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Technische Universität München
Picture of Yonatan Yehezkeally

Yonatan Yehezkeally, Dr.

Technical University of Munich

Associate Professorship of Coding and Cryptography (Prof. Wachter-Zeh)

Postal address

Theresienstr. 90
80333 München

Biography

I received the B.Sc. degree (cum laude) in mathematics and the M.Sc. (summa cum laude) and Ph.D. degrees in electrical and computer engineering from Ben-Gurion University of the Negev (BGU), Beer-Sheva, Israel, in 2013, 2017, and 2020 respectively.

I am currently a senior researcher with the Associate Professorship of Coding and Cryptography (Prof. Wachter-Zeh), School of Computation, Information and Technology, Technical University of Munich (TUM), Munich, Germany. From 2021 to 2024, I was hosted at TUM as a Carl Friedrich von Siemens Post-Doctoral Research Fellow of the Alexander von Humboldt Foundation.

I have studied rank-modulation codes for Flash memories in my master's thesis, which are Gray codes in the symmetric group of finite sets designed to alleviate the read-write imbalance in Flash technology. My doctoral thesis dealt with string-duplication channels, with applications to data storage in DNA (specifically, in vivo DNA data storage).

Research Interests

My research interests center around Coding Theory and algorithms, particularly with applications to nascent storage media. In recent years I've focused on DNA-based data storage, including

  • novel sequencing and synthesis technologies;
  • combined noise models (e.g., substitutions, deletions, insertions, duplications, sliced-information, etc.).

I'm also working on novel coding techniques for memories, such as mixed codes, permutation codes, etc. My interests further include combinatorial analysis and structures in general, as well as algebraic structures.

News

  • Jul. 2024: congratulations to Anisha for winning the ESIT 2024 Best Poster Award for her presentation of our work "Error-Correcting Codes for Nanopore Sequencing."
     
  • Apr. 2024: our manuscript was accepted to ISIT 2024:
    Anisha Banerjee, Yonatan Yehezkeally, Antonia Wachter-Zeh and Eitan Yaakobi, "Correcting a Single Deletion in Reads from a Nanopore Sequencer." (doi pdf)
     
  • Mar. 2024: a new paper in TMBMC Special Issue on DNA-based Data Storage:
    Yonatan Yehezkeally and Nikita Polyanskii, "On Codes for the Noisy Substring Channel." (doi pdf)
     
  • Mar. 2024: a new paper in T-IT:
    Anisha Banerjee, Yonatan Yehezkeally, Antonia Wachter-Zeh and Eitan Yaakobi, "Error-Correcting Codes for Nanopore Sequencing." (doi pdf)
     
  • Nov. 2023: Kick-off of new European-funded project: DiDAX.
     
  • Jun. 2023: a new paper in T-IT:
    Daniella Bar-Lev, Sagi Marcovich, Eitan Yaakobi and Yonatan Yehezkeally, "Adversarial Torn-paper Codes." (doi pdf)

Available Theses

Coding theory for NVMs

Kurzbeschreibung:
Coding problems motivated by properties and asymmetries of NVMs

Beschreibung

Non-volatile memories (NVMs) are electronic data-storage technologies that do not require a continuous power supply to retain data; unlike traditional magnetic or optical media, they do not utilize mechanically movable components and can therefore offer better performance, and allow for three-dimensional scaling of storage devices. Under most realistic workloads, they also offer better energy efficiency.

However, these technologies also feature imbalances in behavior, performance and consequences, between the processes of reading data and writing it. To wit, in memory cells which represent data by the level of held charge (traditionally allowing for representation of several logical levels), the process of charge-injection is a simple and efficient, whereas charge-depletion is both technically complex (requiring the depletion of entire blocks of cells) and destructive, a main driver of cell-degradation over the device's life cycle.

