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haystack/tutorials/Tutorial6_Better_Retrieval_via_DPR.ipynb
Malte Pietsch e91518ee00
Update tutorials (torch versions, ES version, replace Finder with Pipeline) (#814) 
* remove manual torch install on colab

* update elasticsearch version everywhere to 7.9.2

* fix FAQPipeline

* update tutorials with new pipelines

* Add latest docstring and tutorial changes

* revert faqpipeline change. fix field names in tutorial 4

* Add latest docstring and tutorial changes

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2021-02-09 14:56:54 +01:00

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{
"cells": [
{
"cell_type": "markdown",
"metadata": {
"colab_type": "text",
"id": "bEH-CRbeA6NU"
},
"source": [
"# Better Retrieval via \"Dense Passage Retrieval\"\n",
"\n",
"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/deepset-ai/haystack/blob/master/tutorials/Tutorial6_Better_Retrieval_via_DPR.ipynb)\n",
"\n",
"### Importance of Retrievers\n",
"\n",
"The Retriever has a huge impact on the performance of our overall search pipeline.\n",
"\n",
"\n",
"### Different types of Retrievers\n",
"#### Sparse\n",
"Family of algorithms based on counting the occurrences of words (bag-of-words) resulting in very sparse vectors with length = vocab size.\n",
"\n",
"**Examples**: BM25, TF-IDF\n",
"\n",
"**Pros**: Simple, fast, well explainable\n",
"\n",
"**Cons**: Relies on exact keyword matches between query and text\n",
" \n",
"\n",
"#### Dense\n",
"These retrievers use neural network models to create \"dense\" embedding vectors. Within this family there are two different approaches: \n",
"\n",
"a) Single encoder: Use a **single model** to embed both query and passage. \n",
"b) Dual-encoder: Use **two models**, one to embed the query and one to embed the passage\n",
"\n",
"Recent work suggests that dual encoders work better, likely because they can deal better with the different nature of query and passage (length, style, syntax ...). \n",
"\n",
"**Examples**: REALM, DPR, Sentence-Transformers\n",
"\n",
"**Pros**: Captures semantinc similarity instead of \"word matches\" (e.g. synonyms, related topics ...)\n",
"\n",
"**Cons**: Computationally more heavy, initial training of model\n",
"\n",
"\n",
"### \"Dense Passage Retrieval\"\n",
"\n",
"In this Tutorial, we want to highlight one \"Dense Dual-Encoder\" called Dense Passage Retriever. \n",
"It was introdoced by Karpukhin et al. (2020, https://arxiv.org/abs/2004.04906. \n",
"\n",
"Original Abstract: \n",
"\n",
"_\"Open-domain question answering relies on efficient passage retrieval to select candidate contexts, where traditional sparse vector space models, such as TF-IDF or BM25, are the de facto method. In this work, we show that retrieval can be practically implemented using dense representations alone, where embeddings are learned from a small number of questions and passages by a simple dual-encoder framework. When evaluated on a wide range of open-domain QA datasets, our dense retriever outperforms a strong Lucene-BM25 system largely by 9%-19% absolute in terms of top-20 passage retrieval accuracy, and helps our end-to-end QA system establish new state-of-the-art on multiple open-domain QA benchmarks.\"_\n",
"\n",
"Paper: https://arxiv.org/abs/2004.04906 \n",
"Original Code: https://fburl.com/qa-dpr \n",
"\n",
"\n",
"*Use this* [link](https://colab.research.google.com/github/deepset-ai/haystack/blob/master/tutorials/Tutorial6_Better_Retrieval_via_DPR.ipynb) *to open the notebook in Google Colab.*\n"
]
},
{
"cell_type": "markdown",
"metadata": {
"colab_type": "text",
"id": "3K27Y5FbA6NV"
},
"source": [
"### Prepare environment\n",
"\n",
"#### Colab: Enable the GPU runtime\n",
"Make sure you enable the GPU runtime to experience decent speed in this tutorial. \n",
"**Runtime -> Change Runtime type -> Hardware accelerator -> GPU**\n",
