46 citations · 185 across the 18 of their papers we have counts for
20 papers
CertiFlash: A Formal Verification Framework for Flash Translation Layers in Computational Solid State Drives
Harshita Gupta, Mayank Kabra, Rakesh Nadig +10
Data-intensive applications move large amounts of data from storage to the compute unit, incurring significant data movement overhead. Storage-centric computing reduces this overhe…
Storage-Centric System Designs for Enabling Fast, Efficient, and Low-Cost Genomic and Metagenomic Analyses
Nika Mansouri Ghiasi
Genomic and metagenomic analyses play critical roles in many fields, such as precision medicine, urgent clinical settings, discovering early warnings of communicable diseases, ensu…
Enabling Fast, Efficient, and Low-Cost Genomic and Metagenomic Analyses via Storage-Centric System Designs
Nika Mansouri Ghiasi, Onur Mutlu
Due to the challenges of analyzing and storing massive volumes of genomic and metagenomic sequence data, significant efforts have been made to accelerate (meta)genomic analyses and…
GRAINS: Storage-Aware Algorithm-Architecture Co-Design Enabling High-Performance and Low-Cost Graph-Based Genome Analysis
Nika Mansouri Ghiasi, Harun Mustafa, Talu Güloglu +8
Graph-based representations of genome sequences have emerged as a powerful approach for representing massive genomic databases in an expressive and efficient way. Despite their ben…
Architecture for Health Initiative (Arch4Health): Computational Challenges in Health-Related Applications and the Role of Computer Architecture in Addressing Them
Nika Mansouri Ghiasi, Konstantina Koliogeorgi, Onur Mutlu
Recent biotechnological advances enable high-throughput, low-cost, and accurate biological data generation. This wealth of data enables unique opportunities for advancing healthcar…
A decentralized future for the open-science databases
Gaurav Sharma, Viorel Munteanu, Nika Mansouri Ghiasi +18
Continuous and reliable access to curated biological data repositories is indispensable for accelerating rigorous scientific inquiry and fostering reproducible research. Centralize…
MARS: Processing-In-Memory Acceleration of Raw Signal Genome Analysis Inside the Storage Subsystem
Melina Soysal, Konstantina Koliogeorgi, Can Firtina +8
Raw signal genome analysis (RSGA) has emerged as a promising approach to enable real-time genome analysis by directly analyzing raw electrical signals. However, rapid advancements…
Rawsamble: Overlapping and Assembling Raw Nanopore Signals using a Hash-based Seeding Mechanism
Can Firtina, Maximilian Mordig, Harun Mustafa +7
Raw nanopore signal analysis is a common approach in genomics to provide fast and resource-efficient analysis without translating the signals to bases (i.e., without basecalling).…
MegIS: High-Performance, Energy-Efficient, and Low-Cost Metagenomic Analysis with In-Storage Processing
Nika Mansouri Ghiasi, Mohammad Sadrosadati, Harun Mustafa +9
Metagenomics has led to significant advances in many fields. Metagenomic analysis commonly involves the key tasks of determining the species present in a sample and their relative…
Revisiting Main Memory-Based Covert and Side Channel Attacks in the Context of Processing-in-Memory
F. Nisa Bostanci, Konstantinos Kanellopoulos, Ataberk Olgun +6
We introduce IMPACT, a set of high-throughput main memory-based timing attacks that leverage characteristics of processing-in-memory (PiM) architectures to establish covert and sid…
RawAlign: Accurate, Fast, and Scalable Raw Nanopore Signal Mapping via Combining Seeding and Alignment
Joël Lindegger, Can Firtina, Nika Mansouri Ghiasi +3
Nanopore sequencers generate raw electrical signals representing the contents of a biological sequence molecule passing through the nanopore. These signals can be analyzed directly…
Venice: Improving Solid-State Drive Parallelism at Low Cost via Conflict-Free Accesses
Rakesh Nadig, Mohammad Sadrosadati, Haiyu Mao +6
The performance and capacity of solid-state drives (SSDs) are continuously improving to meet the increasing demands of modern data-intensive applications. Unfortunately, communicat…
RawHash: Enabling Fast and Accurate Real-Time Analysis of Raw Nanopore Signals for Large Genomes
Can Firtina, Nika Mansouri Ghiasi, Joel Lindegger +4
Nanopore sequencers generate electrical raw signals in real-time while sequencing long genomic strands. These raw signals can be analyzed as they are generated, providing an opport…
ALP: Alleviating CPU-Memory Data Movement Overheads in Memory-Centric Systems
Nika Mansouri Ghiasi, Nandita Vijaykumar, Geraldo F. Oliveira +7
Partitioning 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,…
Accelerating Time Series Analysis via Processing using Non-Volatile Memories
Ivan Fernandez, Christina Giannoula, Aditya Manglik +6
Time Series Analysis (TSA) is a critical workload to extract valuable information from collections of sequential data, e.g., detecting anomalies in electrocardiograms. Subsequence…
SeGraM: A Universal Hardware Accelerator for Genomic Sequence-to-Graph and Sequence-to-Sequence Mapping
Damla Senol Cali, Konstantinos Kanellopoulos, Joel Lindegger +15
A critical step of genome sequence analysis is the mapping of sequenced DNA fragments (i.e., reads) collected from an individual to a known linear reference genome sequence (i.e.,…
GenStore: A High-Performance and Energy-Efficient In-Storage Computing System for Genome Sequence Analysis
Nika Mansouri Ghiasi, Jisung Park, Harun Mustafa +11
Read mapping is a fundamental, yet computationally-expensive step in many genomics applications. It is used to identify potential matches and differences between fragments (called…
BLEND: A Fast, Memory-Efficient, and Accurate Mechanism to Find Fuzzy Seed Matches in Genome Analysis
Can Firtina, Jisung Park, Mohammed Alser +8
Generating the hash values of short subsequences, called seeds, enables quickly identifying similarities between genomic sequences by matching seeds with a single lookup of their h…
SIMDRAM: An End-to-End Framework for Bit-Serial SIMD Computing in DRAM
Nastaran Hajinazar, Geraldo F. Oliveira, Sven Gregorio +7
Processing-using-DRAM has been proposed for a limited set of basic operations (i.e., logic operations, addition). However, in order to enable full adoption of processing-using-DRAM…
SIMDRAM: A Framework for Bit-Serial SIMD Processing Using DRAM
Nastaran Hajinazar, Geraldo F. Oliveira, Sven Gregorio +7
Processing-using-DRAM has been proposed for a limited set of basic operations (i.e., logic operations, addition). However, in order to enable the full adoption of processing-using-…