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AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes
(2021)arXivAs genome sequencing tools and techniques improve, researchers are able to incrementally assemble more accurate reference genomes, which enable sensitivity in read mapping and downstream analysis such as variant calling. A more sensitive downstream analysis is critical for a better understanding of the genome donor (e.g., health characteristics). Therefore, read sets from sequenced samples should ideally be mapped to the latest available ...Working Paper -
COVIDHunter: An Accurate, Flexible, and Environment-Aware Open-Source COVID-19 Outbreak Simulation Model
(2021)arXivMotivation: Early detection and isolation of COVID-19 patients are essential for successful implementation of mitigation strategies and eventually curbing the disease spread. With a limited number of daily COVID19 tests performed in every country, simulating the COVID-19 spread along with the potential effect of each mitigation strategy currently remains one of the most effective ways in managing the healthcare system and guiding ...Working Paper -
Benchmarking a New Paradigm: An Experimental Analysis of a Real Processing-in-Memory Architecture
(2021)arXivMany 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 and energy. A major reason is that this communication happens through a narrow bus with high latency and limited bandwidth, and the low data reuse in memory-bound workloads is insufficient to amortize ...Working Paper -
TuRaN: True Random Number Generation Using Supply Voltage Underscaling in SRAMs
(2022)arXivPrior works propose SRAM-based TRNGs that extract entropy from SRAM arrays. SRAM arrays are widely used in a majority of specialized or general-purpose chips that perform the computation to store data inside the chip. Thus, SRAM-based TRNGs present a low-cost alternative to dedicated hardware TRNGs. However, existing SRAM-based TRNGs suffer from 1) low TRNG throughput, 2) high energy consumption, 3) high TRNG latency, and 4) the inability ...Working Paper -
TargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering
(2022)arXivBasecalling is an essential step in nanopore sequencing analysis where the raw signals of nanopore sequencers are converted into nucleotide sequences, i.e., reads. State-of-the-art basecallers employ complex deep learning models to achieve high basecalling accuracy. This makes basecalling computationally-inefficient and memory-hungry; bottlenecking the entire genome analysis pipeline. However, for many applications, the majority of reads ...Working Paper -
ALP: Alleviating CPU-Memory Data Movement Overheads in Memory-Centric Systems
(2022)arXivPartitioning applications between NDP and host CPU cores causes inter-segment data movement overhead, which is caused by moving data generated from one segment (e.g., instructions, functions) and used in consecutive segments. Prior works take two approaches to this problem. The first class of works maps segments to NDP or host cores based on the properties of each segment, neglecting the inter-segment data movement overhead. The second ...Working Paper -
A Case for Self-Managing DRAM Chips: Improving Performance, Efficiency, Reliability, and Security via Autonomous in-DRAM Maintenance Operations
(2022)arXivThe memory controller is in charge of managing DRAM maintenance operations (e.g., refresh, RowHammer protection, memory scrubbing) in current DRAM chips. Implementing new maintenance operations often necessitates modifications in the DRAM interface, memory controller, and potentially other system components. Such modifications are only possible with a new DRAM standard, which takes a long time to develop, leading to slow progress in DRAM ...Working Paper -
Packaging, containerization, and virtualization of computational omics methods: Advances, challenges, and opportunities
(2022)arXivOmics software tools have reshaped the landscape of modern biology and become an essential component of biomedical research. The increasing dependence of biomedical scientists on these powerful tools creates a need for easier installation and greater usability. Packaging, virtualization, and containerization are different approaches to satisfy this need by wrapping omics tools in additional software that makes the omics tools easier to ...Working Paper -
Utopia: Efficient Address Translation using Hybrid Virtual-to-Physical Address Mapping
(2022)arXivThe conventional virtual-to-physical address mapping scheme enables a virtual address to flexibly map to any physical address. This flexibility necessitates large data structures to store virtual-to-physical mappings, which incurs significantly high address translation latency and translation-induced interference in the memory hierarchy, especially in data-intensive workloads. Restricting the address mapping so that a virtual address can ...Working Paper -
An Experimental Evaluation of Machine Learning Training on a Real Processing-in-Memory System
(2022)arXivTraining machine learning (ML) algorithms is a computationally intensive process, which is frequently memory-bound due to repeatedly accessing large training datasets. As a result, processor-centric systems (e.g., CPU, GPU) suffer from costly data movement between memory units and processing units, which consumes large amounts of energy and execution cycles. Memory-centric computing systems, i.e., with processing-in-memory (PIM) capabilities, ...Working Paper