Extending the evolvability model to the prokaryotic world: Simulations and results on real data

Sagi Snir, Ben Yohay

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review


In 2006, Valiant introduced a variation to his celebrated PAC model to Biology, by which he wished to explain how such complex life mechanisms evolved in that short time by two simple mechanisms - random variation and natural selection. Soon after, several works extended and specialized his work to more specific processes. To the best of our knowledge, there is no such extension to the prokaryotic world, in which gene sharing is the prevailing mode of evolution. Here we extend the evolvability framework to accommodate horizontal gene transfer (HGT), the transfer of genetic material between unrelated organisms. While in a separate work we focused on the theoretical aspects of this extension and its learnability power, here the focus is on more practical and biological facets of this new model. Specifically, we focus on the evolutionary process of developing a trait and model it as the conjunction function. We demonstrate the speedup in learning time for a variant of conjunction to which learning algorithms are known. We also confront the new model with the recombination model on real data of E. coli strains under the task of developing pathogenicity and obtain results adhering to current existing knowledge. Apart from the sheer extension to the understudied prokaryotic world, our work offers comparisons of three different models of evolution under the same conditions, which we believe is unique and of a separate interest. The code of the simulations is freely available at: https://github.com/byohay/LearningModels.git.

Original languageEnglish
Title of host publicationBioinformatics Research and Applications - 14th International Symposium, ISBRA 2018, Proceedings
EditorsFa Zhang, Shihua Zhang, Zhipeng Cai, Pavel Skums
PublisherSpringer Verlag
Number of pages15
ISBN (Print)9783319949673
StatePublished - 2018
Event14th International Symposium on Bioinformatics Research and Applications, ISBRA 2018 - Beijing, China
Duration: 8 Jun 201811 Jun 2018

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume10847 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349


Conference14th International Symposium on Bioinformatics Research and Applications, ISBRA 2018

Bibliographical note

Publisher Copyright:
© Springer International Publishing AG, part of Springer Nature 2018.


  • E. coli
  • Evolvability
  • Horizontal gene transfer
  • PAC learning
  • Prokaryotic evolution

ASJC Scopus subject areas

  • Theoretical Computer Science
  • General Computer Science


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