---
_id: '7808'
abstract:
- lang: eng
  text: Quantization converts neural networks into low-bit fixed-point computations
    which can be carried out by efficient integer-only hardware, and is standard practice
    for the deployment of neural networks on real-time embedded devices. However,
    like their real-numbered counterpart, quantized networks are not immune to malicious
    misclassification caused by adversarial attacks. We investigate how quantization
    affects a network’s robustness to adversarial attacks, which is a formal verification
    question. We show that neither robustness nor non-robustness are monotonic with
    changing the number of bits for the representation and, also, neither are preserved
    by quantization from a real-numbered network. For this reason, we introduce a
    verification method for quantized neural networks which, using SMT solving over
    bit-vectors, accounts for their exact, bit-precise semantics. We built a tool
    and analyzed the effect of quantization on a classifier for the MNIST dataset.
    We demonstrate that, compared to our method, existing methods for the analysis
    of real-numbered networks often derive false conclusions about their quantizations,
    both when determining robustness and when detecting attacks, and that existing
    methods for quantized networks often miss attacks. Furthermore, we applied our
    method beyond robustness, showing how the number of bits in quantization enlarges
    the gender bias of a predictor for students’ grades.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Mirco
  full_name: Giacobbe, Mirco
  id: 3444EA5E-F248-11E8-B48F-1D18A9856A87
  last_name: Giacobbe
  orcid: 0000-0001-8180-0904
- first_name: Thomas A
  full_name: Henzinger, Thomas A
  id: 40876CD8-F248-11E8-B48F-1D18A9856A87
  last_name: Henzinger
  orcid: 0000-0002-2985-7724
- first_name: Mathias
  full_name: Lechner, Mathias
  id: 3DC22916-F248-11E8-B48F-1D18A9856A87
  last_name: Lechner
citation:
  ama: 'Giacobbe M, Henzinger TA, Lechner M. How many bits does it take to quantize
    your neural network? In: <i>International Conference on Tools and Algorithms for
    the Construction and Analysis of Systems</i>. Vol 12079. Springer Nature; 2020:79-97.
    doi:<a href="https://doi.org/10.1007/978-3-030-45237-7_5">10.1007/978-3-030-45237-7_5</a>'
  apa: 'Giacobbe, M., Henzinger, T. A., &#38; Lechner, M. (2020). How many bits does
    it take to quantize your neural network? In <i>International Conference on Tools
    and Algorithms for the Construction and Analysis of Systems</i> (Vol. 12079, pp.
    79–97). Dublin, Ireland: Springer Nature. <a href="https://doi.org/10.1007/978-3-030-45237-7_5">https://doi.org/10.1007/978-3-030-45237-7_5</a>'
  chicago: Giacobbe, Mirco, Thomas A Henzinger, and Mathias Lechner. “How Many Bits
    Does It Take to Quantize Your Neural Network?” In <i>International Conference
    on Tools and Algorithms for the Construction and Analysis of Systems</i>, 12079:79–97.
    Springer Nature, 2020. <a href="https://doi.org/10.1007/978-3-030-45237-7_5">https://doi.org/10.1007/978-3-030-45237-7_5</a>.
  ieee: M. Giacobbe, T. A. Henzinger, and M. Lechner, “How many bits does it take
    to quantize your neural network?,” in <i>International Conference on Tools and
    Algorithms for the Construction and Analysis of Systems</i>, Dublin, Ireland,
    2020, vol. 12079, pp. 79–97.
  ista: 'Giacobbe M, Henzinger TA, Lechner M. 2020. How many bits does it take to
    quantize your neural network? International Conference on Tools and Algorithms
    for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for
    the Construction and Analysis of Systems, LNCS, vol. 12079, 79–97.'
  mla: Giacobbe, Mirco, et al. “How Many Bits Does It Take to Quantize Your Neural
    Network?” <i>International Conference on Tools and Algorithms for the Construction
    and Analysis of Systems</i>, vol. 12079, Springer Nature, 2020, pp. 79–97, doi:<a
    href="https://doi.org/10.1007/978-3-030-45237-7_5">10.1007/978-3-030-45237-7_5</a>.
  short: M. Giacobbe, T.A. Henzinger, M. Lechner, in:, International Conference on
    Tools and Algorithms for the Construction and Analysis of Systems, Springer Nature,
    2020, pp. 79–97.
conference:
  end_date: 2020-04-30
  location: Dublin, Ireland
  name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems'
  start_date: 2020-04-25
date_created: 2020-05-10T22:00:49Z
date_published: 2020-04-17T00:00:00Z
date_updated: 2023-06-23T07:01:11Z
day: '17'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-030-45237-7_5
file:
- access_level: open_access
  checksum: f19905a42891fe5ce93d69143fa3f6fb
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  creator: dernst
  date_created: 2020-05-26T12:48:15Z
  date_updated: 2020-07-14T12:48:03Z
  file_id: '7893'
  file_name: 2020_TACAS_Giacobbe.pdf
  file_size: 2744030
  relation: main_file
file_date_updated: 2020-07-14T12:48:03Z
has_accepted_license: '1'
intvolume: '     12079'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '04'
oa: 1
oa_version: Published Version
page: 79-97
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: S 11407_N23
  name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: Z211
  name: The Wittgenstein Prize
publication: International Conference on Tools and Algorithms for the Construction
  and Analysis of Systems
publication_identifier:
  eissn:
  - '16113349'
  isbn:
  - '9783030452360'
  issn:
  - '03029743'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
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    status: public
scopus_import: 1
status: public
title: How many bits does it take to quantize your neural network?
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12079
year: '2020'
...
---
_id: '10877'
abstract:
- lang: eng
  text: 'This report presents the results of a friendly competition for formal verification
    of continuous and hybrid systems with piecewise constant dynamics. The friendly
    competition took place as part of the workshop Applied Verification for Continuous
    and Hybrid Systems (ARCH) in 2019. In this third edition, six tools have been
    applied to solve five different benchmark problems in the category for piecewise
    constant dynamics: BACH, Lyse, Hy- COMP, PHAVer/SX, PHAVerLite, and VeriSiMPL.