"\n",
"<img src=\"https://raw.githubusercontent.com/deepset-ai/haystack/master/docs/_src/img/colab_gpu_runtime.jpg\">"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/",
"height": 357
},
"colab_type": "code",
"id": "JlZgP8q1A6NW",
"outputId": "c893ac99-b7a0-4d49-a8eb-1a9951d364d9"
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Mon Aug 24 11:56:45 2020 \r\n",
"+-----------------------------------------------------------------------------+\r\n",
"| NVIDIA-SMI 440.100 Driver Version: 440.100 CUDA Version: 10.2 |\r\n",
"|-------------------------------+----------------------+----------------------+\r\n",
"| GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC |\r\n",
"| Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. |\r\n",
"|===============================+======================+======================|\r\n",
"| 0 Tesla V100-SXM2... Off | 00000000:00:1E.0 Off | 0 |\r\n",
"| N/A 41C P0 39W / 300W | 0MiB / 16160MiB | 0% Default |\r\n",
"+-------------------------------+----------------------+----------------------+\r\n",
" \r\n",
"+-----------------------------------------------------------------------------+\r\n",
"| Processes: GPU Memory |\r\n",
"| GPU PID Type Process name Usage |\r\n",
"|=============================================================================|\r\n",
"| No running processes found |\r\n",
"+-----------------------------------------------------------------------------+\r\n"
]
}
],
"source": [
"# Make sure you have a GPU running\n",
"!nvidia-smi"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/",
"height": 1000
},
"colab_type": "code",
"id": "NM36kbRFA6Nc",
"outputId": "af1a9d85-9557-4d68-ea87-a01f00c584f9"
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Collecting git+https://github.com/deepset-ai/haystack.git\n",
" Cloning https://github.com/deepset-ai/haystack.git to /tmp/pip-req-build-fqgbr4x7\n",
" Running command git clone -q https://github.com/deepset-ai/haystack.git /tmp/pip-req-build-fqgbr4x7\n",
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]
},
{
"name": "stdout",
"output_type": "stream",
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"Building wheels for collected packages: farm-haystack\n",
" Building wheel for farm-haystack (setup.py) ... \u001B[?25ldone\n",
"\u001B[?25h Created wheel for farm-haystack: filename=farm_haystack-0.3.0-py3-none-any.whl size=99007 sha256=c46bad086db77ddc557d67d6a47b0e8ead6a76c20451e21bd7e56e7b3adf5434\n",
" Stored in directory: /tmp/pip-ephem-wheel-cache-s2p1ltpe/wheels/5b/d7/60/7a15bd24f2905dfa70aa762413b9570b9d37add064b151aaf0\n",
"Successfully built farm-haystack\n",
"\u001B[33mWARNING: You are using pip version 20.1.1; however, version 20.2.2 is available.\n",
"You should consider upgrading via the '/home/ubuntu/py3_6/bin/python3.6 -m pip install --upgrade pip' command.\u001B[0m\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Looking in links: https://download.pytorch.org/whl/torch_stable.html\n",
"Collecting torch==1.5.1+cu101\n",
" Downloading https://download.pytorch.org/whl/cu101/torch-1.5.1%2Bcu101-cp36-cp36m-linux_x86_64.whl (704.4 MB)\n",
"\u001B[K |████████████████████████████████| 704.4 MB 9.3 kB/s eta 0:00:011\n",
"\u001B[?25hCollecting torchvision==0.6.1+cu101\n",
" Downloading https://download.pytorch.org/whl/cu101/torchvision-0.6.1%2Bcu101-cp36-cp36m-linux_x86_64.whl (6.6 MB)\n",
"\u001B[K |████████████████████████████████| 6.6 MB 881 kB/s eta 0:00:01\n",
"\u001B[?25hRequirement already satisfied: numpy in /home/ubuntu/py3_6/lib/python3.6/site-packages (from torch==1.5.1+cu101) (1.19.0)\n",
"Requirement already satisfied: future in /home/ubuntu/py3_6/lib/python3.6/site-packages (from torch==1.5.1+cu101) (0.18.2)\n",
"Requirement already satisfied: pillow>=4.1.1 in /home/ubuntu/py3_6/lib/python3.6/site-packages (from torchvision==0.6.1+cu101) (7.2.0)\n",
