Related papers: On the codon assignment of chain termination signa…
We investigate the mutation-selection dynamics for an evolutionary computation model based on Turing Machines that we introduced in a previous article. The use of Turing Machines allows for very simple mechanisms of code growth and code…
Horizontal transfer (HT) of heritable information or `traits' (carried by genetic elements, endosymbionts, or culture) is widespread among living organisms. Yet current ecological and evolutionary theory addressing HT is limited. We present…
The standard genetic code is known to be much more efficient in minimizing adverse effects of misreading errors and one-point mutations in comparison with a random code having the same structure, i.e. the same number of codons coding for…
We call change-point problem (CPP) the identification of changes in the probabilistic behavior of a sequence of observations. Solving the CPP involves detecting the number and position of such changes. In genetics the study of how and what…
We present superconducting quantum circuits which exhibit atomic energy spectrum and selection rules as ladder and lambda three-level configurations designed by means of genetic algorithms. These heuristic optimization techniques are…
In this paper, rate adaptive coded Digital Phase Modulation (DPM) schemes based on punctured ring convolutional codes are presented. We first present an upper bound on symbol error probability for punctured convolutional coded Continuous…
Gene Regulatory Networks (GRNs) consisting of combinations of transcription factors (TFs) and their cis promoters are assumed to be sufficient to direct the development of organisms. Mutations in GRNs are assumed to be the primary drivers…
Motivation: Gene selection has become a common task in most gene expression studies. The objective of such research is often to identify the smallest possible set of genes that can still achieve good predictive performance. The problem of…
Let $G$ be a graph, which represents a social network, and suppose each node $v$ has a threshold value $\tau(v)$. Consider an initial configuration, where each node is either positive or negative. In each discrete time step, a node $v$…
The three-dimensional organization of chromatin is thought to play an important role in controlling gene expression. Specificity in expression is achieved through the interaction of transcription factors and other nuclear proteins with…
Protein sequences are believed to have been selected to provide the stability of, and reliable renaturation to, an encoded unique spatial fold. In recently proposed theoretical schemes, this selection is modeled as ``minimal frustration,''…
Inspired by prior work by Tian and by Cao and Xu, this paper presents an efficient computer-aided framework to characterize the fundamental limits of coded caching systems under the constraint of linear coding. The proposed framework…
Network connectedness is indispensable for the normal operation of transmission networks. However, there still remains a lack of efficient constraints that can be directly added to the problem formulation of optimal transmission switching…
With meteoric developments in communication systems and data storage technologies, the need for secure data transmission is more crucial than ever. The level of security provided by any cryptosystem relies on the sensitivity of the private…
Complex systems with tightly coadapted parts frequently appear in living systems and are difficult to account for through Darwinian evolution, that is random variation and natural selection, if the constituent parts are independently coded…
The problem of minimizing a polynomial over the standard simplex is one of the basic NP-hard nonlinear optimization problems --- it contains the maximum clique problem in graphs as a special case. It is known that the problem allows a…
The evolution in coding DNA sequences brings new flexibility and freedom to the codon words, even as the underlying nucleotides get significantly ordered. These curious contra-rules of gene organisation are observed from the distribution of…
The most common representation in evolutionary computation are bit strings. This is ideal to model binary decision variables, but less useful for variables taking more values. With very little theoretical work existing on how to use…
As the only thiol-bearing amino acid, cysteine (Cys) residues in proteins have the reactive thiol side chain, which is susceptible to a series of post-translational modifications (PTMs). These PTMs participate in a wide range of biological…
When oncologists estimate cancer patient survival, they rely on multimodal data. Even though some multimodal deep learning methods have been proposed in the literature, the majority rely on having two or more independent networks that share…