Please cite the following two papers if you are using our tool. Thanks!

• Jingbo Shang*, Liyuan Liu*, Xiaotao Gu, Xiang Ren, Teng Ren and Jiawei Han, "Learning Named Entity Tagger using Domain-Specific Dictionary", in Proc. of 2018 Conf. on Empirical Methods in Natural Language Processing (EMNLP'18), Brussels, Belgium, Oct. 2018. (* Equal Contribution)
• Jingbo Shang, Jialu Liu, Meng Jiang, Xiang Ren, Clare R Voss, Jiawei Han, "Automated Phrase Mining from Massive Text Corpora", accepted by IEEE Transactions on Knowledge and Data Engineering, Feb. 2018.

• Tokenized Raw Texts
  • Example: data/BC5CDR/raw_text.txt
    • One token per line.
    • An empty line means the end of a sentence.
• Two Dictionaries
  • Core Dictionary w/ Type Info
    • Example: data/BC5CDR/dict_core.txt
      • Two columns (i.e., Type, Tokenized Surface) per line.
      • Tab separated.
    • How to obtain?
      • From domain-specific dictionaries.
  • Full Dictionary w/o Type Info
    • Example: data/BC5CDR/dict_full.txt
      • One tokenized high-quality phrases per line.
    • How to obtain?
      • From domain-specific dictionaries.
      • Applying the high-quality phrase mining tool on domain-specific corpus.
        • AutoPhrase
• Pre-trained word embeddings
  • Train your own or download from the web.
  • The example run uses embedding/bio_embedding.txt, which can be downloaded from our group's server
• [Optional] Development & Test Sets.
  • Example: data/BC5CDR/truth_dev.ck and data/BC5CDR/truth_test.ck
    • Three columns (i.e., token, Tie or Break label, entity type).
    • I is Berak.
    • O is Tie.
    • Two special tokens <s> and <eof> mean the start and end of the sentence.

First, let's create a conda environment using Python 3 and pytorch 0.3.0.

conda create -n env_autoner python=3 mkl=2018 pytorch=0.3.0 -c pytorch -c intel

Then, activate this environment.

source activate env_autoner

Install some more packages (i.e., tqdm and tensorboardx).

conda install -c conda-forge tqdm
conda install -c conda-forge tensorboardx

To train an AutoNER model, please run

./autoner_train.sh

To apply the trained AutoNER model, please run

./autoner_test.sh

You can specify the parameters in the bash files. The variables names are self-explained.