"Installing collected packages: torch, torchvision\n",
" Attempting uninstall: torch\n",
" Found existing installation: torch 1.5.1\n",
" Uninstalling torch-1.5.1:\n",
" Successfully uninstalled torch-1.5.1\n",
"Successfully installed torch-1.5.1+cu101 torchvision-0.6.1+cu101\n",
"\u001B[33mWARNING: You are using pip version 20.1.1; however, version 20.2.2 is available.\n",
"You should consider upgrading via the '/home/ubuntu/py3_6/bin/python3.6 -m pip install --upgrade pip' command.\u001B[0m\n"
]
}
],
"source": [
"# Install the latest release of Haystack in your own environment \n",
"#! pip install farm-haystack\n",
"\n",
"# Install the latest master of Haystack\n",
"!pip install git+https://github.com/deepset-ai/haystack.git\n",
"!pip install urllib3==1.25.4"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "xmRuhTQ7A6Nh"
},
"outputs": [],
"source": [
"from haystack import Finder\n",
"from haystack.preprocessor.cleaning import clean_wiki_text\n",
"from haystack.preprocessor.utils import convert_files_to_dicts, fetch_archive_from_http\n",
"from haystack.reader.farm import FARMReader\n",
"from haystack.reader.transformers import TransformersReader\n",
"from haystack.utils import print_answers"
]
},
{
"cell_type": "markdown",
"metadata": {
"colab_type": "text",
"id": "q3dSo7ZtA6Nl"
},
"source": [
"### Document Store\n",
"\n",
"FAISS is a library for efficient similarity search on a cluster of dense vectors.\n",
"The `FAISSDocumentStore` uses a SQL(SQLite in-memory be default) database under-the-hood\n",
"to store the document text and other meta data. The vector embeddings of the text are\n",
"indexed on a FAISS Index that later is queried for searching answers.\n",
"The default flavour of FAISSDocumentStore is \"Flat\" but can also be set to \"HNSW\" for\n",
"faster search at the expense of some accuracy. Just set the faiss_index_factor_str argument in the constructor.\n",
"For more info on which suits your use case: https://github.com/facebookresearch/faiss/wiki/Guidelines-to-choose-an-index"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/",
"height": 51
},
"colab_type": "code",
"id": "1cYgDJmrA6Nv",
"outputId": "a8aa6da1-9acf-43b1-fa3c-200123e9bdce",
"pycharm": {
"name": "#%%\n"
}
},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"08/25/2020 08:27:51 - INFO - faiss - Loading faiss with AVX2 support.\n",
"08/25/2020 08:27:51 - INFO - faiss - Loading faiss.\n"
]
}
],
"source": [
"from haystack.document_store.faiss import FAISSDocumentStore\n",
"\n",
"document_store = FAISSDocumentStore(faiss_index_factory_str=\"Flat\")"
]
},
{
"cell_type": "markdown",
"metadata": {
"colab_type": "text",
"id": "06LatTJBA6N0",
"pycharm": {
"name": "#%% md\n"
}
},
"source": [
"### Cleaning & indexing documents\n",
"\n",
"Similarly to the previous tutorials, we download, convert and index some Game of Thrones articles to our DocumentStore"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/",
"height": 156
},
"colab_type": "code",
"id": "iqKnu6wxA6N1",
"outputId": "bb5dcc7b-b65f-49ed-db0b-842981af213b",
"pycharm": {
"name": "#%%\n"
}
},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"08/25/2020 08:27:53 - INFO - haystack.indexing.utils - Found data stored in `data/article_txt_got`. Delete this first if you really want to fetch new data.\n"
]
}
],
"source": [
"# Let's first get some files that we want to use\n",
"doc_dir = \"data/article_txt_got\"\n",
"s3_url = \"https://s3.eu-central-1.amazonaws.com/deepset.ai-farm-qa/datasets/documents/wiki_gameofthrones_txt.zip\"\n",
"fetch_archive_from_http(url=s3_url, output_dir=doc_dir)\n",
"\n",
"# Convert files to dicts\n",
"dicts = convert_files_to_dicts(dir_path=doc_dir, clean_func=clean_wiki_text, split_paragraphs=True)\n",
"\n",
"# Now, let's write the dicts containing documents to our DB.\n",
"document_store.write_documents(dicts)"
]
},
{
"cell_type": "markdown",
"metadata": {
