Huang D., Jiang Z., Zou L., Li L. Drug–drug interaction extraction from biomedical literature using support vector machine and long short term memory networks Information Sciences, Volumes 415-416, 2017
git clone [email protected]:yardstick17/DDIExtraction.git
#cd to root directory
bash setup.shPYTHONPATH='.' python main.py
total_files_to_read: 569 from dir: /home/kushwaha/ddi/dataset/DDICorpus/Train/DrugBank/
100%|██████████████████████████████████████████████████████████████████████████████████████████████████| 569/569 [00:01<00:00, 326.29it/s]
total_files_to_read: 569 from dir: /home/kushwaha/ddi/dataset/DDICorpus/Train/DrugBank/
100%|██████████████████████████████████████████████████████████████████████████████████████████████████| 569/569 [00:01<00:00, 370.86it/s]
total_files_to_read: 569 from dir: /home/kushwaha/ddi/dataset/DDICorpus/Train/DrugBank/
100%|██████████████████████████████████████████████████████████████████████████████████████████████████| 569/569 [00:01<00:00, 353.40it/s]
frequent_phrase: [('(e_be', ',_af'), ('(e_be', ',_be'), ('(e_be', '._af'), ('(e_be', '._be'), ('(e_be', 'DRUG')]
total_files_to_read: 569 from dir: /home/kushwaha/ddi/dataset/DDICorpus/Train/DrugBank/
100%|██████████████████████████████████████████████████████████████████████████████████████████████████| 569/569 [00:01<00:00, 361.73it/s]
Unnamed: 0 sentence_text e1 e2 relation_type normalized_sentence
0 0 CANCIDAS reduced the blood AUC0-12 of tacrolim... CANCIDAS tacrolimus mechanism DRUG reduced_be blood_be AUC0-12_be OTHER_DRUG...
1 1 In two clinical studies, cyclosporine (one 4 m... cyclosporine caspofungin mechanism In_bf two_bf clinical_bf studies_bf ,_bf DRUG ...
2 2 There were transient increases in liver ALT an... CANCIDAS cyclosporine effect There_bf transient_bf increases_bf liver_bf AL...
3 3 A drug-drug interaction study with rifampin in... rifampin caspofungin mechanism A_bf drug-drug_bf interaction_bf study_bf DRUG...
4 4 Patients on rifampin should receive 70 mg of C... rifampin CANCIDAS advise Patients_bf DRUG receive_be 70_be mg_be OTHER_...
X: (3006, 26667) Y : [3006]
Score : 0.897009966777
precision recall f1-score support
0 0.88 0.90 0.89 239
1 0.92 0.79 0.85 29
2 0.93 0.89 0.91 194
3 0.88 0.92 0.90 140
avg / total 0.90 0.90 0.90 602
total_files_to_read: 158 from dir: /home/kushwaha/ddi/dataset/DDICorpus/Test/test_for_ddi_extraction_task/DrugBank/
100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 158/158 [00:00<00:00, 327.99it/s]
precision recall f1-score support
0 0.65 0.87 0.74 232
1 0.62 0.12 0.21 80
2 0.86 0.82 0.84 224
3 0.75 0.73 0.74 160
avg / total 0.74 0.74 0.71 696
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