arXiv:2607. 00947v1 Announce Type: new Abstract: Generative models learn data distributions that reside on a low-dimensional manifold within a higher-dimensional ambient space.
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.
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.
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.
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.
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.
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.
arXiv:2607. 02834v1 Announce Type: new Abstract: Molecular optimization often starts from a pretrained generative model that captures a broad prior over valid molecular structures.
arXiv:2606. 11075v1 Announce Type: new Abstract: Aligning text-to-image flow matching models with human preferences via direct reward backpropagation is sample-efficient but hampered by two well-known pathologies: activations cannot be stored across the full sampling trajectory at modern model scale, and chained Jacobian products across steps inflate the reward gradient as it travels back to early indices.
arXiv:2607. 20550v1 Announce Type: cross Abstract: The traditional "one drug, one target" paradigm of structure-based drug design (SBDD) frequently proves inadequate for treating multifactorial diseases such as cancer and neurodegenerative disorders, owing to compensatory signaling pathways and the emergence of drug resistance.
Optimizing 3D shapes within the latent spaces of deep generative models is fundamental to computer assisted engineering, yet remains prone to a critical failure mode we term manifold drift: the tendency of gradient-based optimization to move latent vectors away from the manifold of valid shapes. This problem is exacerbated in state-of-the-art 3D shape generative models that operate in increasingly high-dimensional latent spaces where valid shapes occupy a vanishingly small fraction of the full space.
arXiv:2509. 26405v2 Announce Type: replace Abstract: We introduce InVirtuoGen, a discrete flow generative model for fragmented SMILES for de novo and fragment-constrained generation, and target-property/lead optimization of small molecules.
arXiv:2607. 28553v1 Announce Type: new Abstract: Predicting the 3D structures of atomic systems is fundamental to advancing material science and drug discovery.