Sold by: Waltsoft Inc.
Deployed on AWS
104K monthly downloads. 107-class biomedical NER for FDA submissions, pharmacovigilance, and clinical trial data extraction. Apache-2.0 licensed.
Overview
Biomedical NER All is a token-classification model that extracts 107 distinct biomedical entity types including diseases, drugs, genes, proteins, anatomical structures, clinical procedures, and molecular compounds. Built on BioBERT fine-tuned across multiple biomedical NER corpora (NCBI Disease, BC5CDR, JNLPBA, and others), it provides comprehensive entity coverage for pharmaceutical, regulatory, and clinical informatics pipelines. FDA submissions require structured extraction of adverse events, drug names, and conditions from unstructured clinical text -- this model automates that extraction at scale. At 268MB with Apache-2.0 licensing, it is the most comprehensive open biomedical NER model deployable on commercial infrastructure. Deployed on SageMaker with batch transform for processing research papers, trial protocols, and pharmacovigilance reports.
Highlights
- 107 biomedical entity classes: diseases, drugs, genes, proteins, procedures, and compounds
- Apache-2.0 licensed -- commercially deployable for FDA pharmacovigilance and clinical trial pipelines
- Batch transform support for high-volume processing of medical literature and regulatory documents
Details
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Deployed on AWS
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Dimension | Description | Cost/host/hour |
|---|---|---|
ml.m5.xlarge Inference (Real-Time) Recommended | Model inference on the ml.m5.xlarge instance type, real-time mode | $0.10 |
ml.m5.xlarge Inference (Batch) Recommended | Model inference on the ml.m5.xlarge instance type, batch mode | $0.10 |
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Delivery details
Amazon SageMaker model
An Amazon SageMaker model package is a pre-trained machine learning model ready to use without additional training. Use the model package to create a model on Amazon SageMaker for real-time inference or batch processing. Amazon SageMaker is a fully managed platform for building, training, and deploying machine learning models at scale.
Deploy the model on Amazon SageMaker AI using the following options:
Version release notes
Initial release
Additional details
Inputs
- Summary
104K monthly downloads. 107-class biomedical NER for FDA submissions, pharmacovigilance, and clinical trial data extraction. Apache-2.0 licensed.
- Input MIME type
- application/json
https://waltsoft-marketplace-assets.s3.amazonaws.com/ml-validation/text-sample/sample.jsonl
https://waltsoft-marketplace-assets.s3.amazonaws.com/ml-validation/text-sample/sample.jsonl
Support
Vendor support
Contact support@waltsoft.net for deployment assistance.
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