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Motivated by the development of computer theory, the sorting algorithm is emerging in an endless stream. Inspired by decrease and conquer method, we propose a brand new sorting algorithmUltimately Heapsort. The algorithm consists of two…
In this paper we explore the use of spatial clustering algorithms as a new computational approach for modeling the cosmic web. We demonstrate that such algorithms are efficient in terms of computing time needed. We explore three distinct…
In a previous work a procedure was decribed for dividing the $3 \times N$-dimensional conformational space of a molecular system into a number of discrete cells, this partition allowed the building of a combinatorial structure from data…
Cyclic cellular automata (CCA) are models of excitable media. Started from random initial conditions, they produce several different kinds of spatial structure, depending on their control parameters. We introduce new tools from information…
The alpha complex is a fundamental data structure from computational geometry, which encodes the topological type of a union of balls $B(x; r) \subset \mathbb{R}^m$ for $x\in S$, including a weighted version that allows for varying radii.…
Replication time is among the most important components of a bacterial cell's reproductive fitness. Paradoxically, larger cells replicate in less time than smaller cells despite the fact that building a larger cell requires increased…
We introduce a novel multiobjective optimization algorithm based on the conformational space annealing (CSA) algorithm, MOCSA. It has three characteristic features: (a) Dominance relationship and distance between solutions in the objective…
The structure of topological spaces is analysed here through the lenses of fibrous preorders. Each topological space has an associated fibrous preorder and those fibrous preorders which return a topological space are called spacial. A…
Many biological phenomena are inherently multiscale, i.e. they are characterized by interactions involving different spatial and temporal scales simultaneously. Though several approaches have been proposed to provide "multilayer" models,…
In this paper we propose a novel algorithm to combine two or more cellular complexes, providing a minimal fragmentation of the cells of the resulting complex. We introduce here the idea of arrangement generated by a collection of cellular…
A Genetic Algorithm (GA) is proposed in which each member of the population can change schemata only with its neighbors according to a rule. The rule methodology and the neighborhood structure employ elements from the Cellular Automata (CA)…
We present feature finding and tracking algorithms in 3D in living cells, and demonstrate their utility to measure metrics important in cell biological processes. We developed a computational imaging hybrid approach that combines automated…
We present an algorithm which produces a decomposition of a regular cellular complex with a discrete Morse function analogous to the Morse-Smale decomposition of a smooth manifold with respect to a smooth Morse function. The advantage of…
Cellular automata (CA) are discrete-time dynamical systems with local update rules on a lattice. Despite their elementary definition, CA support a wide spectrum of macroscopic phenomena central to statistical physics: equilibrium and…
Feature matching is a crucial task in the field of computer vision, which involves finding correspondences between images. Previous studies achieve remarkable performance using learning-based feature comparison. However, the pervasive…
This study aims at finding a method for constructing molecular dynamics like models using the formalism of cellular automata for fast simulation of fluid dynamic systems (including compressible phenomena). In as much as the results…
Spatial organization is a core challenge for all large agent-based models with local interactions. In biological tissue models, spatial search and reinsertion are frequently reported as the most expensive steps of the simulation. One of the…
The subject of this paper is the evolution of the concept of information processing in regular structures based on multi-level processing in nested cellular automata. The essence of the proposed model is a discrete space-time containing…
In order to develop systems capable of artificial evolution, we need to identify which systems can produce complex behavior. We present a novel classification method applicable to any class of deterministic discrete space and time dynamical…
Motivation: The rapid growth of diverse biological data allows us to consider interactions between a variety of objects, such as genes, chemicals, molecular signatures, diseases, pathways and environmental exposures. Often, any pair of…