相关论文: PANDA: Processing-in-MRAM Accelerated De Bruijn Gr…

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…

The widespread adoption of Large Language Models (LLMs) has exponentially increased the demand for efficient serving systems. With growing requests and context lengths, key-value (KV)-related operations, including attention computation and…

Large Language Models (LLMs) are increasingly deployed on edge devices with Neural Processing Units (NPUs), yet the decode phase remains memory-intensive, limiting performance. Processing-in-Memory (PIM) offers a promising solution, but…

PANDA is a powerful generic algorithm for answering conjunctive queries (CQs) and disjunctive datalog rules (DDRs) given input degree constraints. In the special case where degree constraints are cardinality constraints and the query is…

Processing in memory (PIM) moves computation into memories with the goal of improving throughput and energy-efficiency compared to traditional von Neumann-based architectures. Most existing PIM architectures are either general-purpose but…

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.…

Analog processing-using-memory (PUM; a.k.a. in-memory computing) makes use of electrical interactions inside memory arrays to perform bulk matrix-vector multiplication (MVM) operations. However, many popular matrix-based kernels need 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…

Because of DNA appealing features as perfect material, including minuscule size, defined structural repeat and rigidity, programmable DNA-mediated processing is a promising computing paradigm, which employs DNAs as information storing and…

The continually increasing volume of DNA sequence data has resulted in a growing demand for fast implementations of core algorithms. Computation of pairwise alignments between candidate haplotypes and sequencing reads using Pair-HMMs is a…

The computing wall and data movement challenges of deep neural networks (DNNs) have exposed the limitations of conventional CMOS-based DNN accelerators. Furthermore, the deep structure and large model size will make DNNs prohibitive to…

Deep sequencing has enabled the investigation of a wide range of environmental microbial ecosystems, but the high memory requirements for {\em de novo} assembly of short-read shotgun sequencing data from these complex populations are an…

Recent research has sought to accelerate cryptographic hash functions as they are at the core of modern cryptography. Traditional designs, however, suffer from the von Neumann bottleneck that originates from the separation of processing and…

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…

To index the increasing volume of data, modern data indexes are typically stored on SSDs and cached in DRAM. However, searching such an index has resulted in significant I/O traffic due to limited access locality and inefficient cache…

PANDA (Passing Attributes between Networks for Data Assimilation) is a gene regulatory network inference method that uses message-passing to integrate multiple sources of 'omics data. PANDA was originally coded in C++. In this application…

Graph neural networks (GNNs) have gained significant interest for applications such as citation network analysis and drug discovery due to their ability to apply machine learning techniques on graph-structured data. GNNs typically employ a…

Recent years have seen a rapid increase in research activity in the field of DRAM-based Processing-In-Memory (PIM) accelerators, where the analog computing capability of DRAM is employed by minimally changing the inherent structure of DRAM…

One of the most computationally intensive tasks in computational biology is de novo genome assembly, the decoding of the sequence of an unknown genome from redundant and erroneous short sequences. A common assembly paradigm identifies…

Triangle counting (TC) is a fundamental problem in graph analysis and has found numerous applications, which motivates many TC acceleration solutions in the traditional computing platforms like GPU and FPGA. However, these approaches suffer…