arXiv AI

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.

arXiv AI
Jul 2

Agentic generation of verifiable rules for deterministic, self-expanding reaction classification

arXiv:2607. 01061v1 Announce Type: new Abstract: Computer-assisted synthesis planning breaks target molecules into accessible precursors using large libraries of reaction rules that assign each transformation a deterministic, interpretable label.

By Daniel Armstrong, Maarten Dobbelaere, Valentas Olikauskas, Helena Avila, Octavian Susanu, J\'er\^ome Waser, Philippe Schwaller
arXiv AI
Aug 11

El Agente Gr\'afico: A Semantic Execution Runtime for Scientific Agents

arXiv:2602. 17902v2 Announce Type: replace Abstract: Large language models (LLMs) can plan scientific workflows and generate code, but these capabilities do not specify how scientific state is validated, transferred and recorded across heterogeneous computational and experimental operations.

By Jiaru Bai, Abdulrahman Aldossary, Thomas Swanick, Marcel M\"uller, Yeonghun Kang, Changhyeok Choi, Naruki Yoshikawa, Zijian Zhang, Jin Won Lee, Tsz Wai Ko, Aiwei Yin, Mohammad Ghazi Vakili, Chris Crebolder, Varinia Bernales, Al\'an Aspuru-Guzik
arXiv AI
Jun 8

MetaConfigurator: AI-Assisted RDF Authoring from JSON Data

arXiv:2606. 07094v1 Announce Type: cross Abstract: Scientific workflows increasingly generate structured JSON data that is easy to exchange but difficult to interpret consistently across systems due to lacking semantic interoperability.

By Felix Neubauer, Mahdi Jafarkhani, Kenichi Endo, J\"urgen Pleiss, Benjamin Uekermann
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
Jun 24

When CQs Go Wrong: Challenges in CQ Verification with OE-Assist

arXiv:2606. 24619v1 Announce Type: new Abstract: Competency Questions (CQs) are the central component of CQ-verification, an established process in which an ontology is evaluated against a set of natural language questions to determine whether the intended purpose of the ontology has been properly modelled.

By Anna Sofia Lippolis, Mohammad Javad Saeedizade, Robin Keskis\"arkk\"a, Aldo Gangemi, Eva Blomqvist, Andrea Giovanni Nuzzolese
arXiv AI
Sep 16

Extracting ontology-compliant knowledge from scientific text describing irradiated materials using large language models

arXiv:2609.17291v1 Announce Type: new Abstract: The quest for new materials increasingly relies on predictive models and comprehensive simulations that span scales from atomic to macroscopic levels....

By Marco Luca Sbodio, Marcos Mart\'inez Galindo, Vanessa Lopez, Blanca Biel, Pablo Canca, Pedro Delgado, Jes\'us I. Mendieta-Moreno, Raphael Tack, Maria J. Caturla
arXiv AI
Sep 18

oMeBench: Towards Robust Benchmarking of LLMs in Organic Mechanism Elucidation and Reasoning

oMeBench is a large-scale, expert-curated benchmark designed to evaluate large language models (LLMs) on organic mechanism reasoning. It contains over 10,000 annotated mechanistic steps, including reaction type labels, intermediate structures, and difficulty ratings, and introduces the oMeS scoring framework to assess logical consistency and chemical structural similarity. Evaluation shows that while current LLMs display promising chemical intuition, they often fail to produce correct and consistent multi-step reasoning, though prompting and fine-tuning can bring smaller models up to the level of closed‑source frontier models.

By Ruiling Xu, Yifan Zhang