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Biomedical queries have become increasingly prevalent in web searches, reflecting the growing interest in accessing biomedical literature. Despite recent research on large-language models (LLMs) motivated by endeavours to attain generalized…

Pre-trained and fine-tuned transformer models like BERT and T5 have improved the state of the art in ad-hoc retrieval and question-answering, but not as yet in high-recall information retrieval, where the objective is to retrieve…

Predicting disease trajectories from electronic health records (EHRs) is a complex task due to major challenges such as data non-stationarity, high granularity of medical codes, and integration of multimodal data. EHRs contain both…

The data available in Electronic Health Records (EHRs) provides the opportunity to transform care, and the best way to provide better care for one patient is through learning from the data available on all other patients. Temporal modelling…

Pre-training models are an important tool in Natural Language Processing (NLP), while the BERT model is a classic pre-training model whose structure has been widely adopted by followers. It was even chosen as the reference model for the…

Objective: Clinical knowledge enriched transformer models (e.g., ClinicalBERT) have state-of-the-art results on clinical NLP (natural language processing) tasks. One of the core limitations of these transformer models is the substantial…

The surge of pre-trained language models has begun a new era in the field of Natural Language Processing (NLP) by allowing us to build powerful language models. Among these models, Transformer-based models such as BERT have become…

Recently, there has been growing interest in the ability of Transformer-based models to produce meaningful embeddings of text with several applications, such as text similarity. Despite significant progress in the field, the explanations…

The multi-head self-attention mechanism of the transformer model has been thoroughly investigated recently. In one vein of study, researchers are interested in understanding why and how transformers work. In another vein, researchers…

Purpose: In this paper, we present an automated method for article classification, leveraging the power of Large Language Models (LLM). The primary focus is on the field of ophthalmology, but the model is extendable to other fields.…

Transformers-based models, such as BERT, have dramatically improved the performance for various natural language processing tasks. The clinical knowledge enriched model, namely ClinicalBERT, also achieved state-of-the-art results when…

We propose a model for tagging unstructured texts with an arbitrary number of terms drawn from a tree-structured vocabulary (i.e., an ontology). We treat this as a special case of sequence-to-sequence learning in which the decoder begins at…

Large-scale pre-trained language models such as BERT are popular solutions for text classification. Due to the superior performance of these advanced methods, nowadays, people often directly train them for a few epochs and deploy the…

Pre-trained language models like BERT achieve superior performances in various NLP tasks without explicit consideration of syntactic information. Meanwhile, syntactic information has been proved to be crucial for the success of NLP…

The goal of text ranking is to generate an ordered list of texts retrieved from a corpus in response to a query. Although the most common formulation of text ranking is search, instances of the task can also be found in many natural…

The Transformer has quickly become the dominant architecture for various pattern recognition tasks due to its capacity for long-range representation. However, transformers are data-hungry models and need large datasets for training. In…

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…

Automatic ICD coding is the task of assigning codes from the International Classification of Diseases (ICD) to medical notes. These codes describe the state of the patient and have multiple applications, e.g., computer-assisted diagnosis or…

Fine-tuning pre-trained models provides significant advantages in downstream performance. The ubiquitous nature of pre-trained models such as BERT and its derivatives in natural language processing has also led to a proliferation of…

Relation extraction (RE) consists in identifying and structuring automatically relations of interest from texts. Recently, BERT improved the top performances for several NLP tasks, including RE. However, the best way to use BERT, within a…