Spark_NLP_Udemy_MOOC/Healthcare_NLP/BertSentenceChunkEmbeddings.ipynb

{"nbformat":4,"nbformat_minor":0,"metadata":{"colab":{"provenance":[],"toc_visible":true},"kernelspec":{"name":"python3","display_name":"Python 3"},"language_info":{"name":"python"}},"cells":[{"cell_type":"markdown","source":["![JohnSnowLabs](https://nlp.johnsnowlabs.com/assets/images/logo.png)\n"],"metadata":{"id":"W0R-4s1jQrV5"}},{"cell_type":"markdown","source":["# **BertSentenceChunkEmbeddings**"],"metadata":{"id":"bewC1SWN-6jB"}},{"cell_type":"markdown","source":["This notebook will cover the different parameters and usages of `BertSentenceChunkEmbeddings` annotator.\n","\n","**📖 Learning Objectives:**\n","\n","1. Understand how to use `BertSentenceChunkEmbeddings`.\n","\n","2. Become comfortable using the different parameters of the annotator.\n","\n","\n","**🔗 Helpful Links:**\n","\n","- Documentation : [BertSentenceChunkEmbeddings](https://nlp.johnsnowlabs.com/docs/en/licensed_annotators#bertsentencechunkembeddings)\n","\n","- Python Docs : [BertSentenceChunkEmbeddings](https://nlp.johnsnowlabs.com/licensed/api/python/reference/autosummary/sparknlp_jsl/annotator/embeddings/bert_sentence_embeddings/index.html#sparknlp_jsl.annotator.embeddings.bert_sentence_embeddings.BertSentenceChunkEmbeddings.name)\n","\n","- Scala Docs : [BertSentenceChunkEmbeddings](https://nlp.johnsnowlabs.com/licensed/api/com/johnsnowlabs/nlp/annotators/embeddings/BertSentenceChunkEmbeddings.html)\n","\n","- For extended examples of usage, see the [Spark NLP Workshop repository](https://github.com/JohnSnowLabs/spark-nlp-workshop/blob/master/healthcare-nlp/05.6.Improved_Entity_Resolution_with_SentenceChunkEmbeddings.ipynb)."],"metadata":{"id":"m048uDkB69Rv"}},{"cell_type":"markdown","source":["## **📜 Background**\n"],"metadata":{"id":"B9Wo54MT8jKU"}},{"cell_type":"markdown","source":["`BertSentenceChunkEmbeddings` annotator which take into account the context of the sentence the chunk appeared in. This is an extension of BertSentenceEmbeddings which combines the embedding of a chunk with the embedding of the surrounding sentence. For each input chunk annotation, it finds the corresponding sentence, computes the BERT sentence embedding of both the chunk and the sentence and averages them. The resulting embeddings are useful in cases, in which one needs a numerical representation of a text chunk which is sensitive to the context it appears in.\n","\n","This model is a subclass of BertSentenceEmbeddings and shares all parameters with it. It can load any pretrained BertSentenceEmbeddings model. Available models can be found at [Models Hub](https://nlp.johnsnowlabs.com/models?task=Embeddings).\n","\n","The default model is `sent_small_bert_L2_768`, if no name is provided.\n","\n","Sources :\n","\n","[BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://arxiv.org/abs/1810.04805)\n","\n","[Sentence-BERT: Sentence Embeddings using Siamese BERT-Networks](https://arxiv.org/pdf/1908.10084.pdf)"],"metadata":{"id":"yaDBNKJsAovm"}},{"cell_type":"markdown","source":["## **🎬 Colab Setup**"],"metadata":{"id":"A4hMnkhd_ik9"}},{"cell_type":"code","source":["# Install the johnsnowlabs library to access Spark-NLP for Healthcare\n","! pip install -q johnsnowlabs"],"metadata":{"id":"xrdvNxjD_yQI"},"execution_count":null,"outputs":[]},{"cell_type":"code","source":["from google.colab import files\n","print('Please Upload your John Snow Labs License using the button below')\n","license_keys = files.upload()"],"metadata":{"id":"3WU-z_e8jYpO"},"execution_count":null,"outputs":[]},{"cell_type":"code","source":["from johnsnowlabs import nlp, medical\n","\n","# After uploading your license run this to install all licensed Python Wheels and pre-download