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Automated annotation of clinical text with standardized medical concepts is critical for enabling structured data extraction and decision support. SNOMED CT provides a rich ontology for labeling clinical entities, but manual annotation is…

Extracting detailed clinical information from free-text medical narratives remains a practical challenge for researchers and healthcare systems. Terminology for immune-mediated and infectious diseases is especially inconsistent across…

Named Entity Recognition (NER) or the extraction of concepts from clinical text is the task of identifying entities in text and slotting them into categories such as problems, treatments, tests, clinical departments, occurrences (such as…

This paper presents BELT, a novel model and learning framework for the pivotal topic of brain-to-language translation research. The translation from noninvasive brain signals into readable natural language has the potential to promote the…

Named entity recognition (NER) models are typically based on the architecture of Bi-directional LSTM (BiLSTM). The constraints of sequential nature and the modeling of single input prevent the full utilization of global information from…

Recently, Natural Language Processing (NLP) has witnessed an impressive progress in many areas, due to the advent of novel, pretrained contextual representation models. In particular, Devlin et al. (2019) proposed a model, called BERT…

Entity Typing (ET) is the process of identifying the semantic types of every entity within a corpus. In contrast to Named Entity Recognition, where each token in a sentence is labelled with zero or one class label, ET involves labelling…

Background: Named Entity Recognition (NER) and Normalisation (NEN) are core components of any text-mining system for biomedical texts. In a traditional concept-recognition pipeline, these tasks are combined in a serial way, which is…

Named entity recognition (NER) is a widely applicable natural language processing task and building block of question answering, topic modeling, information retrieval, etc. In the medical domain, NER plays a crucial role by extracting…

Small and imbalanced datasets commonly seen in healthcare represent a challenge when training classifiers based on deep learning models. So motivated, we propose a novel framework based on BioBERT (Bidirectional Encoder Representations from…

The contextual word embedding model, BERT, has proved its ability on downstream tasks with limited quantities of annotated data. BERT and its variants help to reduce the burden of complex annotation work in many interdisciplinary research…

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…

Learning to represent free text is a core task in many clinical machine learning (ML) applications, as clinical text contains observations and plans not otherwise available for inference. State-of-the-art methods use large language models…

We propose a method for learning disentangled representations of texts that code for distinct and complementary aspects, with the aim of affording efficient model transfer and interpretability. To induce disentangled embeddings, we propose…

With a neural sequence generation model, this study aims to develop a method of writing the patient clinical texts given a brief medical history. As a proof-of-a-concept, we have demonstrated that it can be workable to use medical concept…

The purpose of the study is to investigate the relative effectiveness of four different sentiment analysis techniques: (1) unsupervised lexicon-based model using Sent WordNet; (2) traditional supervised machine learning model using logistic…

Efficient classification of surgical procedures by urgency is paramount to optimize patient care and resource allocation within healthcare systems. This study introduces an unsupervised neural network approach to automatically categorize…

This paper introduces an approach for building a Named Entity Recognition (NER) model built upon a Bidirectional Encoder Representations from Transformers (BERT) architecture, specifically utilizing the SlovakBERT model. This NER model…

Bidirectional Encoder Representations from Transformers (BERT) reach state-of-the-art results in a variety of Natural Language Processing tasks. However, understanding of their internal functioning is still insufficient and unsatisfactory.…

Precision is of utmost importance in the realm of clinical entity extraction from clinical notes and reports. Encoder Models fine-tuned for Named Entity Recognition (NER) are an efficient choice for this purpose, as they don't hallucinate.…