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A challenge in computational topology is to deal with large filtered geometric complexes built from point cloud data such as Vietoris-Rips filtrations. This has led to the development of schemes for parallel computation and compression…

We study theoretically the replication of Kinetoplast DNA consisting of several thousands separate mini-circles found in organisms of the class Kinetoplastida. When the cell is not actively dividing these are topologically connected in a…

Simulation-based approaches to microstructure generation can suffer from a variety of limitations, such as high memory usage, long computational times, and difficulties in generating complex geometries. Generative machine learning models…

This paper presents an evolvable conditional diffusion method such that black-box, non-differentiable multi-physics models, as are common in domains like computational fluid dynamics and electromagnetics, can be effectively used for guiding…

Existing auto-regressive mesh generation approaches suffer from ineffective topology preservation, which is crucial for practical applications. This limitation stems from previous mesh tokenization methods treating meshes as simple…

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…

The proposed method, Discriminator Guidance, aims to improve sample generation of pre-trained diffusion models. The approach introduces a discriminator that gives explicit supervision to a denoising sample path whether it is realistic or…

We describe a new generation of algorithms capable of mapping the structure and conformations of macromolecules and their complexes from large ensembles of heterogeneous snapshots, and demonstrate the feasibility of determining both…

Machine learning in drug discovery has been focused on virtual screening of molecular libraries using discriminative models. Generative models are an entirely different approach that learn to represent and optimize molecules in a continuous…

The generation of drug-like molecules is crucial for drug design. Existing reinforcement learning (RL) methods often overlook structural information. However, feature engineering-based methods usually merely focus on binding affinity…

Navigating the vast chemical space of druggable compounds is a formidable challenge in drug discovery, where generative models are increasingly employed to identify viable candidates. Conditional 3D structure-based drug design (3D-SBDD)…

In digital pathology, the spatial context of cells is important for cell classification, cancer diagnosis and prognosis. To model such complex cell context, however, is challenging. Cells form different mixtures, lineages, clusters and…

Recent research in molecular discovery has primarily been devoted to small, drug-like molecules, leaving many similarly important applications in material design without adequate technology. These applications often rely on more complex…

Constrained generative modeling is fundamental to applications such as robotic control and autonomous driving, where models must respect physical laws and safety-critical constraints. In real-world settings, these constraints rarely take…

Diffusion models, a powerful and universal generative AI technology, have achieved tremendous success in computer vision, audio, reinforcement learning, and computational biology. In these applications, diffusion models provide flexible…

Structural biology relies on accurate three-dimensional biomolecular structures to advance our understanding of biological functions, disease mechanisms, and therapeutics. While recent advances in deep learning have enabled the development…

Pre-trained diffusion models have emerged as powerful generative priors for both unconditional and conditional sample generation, yet their outputs often deviate from the characteristics of user-specific target data. Such mismatches are…

Dataset distillation reduces the storage and computational consumption of training a network by generating a small surrogate dataset that encapsulates rich information of the original large-scale one. However, previous distillation methods…

Diffusion models have become the go-to method for many generative tasks, particularly for image-to-image generation tasks such as super-resolution and inpainting. Current diffusion-based methods do not provide statistical guarantees…

Creating large-scale datasets for training high-performance generative models is often prohibitively expensive, especially when associated attributes or annotations must be provided. As a result, merging existing datasets has become a…