Related papers: Bit catastrophes for the Burrows-Wheeler Transform
We show that the compressed suffix array and the compressed suffix tree for a string of length $n$ over an integer alphabet of size $\sigma\leq n$ can both be built in $O(n)$ (randomized) time using only $O(n\log\sigma)$ bits of working…
A binary string of length $2^k$ induces the Boolean function of $k$ variables whose Shannon expansion is the given binary string. This Boolean function then is representable via a unique reduced ordered binary decision diagram (ROBDD). The…
Until recently, most experts would probably have agreed we cannot backwards-step in constant time with a run-length compressed Burrows-Wheeler Transform (RLBWT), since doing so relies on rank queries on sparse bitvectors and those inherit…
While Transformer-based language models are generally very robust to pruning, there is the recently discovered outlier phenomenon: disabling only 48 out of 110M parameters in BERT-base drops its performance by nearly 30% on MNLI. We…
The worst-case additive sensitivity of a string repetitiveness measure $c$ is defined to be the largest difference between $c(w)$ and $c(w')$, where $w$ is a string of length $n$ and $w'$ is a string that can be obtained by performing a…
Some recent results have introduced external-memory algorithms to compute self-indexes of a set of strings, mainly via computing the Burrows-Wheeler Transform (BWT) of the input strings. The motivations for those results stem from…
Size-Change Termination (SCT) is a method of proving program termination based on the impossibility of infinite descent. To this end we use a program abstraction in which transitions are described by Monotonicity Constraints over (abstract)…
Compact directed acyclic word graphs (CDAWGs) [Blumer et al. 1987] are a fundamental data structure on strings with applications in text pattern searching, data compression, and pattern discovery. Intuitively, the CDAWG of a string $T$ is…
For any $\beta > 1$, let $T_\beta: [0,1)\rightarrow [0,1)$ be the $\beta$-transformation defined by $T_\beta x=\beta x \mod 1$. We study the uniform recurrence properties of the orbit of a point under the $\beta$-transformation to the point…
Given a real number beta>1, a permutation pi of length n is realized by the beta-shift if there is some x in [0,1] such that the relative order of the sequence x,f(x),...,f^{n-1}(x), where f(x) is the factional part of beta*x, is the same…
A palindrome is a string that reads the same forward and backward. A palindromic substring $w$ of a string $T$ is called a minimal unique palindromic substring (MUPS) of $T$ if $w$ occurs only once in $T$ and any proper palindromic…
A constant weight binary code consists of $n$-bit binary codewords, each with exactly $w$ bits equal to 1, such that any two codewords are at least Hamming distance $d$ apart. $A(n,d,w)$ is the maximum size of a constant weight binary code…
Bounded-size rules are dynamic random graph processes which incorporate limited choice along with randomness in the evolution of the system. One starts with the empty graph and at each stage two edges are chosen uniformly at random. One of…
The positional Burrows-Wheeler Transform (PBWT) is commonly used to store haplotype panels compactly in such a way that, given a query haplotype, we can quickly find the set maximal exact matches (SMEMs) between the query and the haplotypes…
In this paper we investigate the problem of partitioning an input string T in such a way that compressing individually its parts via a base-compressor C gets a compressed output that is shorter than applying C over the entire T at once.…
Indexing very large collections of strings, such as those produced by the widespread next generation sequencing technologies, heavily relies on multistring generalization of the Burrows-Wheeler Transform (BWT): large requirements of…
Black holes are interesting astrophysical objects that have been studied as systems sensitive to quantum gravitational data. The accelerated geometry in the exterior of extremal black holes can induce large center-of-mass energies between…
In this paper we propose a flexible and lightweight technique for merging compressed indices based on variants of Burrows-Wheeler transform (BWT), thus addressing the need for algorithms that compute compressed indices over large…
We survey the different methods used for extending the BWT to collections of strings, following largely [Cenzato and Lipt\'ak, CPM 2022, Bioinformatics 2024]. We analyze the specific aspects and combinatorial properties of the resulting BWT…
A string $w$ is said to be a minimal absent word (MAW) for a string $S$ if $w$ does not occur in $S$ and any proper substring of $w$ occurs in $S$. We focus on non-trivial MAWs which are of length at least 2. Finding such non-trivial MAWs…