相关论文: Efficient Construction of a Complete Index for Pan…

Efficient large-scale annotation of genomic intervals is essential for personal genome interpretation in the realm of precision medicine. There are 13 possible relations between two intervals according to Allen's interval algebra.…

Run-length encoding Burrows-Wheeler Transformed strings, resulting in Run-Length BWT (RLBWT), is a powerful tool for processing highly repetitive strings. We propose a new algorithm for online RLBWT working in run-compressed space, which…

Feature selection from a large number of covariates (aka features) in a regression analysis remains a challenge in data science, especially in terms of its potential of scaling to ever-enlarging data and finding a group of scientifically…

Advances in bio-technology have made available massive amounts of functional, structural and genomic data for many biological sequences. This increased availability of heterogeneous biological data has resulted in biological applications…

We present ensemble methods in a machine learning (ML) framework combining predictions from five known motif/binding site exploration algorithms. For a given TF the ensemble starts with position weight matrices (PWM's) for the motif,…

Accurate cardinality estimation of substring queries, which are commonly expressed using the SQL LIKE predicate, is crucial for query optimization in database systems. While both rule-based methods and machine learning-based methods have…

Suffix trees are one of the most versatile data structures in stringology, with many applications in bioinformatics. Their main drawback is their size, which can be tens of times larger than the input sequence. Much effort has been put into…

This paper presents new alternatives to the well-known Bloom filter data structure. The Bloom filter, a compact data structure supporting set insertion and membership queries, has found wide application in databases, storage systems, and…

We study the problem of constructing a dynamic fully indexable dictionary (FID) in the Word-RAM model using space close to the information-theoretic lower bound. A FID is a data-structure that encodes a bit-vector $B$ of length $u$ and…

Large Language Models (LLMs) have demonstrated significant potential as autonomous software engineering (SWE) agents. Recent work has further explored augmenting these agents with memory mechanisms to support long-horizon reasoning.…

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,…

The rank problem in succinct data structures asks to preprocess an array A[1..n] of bits into a data structure using as close to n bits as possible, and answer queries of the form rank(k) = Sum_{i=1}^k A[i]. The problem has been intensely…

Structured security logs are critical for detecting advanced persistent threats (APTs). Large language models (LLMs) struggle in this domain due to limited context and domain mismatch. We propose \textbf{DM-RAG}, a dual-memory…

The Burrows-Wheeler Transform (BWT) of a string is an invertible permutation of the string, which can be used for data compression and compact indexes for string pattern matching. Ganguly et al. [SODA, 2017] introduced the parameterized BWT…

The Burrows-Wheeler transform (BWT) is used by the bzip2 family of compressors. In this paper, we present a hardware architecture that implements an inplace algorithm to compute the BWT. Our design does not have explicit storage for the…

Indexing labeled graphs for pattern matching is a central challenge of pangenomics. Equi et al. (Algorithmica, 2022) developed the Elastic Founder Graph ($\mathsf{EFG}$) representing an alignment of $m$ sequences of length $n$, drawn from…

RNA design aims to identify RNA sequences that fold into a target secondary structure. This task is challenging in terms of computational efficiency. Most existing methods focus on either minimum free energy (MFE)-based or ensemble-based…

Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to…

In a dynamic retrieval system, documents must be ingested as they arrive, and be immediately findable by queries. Our purpose in this paper is to describe an index structure and processing regime that accommodates that requirement for…

This paper introduces a novel indexing and access method, called Feature- Based Adaptive Tolerance Tree (FATT), using wavelet transform is proposed to organize large image data sets efficiently and to support popular image access mechanisms…