Related papers: HemePLM-Diffuse: A Scalable Generative Framework f…

For inhomogeneous systems with interfaces, the inclusion of long-range dispersion interactions is necessary to achieve consistency between molecular simulation calculations and experimental results. For accurate and efficient incorporation…

Molecular generation and molecular property prediction are both crucial for drug discovery, but they are often developed independently. Inspired by recent studies, which demonstrate that diffusion model, a prominent generative approach, can…

Protein structure generative models excel at predicting single protein static structures from sequence, but routinely fail to capture the correct conformational state of protein complexes, critical for protein design and induced proximity…

Diffusion-based generative models in SE(3)-invariant space have demonstrated promising performance in molecular conformation generation, but typically require solving stochastic differential equations (SDEs) with thousands of update steps.…

Large Language Model (LLM) routing is a pivotal technique for navigating a diverse landscape of LLMs, aiming to select the best-performing LLMs tailored to the domains of user queries, while managing computational resources. However,…

Generating molecular dynamics (MD) trajectories using deep generative models has attracted increasing attention, yet remains inherently challenging due to the limited availability of MD data and the complexities involved in modeling…

We propose a novel diffusion map particle system (DMPS) for generative modeling, based on diffusion maps and Laplacian-adjusted Wasserstein gradient descent (LAWGD). Diffusion maps are used to approximate the generator of the corresponding…

This work introduces the generative fractional diffusion model for protein generation (ProT-GFDM), a novel generative framework that employs fractional stochastic dynamics for protein backbone structure modeling. This approach builds on the…

Generative models are spearheading recent progress in deep learning, showcasing strong promise for trajectory sampling in dynamical systems as well. However, whereas latent space modeling paradigms have transformed image and video…

Deep generative models such as diffusion and flow matching are powerful machine learning tools capable of learning and sampling from high-dimensional distributions. They are particularly useful when the training data appears to be…

Molecular conformer generation is a fundamental task in computational chemistry. Several machine learning approaches have been developed, but none have outperformed state-of-the-art cheminformatics methods. We propose torsional diffusion, a…

Diffusion models have become a popular choice for human motion synthesis due to their powerful generative capabilities. However, their high computational complexity and large sampling steps pose challenges for real-time applications.…

The substantial memory bandwidth and computational demands of large language models (LLMs) present critical challenges for efficient inference. To tackle this, the literature has explored heterogeneous systems that combine neural processing…

We investigate whether synthetic images generated by diffusion models can enhance multi-label classification of protein subcellular localization. Specifically, we implement a simplified class-conditional denoising diffusion probabilistic…

Automatically generating high-quality real world 3D scenes is of enormous interest for applications such as virtual reality and robotics simulation. Towards this goal, we introduce NeuralField-LDM, a generative model capable of synthesizing…

Simulations are vital for understanding and predicting the evolution of complex molecular systems. However, despite advances in algorithms and special purpose hardware, accessing the timescales necessary to capture the structural evolution…

The function of biomolecules such as proteins depends on their ability to interconvert between a wide range of structures or "conformations." Researchers have endeavored for decades to develop computational methods to predict the…

Unravelling protein distributions within individual cells is key to understanding their function and state and indispensable to developing new treatments. Here we present the Hybrid subCellular Protein Localiser (HCPL), which learns from…

Generative models of macromolecules carry abundant and impactful implications for industrial and biomedical efforts in protein engineering. However, existing methods are currently limited to modeling protein structures or sequences,…

Protein is linked to almost every life process. Therefore, analyzing the biological structure and property of protein sequences is critical to the exploration of life, as well as disease detection and drug discovery. Traditional protein…