    Compared to last year, a new tool has participated (HyCOMP) and PHAVerLite has
    replaced PHAVer-lite. The result is a snap- shot of the current landscape of tools
    and the types of benchmarks they are particularly suited for. Due to the diversity
    of problems, we are not ranking tools, yet the presented results probably provide
    the most complete assessment of tools for the safety verification of continuous
    and hybrid systems with piecewise constant dynamics up to this date.'
acknowledgement: "The authors gratefully acknowledge \fnancial support by the European
  Commission project\r\nUnCoVerCPS under grant number 643921. Lei Bu is supported
  by the National Natural Science\r\nFoundation of China (No.61572249)."
alternative_title:
- EPiC Series in Computing
article_processing_charge: No
author:
- first_name: Goran
  full_name: Frehse, Goran
  last_name: Frehse
- first_name: Alessandro
  full_name: Abate, Alessandro
  last_name: Abate
- first_name: Dieky
  full_name: Adzkiya, Dieky
  last_name: Adzkiya
- first_name: Anna
  full_name: Becchi, Anna
  last_name: Becchi
- first_name: Lei
  full_name: Bu, Lei
  last_name: Bu
- first_name: Alessandro
  full_name: Cimatti, Alessandro
  last_name: Cimatti
- first_name: Mirco
  full_name: Giacobbe, Mirco
  id: 3444EA5E-F248-11E8-B48F-1D18A9856A87
  last_name: Giacobbe
  orcid: 0000-0001-8180-0904
- first_name: Alberto
  full_name: Griggio, Alberto
  last_name: Griggio
- first_name: Sergio
  full_name: Mover, Sergio
  last_name: Mover
- first_name: Muhammad Syifa'ul
  full_name: Mufid, Muhammad Syifa'ul
  last_name: Mufid
- first_name: Idriss
  full_name: Riouak, Idriss
  last_name: Riouak
- first_name: Stefano
  full_name: Tonetta, Stefano
  last_name: Tonetta
- first_name: Enea
  full_name: Zaffanella, Enea
  last_name: Zaffanella
citation:
  ama: 'Frehse G, Abate A, Adzkiya D, et al. ARCH-COMP19 Category Report: Hybrid systems
    with piecewise constant dynamics. In: Frehse G, Althoff M, eds. <i>ARCH19. 6th
    International Workshop on Applied Verification of Continuous and Hybrid Systems</i>.
    Vol 61. EasyChair; 2019:1-13. doi:<a href="https://doi.org/10.29007/rjwn">10.29007/rjwn</a>'
  apa: 'Frehse, G., Abate, A., Adzkiya, D., Becchi, A., Bu, L., Cimatti, A., … Zaffanella,
    E. (2019). ARCH-COMP19 Category Report: Hybrid systems with piecewise constant
    dynamics. In G. Frehse &#38; M. Althoff (Eds.), <i>ARCH19. 6th International Workshop
    on Applied Verification of Continuous and Hybrid Systems</i> (Vol. 61, pp. 1–13).
    Montreal, Canada: EasyChair. <a href="https://doi.org/10.29007/rjwn">https://doi.org/10.29007/rjwn</a>'
  chicago: 'Frehse, Goran, Alessandro Abate, Dieky Adzkiya, Anna Becchi, Lei Bu, Alessandro
    Cimatti, Mirco Giacobbe, et al. “ARCH-COMP19 Category Report: Hybrid Systems with
    Piecewise Constant Dynamics.” In <i>ARCH19. 6th International Workshop on Applied
    Verification of Continuous and Hybrid Systems</i>, edited by Goran Frehse and
    Matthias Althoff, 61:1–13. EasyChair, 2019. <a href="https://doi.org/10.29007/rjwn">https://doi.org/10.29007/rjwn</a>.'
  ieee: 'G. Frehse <i>et al.</i>, “ARCH-COMP19 Category Report: Hybrid systems with
    piecewise constant dynamics,” in <i>ARCH19. 6th International Workshop on Applied
    Verification of Continuous and Hybrid Systems</i>, Montreal, Canada, 2019, vol.
    61, pp. 1–13.'
  ista: 'Frehse G, Abate A, Adzkiya D, Becchi A, Bu L, Cimatti A, Giacobbe M, Griggio
    A, Mover S, Mufid MS, Riouak I, Tonetta S, Zaffanella E. 2019. ARCH-COMP19 Category
    Report: Hybrid systems with piecewise constant dynamics. ARCH19. 6th International
    Workshop on Applied Verification of Continuous and Hybrid Systems. ARCH: International
    Workshop on Applied Verification on Continuous and Hybrid Systems, EPiC Series
    in Computing, vol. 61, 1–13.'
  mla: 'Frehse, Goran, et al. “ARCH-COMP19 Category Report: Hybrid Systems with Piecewise
    Constant Dynamics.” <i>ARCH19. 6th International Workshop on Applied Verification
    of Continuous and Hybrid Systems</i>, edited by Goran Frehse and Matthias Althoff,
    vol. 61, EasyChair, 2019, pp. 1–13, doi:<a href="https://doi.org/10.29007/rjwn">10.29007/rjwn</a>.'
  short: G. Frehse, A. Abate, D. Adzkiya, A. Becchi, L. Bu, A. Cimatti, M. Giacobbe,
    A. Griggio, S. Mover, M.S. Mufid, I. Riouak, S. Tonetta, E. Zaffanella, in:, G.
    Frehse, M. Althoff (Eds.), ARCH19. 6th International Workshop on Applied Verification
    of Continuous and Hybrid Systems, EasyChair, 2019, pp. 1–13.
conference:
  end_date: 2019-04-15
  location: Montreal, Canada
  name: 'ARCH: International Workshop on Applied Verification on Continuous and Hybrid
    Systems'
  start_date: 2019-04-15
date_created: 2022-03-18T12:29:23Z
date_published: 2019-05-25T00:00:00Z
date_updated: 2022-05-17T07:09:47Z
day: '25'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.29007/rjwn
editor:
- first_name: Goran
  full_name: Frehse, Goran
  last_name: Frehse
- first_name: Matthias
  full_name: Althoff, Matthias
  last_name: Althoff
file:
- access_level: open_access
  checksum: 4b92e333db7b4e2349501a804dfede69
  content_type: application/pdf
  creator: dernst
  date_created: 2022-05-17T06:55:49Z
  date_updated: 2022-05-17T06:55:49Z
  file_id: '11391'
  file_name: 2019_EPiCs_Frehse.pdf
  file_size: 346415
  relation: main_file
  success: 1
file_date_updated: 2022-05-17T06:55:49Z
has_accepted_license: '1'
intvolume: '        61'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 1-13
publication: ARCH19. 6th International Workshop on Applied Verification of Continuous
  and Hybrid Systems
publication_identifier:
  issn:
  - 2398-7340
publication_status: published
publisher: EasyChair
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'ARCH-COMP19 Category Report: Hybrid systems with piecewise constant dynamics'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 61
year: '2019'
...