Jars the Spark Session JVM\n","nlp.install()"],"metadata":{"id":"bUDfeNzUjaO-"},"execution_count":null,"outputs":[]},{"cell_type":"code","source":["from johnsnowlabs import nlp, medical\n","import pandas as pd\n","\n","# Automatically load license data and start a session with all jars user has access to\n","spark = nlp.start()"],"metadata":{"id":"19b2mPsZjbI3"},"execution_count":null,"outputs":[]},{"cell_type":"code","source":["spark"],"metadata":{"colab":{"base_uri":"https://localhost:8080/","height":232},"id":"aFMD5KCS9Xih","outputId":"ee98a5f9-f256-4f48-84e2-8719e8a3ddeb","executionInfo":{"status":"ok","timestamp":1692188516307,"user_tz":-60,"elapsed":149,"user":{"displayName":"Ahmet Emin Tek","userId":"14855809472179427810"}}},"execution_count":null,"outputs":[{"output_type":"execute_result","data":{"text/plain":["<pyspark.sql.session.SparkSession at 0x79dfc08325c0>"],"text/html":["\n","            <div>\n","                <p><b>SparkSession - in-memory</b></p>\n","                \n","        <div>\n","            <p><b>SparkContext</b></p>\n","\n","            <p><a href=\"http://10f0d683aaf5:4040\">Spark UI</a></p>\n","\n","            <dl>\n","              <dt>Version</dt>\n","                <dd><code>v3.1.2</code></dd>\n","              <dt>Master</dt>\n","                <dd><code>local[*]</code></dd>\n","              <dt>AppName</dt>\n","                <dd><code>John-Snow-Labs-Spark-Session 🚀 with Jars for: 🚀Spark-NLP==5.0.1, 💊Spark-Healthcare==5.0.1, running on ⚡ PySpark==3.1.2</code></dd>\n","            </dl>\n","        </div>\n","        \n","            </div>\n","        "]},"metadata":{},"execution_count":5}]},{"cell_type":"code","source":["from pyspark.sql import DataFrame\n","import pyspark.sql.functions as F\n","import pyspark.sql.types as T"],"metadata":{"id":"1SquZfvA_OAX"},"execution_count":null,"outputs":[]},{"cell_type":"markdown","source":["## **🖨️ Input/Output Annotation Types**"],"metadata":{"id":"fdTHvykf8wni"}},{"cell_type":"markdown","source":["- Input: `DOCUMENT`, `CHUNK`\n","\n","- Output: `SENTENCE_EMBEDDINGS`"],"metadata":{"id":"ejYVNcX98y5j"}},{"cell_type":"markdown","source":["## **🔎 Parameters**\n"],"metadata":{"id":"YVa72oJd9Bk_"}},{"cell_type":"markdown","source":["- `inputCols`: The name of the columns containing the input annotations. It can read either a String column or an Array.\n","- `outputCol`: The name of the column in Document type that is generated. We can specify only one column here.\n","- `chunkWeight`: Relative weight of chunk embeddings in comparison to sentence embeddings. The value should between 0 and 1. The default is 0.5, which means the chunk and sentence embeddings are given equal weight.\n","- `setMaxSentenceLength`: Sets max sentence length to process, by default 128.\n","- `caseSensitive`: Determines whether the definitions of the white listed entities are case sensitive.\n","\n","All the parameters can be set using the corresponding set method in camel case. For example, `.setInputcols()`."],"metadata":{"id":"AUbv3YL59D8Q"}},{"cell_type":"markdown","source":["### `inputCols` and `outputCol`"],"metadata":{"id":"EpBqGk7oNc3C"}},{"cell_type":"markdown","source":["Define the column names containing the `SENTENCE` and `CHUNK` annotations needed as input to the `BertSentenceChunkEmbeddings` and the name of the new column containg the identified entities.