Equivariant Asynchronous Diffusion: An Adaptive Denoising Schedule for Accelerated Molecular Conformation Generation

Diffusion models show promise for 3D molecular generation, but face a fundamental trade-off between sampling efficiency and conformational accuracy. While flow-based models are fast, they often produce geometrically inaccurate structures, as they have difficulty capturing the multimodal distributions of molecular conformations. In contrast, denoising diffusion models are more accurate but suffer from slow sampling, a limitation attributed to sub-optimal integration between diffusion dynamics and SE(3)-equivariant architectures. To address this, we propose VEDA, a unified SE(3)-equivariant framework that combines variance-exploding diffusion with annealing to efficiently generate conformationally accurate 3D molecular structures. Specifically, our key technical contributions include: (1) a VE schedule that enables noise injection functionally analogous to simulated annealing, improving 3D accuracy and reducing relaxation energy; (2) a novel preconditioning scheme that reconciles the coordinate-predicting nature of SE(3)-equivariant networks with a residual-based diffusion objective, and (3) a new arcsin-based scheduler that concentrates sampling in critical intervals of the logarithmic signal-to-noise ratio. On the QM9 and GEOM-DRUGS datasets, VEDA matches the sampling efficiency of flow-based models, achieving state-of-the-art valency stability and validity with only 100 sampling steps. More importantly, VEDA's generated structures are remarkably stable, as measured by their relaxation energy during GFN2-xTB optimization. The median energy change is only 1.72 kcal/mol, significantly lower than the 32.3 kcal/mol from its architectural baseline, SemlaFlow. Our framework demonstrates that principled integration of VE diffusion with SE(3)-equivariant architectures can achieve both high chemical accuracy and computational efficiency.

Three-dimensional (3D) molecule generation has been dominated by diffusion models, which achieve strong generation quality but typically require the molecular size to be specified a priori. Recent autoregressive approaches have substantially narrowed the performance gap while naturally supporting variable-length generation and conditioning on partial molecular context. However, balancing unconditional and context-conditioned generation remains challenging. We introduce KRONOS, a latent autoregressive diffusion framework that generates molecules in the latent space of a pre-trained autoencoder, jointly modeling molecular graph topology and geometry, while retaining the flexibility of autoregressive generation. We further introduce a mixed training strategy inspired by Fill-in-the Middle (FIM) paradigm, enabling both unconditional and fragment-conditioned molecular generation within a single left-to-right autoregressive model. Experiments on QM9 and GEOM-Drugs demonstrate that KRONOS achieves leading unconditional generation performance among autoregressive methods, while remaining competitive with diffusion models. Moreover, fragment-conditioned generation is achieved with negligible impact on unconditional generation performance, demonstrating that both generation paradigms can be supported within a single architecture.

Generating molecules that simultaneously satisfy drug-like properties and conform to the 3D structure of a target protein is a core challenge in structure-based drug design (SBDD). Existing generative approaches, however, often rely on costly post-hoc processing during Sampling or require carefully curated datasets during training, yet still achieve modest gains. These limitations are especially pronounced in multi-objective settings, where balancing conflicting criteria remains a core challenge. To address these challenges, We propose FTDiff, a reinforcement learning fine-tuning framework tailored for diffusion-based molecular generation under structural constraints. To ensure stable and sample-efficient optimization, FTDiff adopts a group relative policy optimization (GRPO) style strategy. Furthermore, FTDiff builds upon a time-free pretrained diffusion model and incorporates a fast sampling mechanism that reduces the number of denoising steps, significantly accelerating both training and inference while maintaining generation quality. By optimizing a fixed threshold-aware reward, FTDiff effectively guides the model to produce valid, diverse, and high- quality molecules that balance multiple drug design objectives. Extensive experiments on benchmark datasets demonstrate that FTDiff consistently outperforms prior methods, without requiring expensive post-hoc optimization or intricate data engineering.