---
_id: '6894'
abstract:
- lang: eng
  text: "Hybrid automata combine finite automata and dynamical systems, and model
    the interaction of digital with physical systems. Formal analysis that can guarantee
    the safety of all behaviors or rigorously witness failures, while unsolvable in
    general, has been tackled algorithmically using, e.g., abstraction, bounded model-checking,
    assisted theorem proving.\r\nNevertheless, very few methods have addressed the
    time-unbounded reachability analysis of hybrid automata and, for current sound
    and automatic tools, scalability remains critical. We develop methods for the
    polyhedral abstraction of hybrid automata, which construct coarse overapproximations
    and tightens them incrementally, in a CEGAR fashion. We use template polyhedra,
    i.e., polyhedra whose facets are normal to a given set of directions.\r\nWhile,
    previously, directions were given by the user, we introduce (1) the first method\r\nfor
    computing template directions from spurious counterexamples, so as to generalize
    and\r\neliminate them. The method applies naturally to convex hybrid automata,
    i.e., hybrid\r\nautomata with (possibly non-linear) convex constraints on derivatives
    only, while for linear\r\nODE requires further abstraction. Specifically, we introduce
    (2) the conic abstractions,\r\nwhich, partitioning the state space into appropriate
    (possibly non-uniform) cones, divide\r\ncurvy trajectories into relatively straight
    sections, suitable for polyhedral abstractions.\r\nFinally, we introduce (3) space-time
    interpolation, which, combining interval arithmetic\r\nand template refinement,
    computes appropriate (possibly non-uniform) time partitioning\r\nand template
    directions along spurious trajectories, so as to eliminate them.\r\nWe obtain
    sound and automatic methods for the reachability analysis over dense\r\nand unbounded
    time of convex hybrid automata and hybrid automata with linear ODE.\r\nWe build
    prototype tools and compare—favorably—our methods against the respective\r\nstate-of-the-art
    tools, on several benchmarks."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Mirco
  full_name: Giacobbe, Mirco
  id: 3444EA5E-F248-11E8-B48F-1D18A9856A87
  last_name: Giacobbe
  orcid: 0000-0001-8180-0904
citation:
  ama: Giacobbe M. Automatic time-unbounded reachability analysis of hybrid systems.
    2019. doi:<a href="https://doi.org/10.15479/AT:ISTA:6894">10.15479/AT:ISTA:6894</a>
  apa: Giacobbe, M. (2019). <i>Automatic time-unbounded reachability analysis of hybrid
    systems</i>. Institute of Science and Technology Austria. <a href="https://doi.org/10.15479/AT:ISTA:6894">https://doi.org/10.15479/AT:ISTA:6894</a>
  chicago: Giacobbe, Mirco. “Automatic Time-Unbounded Reachability Analysis of Hybrid
    Systems.” Institute of Science and Technology Austria, 2019. <a href="https://doi.org/10.15479/AT:ISTA:6894">https://doi.org/10.15479/AT:ISTA:6894</a>.
  ieee: M. Giacobbe, “Automatic time-unbounded reachability analysis of hybrid systems,”
    Institute of Science and Technology Austria, 2019.
  ista: Giacobbe M. 2019. Automatic time-unbounded reachability analysis of hybrid
    systems. Institute of Science and Technology Austria.
  mla: Giacobbe, Mirco. <i>Automatic Time-Unbounded Reachability Analysis of Hybrid
    Systems</i>. Institute of Science and Technology Austria, 2019, doi:<a href="https://doi.org/10.15479/AT:ISTA:6894">10.15479/AT:ISTA:6894</a>.
  short: M. Giacobbe, Automatic Time-Unbounded Reachability Analysis of Hybrid Systems,
    Institute of Science and Technology Austria, 2019.
date_created: 2019-09-22T14:08:44Z
date_published: 2019-09-30T00:00:00Z
date_updated: 2023-09-19T09:30:43Z
day: '30'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: ToHe
doi: 10.15479/AT:ISTA:6894
file:
- access_level: open_access
  checksum: 773beaf4a85dc2acc2c12b578fbe1965
  content_type: application/pdf
  creator: mgiacobbe
  date_created: 2019-09-27T14:15:05Z
  date_updated: 2020-07-14T12:47:43Z
  file_id: '6916'
  file_name: giacobbe_thesis.pdf
  file_size: 4100685
  relation: main_file
- access_level: closed
  checksum: 97f1c3da71feefd27e6e625d32b4c75b
  content_type: application/gzip
  creator: mgiacobbe
  date_created: 2019-09-27T14:22:04Z
  date_updated: 2020-07-14T12:47:43Z
  file_id: '6917'
  file_name: giacobbe_thesis_src.tar.gz
  file_size: 7959732
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file_date_updated: 2020-07-14T12:47:43Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '132'
publication_identifier:
  eissn:
  - 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
  record:
  - id: '631'
    relation: part_of_dissertation
    status: public
  - id: '647'
    relation: part_of_dissertation
    status: public
  - id: '140'
    relation: part_of_dissertation
    status: public
status: public
supervisor:
- first_name: Thomas A
  full_name: Henzinger, Thomas A
  id: 40876CD8-F248-11E8-B48F-1D18A9856A87
  last_name: Henzinger
  orcid: 0000−0002−2985−7724
title: Automatic time-unbounded reachability analysis of hybrid systems
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '7453'
abstract:
- lang: eng
  text: We illustrate the ingredients of the state-of-the-art of model-based approach
    for the formal design and verification of cyber-physical systems. To capture the
    interaction between a discrete controller and its continuously evolving environment,
    we use the formal models of timed and hybrid automata. We explain the steps of
    modeling and verification in the tools Uppaal and SpaceEx using a case study based
    on a dual-chamber implantable pacemaker monitoring a human heart. We show how
    to design a model as a composition of components, how to construct models at varying
    levels of detail, how to establish that one model is an abstraction of another,
    how to specify correctness requirements using temporal logic, and how to verify
    that a model satisfies a logical requirement.
