VN-EGNN: E(3)- and SE(3)-Equivariant Graph Neural Networks with Virtual Nodes Enhance Protein Binding Site Identification.

Andreas Mayr Andreas Mayr 0001 University of Marburg, Department of Medical Biometry and Statistics, Germany University of Bonn, Department of Medical Biometrics, Informatics and Epidemiology, Medical Faculty, Germany Ludwig-Maximilians-Universitat Munchen, Department of Statistics, Germany Friedrich-Alexander-Universität Erlangen-Nürnberg, Department of Medical Informatics, Biometry and Epidemiology, Germany https://orcid.org/0000-0001-7106-9732 https://www.wikidata.org/entity/Q59677610 Andreas Mayr 0002 University of Innsbruck, Institute of Geography, Austria https://orcid.org/0000-0001-8305-4765

Florian Sestak Lisa Schneckenreiter Johannes Brandstetter Sepp Hochreiter Andreas Mayr Günter Klambauer VN-EGNN: E(3)- and SE(3)-Equivariant Graph Neural Networks with Virtual Nodes Enhance Protein Binding Site Identification. 11 2026 December 18 J. Cheminformatics 1 https://doi.org/10.1186/s13321-025-01127-9 db/journals/jcheminf/jcheminf18.html#SestakSBHMK26 streams/journals/jcheminf

Richard Freinschlag Timo Bertram Erich Kobler Andreas Mayr Günter Klambauer Symbol-Equivariant Recurrent Reasoning Models. 2026 March abs/2603.02193 CoRR https://doi.org/10.48550/arXiv.2603.02193 db/journals/corr/corr2603.html#abs-2603-02193 streams/journals/corr

Niklas Schmidinger Lisa Schneckenreiter Philipp Seidl Johannes Schimunek Pieter-Jan Hoedt Johannes Brandstetter Andreas Mayr Sohvi Luukkonen Sepp Hochreiter Günter Klambauer Bio-xLSTM: Generative modeling, representation and in-context learning of biological and chemical sequences. 2025 ICLR https://openreview.net/forum?id=IjbXZdugdj conf/iclr/2025 db/conf/iclr/iclr2025.html#SchmidingerSSSH25

Florian Sestak Artur P. Toshev Andreas Fürst Günter Klambauer Andreas Mayr Johannes Brandstetter LaM-SLidE: Latent Space Modeling of Spatial Dynamical Systems via Linked Entities. 2025 February abs/2502.12128 CoRR https://doi.org/10.48550/arXiv.2502.12128 db/journals/corr/corr2502.html#abs-2502-12128 streams/journals/corr

Birgit Vogel-Heuser Fandi Hartl Moritz Wittemer Jingyun Zhao Andreas Mayr Martin Fleischer Theresa Prinz Anne Fischer Jakob Trauer Philipp Schroeder 0002 Ann-Kathrin Goldbach Florian Rothmeyer Markus Zimmermann Kai-Uwe Bletzinger Johannes Fottner Rüdiger Daub Klaus Bengler André Borrmann Michael F. Zaeh Katrin Wudy Long living human-machine systems in construction and production enabled by digital twins: Exploring applications, challenges, and pathways to sustainability. 789-814 2024 September 72 Autom. 9 https://doi.org/10.1515/auto-2023-0227 db/journals/at/at72.html#VogelHeuserHWZMFPFTSGRZ24 streams/journals/at

Lisa Schneckenreiter Richard Freinschlag Florian Sestak Johannes Brandstetter Günter Klambauer Andreas Mayr GNN-VPA: A Variance-Preserving Aggregation Strategy for Graph Neural Networks. 2024 Tiny Papers @ ICLR https://openreview.net/forum?id=2yuAxTs0QV conf/iclr/2024tiny db/conf/iclr/iclr2024tiny.html#Schneckenreiter24 Emese Sükei Elisabeth Rumetshofer Niklas Schmidinger Andreas Mayr Ursula Schmidt-Erfurth Günter Klambauer Hrvoje Bogunovic Improving Clinical Predictions with Multi-Modal Pre-training in Retinal Imaging. 1-5 2024 ISBI https://doi.org/10.1109/ISBI56570.2024.10635447 conf/isbi/2024 db/conf/isbi/isbi2024.html#SukeiRSMSKB24 streams/conf/isbi

