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We study the problem of training named entity recognition (NER) models using only distantly-labeled data, which can be automatically obtained by matching entity mentions in the raw text with entity types in a knowledge base. The biggest…

The clinical named entity recognition (CNER) task seeks to locate and classify clinical terminologies into predefined categories, such as diagnostic procedure, disease disorder, severity, medication, medication dosage, and sign symptom.…

Distantly Supervised Named Entity Recognition (DS-NER) has attracted attention due to its scalability and ability to automatically generate labeled data. However, distant annotation introduces many mislabeled instances, limiting its…

Neural networks (NNs) have become the state of the art in many machine learning applications, especially in image and sound processing [1]. The same, although to a lesser extent [2,3], could be said in natural language processing (NLP)…

We present a weakly-supervised data augmentation approach to improve Named Entity Recognition (NER) in a challenging domain: extracting biomedical entities (e.g., proteins) from the scientific literature. First, we train a neural NER (NNER)…

In this paper, we study the named entity recognition (NER) problem under distant supervision. Due to the incompleteness of the external dictionaries and/or knowledge bases, such distantly annotated training data usually suffer from a high…

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…

Spoken named entity recognition (NER) aims to identify named entities from speech, playing an important role in speech processing. New named entities appear every day, however, annotating their Spoken NER data is costly. In this paper, we…

Existing benchmarks for evaluating the clinical reasoning capabilities of large language models (LLMs) often lack a clear definition of "clinical reasoning" as a construct, fail to capture the full breadth of interdependent tasks within a…

Objective: Develop a cost-effective, large language model (LLM)-based pipeline for automatically extracting Review of Systems (ROS) entities from clinical notes. Materials and Methods: The pipeline extracts ROS section from the clinical…

When comparing entities extracted by a medical entity recognition system with gold standard annotations over a test set, two types of mismatches might occur, label mismatch or span mismatch. Here we focus on span mismatch and show that its…

Clinical concept extraction often begins with clinical Named Entity Recognition (NER). Often trained on annotated clinical notes, clinical NER models tend to struggle with tagging clinical entities in user queries because of the structural…

Named Entity Recognition has traditionally been a key task in natural language processing, aiming to identify and extract important terms from unstructured text data. However, a notable challenge for contemporary deep-learning NER models…

Named entity recognition (NER) is the task to identify mentions of rigid designators from text belonging to predefined semantic types such as person, location, organization etc. NER always serves as the foundation for many natural language…

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…

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…

Medical activities, such as diagnoses, medicine treatments, and laboratory tests, as well as temporal relations between these activities are the basic concepts in clinical research. However, existing relational data model on electronic…

The EQ-5D (EuroQol 5-Dimensions) is a standardized instrument for the evaluation of health-related quality of life. In health economics, systematic literature reviews (SLRs) depend on the correct identification of publications that use the…

Zero-shot named entity recognition (NER) is the task of detecting named entities of specific types (such as 'Person' or 'Medicine') without any training examples. Current research increasingly relies on large synthetic datasets,…

Weak supervision has shown promising results in many natural language processing tasks, such as Named Entity Recognition (NER). Existing work mainly focuses on learning deep NER models only with weak supervision, i.e., without any human…