GPU Parallel Computation of Morse-Smale Complexes

The Morse-Smale complex is a well studied topological structure that represents the gradient flow behavior of a scalar function. It supports multi-scale topological analysis and visualization of large scientific data. Its computation poses significant algorithmic challenges when considering large scale data and increased feature complexity. Several parallel algorithms have been proposed towards the fast computation of the 3D Morse-Smale complex. The non-trivial structure of the saddle-saddle connections are not amenable to parallel computation. This paper describes a fine grained parallel method for computing the Morse-Smale complex that is implemented on a GPU. The saddle-saddle reachability is first determined via a transformation into a sequence of vector operations followed by the path traversal, which is achieved via a sequence of matrix operations. Computational experiments show that the method achieves up to 7x speedup over current shared memory implementations

Diffusion Handles: Enabling 3D Edits for Diffusion Models by Lifting Activations to 3D

Diffusion Handles is a novel approach to enabling 3D object edits on diffusion images. We accomplish these edits using existing pre-trained diffusion models, and 2D image depth estimation, without any fine-tuning or 3D object retrieval. The edited results remain plausible, photo-real, and preserve object identity. Diffusion Handles address a critically missing facet of generative image based creative design, and significantly advance the state-of-the-art in generative image editing. Our key insight is to lift diffusion activations for an object to 3D using a proxy depth, 3D-transform the depth and associated activations, and project them back to image space. The diffusion process applied to the manipulated activations with identity control, produces plausible edited images showing complex 3D occlusion and lighting effects. We evaluate Diffusion Handles: quantitatively, on a large synthetic data benchmark; and qualitatively by a user study, showing our output to be more plausible, and better than prior art at both, 3D editing and identity control. Project Webpage: https://diffusionhandles.github.io/Comment: Project Webpage: https://diffusionhandles.github.io

Morse theory-based segmentation and fabric quantification of granular materials

This article presents a robust Morse theory-based framework for segmenting 3D X-ray computed tomography image (CT) and computing the fabric, relative arrangement of particles, of granular ensembles. The framework includes an algorithm for computing the segmentation, a data structure for storing the segmentation and representing both individual particles and the connectivity network, and visualizations of topological descriptors of the CT image that enable interactive exploration. The Morse theory-based framework produces superior quality segmentation of a granular ensemble as compared to prior approaches based on the watershed transform. The accuracy of the connectivity network also improves. Further, the frame-work supports the efficient computation of various distribution statistics on the segmentation and the connectivity network. Such a comprehensive characterization and quantification of the fabric of granular ensembles is the first step towards a multiple length scale understanding of the behavior.Funding Agencies|Indo-Swedish joint network Project [DST/ INT/ SWD/VR/P-02/2019]; Swedish Research Council (VR)Swedish Research Council [2018-07085]; VR Grant [2019-05487]; Department of Science and Technology, IndiaDepartment of Science &amp; Technology (India) [DST/SJF/ETA-02/2015-16]; Mindtree Chair research grant</p

Exploring the mechanistic insights of Cas scaffolding protein family member 4 with protein tyrosine kinase 2 in Alzheimer’s disease by evaluating protein interactions through molecular docking and dynamic simulations

Cas scaffolding protein family member 4 and protein tyrosine kinase 2 are signaling proteins, which are involved in neuritic plaques burden, neurofibrillary tangles, and disruption of synaptic connections in Alzheimer’s disease. In the current study, a computational approach was employed to explore the active binding sites of Cas scaffolding protein family member 4 and protein tyrosine kinase 2 proteins and their significant role in the activation of downstream signaling pathways. Sequential and structural analyses were performed on Cas scaffolding protein family member 4 and protein tyrosine kinase 2 to identify their core active binding sites. Molecular docking servers were used to predict the common interacting residues in both Cas scaffolding protein family member 4 and protein tyrosine kinase 2 and their involvement in Alzheimer’s disease-mediated pathways. Furthermore, the results from molecular dynamic simulation experiment show the stability of targeted proteins. In addition, the generated root mean square deviations and fluctuations, solvent-accessible surface area, and gyration graphs also depict their backbone stability and compactness, respectively. A better understanding of CAS and their interconnected protein signaling cascade may help provide a treatment for Alzheimer’s disease. Further, Cas scaffolding protein family member 4 could be used as a novel target for the treatment of Alzheimer’s disease by inhibiting the protein tyrosine kinase 2 pathway