import logging # We configure how logging messages should be displayed and which log level should be used before importing Haystack. # Example log message: # INFO - haystack.utils.preprocessing - Converting data/tutorial1/218_Olenna_Tyrell.txt # Default log level in basicConfig is WARNING so the explicit parameter is not necessary but can be changed easily: logging.basicConfig(format="%(levelname)s - %(name)s - %(message)s", level=logging.WARNING) logging.getLogger("haystack").setLevel(logging.INFO) import tempfile from pathlib import Path from haystack.document_stores import ElasticsearchDocumentStore, InMemoryDocumentStore from haystack.pipelines import Pipeline, ExtractiveQAPipeline, DocumentSearchPipeline from haystack.nodes import ( BM25Retriever, DensePassageRetriever, EmbeddingRetriever, FARMReader, PreProcessor, TextConverter, ) from haystack.utils import fetch_archive_from_http, launch_es from haystack.schema import Answer, Document, EvaluationResult, Label, MultiLabel, Span 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/tutorial5" 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/tutorial5/nq_dev_subset_v2.json", doc_index=doc_index, label_index=label_index, preprocessor=preprocessor, ) # Initialize Retriever retriever = BM25Retriever(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, # 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 separated 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=True) ## 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": 5}}, 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) # ## Advanced Label Scopes # Answers are considered correct if the predicted answer matches the gold answer in the labels. # Documents are considered correct if the predicted document ID matches the gold document ID in the labels. # Sometimes, these simple definitions of "correctness" are not sufficient. # There are cases where you want to further specify the "scope" within which an answer or a document is considered correct. # For this reason, `EvaluationResult.calculate_metrics()` offers the parameters `answer_scope` and `document_scope`. # # Say you want to ensure that an answer is only considered correct if it stems from a specific context of surrounding words. # This is especially useful if your answer is very short, like a date (for example, "2011") or a place ("Berlin"). # Such short answer might easily appear in multiple completely different contexts. # Some of those contexts might perfectly fit the actual question and answer it. # Some others might not: they don't relate to the question at all but still contain the answer string. # In that case, you might want to ensure that only answers that stem from the correct context are considered correct. # To do that, specify `answer_scope="context"` in `calculate_metrics()`. # # `answer_scope` takes the following values: # - `any` (default): Any matching answer is considered correct. # - `context`: The answer is only considered correct if its context matches as well. It uses fuzzy matching (see `context_matching` parameters of `pipeline.eval()`). # - `document_id`: The answer is only considered correct if its document ID matches as well. You can specify a custom document ID through the `custom_document_id_field` parameter of `pipeline.eval()`. # - `document_id_and_context`: The answer is only considered correct if its document ID and its context match as well. # # In Question Answering, to enforce that the retrieved document is considered correct whenever the answer is correct, set `document_scope` to `answer` or `document_id_or_answer`. # # `document_scope` takes the following values: # - `document_id`: Specifies that the document ID must match. You can specify a custom document ID through the `custom_document_id_field` parameter of `pipeline.eval()`. # - `context`: Specifies that the content of the document must match. It uses fuzzy matching (see the `context_matching` parameters of `pipeline.eval()`). # - `document_id_and_context`: A Boolean operation specifying that both `'document_id' AND 'context'` must match. # - `document_id_or_context`: A Boolean operation specifying that either `'document_id' OR 'context'` must match. # - `answer`: Specifies that the document contents must include the answer. The selected `answer_scope` is enforced. # - `document_id_or_answer` (default): A Boolean operation specifying that either `'document_id' OR 