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
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
arXiv:2606. 27895v1 Announce Type: cross Abstract: Differentiable partial differential equation (PDE) solvers underpin solver-in-the-loop ML training, gradient-based optimal control, and inverse problems, yet the practical cost of obtaining correct, usable gradients from a given solver on a given problem is largely undocumented.
By Andrin Rehmann, Heiko Zimmermann, Dion H\"afner
arXiv:2410. 10137v5 Announce Type: replace Abstract: We develop Riemannian approaches to variational autoencoders (VAEs) for PDE-type ambient data with regularizing geometric latent dynamics, which we refer to as VAE-DLM, or VAEs with dynamical latent manifolds.
By Andrew Gracyk