Kucukbenli, Emine

9 publications

TMLR 2026 Augmenting Molecular Graphs with Geometries via Machine Learning Interatomic Potentials Cong Fu, Yuchao Lin, Zachary Krueger, Haiyang Yu, Maho Nakata, Jianwen Xie, Emine Kucukbenli, Xiaofeng Qian, Shuiwang Ji

ICLR 2026 La-Proteina: Atomistic Protein Generation via Partially Latent Flow Matching Tomas Geffner, Kieran Didi, Zhonglin Cao, Danny Reidenbach, Zuobai Zhang, Christian Dallago, Emine Kucukbenli, Karsten Kreis, Arash Vahdat

ICLR 2026 Scaling Atomistic Protein Binder Design with Generative Pretraining and Test-Time Compute Kieran Didi, Zuobai Zhang, Guoqing Zhou, Danny Reidenbach, Zhonglin Cao, Sooyoung Cha, Tomas Geffner, Christian Dallago, Jian Tang, Michael M. Bronstein, Martin Steinegger, Emine Kucukbenli, Arash Vahdat, Karsten Kreis

ICLRW 2025 Efficient Molecular Conformer Generation with SO(3) Averaged Flow-Matching and Reflow Zhonglin Cao, Mario Geiger, Allan Dos Santos Costa, Danny Reidenbach, Karsten Kreis, Tomas Geffner, Franco Pellegrini, Guoqing Zhou, Emine Kucukbenli

ICML 2025 Efficient Molecular Conformer Generation with SO(3)-Averaged Flow Matching and Reflow Zhonglin Cao, Mario Geiger, Allan Dos Santos Costa, Danny Reidenbach, Karsten Kreis, Tomas Geffner, Franco Pellegrini, Guoqing Zhou, Emine Kucukbenli

ICLRW 2025 EquiJump: Protein Dynamics Simulation via SO(3)-Equivariant Stochastic Interpolants Allan Dos Santos Costa, Ilan Mitnikov, Franco Pellegrini, Ameya Daigavane, Mario Geiger, Zhonglin Cao, Karsten Kreis, Tess Smidt, Emine Kucukbenli, Joseph Jacobson

ICLR 2025 Proteina: Scaling Flow-Based Protein Structure Generative Models Tomas Geffner, Kieran Didi, Zuobai Zhang, Danny Reidenbach, Zhonglin Cao, Jason Yim, Mario Geiger, Christian Dallago, Emine Kucukbenli, Arash Vahdat, Karsten Kreis

NeurIPS 2025 Tensor Decomposition Networks for Fast Machine Learning Interatomic Potential Computations Yuchao Lin, Cong Fu, Zachary Krueger, Haiyang Yu, Maho Nakata, Jianwen Xie, Emine Kucukbenli, Xiaofeng Qian, Shuiwang Ji

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