"colab_type": "text",
"id": "wgjedxx_A6N6"
},
"source": [
"### Initalize Retriever, Reader, & Finder\n",
"\n",
"#### Retriever\n",
"\n",
"**Here:** We use a `DensePassageRetriever`\n",
"\n",
"**Alternatives:**\n",
"\n",
"- The `ElasticsearchRetriever`with custom queries (e.g. boosting) and filters\n",
"- Use `EmbeddingRetriever` to find candidate documents based on the similarity of embeddings (e.g. created via Sentence-BERT)\n",
"- Use `TfidfRetriever` in combination with a SQL or InMemory Document store for simple prototyping and debugging"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/",
"height": 1000,
"referenced_widgets": [
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"colab_type": "code",
"id": "kFwiPP60A6N7",
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"pycharm": {
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"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"08/25/2020 08:28:12 - INFO - haystack.database.faiss - Updating embeddings for 2497 docs ...\n",
"/pytorch/torch/csrc/utils/python_arg_parser.cpp:756: UserWarning: This overload of nonzero is deprecated:\n",
"\tnonzero(Tensor input, *, Tensor out)\n",
"Consider using one of the following signatures instead:\n",
"\tnonzero(Tensor input, *, bool as_tuple)\n",
"08/25/2020 08:28:13 - INFO - haystack.retriever.dense - Embedded 80 / 2497 texts\n",
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"08/25/2020 08:28:23 - INFO - haystack.retriever.dense - Embedded 1280 / 2497 texts\n",
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]
}
],
"source": [
"from haystack.retriever.dense import DensePassageRetriever\n",
"retriever = DensePassageRetriever(document_store=document_store,\n",
" query_embedding_model=\"facebook/dpr-question_encoder-single-nq-base\",\n",
" passage_embedding_model=\"facebook/dpr-ctx_encoder-single-nq-base\",\n",
" max_seq_len_query=64,\n",
" max_seq_len_passage=256,\n",
" batch_size=16,\n",
" use_gpu=True,\n",
" embed_title=True,\n",
" use_fast_tokenizers=True)\n",
"# Important: \n",
"# Now that after we have the DPR initialized, we need to call update_embeddings() to iterate over all\n",
"# previously indexed documents and update their embedding representation. \n",
"# While this can be a time consuming operation (depending on corpus size), it only needs to be done once. \n",
"# At query time, we only need to embed the query and compare it the existing doc embeddings which is very fast.\n",
"document_store.update_embeddings(retriever)"
]
},
{
"cell_type": "markdown",
"metadata": {
"colab_type": "text",
"id": "rnVR28OXA6OA"
},
"source": [
"#### Reader\n",
"\n",
"Similar to previous Tutorials we now initalize our reader.\n",
"\n",
"Here we use a FARMReader with the *deepset/roberta-base-squad2* model (see: https://huggingface.co/deepset/roberta-base-squad2)\n",
"\n",
"\n",
"\n",
"##### FARMReader"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/",
"height": 739,
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"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"08/25/2020 08:28:54 - INFO - farm.utils - device: cuda n_gpu: 1, distributed training: False, automatic mixed precision training: None\n",
"08/25/2020 08:28:54 - INFO - farm.infer - Could not find `deepset/roberta-base-squad2` locally. Try to download from model hub ...\n",
"08/25/2020 08:28:59 - WARNING - farm.modeling.language_model - Could not automatically detect from language model name what language it is. \n",
"\t We guess it's an *ENGLISH* model ... \n",
"\t If not: Init the language model by supplying the 'language' param.\n",
"08/25/2020 08:29:06 - WARNING - farm.modeling.prediction_head - Some unused parameters are passed to the QuestionAnsweringHead. Might not be a problem. Params: {\"loss_ignore_index\": -1}\n",
"08/25/2020 08:29:09 - INFO - farm.utils - device: cuda n_gpu: 1, distributed training: False, automatic mixed precision training: None\n",
