From fdcaf04f904b39e18d7c86cbea1fc3ed4eda6671 Mon Sep 17 00:00:00 2001 From: mehmetbutgul Date: Mon, 20 Jan 2025 18:55:02 +0000 Subject: [PATCH] deploy: 47fa80b9fde19700de8dcb9500da55b58ebb6387 --- docs/en/licensed_annotators.html | 43 +- en/licensed_annotator_entries/AssertionDL.md | 6 + .../BertSentenceChunkEmbeddings.md | 6 +- .../ContextualEntityFilterer.md | 2 + .../ContextualEntityRuler.md | 16 +- .../DeIdentification.md | 4 + .../FewShotAssertionClassifier.md | 3 + feed.xml | 2 +- sitemap.xml | 2334 ++++++++--------- 9 files changed, 1228 insertions(+), 1188 deletions(-) diff --git a/docs/en/licensed_annotators.html b/docs/en/licensed_annotators.html index 6c8022606c..6770e1aece 100644 --- a/docs/en/licensed_annotators.html +++ b/docs/en/licensed_annotators.html @@ -2289,6 +2289,15 @@

AssertionDL

  • datasetInfo (Str): Descriptive information about the dataset being used.

    • +
  • +

    blackList (list[str]): If defined, list of entities to ignore. The rest will be processed.

    +
    • +
  • +

    whiteList (list[str]): If defined, list of entities to process. The rest will be ignored. Do not include IOB prefix on labels.

    +
    • +
  • +

    caseSensitive (Bool): Determines whether the definitions of the white listed and black listed entities are case sensitive. Default: True.

    +

    • For pretrained models please see the @@ -4981,9 +4990,15 @@

    BertSentenceChunkEmbeddings

  • caseSensitive: Determines whether the definitions of the white listed entities are case sensitive.

    • +
  • +

    strategy: Strategy for computing embeddings. Supported strategies are: sentence_average, scope_average, chunk_only, scope_only. The default is sentence_average.

    +
    • +
  • +

    scopeWindow: cope window to calculate scope embeddings. The scope window is defined by two non-negative integers. The default is [0, 0], which means only the chunk embeddings are used. The first integer defines the number of tokens before the chunk and the second integer defines the number of tokens after the chunk.

    +
    • -

    All the parameters can be set using the corresponding set method in camel case. For example, .setInputcols().

    +

    All the parameters can be set using the corresponding set method in camel case. For example, .setInputCols().

    For more information and examples of BertSentenceChunkEmbeddings annotator, you can check the Spark NLP Workshop, and in special, the notebook 24.1.Improved_Entity_Resolution_with_SentenceChunkEmbeddings.ipynb.

    @@ -10128,6 +10143,8 @@

    ContextualEntityFilterer

  • blackListWords: The black list of words. If a word from this list appears within the scope window, the chunk will be filtered out.
  • whiteListWords: The white list of words. If a word from this list appears within the scope window, the chunk will be kept.
  • confidenceThreshold: The confidence threshold to filter the chunks. Filtering is only applied if the confidence of the chunk is below the threshold.
    • +
  • possibleRegexContext : The possible regex context to filter the chunks. If the regex is found in the context(chunk), the chunk is kept.
    • +
  • impossibleRegexContext : The impossible regex context to filter the chunks. If the regex is found in the context(chunk), the chunk is removed.
    • @@ -10339,11 +10356,11 @@

    ContextualEntityRuler

    Parameters:

    @@ -10444,7 +10459,6 @@

    ContextualEntityRuler

    "replaceEntity" : "Modified_Date", "mode" : "include" } - ] contextual_entity_ruler = medical.ContextualEntityRuler() \ @@ -11595,6 +11609,12 @@

    DeIdentification

    If False, the month will be modified along with the year and day. Default: False.

    +
  • +

    keepTextSizeForObfuscation : Whether to keep the text length same obfuscating entities. If True, the output text will remain the same if a same length fake is available, otherwise length might vary.

    +
    • +
  • +

    fakerLengthOffset : It specifies how much length deviation is accepted in obfuscation, with keepTextSizeForObfuscation enabled. It must be greater than 0.

    +

    • To create a configured DeIdentificationModel, please see the example of DeIdentification.

    @@ -16215,6 +16235,9 @@

    FewShotAssertionClassifierModel

  • batchSize (Int): Batch size
  • caseSensitive (Bool): Whether the classifier is sensitive to text casing
  • maxSentenceLength (Int): The maximum length of the input text
    • +
  • blackList (list[str]): If defined, list of entities to ignore. The rest will be processed.
    • +
  • whiteList (list[str]): If defined, list of entities to process. The rest will be ignored. Do not include IOB prefix on labels.
    • +
  • caseSensitive (Bool): Determines whether the definitions of the white listed and black listed entities are case sensitive. Default: True.

