Related papers: From H&M to Gap for Lightweight BWT Merging
This paper introduces and solves the Generalized Heron-Waist Problem (GHWP), that integrates the classical Heron problem of optimal hub location and the waist problem of minimal-perimeter configuration. The GHWP seeks an optimal closed…
We present a new semi-external algorithm that builds the Burrows--Wheeler transform variant of Bauer et al. (a.k.a., BCR BWT) in linear expected time. Our method uses compression techniques to reduce computational costs when the input is…
Improving the generalization ability of modern deep neural networks (DNNs) is a fundamental challenge in machine learning. Two branches of methods have been proposed to seek flat minima and improve generalization: one led by sharpness-aware…
Recently, Cenzato et al.\ proposed a new text index, called the \emph{suffixient array}, which is a subset of the suffix array and supports locating a single pattern occurrence or finding its maximal exact matches (MEMs), assuming random…
We propose a weighted common subgraph (WCS) matching algorithm to find the most similar subgraphs in two labeled weighted graphs. WCS matching, as a natural generalization of the equal-sized graph matching or subgraph matching, finds wide…
This paper proposes a non-interactive end-to-end solution for secure fusion and matching of biometric templates using fully homomorphic encryption (FHE). Given a pair of encrypted feature vectors, we perform the following ciphertext…
Graph matching plays a central role in such fields as computer vision, pattern recognition, and bioinformatics. Graph matching problems can be cast as two types of quadratic assignment problems (QAPs): Koopmans-Beckmann's QAP or Lawler's…
The Burrows-Wheeler-Transform (BWT), a reversible string transformation, is one of the fundamental components of many current data structures in string processing. It is central in data compression, as well as in efficient query algorithms…
Hierarchical Merging is a technique commonly used to summarize very long texts ($>$100K tokens) by breaking down the input into smaller sections, summarizing those sections individually, and then merging or combining those summaries into a…
At the LHC, tagging boosted heavy particle resonances which decay hadronically, such as top quarks and Higgs bosons, can play an essential role in new physics searches. In events with high multiplicity, however, the standard approach to tag…
Parameterized strings are a generalization of strings in that their characters are drawn from two different alphabets, where one is considered to be the alphabet of static characters and the other to be the alphabet of parameter characters.…
The rapid proliferation of large language models (LLMs) such as GPT-4 and Gemini underscores the intense demand for resources during their training processes, posing significant challenges due to substantial computational and environmental…
The Burrows-Wheeler transform (BWT) is integral to the FM-index, which is used extensively in text compression, indexing, pattern search, and bioinformatic problems as de novo assembly and read alignment. Thus, efficient construction of the…
Large Language Models (LLMs) have the ability to solve a variety of tasks, such as text summarization and mathematical questions, just out of the box, but they are often trained with a single task in mind. Due to high computational costs,…
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…
Given two matroids $\mathcal{M}_1$ and $\mathcal{M}_2$ over the same ground set, the matroid intersection problem is to find the maximum cardinality common independent set. In the weighted version of the problem, the goal is to find a…
Popular sequence alignment tools such as BWA convert a reference genome to an indexing data structure based on the Burrows-Wheeler Transform (BWT), from which matches to individual query sequences can be rapidly determined. However the…
Minimum-weight triangulation (MWT) is NP-hard. It has a polynomial-time constant-factor approximation algorithm, and a variety of effective polynomial- time heuristics that, for many instances, can find the exact MWT. Linear programs (LPs)…
Prior work inspired by compression algorithms has described how the Burrows Wheeler Transform can be used to create a distance measure for bioinformatics problems. We describe issues with this approach that were not widely known, and…
The longest common prefix (LCP) array is a versatile auxiliary data structure in indexed string matching. It can be used to speed up searching using the suffix array (SA) and provides an implicit representation of the topology of an…