https://github.com/nlpatvcu/medacy_model_clinical_notes

A medaCy compatible model for clinical note information extraction.
https://github.com/nlpatvcu/medacy_model_clinical_notes

Last synced: about 1 year ago
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A medaCy compatible model for clinical note information extraction.

• Host: GitHub
• URL: https://github.com/nlpatvcu/medacy_model_clinical_notes
• Owner: NLPatVCU
• License: gpl-3.0
• Created: 2018-12-23T21:42:12.000Z (over 7 years ago)
• Default Branch: master
• Last Pushed: 2020-05-25T19:22:52.000Z (about 6 years ago)
• Last Synced: 2025-03-29T06:11:18.649Z (about 1 year ago)
• Language: Python
• Size: 14.1 MB
• Stars: 11
• Watchers: 4
• Forks: 4
• Open Issues: 3
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
[![spaCy](https://img.shields.io/badge/built%20with-spaCy-09a3d5.svg)](https://spacy.io)

# medaCy

:hospital: Clinical Notes Model for medaCy :hospital:

This repository contains a versioned, medaCy compatible Model for information extraction from clinical notes.

![alt text](https://nlp.cs.vcu.edu/images/Edit_NanomedicineDatabase.png "Nanoinformatics")

# Description

This is the light-weight version (no metamap) of medaCy's model for extracting 9 unique entities from clinical notes:

`Drug, Strength, Duration, Route, Form, ADE, Dosage, Reason, Frequency`

# Results

Model generalization ability is evaluated over 202 patient clinical note files not seen during training. *Strict* indicates exact matches of spans, *Lenient* indicates a fuzzy matching of spans (model predictions are off by single characters).

| Entities | Strict | Lenient |

| :-------: | :----------------: |:-------------:|

|Drug| | |  |

|Strength|  |  |

|Duration | |  |

|Route | |  |

|Form | |  |

|ADE | |  |

|Dosage | |  |

|Reason | |  |

|Frequency | |  |

|**System** | |  |

# Training Data

N2C2 2018 Shared Task

The data used to induce this model is protected by HIPAA privacy regulations and thus cannot be published.

Authors

=======

Andriy Mulyar and Bridget McInnes

Acknowledgments

===============

- [VCU Natural Language Processing Lab](https://nlp.cs.vcu.edu/)     ![alt text](https://nlp.cs.vcu.edu/images/vcu_head_logo "VCU")

- [Nanoinformatics Vertically Integrated Projects](https://rampages.us/nanoinformatics/)