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

CORDIS fournit des liens vers les livrables publics et les publications des projets HORIZON.

Les liens vers les livrables et les publications des projets du 7e PC, ainsi que les liens vers certains types de résultats spécifiques tels que les jeux de données et les logiciels, sont récupérés dynamiquement sur OpenAIRE .

Livrables

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

Auteurs: Zuher Jahshan, Esteban Garzón, Leonid Yavits
Publié dans: IEEE Access, Numéro 12, 2024, ISSN 2169-3536
Éditeur: Institute of Electrical and Electronics Engineers (IEEE)
DOI: 10.1109/access.2024.3367801

Designing Precharge-Free Energy-Efficient Content-Addressable Memories

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

OCCAM: An Error Oblivious CAM

Auteurs: Yuval Harary; Paz Snapir; Eyal Reshef; Esteban Garzón; Leonid Yavits
Publié dans: IEEE Solid-State Circuits Letters, 2024, ISSN 2573-9603
Éditeur: IEEE
DOI: 10.1109/lssc.2024.3362891

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

Auteurs: Safaa Diab, Amir Nassereldine, Mohammed Alser, Juan Gómez Luna, Onur Mutlu, Izzat El Hajj
Publié dans: Bioinformatics, Numéro 39, 2023, ISSN 1367-4811
Éditeur: Oxford University Press (OUP)
DOI: 10.1093/bioinformatics/btad155

Processing-in-Memory for Genomics Workloads

Auteurs: William Andrew Simon, Leonid Yavits, Konstantina Koliogeorgi, Yann Falevoz, Yoshihiro Shibuya, Dominique Lavenier, Irem Boybat, Klea Zambaku, Berkan Şahin, Mohammad Sadrosadati, Onur Mutlu, Abu Sebastian, Rayan Chikhi, The BioPIM Consortium, Can Alkan
Publié dans: IEEE Micro, Numéro 46, 2026, ISSN 0272-1732
Éditeur: Institute of Electrical and Electronics Engineers (IEEE)
DOI: 10.5281/ZENODO.22941196

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

Auteurs: Z. Jahshan, L. Yavits
Publié dans: IEEE Computer Architecture Letters, Numéro 23, 2024, ISSN 1556-6056
Éditeur: 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

Auteurs: Esteban Garzón, Leonid Yavits, Giovanni Finocchio, Mario Carpentieri, Adam Teman, Marco Lanuzza
Publié dans: IEEE Access, Numéro 11, 2024, ISSN 2169-3536
Éditeur: Institute of Electrical and Electronics Engineers (IEEE)
DOI: 10.1109/ACCESS.2023.3245981

DRAMA: Commodity DRAM Based Content Addressable Memory

Auteurs: L. Yavits
Publié dans: IEEE Computer Architecture Letters, Numéro 23, 2024, ISSN 1556-6056
Éditeur: Institute of Electrical and Electronics Engineers (IEEE)
DOI: 10.1109/LCA.2023.3341830

GCOC: A Genome Classifier-On-Chip Based on Similarity Search Content Addressable Memory

Auteurs: Yuval Harary, Paz Snapir, Shir Siman Tov, Chen Kruphman, Eyal Rechef, Zuher Jahshan, Esteban Garzón, Leonid Yavits
Publié dans: IEEE Transactions on Biomedical Circuits and Systems, Numéro 19, 2025, ISSN 1932-4545
Éditeur: Institute of Electrical and Electronics Engineers (IEEE)
DOI: 10.1109/TBCAS.2024.3449788

Approximate Content-Addressable Memories: A Review

Auteurs: Esteban Garzón, Leonid Yavits, Adam Teman, Marco Lanuzza
Publié dans: Chips, Numéro 2, 2025, ISSN 2674-0729
Éditeur: MDPI AG
DOI: 10.3390/chips2020005

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

Auteurs: Joël Lindegger, Can Firtina, Nika Mansouri Ghiasi, Mohammad Sadrosadati, Mohammed Alser, Onur Mutlu
Publié dans: arXiv, 2023, ISSN 2331-8422
Éditeur: arXiv
DOI: 10.5281/ZENODO.15086073

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

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

Constructing and personalizing population pangenome graphs

Auteurs: Rayan Chikhi, Yoann Dufresne, Paul Medvedev
Publié dans: Nature Methods, Numéro 21, 2024, ISSN 1548-7091
Éditeur: Springer Science and Business Media LLC
DOI: 10.5281/ZENODO.15086177

