Improved biomedical word embeddings in the transformer era

Quality of word and concept embeddings in targetted biomedical domains

Embeddings are fundamental resources often reused for building intelligent systems in the biomedical context. As a result, evaluating the quality of previously trained embeddings and ensuring they cover the desired information is critical for the success of applications. This paper proposes a new evaluation methodology to test the coverage of embeddings against a targetted domain of interest. It defines measures to assess the terminology, similarity, and analogy coverage, which are core aspects of the embeddings. Then, it discusses the experimentation carried out on existing biomedical embeddings in the specific context of pulmonary diseases. The proposed methodology and measures are general and may be applied to any application domain.

Year 2021: COVID-19, Information Extraction and BERTization among the Hottest Topics in Medical Natural Language Processing

OBJECTIVES

Analyze the content of publications within the medical natural language processing (NLP) domain in 2021.

METHODS

Automatic and manual preselection of publications to be reviewed, and selection of the best NLP papers of the year. Analysis of the important issues.

RESULTS

Four best papers have been selected in 2021. We also propose an analysis of the content of the NLP publications in 2021, all topics included.

CONCLUSIONS

The main issues addressed in 2021 are related to the investigation of COVID-related questions and to the further adaptation and use of transformer models. Besides, the trends from the past years continue, such as information extraction and use of information from social networks.

Artificial Intelligence in Pharmacovigilance: An Introduction to Terms, Concepts, Applications, and Limitations

The tools of artificial intelligence (AI) have enormous potential to enhance activities in pharmacovigilance. Pharmacovigilance experts need not be AI experts, but they should know enough about AI to explore the possibilities of collaboration with those who are. Modern concepts of AI date from Alan Turing's work, especially his paper on "the imitation game", in the late 1940s and early 1950s. Its scope today includes computational skills, including the formulation of mathematical proofs; visual perception, including facial recognition and virtual reality; decision making by expert systems; aspects of language, such as language processing, speech recognition, creative composition, and translation; and combinations of these, e.g. in self-driving vehicles. Machines can be programmed with the ability to learn, using neural networks that mimic cognitive actions of the human brain, leading to deep structural learning. Limitations of AI include difficulties with language, arising from the need to understand context and interpret ambiguities, which particularly affect translation, and inadequacies of databases, requiring careful preparation and curation. New techniques may cause unforeseen difficulties via unexpected malfunctioning. Relevant terms and concepts include different types of machine learning, neural networks, natural language programming, ontologies, and expert systems. Adoption of the tools of AI in pharmacovigilance has been slow. Machine learning, in conjunction with natural language processing and data mining, to study adverse drug reactions in databases such as those found in electronic health records, claims databases, and social media, has the potential to enhance the characterization of known adverse effects and reactions and detect new signals.