Temporal Logic Based Synthesis of Experimentally Constrained Interaction Networks

Judah Goldfeder; Hillel Kugler

doi:10.1007/978-3-030-19432-1_6

Temporal Logic Based Synthesis of Experimentally Constrained Interaction Networks

Judah Goldfeder, Hillel Kugler

Bar-Ilan University - The Alexander Kofkin Faculty of Engineering

Yeshiva University

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

7 Scopus citations

Abstract

Synthesis methods based on formal reasoning are a powerful way to automate the process of constructing computational models of gene regulatory networks (GRNs) and increase predictive power by considering a set of consistent models that are guaranteed to satisfy known experimental data. Previously, a formal reasoning based approach enabling the synthesis and analysis of biological networks formalized using Abstract Boolean Networks (ABNs) was developed, where the precise interactions and update rules are only partially known. System dynamics can be constrained with specifications of some required behaviors, thereby providing a characterization of the set of all networks capable of reproducing given experimental observations. The synthesis method is supported by a tool, the Reasoning Engine for Interaction Networks (RE:IN). Starting with the synthesis framework supported by RE:IN, we provide translations of experimental observations to temporal logic and semantics of Abstract Boolean Networks, enabling us to use off-the-shelf model checking tools and algorithms. An initial prototype implementation we have developed demonstrates this is a gainful approach, providing speed-up gains for some benchmarks, while also opening the way to study extensions of the experimental observations specification language currently supported in RE:IN by using the rich expressive power of temporal logic.

Original language	English
Title of host publication	Molecular Logic and Computational Synthetic Biology - 1st International Symposium, MLCSB 2018, Revised Selected Papers
Editors	Manuel A. Martins, Madalena Chaves
Publisher	Springer Verlag
Pages	89-104
Number of pages	16
ISBN (Print)	9783030194314
DOIs	https://doi.org/10.1007/978-3-030-19432-1_6
State	Published - 2019
Event	1st International Symposium on Molecular Logic and Computational Synthetic Biology, MLCSB 2018 - Santiago, Chile Duration: 17 Dec 2018 → 18 Dec 2018

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	11415 LNCS
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	1st International Symposium on Molecular Logic and Computational Synthetic Biology, MLCSB 2018
Country/Territory	Chile
City	Santiago
Period	17/12/18 → 18/12/18

Bibliographical note

Publisher Copyright:
© 2019, Springer Nature Switzerland AG.

Funding

Acknowledgment. The research was partially supported by the Horizon 2020 research and innovation programme for the Bio4Comp project under grant agreement number 732482. We also acknowledge the support of the program for Summer Science Research Internships for Yeshiva University Students at Bar-Ilan University. The research was partially supported by the Horizon 2020 research and innovation programme for the Bio4Comp project under grant agreement number 732482. We also acknowledge the support of the program for Summer Science Research Internships for Yeshiva University Students at Bar-Ilan University.

Funders	Funder number
Horizon 2020 Framework Programme	732482
Horizon 2020

Keywords

Boolean networks
Formal verification
Gene regulatory networks
Synthesis
Temporal logic

Access to Document

10.1007/978-3-030-19432-1_6

Cite this

Goldfeder, J., & Kugler, H. (2019). Temporal Logic Based Synthesis of Experimentally Constrained Interaction Networks. In M. A. Martins, & M. Chaves (Eds.), Molecular Logic and Computational Synthetic Biology - 1st International Symposium, MLCSB 2018, Revised Selected Papers (pp. 89-104). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 11415 LNCS). Springer Verlag. https://doi.org/10.1007/978-3-030-19432-1_6

Goldfeder, Judah ; Kugler, Hillel. / Temporal Logic Based Synthesis of Experimentally Constrained Interaction Networks. Molecular Logic and Computational Synthetic Biology - 1st International Symposium, MLCSB 2018, Revised Selected Papers. editor / Manuel A. Martins ; Madalena Chaves. Springer Verlag, 2019. pp. 89-104 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

@inproceedings{2e769d492108421ab902edaa957d113a,

title = "Temporal Logic Based Synthesis of Experimentally Constrained Interaction Networks",

abstract = "Synthesis methods based on formal reasoning are a powerful way to automate the process of constructing computational models of gene regulatory networks (GRNs) and increase predictive power by considering a set of consistent models that are guaranteed to satisfy known experimental data. Previously, a formal reasoning based approach enabling the synthesis and analysis of biological networks formalized using Abstract Boolean Networks (ABNs) was developed, where the precise interactions and update rules are only partially known. System dynamics can be constrained with specifications of some required behaviors, thereby providing a characterization of the set of all networks capable of reproducing given experimental observations. The synthesis method is supported by a tool, the Reasoning Engine for Interaction Networks (RE:IN). Starting with the synthesis framework supported by RE:IN, we provide translations of experimental observations to temporal logic and semantics of Abstract Boolean Networks, enabling us to use off-the-shelf model checking tools and algorithms. An initial prototype implementation we have developed demonstrates this is a gainful approach, providing speed-up gains for some benchmarks, while also opening the way to study extensions of the experimental observations specification language currently supported in RE:IN by using the rich expressive power of temporal logic.",

keywords = "Boolean networks, Formal verification, Gene regulatory networks, Synthesis, Temporal logic",

