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Generative models have achieved remarkable success across various applications, driving the demand for multi-GPU computing. Inter-GPU communication becomes a bottleneck in multi-GPU computing systems, particularly on consumer-grade GPUs. By…
Fast similarity search is a key component in large-scale information retrieval, where semantic hashing has become a popular strategy for representing documents as binary hash codes. Recent advances in this area have been obtained through…
Generating the hash values of short subsequences, called seeds, enables quickly identifying similarities between genomic sequences by matching seeds with a single lookup of their hash values. However, these hash values can be used only for…
Nanopore sequencing technology remains highly error-prone, making efficient error correction essential in DNA-based data storage. Prior work addressed high error rates using convolutional codes with their decoder coupled with the…
Genome assembly from the high-throughput sequencing (HTS) reads is a fundamental yet challenging computational problem. An intrinsic challenge is the uncertainty caused by the widespread repetitive elements. Here we get around the…
Dynamic race detection based on the happens before (HB) partial order has now become the de facto approach to quickly identify data races in multi-threaded software. Most practical implementations for detecting these races use timestamps to…
To support emerging applications ranging from holographic communications to extended reality, next-generation mobile wireless communication systems require ultra-fast and energy-efficient baseband processors. Traditional complementary…
Nanopore sequencing technology has the potential to render other sequencing technologies obsolete with its ability to generate long reads and provide portability. However, high error rates of the technology pose a challenge while generating…
The Segment Anything Model 2 (SAM2) has recently demonstrated exceptional performance in zero-shot prompt segmentation for natural images and videos. However, when the propagation mechanism of SAM2 is applied to medical images, it often…
Nanopore sequencing generates noisy electrical signals that need to be converted into a standard string of DNA nucleotide bases using a computational step called basecalling. The accuracy and speed of basecalling have critical implications…
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…
Background Nucleotide sequences contain multiple codes responsible for organism's functioning and structure. They can be investigated by various signal processing methods. These techniques are well suited for indication of frequently…
Raman spectroscopy can provide insight into the molecular composition of cells and tissue. Consequently, it can be used as a powerful diagnostic tool, e.g. to help identify changes in molecular contents with the onset of disease. But robust…
Assessing the correctness of genome assemblies is an important step in any genome project. Several methods exist, but most are computationally intensive and, in some cases, inappropriate. Here I present baa.pl, a fast and easy-to-use…
Classification in the dissimilarity space has become a very active research area since it provides a possibility to learn from data given in the form of pairwise non-metric dissimilarities, which otherwise would be difficult to cope with.…
DNA sequencing, especially of microbial genomes and metagenomes, has been at the core of recent research advances in large-scale comparative genomics. The data deluge has resulted in exponential growth in genomic datasets over the past…
Image reconstruction from radio-frequency data is pivotal in ultrafast plane wave ultrasound imaging. Unlike the conventional delay-and-sum (DAS) technique, which relies on somewhat imprecise assumptions, deep learning-based methods perform…
We introduce Xampling, a unified framework for signal acquisition and processing of signals in a union of subspaces. The main functions of this framework are two. Analog compression that narrows down the input bandwidth prior to sampling…
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.…
Motivation: De novo transcriptome assembly of non-model organisms is the first major step for many RNA-seq analysis tasks. Current methods for de novo assembly often report a large number of contiguous sequences (contigs), which may be…