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

Auteurs: Itay Merlin, Esteban Garzón, Alexander Fish, Leonid Yavits
Publié dans: IEEE Transactions on Computers, Numéro 73, 2024, ISSN 0018-9340
Éditeur: 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

Auteurs: 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
Publié dans: ACM Transactions on Architecture and Code Optimization, 2024, ISSN 1544-3973
Éditeur: Association for Computing Machinery
DOI: 10.3929/ethz-b-000663170

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

Auteurs: Leonid Yavits
Publié dans: Memories - Materials, Devices, Circuits and Systems, Numéro 4, 2024, ISSN 2773-0646
Éditeur: Elsevier BV
DOI: 10.1016/j.memori.2023.100033

RawHash2: mapping raw nanopore signals using hash-based seeding and adaptive quantization

Auteurs: Can Firtina, Melina Soysal, Joël Lindegger, Onur Mutlu
Publié dans: Bioinformatics, Numéro 40, 2024, ISSN 1367-4811
Éditeur: Oxford University Press (OUP)
DOI: 10.1093/BIOINFORMATICS/BTAE478

LCPan: efficient variation graph construction using locally consistent parsing

Auteurs: Akmuhammet Ashyralyyev, Zülal Bingöl, Begüm Filiz Öz, Kaiyuan Zhu, Salem Malikic, Uzi Vishkin, S. Cenk Sahinalp, Can Alkan
Publié dans: Genome Biology, Numéro 27, 2026, ISSN 1474-760X
Éditeur: Springer Science and Business Media LLC
DOI: 10.5281/ZENODO.22941311

De Bruijn graphs for pangenomics: in-depth performance benchmarking of de Bruijn graph-based tools for read mapping

Auteurs: Zülal Bingöl, Berkan Şahin, Klea Zambaku, Ricardo Roman-Brenes, Konstantina Koliogeorgi, Can Firtina, Onur Mutlu, Can Alkan
Publié dans: Briefings in Bioinformatics, Numéro 27, 2026, ISSN 1467-5463
Éditeur: Oxford University Press (OUP)
DOI: 10.5281/ZENODO.22941530

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

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

Monolithic 3-D-Based Nonvolatile Associative Processor for High-Performance Energy-Efficient Computations

Auteurs: Esteban Garzón, Alessandro Bedoya, Marco Lanuzza, Leonid Yavits
Publié dans: IEEE Journal on Exploratory Solid-State Computational Devices and Circuits, Numéro 10, 2025, ISSN 2329-9231
Éditeur: Institute of Electrical and Electronics Engineers (IEEE)
DOI: 10.1109/JXCDC.2024.3450810

CiMBA: Accelerating Genome Sequencing Through On-Device Basecalling via Compute-in-Memory

Auteurs: William Andrew Simon, Irem Boybat, Riselda Kodra, Elena Ferro, Gagandeep Singh, Mohammed Alser, Shubham Jain, Hsinyu Tsai, Geoffrey W. Burr, Onur Mutlu, Abu Sebastian
Publié dans: IEEE Transactions on Parallel and Distributed Systems, Numéro 36, 2025, ISSN 1045-9219
Éditeur: Institute of Electrical and Electronics Engineers (IEEE)
DOI: 10.1109/TPDS.2025.3550811

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

Auteurs: Luca Denti, Parsoa Khorsand, Paola Bonizzoni, Fereydoun Hormozdiari, Rayan Chikhi
Publié dans: Nature Methods, Numéro 20, 2023, ISSN 1548-7091
Éditeur: 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

Auteurs: Esteban Garzón; Marco Lanuzza; Adam Teman; Leonid Yavits
Publié dans: IEEE Journal on Emerging and Selected Topics in Circuits and Systems, Numéro 1, 2023, ISSN 2156-3365
Éditeur: IEEE
DOI: 10.5281/zenodo.8087076

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

Auteurs: Zuher Jahshan; Leonid Yavits
Publié dans: Bioinformatics, 2024, ISSN 1367-4811
Éditeur: Bioinformatics
DOI: 10.1093/bioinformatics/btae093

