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Gene Ontology (GO) is the most important resource for gene function annotation. It provides a way to unify biological knowledge across different species via a dynamic and controlled vocabulary. GO is now widely represented in the Semantic…

Genomics · Quantitative Biology 2019-09-26 Yanying Wu

Traditional ontologies describe domain structure but cannot generate novel artifacts. Large language models generate fluently but produce outputs lacking structural validity, hallucinating mechanisms without components, goals without end…

Artificial Intelligence · Computer Science 2026-02-10 Benny Cheung

Generative AI models garnered a large amount of public attention and speculation with the release of OpenAIs chatbot, ChatGPT. At least two opinion camps exist: one excited about possibilities these models offer for fundamental changes to…

Artificial Intelligence · Computer Science 2024-06-28 Ann Speed

Large Language Models (LLMs) are transforming AI across industries, but their development and deployment remain complex. This survey reviews 16 key challenges in building and using LLMs and examines how these challenges are addressed by two…

Computation and Language · Computer Science 2025-09-01 Shubham Sharma , Sneha Tuli , Narendra Badam

Of primary importance in formulating a response to the increasing prevalence and power of artificial intelligence (AI) applications in society are questions of ontology. Questions such as: What "are" these systems? How are they to be…

Computers and Society · Computer Science 2019-03-11 Scott H. Hawley

Topic Modeling has become a prominent tool for the study of scientific fields, as they allow for a large scale interpretation of research trends. Nevertheless, the output of these models is structured as a list of keywords which requires a…

Computation and Language · Computer Science 2024-08-14 Diego Kozlowski , Carolina Pradier , Pierre Benz

We evaluated the capability of a generative pre-trained transformer (GPT-4) to automatically generate high-quality learning objectives (LOs) in the context of a practically oriented university course on Artificial Intelligence. Discussions…

Artificial Intelligence · Computer Science 2023-07-03 Pragnya Sridhar , Aidan Doyle , Arav Agarwal , Christopher Bogart , Jaromir Savelka , Majd Sakr

Semantic reasoning aims to infer new knowledge from existing knowledge, with OWL ontologies serving as a standardized framework for organizing information. A key challenge in semantic reasoning is verifying ontology consistency. However,…

Artificial Intelligence · Computer Science 2025-04-29 Justin Mücke , Ansgar Scherp

As large language models (LLMs) have demonstrated their powerful capabilities in plenty of domains and tasks, including context understanding, code generation, language generation, data storytelling, etc., many data analysts may raise…

Computation and Language · Computer Science 2023-10-24 Liying Cheng , Xingxuan Li , Lidong Bing

Recent investigations show that large language models (LLMs), specifically GPT-4, not only have remarkable capabilities in common Natural Language Processing (NLP) tasks but also exhibit human-level performance on various professional and…

Computation and Language · Computer Science 2023-06-05 Zhuo Wang , Rongzhen Li , Bowen Dong , Jie Wang , Xiuxing Li , Ning Liu , Chenhui Mao , Wei Zhang , Liling Dong , Jing Gao , Jianyong Wang

Explainable Artificial Intelligence (XAI) poses a significant challenge in providing transparent and understandable insights into complex AI models. Traditional post-hoc algorithms, while useful, often struggle to deliver interpretable…

Artificial Intelligence · Computer Science 2024-09-24 Adrita Barua , Cara Widmer , Pascal Hitzler

We introduce a neuro-symbolic framework for multi-intent understanding in mobile AI agents by integrating a structured intent ontology with compact language models. Our method leverages retrieval-augmented prompting, logit biasing and…

Artificial Intelligence · Computer Science 2025-11-26 Ioannis Tzachristas , Aifen Sui

Clinical AI systems routinely train on health data structurally distorted by documentation workflows, billing incentives, and terminology fragmentation. Prior work has characterised the mechanisms of this distortion: the three-forces model…

Artificial Intelligence · Computer Science 2026-04-03 Florian Odi Stummer

This research presents a comprehensive methodology for utilizing an ontology-driven structured prompts system in interplay with ChatGPT, a widely used large language model (LLM). The study develops formal models, both information and…

Artificial Intelligence · Computer Science 2023-07-12 Oleksandr Palagin , Vladislav Kaverinskiy , Anna Litvin , Kyrylo Malakhov

High-throughput phenotyping, the automated mapping of patient signs and symptoms to standardized ontology concepts, is essential to gaining value from electronic health records (EHR) in the support of precision medicine. Despite…

Artificial Intelligence · Computer Science 2024-06-24 Syed I. Munzir , Daniel B. Hier , Chelsea Oommen , Michael D. Carrithers

Transforming relational databases into knowledge graphs with enriched ontologies enhances semantic interoperability and unlocks advanced graph-based learning and reasoning over data. However, previous approaches either demand significant…

Large Language Models (LLMs) have drawn a lot of attention due to their strong performance on a wide range of natural language tasks, since the release of ChatGPT in November 2022. LLMs' ability of general-purpose language understanding and…

Computation and Language · Computer Science 2025-03-25 Shervin Minaee , Tomas Mikolov , Narjes Nikzad , Meysam Chenaghlu , Richard Socher , Xavier Amatriain , Jianfeng Gao

The recent swift development of LLMs like GPT-4, Gemini, and GPT-3.5 offers a transformative opportunity in medicine and healthcare, especially in digital diagnostics. This study evaluates each model diagnostic abilities by interpreting a…

Computation and Language · Computer Science 2024-05-14 Gaurav Kumar Gupta , Aditi Singh , Sijo Valayakkad Manikandan , Abul Ehtesham

Tools to explore scientific literature are essential for scientists, especially in biomedicine, where about a million new papers are published every year. Many such tools provide users the ability to search for specific entities (e.g.…

Computation and Language · Computer Science 2021-07-05 Sunil Mohan , Rico Angell , Nick Monath , Andrew McCallum

The advancement of Large Language Models (LLMs), including GPT-4, provides exciting new opportunities for generative design. We investigate the application of this tool across the entire design and manufacturing workflow. Specifically, we…

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