TpT-ADE: Transformer Based Two-Phase ADE Extraction

AbstractExtracting adverse reactions to medications or treatments is a crucial activity in the biomedical domain. The task involves identifying mentions of drugs and their adverse effects/events in raw text, which is challenging due to the unstructured nature of clinical narratives. In this paper, we propose TpT-ADE, a novel joint two-phase transformer model combined with natural language processing (NLP) techniques, to identify adverse events (AEs) caused by drugs. In the first phase of TpT-ADE, entities are extracted and are grounded with their standard terms using the Unified Medical Language System (UMLS) knowledge base. In the second phase, entity and relation classification is performed to determine the presence of a relationship between the drug and AE pairs. TpT-ADE also identifies the intensity of AE entities by constructing a parts-of-speech (POS) embedding model. Unlike previous approaches that use complex classifiers, TpT-ADE employs a shallow neural network and yet outperforms the state-of-the-art methods on the standard ADE corpus.