Mathematical Modeling of the Diversity in Human B and T Cell Receptors using Machine Learning

Susanne Schaller, Johannes Weinberger, Martin Danzer, Christian Gabriel, Rainer Oberbauer, Stephan Winkler

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

3 Citations (Scopus)

Abstract

We here propose an empirical approach based on the analysis of next-generation sequencing (NGS) data for describing the number of distinct clones of B and T-cell receptors in the human immune system. The status of a human immune system is (amongst other features) defined by the diversity of these receptor cells. It is a well-known issue that NGS data have a higher error rate, and therefore the number of distinct sequences found in sequencing data rises with the number of sequences measured by second generation sequencers. We here present a modeling approach that formulates the number of distinct clones depending on the number of read sequences considering two effects. On the one hand there is a true number of distinct sequences which is asymptotically reached by increasing the number of reads, on the other hand the number of randomly found sequences rises linearly due to read errors. The parameters for this combined model are identified using parameter optimization methods using evolution strategies. This modeling approach is evaluated on the basis of immune status data of several human patients. Additionally, the results are compared to those produced by machine learning methods.

Original languageEnglish
Title of host publication26th European Modeling and Simulation Symposium, EMSS 2014
EditorsYuri Merkuryev, Lin Zhang, Emilio Jimenez, Francesco Longo, Michael Affenzeller, Agostino G. Bruzzone
PublisherDIPTEM University of Genova
Pages164-170
Number of pages7
ISBN (Electronic)9788897999324
ISBN (Print)978-88-97999-38-6
Publication statusPublished - 2014
EventThe 26th European Modeling & Simulation Symposium EMSS 2014 - Bordeaux, France
Duration: 10 Sept 201412 Sept 2014
http://www.msc-les.org/conf/emss2014/index.htm

Publication series

Name26th European Modeling and Simulation Symposium, EMSS 2014

Conference

ConferenceThe 26th European Modeling & Simulation Symposium EMSS 2014
Country/TerritoryFrance
CityBordeaux
Period10.09.201412.09.2014
Internet address

Keywords

  • B and T cell diversity analysis
  • Data mining
  • Immune system
  • Model identification
  • Parameter identification

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