Related papers: Local stability and evolution of the genetic code

Analyzing the computational complexity of evolutionary algorithms for binary search spaces has significantly increased their theoretical understanding. With this paper, we start the computational complexity analysis of genetic programming.…

Empirical substitution matrices represent the average tendencies of substitutions over various protein families by sacrificing gene-level resolution. We develop a codon-based model, in which mutational tendencies of codon, a genetic code,…

Adversarial robustness refers to a model's ability to resist perturbation of inputs, while distribution robustness evaluates the performance of the model under data shifts. Although both aim to ensure reliable performance, prior work has…

Stochastic neural networks (SNNs) are random functions whose predictions are gained by averaging over multiple realizations. Consequently, a gradient-based adversarial example is calculated based on one set of samples and its classification…

The genesis of the stand genetic code is considered as a result of a fusion of two AU- and GC-codes distributed in two dominant and two recessive domains. The fusion of these codes is described with simple empirical rules. This formal…

Effective and reliable data retrieval is critical for the feasibility of DNA storage, and the development of random access efficiency plays a key role in its practicality and reliability. In this paper, we study the Random Access Problem,…

Computational RNA secondary structure prediction is rather well established. However, such prediction algorithms always depend on a large number of experimentally measured parameters. Here, we study how sensitive structure prediction…

Stochastic Gradient Descent (SGD) based methods have been widely used for training large-scale machine learning models that also generalize well in practice. Several explanations have been offered for this generalization performance, a…

Though the problem of sequence-reversed protein folding is largely unexplored, one might speculate that reversed native protein sequences should be significantly more foldable than purely random heteropolymer sequences. In this article, we…

Random models of evolution are instrumental in extracting rates of microscopic evolutionary mechanisms from empirical observations on genetic variation in genome sequences. In this context it is necessary to know the statistical properties…

Many works show that node-level predictions of Graph Neural Networks (GNNs) are unrobust to small, often termed adversarial, changes to the graph structure. However, because manual inspection of a graph is difficult, it is unclear if the…

Code generation models have achieved impressive performance. However, they tend to be brittle as slight edits to a prompt could lead to very different generations; these robustness properties, critical for user experience when deployed in…

Under constant selection, each trait has a fixed fitness, and small mutation rates allow populations to efficiently exploit the optimal trait. Therefore it is reasonable to expect mutation rates will evolve downwards. However, we find this…

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…

Accurate prediction of protein stability changes upon single-site variations (DDG) is important for protein design, as well as our understanding of the mechanism of genetic diseases. The performance of high-throughput computational methods…

In this paper, we focus on quantifying model stability as a function of random seed by investigating the effects of the induced randomness on model performance and the robustness of the model in general. We specifically perform a controlled…

This article describes the various experimental bounds on the variation of the fundamental constants of nature. After a discussion on the role of fundamental constants, of their definition and link with metrology, the various constraints on…

Most amino acids are encoded by multiple synonymous codons. For an amino acid, some of its synonymous codons are used much more rarely than others. Analyses of positions of such rare codons in protein sequences revealed that rare codons can…

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…

Functional proteins must fold with some minimal stability to a structure that can perform a biochemical task. Here we use a simple model to investigate the relationship between the stability requirement and the capacity of a protein to…