Installation

Getting started with BioMedICUS

Prerequisites

Create a Virtual Environment

We recommend that you use a Python 3 virtual environment, a local environment of installed packages, to avoid any dependency conflicts.

Linux / MacOS

pip3 install virtualenv
python3 -m virtualenv biomedicus_venv
source biomedicus_venv/bin/activate

Windows

pip3 install virtualenv
python3 -m virtualenv biomedicus_venv
biomedicus_venv\Scripts\activate

Install PyTorch Libraries

BioMedICUS requires PyTorch, a machine learning framework. Installation instructions for PyTorch can be found here. Select your platform and “Pip”, and “None” for CUDA unless you have a NVIDIA graphics card and have installed the CUDA toolkit.

Install BioMedICUS

pip3 install biomedicus

This will install two packages, biomedicus and biomedicus_client, with the command line programs b9 and b9client respectively. The main biomedicus package contains all of the BioMedICUS processor servers and the biomedicus_client package contains functionality for connecting to the servers and processing documents.

Deploy the default BioMedICUS processors

The following command runs a script that will start up all of the BioMedICUS services for processing clinical notes:

b9 deploy

It will ask you to download the BioMedICUS model files if you have not already.

Process a directory of text files using BioMedICUS

After deploying BioMedICUS, you can process a directory of documents using the following command:

b9client run --include-label-text /path/to/input_dir -o /path/to/output_dir

This will process the documents in the directory using BioMedICUS and save the results as json-serialized MTAP Events to output directory.

Viewing results

The default BioMedICUS pipeline and run command will serialize the documents as json. By default the files are not prettified, but you can do that by running the following:

python -m json.tool /path/to/output_file.json