Named entity recognition (NER) stands as a fundamental and pivotal task within the realm of Natural Language Processing. Particularly within the domain of Biomedical Method NER, this task presents notable challenges, stemming from the continual influx of domain-specific terminologies in scholarly literature. Current research in Biomedical Method (BioMethod) NER suffers from a scarcity of resources, primarily attributed to the intricate nature of methodological concepts, which necessitate a profound understanding for precise delineation. In this study, we propose a novel dataset for biomedical method entity recognition, employing an automated BioMethod entity recognition and information retrieval system to assist human annotation. Furthermore, we comprehensively explore a range of conventional and contemporary open-domain NER methodologies, including the utilization of cutting-edge large-scale language models (LLMs) customised to our dataset. Our empirical findings reveal that the large parameter counts of language models surprisingly inhibit the effective assimilation of entity extraction patterns pertaining to biomedical methods. Remarkably, the approach, leveraging the modestly sized ALBERT model (only 11MB), in conjunction with conditional random fields (CRF), achieves state-of-the-art (SOTA) performance.

In scientific research, the method is an indispensable means to solve scientific problems and a critical research object. With the advancement of sciences, many scientific methods are being proposed, modified, and used in academic literature. The authors describe details of the method in the abstract and body text, and key entities in academic literature reflecting names of the method are called method entities. Exploring diverse method entities in a tremendous amount of academic literature helps scholars understand existing methods, select the appropriate method for research tasks, and propose new methods. Furthermore, the evolution of method entities can reveal the development of a discipline and facilitate knowledge discovery. Therefore, this article offers a systematic review of methodological and empirical works focusing on extracting method entities from full-text academic literature and efforts to build knowledge services using these extracted method entities. Definitions of key concepts involved in this review were first proposed. Based on these definitions, we systematically reviewed the approaches and indicators to extract and evaluate method entities, with a strong focus on the pros and cons of each approach. We also surveyed how extracted method entities are used to build new applications. Finally, limitations in existing works as well as potential next steps were discussed.