Related papers: A Realistic Model under which the Genetic Code is …
The adaptation of neural codes to the statistics of their environment is well captured by efficient coding approaches. Here we solve an inverse problem: characterizing the objective and constraint functions that efficient codes appear to be…
The genetic code is considered to be universal. In order to test if some statistical properties of the coding bacterial genome were due to inherent properties of the genetic code, we compared the autocorrelation function, the scaling…
The importance of the notion of symmetry in physics is well established: could it also be the case for the genetic code? In this spirit, a model for the Genetic Code based on continuous symmetries and entitled the "Crystal Basis Model" has…
The present paper is devoted to foundations of p-adic modelling in genomics. Considering nucleotides, codons, DNA and RNA sequences, amino acids, and proteins as information systems, we have formulated the corresponding p-adic formalisms…
In this work it is shown that three pairs of the factors appear to be the key, i.e. main factors of a natural classification of protein (canonical) amino acids within the amino acid (genetic) code. First pair: the factors of the habit of an…
The surface code represents a promising candidate for fault-tolerant quantum computation due to its high error threshold and experimental accessibility with nearest-neighbor interactions. However, current exact surface code threshold…
The surface code, one of the leading candidates for quantum error correction, is known to protect encoded quantum information against stochastic, i.e., incoherent errors. The protection against coherent errors, such as from unwanted gate…
Although several synonymous codons can encode the same aminoacid, this symmetry is generally broken in natural genetic systems. In this article, we show that the symmetry breaking can result from selective pressures due to the violation of…
Randomized benchmarking (RB) is a widely used method for estimating the average fidelity of gates implemented on a quantum computing device. The stochastic error of the average gate fidelity estimated by RB depends on the sampling strategy…
It is becoming increasingly apparent that probabilistic approaches can overcome conservatism and computational complexity of the classical worst-case deterministic framework and may lead to designs that are actually safer. In this paper we…
Genetic algorithms have played an important role in engineering optimization. Traditional GAs treat each gene separately. However, biophysical studies of gene regulatory networks revealed direct associations between different genes. It…
The genetic code underlying protein synthesis is a canonical example of a degenerate biological system. Degeneracies in physical and biological systems can be lifted by external perturbations thus allowing degenerate systems to exhibit a…
We propose genetic algorithms, which are robust optimization techniques inspired by natural selection, to enhance the versatility of digital quantum simulations. In this sense, we show that genetic algorithms can be employed to increase the…
The family of codeword stabilized codes encompasses the stabilizer codes as well as many of the best known nonadditive codes. However, constructing optimal $n$-qubit codeword stabilized codes is made difficult by two main factors. The first…
In genetic association studies, detecting disease-genotype associations is a primary goal. For most diseases, the underlying genetic model is unknown, and we study seven robust test statistics for monotone association. For a given test…
The genetic code is profoundly shaped by an origin in ancient RNA-mediated interactions, needing an extended development to reach the Standard Genetic Code (SGC). That development can serially use RNA specificities, a ribonucleopeptide…
A good feature representation is a determinant factor to achieve high performance for many machine learning algorithms in terms of classification. This is especially true for techniques that do not build complex internal representations of…
Efficient high-performance decoding of topological stabilizer codes has the potential to crucially improve the balance between logical failure rates and the number and individual error rates of the constituent qubits. High-threshold…
This report proposes a novel framework for a rigorous robustness analysis of stochastic biochemical systems. The technique is based on probabilistic model checking. We adapt the general definition of robustness introduced by Kitano to the…
We give new constructions of two classes of algebraic code families which are efficiently list decodable with small output list size from a fraction $1-R-\epsilon$ of adversarial errors where $R$ is the rate of the code, for any desired…