Lisa Schneckenreiter Richard Freinschlag Florian Sestak Johannes Brandstetter Günter Klambauer Andreas Mayr GNN-VPA: A Variance-Preserving Aggregation Strategy for Graph Neural Networks. 2024 abs/2403.04747 CoRR https://doi.org/10.48550/arXiv.2403.04747 db/journals/corr/corr2403.html#abs-2403-04747

Florian Sestak Lisa Schneckenreiter Johannes Brandstetter Sepp Hochreiter Andreas Mayr Günter Klambauer VN-EGNN: E(3)-Equivariant Graph Neural Networks with Virtual Nodes Enhance Protein Binding Site Identification. 2024 abs/2404.07194 CoRR https://doi.org/10.48550/arXiv.2404.07194 db/journals/corr/corr2404.html#abs-2404-07194

Niklas Schmidinger Lisa Schneckenreiter Philipp Seidl Johannes Schimunek Pieter-Jan Hoedt Johannes Brandstetter Andreas Mayr Sohvi Luukkonen Sepp Hochreiter Günter Klambauer Bio-xLSTM: Generative modeling, representation and in-context learning of biological and chemical sequences. 2024 abs/2411.04165 CoRR https://doi.org/10.48550/arXiv.2411.04165 db/journals/corr/corr2411.html#abs-2411-04165 streams/journals/corr

Andreas Mayr Sebastian Lehner Arno Mayrhofer Christoph Kloss Sepp Hochreiter Johannes Brandstetter Boundary Graph Neural Networks for 3D Simulations. 9099-9107 2023 AAAI https://doi.org/10.1609/aaai.v37i8.26092 conf/aaai/2023 db/conf/aaai/aaai2023.html#MayrLMKHB23

Karl Wolf Andreas Mayr Marco Nagiller Leopold Saltuari Matthias Harders Yeongmi Kim PoRi device: portable hand assessment and rehabilitation after stroke. 1003-1017 2022 70 Autom. 11 https://doi.org/10.1515/auto-2022-0037 db/journals/at/at70.html#WolfMNSHK22

Benjamin Lutz Dominik Kißkalt Andreas Mayr Daniel Regulin Matteo Pantano Jörg Franke In-situ identification of material batches using machine learning for machining operations. 1485-1495 2021 32 J. Intell. Manuf. 5 https://doi.org/10.1007/s10845-020-01718-3 db/journals/jim/jim32.html#LutzKMRPF21

Andreas Mayr Sebastian Lehner Arno Mayrhofer Christoph Kloss Sepp Hochreiter Johannes Brandstetter Learning 3D Granular Flow Simulations. 2021 abs/2105.01636 CoRR https://arxiv.org/abs/2105.01636 db/journals/corr/corr2105.html#abs-2105-01636

Andreas Mayr Sebastian Lehner Arno Mayrhofer Christoph Kloss Sepp Hochreiter Johannes Brandstetter Boundary Graph Neural Networks for 3D Simulations. 2021 abs/2106.11299 CoRR https://arxiv.org/abs/2106.11299 db/journals/corr/corr2106.html#abs-2106-11299

Noé Sturm Andreas Mayr Thanh Le Van Vladimir I. Chupakhin Hugo Ceulemans Jörg K. Wegner José Felipe Golib Dzib Nina Jeliazkova Yves Vandriessche Stanislav Böhm Vojtech Cima Jan Martinovic Nigel Greene Tom Vander Aa Thomas J. Ashby Sepp Hochreiter Ola Engkvist Günter Klambauer Hongming Chen 0001 Industry-scale application and evaluation of deep learning for drug target prediction. 26 2020 12 J. Cheminformatics 1 https://doi.org/10.1186/s13321-020-00428-5 db/journals/jcheminf/jcheminf12.html#SturmMVCCWDJVBC20

Jochen Bauer Michael Hechtel Christoph Konrad Martin Holzwarth Hilko Hoffmann Thomas Feld Sven Schneider 0006 Ingo Zinnikus Andreas Mayr Jörg Franke ForeSight - An AI-driven Smart Living Platform, Approach to Add Access Control to openHAB. 432-440 2020 ICOST https://doi.org/10.1007/978-3-030-51517-1_40 conf/icost/2020 db/conf/icost/icost2020.html#BauerHKHHFSZMF20