Different coding theoretic approaches have been explored to alleviate this imbalance, including coding schemes that delay charge-depletion cycles [1]--[3], and such that seek to mitigate the effects of defective memory cells once those appear in a device [4], [5].

Theses are available in extending either approach, as well as combining them.

[1] A. Jiang, R. Mateescu, M. Schwartz and J. Bruck, "Rank Modulation for Flash Memories," in IEEE Transactions on Information Theory, vol. 55, no. 6, pp. 2659-2673, June 2009, doi: 10.1109/TIT.2009.2018336.

[2] M. Horovitz and E. Yaakobi, "On the Capacity of Write-Once Memories," in IEEE Transactions on Information Theory, vol. 63, no. 8, pp. 5124-5137, Aug. 2017, doi: 10.1109/TIT.2017.2689034.

[3] M. Horovitz and T. Etzion, "Local Rank Modulation for Flash Memories," in IEEE Transactions on Information Theory, vol. 65, no. 3, pp. 1705-1713, March 2019, doi: 10.1109/TIT.2018.2859403.

[4] V. Sidorenko, G. Schmidt, E. Gabidulin, M. Bossert and V. Afanassiev, "On polyalphabetic block codes," IEEE Information Theory Workshop, 2005., Rotorua, New Zealand, 2005, pp. 4 pp.-, doi: 10.1109/ITW.2005.1531889.

[5] Y. Yehezkeally, H. A. Kim, S. Puchinger and A. Wachter-Zeh, "Bounds on Mixed Codes with Finite Alphabets," 2023 IEEE Information Theory Workshop (ITW), Saint-Malo, France, 2023, pp. 389-394, doi: 10.1109/ITW55543.2023.10161655.

Betreuer:

DNA-based data storage

Kurzbeschreibung:
Coding theoretic problems motivated by DNA-based stroage

Beschreibung

Contemporary global demand for storage capacity is increasing exponentially, even as traditional magnetic storage media has exhausted its potential for optimization, and requires unsustainable investments for both production and maintenance, in capital, energy and space.

One promising potential medium for archival data storage is DNA; it features high density, extreme longevity, convenient scalability and a lower maintenance footprint. Complete DNA-based storage ecosystems are in active development, raising multiple coding theoretic (as well as engineering, algorithmic, and biotechnological) challenges; correspondingly, increasing attention is recently given to the study of such systems, and they are drawing significant investments from both governments
and the private sector.

The following theses are available (other topics in this domain will also be entertained):

  • The torn paper channel models the effects of DNA strand breakage in storage or processing. It has been studied from both an average-case and a worst-case [1] perspective, with several distinct adversarial models. Recently, the t-break model was studied [2] as a refinement of the previously studied min-max constraint. These developments open the way to study new problems in this setting.
  • Reconstruction from substring spectra is a model motivated by the process of shot-gun sequencing, where short strands are drawn sufficiently many times to reconstruct a long information sequence. Adapting existing literature [3,4] to more realistic models is an open problem.
  • Nanopore sequencing is a nascent technology that reads single-stranded DNA molecules by passing them through a narrow pore while passing electric current through it. More work studying its properties and designing codes capable of handling its relatively high error rate, extending existing literature [5,6], is necessary.
  • Duplications are a type of mutation occurring in the process of cell replication, which may be responsible for large portions of our current genome. For data storage schemes in in vivo DNA (e.g., for watermarking research material) it is an error model that needs to be countered. We aim to extend and build upon existing literature [7,8].



[1] D. Bar-Lev, S. Marcovich, E. Yaakobi and Y. Yehezkeally, "Adversarial Torn-Paper Codes," in IEEE Transactions on Information Theory, vol. 69, no. 10, pp. 6414-6427, Oct. 2023, doi: 10.1109/TIT.2023.3292895.

[2] C. Wang, J. Sima and N. Raviv, "Break-Resilient Codes for Forensic 3D Fingerprinting," arXiv preprint arXiv:2310.03897v1 [cs.IT], Oct. 2023, doi: https://doi.org/10.48550/arXiv.2310.03897.

