Processing-in-memory architectures and programming libraries for bioinformatics algorithms

Leistungen

This report includes survey of different 3D-stacked memories and their various logic layer architectures, including survey on state-of-the art logic layer designs

Workload Characterization Document for Alignment and Search Algorithms - 2

Report about workload characterization for alignment and search algorithms

Workload Characterization Document for Graph Algorithms - 1

Report about workload characterization for graph algorithms

DPU Model Report - 2

Report about DPU model

Data management plan

Plan for data management life cycle of the collected processed andor generated data in the scope of BioPIM including information about procedures quality standards etc

Workload Characterization Document for Graph Algorithms - 2

Report about workload characterization for graph algorithms

DPU Model Report - 4

Report about DPU model

DPU Model Report - 3

Report about DPU model

Workload Characterization Document for Machine Learning and Deep Learning Algorithms - 2

Report about workload characterization for machine learning and deep learning algorithms

DPU Model Report - 1

Report about DPU model

Dissemination, communication and exploitation report - 1

Dissemination, communication and exploitation report

Workload Characterization Document for Machine Learning and Deep Learning Algorithms - 1

Report about workload characterization for machine learning and deep learning algorithms

Workload Characterization Document for Data Structures and Data Mapping - 1

Report about workload characterization for data structures and data mapping

Workload Characterization Document for Data Structures and Data Mapping - 2

Report about workload characterization for data structures and data mapping

Workload Characterization Document for Alignment and Search Algorithms - 1

Report about workload characterization for alignment and search algorithms

Project website and logo

Veröffentlichungen

ViRAL: Vision Transformer Based Accelerator for ReAL Time Lineage Assignment of Viral Pathogens

Autoren: Zuher Jahshan, Esteban Garzón, Leonid Yavits
Veröffentlicht in: IEEE Access, Ausgabe 12, 2024, ISSN 2169-3536
Herausgeber: Institute of Electrical and Electronics Engineers (IEEE)
DOI: 10.1109/access.2024.3367801

Designing Precharge-Free Energy-Efficient Content-Addressable Memories

Autoren: Ramiro Taco, Esteban Garzón, Robert Hanhan, Adam Teman, Leonid Yavits, Marco Lanuzza
Veröffentlicht in: IEEE Transactions on Very Large Scale Integration (VLSI) Systems, Ausgabe 32, 2024, ISSN 1063-8210
Herausgeber: Institute of Electrical and Electronics Engineers (IEEE)
DOI: 10.1109/TVLSI.2024.3475036

OCCAM: An Error Oblivious CAM

Autoren: Yuval Harary; Paz Snapir; Eyal Reshef; Esteban Garzón; Leonid Yavits
Veröffentlicht in: IEEE Solid-State Circuits Letters, 2024, ISSN 2573-9603
Herausgeber: IEEE
DOI: 10.1109/lssc.2024.3362891

A framework for high-throughput sequence alignment using real processing-in-memory systems

Autoren: Safaa Diab, Amir Nassereldine, Mohammed Alser, Juan Gómez Luna, Onur Mutlu, Izzat El Hajj
Veröffentlicht in: Bioinformatics, Ausgabe 39, 2023, ISSN 1367-4811
Herausgeber: Oxford University Press (OUP)
DOI: 10.1093/bioinformatics/btad155

MajorK: Majority Based <i>k</i>mer Matching in Commodity DRAM

Autoren: Z. Jahshan, L. Yavits
Veröffentlicht in: IEEE Computer Architecture Letters, Ausgabe 23, 2024, ISSN 1556-6056
Herausgeber: Institute of Electrical and Electronics Engineers (IEEE)
DOI: 10.1109/LCA.2024.3384259

A Low-Energy DMTJ-Based Ternary Content- Addressable Memory With Reliable Sub-Nanosecond Search Operation

Autoren: Esteban Garzón, Leonid Yavits, Giovanni Finocchio, Mario Carpentieri, Adam Teman, Marco Lanuzza
Veröffentlicht in: IEEE Access, Ausgabe 11, 2024, ISSN 2169-3536
Herausgeber: Institute of Electrical and Electronics Engineers (IEEE)
DOI: 10.1109/ACCESS.2023.3245981

