Related papers: MSPKmerCounter: A Fast and Memory Efficient Approa…

Efficient Maximum Inner Product Search (MIPS) is an important task that has a wide applicability in recommendation systems and classification with a large number of classes. Solutions based on locality-sensitive hashing (LSH) as well as…

In computational genomics, many analyses rely on efficient storage and traversal of $k$-mers, motivating compact representations such as spectrum-preserving string sets (SPSS), which store strings whose $k$-mer spectrum matches that of the…

K-Means algorithm is a popular clustering method. However, it has two limitations: 1) it gets stuck easily in spurious local minima, and 2) the number of clusters k has to be given a priori. To solve these two issues, a multi-prototypes…

Magnetic Resonance (MR) imaging, despite its proven diagnostic utility, remains an inaccessible imaging modality for disease surveillance at the population level. A major factor rendering MR inaccessible is lengthy scan times. An MR scanner…

For taxonomic classification, we are asked to index the genomes in a phylogenetic tree such that later, given a DNA read, we can quickly choose a small subtree likely to contain the genome from which that read was drawn. Although popular…

DNA sequencing is the physical/biochemical process of identifying the location of the four bases (Adenine, Guanine, Cytosine, Thymine) in a DNA strand. As semiconductor technology revolutionized computing, modern DNA sequencing technology…

Next Generation Sequencing (NGS) technologies generate large amounts of short read data for many different organisms. The fact that NGS reads are generally short makes it challenging to assemble the reads and reconstruct the original genome…

Recently, classical kernel methods have been extended by the introduction of suitable tensor kernels so to promote sparsity in the solution of the underlying regression problem. Indeed, they solve an lp-norm regularization problem, with…

Motivation: Read mapping is a computationally expensive process and a major bottleneck in genomics analyses. The performance of read mapping is mainly limited by the performance of three key computational steps: Index Querying, Seed…

This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…

Large Language Models (LLMs) incur significant computational and memory costs when processing long prompts, as full self-attention scales quadratically with input length. Token compression aims to address this challenge by reducing the…

Medical image segmentation is essential for clinical diagnosis and treatment planning. Although transformer-based methods have achieved remarkable results, their high computational cost hinders clinical deployment. To address this issue, we…

The minimum sum-of-squares clustering (MSSC), or k-means type clustering, is traditionally considered an unsupervised learning task. In recent years, the use of background knowledge to improve the cluster quality and promote…

Hyperparameter tuning is one of the the most time-consuming parts in machine learning. Despite the existence of modern optimization algorithms that minimize the number of evaluations needed, evaluations of a single setting may still be…

A genome read data set can be quickly and efficiently remapped from one reference to another similar reference (e.g., between two reference versions or two similar species) using a variety of tools, e.g., the commonly-used CrossMap tool.…

Sequencing a genome to determine an individual's DNA produces an enormous number of short nucleotide subsequences known as reads, which must be reassembled to reconstruct the full genome. We present a method for analyzing this type of data…

Motivation: Single Molecule Real-Time (SMRT) sequencing technology and Oxford Nanopore technologies (ONT) produce reads over 10kbp in length, which have enabled high-quality genome assembly at an affordable cost. However, at present, long…

Large-scale genomic workflows used in precision medicine can process datasets spanning tens to hundreds of gigabytes per sample, leading to high memory spikes, intensive disk I/O, and task failures due to out-of-memory errors. Simple static…

Quantized Spiking Neural Networks (QSNNs) offer superior energy efficiency and are well-suited for deployment on resource-limited edge devices. However, limited bit-width weight and membrane potential result in a notable performance…

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…