Related papers: Potential Score Matching: Debiasing Molecular Stru…

Protein structure prediction (PSP) is computationally a very challenging problem. The challenge largely comes from the fact that the energy function that needs to be minimised in order to obtain the native structure of a given protein is…

Many existing conditional score-based data generation methods utilize Bayes' theorem to decompose the gradients of a log posterior density into a mixture of scores. These methods facilitate the training procedure of conditional score…

Score-based generative models (SGMs) have recently emerged as a promising class of generative models. However, a fundamental limitation is that their sampling process is slow due to a need for many (e.g., 2000) iterations of sequential…

Propensity score matching is a common tool for adjusting for observed confounding in observational studies, but is known to have limitations in the presence of unmeasured confounding. In many settings, researchers are confronted with…

State-space models (SSMs) are a highly expressive model class for learning patterns in time series data and for system identification. Deterministic versions of SSMs (e.g. LSTMs) proved extremely successful in modeling complex time series…

Training energy-based probabilistic models is confronted with apparently intractable sums, whose Monte Carlo estimation requires sampling from the estimated probability distribution in the inner loop of training. This can be approximately…

We resolve difficulties in training and sampling from a discrete generative model by learning a smoothed energy function, sampling from the smoothed data manifold with Langevin Markov chain Monte Carlo (MCMC), and projecting back to the…

Graph structures offer a versatile framework for representing diverse patterns in nature and complex systems, applicable across domains like molecular chemistry, social networks, and transportation systems. While diffusion models have…

Score-based generative modeling (SGM) is a highly successful approach for learning a probability distribution from data and generating further samples. We prove the first polynomial convergence guarantees for the core mechanic behind SGM:…

In this work, we address the challenge of multi-task image generation with limited data for denoising diffusion probabilistic models (DDPM), a class of generative models that produce high-quality images by reversing a noisy diffusion…

Diffusion models have emerged as powerful generative tools with applications in computer vision and scientific machine learning (SciML), where they have been used to solve large-scale probabilistic inverse problems. Traditionally, these…

We focus on the problem of efficient sampling and learning of probability densities by incorporating symmetries in probabilistic models. We first introduce Equivariant Stein Variational Gradient Descent algorithm -- an equivariant sampling…

De novo peptide sequencing algorithms have been widely used in proteomics to analyse tandem mass spectra (MS/MS) and assign them to peptides, but quality-control methods to evaluate the confidence of de novo peptide sequencing are lagging…

Efficient sampling from the Boltzmann distribution given its energy function is a key challenge for modeling complex physical systems such as molecules. Boltzmann Generators address this problem by leveraging continuous normalizing flows to…

This article is concerned with the mathematical analysis of a family of adaptive importance sampling algorithms applied to diffusion processes. These methods, referred to as Adaptive Biasing Potential methods, are designed to efficiently…

Molecular dynamics (MD) has long been the de facto choice for simulating complex atomistic systems from first principles. Recently deep learning models become a popular way to accelerate MD. Notwithstanding, existing models depend on…

Energy-based models (EBMs) offer flexible distribution parametrization. However, due to the intractable partition function, they are typically trained via contrastive divergence for maximum likelihood estimation. In this paper, we propose…

The development of next-generation molecular simulation models requires moving beyond pre-defined functional forms toward machine learning (ML) techniques that directly capture multiscale physics. Here, we demonstrate such an approach using…

Score-based diffusion modeling is a generative machine learning algorithm that can be used to sample from complex distributions. They achieve this by learning a score function, i.e., the gradient of the log-probability density of the data,…

Particle Size Analysis (PSA) is an important process carried out in a number of industries, which can significantly influence the properties of the final product. A ubiquitous instrument for this purpose is the Optical Microscope (OM).…