Related papers: Boosting Low-Resource Biomedical QA via Entity-Awa…

Multi-table entity matching (MEM) addresses the limitations of dual-table approaches by enabling simultaneous identification of equivalent entities across multiple data sources without unique identifiers. However, existing methods relying…

Named entity recognition is a key component of Information Extraction (IE), particularly in scientific domains such as biomedicine and chemistry, where large language models (LLMs), e.g., ChatGPT, fall short. We investigate the…

There is vivid research on adapting Large Language Models (LLMs) to perform a variety of tasks in high-stakes domains such as healthcare. Despite their popularity, there is a lack of understanding of the extent and contributing factors that…

Pre-trained language models (PLMs) have proven to be effective for document re-ranking task. However, they lack the ability to fully interpret the semantics of biomedical and health-care queries and often rely on simplistic patterns for…

Entity linking is the task of linking mentions of named entities in natural language text, to entities in a curated knowledge-base. This is of significant importance in the biomedical domain, where it could be used to semantically annotate…

Neural language models (LM) trained on diverse corpora are known to work well on previously seen entities, however, updating these models with dynamically changing entities such as place names, song titles and shopping items requires…

Most biomedical pretrained language models are monolingual and cannot handle the growing cross-lingual requirements. The scarcity of non-English domain corpora, not to mention parallel data, poses a significant hurdle in training…

Pre-trained transformer language models (LMs) have in recent years become the dominant paradigm in applied NLP. These models have achieved state-of-the-art performance on tasks such as information extraction, question answering, sentiment…

Motivation: State-of-the-art biomedical named entity recognition (BioNER) systems often require handcrafted features specific to each entity type, such as genes, chemicals and diseases. Although recent studies explored using neural network…

Data augmentation is an effective solution to data scarcity in low-resource scenarios. However, when applied to token-level tasks such as NER, data augmentation methods often suffer from token-label misalignment, which leads to…

Entity Matching (EM)--the task of determining whether two data records refer to the same real-world entity--is a core task in data integration. Recent advances in deep learning have set a new standard for EM, particularly through…

Large language models (LLMs) have rapidly improved text embeddings for a growing array of natural-language processing tasks. However, their opaqueness and proliferation into scientific domains such as neuroscience have created a growing…

The overwhelming amount of biomedical scientific texts calls for the development of effective language models able to tackle a wide range of biomedical natural language processing (NLP) tasks. The most recent dominant approaches are…

Prevalent solution for BioNER involves using representation learning techniques coupled with sequence labeling. However, such methods are inherently task-specific, demonstrate poor generalizability, and often require dedicated model for…

Biomedical entity linking is the task of identifying mentions of biomedical concepts in text documents and mapping them to canonical entities in a target thesaurus. Recent advancements in entity linking using BERT-based models follow a…

Specialized entity linking (EL) models are well-trained at mapping mentions to unique knowledge base (KB) entities according to a given context. However, specialized EL models struggle to disambiguate long-tail entities due to their limited…

Word embeddings have been shown adept at capturing the semantic and syntactic regularities of the natural language text, as a result of which these representations have found their utility in a wide variety of downstream content analysis…

Clinical problem-solving requires processing of semantic medical knowledge such as illness scripts and numerical medical knowledge of diagnostic tests for evidence-based decision-making. As large language models (LLMs) show promising…

Biomedical entity linking (EL) consists of named entity recognition (NER) and named entity disambiguation (NED). EL models are trained on corpora labeled by a predefined KB. However, it is a common scenario that only entities within a…

Pre-trained language models induce dense entity representations that offer strong performance on entity-centric NLP tasks, but such representations are not immediately interpretable. This can be a barrier to model uptake in important…