Related papers: Faster Iterative $\phi$ Queries on the Positional …
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…
While short read aligners, which predominantly use the FM-index, are able to easily index one or a few human genomes, they do not scale well to indexing databases containing thousands of genomes. To understand why, it helps to examine the…
When building Burrows-Wheeler Transforms (BWTs) of truly huge datasets, prefix-free parsing (PFP) can use an unreasonable amount of memory. In this paper we show how if a dataset can be broken down into small datasets that are not very…
Structural decomposition methods offer powerful theoretical guarantees for join evaluation, yet they are rarely used in real-world query optimizers. A major reason is the difficulty of combining cost-based plan search and structure-based…
We introduce hp-greedy, a refinement approach for building gravitational wave surrogates as an extension of the standard reduced basis framework. Our proposal is data-driven, with a domain decomposition of the parameter space, local reduced…
Benders decomposition is a widely used method for solving large optimization problems, but its performance is often hindered by the repeated solution of subproblems. We propose a flexible and modular algorithmic framework for accelerating…
Frequency-domain full-waveform inversion (FWI) is suitable for long-offset stationary-recording acquisition, since reliable subsurface models can be reconstructed with a few frequencies and attenuation is easily implemented without…
It is critical to obtain high resolution features with long range dependency for dense prediction tasks such as semantic segmentation. To generate high-resolution output of size $H\times W$ from a low-resolution feature map of size $h\times…
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…
In this paper, we propose a novel Hermite weighted essentially non-oscillatory (HWENO) fast sweeping method to solve the static Hamilton-Jacobi equations efficiently. During the HWENO reconstruction procedure, the proposed method is built…
Wing and Tip decomposition construct a hierarchy of butterfly-dense edge and vertex induced bipartite subgraphs, respectively. They have applications in several domains including e-commerce, recommendation systems and document analysis.…
Purpose: To develop an algorithm for robust partial Fourier (PF) reconstruction applicable to diffusion-weighted (DW) images with non-smooth phase variations. Methods: Based on an unrolled proximal splitting algorithm, a neural network…
Tam [2026] shows that combining Bethel multivariate allocation with Hierarchical Bayes (HB) small area models can substantially reduce survey sample sizes while maintaining domain-level precision and near-nominal coverage of posterior…
The Burrows-Wheeler-Transform (BWT) is a reversible string transformation which plays a central role in text compression and is fundamental in many modern bioinformatics applications. The BWT is a permutation of the characters, which is in…
In the real world datasets (e.g.,DBpedia query log), queries built on well-designed patterns containing only AND and OPT operators (for short, WDAO-patterns) account for a large proportion among all SPARQL queries. In this paper, we present…
Motivated by challenges in pangenomic read alignment, we propose a generalization of Wheeler graphs that we call Wheeler maps. A Wheeler map stores a text $T[1..n]$ and an assignment of tags to the characters of $T$ such that we can…
In this paper we present novel algorithmic techniques with a O(H(N)+N/H(N)) time complexity for performing several types of queries and updates on general rooted trees, binary search trees and lists of size N. For rooted trees we introduce…
Model-Based Iterative Reconstruction (MBIR) is important because direct methods, such as Filtered Back-Projection (FBP) can introduce significant noise and artifacts in sparse-angle tomography, especially for time-evolving samples. Although…
Binary Partition Hierarchies (BPH) and minimum spanning trees are fundamental data structures involved in hierarchical analysis such as quasi-flat zones or watershed. However, classical BPH construction algorithms require to have the whole…
The task of hyper-parameter optimization (HPO) is burdened with heavy computational costs due to the intractability of optimizing both a model's weights and its hyper-parameters simultaneously. In this work, we introduce a new class of HPO…