DRAMA: Commodity DRAM Based Content Addressable Memory

Autoren: L. Yavits
Veröffentlicht in: IEEE Computer Architecture Letters, Ausgabe 23, 2024, ISSN 1556-6056
Herausgeber: Institute of Electrical and Electronics Engineers (IEEE)
DOI: 10.1109/LCA.2023.3341830

Approximate Content-Addressable Memories: A Review

Autoren: Esteban Garzón, Leonid Yavits, Adam Teman, Marco Lanuzza
Veröffentlicht in: Chips, Ausgabe 2, 2025, ISSN 2674-0729
Herausgeber: MDPI AG
DOI: 10.3390/chips2020005

RawAlign: Accurate, Fast, and Scalable Raw Nanopore Signal Mapping via Combining Seeding and Alignment

Autoren: Joël Lindegger, Can Firtina, Nika Mansouri Ghiasi, Mohammad Sadrosadati, Mohammed Alser, Onur Mutlu
Veröffentlicht in: arXiv, 2023, ISSN 2331-8422
Herausgeber: arXiv
DOI: 10.5281/ZENODO.15086073

Constructing and personalizing population pangenome graphs

Autoren: Rayan Chikhi, Yoann Dufresne, Paul Medvedev
Veröffentlicht in: Nature Methods, Ausgabe 21, 2024, ISSN 1548-7091
Herausgeber: Springer Science and Business Media LLC
DOI: 10.1038/s41592-024-02402-7

Efficient mapping of accurate long reads in minimizer space with mapquik

Autoren: Bariş Ekim, Kristoffer Sahlin, Paul Medvedev, Bonnie Berger, Rayan Chikhi
Veröffentlicht in: Genome Research, 2023, ISSN 1088-9051
Herausgeber: Cold Spring Harbor Laboratory
DOI: 10.1101/gr.277679.123

A Low-Complexity Sensing Scheme for Approximate Matching Content-Addressable Memory

Autoren: Esteban Garzón; Roman Golman; Marco Lanuzza; Adam Teman; Leonid Yavits
Veröffentlicht in: IEEE Transactions on Circuits and Systems II: Express Briefs, 2023, ISSN 1558-3791
Herausgeber: IEEE
DOI: 10.1109/tcsii.2023.3286257

DIPER: Detection and Identification of Pathogens Using Edit Distance-Tolerant Resistive CAM

Autoren: Itay Merlin, Esteban Garzón, Alexander Fish, Leonid Yavits
Veröffentlicht in: IEEE Transactions on Computers, Ausgabe 73, 2024, ISSN 0018-9340
Herausgeber: Institute of Electrical and Electronics Engineers (IEEE)
DOI: 10.1109/TC.2023.3315829

ApHMM: Accelerating Profile Hidden Markov Models for Fast and Energy-efficient Genome Analysis

Autoren: Can Firtina; Kamlesh Pillai; Gurpreet S. Kalsi; Bharathwaj Suresh; Damla Senol Cali; Jeremie S. Kim; Taha Shahroodi; Meryem Banu Cavlak; Joël Lindegger; Mohammed Alser; Juan Gómez Luna; Sreenivas Subramoney; Onur Mutlu
Veröffentlicht in: ACM Transactions on Architecture and Code Optimization, 2024, ISSN 1544-3973
Herausgeber: Association for Computing Machinery
DOI: 10.3929/ethz-b-000663170

Will computing in memory become a new dawn of associative processors?

Autoren: Leonid Yavits
Veröffentlicht in: Memories - Materials, Devices, Circuits and Systems, Ausgabe 4, 2024, ISSN 2773-0646
Herausgeber: Elsevier BV
DOI: 10.1016/j.memori.2023.100033

RUBICON: a framework for designing efficient deep learning-based genomic basecallers

Autoren: Gagandeep Singh; Mohammed Alser; Kristof Denolf; Can Firtina; Alireza Khodamoradi; Meryem Banu Cavlak; Henk Corporaal; Onur Mutlu
Veröffentlicht in: Genome Biology, 2024, ISSN 1474-760X
Herausgeber: Genome Biology
DOI: 10.3929/ethz-b-000661676