[3] Y. Yehezkeally, D. Bar-Lev, S. Marcovich and E. Yaakobi, "Generalized Unique Reconstruction From Substrings," in IEEE Transactions on Information Theory, vol. 69, no. 9, pp. 5648-5659, Sept. 2023, doi: 10.1109/TIT.2023.3269124.

[4] H. Wei, M. Schwartz, G. Ge, "Reconstruction from Noisy Substrings," arXiv preprint arXiv:2312.04790v1 [cs.IT], Dec. 2023, doi: 10.48550/arXiv.2312.04790.

[5] A. Banerjee, Y. Yehezkeally, A. Wachter-Zeh and E. Yaakobi, "Error-Correcting Codes for Nanopore Sequencing," in IEEE Transactions on Information Theory, doi: 10.1109/TIT.2024.3380615.

[6] A. Banerjee, Y. Yehezkeally, A. Wachter-Zeh and E. Yaakobi, "Correcting a Single Deletion in Reads from a Nanopore Sequencer," arXiv preprint arXiv:2401.15939v2 [cs.IT], May. 2024, doi: 10.48550/arXiv.2401.15939.

[7] S. Jain, F. Farnoud Hassanzadeh, M. Schwartz and J. Bruck, "Duplication-Correcting Codes for Data Storage in the DNA of Living Organisms," in IEEE Transactions on Information Theory, vol. 63, no. 8, pp. 4996-5010, Aug. 2017, doi: 10.1109/TIT.2017.2688361.

[8] D. Goshkoder, N. Polyanskii and I. Vorobyev, "Codes Correcting Long Duplication Errors," in IEEE Transactions on Molecular, Biological, and Multi-Scale Communications, doi: 10.1109/TMBMC.2024.3403755.

Betreuer:

Theses in Progress

Fault Tolerance in Local Rank Modulation

Stichworte:
nvm; flash memory; ECC; error-correcting codes; rank modulation
Kurzbeschreibung:
This project studies the rate of error-detecting local rank modulation codes

Beschreibung

Non-volatile memories (NVMs) are electronic data-storage technologies that do not require a continuous power supply to retain data; unlike traditional magnetic or optical media, they do not utilize mechanically movable components and can therefore offer better performance, and allow for three-dimensional scaling of storage devices. Under most realistic workloads, they also offer better energy efficiency.

However, these technologies also feature imbalances in behavior, performance and consequences, between the processes of reading data and writing it. To wit, in memory cells which represent data by the level of held charge (traditionally allowing for representation of several logical levels), the process of charge-injection is a simple and efficient, whereas charge-depletion is both technically complex (requiring the depletion of entire blocks of cells) and destructive, a main driver of cell-degradation over the device's life cycle.

Different coding theoretic approaches have been explored to alleviate this imbalance, including coding schemes that delay charge-depletion cycles [1], [2]. This project will build on the work done in [2], by calculating the asymptotic behavior of the number of realizable permutation sequences, when those are restricted to belong to a single Kendall-tau error-detecting code. Possible extensions will be general error-correction capabilities, as well as general window-lengths.

 

[1] A. Jiang, R. Mateescu, M. Schwartz and J. Bruck, "Rank Modulation for Flash Memories," in IEEE Transactions on Information Theory, vol. 55, no. 6, pp. 2659-2673, June 2009, doi: 10.1109/TIT.2009.2018336.

[2] M. Horovitz and T. Etzion, "Local Rank Modulation for Flash Memories," in IEEE Transactions on Information Theory, vol. 65, no. 3, pp. 1705-1713, March 2019, doi: 10.1109/TIT.2018.2859403.