acknowledgement: This research was supported in part by the Austrian Science Fund
  (FWF) under grants S11402-N23(RiSE/SHiNE) and Z211-N23 (Wittgenstein Award). This
  research has received funding from the Sino-Danish Basic Research Centre, IDEA4CPS,
  funded by the Danish National Research Foundation and the National Science Foundation,
  China, the Innovation Fund Denmark centre DiCyPS, as well as the ERC Advanced Grant
  LASSO.
alternative_title:
- Lecture Notes in Computer Science
article_processing_charge: No
author:
- first_name: Rajeev
  full_name: Alur, Rajeev
  last_name: Alur
- first_name: Mirco
  full_name: Giacobbe, Mirco
  id: 3444EA5E-F248-11E8-B48F-1D18A9856A87
  last_name: Giacobbe
  orcid: 0000-0001-8180-0904
- first_name: Thomas A
  full_name: Henzinger, Thomas A
  id: 40876CD8-F248-11E8-B48F-1D18A9856A87
  last_name: Henzinger
  orcid: 0000−0002−2985−7724
- first_name: Kim G.
  full_name: Larsen, Kim G.
  last_name: Larsen
- first_name: Marius
  full_name: Mikučionis, Marius
  last_name: Mikučionis
citation:
  ama: 'Alur R, Giacobbe M, Henzinger TA, Larsen KG, Mikučionis M. Continuous-time
    models for system design and analysis. In: Steffen B, Woeginger G, eds. <i>Computing
    and Software Science</i>. Vol 10000. LNCS. Springer Nature; 2019:452-477. doi:<a
    href="https://doi.org/10.1007/978-3-319-91908-9_22">10.1007/978-3-319-91908-9_22</a>'
  apa: Alur, R., Giacobbe, M., Henzinger, T. A., Larsen, K. G., &#38; Mikučionis,
    M. (2019). Continuous-time models for system design and analysis. In B. Steffen
    &#38; G. Woeginger (Eds.), <i>Computing and Software Science</i> (Vol. 10000,
    pp. 452–477). Springer Nature. <a href="https://doi.org/10.1007/978-3-319-91908-9_22">https://doi.org/10.1007/978-3-319-91908-9_22</a>
  chicago: Alur, Rajeev, Mirco Giacobbe, Thomas A Henzinger, Kim G. Larsen, and Marius
    Mikučionis. “Continuous-Time Models for System Design and Analysis.” In <i>Computing
    and Software Science</i>, edited by Bernhard Steffen and Gerhard Woeginger, 10000:452–77.
    LNCS. Springer Nature, 2019. <a href="https://doi.org/10.1007/978-3-319-91908-9_22">https://doi.org/10.1007/978-3-319-91908-9_22</a>.
  ieee: R. Alur, M. Giacobbe, T. A. Henzinger, K. G. Larsen, and M. Mikučionis, “Continuous-time
    models for system design and analysis,” in <i>Computing and Software Science</i>,
    vol. 10000, B. Steffen and G. Woeginger, Eds. Springer Nature, 2019, pp. 452–477.
  ista: 'Alur R, Giacobbe M, Henzinger TA, Larsen KG, Mikučionis M. 2019.Continuous-time
    models for system design and analysis. In: Computing and Software Science. Lecture
    Notes in Computer Science, vol. 10000, 452–477.'
  mla: Alur, Rajeev, et al. “Continuous-Time Models for System Design and Analysis.”
    <i>Computing and Software Science</i>, edited by Bernhard Steffen and Gerhard
    Woeginger, vol. 10000, Springer Nature, 2019, pp. 452–77, doi:<a href="https://doi.org/10.1007/978-3-319-91908-9_22">10.1007/978-3-319-91908-9_22</a>.
  short: R. Alur, M. Giacobbe, T.A. Henzinger, K.G. Larsen, M. Mikučionis, in:, B.
    Steffen, G. Woeginger (Eds.), Computing and Software Science, Springer Nature,
    2019, pp. 452–477.
date_created: 2020-02-05T10:51:44Z
date_published: 2019-10-05T00:00:00Z
date_updated: 2022-09-06T08:25:52Z
day: '05'
department:
- _id: ToHe
doi: 10.1007/978-3-319-91908-9_22
editor:
- first_name: Bernhard
  full_name: Steffen, Bernhard
  last_name: Steffen
- first_name: Gerhard
  full_name: Woeginger, Gerhard
  last_name: Woeginger
intvolume: '     10000'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1007/978-3-319-91908-9_22
month: '10'
oa: 1
oa_version: Published Version
page: 452-477
project:
- _id: 25F2ACDE-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: S11402-N23
  name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: Z211
  name: The Wittgenstein Prize
publication: Computing and Software Science
publication_identifier:
  eisbn:
  - '9783319919089'
  eissn:
  - 0302-9743
  isbn:
  - '9783319919072'
  issn:
  - 1611-3349
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: LNCS
status: public
title: Continuous-time models for system design and analysis
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10000
year: '2019'
...
---
_id: '140'
abstract:
- lang: eng
  text: Reachability analysis is difficult for hybrid automata with affine differential
    equations, because the reach set needs to be approximated. Promising abstraction
    techniques usually employ interval methods or template polyhedra. Interval methods
    account for dense time and guarantee soundness, and there are interval-based tools
    that overapproximate affine flowpipes. But interval methods impose bounded and
    rigid shapes, which make refinement expensive and fixpoint detection difficult.
    Template polyhedra, on the other hand, can be adapted flexibly and can be unbounded,
    but sound template refinement for unbounded reachability analysis has been implemented
    only for systems with piecewise constant dynamics. We capitalize on the advantages
    of both techniques, combining interval arithmetic and template polyhedra, using
    the former to abstract time and the latter to abstract space. During a CEGAR loop,
    whenever a spurious error trajectory is found, we compute additional space constraints
    and split time intervals, and use these space-time interpolants to eliminate the
    counterexample. Space-time interpolation offers a lazy, flexible framework for
    increasing precision while guaranteeing soundness, both for error avoidance and
    fixpoint detection. To the best of out knowledge, this is the first abstraction
    refinement scheme for the reachability analysis over unbounded and dense time
    of affine hybrid systems, which is both sound and automatic. We demonstrate the
    effectiveness of our algorithm with several benchmark examples, which cannot be
    handled by other tools.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Goran
  full_name: Frehse, Goran
  last_name: Frehse
- first_name: Mirco
  full_name: Giacobbe, Mirco
  id: 3444EA5E-F248-11E8-B48F-1D18A9856A87
  last_name: Giacobbe
  orcid: 0000-0001-8180-0904
- first_name: Thomas A
  full_name: Henzinger, Thomas A
  id: 40876CD8-F248-11E8-B48F-1D18A9856A87
  last_name: Henzinger
  orcid: 0000−0002−2985−7724
citation:
  ama: 'Frehse G, Giacobbe M, Henzinger TA. Space-time interpolants. In: Vol 10981.
