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The Epigenetic Consensus Problem

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Structural Information and Communication Complexity (SIROCCO 2021)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 12810))

Abstract

A distributed computing system is a collection of processors that communicate either by reading and writing from shared memory or by sending messages over some communication network. Most prior biologically inspired distributed computing algorithms rely on message passing as the communication model. Here we show that in the process of genome-wide epigenetic modifications, cells utilize their DNA as a shared memory system. We formulate a particular consensus problem, called the epigenetic consensus problem, that cells attempt to solve using this shared memory model and then present algorithms, derive expected run time and discuss, analyze and simulate improved methods for solving this problem. Analysis of real biological data indicates that the computational methods indeed reflect aspects of the biological process for genome-wide epigenetic modifications.

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Notes

  1. 1.

    In particular, a processor does not have to remember the address (name) of the last memory location it has accessed which will require log N bits of local memory. It only needs to remember one bit which represents the direction in which it is moving. (Recall, that we have assumed that each processor has two bits of local memory.).

  2. 2.

    An agreement on 0 (resp. 1) may correspond to an instruction to deactivate (resp. activate) a specific gene.

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Author information

Authors and Affiliations

  1. Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA

    Sabrina Rashid

  2. The Interdisciplinary Center, Herzliya, Israel

    Gadi Taubenfeld

  3. Machine Learning Department and Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA

    Ziv Bar-Joseph

Authors
  1. Sabrina Rashid
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  2. Gadi Taubenfeld
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  3. Ziv Bar-Joseph
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Corresponding author

Correspondence to Gadi Taubenfeld .

Editor information

Editors and Affiliations

  1. Institute of Computer Science, University of Wrocław, Wroclaw, Poland

    Tomasz Jurdziński

  2. University of Vienna, Vienna, Austria

    Stefan Schmid

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Rashid, S., Taubenfeld, G., Bar-Joseph, Z. (2021). The Epigenetic Consensus Problem. In: Jurdziński, T., Schmid, S. (eds) Structural Information and Communication Complexity. SIROCCO 2021. Lecture Notes in Computer Science(), vol 12810. Springer, Cham. https://doi.org/10.1007/978-3-030-79527-6_9

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  • DOI: https://doi.org/10.1007/978-3-030-79527-6_9

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  • Print ISBN: 978-3-030-79526-9

  • Online ISBN: 978-3-030-79527-6

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