Related papers: A Memory-Efficient FM-Index Constructor for Next-G…
Summary: We present a new method to incrementally construct the FM-index for both short and long sequence reads, up to the size of a genome. It is the first algorithm that can build the index while implicitly sorting the sequences in the…
While short read aligners, which predominantly use the FM-index, are able to easily index one or a few human genomes, they do not scale well to indexing databases containing thousands of genomes. To understand why, it helps to examine the…
Recently, a compressed index for similar strings, called the FM-index of alignment (FMA), has been proposed with the functionalities of pattern search and random access. The FMA is quite efficient in space requirement and pattern search…
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…
We present a new scalable, lightweight algorithm to incrementally construct the BWT and FM-index of large string sets such as those produced by Next Generation Sequencing. The algorithm is designed for massive parallelism and can…
The string graph for a collection of next-generation reads is a lossless data representation that is fundamental for de novo assemblers based on the overlap-layout-consensus paradigm. In this paper, we explore a novel approach to compute…
Genomics is the critical key to enabling precision medicine, ensuring global food security and enforcing wildlife conservation. The massive genomic data produced by various genome sequencing technologies presents a significant challenge for…
Learned indexes use machine learning models to learn the mappings between keys and their corresponding positions in key-value indexes. These indexes use the mapping information as training data. Learned indexes require frequent retrainings…
Deep neural network (DNN) inference relies increasingly on specialized hardware for high computational efficiency. This work introduces a field-programmable gate array (FPGA)-based dynamically configurable accelerator featuring systolic…
Genomics is the foundation of precision medicine, global food security and virus surveillance. Exact-match is one of the most essential operations widely used in almost every step of genomics such as alignment, assembly, annotation, and…
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…
To index the increasing volume of data, modern data indexes are typically stored on SSDs and cached in DRAM. However, searching such an index has resulted in significant I/O traffic due to limited access locality and inefficient cache…
This research introduces an FPGA-based hardware accelerator to optimize the Singular Value Decomposition (SVD) and Fast Fourier transform (FFT) operations in AI models. The proposed design aims to improve processing speed and reduce…
The FM-index is a celebrated compressed data structure for full-text pattern searching. After the first wave of interest in its theoretical developments, we can observe a surge of interest in practical FM-index variants in the last few…
Bitmap index is recognized as a promising candidate for online analytics processing systems, because it effectively supports not only parallel processing but also complex and multi-dimensional queries. However, bitmap index creation is a…
The two most common data-structures for genome indexing, FM-indices and hash-tables, exhibit a fundamental trade-off between memory footprint and performance. We present Ranger, a new indexing technique for nucleotide sequences that is both…
Surface integral equation (SIE) methods are of great interest for the efficient electromagnetic modeling of various devices, from integrated circuits to antenna arrays. Existing acceleration algorithms for SIEs, such as the adaptive…
With the development of hardware-optimized deployment of spiking neural networks (SNNs), SNN processors based on field-programmable gate arrays (FPGAs) have become a research hotspot due to their efficiency and flexibility. However,…
Both industry and academia have extensively investigated hardware accelerations. In this work, to address the increasing demands in computational capability and memory requirement, we propose structured weight matrices (SWM)-based…
Motivation: As a fundamental task in bioinformatics, searching for massive short patterns over a long text is widely accelerated by various compressed full-text indexes. These indexes are able to provide similar searching functionalities to…