Related papers: Simulating Organogenesis in COMSOL: Image-based Mo…
Biological systems are governed by coupled interactions between intracellular metabolism and bioreactor operation that span multiple time scales. Constraint-based metabolic models are widely used to describe intracellular metabolism, but…
Computational models are critical to advance our understanding of how neural, biomechanical, and physical systems interact to orchestrate animal behaviors. Despite the availability of near-complete reconstructions of the Drosophila…
Organoids are self-organized 3D cell clusters that closely mimic the architecture and function of in vivo tissues and organs. Quantification of organoid morphology helps in studying organ development, drug discovery, and toxicity…
Recently, symbolic computation and computer algebra systems have been successfully applied in systems biology, especially in chemical reaction network theory. One advantage of symbolic computation is its potential for qualitative answers to…
Deep learning methods can be found in many medical imaging applications. Recently, those methods were applied directly to the RF ultrasound multi-channel data to enhance the quality of the reconstructed images. In this paper, we apply a…
Agent-based modeling (ABM) is a powerful computational approach for studying complex biological and biomedical systems, yet its widespread use remains limited by significant computational demands. As models become increasingly…
Coarse-grained, mesoscale simulations are invaluable for studying soft condensed matter because of their ability to model systems in which a background solvent plays a significant role but is not the primary interest. Such methods generally…
Discrete-time modeling of acoustic, mechanical and electrical systems is a prominent topic in the musical signal processing literature. Such models are mostly derived by discretizing a mathematical model, given in terms of ordinary or…
Systems Biology has emerged in the last years as a new holistic approach based on the global understanding of cells instead of only being focused on their individual parts (genes or proteins), to better understand the complexity of human…
This paper addresses the challenge of geometric quality assurance in manufacturing, particularly when human assessment is required. It proposes using Blender, an open-source simulation tool, to create synthetic datasets for machine learning…
Neural development represents not only an exciting and complex field of study, with ongoing progress, but it also became the epicentre of neuroscience and developmental biology, as it strives to describe the underlying cellular and…
We consider the task of representation learning for unsupervised segmentation of 3D voxel-grid biomedical images. We show that models that capture implicit hierarchical relationships between subvolumes are better suited for this task. To…
Understanding symptom-image associations is crucial for clinical reasoning. However, existing medical multimodal models often rely on simple one-to-one hard labeling, oversimplifying clinical reality where symptoms relate to multiple…
Declarative modeling uses symbolic expressions to represent models. With such expressions one can formalize high-level mathematical computations on models that would be difficult or impossible to perform directly on a lower-level simulation…
Patient-specific cardiac modeling combines geometries of the heart derived from medical images and biophysical simulations to predict various aspects of cardiac function. However, generating simulation-suitable models of the heart from…
We present a longitudinal MR simulation framework which simulates the future neurodegenerative progression by outputting the predicted follow-up MR image and the voxel-based morphometry (VBM) map. This framework expects the patients to have…
Multi-organ segmentation in medical images is a widely researched task and can save much manual efforts of clinicians in daily routines. Automating the organ segmentation process using deep learning (DL) is a promising solution and…
Mobile genetic elements like conjugative plasmids play a crucial role in shaping the genetic content and population dynamics of bacterial species. Bacterial populations often contain not one, but multiple co-circulating MGEs, which modify…
Understanding the rules underlying organismal development is a major unsolved problem in biology. Each cell in a developing organism responds to signals in its local environment by dividing, excreting, consuming, or reorganizing, yet how…
In this work, we introduce a fast and accurate method for unsupervised 3D medical image registration. This work is built on top of a recent algorithm SAM, which is capable of computing dense anatomical/semantic correspondences between two…