Think Big, Aim High

2022 Publications

2022 Conference and Journal Papers

Geraldo F. Oliveira, Juan Gómez-Luna, Saugata Ghose, Amirali Boroumand, Onur Mutlu, "Accelerating Neural Network Inference With Processing-in-DRAM: From the Edge to the Cloud," in IEEE Micro, Nov - Dec 2022. [arXiv version]

Maciej Besta, Cesare Miglioli, Paolo Sylos Labini, Jakub Tetek, Patrick Iff, Raghavendra Kanakagiri, Saleh Ashkboos, Kacper Janda, Michał Podstawski, Grzegorz Kwasniewski, Niels Gleinig, Flavio Vella, Onur Mutlu, Torsten Hoefler, "ProbGraph: High-Performance and High-Accuracy Graph Mining with Probabilistic Set Representations", Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC), November 2022. SC'22 Best Paper Award

Rahul Bera, Konstantinos Kanellopoulos, Shankar Balachandran, David Novo, Ataberk Olgun, Mohammad Sadrosadat, Onur Mutlu, "Hermes: Accelerating Long-Latency Load Requests via Perceptron-Based Off-Chip Load Prediction," Proceedings of the 55th IEEE/ACM International Symposium on Microarchitecture (MICRO), October 2022. [arXiv version] [Hermes Source Code] MICRO'22 Best Paper Award

Sina Darabi, Mohammad Sadrosadati, Joël Lindegger, Negar Akbarzadeh, Mohammad Hosseini, Jisung Park, Juan Gómez-Luna, Hamid Sarbazi-Azad, Onur Mutlu, "Morpheus: Extending the Last Level Cache Capacityin GPU Systems Using Idle GPU Core Resources",

Proceedings of the 55th IEEE/ACM International Symposium on Microarchitecture (MICRO), October 2022. [Slides (pptx) (pdf)] [arXiv version] [Talk Video (12 minutes)]

Haiyu Mao, Mohammed Alser, Mohammad Sadrosadati, Can Firtina, Akanksha Baranwal, Damla Senol Cali, Aditya Manglik, Nour Almadhoun Alserr, Onur Mutlu, "GenPIP: In-Memory Acceleration of Genome Analysis via Tight Integration of Basecalling and Read Mapping," 2022 55th IEEE/ACM International Symposium on Microarchitecture (MICRO), October 2022. [arXiv version]

A. Giray Yağlikçi, Ataberk Olgun, Minesh Patel, Haocong Luo, Hasan Hassan, Lois Orosa, Oğuz Ergin, Onur Mutlu, "HiRA: Hidden Row Activation for Reducing Refresh Latency of Off-the-Shelf DRAM Chips," 2022 55th IEEE/ACM International Symposium on Microarchitecture (MICRO), October 2022. [arXiv version]

Jawad Haj Yahya, Haris Volos, Davide B. Bartolini, Georgia Antoniou, Jeremie S. Kim, Zhe Wang, Kleovoulos Kalaitzidis, Tom Rollet, Zhirui Chen, Ye Geng, Onur Mutlu, Yiannakis Sazeides, "AgileWatts: An Energy-Efficient CPU Core Idle-State Architecture for Latency-Sensitive Server Applications," 2022 55th IEEE/ACM International Symposium on Microarchitecture (MICRO), October 2022. [arXiv version]

João Dinis Ferreira, Gabriel Falcao, Juan Gómez-Luna, Mohammed Alser, Lois Orosa, Mohammad Sadrosadati, Jeremie S. Kim, Geraldo F. Oliveira, Taha Shahroodi, Anant Nori, Onur Mutlu, "pLUTo: Enabling Massively Parallel Computation in DRAM via Lookup Tables," 2022 55th IEEE/ACM International Symposium on Microarchitecture (MICRO), October 2022. [arXiv version] [pLUTo Source Code]

Jisung Park, Roknoddin Azizi, Geraldo F. Oliveira, Mohammad Sadrosadati, Rakesh Nadig, David Novo, Juan Gómez-Luna, Myungsuk Kim, Onur Mutlu, "Flash-Cosmos: In-Flash Bulk Bitwise Operations Using Inherent Computation Capability of NAND Flash Memory," 2022 55th IEEE/ACM International Symposium on Microarchitecture (MICRO), October 2022. [arXiv version]

Mostafa Hadizadeh, Elham Cheshmikhani, Maysam Rahmanpour, Onur Mutlu, Hossein Asadi, "CoPA: Cold Page Awakening to Overcome Retention Failures in STT-MRAM Based I/O Buffers," in IEEE Transactions on Parallel and Distributed Systems, Oct 2022. [arXiv version]

Taha Shahroodi, Mahdi Zahedi, Can Firtina, Mohammed Alser, Stephan Wong, Onur Mutlu, Said Hamdioui, "Demeter: A Fast and Energy-Efficient Food Profiler Using Hyperdimensional Computing in Memory," in IEEE Access, August 2022.

