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

This paper presents an accurate short-read mapper for next-generation sequencing data which is widely used in the 1000 Genomes Project, and human clinical and other species genome studies.

Accelerators for sparse matrix multiplication are important components in emerging systems. In this paper, we study the main challenges of accelerating Sparse Matrix Multiplication (SpMM). For the situations that data is not stored in the…

Cardiovascular magnetic resonance (CMR) imaging is the gold standard for diagnosing several heart diseases due to its non-invasive nature and proper contrast. MR imaging is time-consuming because of signal acquisition and image formation…

Deep neural networks (DNNs) have been proven to be effective in solving many real-life problems, but its high computation cost prohibits those models from being deployed to edge devices. Pruning, as a method to introduce zeros to model…

Deep Neural Networks (DNN) could forget the knowledge about earlier tasks when learning new tasks, and this is known as \textit{catastrophic forgetting}. While recent continual learning methods are capable of alleviating the catastrophic…

Spiking neural networks (SNNs) provide an energy-efficient solution by utilizing the spike-based and sparse nature of biological systems. Since the advent of Transformers, SNNs have struggled to compete with artificial networks on long…

Magnetic resonance imaging (MRI) is mainly limited by long scanning time and vulnerable to human tissue motion artifacts, in 3D clinical scenarios. Thus, k-space undersampling is used to accelerate the acquisition of MRI while leading to…

Machine learning applications that are implemented with spike-based computation model, e.g., Spiking Neural Network (SNN), have a great potential to lower the energy consumption when they are executed on a neuromorphic hardware. However,…

The computational problem of inferring the full haplotype of a cell starting from read sequencing data is known as haplotype assembly, and consists in assigning all heterozygous Single Nucleotide Polymorphisms (SNPs) to exactly one of the…

Purpose: Compressed sensing MRI (CS-MRI) from single and parallel coils is one of the powerful ways to reduce the scan time of MR imaging with performance guarantee. However, the computational costs are usually expensive. This paper aims to…

The recent framework of compressive statistical learning aims at designing tractable learning algorithms that use only a heavily compressed representation-or sketch-of massive datasets. Compressive K-Means (CKM) is such a method: it…

Motivation: Protein-to-genome alignment is critical to annotating genes in non-model organisms. While there are a few tools for this purpose, all of them were developed over ten years ago and did not incorporate the latest advances in…

Metagenome assembly is the process of transforming a set of short, overlapping, and potentially erroneous DNA segments from environmental samples into the accurate representation of the underlying microbiomes's genomes. State-of-the-art…

The Nystrom method has been popular for generating the low-rank approximation of kernel matrices that arise in many machine learning problems. The approximation quality of the Nystrom method depends crucially on the number of selected…

The Shortest Common Superstring (SCS) problem is a fundamental task in sequence analysis. In genome assembly, however, the double-stranded nature of DNA implies that each fragment may occur either in its original orientation or as its…

Sequence segmentation is a well-studied problem, where given a sequence of elements, an integer K, and some measure of homogeneity, the task is to split the sequence into K contiguous segments that are maximally homogeneous. A classic…

Estimating the number of clusters (K) is a critical and often difficult task in cluster analysis. Many methods have been proposed to estimate K, including some top performers using resampling approach. When performing cluster analysis in…

Sequential pattern mining (SPM) has excellent prospects and application spaces and has been widely used in different fields. The non-overlapping SPM, as one of the data mining techniques, has been used to discover patterns that have…

Subgraph matching is a fundamental problem in graph analysis with a wide range of applications. However, due to its inherent NP-hardness, enumerating subgraph matches efficiently on large real-world graphs remains highly challenging. Most…

This paper describes the adaptation of a well-scaling parallel algorithm for computing Morse-Smale segmentations based on path compression to a distributed computational setting. Additionally, we extend the algorithm to efficiently compute…