---
_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. Acta Informatica. 2017;54(8):765-787.
doi:10.1007/s00236-016-0278-x
apa: Giacobbe, M., Guet, C. C., Gupta, A., Henzinger, T. A., Paixao, T., & Petrov,
T. (2017). Model checking the evolution of gene regulatory networks. Acta Informatica.
Springer. https://doi.org/10.1007/s00236-016-0278-x
chicago: Giacobbe, Mirco, Calin C Guet, Ashutosh Gupta, Thomas A Henzinger, Tiago
Paixao, and Tatjana Petrov. “Model Checking the Evolution of Gene Regulatory Networks.”
Acta Informatica. Springer, 2017. https://doi.org/10.1007/s00236-016-0278-x.
ieee: M. Giacobbe, C. C. Guet, A. Gupta, T. A. Henzinger, T. Paixao, and T. Petrov,
“Model checking the evolution of gene regulatory networks,” Acta Informatica,
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.”
Acta Informatica, vol. 54, no. 8, Springer, 2017, pp. 765–87, doi:10.1007/s00236-016-0278-x.
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: 2023-09-20T11:06:03Z
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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checksum: 4e661d9135d7f8c342e8e258dee76f3e
content_type: application/pdf
creator: dernst
date_created: 2019-01-17T15:57:29Z
date_updated: 2020-07-14T12:44:46Z
file_id: '5841'
file_name: 2017_ActaInformatica_Giacobbe.pdf
file_size: 755241
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intvolume: ' 54'
isi: 1
issue: '8'
language:
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license: https://creativecommons.org/licenses/by/4.0/
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
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Acta Informatica
publication_identifier:
issn:
- '00015903'
publication_status: published
publisher: Springer
publist_id: '5898'
pubrep_id: '649'
quality_controlled: '1'
related_material:
record:
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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: '1230'
abstract:
- lang: eng
text: Concolic testing is a promising method for generating test suites for large
programs. However, it suffers from the path-explosion problem and often fails
to find tests that cover difficult-to-reach parts of programs. In contrast, model
checkers based on counterexample-guided abstraction refinement explore programs
exhaustively, while failing to scale on large programs with precision. In this
paper, we present a novel method that iteratively combines concolic testing and
model checking to find a test suite for a given coverage criterion. If concolic
testing fails to cover some test goals, then the model checker refines its program
abstraction to prove more paths infeasible, which reduces the search space for
concolic testing. We have implemented our method on top of the concolictesting
tool Crest and the model checker CpaChecker. We evaluated our tool on a collection
of programs and a category of SvComp benchmarks. In our experiments, we observed
an improvement in branch coverage compared to Crest from 48% to 63% in the best
case, and from 66% to 71% on average.
acknowledgement: "We thank Andrey Kupriyanov for feedback on the manuscript,\r\nand
Michael Tautschnig for help with preparing the experiments. This research was supported
in part by the European Research Council (ERC) under grant 267989 (QUAREM) and by
the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE) and Z211-N23 (Wittgenstein
Award)."
alternative_title:
- LNCS
author:
- first_name: Przemyslaw
full_name: Daca, Przemyslaw
id: 49351290-F248-11E8-B48F-1D18A9856A87
last_name: Daca
- 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
citation:
ama: 'Daca P, Gupta A, Henzinger TA. Abstraction-driven concolic testing. In: Vol
9583. Springer; 2016:328-347. doi:10.1007/978-3-662-49122-5_16'
apa: 'Daca, P., Gupta, A., & Henzinger, T. A. (2016). Abstraction-driven concolic
testing (Vol. 9583, pp. 328–347). Presented at the VMCAI: Verification, Model
Checking and Abstract Interpretation, St. Petersburg, FL, USA: Springer. https://doi.org/10.1007/978-3-662-49122-5_16'
chicago: Daca, Przemyslaw, Ashutosh Gupta, and Thomas A Henzinger. “Abstraction-Driven
Concolic Testing,” 9583:328–47. Springer, 2016. https://doi.org/10.1007/978-3-662-49122-5_16.
ieee: 'P. Daca, A. Gupta, and T. A. Henzinger, “Abstraction-driven concolic testing,”
presented at the VMCAI: Verification, Model Checking and Abstract Interpretation,
St. Petersburg, FL, USA, 2016, vol. 9583, pp. 328–347.'
ista: 'Daca P, Gupta A, Henzinger TA. 2016. Abstraction-driven concolic testing.
VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS, vol. 9583,
328–347.'
mla: Daca, Przemyslaw, et al. Abstraction-Driven Concolic Testing. Vol. 9583,
Springer, 2016, pp. 328–47, doi:10.1007/978-3-662-49122-5_16.
short: P. Daca, A. Gupta, T.A. Henzinger, in:, Springer, 2016, pp. 328–347.
conference:
end_date: 2016-01-19
location: St. Petersburg, FL, USA
name: 'VMCAI: Verification, Model Checking and Abstract Interpretation'
start_date: 2016-01-17
date_created: 2018-12-11T11:50:50Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2023-09-07T11:58:33Z
day: '01'
department:
- _id: ToHe
doi: 10.1007/978-3-662-49122-5_16
ec_funded: 1
intvolume: ' 9583'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1511.02615
month: '01'
oa: 1
oa_version: Preprint
page: 328 - 347
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication_status: published
publisher: Springer
publist_id: '6104'
quality_controlled: '1'
related_material:
record:
- id: '1155'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Abstraction-driven concolic testing
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9583
year: '2016'
...
---
_id: '1808'
article_number: '7'
author:
- 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
citation:
ama: Gupta A, Henzinger TA. Guest editors’ introduction to special issue on computational
methods in systems biology. ACM Transactions on Modeling and Computer Simulation.
2015;25(2). doi:10.1145/2745799
apa: Gupta, A., & Henzinger, T. A. (2015). Guest editors’ introduction to special
issue on computational methods in systems biology. ACM Transactions on Modeling
and Computer Simulation. ACM. https://doi.org/10.1145/2745799
chicago: Gupta, Ashutosh, and Thomas A Henzinger. “Guest Editors’ Introduction to
Special Issue on Computational Methods in Systems Biology.” ACM Transactions
on Modeling and Computer Simulation. ACM, 2015. https://doi.org/10.1145/2745799.
ieee: A. Gupta and T. A. Henzinger, “Guest editors’ introduction to special issue
on computational methods in systems biology,” ACM Transactions on Modeling
and Computer Simulation, vol. 25, no. 2. ACM, 2015.
ista: Gupta A, Henzinger TA. 2015. Guest editors’ introduction to special issue
on computational methods in systems biology. ACM Transactions on Modeling and
Computer Simulation. 25(2), 7.
mla: Gupta, Ashutosh, and Thomas A. Henzinger. “Guest Editors’ Introduction to Special
Issue on Computational Methods in Systems Biology.” ACM Transactions on Modeling
and Computer Simulation, vol. 25, no. 2, 7, ACM, 2015, doi:10.1145/2745799.
short: A. Gupta, T.A. Henzinger, ACM Transactions on Modeling and Computer Simulation
25 (2015).
date_created: 2018-12-11T11:54:07Z
date_published: 2015-05-01T00:00:00Z
date_updated: 2021-01-12T06:53:20Z
day: '01'
department:
- _id: ToHe
doi: 10.1145/2745799
intvolume: ' 25'
issue: '2'
language:
- iso: eng
month: '05'
oa_version: None
publication: ACM Transactions on Modeling and Computer Simulation
publication_status: published
publisher: ACM
publist_id: '5302'
quality_controlled: '1'
status: public
title: Guest editors' introduction to special issue on computational methods in systems
biology
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2015'
...
