Related papers: String Partition for Building Long Burrows-Wheeler…

We explore for the first time the direct construction of string models on quantum annealers, and investigate their efficiency and effectiveness in the model discovery process. Through a thorough comparison with traditional methods such as…

Genome assembly, the process of reconstructing a long genetic sequence by aligning and merging short fragments, or reads, is known to be NP-hard, either as a version of the shortest common superstring problem or in a Hamiltonian-cycle…

Suffix trees are a fundamental data structure in stringology, but their space usage, though linear, is an important problem for its applications. We design and implement a new compressed suffix tree targeted to highly repetitive texts, such…

Although dominant in natural language processing, transformer-based models remain challenged by the task of long-sequence processing, because the computational cost of self-attention operations in transformers swells quadratically with the…

Symbolic regression that aims to detect underlying data-driven models has become increasingly important for industrial data analysis. For most existing algorithms such as genetic programming (GP), the convergence speed might be too slow for…

Determining the interaction strength between proteins and small molecules is key to analyzing their biological function. Quantum-mechanical calculations such as \emph{Density Functional Theory} (DFT) give accurate and theoretically…

We propose a new technique for creating a space-efficient index for large repetitive text collections, such as pangenomic databases containing sequences of many individuals from the same species. We combine two recent techniques from this…

Bloom filter is a widely used classic data structure for approximate membership queries. Learned Bloom filters improve memory efficiency by leveraging machine learning, with the partitioned learned Bloom filter (PLBF) being among the most…

Converting a set of sequencing reads into a lossless compact data structure that encodes all the relevant biological information is a major challenge. The classical approaches are to build the string graph or the de Bruijn graph. Each has…

In this paper, we introduce zip-tries, which are simple, dynamic, memory-efficient data structures for strings. Zip-tries support search and update operations for $k$-length strings in $\mathcal{O}(k+\log n)$ time in the standard RAM model…

We study the impact that string reversal can have on several repetitiveness measures. First, we exhibit an infinite family of strings where the number, $r$, of runs in the run-length encoding of the Burrows--Wheeler transform (BWT) can…

High-throughput DNA sequencers are becoming indispensable in our understanding of diseases at molecular level, in marker-assisted selection in agriculture and in microbial genetics research. These sequencing instruments produce enormous…

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…

Motivated by challenges in pangenomic read alignment, we propose a generalization of Wheeler graphs that we call Wheeler maps. A Wheeler map stores a text $T[1..n]$ and an assignment of tags to the characters of $T$ such that we can…

For the exploration of large state spaces, symbolic search using binary decision diagrams (BDDs) can save huge amounts of memory and computation time. State sets are represented and modified by accessing and manipulating their…

The rank and select operations over a string of length n from an alphabet of size $\sigma$ have been used widely in the design of succinct data structures. In many applications, the string itself need be maintained dynamically, allowing…

The task of accumulating a portion of a list of values, whose values may be updated at any time, is widely used throughout various applications in computer science. While it is trivial to accomplish this task without any constraints,…

Suffix trees have recently become very successful data structures in handling large data sequences such as DNA or Protein sequences. Consequently parallel architectures have become ubiquitous. We present a novel alphabet-dependent parallel…

Fragment-based shape signature techniques have proven to be powerful tools for computer-aided drug design. They allow scientists to search for target molecules with some similarity to a known active compound. They do not require reference…

Modern language models define distributions over strings, but downstream tasks often require different output formats. For instance, a model that generates byte-pair strings does not directly produce word-level predictions, and a DNA model…