Related papers: FindeR: Accelerating FM-Index-based Exact Pattern …
FM-indexes are a crucial data structure in DNA alignment, for example, but searching with them usually takes at least one random access per character in the query pattern. Ferragina and Fischer observed in 2007 that word-based indexes often…
Generic matrix multiplication (GEMM) and one-dimensional convolution/cross-correlation (CONV) kernels often constitute the bulk of the compute- and memory-intensive processing within image/audio recognition and matching systems. We propose…
Processing-in-memory (PIM) architectures have demonstrated great potential in accelerating numerous deep learning tasks. Particularly, resistive random-access memory (RRAM) devices provide a promising hardware substrate to build PIM…
Mapping gene expression as a quantitative trait using whole genome-sequencing and transcriptome analysis allows to discover the functional consequences of genetic variation. We developed a novel method and ultra-fast software Findr for…
Genome sequencing has become a central focus in computational biology. A genome study typically begins with sequencing, which produces millions to billions of short DNA fragments known as reads. Read mapping aligns these reads to a…
In recent years, pangenomes received increasing attention from the scientific community for their ability to incorporate population variation information and alleviate reference genome bias. Maximal Exact Matches (MEMs) and Maximal Unique…
The advent of next-generation sequencing (NGS) has revolutionized genomic research by enabling cost-effective, high-throughput sequencing of a diverse range of organisms. This breakthrough has unleashed a "Cambrian explosion" in genomic…
Retrieval-Augmented Generation (RAG) enhances large language models (LLMs) by integrating external knowledge retrieval but faces challenges on edge devices due to high storage, energy, and latency demands. Computing-in-Memory (CIM) offers a…
We introduce a new, practical method for conducting an exact search in a uni- and bidirectional FM index in $O(1)$ time per step while using $O(\log \sigma * n) + o(\log \sigma * \sigma * n)$ bits of space. This is done by replacing the…
The continuous shift of computational bottlenecks to the memory access and data transfer, especially for AI applications, poses the urgent needs of re-engineering the computer architecture fundamentals. Many edge computing applications,…
ReRAM-based accelerators exhibit enormous potential to increase computational efficiency for DNN inference tasks, delivering significant performance and energy savings over traditional platforms. By incorporating adaptive scheduling, these…
The advent of highly accurate protein structure prediction methods has fueled an exponential expansion of the protein structure database. Consequently, there is a rising demand for rapid and precise structural homolog search. Traditional…
Mass spectrometry (MS) is essential for proteomics and metabolomics but faces impending challenges in efficiently processing the vast volumes of data. This paper introduces SpecPCM, an in-memory computing (IMC) accelerator designed to…
Recent DNA pre-alignment filter designs employ DRAM for storing the reference genome and its associated meta-data. However, DRAM incurs increasingly high energy consumption background and refresh energy as devices scale. To overcome this…
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…
Motivation: Seed location 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. State-of-the-art read…
Motivation: Next-generation sequencing tools have enabled producing of huge amount of genomic information at low cost. Unfortunately, presence of sequencing errors in such data affects quality of downstream analyzes. Accuracy of them can be…
Next Generation Sequencing (NGS) platforms and, more generally, high-throughput technologies are giving rise to an exponential growth in the size of nucleotide sequence databases. Moreover, many emerging applications of nucleotide datasets…
FM-index is an efficient data structure for string search and is widely used in next-generation sequencing (NGS) applications such as sequence alignment and de novo assembly. Recently, FM-indexing is even performed down to the read level,…
Current computational methods for exon-intron structure prediction from a cluster of transcript (EST, mRNA) data do not exhibit the time and space efficiency necessary to process large clusters of over than 20,000 ESTs and genes longer than…