---
_id: '1992'
abstract:
- lang: eng
text: "We present a method and a tool for generating succinct representations of
sets of concurrent traces. We focus on trace sets that contain all correct or
all incorrect permutations of events from a given trace. We represent trace sets
as HB-Formulas that are Boolean combinations of happens-before constraints between
events. To generate a representation of incorrect interleavings, our method iteratively
explores interleavings that violate the specification and gathers generalizations
of the discovered interleavings into an HB-Formula; its complement yields a representation
of correct interleavings.\r\n\r\nWe claim that our trace set representations can
drive diverse verification, fault localization, repair, and synthesis techniques
for concurrent programs. We demonstrate this by using our tool in three case studies
involving synchronization synthesis, bug summarization, and abstraction refinement
based verification. In each case study, our initial experimental results have
been promising.\r\n\r\nIn the first case study, we present an algorithm for inferring
missing synchronization from an HB-Formula representing correct interleavings
of a given trace. The algorithm applies rules to rewrite specific patterns in
the HB-Formula into locks, barriers, and wait-notify constructs. In the second
case study, we use an HB-Formula representing incorrect interleavings for bug
summarization. While the HB-Formula itself is a concise counterexample summary,
we present additional inference rules to help identify specific concurrency bugs
such as data races, define-use order violations, and two-stage access bugs. In
the final case study, we present a novel predicate learning procedure that uses
HB-Formulas representing abstract counterexamples to accelerate counterexample-guided
abstraction refinement (CEGAR). In each iteration of the CEGAR loop, the procedure
refines the abstraction to eliminate multiple spurious abstract counterexamples
drawn from the HB-Formula."
author:
- 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: Arjun
full_name: Radhakrishna, Arjun
id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87
last_name: Radhakrishna
- first_name: Roopsha
full_name: Samanta, Roopsha
id: 3D2AAC08-F248-11E8-B48F-1D18A9856A87
last_name: Samanta
- first_name: Thorsten
full_name: Tarrach, Thorsten
id: 3D6E8F2C-F248-11E8-B48F-1D18A9856A87
last_name: Tarrach
orcid: 0000-0003-4409-8487
citation:
ama: 'Gupta A, Henzinger TA, Radhakrishna A, Samanta R, Tarrach T. Succinct representation
of concurrent trace sets. In: ACM; 2015:433-444. doi:10.1145/2676726.2677008'
apa: 'Gupta, A., Henzinger, T. A., Radhakrishna, A., Samanta, R., & Tarrach,
T. (2015). Succinct representation of concurrent trace sets (pp. 433–444). Presented
at the POPL: Principles of Programming Languages, Mumbai, India: ACM. https://doi.org/10.1145/2676726.2677008'
chicago: Gupta, Ashutosh, Thomas A Henzinger, Arjun Radhakrishna, Roopsha Samanta,
and Thorsten Tarrach. “Succinct Representation of Concurrent Trace Sets,” 433–44.
ACM, 2015. https://doi.org/10.1145/2676726.2677008.
ieee: 'A. Gupta, T. A. Henzinger, A. Radhakrishna, R. Samanta, and T. Tarrach, “Succinct
representation of concurrent trace sets,” presented at the POPL: Principles of
Programming Languages, Mumbai, India, 2015, pp. 433–444.'
ista: 'Gupta A, Henzinger TA, Radhakrishna A, Samanta R, Tarrach T. 2015. Succinct
representation of concurrent trace sets. POPL: Principles of Programming Languages,
433–444.'
mla: Gupta, Ashutosh, et al. Succinct Representation of Concurrent Trace Sets.
ACM, 2015, pp. 433–44, doi:10.1145/2676726.2677008.
short: A. Gupta, T.A. Henzinger, A. Radhakrishna, R. Samanta, T. Tarrach, in:, ACM,
2015, pp. 433–444.
