Knowledge Extraction from Biomedical Literature with Symbolic and Deep Transfer Learning Methods

The available body of biomedical literature is increasing at a high pace, exceeding the ability of researchers to promptly leverage this knowledge-rich amount of information. Although the outstanding progress in natural language processing (NLP) we observed in the past few years, current technological advances in the field mainly concern newswire and web texts, and do not directly translate in good performance on highly specialized domains such as biomedicine due to linguistic variations along surface, syntax and semantic levels. Given the advances in NLP and the challenges the biomedical domain exhibits, and the explosive growth of biomedical knowledge being currently published, in this thesis we contribute to the biomedical NLP field by providing efficient means for extracting semantic relational information from biomedical literature texts. To this end, we made the following contributions towards the real-world adoption of knowledge extraction methods to support biomedicine: (i) we propose a symbolic high-precision biomedical relation extraction approach to reduce the time-consuming manual curation efforts of extracted relational evidence (Chapter 3), (ii) we conduct a thorough cross-domain study to quantify the drop in performance of deep learning methods for biomedical edge detection shedding lights on the importance of linguistic varieties in biomedicine (Chapter 4), and (iii) we propose a fast and accurate end-to-end solution for biomedical event extraction, leveraging sequential transfer learning and multi-task learning, making it a viable approach for real-world large-scale scenarios (Chapter 5). We then outline the conclusions by highlighting challenges and providing future research directions in the field.