An SMT-Based Framework for Reasoning About Discrete Biological Models

Boyan Yordanov; Sara Jane Dunn; Colin Gravill; Hillel Kugler; Christoph M. Wintersteiger

doi:10.1007/978-3-031-23198-8_11

An SMT-Based Framework for Reasoning About Discrete Biological Models

Boyan Yordanov
, Sara Jane Dunn
, Colin Gravill
, Hillel Kugler
, Christoph M. Wintersteiger

Bar-Ilan University - The Alexander Kofkin Faculty of Engineering

Scientific Technologies
Microsoft USA

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

2 Scopus citations

Abstract

We present a framework called the Reasoning Engine, which implements Satisfiability Modulo Theories (SMT) based methods within a unified computational environment to address diverse biological analysis problems. The reasoning engine was used to reproduce results from key scientific studies, as well as supporting new research in stem cell biology. The framework utilizes an intermediate language for encoding partially specified discrete dynamical systems, which bridges the gap between high-level domain specific languages (DSLs) and low-level SMT solvers. We provide this framework as open source together with various biological case studies, illustrating the synthesis, enumeration, optimization and reasoning over models consistent with experimental observations to reveal novel biological insights.

Original language	English
Title of host publication	Bioinformatics Research and Applications - 18th International Symposium, ISBRA 2022, Proceedings
Editors	Mukul S. Bansal, Zhipeng Cai, Serghei Mangul
Publisher	Springer Science and Business Media Deutschland GmbH
Pages	114-125
Number of pages	12
ISBN (Print)	9783031231971
DOIs	https://doi.org/10.1007/978-3-031-23198-8_11
State	Published - 2022
Event	18th International Symposium on Bioinformatics Research and Applications, ISBRA 2022 - Haifa, Israel Duration: 14 Nov 2022 → 17 Nov 2022

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	13760 LNBI
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	18th International Symposium on Bioinformatics Research and Applications, ISBRA 2022
Country/Territory	Israel
City	Haifa
Period	14/11/22 → 17/11/22

Bibliographical note

Publisher Copyright:
© 2022, The Author(s), under exclusive license to Springer Nature Switzerland AG.

Funding

Acknowledgments. Hillel Kugler’s research was supported by the Horizon 2020 research and innovation programme for the Bio4Comp project under grant agreement number 732482 and by the ISRAEL SCIENCE FOUNDATION (Grant No. 190/19). S.-J. Dunn is now at DeepMind, but completed this work while at MSR Cambridge. H. Kugler: Supported by the Horizon 2020 research and innovation programme for the Bio4Comp project under grant agreement number 732482 and by the ISRAEL SCIENCE FOUNDATION (Grant No. 190/19).

Funders	Funder number
Israel Science Foundation	190/19
Horizon 2020	732482

Access to Document

10.1007/978-3-031-23198-8_11

Cite this

Yordanov, B., Dunn, S. J., Gravill, C., Kugler, H., & Wintersteiger, C. M. (2022). An SMT-Based Framework for Reasoning About Discrete Biological Models. In M. S. Bansal, Z. Cai, & S. Mangul (Eds.), Bioinformatics Research and Applications - 18th International Symposium, ISBRA 2022, Proceedings (pp. 114-125). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 13760 LNBI). Springer Science and Business Media Deutschland GmbH. https://doi.org/10.1007/978-3-031-23198-8_11

Yordanov, Boyan ; Dunn, Sara Jane ; Gravill, Colin et al. / An SMT-Based Framework for Reasoning About Discrete Biological Models. Bioinformatics Research and Applications - 18th International Symposium, ISBRA 2022, Proceedings. editor / Mukul S. Bansal ; Zhipeng Cai ; Serghei Mangul. Springer Science and Business Media Deutschland GmbH, 2022. pp. 114-125 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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Yordanov, B, Dunn, SJ, Gravill, C, Kugler, H & Wintersteiger, CM 2022, An SMT-Based Framework for Reasoning About Discrete Biological Models. in MS Bansal, Z Cai & S Mangul (eds), Bioinformatics Research and Applications - 18th International Symposium, ISBRA 2022, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 13760 LNBI, Springer Science and Business Media Deutschland GmbH, pp. 114-125, 18th International Symposium on Bioinformatics Research and Applications, ISBRA 2022, Haifa, Israel, 14/11/22. https://doi.org/10.1007/978-3-031-23198-8_11

An SMT-Based Framework for Reasoning About Discrete Biological Models. / Yordanov, Boyan; Dunn, Sara Jane; Gravill, Colin et al.
Bioinformatics Research and Applications - 18th International Symposium, ISBRA 2022, Proceedings. ed. / Mukul S. Bansal; Zhipeng Cai; Serghei Mangul. Springer Science and Business Media Deutschland GmbH, 2022. p. 114-125 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 13760 LNBI).

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

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Yordanov B, Dunn SJ, Gravill C, Kugler H, Wintersteiger CM. An SMT-Based Framework for Reasoning About Discrete Biological Models. In Bansal MS, Cai Z, Mangul S, editors, Bioinformatics Research and Applications - 18th International Symposium, ISBRA 2022, Proceedings. Springer Science and Business Media Deutschland GmbH. 2022. p. 114-125. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-031-23198-8_11