Related papers: BioALBERT: A Simple and Effective Pre-trained Lang…

The recent success of question answering systems is largely attributed to pre-trained language models. However, as language models are mostly pre-trained on general domain corpora such as Wikipedia, they often have difficulty in…

This paper presents an iterative approach to performing Scientific Named Entity Recognition (SciNER) using BERT-based models. We leverage transfer learning to fine-tune pretrained models with a small but high-quality set of manually…

Biomedical named entity recognition (BioNER) seeks to automatically recognize biomedical entities in natural language text, serving as a necessary foundation for downstream text mining tasks and applications such as information extraction…

Medical Entity Recognition (MedER) is an essential NLP task for extracting meaningful entities from the medical corpus. Nowadays, MedER-based research outcomes can remarkably contribute to the development of automated systems in the medical…

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.…

Motivation: The proliferation of Biomedical research articles has made the task of information retrieval more important than ever. Scientists and Researchers are having difficulty in finding articles that contain information relevant to…

This paper presents several BERT-based models for Russian language biomedical text mining (RuBioBERT, RuBioRoBERTa). The models are pre-trained on a corpus of freely available texts in the Russian biomedical domain. With this pre-training,…

Named entity recognition (NER) is a widely applicable natural language processing task and building block of question answering, topic modeling, information retrieval, etc. In the medical domain, NER plays a crucial role by extracting…

Large scale self-supervised pre-training of Transformer language models has advanced the field of Natural Language Processing and shown promise in cross-application to the biological `languages' of proteins and DNA. Learning effective…

The use of BERT, one of the most popular language models, has led to improvements in many Natural Language Processing (NLP) tasks. One such task is Named Entity Recognition (NER) i.e. automatic identification of named entities such as…

Biomedical entity linking, a main component in automatic information extraction from health-related texts, plays a pivotal role in connecting textual entities (such as diseases, drugs and body parts mentioned by patients) to their…

Both generic and domain-specific BERT models are widely used for natural language processing (NLP) tasks. In this paper we investigate the vulnerability of BERT models to variation in input data for Named Entity Recognition (NER) through…

Motivation: Biomedical named-entity normalization involves connecting biomedical entities with distinct database identifiers in order to facilitate data integration across various fields of biology. Existing systems for biomedical named…

The Biocreative VII Track-2 challenge consists of named entity recognition, entity-linking (or entity-normalization), and topic indexing tasks -- with entities and topics limited to chemicals for this challenge. Named entity recognition is…

We introduce a new language representation model called BERT, which stands for Bidirectional Encoder Representations from Transformers. Unlike recent language representation models, BERT is designed to pre-train deep bidirectional…

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)…

Deep transformer neural network models have improved the predictive accuracy of intelligent text processing systems in the biomedical domain. They have obtained state-of-the-art performance scores on a wide variety of biomedical and…

Processing information locked within clinical health records is a challenging task that remains an active area of research in biomedical NLP. In this work, we evaluate a broad set of machine learning techniques ranging from simple RNNs to…

Extracting detailed clinical information from free-text medical narratives remains a practical challenge for researchers and healthcare systems. Terminology for immune-mediated and infectious diseases is especially inconsistent across…

Deep learning (DL) based predictive models from electronic health records (EHR) deliver impressive performance in many clinical tasks. Large training cohorts, however, are often required to achieve high accuracy, hindering the adoption of…