FASTA: Revisiting Fully Associative Memories in Computer Microarchitecture

Auteurs: Esteban Garzón, Robert Hanhan, Marco Lanuzza, Adam Teman, Leonid Yavits
Publié dans: IEEE Access, Numéro 12, 2024, ISSN 2169-3536
Éditeur: Institute of Electrical and Electronics Engineers (IEEE)
DOI: 10.1109/access.2024.3355961

ClaPIM: Scalable Sequence Classification Using Processing-in-Memory

Auteurs: Marcel Khalifa, Barak Hoffer, Orian Leitersdorf, Robert Hanhan, Ben Perach, Leonid Yavits, Shahar Kvatinsky
Publié dans: IEEE Transactions on Very Large Scale Integration (VLSI) Systems, Numéro 31, 2023, ISSN 1063-8210
Éditeur: 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

Auteurs: Can Firtina, Nika Mansouri Ghiasi, Joel Lindegger, Gagandeep Singh, Meryem Banu Cavlak, Haiyu Mao, Onur Mutlu
Publié dans: Bioinformatics, Numéro 39, 2023, ISSN 1367-4803
Éditeur: Oxford University Press (OUP)
DOI: 10.1093/bioinformatics/btad272

TargetCall: eliminating the wasted computation in basecalling via pre-basecalling filtering

Auteurs: Meryem Banu Cavlak, Gagandeep Singh, Mohammed Alser, Can Firtina, Joël Lindegger, Mohammad Sadrosadati, Nika Mansouri Ghiasi, Can Alkan, Onur Mutlu
Publié dans: Frontiers in Genetics, Numéro 15, 2024, ISSN 1664-8021
Éditeur: Frontiers Media SA
DOI: 10.5281/ZENODO.22941434

Accelerating Genome Analysis via Algorithm-Architecture Co-Design

Auteurs: Onur Mutlu, Can Firtina
Publié dans: Design Automation Conference (DAC) 2023, 2023, ISSN 2331-8422
Éditeur: arXiv
DOI: 10.5281/zenodo.8087173

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

Auteurs: Meven Mognol, Dominique Lavenier, Julien Legriel
Publié dans: 2024
Éditeur: ACM
DOI: 10.1145/3673038.36730

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

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

MARS: Processing-In-Memory Acceleration of Raw Signal Genome Analysis Inside the Storage Subsystem

Auteurs: M. Soysal, K. Koliogeorgi, C. Firtina, N. M. Ghiasi, R. Nadig, H. Mao, G. F. Oliveira Jr, Y. Liang, K. Zambaku, M. Sadrosadati, O. Mutlu
Publié dans: 2025
Éditeur: Association for Computing Machinery
DOI: 10.1145/3721145.373042

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

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

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

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

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

Auteurs: Florestan de Moor, Meven Mognol, Charles Deltel, Erwan Drezen, Julien Legriel, Dominique Lavenier
Publié dans: 2024
Éditeur: 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

Auteurs: Taha Shahroodi, Gagandeep Singh, Mahdi Zahedi, Haiyu Mao, Joel Lindegger, Can Firtina, Stephan Wong, Onur Mutlu, Said Hamdioui
Publié dans: 2023
Éditeur: Association for Computing Machinery
DOI: 10.1145/3613424.3614252

QUETZAL: Vector Acceleration Framework for Modern Genome Sequence Analysis Algorithms

Auteurs: 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
Publié dans: 2024 ACM/IEEE 51st Annual International Symposium on Computer Architecture (ISCA), 2024
Éditeur: IEEE
DOI: 10.1109/ISCA59077.2024.00050

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

Auteurs: 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
Publié dans: 2024
Éditeur: arXiv
DOI: 10.5281/ZENODO.15085962

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

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

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

Auteurs: Zuher Jahshan, Itay Merlin, Esteban GarzÓN, Leonid Yavits
Publié dans: 56th Annual IEEE/ACM International Symposium on Microarchitecture, 2023
Éditeur: ACM
DOI: 10.1145/3613424.3614262

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

Auteurs: Julien Eudine, Mohammed Alser, Gagandeep Singh, Can Alkan, Onur Mutlu
Publié dans: 2023
Éditeur: arXiv
DOI: 10.48550/arXiv.2309.17063

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

Auteurs: Naomie Abecassis, Juan Gómez-Luna, Onur Mutlu, Ran Ginosar, Aphélie Moisson-Franckhauser, Leonid Yavits
Publié dans: 2024
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.07.26.550623

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