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README.md

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+# Adversarial
+
+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.
+
+## Usage
+### Training
+
+```
+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
+```
+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?
+```

data/example_data.txt

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+Recent studies have provided consistent evidence that treatment with abatacept results in a rapid onset of efficacy that is maintained over the course of treatment in patients with inadequate response to DRUGB and anti- DRUGA therapies .
+16357751.s1	16357751	T1	T2	OTHER
+
+DRUGA inhibitors currently under investigation include the small molecules DRUGB ( Iressa , ZDdgdgdgdg ) and erlotinib ( Tarceva , OSI-dgdgdg ) , as well as monoclonal antibodies such as cetuximab ( IMC-dgdgdg , Erbitux ) .
+14967461.s1	14967461	T22	T1	CLASS1
+
+Taken together , the results of the present study have characterized DRUGA as an inhibitor of matriptase-dg that modulates the synthesis of hepcidin and provides new insights into the regulatory mechanism of DRUGB homoeostasis , with clinical importance for a treatment of iron overload diseases .
+23293962.s1	23293962	T5	T1	OTHER
+
+Taken together , the results of the present study have characterized HAI-dg as an inhibitor of matriptase-dg that modulates the synthesis of DRUGA and provides new insights into the regulatory mechanism of iron homoeostasis , with clinical importance for a treatment of DRUGB overload diseases .
+23293962.s1	23293962	T7	T2	OTHER
+
+DRUGB and bromoacetylalprenololmenthane are competitive slowly reversible antagonists at the DRUGA of rat left atria .
+7678677.s1	7678677	T14	T19	CLASS1
+
+Alprenolol and DRUGB are competitive slowly reversible antagonists at the DRUGA of rat left atria .
+7678677.s1	7678677	T15	T19	CLASS1
+
+DRUGA was chemically bound via linkers to DRUGB -loaded HSA-NP .
+16554356.s1	16554356	T10	T3	OTHER
+
+Apolipoprotein E was chemically bound via linkers to DRUGB -loaded DRUGA -NP .
+16554356.s1	16554356	T3	T11	OTHER
+
+Discovery and optimization of DRUGB as inhibitors of methionine aminopeptidase-dg : a structural basis for the reduction of DRUGA binding .
+16789740.s1	16789740	T4	T13	CLASS1
+
+Discovery and optimization of DRUGB as inhibitors of DRUGA : a structural basis for the reduction of albumin binding .
+16789740.s1	16789740	T4	T14	OTHER
+
+BACKGROUND : Since the introduction of the first DRUGA inhibitor ( ChEI ) in dgdgdgdg , most clinicians and probably most patients would consider the cholinergic drugs , DRUGB , galantamine and rivastigmine , to be the first line pharmacotherapy for mild to moderate Alzheimer 's disease.The drugs have slightly different pharmacological properties , but they all work by inhibiting the breakdown of acetylcholine , an important neurotransmitter associated with memory , by blocking the enzyme acetylcholinesterase .
+16437532.s1	16437532	T39	T11	CLASS1
+
+Mitiglinide ( DRUGB ) , a new anti-diabetic drug , is thought to stimulate insulin secretion by closing the DRUGA in pancreatic beta-cells .
+11716850.s1	11716850	T15	T42	CLASS1

data/train_dev_test/dev_ids.txt

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+14967461
+16357751
+23293962

data/train_dev_test/test_ids.txt

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+23293962
+7678677

data/train_dev_test/train_ids.txt

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+11716850
+16437532
+16554356
+16789740