    Springer; 2018:468-486. doi:<a href="https://doi.org/10.1007/978-3-319-96145-3_25">10.1007/978-3-319-96145-3_25</a>'
  apa: 'Frehse, G., Giacobbe, M., &#38; Henzinger, T. A. (2018). Space-time interpolants
    (Vol. 10981, pp. 468–486). Presented at the CAV: Computer Aided Verification,
    Oxford, United Kingdom: Springer. <a href="https://doi.org/10.1007/978-3-319-96145-3_25">https://doi.org/10.1007/978-3-319-96145-3_25</a>'
  chicago: Frehse, Goran, Mirco Giacobbe, and Thomas A Henzinger. “Space-Time Interpolants,”
    10981:468–86. Springer, 2018. <a href="https://doi.org/10.1007/978-3-319-96145-3_25">https://doi.org/10.1007/978-3-319-96145-3_25</a>.
  ieee: 'G. Frehse, M. Giacobbe, and T. A. Henzinger, “Space-time interpolants,” presented
    at the CAV: Computer Aided Verification, Oxford, United Kingdom, 2018, vol. 10981,
    pp. 468–486.'
  ista: 'Frehse G, Giacobbe M, Henzinger TA. 2018. Space-time interpolants. CAV: Computer
    Aided Verification, LNCS, vol. 10981, 468–486.'
  mla: Frehse, Goran, et al. <i>Space-Time Interpolants</i>. Vol. 10981, Springer,
    2018, pp. 468–86, doi:<a href="https://doi.org/10.1007/978-3-319-96145-3_25">10.1007/978-3-319-96145-3_25</a>.
  short: G. Frehse, M. Giacobbe, T.A. Henzinger, in:, Springer, 2018, pp. 468–486.
conference:
  end_date: 2018-07-17
  location: Oxford, United Kingdom
  name: 'CAV: Computer Aided Verification'
  start_date: 2018-07-14
date_created: 2018-12-11T11:44:50Z
date_published: 2018-07-18T00:00:00Z
date_updated: 2023-09-19T09:30:43Z
day: '18'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1007/978-3-319-96145-3_25
external_id:
  isi:
  - '000491481600025'
file:
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  content_type: application/pdf
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  file_id: '5310'
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  file_size: 563710
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file_date_updated: 2020-07-14T12:44:50Z
has_accepted_license: '1'
intvolume: '     10981'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 468 - 486
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: S 11407_N23
  name: Rigorous Systems Engineering
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: S11402-N23
  name: Moderne Concurrency Paradigms
publication_identifier:
  issn:
  - '03029743'
publication_status: published
publisher: Springer
publist_id: '7783'
pubrep_id: '1010'
quality_controlled: '1'
related_material:
  record:
  - id: '6894'
    relation: dissertation_contains
    status: public
scopus_import: '1'
status: public
title: Space-time interpolants
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10981
year: '2018'
...
---
_id: '631'
abstract:
- lang: eng
  text: Template polyhedra generalize intervals and octagons to polyhedra whose facets
    are orthogonal to a given set of arbitrary directions. They have been employed
    in the abstract interpretation of programs and, with particular success, in the
    reachability analysis of hybrid automata. While previously, the choice of directions
    has been left to the user or a heuristic, we present a method for the automatic
    discovery of directions that generalize and eliminate spurious counterexamples.
    We show that for the class of convex hybrid automata, i.e., hybrid automata with
    (possibly nonlinear) convex constraints on derivatives, such directions always
    exist and can be found using convex optimization. We embed our method inside a
    CEGAR loop, thus enabling the time-unbounded reachability analysis of an important
    and richer class of hybrid automata than was previously possible. We evaluate
    our method on several benchmarks, demonstrating also its superior efficiency for
    the special case of linear hybrid automata.
acknowledgement: This research was supported in part by the Austrian Science Fund
  (FWF) under grants S11402-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), by
  the European Commission under grant 643921 (UnCoVerCPS), and by the ARC project
  DP140104219 (Robust AI Planning for Hybrid Systems).
alternative_title:
- LNCS
author:
- first_name: Sergiy
  full_name: Bogomolov, Sergiy
  id: 369D9A44-F248-11E8-B48F-1D18A9856A87
  last_name: Bogomolov
  orcid: 0000-0002-0686-0365
- first_name: Goran
  full_name: Frehse, Goran
  last_name: Frehse
- first_name: Mirco
  full_name: Giacobbe, Mirco
  id: 3444EA5E-F248-11E8-B48F-1D18A9856A87
  last_name: Giacobbe
  orcid: 0000-0001-8180-0904
- first_name: Thomas A
  full_name: Henzinger, Thomas A
  id: 40876CD8-F248-11E8-B48F-1D18A9856A87
  last_name: Henzinger
  orcid: 0000−0002−2985−7724
citation:
  ama: 'Bogomolov S, Frehse G, Giacobbe M, Henzinger TA. Counterexample guided refinement
    of template polyhedra. In: Vol 10205. Springer; 2017:589-606. doi:<a href="https://doi.org/10.1007/978-3-662-54577-5_34">10.1007/978-3-662-54577-5_34</a>'
  apa: 'Bogomolov, S., Frehse, G., Giacobbe, M., &#38; Henzinger, T. A. (2017). Counterexample
    guided refinement of template polyhedra (Vol. 10205, pp. 589–606). Presented at
    the TACAS: Tools and Algorithms for the Construction and Analysis of Systems,
    Uppsala, Sweden: Springer. <a href="https://doi.org/10.1007/978-3-662-54577-5_34">https://doi.org/10.1007/978-3-662-54577-5_34</a>'
  chicago: Bogomolov, Sergiy, Goran Frehse, Mirco Giacobbe, and Thomas A Henzinger.
