haystack/tutorials/Tutorial5_Evaluation.py

from haystack.document_stores import ElasticsearchDocumentStore
from haystack.nodes import ElasticsearchRetriever, DensePassageRetriever, EmbeddingRetriever, FARMReader, PreProcessor
from haystack.utils import fetch_archive_from_http, launch_es
from haystack.pipelines import ExtractiveQAPipeline, DocumentSearchPipeline
from haystack.schema import Answer, Document, EvaluationResult, Label, MultiLabel, Span

import logging

logger = logging.getLogger(__name__)


def tutorial5_evaluation():

    # make sure these indices do not collide with existing ones, the indices will be wiped clean before data is inserted
    doc_index = "tutorial5_docs"
    label_index = "tutorial5_labels"

    ##############################################
    # Code
    ##############################################
    launch_es()

    # Download evaluation data, which is a subset of Natural Questions development set containing 50 documents with one question per document and multiple annotated answers
    doc_dir = "../data/nq"
    s3_url = "https://s3.eu-central-1.amazonaws.com/deepset.ai-farm-qa/datasets/nq_dev_subset_v2.json.zip"
    fetch_archive_from_http(url=s3_url, output_dir=doc_dir)

    # Connect to Elasticsearch
    document_store = ElasticsearchDocumentStore(
        host="localhost",
        username="",
        password="",
        index=doc_index,
        label_index=label_index,
        embedding_field="emb",
        embedding_dim=768,
        excluded_meta_data=["emb"],
    )

    # Add evaluation data to Elasticsearch document store
    # We first delete the custom tutorial indices to not have duplicate elements
    # and also split our documents into shorter passages using the PreProcessor
    preprocessor = PreProcessor(
        split_by="word",
        split_length=200,
        split_overlap=0,
        split_respect_sentence_boundary=False,
        clean_empty_lines=False,
        clean_whitespace=False,
    )
    document_store.delete_documents(index=doc_index)
    document_store.delete_documents(index=label_index)

    # The add_eval_data() method converts the given dataset in json format into Haystack document and label objects.
    # Those objects are then indexed in their respective document and label index in the document store.
    # The method can be used with any dataset in SQuAD format.
    document_store.add_eval_data(
        filename="../data/nq/nq_dev_subset_v2.json",
        doc_index=doc_index,
        label_index=label_index,
        preprocessor=preprocessor,
    )

    # Initialize Retriever
    from haystack.nodes import ElasticsearchRetriever

    retriever = ElasticsearchRetriever(document_store=document_store)

    # Alternative: Evaluate dense retrievers (EmbeddingRetriever or DensePassageRetriever)
    # The EmbeddingRetriever uses a single transformer based encoder model for query and document.
    # In contrast, DensePassageRetriever uses two separate encoders for both.

    # Please make sure the "embedding_dim" parameter in the DocumentStore above matches the output dimension of your models!
    # Please also take care that the PreProcessor splits your files into chunks that can be completely converted with
    #        the max_seq_len limitations of Transformers
    # The SentenceTransformer model "sentence-transformers/multi-qa-mpnet-base-dot-v1" generally works well with the EmbeddingRetriever on any kind of English text.
    # For more information and suggestions on different models check out the documentation at: https://www.sbert.net/docs/pretrained_models.html

    # from haystack.retriever import EmbeddingRetriever, DensePassageRetriever
    # retriever = EmbeddingRetriever(document_store=document_store, model_format="sentence_transformers",
    #                                embedding_model="sentence-transformers/multi-qa-mpnet-base-dot-v1")
    # retriever = DensePassageRetriever(document_store=document_store,
    #                                   query_embedding_model="facebook/dpr-question_encoder-single-nq-base",
    #                                   passage_embedding_model="facebook/dpr-ctx_encoder-single-nq-base",
    #                                   use_gpu=True,
    #                                   max_seq_len_passage=256,
    #                                   embed_title=True)
    # document_store.update_embeddings(retriever, index=doc_index)

    # Initialize Reader
    reader = FARMReader(model_name_or_path="deepset/roberta-base-squad2", top_k=4, return_no_answer=True)

