medkit - documentation

medkit is a Python library for facilitating the extraction of features from various modalities of patient data: text, audio for now - relational, image, genetic, and others soon. To this end, medkit offers to compose pipelines with modules, developed by us, yourself or others.

We pay particular attention to enable the implementation of non-destructive pipelines (no loss of information when passing from a module to another) and a flexible tracing of data provenance.

medkit aims at accelerating the development of a learning health system, with a strong open-source and community orientation.

Warning

medkit core library is still under development and testing. Some interfaces may change in the future.

This library with its documentation is shared for following reasons:

• helping people with some guidelines for using first medkit versions,

• helping core development team to get user feedback for improving the medkit library.

User Guide

• Installation
• First steps
• Using pipelines
• Provenance tracing
• Make your own module

Medkit components

• Core components
• Text operation modules
• Metrics
• Audio operations
• Metrics
• I/O components
• Training module
• Tools

Examples

• Text spans
• Cleaning text with a predefined operation
• Text segmentation examples
  • Section Tokenizer
  • Syntagma Tokenizer
  • Document splitter
• Brat integration
• Spacy integration
• Creating a custom text operation
• Using EDS-NLP with medkit
• IAMSystem Matcher
• Fine-tuning a Transformers model with medkit
• Detecting text duplicates

API reference

• Generated API documentation
  • medkit.core
  • medkit.text
  • medkit.audio
  • medkit.io
  • medkit.training
  • medkit.tools