\n","\n","Let's define a pipeline to process raw texts into `SENTENCE` and `CHUNK` annotations along with the `BertSentenceChunkEmbeddings`:"],"metadata":{"id":"wOGfzMDiOAXE"}},{"cell_type":"code","source":["documentAssembler = nlp.DocumentAssembler() \\\n","    .setInputCol(\"text\") \\\n","    .setOutputCol(\"document\")\n","\n","sentence = nlp.SentenceDetector() \\\n","    .setInputCols([\"document\"]) \\\n","    .setOutputCol(\"sentence\")\n","\n","tokenizer = nlp.Tokenizer() \\\n","    .setInputCols([\"sentence\"]) \\\n","    .setOutputCol(\"token\")\n","\n","word_embedding = nlp.WordEmbeddingsModel.pretrained('embeddings_clinical', 'en', 'clinical/models') \\\n","    .setInputCols([\"sentence\", \"token\"]) \\\n","    .setOutputCol(\"word_embedding\")\n","\n","nerTagger = medical.NerModel.pretrained('ner_clinical_large', 'en', 'clinical/models') \\\n","    .setInputCols([\"sentence\", \"token\", \"word_embedding\"]) \\\n","    .setOutputCol(\"ner\")\n","\n","nerConverter = medical.NerConverterInternal() \\\n","    .setInputCols([\"sentence\", \"token\",\"ner\"]) \\\n","    .setOutputCol(\"ner_chunk\")\n","\n","sentence_chunk_embeddings = medical.BertSentenceChunkEmbeddings.pretrained() \\\n","    .setInputCols([\"sentence\", \"ner_chunk\"]) \\\n","    .setOutputCol(\"sentence_chunk_embeddings\")\n","\n","pipeline = nlp.Pipeline(\n","    stages = [documentAssembler,\n","              sentence,\n","              tokenizer,\n","              word_embedding,\n","              nerTagger,\n","              nerConverter,\n","              sentence_chunk_embeddings\n","    ])\n","\n"],"metadata":{"id":"c23AbFZ7OV6B","colab":{"base_uri":"https://localhost:8080/"},"outputId":"856bf857-b8f5-49d1-fe17-651cb0416d92","executionInfo":{"status":"ok","timestamp":1692190751815,"user_tz":-60,"elapsed":8800,"user":{"displayName":"Ahmet Emin Tek","userId":"14855809472179427810"}}},"execution_count":null,"outputs":[{"output_type":"stream","name":"stdout","text":["embeddings_clinical download started this may take some time.\n","Approximate size to download 1.6 GB\n","[OK!]\n","ner_clinical_large download started this may take some time.\n","[OK!]\n","sbiobert_base_cased_mli download started this may take some time.\n","[OK!]\n"]}]},{"cell_type":"code","source":["text = \"A 28-year-old female with a history of gestational diabetes mellitus diagnosed eight years prior to presentation and subsequent type two diabetes mellitus ( T2DM ), one prior episode of HTG-induced pancreatitis three years prior to presentation , and associated with an acute hepatitis , presented with a one-week history of polyuria , poor appetite , and vomiting.\"\n","\n","data = spark.createDataFrame([[text]]).toDF(\"text\")\n","\n","result = pipeline.fit(data).transform(data)"],"metadata":{"id":"KB0WFZo5Esw4"},"execution_count":null,"outputs":[]},{"cell_type":"code","source":["result.select(\"sentence_chunk_embeddings\").show(truncate=False)"],"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"d7ZNRQ8N954U","outputId":"fdd86722-eac5-45d0-f75b-aef63e629dc6","executionInfo":{"status":"ok","timestamp":1692190772743,"user_tz":-60,"elapsed":3565,"user":{"displayName":"Ahmet Emin Tek","userId":"14855809472179427810"}}},"execution_count":null,"outputs":[{"output_type":"stream","name":"stdout","text":["+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------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= result.select(F.explode(F.arrays_zip(result.sentence_chunk_embeddings.result,\n","                                                 result.sentence_chunk_embeddings.embeddings)).alias(\"cols\"))\\\n","                  .select(F.expr(\"cols['0']\").alias(\"chunk\"),\n","                          F.expr(\"cols['1']\").alias(\"embeddings\"))\n","\n","result_df.show(50, truncate=False)"],"metadata":{"id":"KfueJP-rALU_","colab":{"base_uri":"https://localhost:8080/"},"outputId":"3afb0a19-4266-4edf-f73e-b6b347dab2eb","executionInfo":{"status":"ok","timestamp":1692190798190,"user_tz":-60,"elapsed":3692,"user":{"displayName":"Ahmet Emin