IMSE: interaction information attention and molecular structure based drug drug interaction extraction

BACKGROUND: Extraction of drug drug interactions from biomedical literature and other textual data is an important component to monitor drug-safety and this has attracted attention of many researchers in healthcare. Existing works are more pivoted around relation extraction using bidirectional long short-term memory networks (BiLSTM) and BERT model which does not attain the best feature representations. RESULTS: Our proposed DDI (drug drug interaction) prediction model provides multiple advantages: (1) The newly proposed attention vector is added to better deal with the problem of overlapping relations, (2) The molecular structure information of drugs is integrated into the model to better express the functional group structure of drugs, (3) We also added text features that combined the T-distribution and chi-square distribution to make the model more focused on drug entities and (4) it achieves similar or better prediction performance (F-scores up to 85.16%) compared to state-of-the-art DDI models when tested on benchmark datasets. CONCLUSIONS: Our model that leverages state of the art transformer architecture in conjunction with multiple features can bolster the performances of drug drug interation tasks in the biomedical domain. In particular, we believe our research would be helpful in identification of potential adverse drug reactions.