Related papers: SE(3)-Stochastic Flow Matching for Protein Backbon…

We introduce a generative model for protein backbone design utilizing geometric products and higher order message passing. In particular, we propose Clifford Frame Attention (CFA), an extension of the invariant point attention (IPA)…

Excitement at the prospect of using data-driven generative models to sample configurational ensembles of biomolecular systems stems from the extraordinary success of these models on a diverse set of high-dimensional sampling tasks. Unlike…

Protein structure prediction is pivotal for understanding the structure-function relationship of proteins, advancing biological research, and facilitating pharmaceutical development and experimental design. While deep learning methods and…

Modeling stochastic and irregularly sampled time series is a challenging problem found in a wide range of applications, especially in medicine. Neural stochastic differential equations (Neural SDEs) are an attractive modeling technique for…

Simulating trajectories of dynamical systems is a fundamental problem in a wide range of fields such as molecular dynamics, biochemistry, and pedestrian dynamics. Machine learning has become an invaluable tool for scaling physics-based…

Protein folding models have achieved groundbreaking results typically via a combination of integrating domain knowledge into the architectural blocks and training pipelines. Nonetheless, given the success of generative models across…

Generative models have emerged as a powerful paradigm for solving physics systems and modeling complex spatiotemporal dynamics. However, achieving high physical accuracy without incurring high computational cost remains a fundamental…

Controlled generation with pre-trained Diffusion and Flow Matching models has vast applications. One strategy for guiding ODE-based generative models is through optimizing a target loss $R(x_1)$ while staying close to the prior…

Deep generative models and neural operators have demonstrated significant potential for 3D aerodynamic inference. However, they often face inherent challenges in maintaining physical consistency and preserving high-frequency features,…

Combining discrete and continuous data is an important capability for generative models. We present Discrete Flow Models (DFMs), a new flow-based model of discrete data that provides the missing link in enabling flow-based generative models…

The multi-step denoising process in diffusion and Flow Matching models causes major efficiency issues, which motivates research on few-step generation. We present Solution Flow Models (SoFlow), a framework for one-step generation from…

Flow Matching (FM) has recently emerged as a leading approach for high-fidelity visual generation, offering a robust continuous-time alternative to ordinary differential equation (ODE) based models. However, despite their success, FM models…

Recently, many generative models for de novo protein structure design have emerged. Yet, only few tackle the difficult task of directly generating fully atomistic structures jointly with the underlying amino acid sequence. This is…

Significant progress in computer hardware and software have enabled molecular dynamics (MD) simulations to model complex biological phenomena such as protein folding. However, enabling MD simulations to access biologically relevant…

Deep generative models that produce novel molecular structures have the potential to facilitate chemical discovery. Diffusion models currently achieve state of the art performance for 3D molecule generation. In this work, we explore the use…

Deep generative models provide a promising approach to de novo 3D peptide design. Most of them jointly model the distributions of peptide's position, orientation, and conformation, attempting to simultaneously converge to the target pocket.…

The recent breakthrough of AlphaFold3 in modeling complex biomolecular interactions, including those between proteins and ligands, nucleotides, or metal ions, creates new opportunities for protein design. In so-called inverse protein…

Elucidating reaction mechanisms hinges on efficiently generating transition states (TSs), products, and complete reaction networks. Recent generative models, such as diffusion models for TS sampling and sequence-based architectures for…

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,…

Computational fluid dynamics (CFD) provides high-fidelity simulations of fluid flows but remains computationally expensive for many-query applications. In recent years deep learning (DL) has been used to construct data-driven fluid-dynamic…