conference:
end_date: 2015-01-17
location: Mumbai, India
name: 'POPL: Principles of Programming Languages'
start_date: 2015-01-15
date_created: 2018-12-11T11:55:05Z
date_published: 2015-01-15T00:00:00Z
date_updated: 2021-01-12T06:54:33Z
day: '15'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1145/2676726.2677008
file:
- access_level: open_access
checksum: f0d4395b600f410a191256ac0b73af32
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:56Z
date_updated: 2020-07-14T12:45:22Z
file_id: '5314'
file_name: IST-2015-317-v1+1_author_version.pdf
file_size: 399462
relation: main_file
file_date_updated: 2020-07-14T12:45:22Z
has_accepted_license: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 433 - 444
publication_identifier:
isbn:
- 978-1-4503-3300-9
publication_status: published
publisher: ACM
publist_id: '5091'
pubrep_id: '317'
quality_controlled: '1'
scopus_import: 1
status: public
title: Succinct representation of concurrent trace sets
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_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:10.1007/978-3-662-46681-0_47
apa: 'Giacobbe, M., Guet, C. C., Gupta, A., Henzinger, T. A., Paixao, T., &
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. https://doi.org/10.1007/978-3-662-46681-0_47'
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. https://doi.org/10.1007/978-3-662-46681-0_47.
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. Model Checking Gene Regulatory Networks. Vol.
9035, Springer, 2015, pp. 469–83, doi:10.1007/978-3-662-46681-0_47.
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: 2023-09-20T11:06:03Z
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'
...
---
_id: '1702'
abstract:
- lang: eng
text: In this paper we present INTERHORN, a solver for recursion-free Horn clauses.
The main application domain of INTERHORN lies in solving interpolation problems
arising in software verification. We show how a range of interpolation problems,
including path, transition, nested, state/transition and well-founded interpolation
can be handled directly by INTERHORN. By detailing these interpolation problems
and their Horn clause representations, we hope to encourage the emergence of a
common back-end interpolation interface useful for diverse verification tools.
alternative_title:
- EPTCS
author:
- first_name: Ashutosh
full_name: Gupta, Ashutosh
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
- first_name: Corneliu
full_name: Popeea, Corneliu
last_name: Popeea
- first_name: Andrey
full_name: Rybalchenko, Andrey
last_name: Rybalchenko
citation:
ama: 'Gupta A, Popeea C, Rybalchenko A. Generalised interpolation by solving recursion
free-horn clauses. In: Electronic Proceedings in Theoretical Computer Science,
EPTCS. Vol 169. Open Publishing; 2014:31-38. doi:10.4204/EPTCS.169.5'
apa: 'Gupta, A., Popeea, C., & Rybalchenko, A. (2014). Generalised interpolation
by solving recursion free-horn clauses. In Electronic Proceedings in Theoretical
Computer Science, EPTCS (Vol. 169, pp. 31–38). Vienna, Austria: Open Publishing.
https://doi.org/10.4204/EPTCS.169.5'
chicago: Gupta, Ashutosh, Corneliu Popeea, and Andrey Rybalchenko. “Generalised
Interpolation by Solving Recursion Free-Horn Clauses.” In Electronic Proceedings
in Theoretical Computer Science, EPTCS, 169:31–38. Open Publishing, 2014.
https://doi.org/10.4204/EPTCS.169.5.
ieee: A. Gupta, C. Popeea, and A. Rybalchenko, “Generalised interpolation by solving
recursion free-horn clauses,” in Electronic Proceedings in Theoretical Computer
Science, EPTCS, Vienna, Austria, 2014, vol. 169, pp. 31–38.
ista: 'Gupta A, Popeea C, Rybalchenko A. 2014. Generalised interpolation by solving
recursion free-horn clauses. Electronic Proceedings in Theoretical Computer Science,
EPTCS. HCVS: Horn Clauses for Verification and Synthesis, EPTCS, vol. 169, 31–38.'
mla: Gupta, Ashutosh, et al. “Generalised Interpolation by Solving Recursion Free-Horn
Clauses.” Electronic Proceedings in Theoretical Computer Science, EPTCS,
vol. 169, Open Publishing, 2014, pp. 31–38, doi:10.4204/EPTCS.169.5.
short: A. Gupta, C. Popeea, A. Rybalchenko, in:, Electronic Proceedings in Theoretical
Computer Science, EPTCS, Open Publishing, 2014, pp. 31–38.
