Using transfer learning-based causality extraction to mine latent factors for Sjögren’s syndrome from biomedical literature

Abstract

Understanding causality is a longstanding goal across many different domains. Different articles, such as those published in medical journals, disseminate newly discovered knowledge that is often causal. In this paper, we use this intuition to build a model that leverages causal relations to unearth factors related to Sjögren's syndrome from biomedical literature. Sjögren's syndrome is an autoimmune disease affecting up to 3.1 million Americans. Due to the uncommon nature of the illness, symptoms across different specialties coupled with common symptoms of other autoimmune conditions such as rheumatoid arthritis, it is difficult for clinicians to diagnose the disease timely. Due to the lack of a dedicated dataset for causal relationships built from biomedical literature, we propose a transfer learning-based approach, where the relationship extraction model is trained on a wide variety of datasets. We conduct an empirical analysis of numerous neural network architectures and data transfer strategies for causal relation extraction. By conducting experiments with various contextual embedding layers and architectural components, we show that an ELECTRA-based sentence-level relation extraction model generalizes better than other architectures across varying web-based sources and annotation strategies. We use this empirical observation to create a pipeline for identifying causal sentences from literature text, extracting the causal relationships from causal sentences, and building a causal network consisting of latent factors related to Sjögren's syndrome. We show that our approach can retrieve such factors with high precision and recall values. Comparative experiments show that this approach leads to 25% improvement in retrieval F1-score compared to several state-of-the-art biomedical models, including BioBERT and Gram-CNN. We apply this model to a corpus of research articles related to Sjögren's syndrome collected from PubMed to create a causal network for Sjögren's syndrome. The proposed causal network for Sjögren's syndrome will potentially help clinicians with a holistic knowledge base for faster diagnosis.