Related papers: On the codon assignment of chain termination signa…
Resource coordination and interference management is the key to achieving the benefits of femtocell networks. Over-the-air signaling is one of the most effective means for distributed dynamic resource coordination and interference…
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…
We report on a theoretical study of point mutations effects on charge transfer properties in the DNA sequence of the tumor-suppressor p53 gene. On the basis of effective single-strand or double-strand tight-binding models which simulate…
We have presented the basic knowledge on the structure of molecules coding the genetic information, mechanisms of transfer of this information from DNA to proteins and phenomena connected with replication of DNA. In particular, we have…
Homeostasis of protein concentrations in cells is crucial for their proper functioning, and this requires concentrations (at their steady-state levels) to be stable to fluctuations. Since gene expression is regulated by proteins such as…
It has been repeatedly proposed to expand the scope for SETI, and one of the suggested alternatives to radio is the biological media. Genomic DNA is already used on Earth to store non-biological information. Though smaller in capacity, but…
For genetic algorithms using a bit-string representation of length~$n$, the general recommendation is to take $1/n$ as mutation rate. In this work, we discuss whether this is really justified for multimodal functions. Taking jump functions…
Horizontal gene transfer consists in exchanging genetic materials between microorganisms during their lives. This is a major mechanism of bacterial evolution and is believed to be of main importance in antibiotics resistance. We consider a…
MDS convolutional codes have the property that their free distance is maximal among all codes of the same rate and the same degree. In this paper we introduce a class of MDS convolutional codes whose column distances reach the generalized…
Certified robustness in machine learning has primarily focused on adversarial perturbations of the input with a fixed attack budget for each point in the data distribution. In this work, we present provable robustness guarantees on the…
This paper provides a source coding theorem for multi-dimensional information signals when, at a given instant, the distribution associated with one arbitrary component of the signal to be compressed is not known and a side information is…
Background: Acceleration of adaptation dynamics by stress-induced hypermutation has been found experimentally. Evolved evolvability is a prominent explanation. We investigate a more generally applicable explanation by a physical constraint.…
Transcription is a fundamental cellular process, and the first step of gene expression. In human cells, it depends on the binding to chromatin of various proteins, including RNA polymerases and numerous transcription factors (TFs).…
What computational structures emerge in transformers trained on next-token prediction? In this work, we provide evidence that transformers implement constrained Bayesian belief updating -- a parallelized version of partial Bayesian…
The evolution of genetic systems has been analyzed through the use of modifier gene models, in which a neutral gene is posited to control the transmission of other genes under selection. Analysis of modifier gene models has found the…
This paper explores the design of convolutional codes for varying constraint lengths, focusing on their role in error correction in digital communication systems. Convolutional codes are essential in achieving reliable data transmission…
Most of compressed sensing (CS) theory to date is focused on incoherent sensing, that is, columns from the sensing matrix are highly uncorrelated. However, sensing systems with naturally occurring correlations arise in many applications,…
Self-attention is usually described as a flexible, content-adaptive way to mix a token with information from its past. We reinterpret causal self-attention transformers, the backbone of modern foundation models, within a probabilistic…
Across many fields, a problem of interest is to predict the transition rates between nodes of a network, given limited stationary state and dynamical information. We give a solution using the principle of Maximum Caliber. We find the…
Conformational transitions are ubiquitous in biomolecular systems, have significant functional roles and are subject to evolutionary pressures. Here we provide a first theoretical framework for topological transition, i.e. conformational…