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

CORDIS oferuje możliwość skorzystania z odnośników do publicznie dostępnych publikacji i rezultatów projektów realizowanych w ramach programów ramowych HORYZONT.

Odnośniki do rezultatów i publikacji związanych z poszczególnymi projektami 7PR, a także odnośniki do niektórych konkretnych kategorii wyników, takich jak zbiory danych i oprogramowanie, są dynamicznie pobierane z systemu OpenAIRE .

Rezultaty

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

Publikacje

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

Autorzy: Zuher Jahshan, Esteban Garzón, Leonid Yavits
Opublikowane w: IEEE Access, Numer 12, 2024, ISSN 2169-3536
Wydawca: Institute of Electrical and Electronics Engineers (IEEE)
DOI: 10.1109/access.2024.3367801

Designing Precharge-Free Energy-Efficient Content-Addressable Memories

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

OCCAM: An Error Oblivious CAM

Autorzy: Yuval Harary; Paz Snapir; Eyal Reshef; Esteban Garzón; Leonid Yavits
Opublikowane w: IEEE Solid-State Circuits Letters, 2024, ISSN 2573-9603
Wydawca: IEEE
DOI: 10.1109/lssc.2024.3362891

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

Autorzy: Safaa Diab, Amir Nassereldine, Mohammed Alser, Juan Gómez Luna, Onur Mutlu, Izzat El Hajj
Opublikowane w: Bioinformatics, Numer 39, 2023, ISSN 1367-4811
Wydawca: Oxford University Press (OUP)
DOI: 10.1093/bioinformatics/btad155

Processing-in-Memory for Genomics Workloads

Autorzy: 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
Opublikowane w: IEEE Micro, Numer 46, 2026, ISSN 0272-1732
Wydawca: Institute of Electrical and Electronics Engineers (IEEE)
DOI: 10.5281/ZENODO.22941196

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

Autorzy: Z. Jahshan, L. Yavits
Opublikowane w: IEEE Computer Architecture Letters, Numer 23, 2024, ISSN 1556-6056
Wydawca: 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

Autorzy: Esteban Garzón, Leonid Yavits, Giovanni Finocchio, Mario Carpentieri, Adam Teman, Marco Lanuzza
Opublikowane w: IEEE Access, Numer 11, 2024, ISSN 2169-3536
Wydawca: Institute of Electrical and Electronics Engineers (IEEE)
DOI: 10.1109/ACCESS.2023.3245981

DRAMA: Commodity DRAM Based Content Addressable Memory

Autorzy: L. Yavits
Opublikowane w: IEEE Computer Architecture Letters, Numer 23, 2024, ISSN 1556-6056
Wydawca: 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

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

Approximate Content-Addressable Memories: A Review

Autorzy: Esteban Garzón, Leonid Yavits, Adam Teman, Marco Lanuzza
Opublikowane w: Chips, Numer 2, 2025, ISSN 2674-0729
Wydawca: MDPI AG
DOI: 10.3390/chips2020005

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

Autorzy: Joël Lindegger, Can Firtina, Nika Mansouri Ghiasi, Mohammad Sadrosadati, Mohammed Alser, Onur Mutlu
Opublikowane w: arXiv, 2023, ISSN 2331-8422
Wydawca: arXiv
DOI: 10.5281/ZENODO.15086073

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

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

Constructing and personalizing population pangenome graphs

Autorzy: Rayan Chikhi, Yoann Dufresne, Paul Medvedev
Opublikowane w: Nature Methods, Numer 21, 2024, ISSN 1548-7091
Wydawca: Springer Science and Business Media LLC
DOI: 10.5281/ZENODO.15086177

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

Autorzy: Itay Merlin, Esteban Garzón, Alexander Fish, Leonid Yavits
Opublikowane w: IEEE Transactions on Computers, Numer 73, 2024, ISSN 0018-9340
Wydawca: 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

Autorzy: 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
Opublikowane w: ACM Transactions on Architecture and Code Optimization, 2024, ISSN 1544-3973
Wydawca: Association for Computing Machinery
DOI: 10.3929/ethz-b-000663170

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

Autorzy: Leonid Yavits
Opublikowane w: Memories - Materials, Devices, Circuits and Systems, Numer 4, 2024, ISSN 2773-0646
Wydawca: Elsevier BV
DOI: 10.1016/j.memori.2023.100033

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

Autorzy: Can Firtina, Melina Soysal, Joël Lindegger, Onur Mutlu
Opublikowane w: Bioinformatics, Numer 40, 2024, ISSN 1367-4811
Wydawca: Oxford University Press (OUP)
DOI: 10.1093/BIOINFORMATICS/BTAE478

LCPan: efficient variation graph construction using locally consistent parsing

Autorzy: Akmuhammet Ashyralyyev, Zülal Bingöl, Begüm Filiz Öz, Kaiyuan Zhu, Salem Malikic, Uzi Vishkin, S. Cenk Sahinalp, Can Alkan
Opublikowane w: Genome Biology, Numer 27, 2026, ISSN 1474-760X
Wydawca: 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

Autorzy: Zülal Bingöl, Berkan Şahin, Klea Zambaku, Ricardo Roman-Brenes, Konstantina Koliogeorgi, Can Firtina, Onur Mutlu, Can Alkan
Opublikowane w: Briefings in Bioinformatics, Numer 27, 2026, ISSN 1467-5463
Wydawca: Oxford University Press (OUP)
DOI: 10.5281/ZENODO.22941530

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

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

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

Autorzy: Esteban Garzón, Alessandro Bedoya, Marco Lanuzza, Leonid Yavits
Opublikowane w: IEEE Journal on Exploratory Solid-State Computational Devices and Circuits, Numer 10, 2025, ISSN 2329-9231
Wydawca: 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

