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Amazon Sagemaker

Amazon SageMaker is a fully-managed platform that enables developers and data scientists to quickly and easily build, train, and deploy machine learning models at any scale. With Amazon SageMaker, all the barriers and complexity that typically slow down developers who want to use machine learning are removed. The service includes models that can be used together or independently to build, train, and deploy your machine learning models.

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Extract Biomarkers Free trial

By:
John Snow Labs
Latest Version:
5.5.4
This model extracts biomarkers, classifies their presence, and links related entities in clinical text
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    Product Overview

    This model is specifically designed to meticulously extract biomarker entities from a diverse array of clinical documents, such as research articles, patient records, and lab reports. By employing sophisticated natural language processing techniques, the model not only detects these critical entities but also classifies sentences to ascertain the presence of biomarkers, providing a nuanced understanding of their context and relevance. Furthermore, it establishes intricate relationships between the extracted entities, which is pivotal for constructing a comprehensive biomarker network. Such capabilities enhance the precision of clinical assessments and facilitate a deeper understanding of patient conditions, potentially leading to more personalized and effective medical interventions.

    Key Data

    Version
    5.5.4
    Usage Instructions
    Release Notes
    By
    John Snow Labs
    Categories
    ML Solutions
    Names Entity Recognition - NER
    Healthcare & Life Sciences
    Type
    Model Package
    Fulfillment Methods
    Amazon SageMaker

    Highlights

    • Extracted Clinical Entity Labels:

      • Biomarker
      • Biomarker_Result

      Relation Extraction Labels: is_finding_of

      Classification Model Labels: 1, 0 Classifies sentences to identify the presence(1) or absence(0) of biomarker entities.

    • Process up to 2 M chars per hour for real-time and up to 3.4 M chars per hour for batch mode.

    Not quite sure what you’re looking for? AWS Marketplace can help you find the right solution for your use case. Contact us

    Pricing Information

    Use this tool to estimate the software and infrastructure costs based your configuration choices. Your usage and costs might be different from this estimate. They will be reflected on your monthly AWS billing reports.

    Contact us to request contract pricing for this product.


    Estimating your costs

    Choose your region and launch option to see the pricing details. Then, modify the estimated price by choosing different instance types.

    Version
    Region

    Software Pricing

    Model Realtime Inference$23.76/hr

    running on ml.m4.xlarge

    Model Batch Transform$47.52/hr

    running on ml.m4.2xlarge

    Infrastructure Pricing

    With Amazon SageMaker, you pay only for what you use. Training and inference is billed by the second, with no minimum fees and no upfront commitments. Pricing within Amazon SageMaker is broken down by on-demand ML instances, ML storage, and fees for data processing in notebooks and inference instances.
    Learn more about SageMaker pricing

    SageMaker Realtime Inference$0.24/host/hr

    running on ml.m4.xlarge

    SageMaker Batch Transform$0.48/host/hr

    running on ml.m4.2xlarge

    About Free trial

    Try this product for 15 days. There will be no software charges, but AWS infrastructure charges still apply. Free Trials will automatically convert to a paid subscription upon expiration.

    Model Realtime Inference

    For model deployment as Real-time endpoint in Amazon SageMaker, the software is priced based on hourly pricing that can vary by instance type. Additional infrastructure cost, taxes or fees may apply.
    InstanceType
    Realtime Inference/hr
    ml.m4.xlarge
    Vendor Recommended
    $23.76

    Usage Information

    Model input and output details

    Input

    Summary
    1. Array of Text Documents { "text": [
       "Text document 1",
 "Text document 2",
 ...
      ] }
    2. Single Text Document { "text": "Single text document" }
      1. JSON Lines (JSONL) Format {"text": "Text document 1"} {"text": "Text document 2"}
    Input MIME type
    application/json, application/jsonlines
    Sample input data
    Expand all input descriptions
    Field name
    text
    Description
    The text of the document that is to be analyzed.
    Required
    Yes
    Data type
    FreeText

    Output

    Summary

    The output provided by the model consists of a JSON object, the detailed information of the structure can be found here

