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Concept normalization in free-form texts is a crucial step in every text-mining pipeline. Neural architectures based on Bidirectional Encoder Representations from Transformers (BERT) have achieved state-of-the-art results in the biomedical…

Named entity recognition (NER) remains challenging when entity mentions can be discontinuous. Existing methods break the recognition process into several sequential steps. In training, they predict conditioned on the golden intermediate…

Building named entity recognition (NER) models for languages that do not have much training data is a challenging task. While recent work has shown promising results on cross-lingual transfer from high-resource languages to low-resource…

For languages with no annotated resources, transferring knowledge from rich-resource languages is an effective solution for named entity recognition (NER). While all existing methods directly transfer from source-learned model to a target…

Deep neural networks have shown promising results for various clinical prediction tasks such as diagnosis, mortality prediction, predicting duration of stay in hospital, etc. However, training deep networks -- such as those based on…

Recurrent Neural Network models are the state-of-the-art for Named Entity Recognition (NER). We present two innovations to improve the performance of these models. The first innovation is the introduction of residual connections between the…

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…

Popular solutions to Named Entity Recognition (NER) include conditional random fields, sequence-to-sequence models, or utilizing the question-answering framework. However, they are not suitable for nested and overlapping spans with large…

The number of biomedical literature on new biomedical concepts is rapidly increasing, which necessitates a reliable biomedical named entity recognition (BioNER) model for identifying new and unseen entity mentions. However, it is…

Named entity recognition (NER) is an extensively studied task that extracts and classifies named entities in a text. NER is crucial not only in downstream language processing applications such as relation extraction and question answering…

Automatically locating named entities in natural language text - named entity recognition - is an important task in the biomedical domain. Many named entity mentions are ambiguous between several bioconcept types, however, causing text…

Traditional named entity recognition (NER) aims to identify text mentions into pre-defined entity types. Continual Named Entity Recognition (CNER) is introduced since entity categories are continuously increasing in various real-world…

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…

Cross-domain NER is a practical yet challenging problem since the data scarcity in the real-world scenario. A common practice is first to learn a NER model in a rich-resource general domain and then adapt the model to specific domains. Due…

We consider the problem of Named Entity Recognition (NER) on biomedical scientific literature, and more specifically the genomic variants recognition in this work. Significant success has been achieved for NER on canonical tasks in recent…

Supervised models trained to predict properties from representations have been achieving high accuracy on a variety of tasks. For instance, the BERT family seems to work exceptionally well on the downstream task from NER tagging to the…

Named entity recognition (NER) is a fundamental component in many applications, such as Web Search and Voice Assistants. Although deep neural networks greatly improve the performance of NER, due to the requirement of large amounts of…

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 the domain of Natural Language Processing (NLP), Named Entity Recognition (NER) stands out as a pivotal mechanism for extracting structured insights from unstructured text. This manuscript offers an exhaustive exploration into the…

Deep neural network models have helped named entity (NE) recognition achieve amazing performance without handcrafting features. However, existing systems require large amounts of human annotated training data. Efforts have been made to…