Related papers: Improving Multi-Word Entity Recognition for Biomed…
KnowNER is a multilingual Named Entity Recognition (NER) system that leverages different degrees of external knowledge. A novel modular framework divides the knowledge into four categories according to the depth of knowledge they convey.…
Objective: This work aimed to demonstrate the effectiveness of a hybrid approach based on Sentence BERT model and retrofitting algorithm to compute relatedness between any two biomedical concepts. Materials and Methods: We generated concept…
In biomedical literature, it is common for entity boundaries to not align with word boundaries. Therefore, effective identification of entity spans requires approaches capable of considering tokens that are smaller than words. We introduce…
For several purposes in Natural Language Processing (NLP), such as Information Extraction, Sentiment Analysis or Chatbot, Named Entity Recognition (NER) holds an important role as it helps to determine and categorize entities in text into…
Many previous models of named entity recognition (NER) suffer from the problem of Out-of-Entity (OOE), i.e., the tokens in the entity mentions of the test samples have not appeared in the training samples, which hinders the achievement of…
Speech Entity Linking aims to recognize and disambiguate named entities in spoken languages. Conventional methods suffer gravely from the unfettered speech styles and the noisy transcripts generated by ASR systems. In this paper, we propose…
Open Named Entity Recognition (NER), which involves identifying arbitrary types of entities from arbitrary domains, remains challenging for Large Language Models (LLMs). Recent studies suggest that fine-tuning LLMs on extensive NER data can…
Mining electronic health records for patients who satisfy a set of predefined criteria is known in medical informatics as phenotyping. Phenotyping has numerous applications such as outcome prediction, clinical trial recruitment, and…
Extracting clinically relevant information from unstructured medical narratives such as admission notes, discharge summaries, and emergency case histories remains a challenge in clinical natural language processing (NLP). Medical Entity…
Integrating named entity recognition (NER) with automatic speech recognition (ASR) can significantly enhance transcription accuracy and informativeness. In this paper, we introduce WhisperNER, a novel model that allows joint speech…
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…
Fine-Grained Named Entity Recognition (FG-NER) is critical for many NLP applications. While classical named entity recognition (NER) has attracted a substantial amount of research, FG-NER is still an open research domain. The current…
In Biomedical Natural Language Processing (BioNLP) tasks, such as Relation Extraction, Named Entity Recognition, and Text Classification, the scarcity of high-quality data remains a significant challenge. This limitation poisons large…
This work investigates multiple approaches to Named Entity Recognition (NER) for text in Electronic Health Record (EHR) data. In particular, we look into the application of (i) rule-based, (ii) deep learning and (iii) transfer learning…
The Bidirectional long short-term memory networks (BiLSTM) have been widely used as an encoder in models solving the named entity recognition (NER) task. Recently, the Transformer is broadly adopted in various Natural Language Processing…
In this article, we present a gold-standard benchmark dataset for Biomedical Urdu Named Entity Recognition (BioUNER), developed by crawling health-related articles from online Urdu news portals, medical prescriptions, and hospital health…
Pretrained language models such as Bidirectional Encoder Representations from Transformers (BERT) have achieved state-of-the-art performance in natural language processing (NLP) tasks. Recently, BERT has been adapted to the biomedical…
Grounded Multimodal Named Entity Recognition (GMNER) task aims to identify named entities, entity types and their corresponding visual regions. GMNER task exhibits two challenging attributes: 1) The tenuous correlation between images and…
The delivery of appropriate targeted therapies to cancer patients requires the complete analysis of the molecular profiling of tumors and the patient's clinical characteristics in the context of existing knowledge and recent findings…
Ever-larger language models with ever-increasing capabilities are by now well-established text processing tools. Alas, information extraction tasks such as named entity recognition are still largely unaffected by this progress as they are…