Related papers: Accelerating DNA Read Mapping with Digital Process…
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…
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…
Processing in-memory (PIM) is promising to accelerate neural networks (NNs) because it minimizes data movement and provides large computational parallelism. Similar to machine learning accelerators, application mapping, which determines the…
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…
DNA sequencing is the physical/biochemical process of identifying the location of the four bases (Adenine, Guanine, Cytosine, Thymine) in a DNA strand. As semiconductor technology revolutionized computing, modern DNA sequencing technology…
Processing-in-memory (PIM) architectures have demonstrated great potential in accelerating numerous deep learning tasks. Particularly, resistive random-access memory (RRAM) devices provide a promising hardware substrate to build PIM…
Genome analysis fundamentally starts with a process known as read mapping, where sequenced fragments of an organism's genome are compared against a reference genome. Read mapping is currently a major bottleneck in the entire genome analysis…
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…
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…
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…
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…
Genome sequencing has become a central focus in computational biology. A genome study typically begins with sequencing, which produces millions to billions of short DNA fragments known as reads. Read mapping aligns these reads to a…
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.…
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…
In-DRAM Processing-In-Memory (DRAM-PIM) has emerged as a promising approach to accelerate memory-intensive workloads by mitigating data transfer overhead between DRAM and the host processor. Bit-serial DRAM-PIM architectures, further…
Processing-in-memory (PIM) has emerged as a promising solution for accelerating memory-intensive workloads as they provide high memory bandwidth to the processing units. This approach has drawn attention not only from the academic community…
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…
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.…
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…
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…