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A fundamental problem in drug discovery is to design molecules that bind to specific proteins. To tackle this problem using machine learning methods, here we propose a novel and effective framework, known as GraphBP, to generate 3D…

The biological functions of proteins often depend on dynamic structural ensembles. In this work, we develop a flow-based generative modeling approach for learning and sampling the conformational landscapes of proteins. We repurpose highly…

A spatiotemporal deep learning framework is proposed that is capable of 2D full-field prediction of fracture in concrete mesostructures. This framework not only predicts fractures but also captures the entire history of the fracture…

Simulating stochastic differential equations (SDEs) in bounded domains, presents significant computational challenges due to particle exit phenomena, which requires accurate modeling of interior stochastic dynamics and boundary…

Recently, 3D generative models have shown promising performances in structure-based drug design by learning to generate ligands given target binding sites. However, only modeling the target-ligand distribution can hardly fulfill one of the…

Spatiotemporal learning is challenging due to the intricate interplay between spatial and temporal dependencies, the high dimensionality of the data, and scalability constraints. These challenges are further amplified in scientific domains,…

Drug combination therapy is a well-established strategy for disease treatment with better effectiveness and less safety degradation. However, identifying novel drug combinations through wet-lab experiments is resource intensive due to the…

Discovering new drug molecules is a pivotal yet challenging process due to the near-infinitely large chemical space and notorious demands on time and resources. Numerous generative models have recently been introduced to accelerate the drug…

Medical image segmentation plays an important role in accurately identifying and isolating regions of interest within medical images. Generative approaches are particularly effective in modeling the statistical properties of segmentation…

Vision Transformers (ViTs) have revolutionized medical image analysis, yet their data-hungry nature clashes with the scarcity and privacy constraints of clinical archives. Formula-Driven Supervised Learning (FDSL) has emerged as a promising…

Recent advances in artificial intelligence have propelled the development of innovative computational materials modeling and design techniques. Generative deep learning models have been used for molecular representation, discovery, and…

Medical image segmentation based on deep learning often fails when deployed on images from a different domain. The domain adaptation methods aim to solve domain-shift challenges, but still face some problems. The transfer learning methods…

Automated 3D scene generation is pivotal for applications spanning virtual reality, digital content creation, and Embodied AI. While computer graphics prioritizes aesthetic layouts, vision and robotics demand scenes that mirror real-world…

As a representative of public transportation, the fundamental issue of managing bike-sharing systems is bike flow prediction. Recent methods overemphasize the spatio-temporal correlations in the data, ignoring the effects of contextual…

Pathology foundation models (PFMs) have emerged as a core approach for learning transferable representations from whole slide images (WSIs), and they are typically benchmarked through downstream clinical endpoints. While such task level…

As the size of accessible compound libraries expands to over 10 billion, the need for more efficient structure-based virtual screening methods is emerging. Different pre-screening methods have been developed for rapid screening, but there…

Designing 3D ligands within a target binding site is a fundamental task in drug discovery. Existing structured-based drug design methods treat all ligand atoms equally, which ignores different roles of atoms in the ligand for drug design…

Structural learning of Bayesian Networks (BNs) is a NP-hard problem, which is further complicated by many theoretical issues, such as the I-equivalence among different structures. In this work, we focus on a specific subclass of BNs, named…

Meshfree particle methods, such as Smoothed Particle Hydrodynamics (SPH) and the Moving Particle Semi-Implicit (MPS) method, are widely used to simulate complex free-surface and multiphase flows. A key challenge in these methods is the…

Motivation: Computational prediction of multiple-type drug-drug interaction (DDI) helps reduce unexpected side effects in poly-drug treatments. Although existing computational approaches achieve inspiring results, they ignore that the…