Related papers: BIBERT-Pipe on Biomedical Nested Named Entity Link…

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…

Entity Linking (EL) is a fundamental task for Information Extraction and Knowledge Graphs. The general form of EL (i.e., end-to-end EL) aims to first find mentions in the given input document and then link the mentions to corresponding…

Biomedical literature is a rapidly expanding field of science and technology. Classification of biomedical texts is an essential part of biomedicine research, especially in the field of biology. This work proposes the fine-tuned DistilBERT,…

Biomedical word embeddings are usually pre-trained on free text corpora with neural methods that capture local and global distributional properties. They are leveraged in downstream tasks using various neural architectures that are designed…

Pretrained language models such as Bidirectional Encoder Representations from Transformers (BERT) have achieved state-of-the-art performance in natural language processing (NLP) tasks. Recently, BERT has been adapted to the biomedical…

Entity Recognition (ER) within a text is a fundamental exercise in Natural Language Processing, enabling further depending tasks such as Knowledge Extraction, Text Summarisation, or Keyphrase Extraction. An entity consists of single words…

In medical information extraction, medical Named Entity Recognition (NER) is indispensable, playing a crucial role in developing medical knowledge graphs, enhancing medical question-answering systems, and analyzing electronic medical…

Language models pre-trained on biomedical corpora, such as BioBERT, have recently shown promising results on downstream biomedical tasks. Many existing pre-trained models, on the other hand, are resource-intensive and computationally heavy…

Pre-trained language models induce dense entity representations that offer strong performance on entity-centric NLP tasks, but such representations are not immediately interpretable. This can be a barrier to model uptake in important…

Named entity recognition (NER) is one of the best studied tasks in natural language processing. However, most approaches are not capable of handling nested structures which are common in many applications. In this paper we introduce a novel…

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…

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…

Processing complex and ambiguous named entities is a challenging research problem, but it has not received sufficient attention from the natural language processing community. In this short paper, we present our participation in the English…

Tools to explore scientific literature are essential for scientists, especially in biomedicine, where about a million new papers are published every year. Many such tools provide users the ability to search for specific entities (e.g.…

Biomedical named entity recognition (NER) and entity linking (EL) strongly depend on annotated corpora, but the utility of these resources for benchmarking is often assumed rather than characterized. We present a corpus-centric framework…

In this paper, we describe the approach that we employed to address the task of Entity Recognition over Wet Lab Protocols -- a shared task in EMNLP WNUT-2020 Workshop. Our approach is composed of two phases. In the first phase, we…

Recent advances in distributed language modeling have led to large performance increases on a variety of natural language processing (NLP) tasks. However, it is not well understood how these methods may be augmented by knowledge-based…

Contextualized word embeddings derived from pre-trained language models (LMs) show significant improvements on downstream NLP tasks. Pre-training on domain-specific corpora, such as biomedical articles, further improves their performance.…

Network Embedding (NE) methods, which map network nodes to low-dimensional feature vectors, have wide applications in network analysis and bioinformatics. Many existing NE methods rely only on network structure, overlooking other…

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…