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Phylogenetic comparative methods correct for shared evolutionary history among a set of non-independent organisms by modeling sample traits as arising from a diffusion process along on the branches of a possibly unknown history. To…
This paper introduces a stochastic adaptive dynamics model for the interplay of several crucial traits and mechanisms in bacterial evolution, namely dormancy, horizontal gene transfer (HGT), mutation and competition. In particular, it…
There is an abundance of prior research on the optimization of production systems, but there is a research gap when it comes to optimizing which components should be included in a design, and how they should be connected. To overcome this…
Multimodal evidence is critical in computational pathology: gigapixel whole slide images capture tumor morphology, while patient-level clinical descriptors preserve complementary context for prognosis. Integrating such heterogeneous signals…
Swarm intelligence algorithms have traditionally been designed for continuous optimization problems, and these algorithms have been modified and extended for application to discrete optimization problems. Notably, their application in…
The evolutionary persistence of symbiotic associations is a puzzle. Adaptation should eliminate cooperative traits if it is possible to enjoy the advantages of cooperation without reciprocating - a facet of cooperation known in game theory…
A spacially extended model of the collective behavior of a large number of locally acting organisms is proposed in which organisms move probabilistically between local cells in space, but with weights dependent on local morphogenetic…
This study introduces a framework that integrates nonlinear feature extraction, classification, and efficient optimization. First, kernel principal component analysis with a radial basis function kernel reduces dimensionality while…
The living-together of distinct organisms in a single termite nest along with the termite builder colony, is emblematic in its ecological and evolutionary significance. On top of preserving biodiversity, these interspecific and…
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…
Some microbial organisms are known to randomly slip into and out of hibernation, irrespective of environmental conditions [1]. In a (genetically) uniform population a typically very small subpopulation becomes metabolically inactive whereas…
Delayed processes are ubiquitous throughout biology. These delays may arise through maturation processes or as the result of complex multi-step networks, and mathematical models with distributed delays are increasingly used to capture the…
In this paper, two multi-objective optimization frameworks in two variants (i.e., NSGA-III-ARM-V1, NSGA-III-ARM-V2; and MOEAD-ARM-V1, MOEAD-ARM-V2) are proposed to find association rules from transactional datasets. The first framework uses…
In the field of evolutionary multi-objective optimization, the approximation of the Pareto front (PF) is achieved by utilizing a collection of representative candidate solutions that exhibit desirable convergence and diversity. Although…
We consider optimizing for different production requirements from the viewpoint of a bio-inspired framework for system flexibility that allows us to study the ability of an algorithm to transfer solutions from previous optimization tasks,…
Cooperative Co-evolution, through the decomposition of the problem space, is a primary approach for solving large-scale global optimization problems. Typically, when the subspaces are disjoint, the algorithms demonstrate significantly both…
The stacked contact process is a three-state spin system that describes the co-evolution of a population of hosts together with their symbionts. In a nutshell, the hosts evolve according to a contact process while the symbionts evolve…
In this paper, a new meta-heuristic algorithm, called beetle swarm optimization algorithm, is proposed by enhancing the performance of swarm optimization through beetle foraging principles. The performance of 23 benchmark functions is…
Feature based steganalysis, an emerging branch in information forensics, aims at identifying the presence of a covert communication by employing the statistical features of the cover and stego image as clues/evidences. Due to the large…
Identification of features is a critical task in microbiome studies that is complicated by the fact that microbial data are high dimensional and heterogeneous. Masked by the complexity of the data, the problem of separating signals from…