'answer'` must match. metrics = saved_eval_result.calculate_metrics(answer_scope="context") 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"]}') document_store.get_all_documents()[0] # Let's try Document Retrieval on a file level (it's sufficient if the correct file identified by its name (for example, 'Book of Life') was retrieved). eval_result_custom_doc_id = pipeline.eval( labels=eval_labels, params={"Retriever": {"top_k": 5}}, custom_document_id_field="name" ) metrics = eval_result_custom_doc_id.calculate_metrics(document_scope="document_id") 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"]}') # Let's enforce the context again: metrics = eval_result_custom_doc_id.calculate_metrics(document_scope="document_id_and_context") 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"]}') # ## Storing results in MLflow # Storing evaluation results in CSVs is fine but not enough if you want to compare and track multiple evaluation runs. MLflow is a handy tool when it comes to tracking experiments. So we decided to use it to track all of `Pipeline.eval()` with reproducability of your experiments in mind. # ### Host your own MLflow or use deepset's public MLflow # If you don't want to use deepset's public MLflow instance under https://public-mlflow.deepset.ai, you can easily host it yourself. # !pip install mlflow # !mlflow server --serve-artifacts # ### Preprocessing the dataset # Preprocessing the dataset works a bit differently than before. Instead of directly generating documents (and labels) out of a SQuAD file, we first save them to disk. This is necessary to experiment with different indexing pipelines. document_store = InMemoryDocumentStore() label_preprocessor = PreProcessor( split_length=200, split_overlap=0, split_respect_sentence_boundary=False, clean_empty_lines=False, clean_whitespace=False, ) # 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. # We only use it to get the evaluation set labels and the corpus files. document_store.add_eval_data( filename="data/tutorial5/nq_dev_subset_v2.json", doc_index=document_store.index, label_index=document_store.label_index, preprocessor=label_preprocessor, ) # the evaluation set to evaluate the pipelines on evaluation_set_labels = document_store.get_all_labels_aggregated(drop_negative_labels=True, drop_no_answers=True) # Pipelines need files as input to be able to test different preprocessors. # Even though this looks a bit cumbersome to write the documents back to files we gain a lot of evaluation potential and reproducibility. docs = document_store.get_all_documents() temp_dir = tempfile.TemporaryDirectory() file_paths = [] for doc in docs: file_name = doc.id + ".txt" file_path = Path(temp_dir.name) / file_name file_paths.append(file_path) with open(file_path, "w") as f: f.write(doc.content) file_metas = [d.meta for d in docs] # ### Run experiments # In this experiment we evaluate extractive QA pipelines with two different retrievers on the evaluation set given the corpus: # **ElasticsearchRetriever vs. EmbeddingRetriever** # helper function to create query and index pipeline def create_pipelines(document_store, preprocessor, retriever, reader): query_pipeline = Pipeline() query_pipeline.add_node(component=retriever, inputs=["Query"], name="Retriever") query_pipeline.add_node(component=reader, inputs=["Retriever"], name="Reader") index_pipeline = Pipeline() index_pipeline.add_node(component=TextConverter(), inputs=["File"], name="TextConverter") index_pipeline.add_node(component=preprocessor, inputs=["TextConverter"], name="Preprocessor") index_pipeline.add_node(component=retriever, inputs=["Preprocessor"], name="Retriever") index_pipeline.add_node(component=document_store, inputs=["Retriever"], name="DocumentStore") return query_pipeline, index_pipeline # Name of the experiment in MLflow EXPERIMENT_NAME = "haystack-tutorial-5" # #### Run using BM25Retriever document_store = ElasticsearchDocumentStore(index="sparse_index", recreate_index=True) preprocessor = PreProcessor( split_length=200, split_overlap=0, split_respect_sentence_boundary=False, clean_empty_lines=False, clean_whitespace=False, ) es_retriever = BM25Retriever(document_store=document_store) reader = FARMReader("deepset/roberta-base-squad2", top_k=3, return_no_answer=True, batch_size=8) query_pipeline, index_pipeline = create_pipelines(document_store, preprocessor, es_retriever, reader) sparse_eval_result = Pipeline.execute_eval_run( index_pipeline=index_pipeline, query_pipeline=query_pipeline, evaluation_set_labels=evaluation_set_labels, corpus_file_paths=file_paths, corpus_file_metas=file_metas, experiment_name=EXPERIMENT_NAME, experiment_run_name="sparse", corpus_meta={"name": "nq_dev_subset_v2.json"}, evaluation_set_meta={"name": "nq_dev_subset_v2.json"}, pipeline_meta={"name": "sparse-pipeline"}, add_isolated_node_eval=True, experiment_tracking_tool="mlflow", experiment_tracking_uri="https://public-mlflow.deepset.ai", reuse_index=True, ) # #### Run using EmbeddingRetriever document_store = ElasticsearchDocumentStore(index="dense_index", recreate_index=True) emb_retriever = EmbeddingRetriever( document_store=document_store, model_format="sentence_transformers", embedding_model="sentence-transformers/multi-qa-mpnet-base-dot-v1", batch_size=8, ) query_pipeline, index_pipeline = create_pipelines(document_store, preprocessor, emb_retriever, reader) dense_eval_result = Pipeline.execute_eval_run( index_pipeline=index_pipeline, query_pipeline=query_pipeline, evaluation_set_labels=evaluation_set_labels, corpus_file_paths=file_paths, corpus_file_metas=file_metas, experiment_name=EXPERIMENT_NAME, experiment_run_name="embedding", corpus_meta={"name": "nq_dev_subset_v2.json"}, evaluation_set_meta={"name": "nq_dev_subset_v2.json"}, pipeline_meta={"name": "embedding-pipeline"}, add_isolated_node_eval=True, experiment_tracking_tool="mlflow", experiment_tracking_uri="https://public-mlflow.deepset.ai", reuse_index=True, answer_scope="context", ) # You can now open MLflow (e.g. https://public-mlflow.deepset.ai/ if you used the public one hosted by deepset) and look for the haystack-eval-experiment experiment. # Try out mlflow's compare function and have fun... # # Note that on our public mlflow instance we are not able to log artifacts like the evaluation results or the piplines.yaml file. ## 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 and setting document_scope to `"document_id"`. # Per default `calculate_metrics()` has document_scope set to `"document_id_or_answer"` which interprets documents as relevant if they either match the gold document ID or contain the answer. metrics = eval_result_with_upper_bounds.calculate_metrics(document_scope="document_id") 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) top_n = reader_eval_results["top_n"] # 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 including no_answers print(f"Reader Top-{top_n}-Accuracy:", reader_eval_results["top_n_accuracy"]) # Reader Top-1-Exact Match is the proportion of questions where the first predicted answer is exactly the same as the correct answer including no_answers print("Reader Top-1-Exact Match:", reader_eval_results["EM"]) # Reader Top-1-F1-Score is the average overlap between the first predicted answers and the correct answers including no_answers print("Reader Top-1-F1-Score:", reader_eval_results["f1"]) # Reader Top-N-Accuracy is the proportion of predicted answers that match with their corresponding correct answer excluding no_answers print(f"Reader Top-{top_n}-Accuracy (without no_answers):", reader_eval_results["top_n_accuracy_text_answer"]) # Reader Top-N-Exact Match is the proportion of questions where the predicted answer within the first n results is exactly the same as the correct answer excluding no_answers (no_answers are always present within top n). print(f"Reader Top-{top_n}-Exact Match (without no_answers):", reader_eval_results["top_n_EM_text_answer"]) # Reader Top-N-F1-Score is the average overlap between the top n predicted answers and the correct answers excluding no_answers (no_answers are always present within top n). print(f"Reader Top-{top_n}-F1-Score (without no_answers):", reader_eval_results["top_n_f1_text_answer"]) # Just as a sanity check, we can compare the top-n exact_match and f1 metrics from `reader.eval()` with the exact_match and f1 from `pipeline.eval(add_isolated_node_eval=True)`. # These two approaches return the same values because pipeline.eval() calculates top-n metrics per default. # Small discrepancies might occur due to string normalization in pipeline.eval()'s answer-to-label comparison. # reader.eval() does not use string normalization. metrics = eval_result_with_upper_bounds.calculate_metrics(eval_mode="isolated") print(metrics["Reader"]["exact_match"]) print(metrics["Reader"]["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/