Stärk, Hannes

35 publications

FnTML 2025 Artificial Intelligence for Science in Quantum, Atomistic, and Continuum Systems Xuan Zhang, Limei Wang, Jacob Helwig, Youzhi Luo, Cong Fu, Yaochen Xie, Meng Liu, Yuchao Lin, Zhao Xu, Keqiang Yan, Keir Adams, Maurice Weiler, Xiner Li, Tianfan Fu, Yucheng Wang, Alex Strasser, Haiyang Yu, Yuqing Xie, Xiang Fu, Shenglong Xu, Yi Liu, Yuanqi Du, Alexandra Saxton, Hongyi Ling, Hannah Lawrence, Hannes Stärk, Shurui Gui, Carl Edwards, Nicholas Gao, Adriana Ladera, Tailin Wu, Elyssa F. Hofgard, Aria Mansouri Tehrani, Rui Wang, Ameya Daigavane, Montgomery Bohde, Jerry Kurtin, Qian Huang, Tuong Phung, Minkai Xu, Chaitanya K. Joshi, Simon V. Mathis, Kamyar Azizzadenesheli, Ada Fang, Alán Aspuru-Guzik, Erik J. Bekkers, Michael M. Bronstein, Marinka Zitnik, Anima Anandkumar, Stefano Ermon, Pietro Liò, Rose Yu, Stephan Günnemann, Jure Leskovec, Heng Ji, Jimeng Sun, Regina Barzilay, Tommi S. Jaakkola, Connor W. Coley, Xiaoning Qian, Xiaofeng Qian, Tess E. Smidt, Shuiwang Ji

ICLRW 2025 FreeFlow: Latent Flow Matching for Free Energy Difference Estimation Ege Erdogan, Radoslav Ralev, Mika Rebensburg, Céline Marquet, Leon Klein, Hannes Stark

ICLR 2025 ProtComposer: Compositional Protein Structure Generation with 3D Ellipsoids Hannes Stark, Bowen Jing, Tomas Geffner, Jason Yim, Tommi Jaakkola, Arash Vahdat, Karsten Kreis

ICLR 2025 Think While You Generate: Discrete Diffusion with Planned Denoising Sulin Liu, Juno Nam, Andrew Campbell, Hannes Stark, Yilun Xu, Tommi Jaakkola, Rafael Gomez-Bombarelli

ICMLW 2024 CodonMPNN for Organism Specific and Codon Optimal Inverse Folding Hannes Stark, Umesh Padia, Julia Balla, Cameron Diao

ICMLW 2024 CodonMPNN for Organism Specific and Codon Optimal Inverse Folding Hannes Stark, Umesh Padia, Julia Balla, Cameron Diao

ICML 2024 Dirichlet Flow Matching with Applications to DNA Sequence Design Hannes Stark, Bowen Jing, Chenyu Wang, Gabriele Corso, Bonnie Berger, Regina Barzilay, Tommi Jaakkola

ICLRW 2024 Dirichlet Flow Matching with Applications to DNA Sequence Design Hannes Stark, Bowen Jing, Chenyu Wang, Gabriele Corso, Bonnie Berger, Regina Barzilay, Tommi Jaakkola

NeurIPS 2024 ET-Flow: Equivariant Flow-Matching for Molecular Conformer Generation Majdi Hassan, Nikhil Shenoy, Jungyoon Lee, Hannes Stärk, Stephan Thaler, Dominique Beaini

ICMLW 2024 Equivariant Flow Matching for Molecular Conformer Generation Majdi Hassan, Nikhil Shenoy, Jungyoon Lee, Hannes Stark, Stephan Thaler, Dominique Beaini

ICMLW 2024 Equivariant Flow Matching for Molecular Conformer Generation Majdi Hassan, Nikhil Shenoy, Jungyoon Lee, Hannes Stark, Stephan Thaler, Dominique Beaini

NeurIPS 2024 Generative Modeling of Molecular Dynamics Trajectories Bowen Jing, Hannes Stärk, Tommi Jaakkola, Bonnie Berger

ICMLW 2024 Generative Modeling of Molecular Dynamics Trajectories Bowen Jing, Hannes Stark, Tommi Jaakkola, Bonnie Berger

ICML 2024 Harmonic Self-Conditioned Flow Matching for Joint Multi-Ligand Docking and Binding Site Design Hannes Stark, Bowen Jing, Regina Barzilay, Tommi Jaakkola

ICMLW 2024 PLINDER: The Protein-Ligand Interactions Dataset and Evaluation Resource Janani Durairaj, Yusuf Adeshina, Zhonglin Cao, Xuejin Zhang, Vladas Oleinikovas, Thomas Duignan, Zachary McClure, Xavier Robin, Emanuele Rossi, Guoqing Zhou, Srimukh Prasad Veccham, Clemens Isert, Yuxing Peng, Prabindh Sundareson, Mehmet Akdel, Gabriele Corso, Hannes Stark, Zachary Wayne Carpenter, Michael M. Bronstein, Emine Kucukbenli, Torsten Schwede, Luca Naef

