Related papers: Biomedical Named Entity Recognition via Dictionary…

Named Entity Recognition (NER) is a fundamental task in Natural Language Processing (NLP) that plays a crucial role in information extraction, question answering, and knowledge-based systems. Traditional deep learning-based NER models often…

Training a neural network-based biomedical named entity recognition (BioNER) model usually requires extensive and costly human annotations. While several studies have employed multi-task learning with multiple BioNER datasets to reduce…

Entity standardization maps noisy mentions from free-form text to standard entities in a knowledge base. The unique challenge of this task relative to other entity-related tasks is the lack of surrounding context and numerous variations in…

Entity linking (or Normalization) is an essential task in text mining that maps the entity mentions in the medical text to standard entities in a given Knowledge Base (KB). This task is of great importance in the medical domain. It can also…

Background and Objective: Biomedical Named Entity Recognition (BioNER) is a foundational task in medical informatics, crucial for downstream applications like drug discovery and clinical trial matching. However, adapting general-domain…

To tackle Named Entity Recognition (NER) tasks, supervised methods need to obtain sufficient cleanly annotated data, which is labor and time consuming. On the contrary, distantly supervised methods acquire automatically annotated data using…

Named Entity Recognition (NER) is a challenging and widely studied task that involves detecting and typing entities in text. So far,NER still approaches entity typing as a task of classification into universal classes (e.g. date, person, or…

In recent years, with the growing amount of biomedical documents, coupled with advancement in natural language processing algorithms, the research on biomedical named entity recognition (BioNER) has increased exponentially. However, BioNER…

Biomedical entity linking (BioEL) has achieved remarkable progress with the help of pre-trained language models. However, existing BioEL methods usually struggle to handle rare and difficult entities due to long-tailed distribution. To…

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…

Background: Finding biomedical named entities is one of the most essential tasks in biomedical text mining. Recently, deep learning-based approaches have been applied to biomedical named entity recognition (BioNER) and showed promising…

Biomedical event extraction is critical in understanding biomolecular interactions described in scientific corpus. One of the main challenges is to identify nested structured events that are associated with non-indicative trigger words. We…

Understanding the meaning of text often involves reasoning about entities and their relationships. This requires identifying textual mentions of entities, linking them to a canonical concept, and discerning their relationships. These tasks…

In this work, we explore the way to perform named entity recognition (NER) using only unlabeled data and named entity dictionaries. To this end, we formulate the task as a positive-unlabeled (PU) learning problem and accordingly propose a…

Knowledge discovery is hindered by the increasing volume of publications and the scarcity of extensive annotated data. To tackle the challenge of information overload, it is essential to employ automated methods for knowledge extraction and…

Mentions of new concepts appear regularly in texts and require automated approaches to harvest and place them into Knowledge Bases (KB), e.g., ontologies and taxonomies. Existing datasets suffer from three issues, (i) mostly assuming that a…

Abstracts derived from biomedical literature possess distinct domain-specific characteristics, including specialised writing styles and biomedical terminologies, which necessitate a deep understanding of the related literature. As a result,…

We introduce biomedical and clinical English model packages for the Stanza Python NLP library. These packages offer accurate syntactic analysis and named entity recognition capabilities for biomedical and clinical text, by combining…

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)…

Unifying multimodal understanding and generation is a compelling frontier that is beginning to emerge in the medical field. However, the limited existing unified medical models typically treat understanding and generation as disjoint…