Related papers: BERT might be Overkill: A Tiny but Effective Biome…

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…

Entity linking involves aligning textual mentions of named entities to their corresponding entries in a knowledge base. Entity linking systems often exploit relations between textual mentions in a document (e.g., coreference) to decide if…

In this paper, we address the problem of learning low dimension representation of entities on relational databases consisting of multiple tables. Embeddings help to capture semantics encoded in the database and can be used in a variety of…

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…

Entity and relation extraction is the necessary step in structuring medical text. However, the feature extraction ability of the bidirectional long short term memory network in the existing model does not achieve the best effect. At the…

This paper introduces a conceptually simple, scalable, and highly effective BERT-based entity linking model, along with an extensive evaluation of its accuracy-speed trade-off. We present a two-stage zero-shot linking algorithm, where each…

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…

Recently, pretrained language models based on BERT have been introduced for the French biomedical domain. Although these models have achieved state-of-the-art results on biomedical and clinical NLP tasks, they are constrained by a limited…

We present, to our knowledge, the first application of BERT to document classification. A few characteristics of the task might lead one to think that BERT is not the most appropriate model: syntactic structures matter less for content…

Entity linking (EL) for biomedical text is typically benchmarked on English-only corpora with flat mentions, leaving the more realistic scenario of nested and multilingual mentions largely unexplored. We present our system for the BioNNE…

Clinical text is rich in information, with mentions of treatment, medication and anatomy among many other clinical terms. Multiple terms can refer to the same core concepts which can be referred as a clinical entity. Ontologies like the…

The Bidirectional Encoder Representations from Transformers (BERT) model has achieved the state-of-the-art performance for many natural language processing (NLP) tasks. Yet, limited research has been contributed to studying its…

Recent advances in natural language processing (NLP) have been driven bypretrained language models like BERT, RoBERTa, T5, and GPT. Thesemodels excel at understanding complex texts, but biomedical literature, withits domain-specific…

Named entity recognition (NER) stands as a fundamental and pivotal task within the realm of Natural Language Processing. Particularly within the domain of Biomedical Method NER, this task presents notable challenges, stemming from the…

Entity Linking (EL) is the process of associating ambiguous textual mentions to specific entities in a knowledge base. Traditional EL methods heavily rely on large datasets to enhance their performance, a dependency that becomes problematic…

Named entity recognition (NER) models generally perform poorly when large training datasets are unavailable for low-resource domains. Recently, pre-training a large-scale language model has become a promising direction for coping with the…

Large, self-supervised transformer-based language representation models have recently received significant amounts of attention, and have produced state-of-the-art results across a variety of tasks simply by scaling up pre-training on…

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…

Language model (LM) pretraining can learn various knowledge from text corpora, helping downstream tasks. However, existing methods such as BERT model a single document, and do not capture dependencies or knowledge that span across…

Relation classification is an important NLP task to extract relations between entities. The state-of-the-art methods for relation classification are primarily based on Convolutional or Recurrent Neural Networks. Recently, the pre-trained…