    “Counterexample Guided Refinement of Template Polyhedra,” 10205:589–606. Springer,
    2017. <a href="https://doi.org/10.1007/978-3-662-54577-5_34">https://doi.org/10.1007/978-3-662-54577-5_34</a>.
  ieee: 'S. Bogomolov, G. Frehse, M. Giacobbe, and T. A. Henzinger, “Counterexample
    guided refinement of template polyhedra,” presented at the TACAS: Tools and Algorithms
    for the Construction and Analysis of Systems, Uppsala, Sweden, 2017, vol. 10205,
    pp. 589–606.'
  ista: 'Bogomolov S, Frehse G, Giacobbe M, Henzinger TA. 2017. Counterexample guided
    refinement of template polyhedra. TACAS: Tools and Algorithms for the Construction
    and Analysis of Systems, LNCS, vol. 10205, 589–606.'
  mla: Bogomolov, Sergiy, et al. <i>Counterexample Guided Refinement of Template Polyhedra</i>.
    Vol. 10205, Springer, 2017, pp. 589–606, doi:<a href="https://doi.org/10.1007/978-3-662-54577-5_34">10.1007/978-3-662-54577-5_34</a>.
  short: S. Bogomolov, G. Frehse, M. Giacobbe, T.A. Henzinger, in:, Springer, 2017,
    pp. 589–606.
conference:
  end_date: 2017-04-29
  location: Uppsala, Sweden
  name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems'
  start_date: 2017-04-22
date_created: 2018-12-11T11:47:36Z
date_published: 2017-03-31T00:00:00Z
date_updated: 2023-09-07T12:53:00Z
day: '31'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-662-54577-5_34
file:
- access_level: open_access
  checksum: f395d0d20102b89aeaad8b4ef4f18f4f
  content_type: application/pdf
  creator: system
  date_created: 2018-12-12T10:11:41Z
  date_updated: 2020-07-14T12:47:27Z
  file_id: '4897'
  file_name: IST-2017-741-v1+1_main.pdf
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  content_type: application/pdf
  creator: system
  date_created: 2018-12-12T10:11:42Z
  date_updated: 2020-07-14T12:47:27Z
  file_id: '4898'
  file_name: IST-2018-741-v2+2_main.pdf
  file_size: 563276
  relation: main_file
file_date_updated: 2020-07-14T12:47:27Z
has_accepted_license: '1'
intvolume: '     10205'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 589 - 606
project:
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: S11402-N23
  name: Moderne Concurrency Paradigms
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: Z211
  name: The Wittgenstein Prize
publication_identifier:
  isbn:
  - 978-366254576-8
publication_status: published
publisher: Springer
publist_id: '7162'
pubrep_id: '966'
quality_controlled: '1'
related_material:
  record:
  - id: '6894'
    relation: dissertation_contains
    status: public
scopus_import: 1
status: public
title: Counterexample guided refinement of template polyhedra
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10205
year: '2017'
...
---
_id: '647'
abstract:
- lang: eng
  text: Despite researchers’ efforts in the last couple of decades, reachability analysis
    is still a challenging problem even for linear hybrid systems. Among the existing
    approaches, the most practical ones are mainly based on bounded-time reachable
    set over-approximations. For the purpose of unbounded-time analysis, one important
    strategy is to abstract the original system and find an invariant for the abstraction.
    In this paper, we propose an approach to constructing a new kind of abstraction
    called conic abstraction for affine hybrid systems, and to computing reachable
    sets based on this abstraction. The essential feature of a conic abstraction is
    that it partitions the state space of a system into a set of convex polyhedral
    cones which is derived from a uniform conic partition of the derivative space.
    Such a set of polyhedral cones is able to cut all trajectories of the system into
    almost straight segments so that every segment of a reach pipe in a polyhedral
    cone tends to be straight as well, and hence can be over-approximated tightly
    by polyhedra using similar techniques as HyTech or PHAVer. In particular, for
    diagonalizable affine systems, our approach can guarantee to find an invariant
    for unbounded reachable sets, which is beyond the capability of bounded-time reachability
    analysis tools. We implemented the approach in a tool and experiments on benchmarks
    show that our approach is more powerful than SpaceEx and PHAVer in dealing with
    diagonalizable systems.
alternative_title:
- LNCS
author:
- first_name: Sergiy
  full_name: Bogomolov, Sergiy
  id: 369D9A44-F248-11E8-B48F-1D18A9856A87
  last_name: Bogomolov
  orcid: 0000-0002-0686-0365
- first_name: Mirco
  full_name: Giacobbe, Mirco
  id: 3444EA5E-F248-11E8-B48F-1D18A9856A87
  last_name: Giacobbe
  orcid: 0000-0001-8180-0904
- first_name: Thomas A
  full_name: Henzinger, Thomas A
  id: 40876CD8-F248-11E8-B48F-1D18A9856A87
  last_name: Henzinger
  orcid: 0000−0002−2985−7724
- first_name: Hui
  full_name: Kong, Hui
  id: 3BDE25AA-F248-11E8-B48F-1D18A9856A87
  last_name: Kong
  orcid: 0000-0002-3066-6941
citation:
  ama: 'Bogomolov S, Giacobbe M, Henzinger TA, Kong H. Conic abstractions for hybrid
    systems. In: Vol 10419. Springer; 2017:116-132. doi:<a href="https://doi.org/10.1007/978-3-319-65765-3_7">10.1007/978-3-319-65765-3_7</a>'
  apa: 'Bogomolov, S., Giacobbe, M., Henzinger, T. A., &#38; Kong, H. (2017). Conic
    abstractions for hybrid systems (Vol. 10419, pp. 116–132). Presented at the FORMATS:
    Formal Modelling and Analysis of Timed Systems, Berlin, Germany: Springer. <a
    href="https://doi.org/10.1007/978-3-319-65765-3_7">https://doi.org/10.1007/978-3-319-65765-3_7</a>'
  chicago: Bogomolov, Sergiy, Mirco Giacobbe, Thomas A Henzinger, and Hui Kong. “Conic
    Abstractions for Hybrid Systems,” 10419:116–32. Springer, 2017. <a href="https://doi.org/10.1007/978-3-319-65765-3_7">https://doi.org/10.1007/978-3-319-65765-3_7</a>.
  ieee: 'S. Bogomolov, M. Giacobbe, T. A. Henzinger, and H. Kong, “Conic abstractions
    for hybrid systems,” presented at the FORMATS: Formal Modelling and Analysis of
    Timed Systems, Berlin, Germany, 2017, vol. 10419, pp. 116–132.'
  ista: 'Bogomolov S, Giacobbe M, Henzinger TA, Kong H. 2017. Conic abstractions for
    hybrid systems. FORMATS: Formal Modelling and Analysis of Timed Systems, LNCS,
    vol. 10419, 116–132.'
  mla: Bogomolov, Sergiy, et al. <i>Conic Abstractions for Hybrid Systems</i>. Vol.