Geraldo F. Oliveira, Juan Gómez-Luna, Saugata Ghose, Onur Mutlu, "Methodologies, Workloads, and Tools for Processing-in-Memory: Enabling the Adoption of Data-Centric Architectures", 2022 IEEE Computer Society Annual Symposium on VLSI (ISVLSI), July 2022. [Slides (pptx) (pdf)]

Ataberk Olgun, Juan Gómez Luna, Konstantinos Kanellopoulos, Behzad Salami, Hasan Hassan, Oğuz Ergin, Onur Mutlu, "PiDRAM: An FPGA-based Framework for End-to-end Evaluation of Processing-in-DRAM Techniques," 2022 IEEE Computer Society Annual Symposium on VLSI (ISVLSI), July 2022. [Slides (pptx) (pdf)]

, "Heterogeneous Data-Centric Architectures for Modern Data-Intensive Applications: Case Studies in Machine Learning and Databases," 2022 IEEE Computer Society Annual Symposium on VLSI (ISVLSI), July 2022. [Slides (pptx) (pdf)]

Ivan Fernandez, Ricardo Quislant, Christina Giannoula, Mohammed Alser, Juan Gómez-Luna, Eladio Gutiérrez, Oscar Plata, Onur Mutlu, "Exploiting Near-Data Processing to Accelerate Time Series Analysis," 2022 IEEE Computer Society Annual Symposium on VLSI (ISVLSI), July 2022. [Slides (pptx) (pdf)]

Nika Mansouri Ghiasi, Jisung Park, Harun Mustafa, Jeremie Kim, Ataberk Olgun, Arvid Gollwitzer, Damla Senol Cali, Can Firtina, Haiyu Mao, Nour Almadhoun Alserr, Rachata Ausavarungnirun, Nandita Vijaykumar, Mohammed Alser, Onur Mutlu, "GenStore: In-Storage Filtering of Genomic Data for High-Performance and Energy-Efficient Genome Analysis," 2022 IEEE Computer Society Annual Symposium on VLSI (ISVLSI), July 2022. [Slides (pptx) (pdf)] [GenStore Source Code]

Christina Giannoula, Ivan Fernandez, Juan Gómez-Luna, Nectarios Koziris, Georgios Goumas, Onur Mutlu, "SparseP: Efficient Sparse Matrix Vector Multiplication on Real Processing-In-Memory Architectures," 2022 IEEE Computer Society Annual Symposium on VLSI (ISVLSI), July 2022. [Slides (pptx) (pdf)]

Juan Gómez-Luna, Yuxin Guo, Sylvan Brocard, Julien Legriel, Remy Cimadomo, Geraldo F. Oliveira, Gagandeep Singh, Onur Mutlu, "Machine Learning Training on a Real Processing-in-Memory System," 2022 IEEE Computer Society Annual Symposium on VLSI (ISVLSI), July 2022. [Slides (pptx) (pdf)]

Zaifeng Pan, Feng Zhang, Yanliang Zhou, Jidong Zhai, Xipeng Shen, Onur Mutlu, Xiaoyong Du, "Exploring Data Analytics Without Decompression on Embedded GPU Systems," in IEEE Transactions on Parallel and Distributed Systems, vol. 33, no. 7, pp. 1553-1568, 1 July 2022.

