A finite model theory for biological hypotheses

Stephen Racunas, Christopher Griffin, Nigam Shah

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

5 Citations (Scopus)

Abstract

We have designed and implemented a set of software tools for the composition and evaluation of hypotheses about gene regulation in biological systems. Our software uses a unified formal grammar for the representation of both diagram-based and text-based hypotheses. The objective of this paper is to show how to use this grammar as the basis for an effective logic for specifying hypotheses about biological systems in precise model-theoretic terms. To accomplish this, we take inspiration from inflationary extensions to fixed point logics and define a new type of logic: a deflationary logic for describing the effects of experiments upon models of biological systems. We present results that characterize decidability, satisfiability, and inflationary/deflationary properties of this logic. We formally define what it means for a set of assertions to be discoverable under this new logic, and show that our software generates discoverable queries. Thus, we lay the groundwork for a formal treatment of machine-aided experimental design under the conceptual framework we have developed for our hypothesis evaluation software.

Original languageEnglish (US)
Title of host publicationProceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004
Pages616-620
Number of pages5
StatePublished - Dec 1 2004
EventProceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004 - Stanford, CA, United States
Duration: Aug 16 2004Aug 19 2004

Publication series

NameProceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004

Conference

ConferenceProceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004
CountryUnited States
CityStanford, CA
Period8/16/048/19/04

Fingerprint

Biological systems
Computability and decidability
Gene expression
Design of experiments
Chemical analysis
Experiments

All Science Journal Classification (ASJC) codes

  • Engineering(all)

Cite this

Racunas, S., Griffin, C., & Shah, N. (2004). A finite model theory for biological hypotheses. In Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004 (pp. 616-620). (Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004).
Racunas, Stephen ; Griffin, Christopher ; Shah, Nigam. / A finite model theory for biological hypotheses. Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004. 2004. pp. 616-620 (Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004).
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Racunas, S, Griffin, C & Shah, N 2004, A finite model theory for biological hypotheses. in Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004. Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004, pp. 616-620, Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004, Stanford, CA, United States, 8/16/04.

A finite model theory for biological hypotheses. / Racunas, Stephen; Griffin, Christopher; Shah, Nigam.

Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004. 2004. p. 616-620 (Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004).

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

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Racunas S, Griffin C, Shah N. A finite model theory for biological hypotheses. In Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004. 2004. p. 616-620. (Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004).