Related papers: A Unified Biomedical Named Entity Recognition Fram…

Named Entity Recognition(NER) is a task of recognizing entities at a token level in a sentence. This paper focuses on solving NER tasks in a multilingual setting for complex named entities. Our team, LLM-RM participated in the recently…

Recognizing entities in texts is a central need in many information-seeking scenarios, and indeed, Named Entity Recognition (NER) is arguably one of the most successful examples of a widely adopted NLP task and corresponding NLP technology.…

Named Entity Recognition (NER) is a critical component of Natural Language Processing with diverse applications in information extraction and conversational AI. However, NER in specific domains for low-resource languages faces challenges…

Entity linking is the task of linking mentions of named entities in natural language text, to entities in a curated knowledge-base. This is of significant importance in the biomedical domain, where it could be used to semantically annotate…

Biomedical entity linking (BEL) is the task of grounding entity mentions to a knowledge base (KB). A popular approach to the task are name-based methods, i.e. those identifying the most appropriate name in the KB for a given mention, either…

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.…

Domain-specific Named Entity Recognition (NER), whose goal is to recognize domain-specific entities and their categories, provides an important support for constructing domain knowledge graphs. Currently, deep learning-based methods are…

We introduce GENomic Encoding REpresentation with Language Model (GENEREL), a framework designed to bridge genetic and biomedical knowledge bases. What sets GENEREL apart is its ability to fine-tune language models to infuse biological…

The increasing depth of parametric domain knowledge in large language models (LLMs) is fueling their rapid deployment in real-world applications. Understanding model vulnerabilities in high-stakes and knowledge-intensive tasks is essential…

Entity linking (EL) for biomedical text is typically benchmarked on English-only corpora with flat mentions, leaving the more realistic scenario of nested and multilingual mentions largely unexplored. We present our system for the BioNNE…

Clinical notes contain valuable unstructured information. Named entity recognition (NER) enables the automatic extraction of medical concepts; however, benchmarks for Portuguese remain scarce. In this study, we aimed to evaluate BERT-based…

Although Large Language Models (LLMs) exhibit remarkable adaptability across domains, these models often fall short in structured knowledge extraction tasks such as named entity recognition (NER). This paper explores an innovative,…

Recent advances in deep neural models allow us to build reliable named entity recognition (NER) systems without handcrafting features. However, such methods require large amounts of manually-labeled training data. There have been efforts on…

Named entity recognition (NER) is a fundamental task of natural language processing (NLP). However, most state-of-the-art research is mainly oriented to high-resource languages such as English and has not been widely applied to low-resource…

Large Language Models (LLMs, e.g., ChatGPT) have shown impressive zero- and few-shot capabilities in Named Entity Recognition (NER). However, these models can only be accessed via online APIs, which may cause data leak and non-reproducible…

Despite the widespread success of self-supervised learning via masked language models (MLM), accurately capturing fine-grained semantic relationships in the biomedical domain remains a challenge. This is of paramount importance for…

Medical Entity Recognition (MedER) is an essential NLP task for extracting meaningful entities from the medical corpus. Nowadays, MedER-based research outcomes can remarkably contribute to the development of automated systems in the medical…

Injecting external domain-specific knowledge (e.g., UMLS) into pretrained language models (LMs) advances their capability to handle specialised in-domain tasks such as biomedical entity linking (BEL). However, such abundant expert knowledge…

Exploring the application of powerful large language models (LLMs) on the named entity recognition (NER) task has drawn much attention recently. This work pushes the performance boundary of zero-shot NER with LLMs by proposing a…

We present BioLunar, developed using the Lunar framework, as a tool for supporting biological analyses, with a particular emphasis on molecular-level evidence enrichment for biomarker discovery in oncology. The platform integrates Large…