activity
20152026
most citedNanopore Sequencing Technology and Tools for Genome Assembly: Computational Analysis of the Current State, Bottlenecks and Future Directions

269 citations · 1.1k across the 57 of their papers we have counts for

collaborators

59 papers

cs.AR2026

PipeDRAM: A Data-Transposition-Free Processing-Using-DRAM Architecture with Hardware/Software Pipelining

Geraldo F. Oliveira, Ataberk Olgun, Ismail Emir Yüksel +6

Processing-using-DRAM (PUD) architectures exploit the analog operational properties of DRAM to perform bulk bitwise Boolean and arithmetic operations inside memory arrays by organi…

cs.AR2026

Leveraging ECRAM for Edge Continual Learning

Nabila Tasnim, Haoran Liu, Qing Cao +1

Several edge computing platforms, such as autonomous vehicles and smart sensing devices, need to adapt to dynamic environments in real time by learning from new data in the field.…

cs.AR2025

Proteus: Enabling High-Performance Processing-Using-DRAM with Dynamic Bit-Precision, Adaptive Data Representation, and Flexible Arithmetic

Geraldo F. Oliveira, Mayank Kabra, Yuxin Guo +8

Processing-using-DRAM (PUD) is a paradigm where the analog operational properties of DRAM are used to perform bulk logic operations. While PUD promises high throughput at low energ…

cs.AR2024

General-Purpose Multicore Architectures

Saugata Ghose

The first years of the 2000s led to an inflection point in computer architectures: while the number of available transistors on a chip continued to grow, crucial transistor scaling…

cs.AR2024★ 1 cited

MIMDRAM: An End-to-End Processing-Using-DRAM System for High-Throughput, Energy-Efficient and Programmer-Transparent Multiple-Instruction Multiple-Data Processing

Geraldo F. Oliveira, Ataberk Olgun, Abdullah Giray Yağlıkçı +4

Processing-using-DRAM (PUD) is a processing-in-memory (PIM) approach that uses a DRAM array's massive internal parallelism to execute very-wide data-parallel operations, in a singl…

cs.AR2023★ 2 cited

DaPPA: A Unified Data-Parallel Programming Framework for Efficient Processing-in-Memory Execution

Geraldo F. Oliveira, Alain Kohli, David Novo +5

Processing-in-memory (PIM) alleviates data-movement bottlenecks by placing computation near or inside memory. Two general-purpose PIM paradigms are now practical: processing-near-m…

cs.AR2022★ 1 cited

Accelerating Neural Network Inference with Processing-in-DRAM: From the Edge to the Cloud

Geraldo F. Oliveira, Juan Gómez-Luna, Saugata Ghose +2

Neural networks (NNs) are growing in importance and complexity. A neural network's performance (and energy efficiency) can be bound either by computation or memory resources. The p…

cs.AR2022

Methodologies, Workloads, and Tools for Processing-in-Memory: Enabling the Adoption of Data-Centric Architectures

Geraldo F. Oliveira, Juan Gómez-Luna, Saugata Ghose +1

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 vo…

cs.AR2022★ 38 cited

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.,…

cs.AR2022

Heterogeneous Data-Centric Architectures for Modern Data-Intensive Applications: Case Studies in Machine Learning and Databases

Geraldo F. Oliveira, Amirali Boroumand, Saugata Ghose +2

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 plac…

cs.AR2022

Enabling High-Performance and Energy-Efficient Hybrid Transactional/Analytical Databases with Hardware/Software Cooperation

Amirali Boroumand, Saugata Ghose, Geraldo F. Oliveira +1

A growth in data volume, combined with increasing demand for real-time analysis (using the most recent data), has resulted in the emergence of database systems that concurrently su…

cs.AR2021★ 1 cited

Extending Memory Capacity in Consumer Devices with Emerging Non-Volatile Memory: An Experimental Study

Geraldo F. Oliveira, Saugata Ghose, Juan Gómez-Luna +8

The number and diversity of consumer devices are growing rapidly, alongside their target applications' memory consumption. Unfortunately, DRAM scalability is becoming a limiting fa…

cs.AR2021★ 2 cited

Google Neural Network Models for Edge Devices: Analyzing and Mitigating Machine Learning Inference Bottlenecks

Amirali Boroumand, Saugata Ghose, Berkin Akin +5

Emerging edge computing platforms often contain machine learning (ML) accelerators that can accelerate inference for a wide range of neural network (NN) models. These models are de…

cs.AR2021★ 2 cited

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…

cs.AR2021

CODIC: A Low-Cost Substrate for Enabling Custom In-DRAM Functionalities and Optimizations

Lois Orosa, Yaohua Wang, Mohammad Sadrosadati +10

DRAM is the dominant main memory technology used in modern computing systems. Computing systems implement a memory controller that interfaces with DRAM via DRAM commands. DRAM exec…

cs.AR2021★ 5 cited

DAMOV: A New Methodology and Benchmark Suite for Evaluating Data Movement Bottlenecks

Geraldo F. Oliveira, Juan Gómez-Luna, Lois Orosa +5

Data movement between the CPU and main memory is a first-order obstacle against improving performance, scalability, and energy efficiency in modern systems. Computer systems employ…

cs.AR2021★ 20 cited

Polynesia: Enabling Effective Hybrid Transactional/Analytical Databases with Specialized Hardware/Software Co-Design

Amirali Boroumand, Saugata Ghose, Geraldo F. Oliveira +1

An exponential growth in data volume, combined with increasing demand for real-time analysis (i.e., using the most recent data), has resulted in the emergence of database systems t…

cs.AR2021★ 20 cited

Mitigating Edge Machine Learning Inference Bottlenecks: An Empirical Study on Accelerating Google Edge Models

Amirali Boroumand, Saugata Ghose, Berkin Akin +5

As the need for edge computing grows, many modern consumer devices now contain edge machine learning (ML) accelerators that can compute a wide range of neural network (NN) models w…

cs.CR2021★ 124 cited

BlockHammer: Preventing RowHammer at Low Cost by Blacklisting Rapidly-Accessed DRAM Rows

Abdullah Giray Yağlıkçı, Minesh Patel, Jeremie S. Kim +9

Aggressive memory density scaling causes modern DRAM devices to suffer from RowHammer, a phenomenon where rapidly activating a DRAM row can cause bit-flips in physically-nearby row…

cs.AR2020

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-…

cs.AR2020★ 27 cited

A Modern Primer on Processing in Memory

Onur Mutlu, Saugata Ghose, Juan Gómez-Luna +3

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…

cs.AR2020★ 84 cited

Accelerating Genome Analysis: A Primer on an Ongoing Journey

Mohammed Alser, Zülal Bingöl, Damla Senol Cali +4

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 i…

cs.AR2020★ 7 cited

FIGARO: Improving System Performance via Fine-Grained In-DRAM Data Relocation and Caching

Yaohua Wang, Lois Orosa, Xiangjun Peng +8

DRAM Main memory is a performance bottleneck for many applications due to the high access latency. In-DRAM caches work to mitigate this latency by augmenting regular-latency DRAM w…

cs.AR2020★ 2 cited

GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis

Damla Senol Cali, Gurpreet S. Kalsi, Zülal Bingöl +13

Genome sequence analysis has enabled significant advancements in medical and scientific areas such as personalized medicine, outbreak tracing, and the understanding of evolution. U…