Related papers: biobambam: tools for read pair collation based alg…
Currently, third-generation sequencing techniques, which allow to obtain much longer DNA reads compared to the next-generation sequencing technologies, are becoming more and more popular. There are many possibilities to combine data from…
Enhancing and preserving the readability of document images, particularly historical ones, is crucial for effective document image analysis. Numerous models have been proposed for this task, including convolutional-based, transformer-based,…
This paper presents a novel method for efficient image retrieval, based on a simple and effective hashing of CNN features and the use of an indexing structure based on Bloom filters. These filters are used as gatekeepers for the database of…
Recent Mamba-based image restoration methods have achieved promising results but remain limited by fixed scanning patterns and inefficient feature utilization. Conventional Mamba architectures rely on predetermined paths that cannot adapt…
Massively parallel sequencing techniques have revolutionized biological and medical sciences by providing unprecedented insight into the genomes of humans, animals, and microbes. Modern sequencing platforms generate enormous amounts of…
Sequence alignment is a fundamental process in computational biology which identifies regions of similarity in biological sequences. With the exponential growth in the volume of data in bioinformatics databases, the time, processing power,…
Recent emergence of next-generation DNA sequencing technology has enabled acquisition of genetic information at unprecedented scales. In order to determine the genetic blueprint of an organism, sequencing platforms typically employ…
State Space Models (SSMs) with selective scan (Mamba) have been adapted into efficient vision models. Mamba, unlike Vision Transformers, achieves linear complexity for token interactions through a recurrent hidden state process. This…
Pyrosequencing is among the emerging sequencing techniques, capable of generating upto 100,000 overlapping reads in a single run. This technique is much faster and cheaper than the existing state of the art sequencing technique such as…
We present a parallel algorithm and scalable implementation for genome analysis, specifically the problem of finding overlaps and alignments for data from "third generation" long read sequencers. While long sequences of DNA offer enormous…
The widespread adoption of Large Language Models (LLMs) has exponentially increased the demand for efficient serving systems. With growing requests and context lengths, key-value (KV)-related operations, including attention computation and…
The continually increasing volume of DNA sequence data has resulted in a growing demand for fast implementations of core algorithms. Computation of pairwise alignments between candidate haplotypes and sequencing reads using Pair-HMMs is a…
Motivation: Recent advances in sequencing technologies promise ultra-long reads of $\sim$100 kilo bases (kb) in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 mega bases (Mb) in length. Existing…
Patch-based methods are widely used in 3D medical image segmentation to address memory constraints in processing high-resolution volumetric data. However, these approaches often neglect the patch's location within the global volume, which…
Motivation: Seed filtering is critical in DNA read mapping, a process where billions of DNA fragments (reads) sampled from a donor are mapped onto a reference genome to identify genomic variants of the donor. Read mappers 1) quickly…
Bit-interleaved coded modulation with iterative decoding (BICM-ID) offers very good error performance over additive white Gaussian noise (AWGN) and fading channels if it uses a wisely designed signal mapping. Further, error performance of…
Reducing the cost of sequencing genomes provided by next-generation sequencing technologies has greatly increased the number of genomic projects. As a result, there is a growing need for better assembly and assembly validation methods. One…
Sequence alignment is a memory bound computation whose performance in modern systems is limited by the memory bandwidth bottleneck. Processing-in-memory architectures alleviate this bottleneck by providing the memory with computing…
Regular expression matching is essential for many applications, such as finding patterns in text, exploring substrings in large DNA sequences, or lexical analysis. However, sequential regular expression matching may be time-prohibitive for…
Genome assembly using high throughput data with short reads, arguably, remains an unresolvable task in repetitive genomes, since when the length of a repeat exceeds the read length, it becomes difficult to unambiguously connect the flanking…