Related papers: Harnessing Large Language Models for Biomedical Na…

Supervised named entity recognition (NER) in the biomedical domain depends on large sets of annotated texts with the given named entities. The creation of such datasets can be time-consuming and expensive, while extraction of new entities…

Processing information locked within clinical health records is a challenging task that remains an active area of research in biomedical NLP. In this work, we evaluate a broad set of machine learning techniques ranging from simple RNNs to…

Developing effective biomedical retrieval models is important for excelling at knowledge-intensive biomedical tasks but still challenging due to the deficiency of sufficient publicly annotated biomedical data and computational resources. We…

Few-shot learning has been studied to adapt models to tasks with very few samples. It holds profound significance, particularly in clinical tasks, due to the high annotation cost of medical images. Several works have explored few-shot…

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,…

Recently, Large Language Models (LLM) have demonstrated impressive capability to solve a wide range of tasks. However, despite their success across various tasks, no prior work has investigated their capability in the biomedical domain yet.…

Large Language Models (LLMs) have swiftly emerged as vital resources for different applications in the biomedical and healthcare domains; however, these models encounter issues such as generating inaccurate information or hallucinations.…

The pervasive deployment of Large Language Models-LLMs in various sectors often neglects the nuanced requirements of individuals and small organizations, who benefit more from models precisely tailored to their specific business contexts…

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…

Fine-tuning of Large Language Models (LLMs) for downstream tasks, performed on domain-specific data has shown significant promise. However, commercial use of such LLMs is limited by the high computational cost required for their deployment…

Automatically locating named entities in natural language text - named entity recognition - is an important task in the biomedical domain. Many named entity mentions are ambiguous between several bioconcept types, however, causing text…

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…

Unlocking deep and interpretable biological reasoning from complex genomic data remains a major AI challenge limiting scientific progress. While current DNA foundation models excel at representing sequences, they struggle with multi-step…

Data selection for fine-tuning large language models (LLMs) aims to choose a high-quality subset from existing datasets, allowing the trained model to outperform baselines trained on the full dataset. However, the expanding body of research…

Large Language Models (LLMs) have demonstrated remarkable versatility in recent years, offering potential applications across specialized domains such as healthcare and medicine. Despite the availability of various open-source LLMs tailored…

The rapid growth of biomedical literature poses challenges for manual knowledge curation and synthesis. Biomedical Natural Language Processing (BioNLP) automates the process. While Large Language Models (LLMs) have shown promise in general…

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,…

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…

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…

Here we present the training and evaluation of NanoNER, a Named Entity Recognition (NER) model for Nanobiology. NER consists in the identification of specific entities in spans of unstructured texts and is often a primary task in Natural…