the text-embedding-3-small model for the retriever and the gpt-3.5-turbo model for the generator, to generate answers to questions in our evaluation dataset. We use the answer_similarity and answer_correctness metrics to measure the overall performance of the RAG chain.
The evaluation shows that the RAG chain produces an answer similarity of 0.8873 and an answer correctness of 0.5922 on our dataset.
The correctness seems a bit low so let’s investigate further. You can convert the results from RAGAS to a pandas dataframe to perform further analysis:
For a more visual analysis, can also create a heatmap of questions vs metrics:
Heatmap visualizing the performance of a RAG application
Upon manually investigating some of the low-scoring results, we observed the following:
  • Some ground-truth answers in the evaluation dataset were in fact incorrect. So although the answer generated by the LLM was right, it didn’t match the ground truth answer, resulting in a low score.
  • Some ground-truth answers were full sentences whereas the LLM-generated answer, although factually correct, was a single word, number, etc.
The above findings emphasize the importance of spot-checking the LLM evaluations, curating accurate and representative evaluation datasets, and highlight yet another challenge with using LLMs for evaluation.

Step 9: Track performance over time

Evaluation should not be a one-time event. Each time you want to change a component in the system, you should evaluate the changes against existing settings to assess how they will impact performance. Then, once the application is deployed in production, you should also have a way to monitor performance in real time and detect changes therein.
In this tutorial, we used MongoDB Atlas as the vector database for our RAG application. You can also use Atlas to monitor the performance of your LLM application via Atlas Charts. All you need to do is write evaluation results and any feedback metrics (e.g., number of thumbs up, thumbs down, response regenerations, etc.) that you want to track to a MongoDB collection:
In the above code snippet, we add a timestamp field containing the current timestamp to the final evaluation result (result) from Step 8, and write it to a collection called metrics in the ragas_evals database using PyMongo’s insert_one method. The result dictionary inserted into MongoDB looks like this:
We can now create a dashboard in Atlas Charts to visualize the data in the metrics collection:
Creating a dashboard in Atlas Charts
Once the dashboard is created, click the Add Chart button and select the metrics collection as the data source for the chart. Drag and drop fields to include, choose a chart type, add a title and description for the chart, and save it to the dashboard:
Creating a chart in Atlas Charts
Here’s what our sample dashboard looks like:
Sample dashboard created using Atlas Charts
Similarly, once your application is in production, you can create a dashboard for any feedback metrics you collect.


In this tutorial, we looked into some of the challenges with evaluating LLM applications, followed by a detailed, step-by-step workflow for evaluating an LLM application, including persisting and tracking evaluation results over time. While we used RAG as our example for evaluation, the concepts and techniques shown in this tutorial can be extended to other LLM applications, including agents.
Now that you have a good foundation on how to evaluate RAG applications, you can take it up as a challenge to evaluate RAG systems from some of our other tutorials:
If you have further questions about LLM evaluations, please reach out to us in our Generative AI community forums and stay tuned for the next tutorial in the RAG series. Previous tutorials from the series can be found below:


If you would like to learn more about evaluating LLM applications, check out the following references:

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