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

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

3D Stacked Memory Model Report - 1

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

Publications

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

Author(s): Zuher Jahshan, Esteban Garzón, Leonid Yavits
Published in: IEEE Access, Issue 12, 2024, ISSN 2169-3536
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
DOI: 10.1109/access.2024.3367801

Designing Precharge-Free Energy-Efficient Content-Addressable Memories

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

OCCAM: An Error Oblivious CAM

Author(s): Yuval Harary; Paz Snapir; Eyal Reshef; Esteban Garzón; Leonid Yavits
Published in: IEEE Solid-State Circuits Letters, 2024, ISSN 2573-9603
Publisher: IEEE
DOI: 10.1109/lssc.2024.3362891

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

Author(s): Safaa Diab, Amir Nassereldine, Mohammed Alser, Juan Gómez Luna, Onur Mutlu, Izzat El Hajj
Published in: Bioinformatics, Issue 39, 2023, ISSN 1367-4811
Publisher: Oxford University Press (OUP)
DOI: 10.1093/bioinformatics/btad155

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

Author(s): Z. Jahshan, L. Yavits
Published in: IEEE Computer Architecture Letters, Issue 23, 2024, ISSN 1556-6056
Publisher: 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

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

DRAMA: Commodity DRAM Based Content Addressable Memory

Author(s): L. Yavits
Published in: IEEE Computer Architecture Letters, Issue 23, 2024, ISSN 1556-6056
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
DOI: 10.1109/LCA.2023.3341830

Approximate Content-Addressable Memories: A Review

Author(s): Esteban Garzón, Leonid Yavits, Adam Teman, Marco Lanuzza
Published in: Chips, Issue 2, 2025, ISSN 2674-0729
Publisher: MDPI AG
DOI: 10.3390/chips2020005

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

Author(s): Joël Lindegger, Can Firtina, Nika Mansouri Ghiasi, Mohammad Sadrosadati, Mohammed Alser, Onur Mutlu
Published in: arXiv, 2024, ISSN 2331-8422
Publisher: arXiv
DOI: 10.48550/arXiv.2310.05037

Constructing and personalizing population pangenome graphs

Author(s): Rayan Chikhi, Yoann Dufresne, Paul Medvedev
Published in: Nature Methods, Issue 21, 2024, ISSN 1548-7091
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/s41592-024-02402-7

Efficient mapping of accurate long reads in minimizer space with mapquik

Author(s): Bariş Ekim, Kristoffer Sahlin, Paul Medvedev, Bonnie Berger, Rayan Chikhi
Published in: Genome Research, 2023, ISSN 1088-9051
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/gr.277679.123

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

Author(s): Esteban Garzón; Roman Golman; Marco Lanuzza; Adam Teman; Leonid Yavits
Published in: IEEE Transactions on Circuits and Systems II: Express Briefs, 2023, ISSN 1558-3791
Publisher: IEEE
DOI: 10.1109/tcsii.2023.3286257

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

Author(s): Itay Merlin, Esteban Garzón, Alexander Fish, Leonid Yavits
Published in: IEEE Transactions on Computers, Issue 73, 2024, ISSN 0018-9340
Publisher: 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

Author(s): 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
Published in: ACM Transactions on Architecture and Code Optimization, 2024, ISSN 1544-3973
Publisher: Association for Computing Machinery
DOI: 10.3929/ethz-b-000663170

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

Author(s): Leonid Yavits
Published in: Memories - Materials, Devices, Circuits and Systems, Issue 4, 2024, ISSN 2773-0646
Publisher: Elsevier BV
DOI: 10.1016/j.memori.2023.100033

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

Author(s): Gagandeep Singh; Mohammed Alser; Kristof Denolf; Can Firtina; Alireza Khodamoradi; Meryem Banu Cavlak; Henk Corporaal; Onur Mutlu
Published in: Genome Biology, 2024, ISSN 1474-760X
Publisher: 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