Betreuer:

Publications

Journal Publications

[9] Anisha Banerjee, Yonatan Yehezkeally, Antonia Wachter-Zeh and Eitan Yaakobi, "Error-Correcting Codes for Nanopore Sequencing," IEEE Trans. Inf. Theory, 70(7), pp. 4956-4967, July 2024. (doi pdf)

[8] Yonatan Yehezkeally and Nikita Polyanskii, "On Codes for the Noisy Substring Channel," IEEE Trans. Mole., Bio., a. Mult. Comm., Special Issue on DNA-Based Data Storage, 10(2), pp. 368-381, June 2024. (doi pdf)

[7] Daniella Bar-Lev, Sagi Marcovich, Eitan Yaakobi and Yonatan Yehezkeally, "Adversarial Torn-paper Codes," IEEE Trans. Inf. Theory, 69(10), pp. 6414-6427, October 2023. (doi pdf)

[6] Yonatan Yehezkeally, Daniella Bar-Lev, Sagi Marcovich and Eitan Yaakobi, "Generalized Unique Reconstruction from Substrings," IEEE Trans. Inf. Theory, 69(9), pp. 5648-5659, September 2023. (doi pdf)

[5] Yonatan Yehezkeally and Moshe Schwartz, "Uncertainty of reconstruction with list-decoding from uniform-tandem-duplication noise," IEEE Trans. Inf. Theory, 67(7), pp. 4276-4287, July 2021. (doi pdf)

[4] Yuanyuan Tang, Yonatan Yehezkeally, Moshe Schwartz, and Farzad Farnoud, "Single-error detection and correction for duplication and substitution channels," IEEE Trans. Inf. Theory, 66(11), pp. 6908-6919, November 2020. (doi pdf)

[3] Yonatan Yehezkeally and Moshe Schwartz, "Reconstruction codes for DNA sequences with uniform tandem-duplication errors," IEEE Trans. Inf. Theory, 66(5), pp. 2658-2668, May 2020. (doi pdf)

[2] Yonatan Yehezkeally and Moshe Schwartz, "Limited-magnitude error-correcting Gray codes for rank modulation," IEEE Trans. Inf. Theory, 63(9), pp. 5774-5792, September 2017. (doi pdf)

[1] Yonatan Yehezkeally and Moshe Schwartz, "Snake-in-the-box codes for rank modulation," IEEE Trans. Inf. Theory, 58(8), pp. 5471-5483, August 2012. (doi pdf)

Conference Publications

[12] Anisha Banerjee, Yonatan Yehezkeally, Antonia Wachter-Zeh and Eitan Yaakobi, "Correcting a Single Deletion in Reads from a Nanopore Sequencer," in Proc. of the 2024 IEEE International Symposium on Information Theory (ISIT), Athens, Greece, July 2024, pp.103-108. (doi pdf)

[11] Anisha Banerjee, Yonatan Yehezkeally, Antonia Wachter-Zeh and Eitan Yaakobi, "Error-Correcting Codes for Nanopore Sequencing," in Proc. of the 2023 IEEE International Symposium on Information Theory (ISIT), Taipei, Taiwan, June 2023, pp. 364-369. (doi pdf)

[10] Yonatan Yehezkeally, Haider Al Kim, Sven Puchinger and Antonia Wachter-Zeh, "Bounds on Mixed Codes with Finite Alphabets," in Proc. of the 2023 IEEE Information Theory Workshop (ITW), St. Malo, France, April 2023, pp.389-394. (doi pdf)

[9] Yonatan Yehezkeally, Daniella Bar-Lev, Sagi Marcovich and Eitan Yaakobi, "Reconstruction from Substrings with Partial Overlap," in Proc. of the 2022 International Symposium on Information Theory and Its Applications (ISITA), Tsukuba, Japan, October 2022, pp. 113-117. (pdf)

[8] Daniella Bar-Lev, Sagi Marcovich, Eitan Yaakobi and Yonatan Yehezkeally, "Adversarial Torn-Paper Codes," in Proc. of the 2022 IEEE International Symposium on Information Theory (ISIT), Espoo, Finland, July 2022, pp. 2934-2939. (doi pdf)

