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Human-Machine Information Extraction Simulator for Biological Collections

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HuMaIN Simulator

Description

The digitization of biocollections is typically performed through crowdsourcing (volunteers) because of the errors that automated information extraction (IE) methods generate.
More specifically, Optical Character Recognition technology still generates errors. The segmentation process and the AI recognition models for handwritten text are two of the most challenging cases.
The HuMaIN simulator expects to promote and accelerate the research in semi-automated IE from biocollections.
The simulated tasks are tasks for which the results have already been computed.
The general recommendation is to simulate all the tasks, except that one that you are trying to improve.

Acknowledgment

HuMaIN is funded by a grant from the National Science Foundation's ACI Division of Advanced Cyberinfrastructure (Award Number: 1535086). Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

Installation

The HuMaIN Simulator requires Python 3 installed in your computer. Please refer to https://www.python.org/downloads/ for instructions about how to download and install Python 3 in your operating system.
To verify the version of Python installed in your computer run:

python3 --version

You should get an answer similar to the following:

Python 3.7.2

The steps to install the simulator are the following:

1) Clone the HuMaIN Simulator repository.

From https://github.com/acislab/HuMaIN_Simulator, download the repository as a zip file and locally extract its content, or clone it with git:

git clone https://github.com/acislab/HuMaIN_Simulator

2) Update the home directory of the simulator.

In the [Installation_Path]/HuMaIN_Simulator/humain/common/constants.py file, update the value of BASE_DIR to the path of the HuMaIN_Simulator in your computer.

3) Update the PYTHONPATH value.

Add the HuMaIN_Simulator directory to PYTHONPATH environment variable of your operating system. For example, in Ubuntu Linux, add the following line to the ~/.bashrc file:

export PYTHONPATH=$PYTHONPATH:.:/home/user/HuMaIN_Simulator

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