    • Input Annotator Types: DOCUMENT, CHUNK

    diff --git a/en/licensed_annotator_entries/AssertionDL.md b/en/licensed_annotator_entries/AssertionDL.md index fd994b983c..de66210190 100644 --- a/en/licensed_annotator_entries/AssertionDL.md +++ b/en/licensed_annotator_entries/AssertionDL.md @@ -33,6 +33,12 @@ Parameters: - `datasetInfo` *(Str)*: Descriptive information about the dataset being used. +- `blackList` *(list[str])*: If defined, list of entities to ignore. The rest will be processed. + +- `whiteList` *(list[str])*: If defined, list of entities to process. The rest will be ignored. Do not include IOB prefix on labels. + +- `caseSensitive` *(Bool)*: Determines whether the definitions of the white listed and black listed entities are case sensitive. Default: True. + For pretrained models please see the [Models Hub](https://nlp.johnsnowlabs.com/models?task=Assertion+Status) for available models. {%- endcapture -%} diff --git a/en/licensed_annotator_entries/BertSentenceChunkEmbeddings.md b/en/licensed_annotator_entries/BertSentenceChunkEmbeddings.md index 82870fbcdd..5d59868cfe 100644 --- a/en/licensed_annotator_entries/BertSentenceChunkEmbeddings.md +++ b/en/licensed_annotator_entries/BertSentenceChunkEmbeddings.md @@ -21,7 +21,11 @@ Parameters: - `caseSensitive`: Determines whether the definitions of the white listed entities are case sensitive. -All the parameters can be set using the corresponding set method in camel case. For example, `.setInputcols()`. +- `strategy`: Strategy for computing embeddings. Supported strategies are: `sentence_average`, `scope_average`, `chunk_only`, `scope_only`. The default is `sentence_average`. + +- `scopeWindow`: cope window to calculate scope embeddings. The scope window is defined by two non-negative integers. The default is [0, 0], which means only the chunk embeddings are used. The first integer defines the number of tokens before the chunk and the second integer defines the number of tokens after the chunk. + +All the parameters can be set using the corresponding set method in camel case. For example, `.setInputCols()`. > For more information and examples of `BertSentenceChunkEmbeddings` annotator, you can check the [Spark NLP Workshop](https://github.com/JohnSnowLabs/spark-nlp-workshop), and in special, the notebook [24.1.Improved_Entity_Resolution_with_SentenceChunkEmbeddings.ipynb](https://github.com/JohnSnowLabs/spark-nlp-workshop/blob/master/tutorials/Certification_Trainings/Healthcare/24.1.Improved_Entity_Resolution_with_SentenceChunkEmbeddings.ipynb). diff --git a/en/licensed_annotator_entries/ContextualEntityFilterer.md b/en/licensed_annotator_entries/ContextualEntityFilterer.md index 6b1afdb37d..1284acc9a2 100644 --- a/en/licensed_annotator_entries/ContextualEntityFilterer.md +++ b/en/licensed_annotator_entries/ContextualEntityFilterer.md @@ -24,6 +24,8 @@ Parameters: - `blackListWords`: The black list of words. If a word from this list appears within the scope window, the chunk will be filtered out. - `whiteListWords`: The white list of words. If a word from this list appears within the scope window, the chunk will be kept. - `confidenceThreshold`: The confidence threshold to filter the chunks. Filtering is only applied if the confidence of the chunk is below the threshold. + - `possibleRegexContext` : The possible regex context to filter the chunks. If the regex is found in the context(chunk), the chunk is kept. + - `impossibleRegexContext` : The impossible regex context to filter the chunks. If the regex is found in the context(chunk), the chunk is removed. {%- endcapture -%} diff --git a/en/licensed_annotator_entries/ContextualEntityRuler.md b/en/licensed_annotator_entries/ContextualEntityRuler.md index 603694ee98..41ddaba45f 100644 --- a/en/licensed_annotator_entries/ContextualEntityRuler.md +++ b/en/licensed_annotator_entries/ContextualEntityRuler.md @@ -14,11 +14,11 @@ It is particularly useful for refining entity recognition results according to s Parameters: -- `setCaseSensitive`: Whether to perform case-sensitive matching. Default is False. -- `setAllowPunctuationInBetween`: Whether to allow punctuation between prefix/suffix patterns and the entity. Default is True. -- `setDropEmptyChunks`: If True, removes chunks with empty content after applying rules. Default is False. -- `setCaseSensitive`: If True, it is case sensitive while checking the context. Default is False. -- `setMergeOverlapping`: If False, it returns both modified entities and the original entities at the same time. Default is True. +- `caseSensitive`: Whether to perform case-sensitive matching. Default is False. +- `allowPunctuationInBetween`: Whether to allow punctuation between prefix/suffix patterns and the entity. Default is True. +- `allowTokensInBetween`: Whether to allow tokens between prefix/suffix patterns and the entity. Default is False. +- `dropEmptyChunks`: