Related papers: EnzymeFlow: Generating Reaction-specific Enzyme Ca…

Metabolomic data sets provide a direct read-out of cellular phenotypes and are increasingly generated to study biological questions. Our previous work revealed the potential of analyzing extracellular metabolomic data in the context of the…

Generative models have become increasingly powerful tools for robot motion generation, enabling flexible and multimodal trajectory generation across various tasks. Yet, most existing approaches remain limited in handling multiple types of…

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…

The enzyme turnover rate is a fundamental parameter in enzyme kinetics, reflecting the catalytic efficiency of enzymes. However, enzyme turnover rates remain scarce across most organisms due to the high cost and complexity of experimental…

Spatio-temporal (3D+t) generative modelling of cardiac shape and motion is crucial for understanding heart structure and function at population scale. Existing generative models for cardiac shape synthesis either adopt volumetric shape…

We introduce $\texttt{PairFlow}$, a lightweight preprocessing step for training Discrete Flow Models (DFMs) to achieve few-step sampling without requiring a pretrained teacher. DFMs have recently emerged as a new class of generative models…

Deep generative models have achieved tremendous success in structure-based drug design in recent years, especially for generating 3D ligand molecules that bind to specific protein pocket. Notably, diffusion models have transformed ligand…

Cells generally convert external nutrient resources to support metabolismand growth. Understanding the thermodynamic efficiency of this conversion is essential to determine the general characteristics of cellular growth. Using a simple…

Functional data, i.e., smooth random functions observed over a continuous domain, are increasingly available in areas such as biomedical research, health informatics, and epidemiology. However, effective statistical analysis for functional…

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…

Generative modelling of entire CT volumes conditioned on clinical reports has the potential to accelerate research through data augmentation, privacy-preserving synthesis and reducing regulator-constraints on patient data while preserving…

Analog/mixed-signal circuits are key for interfacing electronics with the physical world. Their design, however, remains a largely handcrafted process, resulting in long and error-prone design cycles. While the recent rise of AI-based…

Recent advances in reaction prediction have achieved near-saturated accuracy on standard benchmarks (e.g., USPTO), yet most state-of-the-art models formulate the task as a one-shot mapping from reactants to products, offering limited…

Finding a suitable layout represents a crucial task for diverse applications in graphic design. Motivated by simpler and smoother sampling trajectories, we explore the use of Flow Matching as an alternative to current diffusion-based layout…

Generating high-quality time series data has emerged as a critical research topic due to its broad utility in supporting downstream time series mining tasks. A major challenge lies in modeling the intrinsic stochasticity of temporal…

In GPU-accelerated data analytics, the overhead of data transfer from CPU to GPU becomes a performance bottleneck when the data scales beyond GPU memory capacity due to the limited PCIe bandwidth. Data compression has come to rescue for…

We propose Pullback Flow Matching (PFM), a novel framework for generative modeling on data manifolds. Unlike existing methods that assume or learn restrictive closed-form manifold mappings for training Riemannian Flow Matching (RFM) models,…

Predicting gene function from its DNA sequence is a fundamental challenge in biology. Many deep learning models have been proposed to embed DNA sequences and predict their enzymatic function, leveraging information in public databases…

We propose Functional Flow Matching (FFM), a function-space generative model that generalizes the recently-introduced Flow Matching model to operate in infinite-dimensional spaces. Our approach works by first defining a path of probability…

Bacterial growth depends crucially on metabolic fluxes, which are limited by the cell's capacity to maintain metabolic enzymes. The necessary enzyme amount per unit flux is a major determinant of metabolic strategies both in evolution and…