Related papers: Drug and Disease Interpretation Learning with Biom…

Knowledge is acquired by humans through experience, and no boundary is set between the kinds of knowledge or skill levels we can achieve on different tasks at the same time. When it comes to Neural Networks, that is not the case. The…

In this paper we study the problem of predicting clinical diagnoses from textual Electronic Health Records (EHR) data. We show the importance of this problem in medical community and present comprehensive historical review of the problem…

Drug repositioning (DR) refers to identification of novel indications for the approved drugs. The requirement of huge investment of time as well as money and risk of failure in clinical trials have led to surge in interest in drug…

Background : Knowledge is evolving over time, often as a result of new discoveries or changes in the adopted methods of reasoning. Also, new facts or evidence may become available, leading to new understandings of complex phenomena. This is…

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…

Pre-trained contextual language models are ubiquitously employed for language understanding tasks, but are unsuitable for resource-constrained systems. Noncontextual word embeddings are an efficient alternative in these settings. Such…

The rapidly increasing volume of electronic health record (EHR) data underscores a pressing need to unlock biomedical knowledge from unstructured clinical texts to support advancements in data-driven clinical systems, including patient…

Bidirectional Encoder Representations from Transformers (BERT) has recently achieved state-of-the-art performance on a broad range of NLP tasks including sentence classification, machine translation, and question answering. The BERT model…

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…

Named entity recognition is a key component of Information Extraction (IE), particularly in scientific domains such as biomedicine and chemistry, where large language models (LLMs), e.g., ChatGPT, fall short. We investigate the…

Relation extraction (RE) consists in identifying and structuring automatically relations of interest from texts. Recently, BERT improved the top performances for several NLP tasks, including RE. However, the best way to use BERT, within a…

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…

Unlike widely used Named Entity Recognition (NER) data sets in generic domains, biomedical NER data sets often contain mentions consisting of discontinuous spans. Conventional sequence tagging techniques encode Markov assumptions that are…

Named entity disambiguation (NED), which involves mapping textual mentions to structured entities, is particularly challenging in the medical domain due to the presence of rare entities. Existing approaches are limited by the presence of…

The purpose of this study is to analyze the efficacy of transfer learning techniques and transformer-based models as applied to medical natural language processing (NLP) tasks, specifically radiological text classification. We used 1,977…

This study evaluated the effect of BioBERT in medical text processing for the task of medical named entity recognition. Through comparative experiments with models such as BERT, ClinicalBERT, SciBERT, and BlueBERT, the results showed that…

We study whether in-domain pretraining of Bidirectional Encoder Representations from Transformer (BERT) model improves subdomain-level detection of exfiltration at low false positive rates. While previous work mostly examines fine-tuned…

Biomedical entity linking aims to map biomedical mentions, such as diseases and drugs, to standard entities in a given knowledge base. The specific challenge in this context is that the same biomedical entity can have a wide range of names,…

Specialised transformers-based models (such as BioBERT and BioMegatron) are adapted for the biomedical domain based on publicly available biomedical corpora. As such, they have the potential to encode large-scale biological knowledge. We…

Electronic Health Records are large repositories of valuable clinical data, with a significant portion stored in unstructured text format. This textual data includes clinical events (e.g., disorders, symptoms, findings, medications and…