Related papers: p-Adic Degeneracy of the Genetic Code
Gallai's path decomposition conjecture states that if $G$ is a connected graph on $n$ vertices, then the edges of $G$ can be decomposed into at most $\lceil \frac{n }{2} \rceil$ paths. A graph is said to be an odd semi-clique if it can be…
In evolutionary policy search, neural networks are usually represented using a direct mapping: each gene encodes one network weight. Indirect encoding methods, where each gene can encode for multiple weights, shorten the genome to reduce…
Regenerating codes and codes with locality are two schemes that have recently been proposed to ensure data collection and reliability in a distributed storage network. In a situation where one is attempting to repair a failed node,…
In the framework of the crystal basis model of the genetic code, where each codon is assigned to an irreducible representation of $U_{q \to 0}(sl(2) \oplus sl(2))$, single base mutation matrices are introduced. The strength of the mutation…
Belief-propagation (BP) decoders play a vital role in modern coding theory, but they are not suitable to decode quantum error-correcting codes because of a unique quantum feature called error degeneracy. Inspired by an exact mapping between…
We design a heuristic method, a genetic algorithm, for the computation of an upper bound of the minimum distance of a linear code over a finite field. By the use of the row reduced echelon form, we obtain a permutation encoding of the…
In special coordinates (codon position--specific nucleotide frequencies) bacterial genomes form two straight lines in 9-dimensional space: one line for eubacterial genomes, another for archaeal genomes. All the 348 distinct bacterial…
We present a decoding algorithm for quantum convolutional codes that finds the class of degenerate errors with the largest probability conditioned on a given error syndrome. The algorithm runs in time linear with the number of qubits.…
Segmental duplications (SDs), or low-copy repeats (LCR), are segments of DNA greater than 1 Kbp with high sequence identity that are copied to other regions of the genome. SDs are among the most important sources of evolution, a common…
The weak degeneracy of a graph $G$ is a numerical parameter that was recently introduced by the first two authors with the aim of understanding the power of greedy algorithms for graph coloring. Every $d$-degenerate graph is weakly…
Two genomes over the same set of gene families form a canonical pair when each of them has exactly one gene from each family. Different distances of canonical genomes can be derived from a structure called breakpoint graph, which represents…
LDPC code design tools typically rely on asymptotic code behavior and are affected by an unavoidable performance degradation due to model imperfections in the short length regime. We propose an LDPC code design scheme based on an…
Genetic programming (GP) is an evolutionary computation technique to solve problems in an automated, domain-independent way. Rather than identifying the optimum of a function as in more traditional evolutionary optimization, the aim of GP…
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 study of regenerating codes has advanced tremendously in recent years. However, most known constructions require large field size, and hence may be hard to implement in practice. By using notions from the theory of extension fields, we…
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…
The stability of model proteins with designed sequences is assessed in terms of the number of sequences (obtained from the designed sequence through mutations), which fold into 5the ``native'' conformation. By a complete enumeration of the…
Error correction is of utmost necessity for large-scale quantum computing. Quantum error correcting codes can be degenerate, if more than one type of error can map the input state to the same error state. In this paper, we propose a 6-qubit…
Due to its higher data density, longevity, energy efficiency, and ease of generating copies, DNA is considered a promising storage technology for satisfying future needs. However, a diverse set of errors including deletions, insertions,…
The genetic code has been shown to be very error robust compared to randomly selected codes, but to be significantly less error robust than a certain code found by a heuristic algorithm. We formulate this optimisation problem as a Quadratic…