Related papers: BioSEAL: In-Memory Biological Sequence Alignment A…

A genome read data set can be quickly and efficiently remapped from one reference to another similar reference (e.g., between two reference versions or two similar species) using a variety of tools, e.g., the commonly-used CrossMap tool.…

We propose Booster, a novel accelerator for gradient boosting trees based on the unique characteristics of gradient boosting models. We observe that the dominant steps of gradient boosting training (accounting for 90-98% of training time)…

Image segmentation is one of the most essential biomedical image processing problems for different imaging modalities, including microscopy and X-ray in the Internet-of-Medical-Things (IoMT) domain. However, annotating biomedical images is…

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…

Genomic signal processing has been used successfully in bioinformatics to analyze biomolecular sequences and gain varied insights into DNA structure, gene organization, protein binding, sequence evolution, etc. But challenges remain in…

Sequence alignment is a memory bound computation whose performance in modern systems is limited by the memory bandwidth bottleneck. Processing-in-memory architectures alleviate this bottleneck by providing the memory with computing…

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…

Complex, high-throughput data acquisition and processing systems, such as those used in high-energy physics experiments, are increasingly moving sophisticated pattern recognition and data compression algorithms closer to the sensors…

Deep learning (DL) accelerators are increasingly deployed on edge devices to support fast local inferences. However, they suffer from a new security problem, i.e., being vulnerable to physical access based attacks. An adversary can easily…

Nanopore sequencers generate raw electrical signals representing the contents of a biological sequence molecule passing through the nanopore. These signals can be analyzed directly, avoiding basecalling entirely. We observe that while…

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…

Modeling biological sequences such as DNA, RNA, and proteins is crucial for understanding complex processes like gene regulation and protein synthesis. However, most current models either focus on a single type or treat multiple types of…

We introduce a parallel algorithmic architecture for metagenomic sequence assembly, termed MetaPar, which allows for significant reductions in assembly time and consequently enables the processing of large genomic datasets on computers with…

This article introduces an innovative Retrieval Augmented Generation approach to similarity search. The proposed method uses a generative model to capture nuanced semantic information and retrieve similarity scores based on advanced context…

The massively parallel nature of biological information processing plays an important role for its superiority to human-engineered computing devices. In particular, it may hold the key to overcoming the von Neumann bottleneck that limits…

It is demonstrated earlier that the exact Smith-Waterman algorithm yields more accurate results than the members of the heuristic BLAST family of algorithms. Unfortunately, the Smith-Waterman algorithm is much slower than the BLAST and its…

Aligning millions of short DNA or RNA reads, of 75 to 250 base pairs each, to a reference genome is a significant computation problem in bioinformatics. We present a flexible and fast FPGA-based short read alignment tool. Our aligner makes…

The Jaccard similarity index is an important measure of the overlap of two sets, widely used in machine learning, computational genomics, information retrieval, and many other areas. We design and implement SimilarityAtScale, the first…

Atomic-level simulations are widely used to study biomolecules and their dynamics. A common goal in such studies is to compare simulations of a molecular system under several conditions -- for example, with various mutations or bound…

Resistive random-access memory is one of the most promising candidates for the next generation of non-volatile memory technology. However, its crossbar structure causes severe "sneak-path" interference, which also leads to strong inter-cell…