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cdf1035c34ec380218a8cc9a43d438f9-AuthorFeedback.pdf
R2 considered our method requiring a "discretized proxy." First of all, a different, more challenging optimization problem is studied in our work. The variables in the16 barycenter problem we consider include not only the individual transport plan from each source to the barycenter,17 but importantly also the barycenter itself. Wewould33 like to point out that there are three accepted papers at NeurIPS last year inspired by Wasserstein barycenters. These are37 challenging questions that depend on the specific structure of parameterization and the particular recovery method.38
Enhanced Diffusion Sampling: Efficient Rare Event Sampling and Free Energy Calculation with Diffusion Models
Xie, Yu, Winkler, Ludwig, Sun, Lixin, Lewis, Sarah, Foster, Adam E., Luna, José Jiménez, Hempel, Tim, Gastegger, Michael, Chen, Yaoyi, Zaporozhets, Iryna, Clementi, Cecilia, Bishop, Christopher M., Noé, Frank
The rare-event sampling problem has long been the central limiting factor in molecular dynamics (MD), especially in biomolecular simulation. Recently, diffusion models such as BioEmu have emerged as powerful equilibrium samplers that generate independent samples from complex molecular distributions, eliminating the cost of sampling rare transition events. However, a sampling problem remains when computing observables that rely on states which are rare in equilibrium, for example folding free energies. Here, we introduce enhanced diffusion sampling, enabling efficient exploration of rare-event regions while preserving unbiased thermodynamic estimators. The key idea is to perform quantitatively accurate steering protocols to generate biased ensembles and subsequently recover equilibrium statistics via exact reweighting. We instantiate our framework in three algorithms: UmbrellaDiff (umbrella sampling with diffusion models), $Δ$G-Diff (free-energy differences via tilted ensembles), and MetaDiff (a batchwise analogue for metadynamics). Across toy systems, protein folding landscapes and folding free energies, our methods achieve fast, accurate, and scalable estimation of equilibrium properties within GPU-minutes to hours per system -- closing the rare-event sampling gap that remained after the advent of diffusion-model equilibrium samplers.
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Diversity-Driven Synthesis: Enhancing Dataset Distillation through Directed Weight Adjustment
To avoid redundancy in these synthetic datasets, it is crucial that each element contains unique features and remains diverse from others during the synthesis stage. In this paper, we provide a thorough theoretical and empirical analysis of diversity within synthesized datasets. We argue that enhancing diversity can improve the parallelizable yet isolated synthesizing approach.
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