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Hypertree decompositions (HDs), as well as the more powerful generalized hypertree decompositions (GHDs), and the yet more general fractional hypertree decompositions (FHDs) are hypergraph decomposition methods successfully used for…
The Burrows-Wheeler-Transform (BWT), a reversible string transformation, is one of the fundamental components of many current data structures in string processing. It is central in data compression, as well as in efficient query algorithms…
The Burrows-Wheeler Transform (BWT) is a word transformation introduced in 1994 for Data Compression. It has become a fundamental tool for designing self-indexing data structures, with important applications in several area in science and…
The Burrows-Wheeler Transform (BWT) is a string transformation technique widely used in areas such as bioinformatics and file compression. Many applications combine a run-length encoding (RLE) with the BWT in a way which preserves the…
Hypertree decompositions, as well as the more powerful generalized hypertree decompositions (GHDs), and the yet more general fractional hypertree decompositions (FHD) are hypergraph decomposition methods successfully used for answering…
Persistent homology is a tool that can be employed to summarize the shape of data by quantifying homological features. When the data is an object in $\mathbb{R}^d$, the (augmented) persistent homology transform ((A)PHT) is a family of…
We study problems connected to first-order logic in graphs of bounded twin-width. Inspired by the approach of Bonnet et al. [FOCS 2020], we introduce a robust methodology of local types and describe their behavior in contraction sequences…
A bi-level optimization framework (BiOPT) was proposed in [3] for convex composite optimization, which is a generalization of bi-level unconstrained minimization framework (BLUM) given in [20]. In this continuation paper, we introduce a…
In order to avoid the reference bias introduced by mapping reads to a reference genome, bioinformaticians are investigating reference-free methods for analyzing sequenced genomes. With large projects sequencing thousands of individuals,…
The Burrows-Wheeler transform (BWT) is a permutation whose applications are prevalent in data compression and text indexing. The bijective BWT (BBWT) is a bijective variant of it. Although it is known that the BWT can be constructed in…
Invariant-based models for incompressible isotropic hyperelasticity are typically formulated as functions of the first and second invariants, $W = W(\bar{I}_1, \bar{I}_2)$. A widely used class of models employs separable representations of…
The Burrows-Wheeler Transform is a string transformation that plays a fundamental role for the design of self-indexing compressed data structures. Over the years, researchers have successfully extended this transformation outside the…
Prefix-free parsing (PFP) was introduced by Boucher et al. (2019) as a preprocessing step to ease the computation of Burrows-Wheeler Transforms (BWTs) of genomic databases. Given a string $S$, it produces a dictionary $D$ and a parse $P$ of…
The compression of highly repetitive strings (i.e., strings with many repetitions) has been a central research topic in string processing, and quite a few compression methods for these strings have been proposed thus far. Among them, an…
The Burrows-Wheeler Transform (BWT) serves as the basis for many important sequence indexes. On very large datasets (e.g. genomic databases), classical BWT construction algorithms are often infeasible because they usually need to have the…
Expander decompositions have become one of the central frameworks in the design of fast algorithms. For an undirected graph $G=(V,E)$, a near-optimal $\phi$-expander decomposition is a partition $V_1, V_2, \ldots, V_k$ of the vertex set $V$…
In this paper, we consider the problem of compressing a trie while supporting the powerful \emph{locate} queries: to return the pre-order identifiers of all nodes reached by a path labeled with a given query pattern. Our result builds on…
Inference-time optimization scales computation to derive deliberate reasoning steps for effective performance. While previous search-based strategies address the short-sightedness of auto-regressive generation, the vast search space leads…
The Burrows-Wheeler-Transform (BWT) is an invertible permutation of a text known to be highly compressible but also useful for sequence analysis, what makes the BWT highly attractive for lossless data compression. In this paper, we present…
Burrows-Wheeler transform (BWT) is an invertible text transformation that, given a text $T$ of length $n$, permutes its symbols according to the lexicographic order of suffixes of $T$. BWT is one of the most heavily studied algorithms in…