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Build an ML classifier to match procedure at each site to a ground truth ontology defined by imaging repository (radlex/LOINC)

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Sharing is Caring: Medical image consolidation using machine learning

Description

This work started off as a course project, so the code acts as an archive of methods we explored.

main.py contains the code to generate the evaluation in the paper. A majority of the code was run on a server with a 14 core/28 thread Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz. The server has 128Gb of ram and Nvidia Quadro P4000 (8Gb). On this server, training took anywhere from under a minute up to 12 hours depending on the representation/model used.

Directory Structure

input_data/ contains the input data as csv (not uploaded due to privacy concerns/restrictions)

output/ should be where all output is stored

data_reader.py contains DataReader which is a class that reads csv's from input_data and presents them as a pandas dataframe

data_manipulator.py is a library that has functions for manipulating data, such as splitting the dataframe into train/test

Models/ Contains all the models we tried

main.py shows the code used to generate results shown in the paper.

Development

To get started, download the .csv files from the Google Drive and paste them into input_data. From there, you can do the following:

* To create a new model, create a new subclass of Model in Models. Implement the abstract methods of Models and add any additional needed methods.

* To modify how data is read, add a method to the DataReader class inside data_reader.py

* To transform the data, implement a method inside data_manipulator.py
    
* Run main.py to see results

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Build an ML classifier to match procedure at each site to a ground truth ontology defined by imaging repository (radlex/LOINC)

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