Markus Hofmarcher Andreas Mayr Elisabeth Rumetshofer Peter Ruch Philipp Renz Johannes Schimunek Philipp Seidl Andreu Vall Michael Widrich Sepp Hochreiter Günter Klambauer Large-scale ligand-based virtual screening for SARS-CoV-2 inhibitors using deep neural networks. 2020 abs/2004.00979 CoRR https://arxiv.org/abs/2004.00979 db/journals/corr/corr2004.html#abs-2004-00979

Thomas Adler Johannes Brandstetter Michael Widrich Andreas Mayr David P. Kreil Michael Kopp 0001 Günter Klambauer Sepp Hochreiter Cross-Domain Few-Shot Learning by Representation Fusion. 2020 abs/2010.06498 CoRR https://arxiv.org/abs/2010.06498 db/journals/corr/corr2010.html#abs-2010-06498

Noé Sturm Jiangming Sun Yves Vandriessche Andreas Mayr Günter Klambauer Lars Carlsson Ola Engkvist Hongming Chen 0001 Application of Bioactivity Profile-Based Fingerprints for Building Machine Learning Models. 962-972 2019 59 J. Chem. Inf. Model. 3 https://doi.org/10.1021/acs.jcim.8b00550 https://www.wikidata.org/entity/Q58565747 db/journals/jcisd/jcisd59.html#SturmSVMKCEC19

Jochen Bauer Hilko Hoffmann Thomas Feld Mathias Runge Oliver Hinz Andreas Mayr Kristina Förster Franz Teske Franziska Schäfer Christoph Konrad Jörg Franke ForeSight - Platform Approach for Enabling AI-based Services for Smart Living. 204-211 2019 ICOST https://doi.org/10.1007/978-3-030-32785-9_19 conf/icost/2019 db/conf/icost/icost2019.html#BauerHFRHMFTSKF19 Günter Klambauer Thomas Unterthiner Andreas Mayr Sepp Hochreiter Self-Normalizing Neural Networks. 971-980 2017 NIPS https://proceedings.neurips.cc/paper/2017/hash/5d44ee6f2c3f71b73125876103c8f6c4-Abstract.html http://papers.nips.cc/paper/6698-self-normalizing-neural-networks conf/nips/2017 db/conf/nips/nips2017.html#KlambauerUMH17

Günter Klambauer Thomas Unterthiner Andreas Mayr Sepp Hochreiter Self-Normalizing Neural Networks. 2017 abs/1706.02515 CoRR http://arxiv.org/abs/1706.02515 db/journals/corr/corr1706.html#KlambauerUMH17

Günter Klambauer Martin Wischenbart Michael Mahr Thomas Unterthiner Andreas Mayr Sepp Hochreiter Rchemcpp: a web service for structural analoging in ChEMBL, Drugbank and the Connectivity Map. 3392-3394 2015 31 Bioinform. 20 https://doi.org/10.1093/bioinformatics/btv373 https://www.wikidata.org/entity/Q40822032 db/journals/bioinformatics/bioinformatics31.html#KlambauerWMUMH15

Djork-Arné Clevert Andreas Mayr Thomas Unterthiner Sepp Hochreiter Rectified Factor Networks. 1855-1863 2015 NIPS https://proceedings.neurips.cc/paper/2015/hash/df0aab058ce179e4f7ab135ed4e641a9-Abstract.html http://papers.nips.cc/paper/5963-rectified-factor-networks conf/nips/2015 db/conf/nips/nips2015.html#ClevertMUH15

Djork-Arné Clevert Thomas Unterthiner Andreas Mayr Hubert Ramsauer Sepp Hochreiter Rectified Factor Networks. 2015 abs/1502.06464 CoRR http://arxiv.org/abs/1502.06464 db/journals/corr/corr1502.html#ClevertUMRH15

Thomas Unterthiner Andreas Mayr Günter Klambauer Sepp Hochreiter Toxicity Prediction using Deep Learning. 2015 abs/1503.01445 CoRR http://arxiv.org/abs/1503.01445 db/journals/corr/corr1503.html#UnterthinerMKH15