Autorzy: William Andrew Simon, Irem Boybat, Riselda Kodra, Elena Ferro, Gagandeep Singh, Mohammed Alser, Shubham Jain, Hsinyu Tsai, Geoffrey W. Burr, Onur Mutlu, Abu Sebastian
Opublikowane w: IEEE Transactions on Parallel and Distributed Systems, Numer 36, 2025, ISSN 1045-9219
Wydawca: 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

Autorzy: Luca Denti, Parsoa Khorsand, Paola Bonizzoni, Fereydoun Hormozdiari, Rayan Chikhi
Opublikowane w: Nature Methods, Numer 20, 2023, ISSN 1548-7091
Wydawca: 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

Autorzy: Esteban Garzón; Marco Lanuzza; Adam Teman; Leonid Yavits
Opublikowane w: IEEE Journal on Emerging and Selected Topics in Circuits and Systems, Numer 1, 2023, ISSN 2156-3365
Wydawca: IEEE
DOI: 10.5281/zenodo.8087076

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

Autorzy: Zuher Jahshan; Leonid Yavits
Opublikowane w: Bioinformatics, 2024, ISSN 1367-4811
Wydawca: Bioinformatics
DOI: 10.1093/bioinformatics/btae093

FASTA: Revisiting Fully Associative Memories in Computer Microarchitecture

Autorzy: Esteban Garzón, Robert Hanhan, Marco Lanuzza, Adam Teman, Leonid Yavits
Opublikowane w: IEEE Access, Numer 12, 2024, ISSN 2169-3536
Wydawca: Institute of Electrical and Electronics Engineers (IEEE)
DOI: 10.1109/access.2024.3355961

ClaPIM: Scalable Sequence Classification Using Processing-in-Memory

Autorzy: Marcel Khalifa, Barak Hoffer, Orian Leitersdorf, Robert Hanhan, Ben Perach, Leonid Yavits, Shahar Kvatinsky
Opublikowane w: IEEE Transactions on Very Large Scale Integration (VLSI) Systems, Numer 31, 2023, ISSN 1063-8210
Wydawca: 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

Autorzy: Can Firtina, Nika Mansouri Ghiasi, Joel Lindegger, Gagandeep Singh, Meryem Banu Cavlak, Haiyu Mao, Onur Mutlu
Opublikowane w: Bioinformatics, Numer 39, 2023, ISSN 1367-4803
Wydawca: Oxford University Press (OUP)
DOI: 10.1093/bioinformatics/btad272

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

Autorzy: Meryem Banu Cavlak, Gagandeep Singh, Mohammed Alser, Can Firtina, Joël Lindegger, Mohammad Sadrosadati, Nika Mansouri Ghiasi, Can Alkan, Onur Mutlu
Opublikowane w: Frontiers in Genetics, Numer 15, 2024, ISSN 1664-8021
Wydawca: Frontiers Media SA
DOI: 10.5281/ZENODO.22941434

Accelerating Genome Analysis via Algorithm-Architecture Co-Design

Autorzy: Onur Mutlu, Can Firtina
Opublikowane w: Design Automation Conference (DAC) 2023, 2023, ISSN 2331-8422
Wydawca: arXiv
DOI: 10.5281/zenodo.8087173

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

Autorzy: Meven Mognol, Dominique Lavenier, Julien Legriel
Opublikowane w: 2024
Wydawca: ACM
DOI: 10.1145/3673038.36730

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

Autorzy: Yann Falevoz, Julien Legriel
Opublikowane w: Lecture Notes in Computer Science, Euro-Par 2023: Parallel Processing Workshops, 2024
Wydawca: 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

Autorzy: 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
Opublikowane w: 2025
Wydawca: Association for Computing Machinery
DOI: 10.1145/3721145.373042

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

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

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

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

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

Autorzy: Florestan de Moor, Meven Mognol, Charles Deltel, Erwan Drezen, Julien Legriel, Dominique Lavenier
Opublikowane w: 2024
Wydawca: 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

Autorzy: Taha Shahroodi, Gagandeep Singh, Mahdi Zahedi, Haiyu Mao, Joel Lindegger, Can Firtina, Stephan Wong, Onur Mutlu, Said Hamdioui
Opublikowane w: 2023
Wydawca: Association for Computing Machinery
DOI: 10.1145/3613424.3614252

QUETZAL: Vector Acceleration Framework for Modern Genome Sequence Analysis Algorithms

Autorzy: 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
Opublikowane w: 2024 ACM/IEEE 51st Annual International Symposium on Computer Architecture (ISCA), 2024
Wydawca: IEEE
DOI: 10.1109/ISCA59077.2024.00050

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

Autorzy: 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
Opublikowane w: 2024
Wydawca: arXiv
DOI: 10.5281/ZENODO.15085962

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

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

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

Autorzy: Zuher Jahshan, Itay Merlin, Esteban GarzÓN, Leonid Yavits
Opublikowane w: 56th Annual IEEE/ACM International Symposium on Microarchitecture, 2023
Wydawca: ACM
DOI: 10.1145/3613424.3614262

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

Autorzy: Julien Eudine, Mohammed Alser, Gagandeep Singh, Can Alkan, Onur Mutlu
Opublikowane w: 2023
Wydawca: arXiv
DOI: 10.48550/arXiv.2309.17063

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

Autorzy: Naomie Abecassis, Juan Gómez-Luna, Onur Mutlu, Ran Ginosar, Aphélie Moisson-Franckhauser, Leonid Yavits
Opublikowane w: 2024
Wydawca: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.07.26.550623

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