Related papers: Ant Colony Optimization for Inferring Key Gene Int…
In Part I of this series, we established a rigorous mathematical isomorphism between ant colony decision-making and random forest learning, demonstrating that variance reduction through decorrelation is a universal principle shared by…
This study proposes a distributed algorithm that makes agents' adaptive grouping entrap multiple targets via automatic decision making, smooth flocking, and well-distributed entrapping. Agents make their own decisions about which targets to…
Neural network models of real-world systems, such as industrial processes, made from sensor data must often rely on incomplete data. System states may not all be known, sensor data may be biased or noisy, and it is not often known which…
Some recent studies have pointed that, the self-organization of neurons into brain-like structures, and the self-organization of ants into a swarm are similar in many respects. If possible to implement, these features could lead to…
This work aims at optimizing injection networks, which consist in adding a set of long-range links (called bypass links) in mobile multi-hop ad hoc networks so as to improve connectivity and overcome network partitioning. To this end, we…
Efficient transportation, a hot topic in nonlinear science, is essential for modern societies and the survival of biological species. Biological evolution has generated a rich variety of successful solutions, which have inspired engineers…
Ant Colony Optimization (ACO) is renowned for its effectiveness in solving Traveling Salesman Problems, yet it faces computational challenges in CPU-based environments, particularly with large-scale instances. In response, we introduce a…
The behavior of ecological systems mainly relies on the interactions between the species it involves. We consider the problem of inferring the species interaction network from abundance data. To be relevant, any network inference…
Evolutionary processes proved very useful for solving optimization problems. In this work, we build a formalization of the notion of cooperation and competition of multiple systems working toward a common optimization goal of the population…
Specific protein-protein interactions are crucial in the cell, both to ensure the formation and stability of multi-protein complexes, and to enable signal transduction in various pathways. Functional interactions between proteins result in…
Ant algorithms are inspired in real ants and the main idea is to create virtual ants that travel into the space of possible solution depositing virtual pheromone proportional to how good a specific solution is. This creates a autocatalytic…
Solving large traveling salesman problem (TSP) in an efficient way is a challenging area for the researchers of computer science. This paper presents a modified version of the ant colony system (ACS) algorithm called Red-Black Ant Colony…
A system level view of cellular processes for human and several organisms can be cap- tured by analyzing molecular interaction networks. A molecular interaction network formed of differentially expressed genes and their interactions helps…
Congestion is a problem of paramount importance in resource constrained Wireless Sensor Networks, especially for large networks, where the traffic loads exceed the available capacity of the resources. Sensor nodes are prone to failure and…
The inference of gene regulatory networks from high throughput gene expression data is one of the major challenges in systems biology. This paper aims at analysing and comparing two different algorithmic approaches. The first approach uses…
We wish to minimize the resources used for network coding while achieving the desired throughput in a multicast scenario. We employ evolutionary approaches, based on a genetic algorithm, that avoid the computational complexity that makes…
Evolutionary algorithms, inspired by natural evolution, aim to optimize difficult objective functions without computing derivatives. Here we detail the relationship between population genetics and evolutionary optimization and formulate a…
Gene interaction graphs aim to capture various relationships between genes and can represent decades of biology research. When trying to make predictions from genomic data, those graphs could be used to overcome the curse of dimensionality…
For many complex diseases, prognosis is of essential importance. It has been shown that, beyond the main effects of genetic (G) and environmental (E) risk factors, the gene-environment (G$\times$E) interactions also play a critical role. In…
The past decade has seen the rapid development of the online newsroom. News published online are the main outlet of news surpassing traditional printed newspapers. This poses challenges to the production and to the consumption of those…