SVDSS: structural variation discovery in hard-to-call genomic regions using sample-specific strings from accurate long reads

Autoren: Luca Denti, Parsoa Khorsand, Paola Bonizzoni, Fereydoun Hormozdiari, Rayan Chikhi
Veröffentlicht in: Nature Methods, Ausgabe 20, 2023, ISSN 1548-7091
Herausgeber: Springer Science and Business Media LLC
DOI: 10.1038/s41592-022-01674-1

AM4: MRAM Crossbar Based CAM/TCAM/ACAM/AP for In-Memory Computing

Autoren: Esteban Garzón; Marco Lanuzza; Adam Teman; Leonid Yavits
Veröffentlicht in: IEEE Journal on Emerging and Selected Topics in Circuits and Systems, Ausgabe 1, 2023, ISSN 2156-3365
Herausgeber: IEEE
DOI: 10.5281/zenodo.8087076

ViTAL: Vision TrAnsformer based Low coverage SARS-CoV-2 lineage assignment

Autoren: Zuher Jahshan; Leonid Yavits
Veröffentlicht in: Bioinformatics, 2024, ISSN 1367-4811
Herausgeber: Bioinformatics
DOI: 10.1093/bioinformatics/btae093

FASTA: Revisiting Fully Associative Memories in Computer Microarchitecture

Autoren: Esteban Garzón, Robert Hanhan, Marco Lanuzza, Adam Teman, Leonid Yavits
Veröffentlicht in: IEEE Access, Ausgabe 12, 2024, ISSN 2169-3536
Herausgeber: Institute of Electrical and Electronics Engineers (IEEE)
DOI: 10.1109/access.2024.3355961

ClaPIM: Scalable Sequence Classification Using Processing-in-Memory

Autoren: Marcel Khalifa, Barak Hoffer, Orian Leitersdorf, Robert Hanhan, Ben Perach, Leonid Yavits, Shahar Kvatinsky
Veröffentlicht in: IEEE Transactions on Very Large Scale Integration (VLSI) Systems, Ausgabe 31, 2023, ISSN 1063-8210
Herausgeber: Institute of Electrical and Electronics Engineers (IEEE)
DOI: 10.1109/TVLSI.2023.3293038

RawHash: enabling fast and accurate real-time analysis of raw nanopore signals for large genomes

Autoren: Can Firtina, Nika Mansouri Ghiasi, Joel Lindegger, Gagandeep Singh, Meryem Banu Cavlak, Haiyu Mao, Onur Mutlu
Veröffentlicht in: Bioinformatics, Ausgabe 39, 2023, ISSN 1367-4803
Herausgeber: Oxford University Press (OUP)
DOI: 10.1093/bioinformatics/btad272

Accelerating Genome Analysis via Algorithm-Architecture Co-Design

Autoren: Onur Mutlu, Can Firtina
Veröffentlicht in: Design Automation Conference (DAC) 2023, 2023, ISSN 2331-8422
Herausgeber: arXiv
DOI: 10.5281/zenodo.8087173

Parallelization of the Banded Needleman & Wunsch Algorithm on UPMEM PiM Architecture for Long DNA Sequence Alignment

Autoren: Meven Mognol, Dominique Lavenier, Julien Legriel
Veröffentlicht in: 2024
Herausgeber: ACM
DOI: 10.1145/3673038.36730

Energy Efficiency Impact of Processing in Memory: A Comprehensive Review of Workloads on the UPMEM Architecture

Autoren: Yann Falevoz, Julien Legriel
Veröffentlicht in: Lecture Notes in Computer Science, Euro-Par 2023: Parallel Processing Workshops, 2024
Herausgeber: Springer Nature Switzerland
DOI: 10.1007/978-3-031-48803-0_13

TransPimLib: Efficient Transcendental Functions for Processing-in-Memory Systems

Autoren: Maurus Item, Geraldo F. Oliveira, Juan Gómez-Luna, Mohammad Sadrosadati, Yuxin Guo, Onur Mutlu
Veröffentlicht in: 2023 IEEE International Symposium on Performance Analysis of Systems and Software (ISPASS), 2023
Herausgeber: IEEE
DOI: 10.1109/ISPASS57527.2023.00031

