Related papers: Bit catastrophes for the Burrows-Wheeler Transform
A standard format used for storing the output of high-throughput sequencing experiments is the FASTQ format. It comprises three main components: (i) headers, (ii) bases (nucleotide sequences), and (iii) quality scores. FASTQ files are…
We present an improved wavelet tree construction algorithm and discuss its applications to a number of rank/select problems for integer keys and strings. Given a string of length n over an alphabet of size $\sigma\leq n$, our method builds…
Benford's Law predicts that the first significant digit on the leftmost side of numbers in real-life data is proportioned between all possible 1 to 9 digits approximately as in LOG(1 + 1/digit), so that low digits occur much more frequently…
Multiple studies have shown that Transformers are remarkably robust to pruning. Contrary to this received wisdom, we demonstrate that pre-trained Transformer encoders are surprisingly fragile to the removal of a very small number of…
We propose that the widely observed and universal Gutenberg-Richter relation is a mathematical consequence of the critical branching nature of earthquake process in a brittle fracture environment. These arguments, though preliminary, are…
A well-known fact in the field of lossless text compression is that high-order entropy is a weak model when the input contains long repetitions. Motivated by this, decades of research have generated myriads of so-called dictionary…
Logically constrained term rewriting is a relatively new rewriting formalism that naturally supports built-in data structures, such as integers and bit vectors. In the analysis of logically constrained term rewrite systems (LCTRSs),…
The $\beta$-shift is the transformation from the unit interval to itself that maps $x$ to the fractional part of $\beta x$. Permutations realized by the relative order of the elements in the orbits of these maps have been studied for…
The substring edit error is the operation of replacing a substring $u$ of $x$ with another string $v$, where the lengths of $u$ and $v$ are bounded by a given constant $k$. It encompasses localized insertions, deletions, and substitutions…
In the first part of the present work we consider periodically or quasiperiodically forced systems of the form $(d/dt)x = \epsilon f(x,t \omega )$, where $\epsilon\ll 1$, $\omega\in\mathbb{R}^d$ is a nonresonant vector of frequencies and…
The error threshold transition in a stochastic (i.e. finite population) version of the quasispecies model of molecular evolution is studied using finite-size scaling. For the single-sharp-peak replication landscape, the deterministic model…
The AdS/CFT correspondence is applied to a close analogue of the little hierarchy problem in $AdS_{d+1}$, $d \geq 3$. The new mechanism requires a Maxwell field that gauges a $U(1)_R$ symmetry in a bulk supergravity theory with a negative…
String kernels are typically used to compare genome-scale sequences whose length makes alignment impractical, yet their computation is based on data structures that are either space-inefficient, or incur large slowdowns. We show that a…
Spin-transfer-torque random access memory (STT-RAM) is a promising candidate for the next-generation of random-access-memory due to improved scalability, read-write speeds and endurance. However, the write pulse duration must be long enough…
Given a string of length $n$ that is composed of $r$ runs of letters from the alphabet $\{0,1,\ldots,\sigma{-}1\}$ such that $2 \le \sigma \le r$, we describe a data structure that, provided $r \le n / \log^{\omega(1)} n$, stores the string…
A fundamental issue in the renormalization-group (RG) theory of critical phenomena concerns the allowed values of critical exponents that are consistent with the continuous nature of a phase transition. Here we conjecture a lower bound for…
Binary search trees (BST) are a popular type of data structure when dealing with ordered data. Indeed, they enable one to access and modify data efficiently, with their height corresponding to the worst retrieval time. From a probabilistic…
Recently, codes for correcting a burst of errors have attracted significant attention. One of the most important reasons is that bursts of errors occur in certain emerging techniques, such as DNA storage. In this paper, we investigate a…
A string $w$ is said to be a minimal unique substring (MUS) of a string $T$ if $w$ occurs exactly once in $T$, and any proper substring of $w$ occurs at least twice in $T$. It is known that the number of MUSs in a string $T$ of length $n$…
The longest common prefix array is a very advantageous data structure that, combined with the suffix array and the Burrows-Wheeler transform, allows to efficiently compute some combinatorial properties of a string useful in several…