Related papers: Optimal-Time Mapping in Run-Length Compressed PBWT
A longest repeat query on a string, motivated by its applications in many subfields including computational biology, asks for the longest repetitive substring(s) covering a particular string position (point query). In this paper, we extend…
The suffix tree is arguably the most fundamental data structure on strings: introduced by Weiner (SWAT 1973) and McCreight (JACM 1976), it allows solving a myriad of computational problems on strings in linear time. Motivated by its large…
A Longest Common Extension (LCE) query on a text $T$ of length $N$ asks for the length of the longest common prefix of suffixes starting at given two positions. We show that the signature encoding $\mathcal{G}$ of size $w = O(\min(z \log N…
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…
Binary relations are commonly used in Computer Science for modeling data. In addition to classical representations using matrices or lists, some compressed data structures have recently been proposed to represent binary relations in compact…
With the growing scale of big data, probabilistic structures receive increasing popularity for efficient approximate storage and query processing. For example, Bloom filters (BF) can achieve satisfactory performance for approximate…
Backpressure (BP) routing is a well-established framework for distributed routing and scheduling in wireless multi-hop networks. However, the basic BP scheme suffers from poor end-to-end delay due to the drawbacks of slow startup, random…
A degenerate or indeterminate string on an alphabet $\Sigma$ is a sequence of non-empty subsets of $\Sigma$. Given a degenerate string $t$ of length $n$, we present a new method based on the Burrows--Wheeler transform for searching for a…
Recently, Holt and McMillan [Bionformatics 2014, ACM-BCB 2014] have proposed a simple and elegant algorithm to merge the Burrows-Wheeler transforms of a family of strings. In this paper we show that the H&M algorithm can be improved so…
Pretrained Foundation Models (PFMs) have transformed numerous applications by enabling efficient adaptation to customized tasks. Parameter-Efficient Fine-Tuning (PEFT) has emerged as a resource-efficient alternative to full fine-tuning,…
Optimal Transport (OT) has established itself as a robust framework for quantifying differences between distributions, with applications that span fields such as machine learning, data science, and computer vision. This paper offers a…
The offline pickup and delivery problem with time windows (PDPTW) is a classical combinatorial optimization problem in the transportation community, which has proven to be very challenging computationally. Due to the complexity of the…
We propose a novel framework for fast integral operations by uncovering hidden geometries in the row and column structures of the underlying operators. This is accomplished through the \texttt{Questionnaire} algorithm, an iterative…
Modern retrieval system often requires recomputing the representation of every piece of data in the gallery when updating to a better representation model. This process is known as backfilling and can be especially costly in the real world…
Motivation: Predicting the secondary structure of an RNA sequence is useful in many applications. Existing algorithms (based on dynamic programming) suffer from a major limitation: their runtimes scale cubically with the RNA length, and…
Recently, several works have shown that natural modifications of the classical conditional gradient method (aka Frank-Wolfe algorithm) for constrained convex optimization, provably converge with a linear rate when: i) the feasible set is a…
Language models (LMs) pretrained on a large text corpus and fine-tuned on a downstream text corpus and fine-tuned on a downstream task becomes a de facto training strategy for several natural language processing (NLP) tasks. Recently, an…
Subset-Sum is an NP-complete problem where one must decide if a multiset of $n$ integers contains a subset whose elements sum to a target value $m$. The best-known classical and quantum algorithms run in time $\tilde{O}(2^{n/2})$ and…
Large Language Reasoning Models have demonstrated remarkable success on static tasks, yet their application to multi-round agentic planning in interactive environments faces two fundamental challenges. First, the intractable credit…
We introduce probabilistic language tries (PLTs), a unified representation that makes explicit the prefix structure implicitly defined by any generative model over sequences. By assigning to each outgoing edge the conditional probability of…