### 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 language | English (US) |
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Title of host publication | Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004 |

Pages | 616-620 |

Number of pages | 5 |

State | Published - Dec 1 2004 |

Event | Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004 - Stanford, CA, United States Duration: Aug 16 2004 → Aug 19 2004 |

### Publication series

Name | Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004 |
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### Conference

Conference | Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004 |
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Country | United States |

City | Stanford, CA |

Period | 8/16/04 → 8/19/04 |

### Fingerprint

### All Science Journal Classification (ASJC) codes

- Engineering(all)

### Cite this

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

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*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.

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

TY - GEN

T1 - A finite model theory for biological hypotheses

AU - Racunas, Stephen

AU - Griffin, Christopher

AU - Shah, Nigam

PY - 2004/12/1

Y1 - 2004/12/1

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=14044254817&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=14044254817&partnerID=8YFLogxK

M3 - Conference contribution

SN - 0769521940

SN - 9780769521947

T3 - Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004

SP - 616

EP - 620

BT - Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004

ER -