    10419, Springer, 2017, pp. 116–32, doi:<a href="https://doi.org/10.1007/978-3-319-65765-3_7">10.1007/978-3-319-65765-3_7</a>.
  short: S. Bogomolov, M. Giacobbe, T.A. Henzinger, H. Kong, in:, Springer, 2017,
    pp. 116–132.
conference:
  end_date: 2017-09-07
  location: Berlin, Germany
  name: 'FORMATS: Formal Modelling and Analysis of Timed Systems'
  start_date: 2017-09-05
date_created: 2018-12-11T11:47:41Z
date_published: 2017-09-01T00:00:00Z
date_updated: 2023-09-07T12:53:00Z
day: '01'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1007/978-3-319-65765-3_7
file:
- access_level: open_access
  checksum: faf546914ba29bcf9974ee36b6b16750
  content_type: application/pdf
  creator: system
  date_created: 2018-12-12T10:12:38Z
  date_updated: 2020-07-14T12:47:31Z
  file_id: '4956'
  file_name: IST-2017-831-v1+1_main.pdf
  file_size: 3806864
  relation: main_file
file_date_updated: 2020-07-14T12:47:31Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 116 - 132
project:
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: S11402-N23
  name: Moderne Concurrency Paradigms
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: Z211
  name: The Wittgenstein Prize
publication_identifier:
  isbn:
  - 978-331965764-6
publication_status: published
publisher: Springer
publist_id: '7129'
pubrep_id: '831'
quality_controlled: '1'
related_material:
  record:
  - id: '6894'
    relation: dissertation_contains
    status: public
scopus_import: 1
status: public
title: Conic abstractions for hybrid systems
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: '10419 '
year: '2017'
...
---
_id: '1351'
abstract:
- lang: eng
  text: The behaviour of gene regulatory networks (GRNs) is typically analysed using
    simulation-based statistical testing-like methods. In this paper, we demonstrate
    that we can replace this approach by a formal verification-like method that gives
    higher assurance and scalability. We focus on Wagner’s weighted GRN model with
    varying weights, which is used in evolutionary biology. In the model, weight parameters
    represent the gene interaction strength that may change due to genetic mutations.
    For a property of interest, we synthesise the constraints over the parameter space
    that represent the set of GRNs satisfying the property. We experimentally show
    that our parameter synthesis procedure computes the mutational robustness of GRNs—an
    important problem of interest in evolutionary biology—more efficiently than the
    classical simulation method. We specify the property in linear temporal logic.
    We employ symbolic bounded model checking and SMT solving to compute the space
    of GRNs that satisfy the property, which amounts to synthesizing a set of linear
    constraints on the weights.
article_processing_charge: No
author:
- first_name: Mirco
  full_name: Giacobbe, Mirco
  id: 3444EA5E-F248-11E8-B48F-1D18A9856A87
  last_name: Giacobbe
  orcid: 0000-0001-8180-0904
- first_name: Calin C
  full_name: Guet, Calin C
  id: 47F8433E-F248-11E8-B48F-1D18A9856A87
  last_name: Guet
  orcid: 0000-0001-6220-2052
- first_name: Ashutosh
  full_name: Gupta, Ashutosh
  id: 335E5684-F248-11E8-B48F-1D18A9856A87
  last_name: Gupta
- first_name: Thomas A
  full_name: Henzinger, Thomas A
  id: 40876CD8-F248-11E8-B48F-1D18A9856A87
  last_name: Henzinger
  orcid: 0000−0002−2985−7724
- first_name: Tiago
  full_name: Paixao, Tiago
  id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
  last_name: Paixao
  orcid: 0000-0003-2361-3953
- first_name: Tatjana
  full_name: Petrov, Tatjana
  id: 3D5811FC-F248-11E8-B48F-1D18A9856A87
  last_name: Petrov
  orcid: 0000-0002-9041-0905
citation:
  ama: Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. Model checking
    the evolution of gene regulatory networks. <i>Acta Informatica</i>. 2017;54(8):765-787.
    doi:<a href="https://doi.org/10.1007/s00236-016-0278-x">10.1007/s00236-016-0278-x</a>
  apa: Giacobbe, M., Guet, C. C., Gupta, A., Henzinger, T. A., Paixao, T., &#38; Petrov,
    T. (2017). Model checking the evolution of gene regulatory networks. <i>Acta Informatica</i>.
    Springer. <a href="https://doi.org/10.1007/s00236-016-0278-x">https://doi.org/10.1007/s00236-016-0278-x</a>
  chicago: Giacobbe, Mirco, Calin C Guet, Ashutosh Gupta, Thomas A Henzinger, Tiago
    Paixao, and Tatjana Petrov. “Model Checking the Evolution of Gene Regulatory Networks.”
    <i>Acta Informatica</i>. Springer, 2017. <a href="https://doi.org/10.1007/s00236-016-0278-x">https://doi.org/10.1007/s00236-016-0278-x</a>.
  ieee: M. Giacobbe, C. C. Guet, A. Gupta, T. A. Henzinger, T. Paixao, and T. Petrov,
    “Model checking the evolution of gene regulatory networks,” <i>Acta Informatica</i>,
    vol. 54, no. 8. Springer, pp. 765–787, 2017.
  ista: Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. 2017. Model
    checking the evolution of gene regulatory networks. Acta Informatica. 54(8), 765–787.
  mla: Giacobbe, Mirco, et al. “Model Checking the Evolution of Gene Regulatory Networks.”
