IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v16y2025i1d10.1038_s41467-025-58499-7.html
   My bibliography  Save this article

A multi-modal transformer for predicting global minimum adsorption energy

Author

Listed:
  • Junwu Chen

    (Ecole Polytechnique Fédérale de Lausanne (EPFL)
    Ecole Polytechnique Fédérale de Lausanne (EPFL))

  • Xu Huang

    (Ecole Polytechnique Fédérale de Lausanne (EPFL)
    Shanghai Jiao Tong University)

  • Cheng Hua

    (Shanghai Jiao Tong University)

  • Yulian He

    (Shanghai Jiao Tong University
    University of Michigan-Shanghai Jiao Tong University Joint Institute (UM-SJTU JI))

  • Philippe Schwaller

    (Ecole Polytechnique Fédérale de Lausanne (EPFL)
    Ecole Polytechnique Fédérale de Lausanne (EPFL))

Abstract

The fast assessment of the global minimum adsorption energy (GMAE) between catalyst surfaces and adsorbates is crucial for large-scale catalyst screening. However, multiple adsorption sites and numerous possible adsorption configurations for each surface/adsorbate combination make it prohibitively expensive to calculate the GMAE through density functional theory (DFT). Thus, we designed a multi-modal transformer called AdsMT to rapidly predict the GMAE based on surface graphs and adsorbate feature vectors without site-binding information. The AdsMT model effectively captures the intricate relationships between adsorbates and surface atoms through the cross-attention mechanism, hence avoiding the enumeration of adsorption configurations. Three diverse benchmark datasets were introduced, providing a foundation for further research on the challenging GMAE prediction task. Our AdsMT framework demonstrates excellent performance by adopting the tailored graph encoder and transfer learning, achieving mean absolute errors of 0.09, 0.14, and 0.39 eV, respectively. Beyond GMAE prediction, AdsMT’s cross-attention scores showcase the interpretable potential to identify the most energetically favorable adsorption sites. Additionally, uncertainty quantification was integrated into our models to enhance the trustworthiness of the predictions.

