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Generative models for structure-based molecular design hold significant promise for drug discovery, with the potential to speed up the hit-to-lead development cycle, while improving the quality of drug candidates and reducing costs. Data…

Physics-based simulations are often used to model and understand complex physical systems and processes in domains like fluid dynamics. Such simulations, although used frequently, have many limitations which could arise either due to the…

We introduce structural causal bottleneck models (SCBMs), a novel class of structural causal models. At the core of SCBMs lies the assumption that causal effects between high-dimensional variables only depend on low-dimensional summary…

Designing molecules that bind to specific target proteins is a fundamental task in drug discovery. Recent models leverage geometric constraints to generate ligand molecules that bind cohesively with specific protein pockets. However, these…

Physics simulations like computational fluid dynamics (CFD) are a computational bottleneck in computer-aided design (CAD) optimization processes. To overcome this bottleneck, one requires either an optimization framework that is highly…

Billions of organic molecules are known, but only a tiny fraction of the functional inorganic materials have been discovered, a particularly relevant problem to the community searching for new quantum materials. Recent advancements in…

Diffusion models have emerged as a leading framework in generative modeling, poised to transform the traditionally slow and costly process of drug discovery. This review provides a systematic comparison of their application in designing two…

The accurate and efficient simulation of Partial Differential Equations (PDEs) in and around arbitrarily defined geometries is critical for many application domains. Immersed boundary methods (IBMs) alleviate the usually laborious and…

Generating novel active molecules for a given protein is an extremely challenging task for generative models that requires an understanding of the complex physical interactions between the molecule and its environment. In this paper, we…

The goal of spatial-configuration-based classification is to build a classifier to distinguish two classes (e.g., responder, non-responder) based on the spatial arrangements (e.g., spatial interactions between different point categories)…

Traditional drug design faces significant challenges due to inherent chemical and biological complexities, often resulting in high failure rates in clinical trials. Deep learning advancements, particularly generative models, offer potential…

Spatial profiling technologies in biology, such as imaging mass cytometry (IMC) and spatial transcriptomics (ST), generate high-dimensional, multi-channel data with strong spatial alignment and complex inter-channel relationships.…

Spatial transcriptomics (ST) has emerged as a powerful technology for bridging histology imaging with gene expression profiling. However, its application has been limited by low throughput and the need for specialized experimental…

Generative models for 3D shapes represented by hierarchies of parts can generate realistic and diverse sets of outputs. However, existing models suffer from the key practical limitation of modelling shapes holistically and thus cannot…

Generative deep learning has become pivotal in molecular design for drug discovery, materials science, and chemical engineering. A widely used paradigm is to pretrain neural networks on string representations of molecules and fine-tune them…

The computational design of antibodies with high specificity and affinity is a cornerstone of modern therapeutic development. While deep generative models have demonstrated potential, they often struggle to balance high-fidelity geometric…

As deep neural networks (DNNs) are increasingly deployed on edge devices, optimizing models for constrained computational resources is critical. Existing auto-pruning methods face challenges due to the diversity of DNN models, various…

Physiologically Based Pharmacokinetic (PBPK) modeling is a cornerstone of model-informed drug development (MIDD), providing a mechanistic framework to predict drug absorption, distribution, metabolism, and excretion (ADME). Despite its…

We developed Distilled Graph Attention Policy Network (DGAPN), a reinforcement learning model to generate novel graph-structured chemical representations that optimize user-defined objectives by efficiently navigating a physically…

Rapid and accurate simulations of fluid dynamics around complicated geometric bodies are critical in a variety of engineering and scientific applications, including aerodynamics and biomedical flows. However, while scientific machine…