    <i>Acta Informatica</i>, vol. 54, no. 8, Springer, 2017, pp. 765–87, doi:<a href="https://doi.org/10.1007/s00236-016-0278-x">10.1007/s00236-016-0278-x</a>.
  short: M. Giacobbe, C.C. Guet, A. Gupta, T.A. Henzinger, T. Paixao, T. Petrov, Acta
    Informatica 54 (2017) 765–787.
date_created: 2018-12-11T11:51:32Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2025-05-28T11:57:04Z
day: '01'
ddc:
- '006'
- '576'
department:
- _id: ToHe
- _id: CaGu
- _id: NiBa
doi: 10.1007/s00236-016-0278-x
ec_funded: 1
external_id:
  isi:
  - '000414343200003'
file:
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intvolume: '        54'
isi: 1
issue: '8'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 765 - 787
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '267989'
  name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: S 11407_N23
  name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: Z211
  name: The Wittgenstein Prize
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
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  name: Speed of Adaptation in Population Genetics and Evolutionary Computation
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  name: Limits to selection in biology and in evolutionary computation
publication: Acta Informatica
publication_identifier:
  issn:
  - '00015903'
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publisher: Springer
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related_material:
  record:
  - id: '1835'
    relation: earlier_version
    status: public
scopus_import: '1'
status: public
title: Model checking the evolution of gene regulatory networks
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 54
year: '2017'
...
---
_id: '1835'
abstract:
- lang: eng
  text: The behaviour of gene regulatory networks (GRNs) is typically analysed using
    simulation-based statistical testing-like methods. In this paper, we demonstrate
    that we can replace this approach by a formal verification-like method that gives
    higher assurance and scalability. We focus on Wagner’s weighted GRN model with
    varying weights, which is used in evolutionary biology. In the model, weight parameters
    represent the gene interaction strength that may change due to genetic mutations.
    For a property of interest, we synthesise the constraints over the parameter space
    that represent the set of GRNs satisfying the property. We experimentally show
    that our parameter synthesis procedure computes the mutational robustness of GRNs
    –an important problem of interest in evolutionary biology– more efficiently than
    the classical simulation method. We specify the property in linear temporal logics.
    We employ symbolic bounded model checking and SMT solving to compute the space
    of GRNs that satisfy the property, which amounts to synthesizing a set of linear
    constraints on the weights.
acknowledgement: "SNSF Early Postdoc.Mobility Fellowship, the grant number P2EZP2
  148797.\r\n"
alternative_title:
- LNCS
author:
- first_name: Mirco
  full_name: Giacobbe, Mirco
  id: 3444EA5E-F248-11E8-B48F-1D18A9856A87
  last_name: Giacobbe
  orcid: 0000-0001-8180-0904
- first_name: Calin C
  full_name: Guet, Calin C
  id: 47F8433E-F248-11E8-B48F-1D18A9856A87
  last_name: Guet
  orcid: 0000-0001-6220-2052
- first_name: Ashutosh
  full_name: Gupta, Ashutosh
  id: 335E5684-F248-11E8-B48F-1D18A9856A87
  last_name: Gupta
- first_name: Thomas A
  full_name: Henzinger, Thomas A
  id: 40876CD8-F248-11E8-B48F-1D18A9856A87
  last_name: Henzinger
  orcid: 0000−0002−2985−7724
- first_name: Tiago
  full_name: Paixao, Tiago
  id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
  last_name: Paixao
  orcid: 0000-0003-2361-3953
- first_name: Tatjana
  full_name: Petrov, Tatjana
  id: 3D5811FC-F248-11E8-B48F-1D18A9856A87
  last_name: Petrov
  orcid: 0000-0002-9041-0905
citation:
  ama: Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. Model checking
    gene regulatory networks. 2015;9035:469-483. doi:<a href="https://doi.org/10.1007/978-3-662-46681-0_47">10.1007/978-3-662-46681-0_47</a>
  apa: 'Giacobbe, M., Guet, C. C., Gupta, A., Henzinger, T. A., Paixao, T., &#38;
    Petrov, T. (2015). Model checking gene regulatory networks. Presented at the TACAS:
    Tools and Algorithms for the Construction and Analysis of Systems, London, United
    Kingdom: Springer. <a href="https://doi.org/10.1007/978-3-662-46681-0_47">https://doi.org/10.1007/978-3-662-46681-0_47</a>'
  chicago: Giacobbe, Mirco, Calin C Guet, Ashutosh Gupta, Thomas A Henzinger, Tiago
    Paixao, and Tatjana Petrov. “Model Checking Gene Regulatory Networks.” Lecture
    Notes in Computer Science. Springer, 2015. <a href="https://doi.org/10.1007/978-3-662-46681-0_47">https://doi.org/10.1007/978-3-662-46681-0_47</a>.
  ieee: M. Giacobbe, C. C. Guet, A. Gupta, T. A. Henzinger, T. Paixao, and T. Petrov,
    “Model checking gene regulatory networks,” vol. 9035. Springer, pp. 469–483, 2015.
  ista: Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. 2015. Model
    checking gene regulatory networks. 9035, 469–483.
  mla: Giacobbe, Mirco, et al. <i>Model Checking Gene Regulatory Networks</i>. Vol.
    9035, Springer, 2015, pp. 469–83, doi:<a href="https://doi.org/10.1007/978-3-662-46681-0_47">10.1007/978-3-662-46681-0_47</a>.
  short: M. Giacobbe, C.C. Guet, A. Gupta, T.A. Henzinger, T. Paixao, T. Petrov, 9035
    (2015) 469–483.
conference:
  end_date: 2015-04-18
  location: London, United Kingdom
  name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems'
  start_date: 2015-04-11
date_created: 2018-12-11T11:54:16Z
date_published: 2015-04-01T00:00:00Z
date_updated: 2025-05-28T11:57:04Z
day: '01'
department:
- _id: ToHe
- _id: CaGu
- _id: NiBa
doi: 10.1007/978-3-662-46681-0_47
ec_funded: 1
intvolume: '      9035'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: http://arxiv.org/abs/1410.7704
month: '04'
oa: 1
oa_version: Preprint
page: 469 - 483
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '267989'
  name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: S 11407_N23
  name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: Z211
  name: The Wittgenstein Prize
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '618091'
  name: Speed of Adaptation in Population Genetics and Evolutionary Computation
- _id: 25B07788-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '250152'
  name: Limits to selection in biology and in evolutionary computation
- _id: 25681D80-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '291734'
  name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: Springer
publist_id: '5267'
quality_controlled: '1'
related_material:
  record:
  - id: '1351'
    relation: later_version
    status: public
scopus_import: 1
series_title: Lecture Notes in Computer Science
status: public
title: Model checking gene regulatory networks
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9035
year: '2015'
...
