Related papers: Data Mining in Clinical Trial Text: Transformers f…
Retrieving answer passages from long documents is a complex task requiring semantic understanding of both discourse and document context. We approach this challenge specifically in a clinical scenario, where doctors retrieve cohorts of…
Objective: Causality mining is an active research area, which requires the application of state-of-the-art natural language processing techniques. In the healthcare domain, medical experts create clinical text to overcome the limitation of…
Natural language processing (NLP) of clinical trial documents can be useful in new trial design. Here we identify entity types relevant to clinical trial design and propose a framework called CT-BERT for information extraction from clinical…
Clinical notes contain an extensive record of a patient's health status, such as smoking status or the presence of heart conditions. However, this detail is not replicated within the structured data of electronic health systems.…
The massive scale and growth of textual biomedical data have made its indexing and classification increasingly important. However, existing research on this topic mainly utilized convolutional and recurrent neural networks, which generally…
The Transformer architecture has become prominent in developing large causal language models. However, mechanisms to explain its capabilities are not well understood. Focused on the training process, here we establish a meta-learning view…
Tracking entities in procedural language requires understanding the transformations arising from actions on entities as well as those entities' interactions. While self-attention-based pre-trained language encoders like GPT and BERT have…
This study explores the optimization of the DRAGON Longformer base model for clinical text classification, specifically targeting the binary classification of medical case descriptions. A dataset of 500 clinical cases containing structured…
The fundamental process of evidence extraction and synthesis in evidence-based medicine involves extracting PICO (Population, Intervention, Comparison, and Outcome) elements from biomedical literature. However, Outcomes, being the most…
Automatic phenotyping is a task of identifying cohorts of patients that match a predefined set of criteria. Phenotyping typically involves classifying long clinical documents that contain thousands of tokens. At the same time, recent…
Automatic extraction of clinical concepts is an essential step for turning the unstructured data within a clinical note into structured and actionable information. In this work, we propose a clinical concept extraction model for automatic…
Opinion mining, also known as sentiment analysis, is a subfield of natural language processing (NLP) that focuses on identifying and extracting subjective information in textual material. This can include determining the overall sentiment…
Transformers are widely used in natural language processing, where they consistently achieve state-of-the-art performance. This is mainly due to their attention-based architecture, which allows them to model rich linguistic relations…
Clinical notes in electronic health records contain highly heterogeneous writing styles, including non-standard terminology or abbreviations. Using these notes in predictive modeling has traditionally required preprocessing (e.g. taking…
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…
Electronic Health Records are large repositories of valuable clinical data, with a significant portion stored in unstructured text format. This textual data includes clinical events (e.g., disorders, symptoms, findings, medications and…
Neural network-based representations ("embeddings") have dramatically advanced natural language processing (NLP) tasks, including clinical NLP tasks such as concept extraction. Recently, however, more advanced embedding methods and…
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…
Recent trends in natural language processing research and annotation tasks affirm a paradigm shift from the traditional reliance on a single ground truth to a focus on individual perspectives, particularly in subjective tasks. In scenarios…
Many NLP applications require models to be interpretable. However, many successful neural architectures, including transformers, still lack effective interpretation methods. A possible solution could rely on building explanations from…