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Gur Yaari

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3 published item(s)

preprint2026arXiv

Flashback: A Reversible Bilateral Run-Peeling Decomposition of Strings

We introduce Flashback, a reversible string decomposition that repeatedly peels the maximal leading and trailing character runs from a sentinel-wrapped input, recording each pair as one bilateral token. Decomposition and reconstruction both run in O(n) time and space. Our central result is a run-pairing theorem: Flashback is equivalent to pairing the first run of the string with the last, the second with the second-to-last, and so on. This gives an exact token count of 1+[r/2] for a string with r maximal runs, and matches a lower bound that holds for any admissible bilateral run-peeling scheme. From the run-pairing theorem the main structural properties follow as corollaries: the irreducible peeling kernel uses at most two symbols; palindromes are precisely the strings whose run-length encoding is symmetric with an odd number of runs; the image of the decomposition admits an explicit finite-state characterisation; and changing one run length rewrites exactly one content token.

preprint2021arXiv

Diversity in immunogenomics: the value and the challenge

With the advent of high-throughput sequencing technologies, the fields of immunogenomics and adaptive immune receptor repertoire research are facing both opportunities and challenges. Adaptive immune receptor repertoire sequencing (AIRR-seq) has become an increasingly important tool to characterize T and B cell responses in settings of interest. However, the majority of AIRR-seq studies conducted so far were performed in individuals of European ancestry, restricting the ability to identify variation in human adaptive immune responses across populations and limiting their applications. As AIRR-seq studies depend on the ability to assign VDJ sequence reads to the correct germline gene segments, efforts to characterize the genomic loci that encode adaptive immune receptor genes in different populations are urgently needed. The availability of comprehensive germline gene databases and further applications of AIRR-seq studies to individuals of non-European ancestry will substantially enhance our understanding of human adaptive immune responses, promote the development of effective diagnostics and treatments, and eventually advance precision medicine.

preprint2010arXiv

Cooperation Evolution in Random Multiplicative Environments

Most real life systems have a random component: the multitude of endogenous and exogenous factors influencing them result in stochastic fluctuations of the parameters determining their dynamics. These empirical systems are in many cases subject to noise of multiplicative nature. The special properties of multiplicative noise as opposed to additive noise have been noticed for a long while. Even though apparently and formally the difference between free additive vs. multiplicative random walks consists in just a move from normal to log-normal distributions, in practice the implications are much more far reaching. While in an additive context the emergence and survival of cooperation requires special conditions (especially some level of reward, punishment, reciprocity), we find that in the multiplicative random context the emergence of cooperation is much more natural and effective. We study the various implications of this observation and its applications in various contexts.