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This paper presents a new approach to statistical similarity assessment based on sequence alignment. The algorithm performs mutual matching of two random sequences by successively searching for common elements and by applying sequence…
DNA sequence alignment is important today as it is usually the first step in finding gene mutation, evolutionary similarities, protein structure, drug development and cancer treatment. Covid-19 is one recent example. There are many…
Genomic sequence alignment is an important research topic in bioinformatics and continues to attract significant efforts. As genomic data grow exponentially, however, most of alignment methods face challenges due to their huge computational…
Molecular similarity search has been widely used in drug discovery to identify structurally similar compounds from large molecular databases rapidly. With the increasing size of chemical libraries, there is growing interest in the efficient…
High-throughput sequencing (HTS) technologies have revolutionized the field of genomics, enabling rapid and cost-effective genome analysis for various applications. However, the increasing volume of genomic data generated by HTS…
The maximal sensitivity of the Smith-Waterman (SW) algorithm has enabled its wide use in biological sequence database search. Unfortunately, the high sensitivity comes at the expense of quadratic time complexity, which makes the algorithm…
Genome sequence analysis has enabled significant advancements in medical and scientific areas such as personalized medicine, outbreak tracing, and the understanding of evolution. Unfortunately, it is currently bottlenecked by the…
Hardware acceleration of database query processing can be done with the help of FPGAs. In particular, they are partially reconfigurable during runtime, which allows for the runtime adaption of the hardware to a variety of queries.…
We now need more than ever to make genome analysis more intelligent. We need to read, analyze, and interpret our genomes not only quickly, but also accurately and efficiently enough to scale the analysis to population level. There currently…
DNA sequence alignment is an important workload in computational genomics. Reference-guided DNA assembly involves aligning many read sequences against candidate locations in a long reference genome. To reduce the computational load of this…
Motivation: Read mapping is a computationally expensive process and a major bottleneck in genomics analyses. The performance of read mapping is mainly limited by the performance of three key computational steps: Index Querying, Seed…
AI acceleration has been dominated by GPUs, but the growing need for lower latency, energy efficiency, and fine-grained hardware control exposes the limits of fixed architectures. In this context, Field-Programmable Gate Arrays (FPGAs)…
Fluorescence lifetime imaging (FLI) is a widely used technique in the biomedical field for measuring the decay times of fluorescent molecules, providing insights into metabolic states, protein interactions, and ligand-receptor bindings.…
Packet classification is a vital and complicated task as the processing of packets should be done at a specified line speed. In order to classify a packet as belonging to a particular flow or set of flows, network nodes must perform a…
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…
The rapid advancements in artificial intelligence (AI), particularly the Large Language Models (LLMs), have profoundly affected our daily work and communication forms. However, it is still a challenge to deploy LLMs on resource-constrained…
Third-generation nanopore sequencers offer a feature called selective sequencing or 'Read Until' that allows genomic reads to be analyzed in real-time and abandoned halfway, if not belonging to a genomic region of 'interest'. This selective…
Filtering data based on predicates is one of the most fundamental operations for any modern data warehouse. Techniques to accelerate the execution of filter expressions include clustered indexes, specialized sort orders (e.g., Z-order),…
We present the Scalable Nucleotide Alignment Program (SNAP), a new short and long read aligner that is both more accurate (i.e., aligns more reads with fewer errors) and 10-100x faster than state-of-the-art tools such as BWA. Unlike recent…
While many hardware accelerators have recently been proposed to address the inefficiency problem of fully homomorphic encryption (FHE) schemes, none of them is able to deliver optimal performance when facing real-world FHE workloads…