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Unsupervised domain adaptation method for relation extraction
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data first commit Mar 21, 2018
models Update Jul 16, 2018 Update Apr 5, 2018 first commit Mar 21, 2018


This repo contains code for our unsupervised domain adaptation method for relation extraction.

Note: Examples of the data format can be found in the data/ folder.



python --num_epochs 50 --checkpoint_dir /checkpoint/dir/experiments/checkpoints/ --checkpoint_name my_checkpoint --min_df 5 --lr 0.001 --penalty 0. --adv_train_data_X  /my/data/data1/all_train.txt --adv_test_data_X  /my/data/biogrid_train_test/all_test.txt --test_data /my/data/test_data.txt --train_data /my/data/train_data.txt --train_data_X /my/data/data2/train.txt --val_data_X /my/data/data2/test.txt --num_iters 10000 --num_disc_updates 1 --emb_reg --adv --pos_reg --hidden_state 128 --adv --seed 42
usage: [-h] [--num_epochs NUM_EPOCHS]
                          [--hidden_state HIDDEN_STATE]
                          [--checkpoint_dir CHECKPOINT_DIR]
                          [--checkpoint_name CHECKPOINT_NAME]
                          [--min_df MIN_DF] [--lr LR] [--penalty PENALTY]
                          [--train_data_X TRAIN_DATA_X]
                          [--train_data TRAIN_DATA] [--test_data TEST_DATA]
                          [--val_data_X VAL_DATA_X]
                          [--adv_train_data_X ADV_TRAIN_DATA_X]
                          [--adv_test_data_X ADV_TEST_DATA_X]
                          [--num_iters NUM_ITERS] [--grad_clip GRAD_CLIP]
                          [--num_disc_updates NUM_DISC_UPDATES] [--seed SEED]
                          [--adv] [--emb_reg] [--pos_reg]

Train Neural Network.

optional arguments:
  -h, --help            show this help message and exit
  --num_epochs NUM_EPOCHS
                        Number of updates to make.
  --hidden_state HIDDEN_STATE
                        LSTM hidden state size.
  --checkpoint_dir CHECKPOINT_DIR
                        Checkpoint directory.
  --checkpoint_name CHECKPOINT_NAME
                        Checkpoint File Name.
  --min_df MIN_DF       Min word count.
  --lr LR               Learning Rate.
  --penalty PENALTY     Regularization Parameter.
  --train_data_X TRAIN_DATA_X
                        Training Data.
  --train_data TRAIN_DATA
                        Training Data.
  --test_data TEST_DATA
                        Training Data.
  --val_data_X VAL_DATA_X
                        Validation Data.
  --adv_train_data_X ADV_TRAIN_DATA_X
                        Validation Data.
  --adv_test_data_X ADV_TEST_DATA_X
                        Validation Data.
  --num_iters NUM_ITERS
                        Validation Data.
  --grad_clip GRAD_CLIP
                        Gradient Clip Value.
  --num_disc_updates NUM_DISC_UPDATES
                        Number of time to update discriminator.
  --seed SEED           Random seed.
  --adv                 Adversarial training?
  --emb_reg             Regularize word embeddings?
  --pos_reg             Regularize pos embeddings?


Anthony Rios, Ramakanth Kavuluru, and Zhiyong Lu. "Generalizing Biomedical Relation Classification with Neural Adversarial Domain Adaptation". Bioinformatics 2018

  title={Generalizing Biomedical Relation Classification with Neural Adversarial Domain Adaptation},
  author={Rios, Anthony and Kavuluru, Ramakanth and Lu, Zhiyong},

Written by Anthony Rios (anthonymrios at gmail dot com)

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