Related papers: Boosting Low-Resource Biomedical QA via Entity-Awa…

Entity linking (mapping ambiguous mentions in text to entities in a knowledge base) is a foundational step in tasks such as knowledge graph construction, question-answering, and information extraction. Our method, LELA, is a modular…

Named entity recognition (NER) stands as a fundamental and pivotal task within the realm of Natural Language Processing. Particularly within the domain of Biomedical Method NER, this task presents notable challenges, stemming from the…

Clinical text is rich in information, with mentions of treatment, medication and anatomy among many other clinical terms. Multiple terms can refer to the same core concepts which can be referred as a clinical entity. Ontologies like the…

Large Language Model (LLM) has gained popularity and achieved remarkable results in open-domain tasks, but its performance in real industrial domain-specific scenarios is average due to its lack of specific domain knowledge. This issue has…

The paper introduces a framework for the evaluation of the encoding of factual scientific knowledge, designed to streamline the manual evaluation process typically conducted by domain experts. Inferring over and extracting information from…

Effective Question Answering (QA) on large biomedical document collections requires effective document retrieval techniques. The latter remains a challenging task due to the domain-specific vocabulary and semantic ambiguity in user queries.…

Biomedical named entity recognition (NER) is a fundamental task in text mining of medical documents and has many applications. Deep learning based approaches to this task have been gaining increasing attention in recent years as their…

Although biomedical entity linking (BioEL) has made significant progress with pre-trained language models, challenges still exist for fine-grained and long-tailed entities. To address these challenges, we present BioELQA, a novel model that…

Knowledge-Based Visual Question Answering (KBVQA) is a bi-modal task requiring external world knowledge in order to correctly answer a text question and associated image. Recent single modality text work has shown knowledge injection into…

The Biomedical Entity Normalization (BEN) task aims to align raw, unstructured medical entities to standard entities, thus promoting data coherence and facilitating better downstream medical applications. Recently, prompt learning methods…

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…

Despite recent progress, Biomedical Entity Linking (BEL) with large language models (LLMs) remains computationally inefficient and challenging to deploy in practical settings. In this work, we demonstrate that instruction-tuning of…

Large Language Models (LLMs) demonstrate remarkable versatility in various NLP tasks but encounter distinct challenges in biomedical due to the complexities of language and data scarcity. This paper investigates LLMs application in the…

Background and Objective: Biomedical Named Entity Recognition (BioNER) is a foundational task in medical informatics, crucial for downstream applications like drug discovery and clinical trial matching. However, adapting general-domain…

Factoid question answering (QA) has recently benefited from the development of deep learning (DL) systems. Neural network models outperform traditional approaches in domains where large datasets exist, such as SQuAD (ca. 100,000 questions)…

The progress introduced by pre-trained language models and their fine-tuning has resulted in significant improvements in most downstream NLP tasks. The unsupervised training of a language model combined with further target task fine-tuning…

Although pre-training models have achieved great success in dialogue generation, their performance drops dramatically when the input contains an entity that does not appear in pre-training and fine-tuning datasets (unseen entity). To…

Background: Biomedical entity normalization is critical to biomedical research because the richness of free-text clinical data, such as progress notes, can often be fully leveraged only after translating words and phrases into structured…

Due to large number of entities in biomedical knowledge bases, only a small fraction of entities have corresponding labelled training data. This necessitates entity linking models which are able to link mentions of unseen entities using…

Language Models (LMs) have performed well on biomedical natural language processing applications. In this study, we conducted some experiments to use prompt methods to extract knowledge from LMs as new knowledge Bases (LMs as KBs). However,…