Suggested Citation

  • Junwu Chen & Xu Huang & Cheng Hua & Yulian He & Philippe Schwaller, 2025. "A multi-modal transformer for predicting global minimum adsorption energy," Nature Communications, Nature, vol. 16(1), pages 1-12, December.
  • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-58499-7
    DOI: 10.1038/s41467-025-58499-7
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-025-58499-7
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-025-58499-7?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Miao Zhong & Kevin Tran & Yimeng Min & Chuanhao Wang & Ziyun Wang & Cao-Thang Dinh & Phil De Luna & Zongqian Yu & Armin Sedighian Rasouli & Peter Brodersen & Song Sun & Oleksandr Voznyy & Chih-Shan Ta, 2020. "Accelerated discovery of CO2 electrocatalysts using active machine learning," Nature, Nature, vol. 581(7807), pages 178-183, May.
    2. Pushkar G. Ghanekar & Siddharth Deshpande & Jeffrey Greeley, 2022. "Adsorbate chemical environment-based machine learning framework for heterogeneous catalysis," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    3. Rafael B. Araujo & Gabriel L. S. Rodrigues & Egon Campos Santos & Lars G. M. Pettersson, 2022. "Adsorption energies on transition metal surfaces: towards an accurate and balanced description," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    4. Shuqi Lu & Zhifeng Gao & Di He & Linfeng Zhang & Guolin Ke, 2024. "Author Correction: Data-driven quantum chemical property prediction leveraging 3D conformations with Uni-Mol+," Nature Communications, Nature, vol. 15(1), pages 1-1, December.
    5. Shuqi Lu & Zhifeng Gao & Di He & Linfeng Zhang & Guolin Ke, 2024. "Data-driven quantum chemical property prediction leveraging 3D conformations with Uni-Mol+," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    6. Keith T. Butler & Daniel W. Davies & Hugh Cartwright & Olexandr Isayev & Aron Walsh, 2018. "Machine learning for molecular and materials science," Nature, Nature, vol. 559(7715), pages 547-555, July.
    7. Victor Fung & Guoxiang Hu & P. Ganesh & Bobby G. Sumpter, 2021. "Machine learned features from density of states for accurate adsorption energy prediction," Nature Communications, Nature, vol. 12(1), pages 1-11, December.
    8. Wang Gao & Yun Chen & Bo Li & Shan-Ping Liu & Xin Liu & Qing Jiang, 2020. "Determining the adsorption energies of small molecules with the intrinsic properties of adsorbates and substrates," Nature Communications, Nature, vol. 11(1), pages 1-11, December.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Kihoon Bang & Doosun Hong & Youngtae Park & Donghun Kim & Sang Soo Han & Hyuck Mo Lee, 2023. "Machine learning-enabled exploration of the electrochemical stability of real-scale metallic nanoparticles," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    2. Xiaoyun Lin & Xiaowei Du & Shican Wu & Shiyu Zhen & Wei Liu & Chunlei Pei & Peng Zhang & Zhi-Jian Zhao & Jinlong Gong, 2024. "Machine learning-assisted dual-atom sites design with interpretable descriptors unifying electrocatalytic reactions," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    3. Zhiyuan Han & An Chen & Zejian Li & Mengtian Zhang & Zhilong Wang & Lixue Yang & Runhua Gao & Yeyang Jia & Guanjun Ji & Zhoujie Lao & Xiao Xiao & Kehao Tao & Jing Gao & Wei Lv & Tianshuai Wang & Jinji, 2024. "Machine learning-based design of electrocatalytic materials towards high-energy lithium||sulfur batteries development," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    4. Gang Wang & Shinya Mine & Duotian Chen & Yuan Jing & Kah Wei Ting & Taichi Yamaguchi & Motoshi Takao & Zen Maeno & Ichigaku Takigawa & Koichi Matsushita & Ken-ichi Shimizu & Takashi Toyao, 2023. "Accelerated discovery of multi-elemental reverse water-gas shift catalysts using extrapolative machine learning approach," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    5. Zhilong Song & Linfeng Fan & Shuaihua Lu & Chongyi Ling & Qionghua Zhou & Jinlan Wang, 2025. "Inverse design of promising electrocatalysts for CO2 reduction via generative models and bird swarm algorithm," Nature Communications, Nature, vol. 16(1), pages 1-10, December.
    6. Kangming Li & Daniel Persaud & Kamal Choudhary & Brian DeCost & Michael Greenwood & Jason Hattrick-Simpers, 2023. "Exploiting redundancy in large materials datasets for efficient machine learning with less data," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    7. Manu Suvarna & Tangsheng Zou & Sok Ho Chong & Yuzhen Ge & Antonio J. Martín & Javier Pérez-Ramírez, 2024. "Active learning streamlines development of high performance catalysts for higher alcohol synthesis," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    8. Han Li & Ruotian Zhang & Yaosen Min & Dacheng Ma & Dan Zhao & Jianyang Zeng, 2023. "A knowledge-guided pre-training framework for improving molecular representation learning," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    9. Cheng Du & Joel P. Mills & Asfaw G. Yohannes & Wei Wei & Lei Wang & Siyan Lu & Jian-Xiang Lian & Maoyu Wang & Tao Guo & Xiyang Wang & Hua Zhou & Cheng-Jun Sun & John Z. Wen & Brian Kendall & Martin Co, 2023. "Cascade electrocatalysis via AgCu single-atom alloy and Ag nanoparticles in CO2 electroreduction toward multicarbon products," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    10. Tian Xie & Arthur France-Lanord & Yanming Wang & Jeffrey Lopez & Michael A. Stolberg & Megan Hill & Graham Michael Leverick & Rafael Gomez-Bombarelli & Jeremiah A. Johnson & Yang Shao-Horn & Jeffrey C, 2022. "Accelerating amorphous polymer electrolyte screening by learning to reduce errors in molecular dynamics simulated properties," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    11. Li, Yi & Liu, Kailong & Foley, Aoife M. & Zülke, Alana & Berecibar, Maitane & Nanini-Maury, Elise & Van Mierlo, Joeri & Hoster, Harry E., 2019. "Data-driven health estimation and lifetime prediction of lithium-ion batteries: A review," Renewable and Sustainable Energy Reviews, Elsevier, vol. 113(C), pages 1-1.
    12. O. V. Mythreyi & M. Rohith Srinivaas & Tigga Amit Kumar & R. Jayaganthan, 2021. "Machine-Learning-Based Prediction of Corrosion Behavior in Additively Manufactured Inconel 718," Data, MDPI, vol. 6(8), pages 1-16, July.
    13. Jian Cheng & Ling Chen & Yanzhi Zhang & Min Wang & Zhangyi Zheng & Lin Jiang & Zhao Deng & Zhihe Wei & Mutian Ma & Likun Xiong & Wei Hua & Daqi Song & Wenxuan Huo & Yuebin Lian & Wenjun Yang & Fenglei, 2025. "Metal-organic double layer to stabilize selective multi-carbon electrosynthesis," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
    14. Guolin Cao & Sha Yang & Ji-Chang Ren & Wei Liu, 2025. "Electronic descriptors for designing high-entropy alloy electrocatalysts by leveraging local chemical environments," Nature Communications, Nature, vol. 16(1), pages 1-11, December.
    15. Sarmad Dashti Latif & Ali Najah Ahmed, 2023. "A review of deep learning and machine learning techniques for hydrological inflow forecasting," Environment, Development and Sustainability: A Multidisciplinary Approach to the Theory and Practice of Sustainable Development, Springer, vol. 25(11), pages 12189-12216, November.
    16. Snehi Shrestha & Kieran James Barvenik & Tianle Chen & Haochen Yang & Yang Li & Meera Muthachi Kesavan & Joshua M. Little & Hayden C. Whitley & Zi Teng & Yaguang Luo & Eleonora Tubaldi & Po-Yen Chen, 2024. "Machine intelligence accelerated design of conductive MXene aerogels with programmable properties," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    17. Oscar Méndez-Lucio & Christos A. Nicolaou & Berton Earnshaw, 2024. "MolE: a foundation model for molecular graphs using disentangled attention," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
    18. Xinyu Chen & Shuaihua Lu & Qian Chen & Qionghua Zhou & Jinlan Wang, 2024. "From bulk effective mass to 2D carrier mobility accurate prediction via adversarial transfer learning," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
    19. SJ, Balaji & Babu, Suresh Chandra & Pal, Suresh, 2021. "Understanding Science and Policy Making in Agriculture: A Machine Learning Application for India," 2021 Conference, August 17-31, 2021, Virtual 315227, International Association of Agricultural Economists.
    20. Niklas W. A. Gebauer & Michael Gastegger & Stefaan S. P. Hessmann & Klaus-Robert Müller & Kristof T. Schütt, 2022. "Inverse design of 3d molecular structures with conditional generative neural networks," Nature Communications, Nature, vol. 13(1), pages 1-11, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-58499-7. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.