Marc Streit Samuel Gratzl Michael Gillhofer Andreas Mayr Andreas Mitterecker Sepp Hochreiter Furby: fuzzy force-directed bicluster visualization. S4 2014 15 BMC Bioinform. S-6 https://doi.org/10.1186/1471-2105-15-S6-S4 https://www.wikidata.org/entity/Q35216264 db/journals/bmcbi/bmcbi15S.html#StreitGGMMH14

Stefan Vonolfen Andreas Beham Michael Affenzeller Stefan Wagner 0002 Andreas Mayr Combination and Comparison of Different Genetic Encodings for the Vehicle Routing Problem. 327-334 2011 EUROCAST (1) https://doi.org/10.1007/978-3-642-27549-4_42 conf/eurocast/2011-1 db/conf/eurocast/eurocast2011-1.html#VonolfenBAWM11

Sepp Hochreiter Ulrich Bodenhofer Martin Heusel Andreas Mayr Andreas Mitterecker Adetayo Kasim Tatsiana Khamiakova Suzy Van Sanden Dan Lin 0004 Willem Talloen Luc Bijnens Hinrich W. H. Göhlmann Ziv Shkedy Djork-Arné Clevert FABIA: factor analysis for bicluster acquisition. 1520-1527 2010 26 Bioinform. 12 https://doi.org/10.1093/bioinformatics/btq227 https://www.wikidata.org/entity/Q24599474 db/journals/bioinformatics/bioinformatics26.html#HochreiterBHMMKKSLTBGSC10

Tom Vander Aa Thomas Adler Michael Affenzeller Thomas J. Ashby Jochen Bauer Andreas Beham Klaus Bengler Timo Bertram Luc Bijnens Kai-Uwe Bletzinger Ulrich Bodenhofer Hrvoje Bogunovic Stanislav Böhm André Borrmann Johannes Brandstetter Lars Carlsson Hugo Ceulemans Hongming Chen 0001 Vladimir I. Chupakhin Vojtech Cima Djork-Arné Clevert Rüdiger Daub José Felipe Golib Dzib Ola Engkvist Thomas Feld Anne Fischer Martin Fleischer Kristina Förster Johannes Fottner Jörg Franke Richard Freinschlag Andreas Fürst Michael Gillhofer Hinrich W. H. Göhlmann Ann-Kathrin Goldbach Samuel Gratzl Nigel Greene Matthias Harders Fandi Hartl Michael Hechtel Martin Heusel Oliver Hinz Sepp Hochreiter Pieter-Jan Hoedt Hilko Hoffmann Markus Hofmarcher Martin Holzwarth Nina Jeliazkova Adetayo Kasim Tatsiana Khamiakova Yeongmi Kim Dominik Kißkalt Günter Klambauer Christoph Kloss Erich Kobler Christoph Konrad Michael Kopp 0001 David P. Kreil Sebastian Lehner Dan Lin 0004 Benjamin Lutz Sohvi Luukkonen Michael Mahr Jan Martinovic Arno Mayrhofer Andreas Mitterecker Marco Nagiller Matteo Pantano Theresa Prinz Hubert Ramsauer Daniel Regulin Philipp Renz Florian Rothmeyer Peter Ruch Elisabeth Rumetshofer Mathias Runge Leopold Saltuari Suzy Van Sanden Franziska Schäfer Johannes Schimunek Niklas Schmidinger Ursula Schmidt-Erfurth Lisa Schneckenreiter Sven Schneider 0006 Philipp Schroeder 0002 Philipp Seidl Florian Sestak Ziv Shkedy Marc Streit Noé Sturm Emese Sükei Jiangming Sun Willem Talloen Franz Teske Artur P. Toshev Jakob Trauer Thomas Unterthiner Andreu Vall Thanh Le Van Yves Vandriessche Birgit Vogel-Heuser Stefan Vonolfen Stefan Wagner 0002 Jörg K. Wegner Michael Widrich Martin Wischenbart Moritz Wittemer Karl Wolf Katrin Wudy Michael F. ZähMichael F. Zaeh Jingyun Zhao Markus Zimmermann Ingo Zinnikus