The present invention provides methods, systems and devices for drug-drug interaction and adverse event analysis. Chemical structures for one or more pairs of drugs are obtained from at least one of a user and a database. A chemical fingerprint is generated for each drug of the one or more pairs of drugs based on the chemical structure of the drug. Drug-drug interaction prediction is performed for each pair of drugs based on the chemical fingerprints. Adverse event prediction is performed based on the predicted drug-drug interaction for the one or more pairs of drugs.