    Output MIME type
    application/json, application/jsonlines
    Sample output data
    Expand all output descriptions
    Field name
    ner_predictions
    Description
    Array containing information about the named entity chunk, label of the detected entity for the chunk,confidence score
    Always returned
    Yes
    Data type
    FreeText
    Field name
    ner_chunk
    Description
    The text of the entity
    Always returned
    Yes
    Data type
    FreeText
    Field name
    begin
    Description
    Starting index of the named entity chunk within the document.
    Always returned
    Yes
    Data type
    Integer
    Range
    Field name
    end
    Description
    Ending index of the named entity chunk within the document.
    Always returned
    Yes
    Data type
    Integer
    Range
    Field name
    ner_label
    Description
    The label of the entity, as determined by the NER model.
    Always returned
    Yes
    Data type
    Categorical
    Allowed values
    Biomarker, Biomarker_Result
    Field name
    ner_confidence
    Description
    Confidence score associated with the NER prediction
    Always returned
    Yes
    Data type
    Continuous (Float)
    Range
    Min: 0
    Max: 1
    Field name
    relation_predictions
    Description
    Array with information about the relation type between two specific labels of two different text chunks and the confidence score for that relation type
    Always returned
    Yes
    Data type
    FreeText
    Field name
    ner_chunk1
    Description
    First named entity involved in the relation.
    Always returned
    Yes
    Data type
    FreeText
    Field name
    ner_chunk1_begin
    Description
    Starting index of the first named entity chunk within the document.
    Always returned
    Yes
    Data type
    Integer
    Range
    Field name
    ner_chunk1_end
    Description
    Ending index of the first named entity chunk within the document.
    Always returned
    Yes
    Data type
    Integer
    Range
    Field name
    ner_label1
    Description
    Label assigned to the first named entity.
    Always returned
    Yes
    Data type
    Categorical
    Allowed values
    Biomarker, Biomarker_Result
    Field name
    ner_chunk2
    Description
    Second named entity involved in the relation.
    Always returned
    Yes
    Data type
    FreeText
    Field name
    ner_chunk2_begin
    Description
    Starting index of the second named entity chunk within the document.
    Always returned
    Yes
    Data type
    Integer
    Range
    Field name
    ner_chunk2_end
    Description
    Ending index of the second named entity chunk within the document.
    Always returned
    Yes
    Data type
    Integer
    Range
    Field name
    ner_label2
    Description
    Label assigned to the second named entity.
    Always returned
    Yes
    Data type
    Categorical
    Allowed values
    Biomarker, Biomarker_Result
    Field name
    relation
    Description
    Type of relation identified.
    Always returned
    Yes
    Data type
    Categorical
    Allowed values
    is_finding_of
    Field name
    relation_confidence
    Description
    Confidence score associated with the relation prediction.
    Always returned
    Yes
    Data type
    Integer
    Range
    Field name
    classification_predictions
    Description
    Array with infrmation about extracted sentences, predicted class the for each sentence whether they contain biomarker entities or not, and the confidence score associated with the predicted class.
    Always returned
    Yes
    Data type
    FreeText
    Field name
    sentence
    Description
    The extracted sentence from the document.
    Always returned
    Yes
    Data type
    FreeText
    Field name
    begin
    Description
    The starting character index of the sentence within the document.
    Always returned
    Yes
    Data type
    Integer
    Range
    Field name
    end
    Description
    The ending character index of the sentence within the document.
    Always returned
    Yes
    Data type
    Integer
    Range
    Field name
    class
    Description
    The predicted label for the corresponding sentence.
    Always returned
    Yes
    Data type
    Categorical
    Allowed values
    1, 0
    Field name
    class_confidence
    Description
    The confidence score associated with the predicted class, indicating the model's certainty in its prediction.
    Always returned
    Yes
    Data type
    Continuous (Float)
    Range
    Min: 0
    Max: 1

    Sample notebook

    Additional Resources

    End User License Agreement

    By subscribing to this product you agree to terms and conditions outlined in the product End user License Agreement (EULA)

    Support Information

    Extract Biomarkers

    For any assistance, please reach out to support@johnsnowlabs.com.

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