Related papers: Optimal-Time Mapping in Run-Length Compressed PBWT
A self-index is a compressed data structure that supports locate queries -- reporting all positions where a given pattern occurs in a string while maintaining the string in compressed form. While many self-indexes have been proposed,…
We deal with the problem of maintaining the suffix tree indexing structure for a fully-online collection of multiple strings, where a new character can be prepended to any string in the collection at any time. The only previously known…
Comparing data defined over space and time is notoriously hard, because it involves quantifying both spatial and temporal variability, while at the same time taking into account the chronological structure of data. Dynamic Time Warping…
We present a new scalable, lightweight algorithm to incrementally construct the BWT and FM-index of large string sets such as those produced by Next Generation Sequencing. The algorithm is designed for massive parallelism and can…
The sort transform (ST) is a modification of the Burrows-Wheeler transform (BWT). Both transformations map an arbitrary word of length n to a pair consisting of a word of length n and an index between 1 and n. The BWT sorts all rotation…
Under the word RAM model, we design three data structures that can be constructed in $O(n\sqrt{\lg n})$ time over $n$ points in an $n \times n$ grid. The first data structure is an $O(n\lg^{\epsilon} n)$-word structure supporting orthogonal…
Modern genomic analyses increasingly rely on pangenomes, that is, representations of the genome of entire populations. The simplest representation of a pangenome is a set of individual genome sequences. Compared to e.g. sequence graphs,…
We present an efficient algorithm for finding all approximate occurrences of a given pattern $p$ of length $m$ in a text $t$ of length $n$ allowing for translocations of equal length adjacent factors and inversions of factors. The algorithm…
In this paper we propose a new family of RRT based algorithms, named RRT+ , that are able to find faster solutions in high-dimensional configuration spaces compared to other existing RRT variants by finding paths in lower dimensional…
Effectively modeling non-stationary dynamics in probabilistic multivariate time series(MTS) forecasting requires balancing expressiveness with robustness. Existing parametric approaches benefit from strong inductive biases but lack…
LLMs exhibit advanced reasoning capabilities, offering the potential to transform natural language questions into mathematical models. However, existing open-source datasets in operations research domain lack detailed annotations of the…
Emerging applications in Printed Circuit Board (PCB) routing impose new challenges on automatic length matching, including adaptability for any-direction traces with their original routing preserved for interactiveness. The challenges can…
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…
The Lawler-Moore dynamic programming framework is a classical tool in scheduling on parallel machines. It applies when the objective is regular, i.e. monotone in job completion times, and each machine follows a fixed priority order such as…
In this paper, we present the first study of the computational complexity of converting an automata-based text index structure, called the Compact Directed Acyclic Word Graph (CDAWG), of size $e$ for a text $T$ of length $n$ into other text…
Binary jumbled pattern matching asks to preprocess a binary string $S$ in order to answer queries $(i,j)$ which ask for a substring of $S$ that is of length $i$ and has exactly $j$ 1-bits. This problem naturally generalizes to…
Let $T [1..n]$ be a text over an alphabet of size $\sigma \in \mathrm{polylog} (n)$, let $r^*$ be the sum of the numbers of runs in the Burrows-Wheeler Transforms of $T$ and its reverse, and let $z$ be the number of phrases in the LZ77…
There are many classical problems in P whose time complexities have not been improved over the past decades. Recent studies of "Hardness in P" have revealed that, for several of such problems, the current fastest algorithm is the best…
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…
Transformers have emerged as the cornerstone of state-of-the-art natural language processing models, showcasing exceptional performance across a wide range of AI applications. However, the memory demands posed by the self-attention…