ICLRW 2023 DiffDock-PP: Rigid Protein-Protein Docking with Diffusion Models Mohamed Amine Ketata, Cedrik Laue, Ruslan Mammadov, Hannes Stark, Menghua Wu, Gabriele Corso, Céline Marquet, Regina Barzilay, Tommi S. Jaakkola

NeurIPSW 2023 DiffDock-Pocket: Diffusion for Pocket-Level Docking with Sidechain Flexibility Michael Plainer, Marcella Toth, Simon Dobers, Hannes Stark, Gabriele Corso, Céline Marquet, Regina Barzilay

ICLR 2023 DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking Gabriele Corso, Hannes Stärk, Bowen Jing, Regina Barzilay, Tommi S. Jaakkola

NeurIPSW 2023 Harmonic Prior Self-Conditioned Flow Matching for Multi-Ligand Docking and Binding Site Design Hannes Stark, Bowen Jing, Regina Barzilay, Tommi Jaakkola

NeurIPSW 2023 Harmonic Prior Self-Conditioned Flow Matching for Multi-Ligand Docking and Binding Site Design Hannes Stark, Bowen Jing, Regina Barzilay, Tommi Jaakkola

NeurIPSW 2023 Latent Space Simulator for Unveiling Molecular Free Energy Landscapes and Predicting Transition Dynamics Simon Dobers, Hannes Stark, Xiang Fu, Dominique Beaini, Stephan Günnemann

ICLRW 2023 Task-Agnostic Graph Neural Network Evaluation via Adversarial Collaboration Xiangyu Zhao, Hannes Stärk, Dominique Beaini, Yiren Zhao, Pietro Lio

NeurIPSW 2023 Transition Path Sampling with Boltzmann Generator-Based MCMC Moves Michael Plainer, Hannes Stark, Charlotte Bunne, Stephan Günnemann

NeurIPSW 2023 Transition Path Sampling with Boltzmann Generator-Based MCMC Moves Michael Plainer, Hannes Stark, Charlotte Bunne, Stephan Günnemann

ICML 2022 3D Infomax Improves GNNs for Molecular Property Prediction Hannes Stärk, Dominique Beaini, Gabriele Corso, Prudencio Tossou, Christian Dallago, Stephan Günnemann, Pietro Lió

NeurIPSW 2022 DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking Gabriele Corso, Hannes Stärk, Bowen Jing, Regina Barzilay, Tommi S. Jaakkola

NeurIPSW 2022 DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking Gabriele Corso, Hannes Stärk, Bowen Jing, Regina Barzilay, Tommi S. Jaakkola

ICML 2022 EquiBind: Geometric Deep Learning for Drug Binding Structure Prediction Hannes Stärk, Octavian Ganea, Lagnajit Pattanaik, Dr.Regina Barzilay, Tommi Jaakkola

ICLRW 2022 EquiBind: Geometric Deep Learning for Drug Binding Structure Prediction Hannes Stärk, Octavian-Eugen Ganea, Lagnajit Pattanaik, Regina Barzilay, Tommi S. Jaakkola

NeurIPSW 2022 Equivariant 3D-Conditional Diffusion Models for Molecular Linker Design Ilia Igashov, Hannes Stärk, Clement Vignac, Victor Garcia Satorras, Pascal Frossard, Max Welling, Michael M. Bronstein, Bruno Correia

NeurIPSW 2022 Generalized Laplacian Positional Encoding for Graph Representation Learning Sohir Maskey, Ali Parviz, Maximilian Thiessen, Hannes Stärk, Ylli Sadikaj, Haggai Maron

ICLRW 2022 Graph Anisotropic Diffusion Ahmed A. A. Elhag, Gabriele Corso, Hannes Stärk, Michael M. Bronstein

ICLRW 2022 Graph Anisotropic Diffusion for Molecules Ahmed A. A. Elhag, Gabriele Corso, Hannes Stärk, Michael M. Bronstein

LoG 2022 The First Learning on Graphs Conference: Preface Bastian Rieck, Razvan Pascanu, Yuanqi Du, Hannes Stärk, Derek Lim, Chaitanya K. Joshi, Andreea Deac, Iulia Duta, Joshua Robinson, Gabriele Corso, Leonardo Cotta, Yanqiao Zhu, Kexin Huang, Michelle Li, Sofia Bourhim, Ilia Igashov

NeurIPSW 2021 3D Infomax Improves GNNs for Molecular Property Prediction Hannes Stärk, Dominique Beaini, Gabriele Corso, Prudencio Tossou, Christian Dallago, Stephan Günnemann, Pietro Lio