Related papers: Can Large Language Models Augment a Biomedical Ont…

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…

Ontology, and more broadly, Knowledge Graph Matching is a challenging task in which expressiveness has not been fully addressed. Despite the increasing use of embeddings and language models for this task, approaches for generating…

Large Language Models (LLMs) have been extensively adopted in Knowledge Graph Completion (KGC), showcasing significant research advancements. However, as black-box models driven by deep neural architectures, current LLM-based KGC methods…

Automated clinical text anonymization has the potential to unlock the widespread sharing of textual health data for secondary usage while assuring patient privacy and safety. Despite the proposal of many complex and theoretically successful…

Large Language Models (LLMs) have been successfully used in many natural-language tasks and applications including text generation and AI chatbots. They also are a promising new technology for concept-oriented deep learning (CODL). However,…

The rapid advancement of large language models (LLMs) has opened new boundaries in the extraction and synthesis of medical knowledge, particularly within evidence synthesis. This paper reviews the state-of-the-art applications of LLMs in…

OWL (Web Ontology Language) ontologies which are able to formally represent complex knowledge and support semantic reasoning have been widely adopted across various domains such as healthcare and bioinformatics. Recently, ontology…

Mentions of new concepts appear regularly in texts and require automated approaches to harvest and place them into Knowledge Bases (KB), e.g., ontologies and taxonomies. Existing datasets suffer from three issues, (i) mostly assuming that a…

Large language models (LLMs) have shown significant achievements in solving a wide range of tasks. Recently, LLMs' capability to store, retrieve and infer with symbolic knowledge has drawn a great deal of attention, showing their potential…

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…

Managing clinical trial information is currently a significant challenge for the medical industry, as traditional methods are both time-consuming and costly. This paper proposes a simple yet effective methodology to extract and integrate…

Large language models (LLMs) have recently demonstrated their potential in clinical applications, providing valuable medical knowledge and advice. For example, a large dialog LLM like ChatGPT has successfully passed part of the US medical…

Genes, proteins and other biological entities influence one another via causal molecular networks. Causal relationships in such networks are mediated by complex and diverse mechanisms, through latent variables, and are often specific to…

Large language models (LLMs) are introducing a paradigm shift in molecular discovery by enabling text-guided interaction with chemical spaces through natural language, symbolic notations, with emerging extensions to incorporate multi-modal…

We propose the LLMs4OL approach, which utilizes Large Language Models (LLMs) for Ontology Learning (OL). LLMs have shown significant advancements in natural language processing, demonstrating their ability to capture complex language…

This study applies Large Language Models (LLMs) to two foundational Electronic Health Record (EHR) data science tasks: structured data querying (using programmatic languages, Python/Pandas) and information extraction from unstructured…

Recent advances in Language Models (LMs) have failed to mask their shortcomings particularly in the domain of reasoning. This limitation impacts several tasks, most notably those involving ontology engineering. As part of a PhD research, we…

In our work, we systematize and analyze implicit ontological commitments in the responses generated by large language models (LLMs), focusing on ChatGPT 3.5 as a case study. We investigate how LLMs, despite having no explicit ontology,…

Using different sources of information to support automated extracting of relations between biomedical concepts contributes to the development of our understanding of biological systems. The primary comprehensive source of these relations…

Aligning terminological resources, including ontologies, controlled vocabularies, taxonomies, and value sets is a critical part of data integration in many domains such as healthcare, chemistry, and biomedical research. Entity mapping is…