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Materials informatics with large scale materials databases: Semantic modeling and data-driven crystal structure generation
Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.ORCID iD: 0009-0003-6158-1857
2026 (English)Licentiate thesis, comprehensive summary (Other academic)
Abstract [en]

Materials design has evolved from experimental trial-and-error, to model-based theoretical science and physics-based computational methods, and have now entered the paradigm of data-driven methods. During the past decades physics-based methods such as density functional theory (DFT) has been the driving force of computational materials design, and have been used to produce large sets of materials data by academic groups across the world. Since different databases use different technologies and data formats, the data production has resulted in scattered heterogeneous materials database designs. Data driven design of materials relies on data and methods operating on the data such as machine learning, neural networks, and analysis tools. To enable the full potential of the emerging data operational methods, especially the learning-based methods which commonly improves in correlation to the amount of training data, we need to make the data collectively accessible.

Database integration and interoperability are used to make the data collectively and viably accessible, where ontologies are key to, e.g., make data storages machine interpretable and unification of heterogenous data descriptions. This thesis presents an ontology for units of measures specifically targeting challenges of handling units across databases of computational and experimental data. The ontology is created using definition files part of the property definitions in release 1.2, from the community-driven OPTIMADE standard for a common application programming interface (API) for materials databases. The resulting ontology allows addressing data integration challenges encountered in that effort, which were unsolvable with available tools. These challenges include reference to specific and generalized units that have changed over time, using relevant symbols for different scientific domains, specification of relationships between units, and representation of units not part of System of Units (SI) without defining them in SI units or using SI system conventions.

Developments of structure-to-property machine learning and artificial intelligence (AI) mod-els part of data-driven methods has sped-up traditional physics-based simulation methods. Despite the speed increase of structure-to-property predictions, all possible materials is a massive space which is intractable to screen exhaustively, which leads to the idea of in-verse materials design using property-to-structure prediction. Generative AI models are promising candidates for property-to-structure prediction. Most existing crystal structure generative AI models does not account for symmetry, resulting in generation of high concentration of low-symmetry crystal structures. This thesis presents a generative AI model, capable of generating novel and stable symmetry-based descriptions of crystal structures, which inherently accounts for crystal structure symmetry.

Place, publisher, year, edition, pages
Linköping: Linköping University Electronic Press, 2026. , p. 47
Series
Linköping Studies in Science and Technology. Licentiate Thesis, ISSN 0280-7971 ; 2038
National Category
Computer Sciences Artificial Intelligence
Identifiers
URN: urn:nbn:se:liu:diva-226733DOI: 10.3384/9789181186741ISBN: 9789181186734 (print)ISBN: 9789181186741 (electronic)OAI: oai:DiVA.org:liu-226733DiVA, id: diva2:2092222
Presentation
2026-09-11, Nobel (BL32), B-building, Campus Valla, Linköping, 10:15 (English)
Opponent
Supervisors
Available from: 2026-08-14 Created: 2026-08-14 Last updated: 2026-08-19Bibliographically approved
List of papers
1. An ontology for units of measures across history,standards, and scientific and technology domains
Open this publication in new window or tab >>An ontology for units of measures across history,standards, and scientific and technology domains
2024 (English)In: Proceedings of the First International Workshop on Semantic Materials Science: Harnessing the Power of Semantic Web Technologies in Materials Science: co-located with the 20th International Conference on Semantic Systems (SEMANTiCS 2024) / [ed] Andre Valdestilhas, Huanyu Li, Patrick Lambrix, Harald Sack, Aachen, Germany: CEUR Workshop Proceedings , 2024, p. 15-28Conference paper, Published paper (Refereed)
Abstract [en]

Units of measure are central in all areas of science and technology. There are several ontologicalframeworks aiming to improve interoperability and precision in digital data exchange of quantitiesinvolving units. We introduce an ontology that specifically targets challenges for handling units acrossdatabases of computational and experimental data from various sources. The ontology is created usingdefinition files from the community-driven OPTIMADE standard for a common API for materialsdatabases. The resulting ontology allows addressing data integration challenges encountered in thateffort, including (i) referencing both specific and more general instances of units that have changedover time; (ii) the use of unit systems to define short domain-relevant identifiers for a collection of unitsthat make sense within a specific subdomain, rather than having to adopt globally standardized namingschemes; (iii) specifications of relationships between units that enables tools to convert between them;and (iv) units not part of the International System of Units (SI) can be represented without defining themin SI units or using SI system conventions. This paper provides a brief survey of existing ontologiesfor units of measure and then presents the design and discuss features of an ontology based on theOPTIMADE unit definitions.

