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Pre-trained contextual representations like BERT have achieved great success in natural language processing. However, the sentence embeddings from the pre-trained language models without fine-tuning have been found to poorly capture…

Although deep learning has advanced automated electrocardiogram (ECG) diagnosis, prevalent supervised methods typically treat recordings as undifferentiated one-dimensional (1D) signals or two-dimensional (2D) images. This formulation…

Pre-training large-scale neural language models on raw texts has made a significant contribution to improving transfer learning in natural language processing (NLP). With the introduction of transformer-based language models, such as…

In this paper, we present our approach to extracting structured information from unstructured Electronic Health Records (EHR) [2] which can be used to, for example, study adverse drug reactions in patients due to chemicals in their…

Pretrained text encoders, such as BERT, have been applied increasingly in various natural language processing (NLP) tasks, and have recently demonstrated significant performance gains. However, recent studies have demonstrated the existence…

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…

Neural network-based representations ("embeddings") have dramatically advanced natural language processing (NLP) tasks, including clinical NLP tasks such as concept extraction. Recently, however, more advanced embedding methods and…

Named Entity Recognition (NER) is a fundamental Natural Language Processing (NLP) task to extract entities from unstructured data. The previous methods for NER were based on machine learning or deep learning. Recently, pre-training models…

Using deep learning models pre-trained on Imagenet is the traditional solution for medical image classification to deal with data scarcity. Nevertheless, relevant literature supports that this strategy may offer limited gains due to the…

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…

Biomedical entity linking (EL) consists of named entity recognition (NER) and named entity disambiguation (NED). EL models are trained on corpora labeled by a predefined KB. However, it is a common scenario that only entities within a…

Existing state of the art neural entity linking models employ attention-based bag-of-words context model and pre-trained entity embeddings bootstrapped from word embeddings to assess topic level context compatibility. However, the latent…

Clinical named entity recognition (NER) aims to retrieve important entities within clinical narratives. Recent works have demonstrated that large language models (LLMs) can achieve strong performance in this task. While previous works focus…

In practical scenario, relation extraction needs to first identify entity pairs that have relation and then assign a correct relation class. However, the number of non-relation entity pairs in context (negative instances) usually far…

Named entity recognition (NER) of chemicals and drugs is a critical domain of information extraction in biochemical research. NER provides support for text mining in biochemical reactions, including entity relation extraction, attribute…

Named Entity Recognition (NER) in biomedical domains faces challenges due to data scarcity and imbalanced label distributions, especially with fine-grained entity types. We propose ReProCon, a novel few-shot NER framework that combines…

We study the problem of incorporating prior knowledge into a deep Transformer-based model,i.e.,Bidirectional Encoder Representations from Transformers (BERT), to enhance its performance on semantic textual matching tasks. By probing and…

Entities lie in the heart of biomedical natural language understanding, and the biomedical entity linking (EL) task remains challenging due to the fine-grained and diversiform concept names. Generative methods achieve remarkable…

The application of Natural Language Processing (NLP) has achieved a high level of relevance in several areas. In the field of software engineering (SE), NLP applications are based on the classification of similar texts (e.g. software…

Recognizing spans of biomedical concepts and their types (e.g., drug or gene) in free text, often called biomedical named entity recognition (NER), is a basic component of information extraction (IE) pipelines. Without a strong NER…