If True, removes chunks with empty content after applying rules. Default is False. +- `mergeOverlapping`: If False, it returns both modified entities and the original entities at the same time. Default is True. - `rules`: The updating rules. Each rule is a dictionary with the following keys: - `entity`: The target entity label to modify. Example: `"AGE"`. @@ -38,9 +38,8 @@ Parameters: Example: `["\\b(old|young)\\b"]` matches words like "old" or "young" as suffixes. - `replaceEntity`: Optional string specifying the new entity label to replace with the target entity label. Example: `"MODIFIED_AGE"` replaces `"AGE"` with `"MODIFIED_AGE"` in matching cases. - - `mode`: Specifies the operational mode for the rules. - Possible values depend on the use case (e.g., `"include"`, `"exclude"`). - Default: `"include"` + - `mode`: Specifies the operational mode for the rules. Options: `include`, `exclude`, or `replace_label_only`. Default is `include`. + {%- endcapture -%} {%- capture model_input_anno -%} @@ -101,7 +100,6 @@ rules = [ { "replaceEntity" : "Modified_Date", "mode" : "include" } - ] contextual_entity_ruler = medical.ContextualEntityRuler() \ diff --git a/en/licensed_annotator_entries/DeIdentification.md b/en/licensed_annotator_entries/DeIdentification.md index 377bb03e95..545d90d58b 100644 --- a/en/licensed_annotator_entries/DeIdentification.md +++ b/en/licensed_annotator_entries/DeIdentification.md @@ -123,6 +123,10 @@ If True, the month will remain unchanged during the obfuscation process. If False, the month will be modified along with the year and day. Default: False. +- `keepTextSizeForObfuscation` : Whether to keep the text length same obfuscating entities. If `True`, the output text will remain the same if a same length fake is available, otherwise length might vary. + +- `fakerLengthOffset` : It specifies how much length deviation is accepted in obfuscation, with `keepTextSizeForObfuscation` enabled. It must be greater than 0. + To create a configured DeIdentificationModel, please see the example of DeIdentification. {%- endcapture -%} diff --git a/en/licensed_annotator_entries/FewShotAssertionClassifier.md b/en/licensed_annotator_entries/FewShotAssertionClassifier.md index dc2cbb00e6..f0b3fb813e 100644 --- a/en/licensed_annotator_entries/FewShotAssertionClassifier.md +++ b/en/licensed_annotator_entries/FewShotAssertionClassifier.md @@ -16,6 +16,9 @@ Parameters: - `batchSize` *(Int)*: Batch size - `caseSensitive` *(Bool)*: Whether the classifier is sensitive to text casing - `maxSentenceLength` *(Int)*: The maximum length of the input text +- `blackList` *(list[str])*: If defined, list of entities to ignore. The rest will be processed. +- `whiteList` *(list[str])*: If defined, list of entities to process. The rest will be ignored. Do not include IOB prefix on labels. +- `caseSensitive` *(Bool)*: Determines whether the definitions of the white listed and black listed entities are case sensitive. Default: True. {%- endcapture -%} diff --git a/feed.xml b/feed.xml index 1c2da3d492..f2906965e9 100644 --- a/feed.xml +++ b/feed.xml @@ -1,4 +1,4 @@ -Jekyll2025-01-20T18:46:09+00:00/feed.xmlSpark NLPHigh Performance NLP with Apache Spark +Jekyll2025-01-20T18:53:47+00:00/feed.xmlSpark NLPHigh Performance NLP with Apache Spark {"type"=>nil, "name"=>nil, "url"=>nil, "avatar"=>nil, "bio"=>nil, "email"=>nil, "facebook"=>nil, "twitter"=>nil, "weibo"=>nil, "googleplus"=>nil, "telegram"=>nil, "medium"=>nil, "zhihu"=>nil, "douban"=>nil, "linkedin"=>nil, "github"=>nil, "npm"=>nil}Clinical Deidentification Pipeline (Document Wise - Benchmark)2025-01-16T00:00:00+00:002025-01-16T00:00:00+00:00/2025/01/16/clinical_deidentification_docwise_benchmark_en## Description This pipeline can be used to deidentify PHI information from medical texts. The PHI information will be masked and obfuscated in the resulting text. The pipeline can mask and obfuscate `NAME`, `IDNUM`, `CONTACT`, `LOCATION`, `AGE`, `DATE` entities. diff --git a/sitemap.xml b/sitemap.xml index 6f5aa2ad2d..49430fc361 100644 --- a/sitemap.xml +++ b/sitemap.xml @@ -19355,4670 +19355,4670 @@ /assets/plugins/elegant_font/css/ -2025-01-20T18:44:21+00:00 +2025-01-20T18:51:51+00:00 /assets/plugins/jquery-match-height/test.html -2025-01-20T18:44:21+00:00 +2025-01-20T18:51:51+00:00 /assets/plugins/jquery-scrollTo/demo/ -2025-01-20T18:44:21+00:00 +2025-01-20T18:51:51+00:00 /assets/plugins/jquery-scrollTo/demo/index.old.html -2025-01-20T18:44:21+00:00 +2025-01-20T18:51:51+00:00 /assets/plugins/jquery-scrollTo/tests/ElemMaxY-compat.html -2025-01-20T18:44:21+00:00 +2025-01-20T18:51:51+00:00 /assets/plugins/jquery-scrollTo/tests/ElemMaxY-quirks.html -2025-01-20T18:44:21+00:00 +2025-01-20T18:51:51+00:00 /assets/plugins/jquery-scrollTo/tests/WinMaxY-compat.html -2025-01-20T18:44:21+00:00 +2025-01-20T18:51:51+00:00 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