Knowledge of a disease includes information of various aspects of the disease, such as signs and symptoms, diagnosis and treatment. This disease knowledge is critical for many health-related and biomedical tasks, including consumer health question answering, medical language inference and disease name recognition. While pre-trained language models like BERT have shown success in capturing syntactic, semantic, and world knowledge from text, we find they can be further complemented by specific information like knowledge of symptoms, diagnoses, treatments, and other disease aspects. Hence, we integrate BERT with disease knowledge for improving these important tasks. Specifically, we propose a new disease knowledge infusion training procedure and evaluate it on a suite of BERT models including BERT, BioBERT, SciBERT, ClinicalBERT, BlueBERT, and ALBERT. Experiments over the three tasks show that these models can be enhanced in nearly all cases, demonstrating the viability of disease knowledge infusion. For example, accuracy of BioBERT on consumer health question answering is improved from 68.29% to 72.09%, while new SOTA results are observed in two datasets. We make our data and code freely available.

We present a new benchmark dataset called PARADE for paraphrase identification that requires specialized domain knowledge. PARADE contains paraphrases that overlap very little at the lexical and syntactic level but are semantically equivalent based on computer science domain knowledge, as well as non-paraphrases that overlap greatly at the lexical and syntactic level but are not semantically equivalent based on this domain knowledge. Experiments show that both state-of-the-art neural models and non-expert human annotators have poor performance on PARADE. For example, BERT after fine-tuning achieves an F1 score of 0.709, which is much lower than its performance on other paraphrase identification datasets. PARADE can serve as a resource for researchers interested in testing models that incorporate domain knowledge. We make our data and code freely available.