A. Giray Yağlıkçı, Haocong Luo, Geraldo F. de Oliviera, Ataberk Olgun, Minesh Patel, Jisung Park, Hasan Hassan, Jeremie S. Kim, Lois Orosa, and Onur Mutlu, "Understanding RowHammer Under Reduced Wordline Voltage: An Experimental Study Using Real DRAM Devices", Proceedings of the 52nd Annual IEEE/IFIP International Conference on Dependable Systems and Networks (DSN), Baltimore, MD, USA, June 2022.
[Slides (pptx) (pdf)] [Lightning Talk Slides (pptx) (pdf)] [arXiv version] [Talk Video (34 minutes, including Q&A)] [Lightning Talk Video (2 minutes)]

Gagandeep Singh, Rakesh Nadig, Jisung Park, Rahul Bera, Nastaran Hajinazar, David Novo, Juan Gomez-Luna, Sander Stuijk, Henk Corporaal, and Onur Mutlu, "Sibyl: Adaptive and Extensible Data Placement in Hybrid Storage Systems Using Online Reinforcement Learning", Proceedings of the 49th International Symposium on Computer Architecture (ISCA), New York, June 2022.

[Slides (pptx) (pdf)] [arXiv version] [Sibyl Source Code] [Talk Video (16 minutes)]

Damla Senol Cali, Konstantinos Kanellopoulos, Joel Lindegger, Zulal Bingol, Gurpreet S. Kalsi, Ziyi Zuo, Can Firtina, Meryem Banu Cavlak, Jeremie Kim, Nika MansouriGhiasi, Gagandeep Singh, Juan Gomez-Luna, Nour Almadhoun Alserr, Mohammed Alser, Sreenivas Subramoney, Can Alkan, Saugata Ghose, and Onur Mutlu, "SeGraM: A Universal Hardware Accelerator for Genomic Sequence-to-Graph and Sequence-to-Sequence Mapping", Proceedings of the 49th International Symposium on Computer Architecture (ISCA), New York, June 2022

[Slides (pptx) (pdf)] [arXiv version] [Talk Video (22 minutes)] [SeGraM Source Code and Datasets]

Christina Giannoula, Ivan Fernandez, Juan Gomez-Luna, Nectarios Koziris, Georgios Goumas, and Onur Mutlu, "SparseP: Towards Efficient Sparse Matrix Vector Multiplication on Real Processing-In-Memory Architectures", Proceedings of the ACM International Conference on Measurement and Modeling of Computer Systems (SIGMETRICS), Mumbai, India, June 2022.
[Extended arXiv Version] [Abstract] [Slides (pptx) (pdf)] [Long Talk Slides (pptx) (pdf)] [SparseP Source Code] [Talk Video (16 minutes)] [Long Talk Video (55 minutes)]

Mohammed Alser, Jeremie S. Kim, Nour Almadhoun Alserr, Stefan W. Tell, and Onur Mutlu,
"COVIDHunter: COVID-19 pandemic wave prediction and mitigation via seasonality aware modeling", Frontiers in Public Health, June 2022.

[arXiv version with all Supplementary Materials] [COVIDHunter Source Code] [Switzerland Case Study] [Short Talk Video at ISMB/ECCB 2021 (7 minutes)]

Nandita Vijaykumar, Ataberk Olgun, Konstantinos Kanellopoulos, F. Nisa Bostanci, Hasan Hassan, Mehrshad Lotfi, Phillip B. Gibbons, and Onur Mutlu, "MetaSys: A Practical Open-source Metadata Management System to Implement and Evaluate Cross-layer Optimizations", ACM Transactions on Architecture and Code Optimization (TACO), June 2022. [arXiv version] [Slides (pptx) (pdf)] [MetaSys Source Code] [Preliminary Talk Video (14 minutes)]

Juan Gomez-Luna, Izzat El Hajj, Ivan Fernandez, Christina Giannoula, Geraldo F. Oliveira, and Onur Mutlu, "Benchmarking a New Paradigm: Experimental Analysis and Characterization of a Real Processing-in-Memory System", IEEE Access, 10 May 2022.
[arXiv version] [PrIM Benchmarks Source Code] [Slides (pptx) (pdf)] [Long Talk Slides (pptx) (pdf)] [Short Talk Slides (pptx) (pdf)] [SAFARI Live Seminar Slides (pptx) (pdf)] [SAFARI Live Seminar Video (2 hrs 57 mins)] [Lightning Talk Video (3 minutes)]
[Short Talk Video (21 minutes)] [1-hour Talk Video (58 minutes)]

[ETH New for Industry Article]

Joel Lindegger, Damla Senol Cali, Mohammed Alser, Juan Gomez-Luna, and Onur Mutlu,
"Algorithmic Improvement and GPU Acceleration of the GenASM Algorithm", Proceedings of the 21st IEEE International Workshop on High Performance Computational Biology (HICOMB), Virtual, May 2022.
[arXiv version] [Slides (pptx) (pdf)]