"08/25/2020 08:29:10 - INFO - farm.infer - Got ya 7 parallel workers to do inference ...\n",
"08/25/2020 08:29:10 - INFO - farm.infer - 0 0 0 0 0 0 0 \n",
"08/25/2020 08:29:10 - INFO - farm.infer - /w\\ /w\\ /w\\ /w\\ /w\\ /w\\ /w\\\n",
"08/25/2020 08:29:10 - INFO - farm.infer - /'\\ / \\ /'\\ /'\\ / \\ / \\ /'\\\n",
"08/25/2020 08:29:10 - INFO - farm.infer - \n"
]
}
],
"source": [
"# Load a local model or any of the QA models on\n",
"# Hugging Face's model hub (https://huggingface.co/models)\n",
"\n",
"reader = FARMReader(model_name_or_path=\"deepset/roberta-base-squad2\", use_gpu=True)"
]
},
{
"cell_type": "markdown",
"metadata": {
"colab_type": "text",
"id": "unhLD18yA6OF"
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"source": [
"### Pipeline\n",
"\n",
"With a Haystack `Pipeline` you can stick together your building blocks to a search pipeline.\n",
"Under the hood, `Pipelines` are Directed Acyclic Graphs (DAGs) that you can easily customize for your own use cases.\n",
"To speed things up, Haystack also comes with a few predefined Pipelines. One of them is the `ExtractiveQAPipeline` that combines a retriever and a reader to answer our questions.\n",
"You can learn more about `Pipelines` in the [docs](https://haystack.deepset.ai/docs/latest/pipelinesmd)."
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "TssPQyzWA6OG"
},
"outputs": [],
"source": [
"from haystack.pipeline import ExtractiveQAPipeline\n",
"pipe = ExtractiveQAPipeline(reader, retriever)"
]
},
{
"cell_type": "markdown",
"metadata": {
"colab_type": "text",
"id": "bXlBBxKXA6OL"
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"source": [
"## Voilà! Ask a question!"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/",
"height": 275
},
"colab_type": "code",
"id": "Zi97Hif2A6OM",
"outputId": "5eb9363d-ba92-45d5-c4d0-63ada3073f02"
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"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"08/25/2020 08:30:28 - INFO - haystack.finder - Reader is looking for detailed answer in 9168 chars ...\n",
"Inferencing Samples: 0%| | 0/1 [00:00<?, ? Batches/s]/home/ubuntu/deepset/FARM/farm/modeling/prediction_head.py:1073: UserWarning: Implicit dimension choice for softmax has been deprecated. Change the call to include dim=X as an argument.\n",
" start_logits_normalized = nn.functional.softmax(start_logits)\n",
"/home/ubuntu/deepset/FARM/farm/modeling/prediction_head.py:1076: UserWarning: Implicit dimension choice for softmax has been deprecated. Change the call to include dim=X as an argument.\n",
" end_logits_normalized = nn.functional.softmax(end_logits)\n",
"Inferencing Samples: 100%|██████████| 1/1 [00:00<00:00, 3.56 Batches/s]\n",
"Inferencing Samples: 100%|██████████| 1/1 [00:00<00:00, 38.79 Batches/s]\n",
"Inferencing Samples: 100%|██████████| 1/1 [00:00<00:00, 39.61 Batches/s]\n",
"Inferencing Samples: 100%|██████████| 1/1 [00:00<00:00, 53.05 Batches/s]\n",
"Inferencing Samples: 100%|██████████| 1/1 [00:00<00:00, 37.39 Batches/s]\n",
"Inferencing Samples: 100%|██████████| 1/1 [00:00<00:00, 67.21 Batches/s]\n",
"Inferencing Samples: 100%|██████████| 1/1 [00:00<00:00, 67.10 Batches/s]\n",
"Inferencing Samples: 100%|██████████| 1/1 [00:00<00:00, 66.66 Batches/s]\n",
"Inferencing Samples: 100%|██████████| 1/1 [00:00<00:00, 47.91 Batches/s]\n",
"Inferencing Samples: 100%|██████████| 1/1 [00:00<00:00, 33.05 Batches/s]\n"
]
}
],
"source": [
"# You can configure how many candidates the reader and retriever shall return\n",
"# The higher top_k_retriever, the better (but also the slower) your answers.\n",
"prediction = pipe.run(query=\"Who created the Dothraki vocabulary?\", top_k_retriever=10, top_k_reader=5)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"print_answers(prediction, details=\"minimal\")\n",
"\n"
]
}
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