Creating large datasets for biomedical relation classification can be prohibitively expensive. While some datasets have been curated to extract protein-protein and drug-drug interactions from text, we are also interested in other interactions including gene-disease and chemical-protein connections. Also, many biomedical researchers have begun to explore ternary relationships. Even when annotated data is available, many datasets used for relation classification are inherently biased. For example, issues such as sample selection bias typically prevent models from generalizing in the wild. To address the problem of cross-corpora generalization, in this repository, we host code for a novel adversarial learning algorithm for unsupervised domain adaptation tasks where no labeled data is available for the target domain. Instead, our method takes advantage of unlabeled data to improve biased classifiers by learning domain-invariant features via a 2-stage adversarial training process using neural networks.
Note: Examples of the data format can be found in the data/ directory and the source code for the models are available in the models/ directory.
Below we display an example command-line configuration to train a new model from scratch:
python train_final_cnn.py --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
The available command-line arguments are listed below:
usage: train_final_cnn.py [-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?
val_data should contain a list of IDs in the source dataset to use to avoid over-fitting during stage 1 of the training process. We provide examples of the format and structure of the train, dev, and test datasets in the data/ directory. Also, note that while we checkpoint the model using the checkpoint_dir and checkpoint_name parameters, after stage 2 of the training process the provided source code will also make predictions on the provided test data if the test_data_X (the target test set) is used.
If you find this useful or relevant to your research, please cite the following paper:
Anthony Rios, Ramakanth Kavuluru, and Zhiyong Lu. "Generalizing Biomedical Relation Classification with Neural Adversarial Domain Adaptation". Bioinformatics 2018
@article{rios2018advrel,
title={Generalizing Biomedical Relation Classification with Neural Adversarial Domain Adaptation},
author={Rios, Anthony and Kavuluru, Ramakanth and Lu, Zhiyong},
journal={Bioinformatics},
year={2018}
}
Written by Anthony Rios (anthonymrios at gmail dot com)