Related papers: SparseAssembler2: Sparse k-mer Graph for Memory Ef…

Motivation: De Bruijn graphs have been proposed as a data structure to facilitate the analysis of related whole genome sequences, in both a population and comparative genomic settings. However, current approaches do not scale well to many…

High throughput sequencing of RNA (RNA-Seq) can provide us with millions of short fragments of RNA transcripts from a sample. How to better recover the original RNA transcripts from those fragments (RNA-Seq assembly) is still a difficult…

Sparse matrix-vector and matrix-matrix multiplication (SpMV and SpMM) are fundamental in both conventional (graph analytics, scientific computing) and emerging (sparse DNN, GNN) domains. Workload-balancing and parallel-reduction are…

Multiplying two sparse matrices (SpGEMM) is a common computational primitive used in many areas including graph algorithms, bioinformatics, algebraic multigrid solvers, and randomized sketching. Distributed-memory parallel algorithms for…

Structured sparsity enables deploying large language models (LLMs) on resource-constrained systems. Approaches like dense-to-sparse fine-tuning are particularly compelling, achieving remarkable structured sparsity by reducing the model size…

We consider a sparse matrix-matrix multiplication (SpGEMM) setting where one matrix is square and the other is tall and skinny. This special variant, called TS-SpGEMM, has important applications in multi-source breadth-first search,…

Resistive Random-Access-Memory (ReRAM) crossbar is a promising technique for deep neural network (DNN) accelerators, thanks to its in-memory and in-situ analog computing abilities for Vector-Matrix Multiplication-and-Accumulations (VMMs).…

Distributed approaches based on the map-reduce programming paradigm have started to be proposed in the bioinformatics domain, due to the large amount of data produced by the next-generation sequencing techniques. However, the use of…

Sparse general matrix multiplication (SpGEMM) is a fundamental building block for many real-world applications. Since SpGEMM is a well-known memory-bounded application with vast and irregular memory accesses, considering the memory access…

Motivations Short-read accuracy is important for downstream analyses such as genome assembly and hybrid long-read correction. Despite much work on short-read correction, present-day correctors either do not scale well on large data sets or…

We introduce a new concept of a subgraph class called a superbubble for analyzing assembly graphs, and propose an efficient algorithm for detecting it. Most assembly algorithms utilize assembly graphs like the de Bruijn graph or the overlap…

We introduce Tiered Sampling, a novel technique for approximate counting sparse motifs in massive graphs whose edges are observed in a stream. Our technique requires only a single pass on the data and uses a memory of fixed size $M$, which…

Searching for similar genomic sequences is an essential and fundamental step in biomedical research and an overwhelming majority of genomic analyses. State-of-the-art computational methods performing such comparisons fail to cope with the…

The analysis of biological sequencing data has been one of the biggest applications of string algorithms. The approaches used in many such applications are based on the analysis of k-mers, which are short fixed-length strings present in a…

Genome assembly is a fundamental problem in Bioinformatics, requiring to reconstruct a source genome from an assembly graph built from a set of reads (short strings sequenced from the genome). A notion of genome assembly solution is that of…

Counting the frequencies of k-mers in read libraries is often a first step in the analysis of high-throughput sequencing experiments. Infrequent k-mers are assumed to be a result of sequencing errors. The frequent k-mers constitute a…

In generating large quantities of DNA data, high-throughput sequencing technologies require advanced bioinformatics infrastructures for efficient data analysis. k-mer counting, the process of quantifying the frequency of fixed-length k DNA…

Generalized Sparse Matrix-Matrix Multiplication (SpGEMM) is a ubiquitous task in various engineering and scientific applications. However, inner product based SpGENN introduces redundant input fetches for mismatched nonzero operands, while…

Expander graphs have been recently proposed to construct efficient compressed sensing algorithms. In particular, it has been shown that any $n$-dimensional vector that is $k$-sparse (with $k\ll n$) can be fully recovered using…

Sparse deep learning has reduced computation significantly, but its irregular non-zero data distribution complicates the data flow and hinders data reuse, increasing on-chip SRAM access and thus power consumption of the chip. This paper…