arXiv AI

An Ontology for Machine Learning Interatomic Potentials

arXiv:2607. 23219v1 Announce Type: new Abstract: Machine learning interatomic potentials (MLIPs) approximate quantum-mechanical energies and forces---conventionally computed by density functional theory (DFT) or wave-function methods---at a fraction of the cost.

arXiv AI
2d ago

Ontology-Grounded, Reasoner-Verified Benchmarks for Evaluating LLM Reasoning in Scientific AI

The paper introduces a pipeline that automatically creates ontology‑grounded multiple‑choice question benchmarks for evaluating large language models (LLMs) on logical reasoning tasks in scientific AI. By using OWL 2 ontologies, correct answers are guaranteed by design and distractors are generated and formally verified as incorrect through an OWL reasoner. Experiments on three ontologies—Pizza, PMDco, and DOID—yielded 112, 2,491, and 15,216 MCQs, respectively, with high natural‑language quality and challenging zero‑shot performance for six LLMs.

By Nishtha N. Vaidya, Stephan Grimm, Thomas Hubauer, Thomas A. Runkler
arXiv AI
Jul 28

Retrieval-Augmented Generation of Ontologies from Relational Databases

arXiv:2506. 01232v2 Announce Type: replace-cross Abstract: Deriving OWL ontologies from relational database schemas supports semantic interoperability and downstream tasks such as knowledge graph population, ontology-based data access, graph-based learning, and automated reasoning.

By Nadeen Fathallah, Mojtaba Nayyeri, Athish A Yogi, Ratan Bahadur Thapa, Hans-Michael Tautenhahn, Anton Schnurpel, Steffen Staab
arXiv AI
Jul 9

Accurate, Interdisciplinary and Transparent Structure-property Understanding with Deep Native Structural Reasoning

arXiv:2607. 07708v1 Announce Type: cross Abstract: Structure-property relationships are foundational to biology, chemistry and materials science, where function, reactivity and physical response emerge from spatial, chemical and periodic organization.

By Chen Tang, Yizhou Wang, Jianyu Wu, Lintao Wang, Shixiang Tang, Pengze Li, Encheng Su, Jun Yao, Jiabei Xiao, Yuqi Shi, Jielan Li, Hongxia Hao, Zhangyang Gao, Fang Wu, Ben Fei, Xiangyu Yue, Pan Tan, Bozitao Zhong, Jinouwen Zhang, Aoran Wang, Yan Lu, Jiaheng Liu, Xinzhu Ma, Liang Hong, Mingyue Zheng, Phil Torr, Bowen Zhou, Wanli Ouyang, Lei Bai
arXiv AI
Aug 28

A Task-Centric Ontology and Deterministic Domain Rules as a Verifiable Core for AI-Assisted Chemistry Problem Solving

The paper introduces ChemOntoRule, a symbolic core designed to aid AI in solving school‑level chemistry problems. It uses a task‑centric ontology built around the specific concepts and procedures needed for a defined set of problems, combined with deterministic Python rules for electronic structure, periodic trends, oxidation states, and related reasoning patterns. Evaluated on 300 human‑authored problems, the system matched 296 reference answers (98.67%), with the ontology‑driven rules covering 269 problems and achieving 98.88% accuracy.

By Ibrokhimsho Abduchaborov
arXiv Machine Learning
Jul 1

ElemeNet: Multiscale Molecular Machine Learning with Uncertainty Quantification Across the Periodic Table

arXiv:2606. 30961v1 Announce Type: cross Abstract: Advances in deep learning architectures and representations have enabled ML-driven chemical property prediction, but state-of-the-art (SOTA) models have remained largely confined to independent codebases and lack support for diverse chemical species.

By Jacob W. Toney, Samir Darouich, Yiran Wang, Aaron G. Garrison, Johannes K\"astner, Heather J. Kulik