Related papers: A Unified Theory on Construction and Evolution of …
Heterozygote disadvantage is potentially a potent driver of population genetic divergence. Also referred to as underdominance, this phenomena describes a situation where a genetic heterozygote has a lower overall fitness than either…
The problem-solving performance of many evolutionary algorithms, including genetic programming systems used for program synthesis, depends on the values of hyperparameters including mutation rates. The mutation method used to produce some…
Making use of a simplified model for protein folding, it can be shown that conformations which are particularly stable when their energy is minimized with respect to amino acid sequence (in the sense that they display a large energy gap to…
To overcome the restriction of identical distribution assumption, invariant representation learning for unsupervised domain adaptation (UDA) has made significant advances in computer vision and pattern recognition communities. In UDA…
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…
This paper presents new lower and upper bounds for the compression rate of binary prefix codes optimized over memoryless sources according to various nonlinear codeword length objectives. Like the most well-known redundancy bounds for…
Proteins have evolved through mutations, amino acid substitutions, since life appeared on Earth, some 109 years ago. The study of these phenomena has been of particular significance because of their impact on protein stability, function,…
A class of rate-adaptive protograph MacKay-Neal (MN) codes is introduced and analyzed. The code construction employs an outer distribution matcher (DM) to adapt the rate of the scheme. The DM is coupled with an inner protograph-based…
Transcription factors (TFs) exert their regulatory action by binding to DNA with specific sequence preferences. However, different TFs can partially share their binding sequences due to their common evolutionary origin. This `redundancy' of…
Grammar-Guided Genetic Programming (GGGP) employs a variety of insights from evolutionary theory to autonomously design solutions for a given task. Recent insights from evolutionary biology can lead to further improvements in GGGP…
We introduce a model of DNA sequence evolution which can account for biases in mutation rates that depend on the identity of the neighboring bases. An analytic solution for this class of non-equilibrium models is developed by adopting…
In the near future, all the human genes will be identified. But understanding the functions coded in the genes is a much harder problem. For example, by using block entropy, one has that the DNA code is closer to a random code then written…
The standard genetic code is well known to be optimized for minimizing the phenotypic effects of single nucleotide substitutions, a property that was likely selected for during the emergence of a universal code. Given the fitness advantage…
In the Minimum Description Length (MDL) principle, learning from the data is equivalent to an optimal coding problem. We show that the codes that achieve optimal compression in MDL are critical in a very precise sense. First, when they are…
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…
Evolutionary dynamics is often viewed as a subtle process of change accumulation that causes a divergence among organisms and their genomes. However, this interpretation is an inheritance of a gradualistic view that has been challenged at…
Evolution has fascinated quantitative and physical scientists for decades: how can the random process of mutation, recombination, and duplication of genetic information generate the diversity of life? What determines the rate of evolution?…
The mathematical concept of q-deformations, in particular the one of qnumbers, is used to study the genetic code(s). After considering two kinds of q-numbers, for comparison, a phenomenological classification scheme of the genetic code…
The prevalence of neutral mutations implies that biological systems typically have many more genotypes than phenotypes. But can the way that genotypes are distributed over phenotypes determine evolutionary outcomes? Answering such questions…
The minimum average number of bits need to describe a random variable is its entropy, assuming knowledge of the underlying statistics On the other hand, universal compression supposes that the distribution of the random variable, while…