Manifold Aware Denoising Score Matching (MAD)

A major focus in designing methods for learning distributions defined on manifolds is to alleviate the need to implicitly learn the manifold so that learning can concentrate on the data distribution within the manifold. However, accomplishing this often leads to compute-intensive solutions. In this work, we propose a simple modification to denoising score-matching in the ambient space to implicitly account for the manifold, thereby reducing the burden of learning the manifold while maintaining computational efficiency. Specifically, we propose a simple decomposition of the score function into a known component $s^{base}$ and a remainder component $s-s^{base}$ (the learning target), with the former implicitly including information on where the data manifold resides. We derive known components $s^{base}$ in analytical form for several important cases, including distributions over rotation matrices and discrete distributions, and use them to demonstrate the utility of this approach in those cases.

Meta Flow Maps enable scalable reward alignment

Controlling generative models is computationally expensive. This is because optimal alignment with a reward function--whether via inference-time steering or fine-tuning--requires estimating the value function. This task demands access to the conditional posterior $p_{1|t}(x_1|x_t)$, the distribution of clean data $x_1$ consistent with an intermediate state $x_t$, a requirement that typically compels methods to resort to costly trajectory simulations. To address this bottleneck, we introduce Meta Flow Maps (MFMs), a framework extending consistency models and flow maps into the stochastic regime. MFMs are trained to perform stochastic one-step posterior sampling, generating arbitrarily many i.i.d. draws of clean data $x_1$ from any intermediate state. Crucially, these samples provide a differentiable reparametrization that unlocks efficient value function estimation. We leverage this capability to solve bottlenecks in both paradigms: enabling inference-time steering without inner rollouts, and facilitating unbiased, off-policy fine-tuning to general rewards. Empirically, our single-particle steered-MFM sampler outperforms a Best-of-1000 baseline on ImageNet across multiple rewards at a fraction of the compute.

SigmaDock: Untwisting Molecular Docking With Fragment-Based SE(3) Diffusion

Determining the binding pose of a ligand to a protein, known as molecular docking, is a fundamental task in drug discovery. Generative approaches promise faster, improved, and more diverse pose sampling than physics-based methods, but are often hindered by chemically implausible outputs, poor generalisability, and high computational cost. To address these challenges, we introduce a novel fragmentation scheme, leveraging inductive biases from structural chemistry, to decompose ligands into rigid-body fragments. Building on this decomposition, we present SigmaDock, an SE(3) Riemannian diffusion model that generates poses by learning to reassemble these rigid bodies within the binding pocket. By operating at the level of fragments in SE(3), SigmaDock exploits well-established geometric priors while avoiding overly complex diffusion processes and unstable training dynamics. Experimentally, we show SigmaDock achieves state-of-the-art performance, reaching Top-1 success rates (RMSD<2 & PB-valid) above 79.9% on the PoseBusters set, compared to 12.7-30.8% reported by recent deep learning approaches, whilst demonstrating consistent generalisation to unseen proteins. SigmaDock is the first deep learning approach to surpass classical physics-based docking under the PB train-test split, marking a significant leap forward in the reliability and feasibility of deep learning for molecular modelling.