    # Define a pipeline consisting of the initialized retriever and reader
    # Here we evaluate retriever and reader in an integrated (a.k.a. open domain) fashion on the full corpus of documents
    # i.e. a document is considered
    # correctly retrieved if it contains the gold answer string within it. The reader is evaluated based purely on the
    # predicted answer string, regardless of which document this came from and the position of the extracted span.
    # The generation of predictions is seperated from the calculation of metrics.
    # This allows you to run the computation-heavy model predictions only once and then iterate flexibly on the metrics or reports you want to generate.

    pipeline = ExtractiveQAPipeline(reader=reader, retriever=retriever)

    # The evaluation also works with any other pipeline.
    # For example you could use a DocumentSearchPipeline as an alternative:
    # pipeline = DocumentSearchPipeline(retriever=retriever)

    # We can load evaluation labels from the document store
    # We are also opting to filter out no_answer samples
    eval_labels = document_store.get_all_labels_aggregated(drop_negative_labels=True, drop_no_answers=False)
    eval_labels = [label for label in eval_labels if not label.no_answer]

    ## Alternative: Define queries and labels directly
    # eval_labels = [
    #     MultiLabel(
    #         labels=[
    #             Label(
    #                 query="who is written in the book of life",
    #                 answer=Answer(
    #                     answer="every person who is destined for Heaven or the World to Come",
    #                     offsets_in_context=[Span(374, 434)]
    #                 ),
    #                 document=Document(
    #                     id='1b090aec7dbd1af6739c4c80f8995877-0',
    #                    content_type="text",
    #                    content='Book of Life - wikipedia Book of Life Jump to: navigation, search This article is
    #                       about the book mentioned in Christian and Jewish religious teachings...'
    #                 ),
    #                 is_correct_answer=True,
    #                 is_correct_document=True,
    #                 origin="gold-label"
    #             )
    #         ]
    #     )
    # ]

    # Similar to pipeline.run() we can execute pipeline.eval()
    eval_result = pipeline.eval(labels=eval_labels, params={"Retriever": {"top_k": 5}})

    # The EvaluationResult contains a pandas dataframe for each pipeline node.
    # That's why there are two dataframes in the EvaluationResult of an ExtractiveQAPipeline.

    retriever_result = eval_result["Retriever"]
    retriever_result.head()

    reader_result = eval_result["Reader"]
    reader_result.head()

    # We can filter for all documents retrieved for a given query
    query = "who is written in the book of life"
    retriever_book_of_life = retriever_result[retriever_result["query"] == query]

    # We can also filter for all answers predicted for a given query
    reader_book_of_life = reader_result[reader_result["query"] == "who is written in the book of life"]

    # Save the evaluation result so that we can reload it later
    # and calculate evaluation metrics without running the pipeline again.
    eval_result.save("../")

    ## Calculating Evaluation Metrics
    # Load an EvaluationResult to quickly calculate standard evaluation metrics for all predictions,
    # such as F1-score of each individual prediction of the Reader node or recall of the retriever.
    # To learn more about the metrics, see [Evaluation Metrics](https://haystack.deepset.ai/guides/evaluation#metrics-retrieval)

    saved_eval_result = EvaluationResult.load("../")
    metrics = saved_eval_result.calculate_metrics()
    print(f'Retriever - Recall (single relevant document): {metrics["Retriever"]["recall_single_hit"]}')
    print(f'Retriever - Recall (multiple relevant documents): {metrics["Retriever"]["recall_multi_hit"]}')
    print(f'Retriever - Mean Reciprocal Rank: {metrics["Retriever"]["mrr"]}')
    print(f'Retriever - Precision: {metrics["Retriever"]["precision"]}')
    print(f'Retriever - Mean Average Precision: {metrics["Retriever"]["map"]}')

    print(f'Reader - F1-Score: {metrics["Reader"]["f1"]}')
    print(f'Reader - Exact Match: {metrics["Reader"]["exact_match"]}')

    ## Generating an Evaluation Report
    # A summary of the evaluation results can be printed to get a quick overview.
    # It includes some aggregated metrics and also shows a few wrongly predicted examples.

    pipeline.print_eval_report(saved_eval_result)

