Related papers: EXMA: A Genomics Accelerator for Exact-Matching

Breast cancer is one of the leading causes of death globally, and thus there is an urgent need for early and accurate diagnostic techniques. Although ultrasound imaging is a widely used technique for breast cancer screening, it faces…

Linear mixed models (LMM) are widely adopted in genome-wide association studies (GWAS) to account for population stratification and cryptic relatedness. However, the parameter estimation of LMMs imposes substantial computational burdens due…

MONI (Rossi et al., {\it JCB} 2022) is a BWT-based compressed index for computing the matching statistics and maximal exact matches (MEMs) of a pattern (usually a DNA read) with respect to a highly repetitive text (usually a database of…

Programs based on hash tables and Burrows-Wheeler are very fast for mapping short reads to genomes but have low accuracy in the presence of mismatches and gaps. Such reads can be aligned accurately with the Smith-Waterman algorithm but it…

Existing attention accelerators often trade exact softmax semantics, depend on fused Tensor Core kernels, or incur sequential depth that limits FP32 throughput on long sequences. We present \textbf{ELSA}, an algorithmic reformulation of…

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…

Motivation: Despite significant advances in Third-Generation Sequencing (TGS) technologies, Next-Generation Sequencing (NGS) technologies remain dominant in the current sequencing market. This is due to the lower error rates and richer…

The Partitioning Min-Max Weighted Matching (PMMWM) problem, being a practical NP-hard problem, integrates the task of partitioning the vertices of a bipartite graph into disjoint sets of limited size with the classical Maximum-Weight…

While graph-based dynamic programming (DP) is a cornerstone of genomics and network analytics, its efficiency is hampered by fundamentally conflicting computational patterns. Matrix-centric DP drives regular, compute-bound network…

Rapid development of modern sequencing platforms enabled an unprecedented growth of protein families databases. The abundance of sets composed of hundreds of thousands sequences is a great challenge for multiple sequence alignment…

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…

Mixed-precision quantization is a popular approach for compressing deep neural networks (DNNs). However, it is challenging to scale the performance efficiently with mixed-precision DNNs given the current FPGA architecture and conventional…

With the rise of compute-in-memory (CIM) accelerators, floating-point multiply-and-accumulate (FP-MAC) operations have gained extensive attention for their higher accuracy over integer MACs in neural networks. However, the hardware overhead…

The design of DNN accelerators includes two key parts: HW resource configuration and mapping strategy. Intensive research has been conducted to optimize each of them independently. Unfortunately, optimizing for both together is extremely…

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…

Neural Network (NN) accelerators with emerging ReRAM (resistive random access memory) technologies have been investigated as one of the promising solutions to address the \textit{memory wall} challenge, due to the unique capability of…

Accelerating finite automata processing is critical for advancing real-time analytic in pattern matching, data mining, bioinformatics, intrusion detection, and machine learning. Recent in-memory automata accelerators leveraging SRAMs and…

Motivation: Exome or targeted sequencing data exerts analytical challenge to test single nucleotide polymorphisms (SNPs) with extremely small minor allele frequency (MAF). Various rare variant tests were proposed to increase power by…

Deep Neural Networks (DNNs) predominantly rely on General Matrix Multiply (GEMM) kernels, which are often accelerated using specialized hardware architectures. Recently, analog photonic GEMM accelerators have emerged as a promising…

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…