Related papers: Efficient Construction of a Complete Index for Pan…

Bit vectors are fundamental building blocks of many succinct data structures. They can be used to represent graphs, are an important part of many text indices in the form of the wavelet tree, and can be used to encode ordered sequences of…

The wavelet tree (Grossi et al. [SODA, 2003]) and wavelet matrix (Claude et al. [Inf. Syst., 47:15--32, 2015]) are compact indices for texts over an alphabet $[0,\sigma)$ that support rank, select and access queries in $O(\lg \sigma)$ time.…

Agentic memory systems have become critical for enabling LLM agents to maintain long-term context and retrieve relevant information efficiently. However, existing memory frameworks suffer from a fundamental limitation: they perform…

In the last decades, the necessity to process massive amounts of textual data fueled the development of compressed text indexes: data structures efficiently answering queries on a given text while occupying space proportional to the…

In this article we extend the elegant in-place Burrows-Wheeler transform (BWT) algorithm proposed by Crochemore et al. (Crochemore et al., 2015). Our extension is twofold: we first show how to compute simultaneously the longest common…

Gagie, Navarro and Prezza's $r$-index (SODA, 2018) promises to speed up DNA alignment and variation calling by allowing us to index entire genomic databases, provided certain obstacles can be overcome. In this paper we first strengthen and…

Gliomas are the most prevalent type of primary brain tumors, and their accurate segmentation from MRI is critical for diagnosis, treatment planning, and longitudinal monitoring. However, the scarcity of high-quality annotated imaging data…

We design the first learned index that solves the dictionary problem with time and space complexity provably better than classic data structures for hierarchical memories, such as B-trees, and modern learned indexes. We call our solution…

Sublinear time quantum algorithms have been established for many fundamental problems on strings. This work demonstrates that new, faster quantum algorithms can be designed when the string is highly compressible. We focus on two popular and…

Engineering LLMs to accelerate life sciences research requires a robust alignment with biomedical knowledge. We observe that biomedical text exhibits a fundamentally different uncertainty structure from general text: dense low-confidence…

Biomedical question-answering (QA) systems require effective retrieval and generation components to ensure accuracy, efficiency, and scalability. This study systematically examines a Retrieval-Augmented Generation (RAG) system for…

Data subset selection aims to find a smaller yet informative subset of a large dataset that can approximate the full-dataset training, addressing challenges associated with training neural networks on large-scale datasets. However, existing…

Personalization of machine learning (ML) predictions for individual users/domains/enterprises is critical for practical recommendation systems. Standard personalization approaches involve learning a user/domain specific embedding that is…

To store and search genomic databases efficiently, researchers have recently started building compressed self-indexes based on grammars. In this paper we show how, given a straight-line program with $r$ rules for a string (S [1..n]) whose…

With small-scale quantum processors transitioning from experimental physics labs to industrial products, these processors allow us to efficiently compute important algorithms in various fields. In this paper, we propose a quantum algorithm…

An algorithm (bliss) is proposed to speed up the construction of slow adaptive walks. Slow adaptive walks are adaptive walks biased towards closer points or smaller move steps. They were previously introduced to explore a search space, e.g.…

Natural language text corpora are often available as sets of syntactically parsed trees. A wide range of expressive tree queries are possible over such parsed trees that open a new avenue in searching over natural language text. They not…

Indexes facilitate efficient querying when the selection predicate is on an indexed key. As a result, when loading data, if we anticipate future selective (point or range) queries, we typically maintain an index that is gradually populated…

Range Minimum Query (RMQ) is an important building brick of many compressed data structures and string matching algorithms. Although this problem is essentially solved in theory, with sophisticated data structures allowing for constant time…

With novel developments in sequencing technologies, time-sampled data are becoming more available and accessible. Naturally, there have been efforts in parallel to infer population genetic parameters from these datasets. Here, we compare…