Related papers: Deriving a genetic regulatory network from an opti…
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…
Gene regulatory networks typically have low in-degrees, whereby any given gene is regulated by few of the genes in the network. What mechanisms might be responsible for these low in-degrees? Starting with an accepted framework of the…
Information theory has explained the organization of many biological phenomena, from the physiology of sensory receptive fields to the variability of certain DNA sequence ensembles. Some scholars have proposed that information should…
Elucidating the fitness measures optimized during the evolution of complex biological systems is a major challenge in evolutionary theory. We present experimental evidence and an analytical framework demonstrating how biochemical networks…
In this paper, we propose an optimization-based mechanism to explain power law distributions, where the function that the optimization process is seeking to optimize is derived mathematically, then the behavior and interpretation of this…
Gene expression-based heterogeneity analysis has been extensively conducted. In recent studies, it has been shown that network-based analysis, which takes a system perspective and accommodates the interconnections among genes, can be more…
The network information system is a military information network system with evolution characteristics. Evolution is a process of replacement between disorder and order, chaos and equilibrium. Given that the concept of evolution originates…
We present an analysis of the topologies of a class of networks which are optimal in terms of the requirements of having as short a route as possible between any two nodes while yet keeping the congestion in the network as low as possible.…
Lots of bio-inspired research works have been conducted in self-adaptive software. They have focused on the external behavior of biological entities without their genetic material that causes this behavior and constitutes the challenge this…
We consider a model of large regulatory gene expression networks where the thresholds activating the sigmoidal interactions between genes and the signs of these interactions are shuffled randomly. Such an approach allows for a qualitative…
Biological structure and function depend on complex regulatory interactions between many genes. A wealth of gene expression data is available from high-throughput genome-wide measurement technologies, but effective gene regulatory network…
The mammalian brain is a metabolically expensive device, and evolutionary pressures have presumably driven it to make productive use of its resources. For sensory areas, this concept has been expressed more formally as an optimality…
While evolutionary algorithms are known to be very successful for a broad range of applications, the algorithm designer is often left with many algorithmic choices, for example, the size of the population, the mutation rates, and the…
Despite the significant advances in identifying the driver nodes and energy requiring in network control, a framework that incorporates more complicated dynamics remains challenging. Here, we consider the conformity behavior into network…
In this paper, we tested several sparse optimization algorithms based on the public dataset of the DREAM5 Gene Regulatory Network Inference Challenge. And we find that introducing 20% of the regulatory network as a priori known data can…
We consider two variational models for transport networks, an urban planning and a branched transport model, in which the degree of network complexity and ramification is governed by a small parameter $\varepsilon>0$. Smaller $\varepsilon$…
Biomolecular networks have already found great utility in characterizing complex biological systems arising from pair-wise interactions amongst biomolecules. Here, we review how graph theoretical approaches can be applied not only for a…
Living organisms must respond to environmental changes. Generally, accurate and rapid responses are provided by simple, unidirectional networks that connect inputs with outputs. Besides accuracy and speed, biological responses should also…
Two ideas taken from Bayesian optimization and classifier systems are presented for personnel scheduling based on choosing a suitable scheduling rule from a set for each persons assignment. Unlike our previous work of using genetic…
The field of optimal control typically requires the assumption of perfect knowledge of the system one desires to control, which is an unrealistic assumption for biological systems, or networks, typically affected by high levels of…