Representing and reasoning about signal networks: An illustration using NFκB dependent signaling pathways

Chitta Baral, K. Chancellor, N. Tran, N. Tran

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

Abstract

We propose a formal language to represent and reason about signal transduction networks. The existing approaches such as ones based on Petri nets, and π-calculus fall short in many ways and our work suggests that an artificial intelligence (AI) based approach may be well suited for many aspects. We apply a form of action language to represent and reason about NFκB dependent signaling pathways. Our language supports several essential features of reasoning with signal transduction knowledge, such as: reasoning with partial (or incomplete) knowledge, and reasoning about triggered evolutions of the world and elaboration tolerance. Because of its growing important role in cellular functions, we select NFκB dependent signaling to be our test bed. NFκB is a central mediator of the immune response, and it can regulate stress responses, as well as cell death/survival in several cell types. While many extracellular signals may lead to the activation of NFκB, few related pathways are elucidated. We study the tasks of representation of pathways, reasoning with pathways, explaining observations, and planning to alter the outcomes; and show that all of them can be well formulated in our framework. Thus our work shows that our AI based approach is a good candidate for feasible and practical representation of and reasoning about signal networks.

Original languageEnglish (US)
Title of host publicationProceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages623-628
Number of pages6
ISBN (Electronic)0769520006, 9780769520001
DOIs
StatePublished - Jan 1 2003
Event2nd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003 - Stanford, United States
Duration: Aug 11 2003Aug 14 2003

Publication series

NameProceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003

Other

Other2nd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003
CountryUnited States
CityStanford
Period8/11/038/14/03

ASJC Scopus subject areas

  • Electrical and Electronic Engineering
  • Computer Science Applications

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    Baral, C., Chancellor, K., Tran, N., & Tran, N. (2003). Representing and reasoning about signal networks: An illustration using NFκB dependent signaling pathways. In Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003 (pp. 623-628). [1227427] (Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/CSB.2003.1227427