Related papers: Regularized arrangements of cellular complexes
This article describes algorithms for the hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-range forces. The parallelization method combines domain decomposition with a thread-based parallelization…
Accurate segmentation of 3-D cell nuclei in microscopy images is essential for the study of nuclear organization, gene expression, and cell morphodynamics. Current image segmentation methods are challenged by the complexity and variability…
The alpha complex, a subset of the Delaunay triangulation, has been extensively used as the underlying representation for biomolecular structures. We propose a GPU-based parallel algorithm for the computation of the alpha complex, which…
Modeling the 3D structures of cells and tissues is crucial in biology. Sequential cross-sectional images from electron microscopy provide high-resolution intracellular structure information. The segmentation of complex cell structures…
The simulation of large ensembles of particles is usually parallelized by partitioning the domain spatially and using message passing to communicate between the processes handling neighboring subdomains. The particles are represented as…
We study the complexity of the following cell connection and separation problems in segment arrangements. Given a set of straight-line segments in the plane and two points $a$ and $b$ in different cells of the induced arrangement: (i)…
This study focuses on the classification of cancerous and healthy slices from multimodal lung images. The data used in the research comprises Computed Tomography (CT) and Positron Emission Tomography (PET) images. The proposed strategy…
Vertical decomposition is a widely used general technique for decomposing the cells of arrangements of semi-algebraic sets in ${{\mathbb R}}^d$ into constant-complexity subcells. In this paper, we settle in the affirmative a few…
The current computer architecture has moved towards the multi/many-core structure. However, the algorithms in the current sequential dense numerical linear algebra libraries (e.g. LAPACK) do not parallelize well on multi/many-core…
Perfectly-Matched Layers (PML) are widely used in Particle-In-Cell simulations, in order to absorb electromagnetic waves that propagate out of the simulation domain. However, when charged particles cross the interface between the simulation…
We are entering a new era in which software systems are becoming more and more complex and larger. So, the composition of such systems is becoming infeasible by manual means. To address this challenge, self-organising software models…
This note makes an observation that significantly simplifies a number of previous parallel, two-way merge algorithms based on binary search and sequential merge in parallel. First, it is shown that the additional merge step of distinguished…
Finite mixture modelling is a popular method in the field of clustering and is beneficial largely due to its soft cluster membership probabilities. A common method for fitting finite mixture models is to employ spectral clustering, which…
Electron Microscopy (EM) image (or volume) segmentation has become significantly important in recent years as an instrument for connectomics. This paper proposes a novel agglomerative framework for EM segmentation. In particular, given an…
Many approaches to 3D image segmentation are based on hierarchical clustering of supervoxels into image regions. Here we describe a distributed algorithm capable of handling a tremendous number of supervoxels. The algorithm works…
Model merging combines fine-tuned checkpoints into a single multi-task model without retraining. Existing methods - such as task arithmetic, model soups, TIES, and DARE - are computationally efficient and empirically successful, but rely on…
Spectral clustering approaches have led to well-accepted algorithms for finding accurate clusters in a given dataset. However, their application to large-scale datasets has been hindered by computational complexity of eigenvalue…
In this paper, we analyze the algebraic structure of some null boundary as well as some periodic boundary 2-D Cellular Automata (CA) rules by introducing a new matrix multiplication operation using only AND, OR instead of most commonly used…
We study the problem of instance segmentation in biological images with crowded and compact cells. We formulate this task as an integer program where variables correspond to cells and constraints enforce that cells do not overlap. To solve…
Finite mixture models are powerful tools for modelling and analyzing heterogeneous data. Parameter estimation is typically carried out using maximum likelihood estimation via the Expectation-Maximization (EM) algorithm. Recently, the…