Place, publisher, year, edition, pages
Aachen, Germany: CEUR Workshop Proceedings, 2024
Series
CEUR Workshop Proceedings, ISSN 1613-0073 ; 3760
Keywords
Ontology, Units of measure, Unit ontologies, Materials Science
National Category
Computer Sciences Materials Engineering
Identifiers
urn:nbn:se:liu:diva-207726 (URN)
Conference
First International Workshop on Semantic Materials Science: Harnessing the Power of Semantic Web Technologies in Materials Science, Amsterdam, The Netherlands, September 17, 2024.
Funder
Swedish Research Council, 2020-05402Swedish e‐Science Research CenterCUGS (National Graduate School in Computer Science)EU, Horizon Europe, 101058682
Available from: 2024-09-18 Created: 2024-09-18 Last updated: 2026-09-08Bibliographically approved
2. Developments and applications of the OPTIMADE API for materials discovery, design, and data exchange
Open this publication in new window or tab >>Developments and applications of the OPTIMADE API for materials discovery, design, and data exchange
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2024 (English)In: Digital Discovery, E-ISSN 2635-098X, Vol. 3, no 8, p. 1509-1533Article in journal (Refereed) Published
Abstract [en]

The Open Databases Integration for Materials Design (OPTIMADE) application programming interface (API) empowers users with holistic access to a growing federation of databases, enhancing the accessibility and discoverability of materials and chemical data. Since the first release of the OPTIMADE specification (v1.0), the API has undergone significant development, leading to the v1.2 release, and has underpinned multiple scientific studies. In this work, we highlight the latest features of the API format, accompanying software tools, and provide an update on the implementation of OPTIMADE in contributing materials databases. We end by providing several use cases that demonstrate the utility of the OPTIMADE API in materials research that continue to drive its ongoing development. The Open Databases Integration for Materials Design (OPTIMADE) application programming interface (API) empowers users with holistic access to a federation of databases, enhancing the accessibility and discoverability of materials and chemical data.

Place, publisher, year, edition, pages
ROYAL SOC CHEMISTRY, 2024
National Category
Computer Engineering
Identifiers
urn:nbn:se:liu:diva-206760 (URN)10.1039/d4dd00039k (DOI)001253257300001 ()39118978 (PubMedID)
Note

Funding Agencies|CECAM in Lausanne (Switzerland); Lorentz Center in Leiden (Netherlands); Psi-k; NCCR MARVEL (National Centre of Competence in Research-Swiss National Science Foundation) [205602]; Swedish e-Science Research Centre (SeRC); Royal Society; Wallonia-Brussels Federation under European Commission [847587]; NSF [DMR-2219788]; German Research Foundation (DFG) through the NFDI consortium FAIRmat [460197019]; Open Research Data Program of the ETH Board; Vetenskapsradet [2020-05402]; Swedish e-Science Research Centre; Programme "University Excellence Initiatives" of the Ministry of Education, Science and Sports of the Republic of Lithuania [12-001-01-01-01]; EPSRC [EP/T026642/1, EP/T026375/1, EP/P022561/1, EP/T022221/1]; U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering Division [DE-AC02-05-CH11231]; Materials Project program (KC23MP); European Union [675728, 823830, 720270, 785907, 945539]; Horizon Europe Programme [101093290, 101094651]; CHIPS Metrology Program, part of CHIPS for America, National Institute of Standards and Technology, U.S. Department of Commerce; National Natural Science Foundation of China (NSFC) [62376258]

Available from: 2024-08-26 Created: 2024-08-26 Last updated: 2026-09-08Bibliographically approved
3. WyckoffDiff– A Generative Diffusion Model for Crystal Symmetry
Open this publication in new window or tab >>WyckoffDiff– A Generative Diffusion Model for Crystal Symmetry
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2025 (English)In: Proceedings of the 42nd International Conference on Machine Learning, PMLR , 2025, Vol. 267, p. 15130-15147Conference paper, Published paper (Refereed)
Abstract [en]

Crystalline materials often exhibit a high level of symmetry. However, most generative models do not account for symmetry, but rather model each atom without any constraints on its position or element. We propose a generative model, Wyckoff Diffusion (WyckoffDiff), which generates symmetry-based descriptions of crystals. This is enabled by considering a crystal structure representation that encodes all symmetry, and we design a novel neural network architecture which enables using this representation inside a discrete generative model framework. In addition to respecting symmetry by construction, the discrete nature of our model enables fast generation. We additionally present a new metric, Fréchet Wrenformer Distance, which captures the symmetry aspects of the materials generated, and we benchmark WyckoffDiff against recently proposed generative models for crystal generation. As a proof-of-concept study, we use WyckoffDiff to find new materials below the convex hull of thermodynamical stability.

Place, publisher, year, edition, pages
PMLR, 2025
Series
Proceedings of Machine Learning Research, ISSN 2640-3498
National Category
Condensed Matter Physics Artificial Intelligence
Identifiers
urn:nbn:se:liu:diva-218524 (URN)001693104000283 ()
Conference
ICML 2025, Forty-Second International Conference on Machine Learning, Vancouver Convention Center, Sun. July 13th through Sat. July 19th
Note

Funding: Knut and Alice Wallenberg Foundation (KAW) via the Wallenberg AI, Autonomous Systems and Software Program (WASP); Wallenberg Initiative Material Science for Sustainability (WISE); Swedish Research Council (VR) [2020-05402]; Excellence Center at Linkoping-Lund in Information Technology (ELLIIT); Swedish e-Science Centre (SeRC); Knut and Alice Wallenberg Foundation at the National Supercomputer Centre (NSC); Chalmers Centre for Computational Science and Engineering (C3SE) - Swedish Research Council [2022-06725]

Available from: 2025-10-07 Created: 2025-10-07 Last updated: 2026-09-08

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Andersson, Oskar

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