An Experimental Evaluation of Machine Learning Training on a Real Processing-in-Memory System

Autoren: Juan Gómez Luna, Yuxin Guo, Sylvan Brocard, Julien Legriel, Remy Cimadomo, Geraldo F. Oliveira, Gagandeep Singh, Onur Mutlu
Veröffentlicht in: ISPASS, 2022, ISSN 2331-8422
Herausgeber: arXiv
DOI: 10.5281/ZENODO.8087127

MiMyCS: A Processing-in-Memory Read Mapper for Compressing Next-Gen Sequencing Datasets

Autoren: Florestan de Moor, Meven Mognol, Charles Deltel, Erwan Drezen, Julien Legriel, Dominique Lavenier
Veröffentlicht in: 2024
Herausgeber: Hal open science
DOI: 10.1109/BIBM62325.2024.10821790

Swordfish: A Framework for Evaluating Deep Neural Network-based Basecalling using Computation-In-Memory with Non-Ideal Memristors

Autoren: Taha Shahroodi, Gagandeep Singh, Mahdi Zahedi, Haiyu Mao, Joel Lindegger, Can Firtina, Stephan Wong, Onur Mutlu, Said Hamdioui
Veröffentlicht in: 2023
Herausgeber: Association for Computing Machinery
DOI: 10.1145/3613424.3614252

QUETZAL: Vector Acceleration Framework for Modern Genome Sequence Analysis Algorithms

Autoren: Julian Pavon, Ivan Vargas Valdivieso, Carlos Rojas, Cesar Hernandez, Mehmet Aslan, Roger Figueras, Yichao Yuan, Joël Lindegger, Mohammed Alser, Francesc Moll, Santiago Marco-Sola, Oguz Ergin, Nishil Talati, Onur Mutlu, Osman Unsal, Mateo Valero, Adrian Cristal
Veröffentlicht in: 2024 ACM/IEEE 51st Annual International Symposium on Computer Architecture (ISCA), 2024
Herausgeber: IEEE
DOI: 10.1109/ISCA59077.2024.00050

MegIS: High-Performance, Energy-Efficient, and Low-Cost Metagenomic Analysis with In-Storage Processing

Autoren: Nika Mansouri Ghiasi, Mohammad Sadrosadati, Harun Mustafa, Arvid Gollwitzer, Can Firtina, Julien Eudine, Haiyu Mao, Joël Lindegger, Meryem Banu Cavlak, Mohammed Alser, Jisung Park, Onur Mutlu
Veröffentlicht in: 2024
Herausgeber: arXiv
DOI: 10.5281/ZENODO.15085962

SimplePIM: A Software Framework for Productive and Efficient Processing-in-Memory

Autoren: Jinfan Chen, Juan Gómez-Luna, Izzat El Hajj, Yuxin Guo, Onur Mutlu
Veröffentlicht in: 2023 32nd International Conference on Parallel Architectures and Compilation Techniques (PACT), 2024
Herausgeber: IEEE
DOI: 10.1109/PACT58117.2023.00017

DASH-CAM: Dynamic Approximate SearcH Content Addressable Memory for genome classification

Autoren: Zuher Jahshan, Itay Merlin, Esteban GarzÓN, Leonid Yavits
Veröffentlicht in: 56th Annual IEEE/ACM International Symposium on Microarchitecture, 2023
Herausgeber: ACM
DOI: 10.1145/3613424.3614262

GateSeeder: Near-memory CPU-FPGA Acceleration of Short and Long Read Mapping

Autoren: Julien Eudine, Mohammed Alser, Gagandeep Singh, Can Alkan, Onur Mutlu
Veröffentlicht in: 2023
Herausgeber: arXiv
DOI: 10.48550/arXiv.2309.17063

GAPiM: Discovering Genetic Variations on a Real Processing-in-Memory System

Autoren: Naomie Abecassis, Juan Gómez-Luna, Onur Mutlu, Ran Ginosar, Aphélie Moisson-Franckhauser, Leonid Yavits
Veröffentlicht in: 2024
Herausgeber: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.07.26.550623

Leistungen

Veröffentlichungen

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