Related papers: FiltPIM: In-Memory Filter for DNA Sequencing

DNA sequence classification is a fundamental task in computational biology with vast implications for applications such as disease prevention and drug design. Therefore, fast high-quality sequence classifiers are significantly important.…

Motivation: Seed location 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. State-of-the-art read…

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…

Low-cost, high-throughput DNA and RNA sequencing (HTS) data is the backbone of the life sciences. Genome sequencing is now becoming a part of Predictive, Preventive, Personalized, and Participatory (termed 'P4') medicine. All genomic data…

In-memory database query processing frequently involves substantial data transfers between the CPU and memory, leading to inefficiencies due to Von Neumann bottleneck. Processing-in-Memory (PIM) architectures offer a viable solution to…

Processing-in-memory (PIM) seeks to eliminate computation/memory data transfer using devices that support both storage and logic. Stateful logic techniques such as IMPLY, MAGIC and FELIX can perform logic gates within memristive crossbar…

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…

Genome analysis has revolutionized fields such as personalized medicine and forensics. Modern sequencing machines generate vast amounts of fragmented strings of genome data called reads. The alignment of these reads into a complete DNA…

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…

Data movement between memory and processors is a major bottleneck in modern computing systems. The processing-in-memory (PIM) paradigm aims to alleviate this bottleneck by performing computation inside memory chips. Real PIM hardware (e.g.,…

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…

Nanopore sequencing is a widely-used high-throughput genome sequencing technology that can sequence long fragments of a genome into raw electrical signals at low cost. Nanopore sequencing requires two computationally-costly processing steps…

The Discrete Fourier Transform (DFT) is essential for various applications ranging from signal processing to convolution and polynomial multiplication. The groundbreaking Fast Fourier Transform (FFT) algorithm reduces DFT time complexity…

Processing-in-Memory (PIM) enhances memory with computational capabilities, potentially solving energy and latency issues associated with data transfer between memory and processors. However, managing concurrent computation and data flow…

Processing-in-memory (PIM) architectures are emerging to reduce data movement in data-intensive applications. These architectures seek to exploit the same physical devices for both information storage and logic, thereby dwarfing the…

Memristive in-memory sorting has been proposed recently to improve hardware sorting efficiency. Using iterative in-memory min computations, data movements between memory and external processing units can be eliminated for improved latency…

The utilization of large-scale neural networks on Processing-In-Memory (PIM) accelerators encounters challenges due to constrained on-chip memory capacity. To tackle this issue, current works explore model compression algorithms to reduce…

Processing-in-cache (PiC) and Processing-in-memory (PiM) architectures, especially those utilizing bit-line computing, offer promising solutions to mitigate data movement bottlenecks within the memory hierarchy. While previous studies have…

Privacy-preserving computation techniques like homomorphic encryption (HE) and secure multi-party computation (SMPC) enhance data security by enabling processing on encrypted data. However, the significant computational and CPU-DRAM data…

Convolutional neural networks (CNN) have become a ubiquitous algorithm with growing applications in mobile and edge settings. We describe a compute-in-memory (CIM) technique called FPIRM using Racetrack Memory (RM) to accelerate CNNs for…