[7] Yonatan Yehezkeally, Sagi Marcovich and Eitan Yaakobi, "Multi-strand Reconstruction from Substrings," in Proc. of the 2021 IEEE Information Theory Workshop (ITW), Kanazawa, Japan (held virtually), October 2021. (doi pdf)

[6] Yonatan Yehezkeally and Nikita Polyanskii, "On Codes for the Noisy Substring Channel," in Proc. of the 2021 IEEE International Symposium on Information Theory (ISIT), Melbourne, Victoria, Australia (held virtually), July 2021, pp. 1700-1705. (doi pdf)

[5] Yonatan Yehezkeally and Moshe Schwartz, "Uncertainty of Reconstructing Multiple Messages from Uniform-Tandem-Duplication Noise," in Proc. of the 2020 IEEE International Symposium on Information Theory (ISIT), Los Angeles, CA, USA (held virtually), June 2020, pp. 126-131. (doi pdf)

[4] Yuanyuan Tang, Yonatan Yehezkeally, Moshe Schwartz, and Farzad Farnoud (Hassanzadeh), "Single-error detection and correction for duplication and substitution channels," in Proc. of the 2019 IEEE International Symposium on Information Theory (ISIT), Paris, France, July 2019, pp. 300-304. (doi pdf)

[3] Yonatan Yehezkeally and Moshe Schwartz, "Reconstruction codes for DNA sequences with uniform tandem-duplication errors," in Proc. of the 2018 IEEE International Symposium on Information Theory (ISIT), Vail, CO, U.S.A., June 2018, pp. 2535-2539. (doi pdf)

[2] Yonatan Yehezkeally and Moshe Schwartz, "Limited-magnitude error-correcting Gray codes for rank modulation," in Proc. of the 2016 IEEE International Symposium on Information Theory (ISIT), Barcelona, Spain, July 2016, pp. 2829-2833. (doi pdf)

[1] Yonatan Yehezkeally and Moshe Schwartz, "Snake-in-the-box codes for rank modulation," in Proc. of the 2012 IEEE International Symposium on Information Theory (ISIT), Boston, MA, U.S.A., July 2012, pp. 2993-2997. (doi pdf)

Theses

[2] Yonatan Yehezkeally, "Coding for duplicatoin channels with application to DNA storage," Ben-Gurion University of the Negev, Beer-Sheva, Israel, Jun. 2020. (permalink pdf)

[1] Yonatan Yehezkeally, "Snake-in-the-box codes for rank modulation," Ben-Gurion University of the Negev, Beer-Sheva, Israel, Jun. 2016. (permalink pdf)

Invited talks

[6] "DNA-bases Storage Systems: Coding Theory and Algorithms," School of Computing, Newcastle University, Newcastle, UK, Oct. 17, 2024.

[5] "Coding-theoretic Challenges for DNA-based Storage/Communication Systems," 6G-life Workshop on Molecular Communications, Munich, Germany, Jul. 21, 2023.

[4] "Resilient Repeat-free Codes," Coding Theory Seminar, the Taub Faculty of Computer Science, Technion---Israel Institute of Technology, Haifa, Israel, Jun. 18, 2023.

[3] "Between reconstruction and list decoding: the associative memory model for uniform tandem-duplication noise," Applied Information Theory group, Skoltech (Skolkovo Institute of Science and Technology), Moscow, Russia (held virtually), Dec. 14, 2020.

[2] "Coding for Duplication Channels with Applications to DNA data Storage," Institute for Communications Engineering, Technical University of Munich, Munich, Germany, Feb. 11, 2020.

[1] "Coding for Duplication Channels with Applications to DNA data Storage," School of Electrical Engineering - Systems, Tel-Aviv University, Tel-Aviv, Israel, Jan. 16, 2020.

