arXiv:2607. 27431v1 Announce Type: new Abstract: Generative modeling of protein backbones promises the de novo design of proteins with prescribed structural and functional properties.
By Yikun Bai, Binghang Lu, Yikai Liu, Elaheh Akbari, Soheil Kolouri, Linxuan Wang, Ping He, Shuchan Wang, Ruqi Zhang, Guang Lin
arXiv:2607. 22004v1 Announce Type: new Abstract: Energy natural gradient descent (ENGD) aligns parameter updates with the curvature of an underlying function-space energy, but existing formulations assume an unconstrained Euclidean parameter domain.
By Zhangyong Liang, Huanhuan Gao
arXiv:2606. 08375v1 Announce Type: new Abstract: All-atom generative modeling of 3D biomolecular complexes has emerged as the dominant paradigm for predicting the structure of proteins and protein-ligand systems.
By Gianluca Scarpellini, Ron Shprints, Peter Holderrieth, Juno Nam, Pranav Murugan, Rafael G\'omez-Bombarelli, Tommi Jaakola, Maruan Al-Shedivat, Nicholas Matthew Boffi, Avishek Joey Bose
RW-Flow presents a new one‑step generative framework for data on compact manifolds, leveraging Wasserstein gradient flows. The authors derive a necessary and sufficient identifiability condition for velocity fields on compact, connected Riemannian manifolds, showing that a symmetric, Lipschitz‑continuous cost function yields identifiability iff its Gibbs kernel is nondegenerate. Experiments on geospatial events, protein and RNA torsion angles, and discretized manifolds demonstrate that RW‑Flow surpasses existing one‑step methods across most benchmark settings.
By Ualibyek Nurgulan, Seungwoo Yoo, Prin Phunyaphibarn, Minhyuk Sung
arXiv:2510.03095v4 Announce Type: replace
Abstract: Diffusion- and flow-based generative models have recently demonstrated strong performance in protein backbone generation tasks, offering unpreceden...
By Liyang Xie, Haoran Zhang, Zhendong Wang, Wesley Tansey, Mingyuan Zhou
arXiv:2510. 08906v2 Announce Type: replace-cross Abstract: Training set sampling methods are used to improve model performance and lower data costs in machine learning problems relevant to chemistry.
By Morris Trestman, Stefan Gugler, Felix A. Faber, O. A. von Lilienfeld