Related papers: Processing-in-memory for genomics workloads
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…
The increasing prevalence and growing size of data in modern applications have led to high costs for computation in traditional processor-centric computing systems. Moving large volumes of data between memory devices (e.g., DRAM) and…
Many modern and emerging applications must process increasingly large volumes of data. Unfortunately, prevalent computing paradigms are not designed to efficiently handle such large-scale data: the energy and performance costs to move this…
Today's systems are overwhelmingly designed to move data to computation. This design choice goes directly against at least three key trends in systems that cause performance, scalability and energy bottlenecks: (1) data access from memory…
This paper discusses recent research that aims to enable computation close to data, an approach we broadly call processing-in-memory (PIM). PIM places computation mechanisms in or near where the data is stored (i.e., inside memory chips or…
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…
Aligning the entire genome of an organism is a compute-intensive task. Pre-alignment filters substantially reduce computation complexity by filtering potential alignment locations. The base-count filter successfully removes over 68% of the…
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…
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.…
Today's computing systems require moving data back-and-forth between computing resources (e.g., CPUs, GPUs, accelerators) and off-chip main memory so that computation can take place on the data. Unfortunately, this data movement is a major…
Many modern workloads such as neural network inference and graph processing are fundamentally memory-bound. For such workloads, data movement between memory and CPU cores imposes a significant overhead in terms of both latency and energy. A…
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.,…
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…
Modern computing systems suffer from the dichotomy between computation on one side, which is performed only in the processor (and accelerators), and data storage/movement on the other, which all other parts of the system are dedicated to.…
Many modern workloads, such as neural networks, databases, and graph processing, are fundamentally memory-bound. For such workloads, the data movement between main memory and CPU cores imposes a significant overhead in terms of both latency…
Cryptographic algorithms such as AES-128 and SHA-256 are fundamental to ensuring data security and integrity. Although these algorithms are computationally efficient, their performance is often constrained by the processor-centric…
The widespread adoption of cloud-based solutions introduces privacy and security concerns. Techniques such as homomorphic encryption (HE) mitigate this problem by allowing computation over encrypted data without the need for decryption.…
Processing-In-Memory (PIM) is a novel approach that augments existing DRAM memory chips with lightweight logic. By allowing to offload computations to the PIM system, this architecture allows for circumventing the data-bottleneck problem…
Genome sequence analysis plays a pivotal role in enabling many medical and scientific advancements in personalized medicine, outbreak tracing, and forensics. However, the analysis of genome sequencing data is currently bottlenecked by the…
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…