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Recent advances in distance-based protein folding have led to a paradigm shift in protein structure prediction. Through sufficiently precise estimation of the inter-residue distance matrix for a protein sequence, it is now feasible to…
LiDAR-based 3D object detectors often struggle to detect far-field objects due to the sparsity of point clouds at long ranges, which limits the availability of reliable geometric cues. To address this, prior approaches augment LiDAR data…
Interactive molecular graphics applications facilitate analysis of three dimensional protein structures. Naturally, non-interactive 2-D snapshots of the protein structures do not convey the same level of geometric detail. Several 2-D…
In this manuscript, we will introduce a recently developed program GPView, which can be used for wave function analysis and visualization. The wave function analysis module can calculate and generate 3D cubes for various types of molecular…
In the modern drug discovery process, medicinal chemists deal with the complexity of analysis of large ensembles of candidate molecules. Computational tools, such as dimensionality reduction (DR) and classification, are commonly used to…
Three-dimensional particle tracking velocimetry (3D-PTV) technique is widely used to acquire the complicated trajectories of particles and flow fields. It is known that the accuracy of 3D-PTV depends on the mapping function to reconstruct…
Recent progress in deep generative models has led to tremendous breakthroughs in image generation. However, while existing models can synthesize photorealistic images, they lack an understanding of our underlying 3D world. We present a new…
We present ReViVD, a tool for exploring and filtering large trajectory-based datasets using virtual reality. ReViVD's novelty lies in using simple 3D shapes -- such as cuboids, spheres and cylinders -- as queries for users to select and…
Rich data and powerful machine learning models allow us to design drugs for a specific protein target \textit{in silico}. Recently, the inclusion of 3D structures during targeted drug design shows superior performance to other target-free…
The study of complex many-body systems via analysis of the trajectories of the units that dynamically move and interact within them is a non-trivial task. The workflow for extracting meaningful information from the raw trajectory data is…
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…
Intraoperative observation of tissue internal structure is often difficult. Hence, real-time soft tissue deformation is essential for the localization of tumor and other internal structures. We propose a method to simulate the internal…
We develop methodology for three-dimensional (3D) radial visualization (RadViz) of multidimensional datasets. The classical two-dimensional (2D) RadViz visualizes multivariate data in the 2D plane by mapping every observation to a point…
All that structure from motion algorithms "see" are sets of 2D points. We show that these impoverished views of the world can be faked for the purpose of reconstructing objects in challenging settings, such as from a single image, or from a…
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…
We present High-Density Visual Particle Dynamics (HD-VPD), a learned world model that can emulate the physical dynamics of real scenes by processing massive latent point clouds containing 100K+ particles. To enable efficiency at this scale,…
Human vision possesses a special type of visual processing systems called peripheral vision. Partitioning the entire visual field into multiple contour regions based on the distance to the center of our gaze, the peripheral vision provides…
IVISIT is a generic interactive visual simulation tool that is based on Python/Numpy and can be used for system simulation, parameter optimization, parameter management, and visualization of system dynamics as required, for example,for…
Learning powerful deep generative models for 3D shape synthesis is largely hindered by the difficulty in ensuring plausibility encompassing correct topology and reasonable geometry. Indeed, learning the distribution of plausible 3D shapes…
We develop the analysis of x-ray intensity correlations from dilute ensembles of identical particles in a number of ways. First, we show that the 3D particle structure can be determined if the particles can be aligned with respect to a…