Services to community

Organizer

  • Future Dagstuhl Seminar (24511): "Coding Theory and Algorithms for Emerging Technologies in Synthetic Biology."

Technical Program Committee Member

  • 2024 International Symposium on Information Theory and Its Applications (ISITA), Taiwan, Taipei.

Session chair

  • 2022 IEEE International Symposium on Information Theory
  • 2022 Munich Workshop on Coding and Cryptography

Reviewer, Foundations

  • Israel Science Foundation (ISF)

Reviewer, Journals

  • Nature Comput. Sci. (2024)
  • IEEE Trans. on Comm. (2024)
  • IEEE Trans. on Inform. Theory (2015-2024)
  • Cryptography and Communications (2023-2024)
  • J. Combin. Theory Ser. A (2023-2024)
  • IEEE Trans. Mol., Bio. and Multi-Scale Commun (2024)
  • IEEE J. on Selec. Areas in Inform. Theory (2023)
  • Disc. Math. (2023)
  • Designs, Codes and Cryptography (2019-2021)

Reviewer, Conferences

  • IEEE International Symposium on Information Theory (ISIT): 9 years (2012--2024)
  • IEEE Information Theory Workshop (ITW): 3 years (2019--2022)
  • IEEE International Symposium on Topics in Coding (ISTC): 1 year (2021)
  • International Symposium on Information Theory and Its Applications (ISITA): 1 year (2020)

Teaching

Lecturer

  • Digital Systems (at BGU; mandatory module for Bachelor students), Winters 2018/19,2019/20.
  • Calculus 1 (at BGU; prep. module for Bachelor students), Summer 2017

Honors and awards

2020

Awarded a Carl Friedrich von Siemens Research Fellowship of the Alexander von Humboldt Foundation for postdoctoral researchers.
2020

Awarded a Minerva Fellowship for a research residency at TU Munich, EI, LNT (host: Prof. Antonia Wachter-Zeh) from the Minerva Stiftung. (Declined due to conflict with Humboldt Research Fellowship.)
2020

Received the Dr. Max Fogiel and Helen J. Kaufmann Award for Highest Student Achievment in Electrical Engineering, from the School of Electrical and Computer Engineering, Ben-Gurion University of the Negev.
2017

Awarded a Negev-Faran scholarship from the Kreitman School of Advanced Graduate Studies, Ben-Gurion University of the Negev.
2008

Winner of the Intel Prize (Israel) for excellent B.Sc. students in relevant fields of study.

 

Work Experience

19.10.2020-
current		 Senior Researcher
Institute for Communications Engineering, School of Computation, Information and Technology
Technical University of Munich
01.04.2021-
31.03.2024		 Carl Friedrich von Siemens Postdoctoral Research Fellow of the Alexander von Humboldt Foundation
Institute for Communications Engineering, School of Computation, Information and Technology
Technical University of Munich

01.07.2020-
30.09.2020

 Postdoctoral researcher
School of Electrical and Computer Engineering
Ben-Gurion University of the Negev
01.10.2018-
31.08.2020		 Lecturer and Teaching Assistant
School of Electrical and Computer Engineering
Ben-Gurion University of the Negev
01.10.2011-
30.09.2018		 Teaching Assistant
Department of Mathematics
Ben-Gurion University of the Negev
2001-2006 Officer (mandatory service)
Israeli Defense Forces

 

Education

2016-2020 Ph.D. in Electrical and Computer Engineering
Ben-Gurion University of the Negev
Supervisor: Prof. Moshe Schwartz
Thesis: "Coding for Duplication Channels with Applications to DNA Storage"
2014-2017 M.Sc. (summa cum laude) in Electrical and Computer Engineering
Ben-Gurion University of the Negev
Supervisor: Prof. Moshe Schwartz
Thesis: "Snake-in-the-Box Codes for Rank Modulation"
2006-2013 B.Sc. (cum laude) in Mathematics
Ben-Gurion University of the Negev

 

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