Related papers: Potential Score Matching: Debiasing Molecular Stru…

Controllable molecular graph generation is essential for material and drug discovery, where generated molecules must satisfy diverse property constraints. While recent advances in graph diffusion models have improved generation quality,…

Particle-based modeling of materials at atomic scale plays an important role in the development of new materials and understanding of their properties. The accuracy of particle simulations is determined by interatomic potentials, which…

Molecule generation is advancing rapidly in chemical discovery and drug design. Flow matching methods have recently set the state of the art (SOTA) in unconditional molecule generation, surpassing score-based diffusion models. However,…

Despite the remarkable empirical success of score-based diffusion models, their statistical guarantees remain underdeveloped. Existing analyses often provide pessimistic convergence rates that do not reflect the intrinsic low-dimensional…

Sequential Monte Carlo (SMC) samplers are powerful tools for Bayesian inference but suffer from high computational costs due to their reliance on large particle ensembles for accurate estimates. We introduce persistent sampling (PS), an…

Diffusion models have shown promising potential for advancing Boltzmann Generators. However, two critical challenges persist: (1) inherent errors in samples due to model imperfections, and (2) the requirement of hundreds of functional…

Score-based generative models (SGMs) have gained prominence in sparse-view CT reconstruction for their precise sampling of complex distributions. In SGM-based reconstruction, data consistency in the score-based diffusion model ensures close…

Time course measurement of single molecules on a cell surface provides detailed information on the dynamics of the molecules, which is otherwise inaccessible. To extract the quantitative information, single particle tracking (SPT) is…

Finding parameters that minimise a loss function is at the core of many machine learning methods. The Stochastic Gradient Descent algorithm is widely used and delivers state of the art results for many problems. Nonetheless, Stochastic…

Predicting stable and metastable structures is central to molecular and materials discovery, but remains limited by the cost of searching high-dimensional energy landscapes. Deep generative models offer efficient structure sampling, yet…

This is an expository article on the score-based diffusion models, with a particular focus on the formulation via stochastic differential equations (SDE). After a gentle introduction, we discuss the two pillars in the diffusion modeling --…

Recent score-based diffusion models (SBDMs) show promising results in unpaired image-to-image translation (I2I). However, existing methods, either energy-based or statistically-based, provide no explicit form of the interfered intermediate…

Reward-based fine-tuning steers a pretrained diffusion or flow-based generative model toward higher-reward samples while remaining close to the pretrained model. Although existing methods are derived from different perspectives, we show…

Energy-Based Models (EBMs) have been widely used for generative modeling. Contrastive Divergence (CD), a prevailing training objective for EBMs, requires sampling from the EBM with Markov Chain Monte Carlo methods (MCMCs), which leads to an…

Solving partial differential equations (PDEs) on fine spatio-temporal scales for high-fidelity solutions is critical for numerous scientific breakthroughs. Yet, this process can be prohibitively expensive, owing to the inherent complexities…

Probability proportional to size (PPS) sampling schemes with a target sample size aim to produce a sample comprising a specified number $n$ of items while ensuring that each item in the population appears in the sample with a probability…

Diffusion probabilistic models (DPMs) have emerged as a promising technique in generative modeling. The success of DPMs relies on two ingredients: time reversal of diffusion processes and score matching. In view of possibly unguaranteed…

Score-based generative models have recently achieved remarkable success. While they are usually parameterized by the score, an alternative way is to use a series of time-dependent energy-based models (EBMs), where the score is obtained from…

Recently, diffusion model have demonstrated impressive image generation performances, and have been extensively studied in various computer vision tasks. Unfortunately, training and evaluating diffusion models consume a lot of time and…

The success of metabolomics studies depends upon the "fitness" of each biological sample used for analysis: it is critical that metabolite levels reported for a biological sample represent an accurate snapshot of the studied organism's…