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The current UMLS (Unified Medical Language System) Metathesaurus construction process for integrating over 200 biomedical source vocabularies is expensive and error-prone as it relies on the lexical algorithms and human editors for deciding…

Pre-trained language models have attracted increasing attention in the biomedical domain, inspired by their great success in the general natural language domain. Among the two main branches of pre-trained language models in the general…

Recent advancements in language models based on recurrent neural networks and transformers architecture have achieved state-of-the-art results on a wide range of natural language processing tasks such as pos tagging, named entity…

Clinical word embeddings are extensively used in various Bio-NLP problems as a state-of-the-art feature vector representation. Although they are quite successful at the semantic representation of words, due to the dataset - which…

Developing high-performing systems for detecting biomedical named entities has major implications. State-of-the-art deep-learning based solutions for entity recognition often require large annotated datasets, which is not available in the…

This paper presents a framework for Named Entity Recognition (NER) leveraging the Bidirectional Encoder Representations from Transformers (BERT) model in natural language processing (NLP). NER is a fundamental task in NLP with broad…

Biomedical text embeddings have primarily been developed using research literature from PubMed, yet clinical cardiology practice relies heavily on procedural knowledge and specialized terminology found in comprehensive textbooks rather than…

NER has been traditionally formulated as a sequence labeling task. However, there has been recent trend in posing NER as a machine reading comprehension task (Wang et al., 2020; Mengge et al., 2020), where entity name (or other information)…

Named Entity Recognition (NER), a classic sequence labelling task, is an essential component of natural language understanding (NLU) systems in task-oriented dialog systems for slot filling. For well over a decade, different methods from…

In this work, we examine the extent to which embeddings may encode marginalized populations differently, and how this may lead to a perpetuation of biases and worsened performance on clinical tasks. We pretrain deep embedding models (BERT)…

The aim of Named Entity Recognition (NER) is to identify references of named entities in unstructured documents, and to classify them into pre-defined semantic categories. NER often aids from added background knowledge in the form of…

We aimed to enhance the performance of a supervised model for clinical named-entity recognition (NER) using medical terminologies. In order to evaluate our system in French, we built a corpus for 5 types of clinical entities. We used a…

Large Language Models (LLMs) demonstrate remarkable versatility in various NLP tasks but encounter distinct challenges in biomedical due to the complexities of language and data scarcity. This paper investigates LLMs application in the…

Pre-trained Transformers (\eg BERT) have been commonly used in existing dense retrieval methods for parameter initialization, and recent studies are exploring more effective pre-training tasks for further improving the quality of dense…

The recently proposed BERT has shown great power on a variety of natural language understanding tasks, such as text classification, reading comprehension, etc. However, how to effectively apply BERT to neural machine translation (NMT) lacks…

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…

Current systems of fine-grained entity typing use distant supervision in conjunction with existing knowledge bases to assign categories (type labels) to entity mentions. However, the type labels so obtained from knowledge bases are often…

Named Entity Recognition (NER) encounters the challenge of unbalanced labels, where certain entity types are overrepresented while others are underrepresented in real-world datasets. This imbalance can lead to biased models that perform…

We propose two neural network architectures for nested named entity recognition (NER), a setting in which named entities may overlap and also be labeled with more than one label. We encode the nested labels using a linearized scheme. In our…

Pre-trained BERT models have achieved impressive accuracy on natural language processing (NLP) tasks. However, their excessive amount of parameters hinders them from efficient deployment on edge devices. Binarization of the BERT models can…