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The innovation of next-generation sequencing (NGS) techniques has significantly reduced the price of genome sequencing, lowering barriers to future medical research; it is now feasible to apply genome sequencing to studies where it would…
Genetic and comparative genomic studies indicate that extant genomes are more properly considered to be a fusion product of random mutations over generations and genomic material transfers between individuals of different lineages. This has…
Multivariate time series (MTS) analysis prevails in real-world applications such as finance, climate science and healthcare. The various self-attention mechanisms, the backbone of the state-of-the-art Transformer-based models, efficiently…
Convolutional neural networks are based on a huge number of trained weights. Consequently, they are often data-greedy, sensitive to overtraining, and learn slowly. We follow the line of research in which filters of convolutional neural…
Cells receive a wide variety of cellular and environmental signals, which must be processed combinatorially to generate specific and timely genetic responses. We present here a theoretical study on the combinatorial control and integration…
We argue that the freezing transition scenario, previously explored in the statistical mechanics of 1/f-noise random energy models, also determines the value distribution of the maximum of the modulus of the characteristic polynomials of…
We revisit the dynamics of a gene repressed by its own protein in the case where the transcription rate does not adapt instantaneously to protein concentration but is a dynamical variable. We derive analytical criteria for the appearance of…
Coded caching is a promising technique to create coded multicast opportunities for cache-aided networks. By splitting each file into $F$ equal packets (i.e., the subpacketization level $F$) and letting each user cache a set of packets, the…
In this work, we take the initiative in studying the information-theoretic tradeoff between communication and quickest change detection (QCD) under an integrated sensing and communication setting. We formally establish a joint communication…
Vulnerability detection is garnering increasing attention in software engineering, since code vulnerabilities possibly pose significant security. Recently, reusing various code pre-trained models has become common for code embedding without…
This contribution is concerned with mathematical models for the dynamics of the genetic composition of populations evolving under recombination. Recombination is the genetic mechanism by which two parent individuals create the mixed type of…
Apart from few exceptions, the mathematical runtime analysis of evolutionary algorithms is mostly concerned with expected runtimes. In this work, we argue that stochastic domination is a notion that should be used more frequently in this…
A set of linearly constrained permutation matrices are proposed for constructing a class of permutation codes. Making use of linear constraints imposed on the permutation matrices, we can formulate a minimum Euclidian distance decoding…
Approaches to gene interactions based on sign epistasis have been highly influential in recent time. Sign epistasis is useful for relating local and global properties of fitness landscapes, as well as for analyzing evolutionary trajectories…
Statistical analysis of alignments of large numbers of protein sequences has revealed "sectors" of collectively coevolving amino acids in several protein families. Here, we show that selection acting on any functional property of a protein,…
The heavy-tailed mutation operator proposed in Doerr, Le, Makhmara, and Nguyen (GECCO 2017), called \emph{fast mutation} to agree with the previously used language, so far was proven to be advantageous only in mutation-based algorithms.…
The possible role of quantum effects in transfer of genetic information is studied. It's argued that the nucleotides selection during DNA replication is performed by means of proton tunneling between nucleotide and DNA-polimerase bound by…
Motivated by mutation processes occurring in in-vivo DNA-storage applications, a channel that mutates stored strings by duplicating substrings as well as substituting symbols is studied. Two models of such a channel are considered: one in…
Efficient communication in wireless networks is typically challenged by the possibility of interference among several transmitting nodes. Much important research has been invested in decreasing the number of collisions in order to obtain…
Delineating and planning with respect to regions suspected to contain microscopic tumor cells is an inherently uncertain task in radiotherapy. The recently proposed \textit{clinical target distribution} (CTD) is an alternative to the…