    ## Advanced Evaluation Metrics
    # Semantic Answer Similarity (SAS) is an advanced evaluation metric can be calculated in Haystack.
    # This metric takes into account whether the meaning of a predicted answer is similar to the annotated gold answer
    # rather than just doing string comparison. To this end SAS relies on pre-trained models.
    # For English, we recommend "cross-encoder/stsb-roberta-large", whereas for German we recommend "deepset/gbert-large-sts".
    # A good multilingual model is "sentence-transformers/paraphrase-multilingual-mpnet-base-v2".
    # More info on this metric can be found in our [paper](https://arxiv.org/abs/2108.06130)
    # or in our [blog post](https://www.deepset.ai/blog/semantic-answer-similarity-to-evaluate-qa).

    advanced_eval_result = pipeline.eval(
        labels=eval_labels,
        params={"Retriever": {"top_k": 1}},
        sas_model_name_or_path="cross-encoder/stsb-roberta-large",
    )

    metrics = advanced_eval_result.calculate_metrics()
    print(metrics["Reader"]["sas"])

    ## Isolated Evaluation Mode
    # The isolated node evaluation uses labels as input to the Reader node instead of the output of the preceeding retriever node.
    # Thereby, we can additionally calculate the upper bounds of the evaluation metrics of the Reader.
    # Note that even with isolated evaluation enabled, integrated evaluation will still be running.
    eval_result_with_upper_bounds = pipeline.eval(
        labels=eval_labels, params={"Retriever": {"top_k": 5}}, add_isolated_node_eval=True
    )
    pipeline.print_eval_report(eval_result_with_upper_bounds)

    ## Evaluation of Individual Components
    # Sometimes you might want to evaluate individual components,
    # for example, if you don't have a pipeline but only a retriever or a reader with a model that you trained yourself.

    # Evaluate Retriever on its own
    # Here we evaluate only the retriever, based on whether the gold_label document is retrieved.
    # Note that no_answer samples are omitted when evaluation is performed with this method
    retriever_eval_results = retriever.eval(top_k=5, label_index=label_index, doc_index=doc_index)

    ## Retriever Recall is the proportion of questions for which the correct document containing the answer is
    ## among the correct documents
    print("Retriever Recall:", retriever_eval_results["recall"])
    ## Retriever Mean Avg Precision rewards retrievers that give relevant documents a higher rank
    print("Retriever Mean Avg Precision:", retriever_eval_results["map"])

    # Just as a sanity check, we can compare the recall from `retriever.eval()`
    # with the multi hit recall from `pipeline.eval(add_isolated_node_eval=True)`.
    # These two recall metrics are only comparable since we chose to filter out no_answer samples when generating eval_labels.
    metrics = eval_result_with_upper_bounds.calculate_metrics()
    print(metrics["Retriever"]["recall_multi_hit"])

    # Evaluate Reader on its own
    # Here we evaluate only the reader in a closed domain fashion i.e. the reader is given one query
    # and its corresponding relevant document and metrics are calculated on whether the right position in this text is selected by
    # the model as the answer span (i.e. SQuAD style)
    reader_eval_results = reader.eval(document_store=document_store, label_index=label_index, doc_index=doc_index)
    # Evaluation of Reader can also be done directly on a SQuAD-formatted file without passing the data to Elasticsearch
    # reader_eval_results = reader.eval_on_file("../data/nq", "nq_dev_subset_v2.json")

    ## Reader Top-N-Accuracy is the proportion of predicted answers that match with their corresponding correct answer
    print("Reader Top-N-Accuracy:", reader_eval_results["top_n_accuracy"])
    ## Reader Exact Match is the proportion of questions where the predicted answer is exactly the same as the correct answer
    print("Reader Exact Match:", reader_eval_results["EM"])
    ## Reader F1-Score is the average overlap between the predicted answers and the correct answers
    print("Reader F1-Score:", reader_eval_results["f1"])


if __name__ == "__main__":
    tutorial5_evaluation()

# This Haystack script was made with love by deepset in Berlin, Germany
# Haystack: https://github.com/deepset-ai/haystack
# deepset: https://deepset.ai/