Safaa Diab, Amir Nassereldine, Mohammed Alser, Juan Gomez-Luna, Onur Mutlu, and Izzat El Hajj, "High-throughput Pairwise Alignment with the Wavefront Algorithm using Processing-in-Memory", Proceedings of the 21st IEEE International Workshop on High Performance Computational Biology (HICOMB), Virtual, May 2022.
[arXiv version] [Slides (pptx) (pdf)]

Amirali Boroumand, Saugata Ghose, Geraldo F. Oliveira, and Onur Mutlu, "Polynesia: Enabling High-Performance and Energy-Efficient Hybrid Transactional/Analytical Databases with Hardware/Software Co-Design", Proceedings of the 38th International Conference on Data Engineering (ICDE), Virtual, May 2022.
[arXiv version] [Slides (pptx) (pdf)] [Short Talk Slides (pptx) (pdf)]

F. Nisa Bostanci, Ataberk Olgun, Lois Orosa, A. Giray Yaglikci, Jeremie S. Kim, Hasan Hassan, Oguz Ergin, and Onur Mutlu, "DR-STRaNGe: End-to-End System Design for DRAM-based True Random Number Generators", Proceedings of the 28th International Symposium on High-Performance Computer Architecture (HPCA), Virtual, April 2022.
[Slides (pptx) (pdf)] [Short Talk Slides (pptx) (pdf)] [Talk Video (24 minutes)]

Jawad Haj Yahya, Jeremie S. Kim, A. Giray Yaglikci, Jisung Park, Efraim Rotem, Yanos Sazeides, and Onur Mutlu, "DarkGates: A Hybrid Power-Gating Architecture to Mitigate the Performance Impact of Dark-Silicon in High Performance Processors", Proceedings of the 28th International Symposium on High-Performance Computer Architecture (HPCA), Virtual, April 2022. [Slides (pptx) (pdf)] [Short Talk Slides (pptx) (pdf)]

Mhd Ghaith Olabi, Juan Gomez Luna, Onur Mutlu, Wen-mei Hwu, and Izzat El Hajj, "A Compiler Framework for Optimizing Dynamic Parallelism on GPUs", Proceedings of the International Symposium on Code Generation and Optimization (CGO), Virtual, April 2022. Officially artifact evaluated as available, reusable and reproducible.
[Slides (pptx) (pdf)] [Short Talk Slides (pptx) (pdf)] [Source Code (Officially Artifact Evaluated with All Badges)]

Hai “Helen” Li, Alaa R. Alameldeen, Onur Mutlu, "Guest Editors’ Introduction: Near-Memory and In-Memory Processing," in IEEE Design & Test, April 2022.

Nika Mansouri Ghiasi, Jisung Park, Harun Mustafa, Jeremie Kim, Ataberk Olgun, Arvid Gollwitzer, Damla Senol Cali, Can Firtina, Haiyu Mao, Nour Almadhoun Alserr, Rachata Ausavarungnirun, Nandita Vijaykumar, Mohammed Alser, and Onur Mutlu, "GenStore: A High-Performance and Energy-Efficient In-Storage Computing System for Genome Sequence Analysis", Proceedings of the 27th International Conference on Architectural Support for Programming Languages and Operating Systems (ASPLOS), Virtual, February-March 2022. [Talk Slides (pptx) (pdf)] [Lightning Talk Slides (pptx) (pdf)] [Lightning Talk Video (90 seconds)] [Talk Video (17 minutes)]

Jisung Park, Jeonggyun Kim, Yeseong Kim, Sungjin Lee, and Onur Mutlu, "DeepSketch: A New Machine Learning-Based Reference Search Technique for Post-Deduplication Delta Compression", Proceedings of the 20th USENIX Conference on File and Storage Technologies (FAST), Santa Clara, CA, USA, February 2022.
[Slides (pptx) (pdf)] [Talk Video (15 minutes)]

Feng Zhang, Jidong Zhai, Xipeng Shen, Onur Mutlu, Xiaoyong Du, "POCLib: A High-Performance Framework for Enabling Near Orthogonal Processing on Compression," in IEEE Transactions on Parallel and Distributed Systems, vol. 33, no. 2, pp. 459-475, 1 Feb. 2022.