Tek","userId":"14855809472179427810"}}},"execution_count":null,"outputs":[{"output_type":"stream","name":"stdout","text":["+-------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n","|chunk 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|\n","+-------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n","\n"]}]},{"cell_type":"code","source":["sentence_chunk_embeddings.getStorageRef()"],"metadata":{"colab":{"base_uri":"https://localhost:8080/","height":58},"id":"vg44awUQrv0Q","outputId":"784e0b60-3be4-41fd-9331-4b7e1b9bf121","executionInfo":{"status":"ok","timestamp":1692190862690,"user_tz":-60,"elapsed":514,"user":{"displayName":"Ahmet Emin Tek","userId":"14855809472179427810"}}},"execution_count":null,"outputs":[{"output_type":"execute_result","data":{"text/plain":["'BERT_SENTENCE_EMBEDDINGS_0bee53f1b2cc'"],"application/vnd.google.colaboratory.intrinsic+json":{"type":"string"}},"metadata":{},"execution_count":26}]},{"cell_type":"code","source":["sentence_chunk_embeddings.getDimension()"],"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"choz-EaSrv5g","outputId":"5bea1c53-df1b-45c2-83ee-7007f42a6efb","executionInfo":{"status":"ok","timestamp":1692190889358,"user_tz":-60,"elapsed":209,"user":{"displayName":"Ahmet Emin Tek","userId":"14855809472179427810"}}},"execution_count":null,"outputs":[{"output_type":"execute_result","data":{"text/plain":["768"]},"metadata":{},"execution_count":27}]},{"cell_type":"code","source":["sentence_chunk_embeddings.getMaxSentenceLength()"],"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"_xOkjhNHrvxu","outputId":"3fb9ab3a-1820-430c-cd89-81aede1416f5","executionInfo":{"status":"ok","timestamp":1692190903122,"user_tz":-60,"elapsed":314,"user":{"displayName":"Ahmet Emin Tek","userId":"14855809472179427810"}}},"execution_count":null,"outputs":[{"output_type":"execute_result","data":{"text/plain":["128"]},"metadata":{},"execution_count":28}]},{"cell_type":"code","source":["sentence_chunk_embeddings.getCaseSensitive()"],"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"x6VIMgc7kCRc","outputId":"1fc0a233-f36e-48fa-efcd-ae14fbb1917e","executionInfo":{"status":"ok","timestamp":1692190920104,"user_tz":-60,"elapsed":206,"user":{"displayName":"Ahmet Emin Tek","userId":"14855809472179427810"}}},"execution_count":null,"outputs":[{"output_type":"execute_result","data":{"text/plain":["True"]},"metadata":{},"execution_count":29}]},{"cell_type":"markdown","source":["### `chunkWeight`\n","\n","Relative weight of chunk embeddings in comparison to sentence embeddings.\n","\n","The value should between 0 and 1.The default is 0.5, which means the chunk and sentence embeddings are given equal weight."],"metadata":{"id":"VkIDKSEG_AZb"}},{"cell_type":"markdown","source":["**.setChunkWeight(0)**\n","\n","When we set the chunkWeight parameter value to 0, the weight for the chunk will be 0 and the sentence's total embedding value will returned."],"metadata":{"id":"mnmTA3z5GIcv"}},{"cell_type":"code","source":["sentence_chunk_embeddings = medical.BertSentenceChunkEmbeddings.pretrained() \\\n","    .setInputCols([\"sentence\", \"ner_chunk\"]) \\\n","    .setOutputCol(\"sentence_chunk_embeddings\")\\\n","    .setChunkWeight(0)\n","\n","pipeline = nlp.Pipeline(\n","    stages = [documentAssembler,\n","              sentence,\n","              tokenizer,\n","              word_embedding,\n","              nerTagger,\n","              nerConverter,\n","              sentence_chunk_embeddings\n","              ])\n"],"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"iQsbMopI_iMn","outputId":"e7dfad95-a01e-4506-f0a7-e746bab75b4c","executionInfo":{"status":"ok","timestamp":1692191775573,"user_tz":-60,"elapsed":2806,"user":{"displayName":"Ahmet Emin Tek","userId":"14855809472179427810"}}},"execution_count":null,"outputs":[{"output_type":"stream","name":"stdout","text":["sbiobert_base_cased_mli download started this may take some time.