author = "Judah Goldfeder and Hillel Kugler",

note = "Publisher Copyright: {\textcopyright} 2019, Springer Nature Switzerland AG.; 1st International Symposium on Molecular Logic and Computational Synthetic Biology, MLCSB 2018 ; Conference date: 17-12-2018 Through 18-12-2018",

year = "2019",

doi = "10.1007/978-3-030-19432-1_6",

language = "אנגלית",

isbn = "9783030194314",

series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",

publisher = "Springer Verlag",

pages = "89--104",

editor = "Martins, {Manuel A.} and Madalena Chaves",

booktitle = "Molecular Logic and Computational Synthetic Biology - 1st International Symposium, MLCSB 2018, Revised Selected Papers",

address = "גרמניה",

}

Goldfeder, J & Kugler, H 2019, Temporal Logic Based Synthesis of Experimentally Constrained Interaction Networks. in MA Martins & M Chaves (eds), Molecular Logic and Computational Synthetic Biology - 1st International Symposium, MLCSB 2018, Revised Selected Papers. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 11415 LNCS, Springer Verlag, pp. 89-104, 1st International Symposium on Molecular Logic and Computational Synthetic Biology, MLCSB 2018, Santiago, Chile, 17/12/18. https://doi.org/10.1007/978-3-030-19432-1_6

Temporal Logic Based Synthesis of Experimentally Constrained Interaction Networks. / Goldfeder, Judah; Kugler, Hillel.
Molecular Logic and Computational Synthetic Biology - 1st International Symposium, MLCSB 2018, Revised Selected Papers. ed. / Manuel A. Martins; Madalena Chaves. Springer Verlag, 2019. p. 89-104 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 11415 LNCS).

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

TY - GEN

T1 - Temporal Logic Based Synthesis of Experimentally Constrained Interaction Networks

AU - Goldfeder, Judah

AU - Kugler, Hillel

PY - 2019

Y1 - 2019

N2 - Synthesis methods based on formal reasoning are a powerful way to automate the process of constructing computational models of gene regulatory networks (GRNs) and increase predictive power by considering a set of consistent models that are guaranteed to satisfy known experimental data. Previously, a formal reasoning based approach enabling the synthesis and analysis of biological networks formalized using Abstract Boolean Networks (ABNs) was developed, where the precise interactions and update rules are only partially known. System dynamics can be constrained with specifications of some required behaviors, thereby providing a characterization of the set of all networks capable of reproducing given experimental observations. The synthesis method is supported by a tool, the Reasoning Engine for Interaction Networks (RE:IN). Starting with the synthesis framework supported by RE:IN, we provide translations of experimental observations to temporal logic and semantics of Abstract Boolean Networks, enabling us to use off-the-shelf model checking tools and algorithms. An initial prototype implementation we have developed demonstrates this is a gainful approach, providing speed-up gains for some benchmarks, while also opening the way to study extensions of the experimental observations specification language currently supported in RE:IN by using the rich expressive power of temporal logic.

AB - Synthesis methods based on formal reasoning are a powerful way to automate the process of constructing computational models of gene regulatory networks (GRNs) and increase predictive power by considering a set of consistent models that are guaranteed to satisfy known experimental data. Previously, a formal reasoning based approach enabling the synthesis and analysis of biological networks formalized using Abstract Boolean Networks (ABNs) was developed, where the precise interactions and update rules are only partially known. System dynamics can be constrained with specifications of some required behaviors, thereby providing a characterization of the set of all networks capable of reproducing given experimental observations. The synthesis method is supported by a tool, the Reasoning Engine for Interaction Networks (RE:IN). Starting with the synthesis framework supported by RE:IN, we provide translations of experimental observations to temporal logic and semantics of Abstract Boolean Networks, enabling us to use off-the-shelf model checking tools and algorithms. An initial prototype implementation we have developed demonstrates this is a gainful approach, providing speed-up gains for some benchmarks, while also opening the way to study extensions of the experimental observations specification language currently supported in RE:IN by using the rich expressive power of temporal logic.

KW - Boolean networks

KW - Formal verification

KW - Gene regulatory networks

KW - Synthesis

KW - Temporal logic

UR - http://www.scopus.com/inward/record.url?scp=85065784743&partnerID=8YFLogxK

U2 - 10.1007/978-3-030-19432-1_6

DO - 10.1007/978-3-030-19432-1_6

M3 - ???researchoutput.researchoutputtypes.contributiontobookanthology.conference???

AN - SCOPUS:85065784743

SN - 9783030194314

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 89

EP - 104

BT - Molecular Logic and Computational Synthetic Biology - 1st International Symposium, MLCSB 2018, Revised Selected Papers

A2 - Martins, Manuel A.

A2 - Chaves, Madalena

PB - Springer Verlag

T2 - 1st International Symposium on Molecular Logic and Computational Synthetic Biology, MLCSB 2018

Y2 - 17 December 2018 through 18 December 2018

ER -

Goldfeder J, Kugler H. Temporal Logic Based Synthesis of Experimentally Constrained Interaction Networks. In Martins MA, Chaves M, editors, Molecular Logic and Computational Synthetic Biology - 1st International Symposium, MLCSB 2018, Revised Selected Papers. Springer Verlag. 2019. p. 89-104. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-030-19432-1_6

Temporal Logic Based Synthesis of Experimentally Constrained Interaction Networks

Abstract

Publication series

Conference

Bibliographical note

Funding

Keywords

Access to Document

Other files and links

Fingerprint

Cite this