To our publications

Open Source Releases

We released many research artifacts and tools in 2022. All are available on GitHub:

Genome-on-Diet is a software tool that exemplifies sparsified genomics, which greatly reduces the amount of data used for certain genome analytics tasks to improve both performance and energy efficiency, while preserving analysis accuracy. Alser et al. https://arxiv.org/abs/2211.08157.

SeGraM is a universal genomic mapping accelerator that supports both sequence-to-graph mapping and sequence-to sequence mapping, for both short and long reads. Senol Cali et al., "SeGraM: A Universal Hardware Accelerator for Genomic Sequence-to-Graph and Sequence-to-Sequence Mapping", ISCA'22.

Sibyl is a hybrid storage system (HSS) uses multiple different storage devices to provide high and scalable storage capacity at high performance. Data placement across different devices is critical to maximize the benefits of such a hybrid system. Singh et al., "Sibyl: Adaptive and Extensible Data Placement in Hybrid Storage Systems using Online Reinforcement Learning", ISCA'22

Scrooge is a high-performance pairwise sequence aligner based on the GenASM algorithm. Scrooge includes three novel algorithmic improvements on top of GenASM, and high-performance CPU and GPU implementations. Lindegger et al. https://doi.org/10.48550/arXiv.2208.09985

Molecules2Variations is the first work to provide a comprehensive survey of a prominent set of algorithmic improvement and hardware acceleration efforts for the entire genome analysis pipeline used for the three most prominent sequencing data, short reads (Illumina), ultra-long reads (ONT), and accurate long reads (HiFi). Alser et al., https://arxiv.org/abs/2205.07957

SparseP is the first open-source Sparse Matrix Vector Multiplication (SpMV) software package for real-world Processing-In-Memory (PIM) architectures. SparseP is developed to evaluate and characterize the first publicly-available real-world PIM architecture, the UPMEM PIM architecture. Giannoula et al.

"SparseP: Towards Efficient Sparse Matrix Vector Multiplication on Real Processing-In-Memory Architectures", SIGMETRICS'22.

Metasys is the first open-source FPGA-based infrastructure with a prototype in a RISC-V core, to enable the rapid implementation and evaluation of a wide range of cross-layer software/hardware cooperative techniques techniques in real hardware. Vijaykumar, Olgun, et al., "MetaSys: A Practical Open-source Metadata Management System to Implement and Evaluate Cross-layer Optimizations", TACO'22

BlockHammer is a low-cost, effective, and easy-to-adopt RowHammer mitigation mechanism that overcomes the two key challenges by selectively throttling memory accesses that could otherwise cause RowHammer bit-flips.
Yaglikci et al., "BlockHammer: Preventing RowHammer at Low Cost by Blacklisting Rapidly-Accessed DRAM Rows", HPCA'21.

DRAM Bender is the first open source DRAM testing infrastructure that can be used to easily and comprehensively test state-of-the-art DDR4 modules of different form factors. Four prototypes are available on different FPGA boards. Olgun et al. https://arxiv.org/pdf/2211.05838.pdf

Hermes is a speculative mechanism to accelerate long-latency off-chip load requests by removing on-chip cache access latency from their critical path. Bera et al., "Hermes: Accelerating Long-Latency Load Requests via Perceptron-Based Off-Chip Load Prediction", MICRO'22

pLUTo is a DRAM-based Processing-using-Memory architecture that leverages the high density of DRAM to enable the massively parallel storing and querying of lookup tables (LUTs). Ferreira et al., "pLUTo: Enabling Massively Parallel Computation in DRAM via Lookup Tables", MICRO'22.

ApHMM-GPU is the first GPU implementation of the Baum-Welch algorithm for profile Hidden Markov Models (pHMMs). Firtina et al. https://arxiv.org/abs/2207.09765.

GenStore is the first in-storage processing system designed for genome sequence analysis that greatly reduces both data movement and computational overheads of genome sequence analysis by exploiting low-cost and accurate in-storage filters. Mansouri Ghiasi et al., "GenStore: A High-Performance and Energy-Efficient In-Storage Computing System for Genome Sequence Analysis", ASPLOS'22.

FastRemap Source Code is a tool for Quickly Remapping Reads between Genome Assemblies. Kim, et al. https://arxiv.org/pdf/2201.06255.pdf

TargetCall is the first pre-basecalling filter that is applicable to a wide range of use cases to eliminate wasted computation in basecalling. Cavlak et al., https://arxiv.org/abs/2212.04953

Think Big, Aim High

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December 2021