Author(s): Luca Denti, Parsoa Khorsand, Paola Bonizzoni, Fereydoun Hormozdiari, Rayan Chikhi
Published in: Nature Methods, Issue 20, 2023, ISSN 1548-7091
Publisher: 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

Author(s): Esteban Garzón; Marco Lanuzza; Adam Teman; Leonid Yavits
Published in: IEEE Journal on Emerging and Selected Topics in Circuits and Systems, Issue 1, 2023, ISSN 2156-3365
Publisher: IEEE
DOI: 10.5281/zenodo.8087076

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

Author(s): Zuher Jahshan; Leonid Yavits
Published in: Bioinformatics, 2024, ISSN 1367-4811
Publisher: Bioinformatics
DOI: 10.1093/bioinformatics/btae093

FASTA: Revisiting Fully Associative Memories in Computer Microarchitecture

Author(s): Esteban Garzón, Robert Hanhan, Marco Lanuzza, Adam Teman, Leonid Yavits
Published in: IEEE Access, Issue 12, 2024, ISSN 2169-3536
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
DOI: 10.1109/access.2024.3355961

ClaPIM: Scalable Sequence Classification Using Processing-in-Memory

Author(s): Marcel Khalifa, Barak Hoffer, Orian Leitersdorf, Robert Hanhan, Ben Perach, Leonid Yavits, Shahar Kvatinsky
Published in: IEEE Transactions on Very Large Scale Integration (VLSI) Systems, Issue 31, 2023, ISSN 1063-8210
Publisher: 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

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

Accelerating Genome Analysis via Algorithm-Architecture Co-Design

Author(s): Onur Mutlu, Can Firtina
Published in: Design Automation Conference (DAC) 2023, 2023, ISSN 2331-8422
Publisher: arXiv
DOI: 10.5281/zenodo.8087173

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

Author(s): Meven Mognol, Dominique Lavenier, Julien Legriel
Published in: 2024
Publisher: ACM
DOI: 10.1145/3673038.36730

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

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

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

Author(s): Juan Gómez Luna, Yuxin Guo, Sylvan Brocard, Julien Legriel, Remy Cimadomo, Geraldo F. Oliveira, Gagandeep Singh, Onur Mutlu
Published in: ISPASS, 2023, ISSN 2331-8422
Publisher: arXiv
DOI: 10.48550/arXiv.2207.07886

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

Author(s): Florestan de Moor, Meven Mognol, Charles Deltel, Erwan Drezen, Julien Legriel, Dominique Lavenier
Published in: 2024
Publisher: 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

Author(s): Taha Shahroodi, Gagandeep Singh, Mahdi Zahedi, Haiyu Mao, Joel Lindegger, Can Firtina, Stephan Wong, Onur Mutlu, Said Hamdioui
Published in: 2023
Publisher: Association for Computing Machinery
DOI: 10.1145/3613424.3614252

QUETZAL: Vector Acceleration Framework for Modern Genome Sequence Analysis Algorithms

Author(s): 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
Published in: 2024 ACM/IEEE 51st Annual International Symposium on Computer Architecture (ISCA), 2024
Publisher: IEEE
DOI: 10.1109/ISCA59077.2024.00050

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

Author(s): 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
Published in: 2024
Publisher: arXiv
DOI: 10.48550/arXiv.2406.19113

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

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

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

Author(s): Zuher Jahshan, Itay Merlin, Esteban GarzÓN, Leonid Yavits
Published in: 56th Annual IEEE/ACM International Symposium on Microarchitecture, 2023
Publisher: ACM
DOI: 10.1145/3613424.3614262

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

Author(s): Julien Eudine, Mohammed Alser, Gagandeep Singh, Can Alkan, Onur Mutlu
Published in: 2023
Publisher: arXiv
DOI: 10.48550/arXiv.2309.17063

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

Author(s): Naomie Abecassis, Juan Gómez-Luna, Onur Mutlu, Ran Ginosar, Aphélie Moisson-Franckhauser, Leonid Yavits
Published in: 2024
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.07.26.550623

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