Related papers: Coarse-Grained Boltzmann Generators
In this study, we address the challenge of using energy-based models to produce high-quality, label-specific data in complex structured datasets, such as population genetics, RNA or protein sequences data. Traditional training methods…
We introduce a method for imposing higher-level structure on generated, polyphonic music. A Convolutional Restricted Boltzmann Machine (C-RBM) as a generative model is combined with gradient descent constraint optimisation to provide…
Boltzmann machine is a powerful machine learning model with many real-world applications, for example by constructing deep belief networks. Statistical inference on a Boltzmann machine can be carried out by sampling from its posterior…
Coarse-grained (CG) modeling simplifies molecular systems by mapping groups of atoms into representative units. However, traditional CG approaches rely on fixed mapping rules, which limit their ability to handle diverse chemical systems and…
The Boltzmann distribution of a protein provides a roadmap to all of its functional states. Normalizing flows are a promising tool for modeling this distribution, but current methods are intractable for typical pharmacological targets; they…
Extracting automatically the complex set of features composing real high-dimensional data is crucial for achieving high performance in machine--learning tasks. Restricted Boltzmann Machines (RBM) are empirically known to be efficient for…
Molecular dynamics simulations provide theoretical insight into the microscopic behavior of materials in condensed phase and, as a predictive tool, enable computational design of new compounds. However, because of the large temporal and…
Restricted Boltzmann Machines are simple and powerful generative models that can encode any complex dataset. Despite all their advantages, in practice the trainings are often unstable and it is difficult to assess their quality because the…
Molecular dynamics (MD) is a crucial technique for simulating biological systems, enabling the exploration of their dynamic nature and fostering an understanding of their functions and properties. To address exploration inefficiency,…
A hallmark of meso-scale interfacial fluids is the multi-faceted, scale-dependent interfacial energy, which often manifests different characteristics across the molecular and continuum scale. The multi-scale nature imposes a challenge to…
Driven by the critical needs of biomanufacturing 4.0, we introduce a probabilistic knowledge graph hybrid model characterizing the risk- and science-based understanding of bioprocess mechanisms. It can faithfully capture the important…
We review Boltzmann machines and energy-based models. A Boltzmann machine defines a probability distribution over binary-valued patterns. One can learn parameters of a Boltzmann machine via gradient based approaches in a way that log…
The restricted Boltzmann machine (RBM) is a neural network based on the Ising model, well known for its ability to learn probability distributions and stochastically generate new content. However, the high computational cost of Gibbs…
Quantum generative modeling has emerged as a promising application of quantum computers, aiming to model complex probability distributions beyond the reach of classical methods. In practice, however, training such models often requires…
We introduce a generalized machine learning framework to probabilistically parameterize upper-scale models in the form of nonlinear PDEs consistent with a continuum theory, based on coarse-grained atomistic simulation data of mechanical…
Machine learning has recently entered into the mainstream of coarse-grained (CG) molecular modeling and simulation. While a variety of methods for incorporating deep learning into these models exist, many of them involve training neural…
Markov state models (MSMs)---or discrete-time master equation models---are a powerful way of modeling the structure and function of molecular systems like proteins. Unfortunately, MSMs with sufficiently many states to make a quantitative…
In order to scale standard Gaussian process (GP) regression to large-scale datasets, aggregation models employ factorized training process and then combine predictions from distributed experts. The state-of-the-art aggregation models,…
Sampling from Boltzmann distributions, particularly those tied to high dimensional and complex energy functions, poses a significant challenge in many fields. In this work, we present the Energy-Based Diffusion Generator (EDG), a novel…
We build a new class of generative algorithms capable of efficiently learning an arbitrary target distribution from possibly scarce, high-dimensional data and subsequently generate new samples. These generative algorithms are particle-based…