NeuroNER is a program that performs named-entity recognition (NER). Website: neuroner.com.

This page gives step-by-step instructions to install and use NeuroNER. If you already have Python 3.5 and TensorFlow 1.0, you can directly jump to the Running NeuroNER section.

Alternatively, you can use this installation script for Ubuntu, which:

1. Installs TensorFlow (CPU only), Python 3.5, and BRAT.
2. Downloads the NeuroNER code as well as word embeddings.
3. Starts training on the CoNLL-2003 dataset (the F1-score on the test set should be around 0.90, i.e. on par with state-of-the-art systems).

To use this script, run the following command from the terminal:

wget https://raw.githubusercontent.com/Franck-Dernoncourt/NeuroNER/master/install_ubuntu.sh; bash install_ubuntu.sh

NeuroNER relies on BRAT, Python 3.5, and TensorFlow 1.0:

• BRAT is a web-based annotation tool. It only needs to be installed if you wish to conveniently create annotations or view the predictions made by NeuroNER. Official website: http://brat.nlplab.org
• Python 3.5: NeuroNER does not work with Python 2.x.
• TensorFlow is a library for machine learning. NeuroNER uses it for its NER engine, which is based on neural networks. Official website: https://www.tensorflow.org/

Installation instructions for TensorFlow, Python 3.5, and (optional) BRAT are given below for different types of operating systems:

• Mac
• Ubuntu
• Windows

###Running NeuroNER

To download NeuroNER code, download and unzip http://neuroner.com/NeuroNER-master.zip, which can be done on Ubuntu and Mac OS X with:

wget https://github.com/Franck-Dernoncourt/NeuroNER/archive/master.zip
sudo apt-get install -y unzip
unzip master.zip

It also needs some word embeddings, which should be downloaded from http://neuroner.com/data/word_vectors/glove.6B.100d.zip, unzipped and placed in /data/word_vectors. This can be done on Ubuntu and Mac OS X with:

# Download some word embeddings
mkdir NeuroNER-master/data/word_vectors
cd NeuroNER-master/data/word_vectors
wget http://neuroner.com/data/word_vectors/glove.6B.100d.zip
unzip glove.6B.100d.zip

NeuroNER is now ready to run! By default NeuroNER is configured to train and test on CoNLL-2003. To start the training:

# To use the CPU if you have installed tensorflow, or use the GPU if you have installed tensorflow-gpu:
python3.5 main.py

# To use the CPU only if you have installed tensorflow-gpu:
CUDA_VISIBLE_DEVICES="" python3.5 main.py

# To use the GPU 1 only if you have installed tensorflow-gpu:
CUDA_VISIBLE_DEVICES=1 python3.5 main.py

If you wish to change the dataset or NeuroNER parameters, you should change the src/parameters.ini configuration file.