相关论文: Learning Collective Variables from BioEmu with Tim…

Developing accurate and efficient coarse-grained representations of proteins is crucial for understanding their folding, function, and interactions over extended timescales. Our methodology involves simulating proteins with molecular…

Molecular dynamics simulations hold great promise for providing insight into the microscopic behavior of complex molecular systems. However, their effectiveness is often constrained by long timescales associated with rare events. Enhanced…

An energy-based model (EBM) is a popular generative framework that offers both explicit density and architectural flexibility, but training them is difficult since it is often unstable and time-consuming. In recent years, various training…

Current state-of-the-art generative approaches frequently rely on a two-stage training procedure, where an autoencoder (often a VAE) first performs dimensionality reduction, followed by training a generative model on the learned latent…

The most popular and universally predictive protein simulation models employ all-atom molecular dynamics (MD), but they come at extreme computational cost. The development of a universal, computationally efficient coarse-grained (CG) model…

Without knowledge of specific pockets, generating ligands based on the global structure of a protein target plays a crucial role in drug discovery as it helps reduce the search space for potential drug-like candidates in the pipeline.…

In this paper, we investigate the problem of string-based molecular generation via variational autoencoders (VAEs) that have served a popular generative approach for various tasks in artificial intelligence. We propose a simple, yet…

Deep generative models such as conditional variational autoencoders (CVAEs) have shown great promise for predicting trajectories of surrounding agents in autonomous vehicle planning. State-of-the-art models have achieved remarkable accuracy…

In this report, we present an unsupervised machine learning method for determining groups of molecular systems according to similarity in their dynamics or structures using Ward's minimum variance objective function. We first apply the…

The heat shock protein 90 (Hsp90) is a molecular chaperone that controls the folding and activation of client proteins using the free energy of ATP hydrolysis. The Hsp90 active site is in its N-terminal domain (NTD). Our goal is to…

This work proposes a model for continual learning on tasks involving temporal sequences, specifically, human motions. It improves on a recently proposed brain-inspired replay model (BI-R) by building a biologically-inspired conditional…

Charged particle dynamics under the influence of electromagnetic fields is a challenging spatiotemporal problem. Many high performance physics-based simulators for predicting behavior in a charged particle beam are computationally…

Cross-validation (CV) is one of the main tools for performance estimation and parameter tuning in machine learning. The general recipe for computing CV estimate is to run a learning algorithm separately for each CV fold, a computationally…

PLUMED-GUI is an interactive environment to develop and test complex PLUMED scripts within the Visual Molecular Dynamics (VMD) environment. Computational biophysicists can take advantage of both PLUMED's rich syntax to define collective…

Machine-learned coarse-grained (MLCG) molecular dynamics is a promising option for modeling biomolecules. However, MLCG models currently require large amounts of data from reference atomistic molecular dynamics or substantial computation…

Given a probability distribution $\mu$ in $\mathbb{R}^d$ represented by data, we study in this paper the generative modeling of the corresponding conditional probability distributions on the level-sets of a collective variable…

Cryo-electron microscopy (cryo-EM) has revolutionized experimental protein structure determination. Despite advances in high resolution reconstruction, a majority of cryo-EM experiments provide either a single state of the studied…

Learning compact and interpretable representations of data is a critical challenge in scientific image analysis. Here, we introduce Affinity-VAE, a generative model that enables us to impose our scientific intuition about the similarity of…

We investigate large-scale latent variable models (LVMs) for neural story generation -- an under-explored application for open-domain long text -- with objectives in two threads: generation effectiveness and controllability. LVMs,…

Many modern data analyses benefit from explicitly modeling dependence structure in data -- such as measurements across time or space, ordered words in a sentence, or genes in a genome. A gold standard evaluation technique is structured…