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Named Entity Recognition (NER) is one of the most common tasks of the natural language processing. The purpose of NER is to find and classify tokens in text documents into predefined categories called tags, such as person names, quantity…

Pretraining large neural language models, such as BERT, has led to impressive gains on many natural language processing (NLP) tasks. However, most pretraining efforts focus on general domain corpora, such as newswire and Web. A prevailing…

With increasing applications in areas such as biomedical information extraction pipelines and social media analytics, Named Entity Recognition (NER) has become an indispensable tool for knowledge extraction. However, with the gradual shift…

We explore the suitability of unsupervised representation learning methods on biomedical text -- BioBERT, SciBERT, and BioSentVec -- for biomedical question answering. To further improve unsupervised representations for biomedical QA, we…

Named Entity Recognition (NER) is a fundamental task in the fields of natural language processing and information extraction. NER has been widely used as a standalone tool or an essential component in a variety of applications such as…

Background: Biomedical entity normalization is critical to biomedical research because the richness of free-text clinical data, such as progress notes, can often be fully leveraged only after translating words and phrases into structured…

Clinical data in hospitals are increasingly accessible for research through clinical data warehouses. However these documents are unstructured and it is therefore necessary to extract information from medical reports to conduct clinical…

The Bidirectional Encoder Representations from Transformers (BERT) model has been radically improving the performance of many Natural Language Processing (NLP) tasks such as Text Classification and Named Entity Recognition (NER)…

Named entity recognition (NER) plays an important role in text-based information retrieval. In this paper, we combine Bidirectional Long Short-Term Memory (Bi-LSTM) \cite{hochreiter1997,schuster1997} with Conditional Random Field (CRF)…

The overwhelming amount of biomedical scientific texts calls for the development of effective language models able to tackle a wide range of biomedical natural language processing (NLP) tasks. The most recent dominant approaches are…

Pre-trained cross-lingual encoders such as mBERT (Devlin et al., 2019) and XLMR (Conneau et al., 2020) have proven to be impressively effective at enabling transfer-learning of NLP systems from high-resource languages to low-resource…

Named entity recognition (NER) is the task to identify mentions of rigid designators from text belonging to predefined semantic types such as person, location, organization etc. NER always serves as the foundation for many natural language…

Named-entity recognition (NER) detects texts with predefined semantic labels and is an essential building block for natural language processing (NLP). Notably, recent NER research focuses on utilizing massive extra data, including…

Domain adaptation of Pretrained Language Models (PTLMs) is typically achieved by unsupervised pretraining on target-domain text. While successful, this approach is expensive in terms of hardware, runtime and CO_2 emissions. Here, we propose…

Pre-trained language models (PLMs) have proven to be effective for document re-ranking task. However, they lack the ability to fully interpret the semantics of biomedical and health-care queries and often rely on simplistic patterns for…

Recently, neural methods have achieved state-of-the-art (SOTA) results in Named Entity Recognition (NER) tasks for many languages without the need for manually crafted features. However, these models still require manually annotated…

This paper presents a comprehensive study to efficiently build named entity recognition (NER) systems when a small number of in-domain labeled data is available. Based upon recent Transformer-based self-supervised pre-trained language…

There are a few challenges related to the task of biomedical named entity recognition, which are: the existing methods consider a fewer number of biomedical entities (e.g., disease, symptom, proteins, genes); and these methods do not…

Multilingual pre-trained models have achieved remarkable performance on cross-lingual transfer learning. Some multilingual models such as mBERT, have been pre-trained on unlabeled corpora, therefore the embeddings of different languages in…

A BERT-based Neural Ranking Model (NRM) can be either a crossencoder or a bi-encoder. Between the two, bi-encoder is highly efficient because all the documents can be pre-processed before the actual query time. In this work, we show two…