\n","[OK!]\n"]}]},{"cell_type":"code","source":["result = pipeline.fit(data).transform(data)\n","\n","result_df = result.select(F.explode(F.arrays_zip(result.sentence_chunk_embeddings.result,\n","                                                 result.sentence_chunk_embeddings.embeddings)).alias(\"cols\"))\\\n","                  .select(F.expr(\"cols['0']\").alias(\"chunk\"),\n","                          F.expr(\"cols['1']\").alias(\"embeddings\"))\n","\n","result_df.show(50, truncate=False)"],"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"h3MDnxsYBUmE","outputId":"643e9432-0164-46c8-fdf3-89c5d902cfe4","executionInfo":{"status":"ok","timestamp":1692191786589,"user_tz":-60,"elapsed":5099,"user":{"displayName":"Ahmet Emin Tek","userId":"14855809472179427810"}}},"execution_count":null,"outputs":[{"output_type":"stream","name":"stdout","text":["+-------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------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                               |embeddings                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               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0.6746282]|\n","+-------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n","\n"]}]},{"cell_type":"markdown","source":["**.setChunkWeight(1)**\n","\n","When we set the chunkWeight parameter value to 1, the weight for the chunk will be 1 and the sentence's total embedding value will be disabled."],"metadata":{"id":"_bhX9D1tGNCv"}},{"cell_type":"code","source":["sentence_chunk_embeddings = medical.BertSentenceChunkEmbeddings.pretrained() \\\n","    .setInputCols([\"sentence\", \"ner_chunk\"]) \\\n","    .setOutputCol(\"sentence_chunk_embeddings\")\\\n","    .setChunkWeight(1)\n","\n","pipeline = nlp.Pipeline(\n","    stages = [documentAssembler,\n","              sentence,\n","              tokenizer,\n","              word_embedding,\n","              nerTagger,\n","              nerConverter,\n","              sentence_chunk_embeddings\n","              ])\n"],"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"n8r_3jqWEJjA","outputId":"5a044ff9-af8a-4f0c-b298-aaa235c9caa3","executionInfo":{"status":"ok","timestamp":1692191825574,"user_tz":-60,"elapsed":2732,"user":{"displayName":"Ahmet Emin Tek","userId":"14855809472179427810"}}},"execution_count":null,"outputs":[{"output_type":"stream","name":"stdout","text":["sbiobert_base_cased_mli download started this may take some time.\n","[OK!]\n"]}]},{"cell_type":"code","source":["result = pipeline.fit(data).transform(data)\n","\n","result_df = result.select(F.explode(F.arrays_zip(result.sentence_chunk_embeddings.result,\n","                                                 result.sentence_chunk_embeddings.embeddings)).alias(\"cols\"))\\\n","                  .select(F.expr(\"cols['0']\").alias(\"chunk\"),\n","                          F.expr(\"cols['1']\").alias(\"embeddings\"))\n","\n","result_df.show(50, truncate=False)"],"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"g111TBGCEJgY","outputId":"0787904c-4d89-4660-bb4e-eaf9b66caa88","executionInfo":{"status":"ok","timestamp":1692191837234,"user_tz":-60,"elapsed":3842,"user":{"displayName":"Ahmet Emin Tek","userId":"14855809472179427810"}}},"execution_count":null,"outputs":[{"output_type":"stream","name":"stdout","text":["+-------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------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------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n","|gestational 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