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We present DiSH-Sim, a simulator for large discrete models of biological signal transduction pathways, capable of simulating networks with multi-valued elements in both deterministic and stochastic manner. We focus on order of update and…

Molecular Networks · Quantitative Biology 2017-05-09 Khaled Sayed , Yu-Hsin Kuo , Anuva Kulkarni , Natasa Miskov-Zivanov

The locality of solution features in cardiac electrophysiology simulations calls for adaptive methods. Due to the overhead incurred by established mesh refinement and coarsening, however, such approaches failed in accelerating the…

Numerical Analysis · Mathematics 2023-11-14 Fatemeh Chegini , Thomas Steinke , Martin Weiser

We present a novel approach for the reconstruction of dynamic geometric shapes using a single hand-held consumer-grade RGB-D sensor at real-time rates. Our method does not require a pre-defined shape template to start with and builds up the…

Computer Vision and Pattern Recognition · Computer Science 2016-08-02 Matthias Innmann , Michael Zollhöfer , Matthias Nießner , Christian Theobalt , Marc Stamminger

Origami-inspired mechanisms can transform flat sheets into functional three-dimensional dynamic structures that are lightweight, compact, and capable of complex motion. These properties make origami increasingly valuable in robotic and…

Robotics · Computer Science 2026-05-05 Tianhui Han , Shashwat Singh , Sarvesh Patil , Zeynep Temel

We show that physics-based simulations can be seamlessly integrated with NeRF to generate high-quality elastodynamics of real-world objects. Unlike existing methods, we discretize nonlinear hyperelasticity in a meshless way, obviating the…

Computer Vision and Pattern Recognition · Computer Science 2024-03-29 Yutao Feng , Yintong Shang , Xuan Li , Tianjia Shao , Chenfanfu Jiang , Yin Yang

Generative modeling of anatomical structures plays a crucial role in virtual imaging trials, which allow researchers to perform studies without the costs and constraints inherent to in vivo and phantom studies. For clinical relevance,…

Computer Vision and Pattern Recognition · Computer Science 2025-04-07 Bram de Wilde , Max T. Rietberg , Guillaume Lajoinie , Jelmer M. Wolterink

Soft robotic systems offer benefits over traditional rigid systems through reduced contact trauma with soft tissues and by enabling access through tortuous paths in minimally invasive surgery. However, the inherent deformability of soft…

Robotics · Computer Science 2020-05-04 James Avery , Mark Runciman , Ara Darzi , George P. Mylonas

Shape-morphing metamaterials enable adaptive structures capable of complex functional deformations, with applications ranging from reconfigurable structures and soft robotics to medical devices. However, their design remains challenging due…

Computational Engineering, Finance, and Science · Computer Science 2026-05-11 Jipeng Cui , Wei "Wayne" Chen

Objective: Deformable image registration is a fundamental problem in medical image analysis, with applications such as longitudinal studies, population modeling, and atlas based image segmentation. Registration is often phrased as an…

Computer Vision and Pattern Recognition · Computer Science 2018-10-22 Simon Ekström , Filip Malmberg , Håkan Ahlström , Joel Kullberg , Robin Strand

While the Segment Anything Model (SAM) excels in semantic segmentation for general-purpose images, its performance significantly deteriorates when applied to medical images, primarily attributable to insufficient representation of medical…

Computer Vision and Pattern Recognition · Computer Science 2023-11-07 Yiming Zhang , Tianang Leng , Kun Han , Xiaohui Xie

The objective of this paper is to significantly reduce the manual workload required from medical professionals in complex 3D segmentation tasks that cannot be yet fully automated. For instance, in radiotherapy planning, organs at risk must…

User interfaces provide an interactive window between physical and virtual environments. A new concept in the field of human-computer interaction is a soft user interface; a compliant surface that facilitates touch interaction through…

Human-Computer Interaction · Computer Science 2018-03-28 Chris Larson , Josef Spjut , Ross Knepper , Robert Shepherd

Mathematical Modelling has a long history in developmental biology. Advances in experimental techniques and computational algorithms now permit the development of increasingly more realistic models of organogenesis. In particular, 3D…

Computational Engineering, Finance, and Science · Computer Science 2014-08-08 Zahra Karimaddini , Erkan Unal , Denis Menshykau , Dagmar Iber

In this work, we develop an approach for guiding robots to automatically localize and find the shapes of tumors and other stiff inclusions present in the anatomy. Our approach uses Gaussian processes to model the stiffness distribution and…

Magnetic soft robots embedded with hard magnetic particles enable untethered actuation via external magnetic fields, offering remote, rapid, and precise control, which is highly promising for biomedical applications. However, designing such…

Robotics · Computer Science 2025-07-15 Liwei Wang

Specifying a governing physical model in the presence of missing physics and recovering its parameters are two intertwined and fundamental problems in science. Modern machine learning allows one to circumvent these, via emulators and…

Machine Learning · Computer Science 2020-06-30 Daniel J. Tait , Theodoros Damoulas

Modeling of respiratory motion is important for a more accurate understanding and accounting of its effect on dose to cancers in the thorax and abdomen by radiotherapy. We have developed a model of respiration-induced organ motion in the…

How pattern and form are generated in a reproducible manner during embryogenesis remains poorly understood. Intestinal organoid morphogenesis involves a number of mechanochemical regulators, including cell-type specific cytoskeletal forces…

Tissues and Organs · Quantitative Biology 2024-04-01 Shi-Lei Xue , Qiutan Yang , Prisca Liberali , Edouard Hannezo

In medical imaging, the diffusion models have shown great potential for synthetic image generation tasks. However, these approaches often lack the interpretable connections between the generated and real images and can create anatomically…

Image and Video Processing · Electrical Eng. & Systems 2026-02-12 Jian-Qing Zheng , Yuanhan Mo , Yang Sun , Jiahua Li , Fuping Wu , Ziyang Wang , Tonia Vincent , Bartłomiej W. Papież

Large image generation and vision models, combined with differentiable rendering technologies, have become powerful tools for generating paths that can be drawn or painted by a robot. However, these tools often overlook the intrinsic…