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We introduce a new framework for molecular graph generation with 3D molecular generative models. Our Synthetic Coordinate Embedding (SyCo) framework maps molecular graphs to Euclidean point clouds via synthetic conformer coordinates and…

Generative models see increasing use in computer-aided drug design. However, while performing well at capturing distributions of molecular motifs, they often produce synthetically inaccessible molecules. To address this, we introduce…

Structure-Based Drug Design (SBDD) has revolutionized drug discovery by enabling the rational design of molecules for specific protein targets. Despite significant advancements in improving docking scores, advanced 3D-SBDD generative models…

The task of deducing three-dimensional molecular configurations from their two-dimensional graph representations holds paramount importance in the fields of computational chemistry and pharmaceutical development. The rapid advancement of…

The evolve-filter (EF) model is a filter-based numerical stabilization for under-resolved convection-dominated flows. EF is a simple, modular, and effective strategy for both full-order models (FOMs) and reduced-order models (ROMs). It is…

Structure-based drug design (SBDD), which maps target proteins to candidate molecular ligands, is a fundamental task in drug discovery. Effectively aligning protein structural representations with molecular representations, and ensuring…

Breakthroughs in high-accuracy protein structure prediction, such as AlphaFold, have established receptor-based molecule design as a critical driver for rapid early-phase drug discovery. However, most approaches still struggle to balance…

A central goal in systems biology and drug discovery is to predict the transcriptional response of cells to perturbations. This task is challenging due to the noisy and sparse nature of single-cell measurements, as well as the fact that…

Equivocal 3D lesion segmentation exhibits high inter-observer variability. Conventional deterministic models ignore this aleatoric uncertainty, producing over-confident masks that obscure clinical risks. Conversely, while generative methods…

Diffusion models (DMs) represent state-of-the-art generative models for continuous inputs. DMs work by constructing a Stochastic Differential Equation (SDE) in the input space (ie, position space), and using a neural network to reverse it.…

Many real-world problems require reasoning across multiple scales, demanding models which operate not on single data points, but on entire distributions. We introduce generative distribution embeddings (GDE), a framework that lifts…

Diffusion generative models (DMs) have achieved promising results in image and graph generation. However, real-world graphs, such as social networks, molecular graphs, and traffic graphs, generally share non-Euclidean topologies and hidden…

The evolutionary fitness landscape of biological molecules is extremely sparse and heterogeneous, with functional sequences forming isolated dense ``islands'' within a vast combinatorial space of largely non-functional variants. Protein…

Recent years have witnessed significant progress in developing effective training and fast sampling techniques for diffusion models. A remarkable advancement is the use of stochastic differential equations (SDEs) and their…

We propose Evolutionary Dynamic Loss (EDL), a framework that learns a transferable classification loss in the probability space using unlimited synthetic prediction-label pairs, without accessing real samples during the main loss…

Modeling transformations between arbitrary data distributions is a fundamental scientific challenge, arising in applications like drug discovery and evolutionary simulation. While flow matching offers a natural framework for this task, its…

Many generative applications, such as synthesis-based 3D molecular design, involve constructing compositional objects with continuous features. Here, we introduce Compositional Generative Flows (CGFlow), a novel framework that extends flow…

We construct a reduced, data-driven, parameter dependent effective Stochastic Differential Equation (eSDE) for electric-field mediated colloidal crystallization using data obtained from Brownian Dynamics Simulations. We use Diffusion Maps…

While existing equivariant methods enhance data efficiency, they suffer from high computational intensity, reliance on single-modality inputs, and instability when combined with fast-sampling methods. In this work, we propose E3Flow, a…

A novel volume of fluid model (VoF) called explicit volume diffusion (EVD) is developed for the simulation of interfacial flows, including those with turbulence and primary spray atomisation. The EVD model is derived by volume averaging the…