conference:
end_date: 2014-07-17
location: Vienna, Austria
name: 'HCVS: Horn Clauses for Verification and Synthesis'
start_date: 2014-07-17
date_created: 2018-12-11T11:53:33Z
date_published: 2014-12-02T00:00:00Z
date_updated: 2021-01-12T06:52:38Z
day: '02'
department:
- _id: ToHe
doi: 10.4204/EPTCS.169.5
intvolume: ' 169'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1303.7378v2
month: '12'
oa: 1
oa_version: Submitted Version
page: 31 - 38
publication: Electronic Proceedings in Theoretical Computer Science, EPTCS
publication_status: published
publisher: Open Publishing
publist_id: '5435'
quality_controlled: '1'
status: public
title: Generalised interpolation by solving recursion free-horn clauses
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 169
year: '2014'
...
---
_id: '1869'
abstract:
- lang: eng
text: Boolean controllers for systems with complex datapaths are often very difficult
to implement correctly, in particular when concurrency is involved. Yet, in many
instances it is easy to formally specify correctness. For example, the specification
for the controller of a pipelined processor only has to state that the pipelined
processor gives the same results as a non-pipelined reference design. This makes
such controllers a good target for automated synthesis. However, an efficient
abstraction for the complex datapath elements is needed, as a bit-precise description
is often infeasible. We present Suraq, the first controller synthesis tool which
uses uninterpreted functions for the abstraction. Quantified firstorder formulas
(with specific quantifier structure) serve as the specification language from
which Suraq synthesizes Boolean controllers. Suraq transforms the specification
into an unsatisfiable SMT formula, and uses Craig interpolation to compute its
results. Using Suraq, we were able to synthesize a controller (consisting of two
Boolean signals) for a five-stage pipelined DLX processor in roughly one hour
and 15 minutes.
acknowledgement: The work presented in this paper was supported in part by the European
Research Council (ERC) under grant agreement QUAINT (I774-N23)
alternative_title:
- LNCS
author:
- first_name: Georg
full_name: Hofferek, Georg
last_name: Hofferek
- first_name: Ashutosh
full_name: Gupta, Ashutosh
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
citation:
ama: 'Hofferek G, Gupta A. Suraq - a controller synthesis tool using uninterpreted
functions. In: Yahav E, ed. HVC 2014. Vol 8855. Springer; 2014:68-74. doi:10.1007/978-3-319-13338-6_6'
apa: 'Hofferek, G., & Gupta, A. (2014). Suraq - a controller synthesis tool
using uninterpreted functions. In E. Yahav (Ed.), HVC 2014 (Vol. 8855,
pp. 68–74). Haifa, Israel: Springer. https://doi.org/10.1007/978-3-319-13338-6_6'
chicago: Hofferek, Georg, and Ashutosh Gupta. “Suraq - a Controller Synthesis Tool
Using Uninterpreted Functions.” In HVC 2014, edited by Eran Yahav, 8855:68–74.
Springer, 2014. https://doi.org/10.1007/978-3-319-13338-6_6.
ieee: G. Hofferek and A. Gupta, “Suraq - a controller synthesis tool using uninterpreted
functions,” in HVC 2014, Haifa, Israel, 2014, vol. 8855, pp. 68–74.
ista: 'Hofferek G, Gupta A. 2014. Suraq - a controller synthesis tool using uninterpreted
functions. HVC 2014. HVC: Haifa Verification Conference, LNCS, vol. 8855, 68–74.'
mla: Hofferek, Georg, and Ashutosh Gupta. “Suraq - a Controller Synthesis Tool Using
Uninterpreted Functions.” HVC 2014, edited by Eran Yahav, vol. 8855, Springer,
2014, pp. 68–74, doi:10.1007/978-3-319-13338-6_6.
short: G. Hofferek, A. Gupta, in:, E. Yahav (Ed.), HVC 2014, Springer, 2014, pp.
68–74.
conference:
end_date: 2014-11-20
location: Haifa, Israel
name: 'HVC: Haifa Verification Conference'
start_date: 2014-11-18
date_created: 2018-12-11T11:54:27Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:53:44Z
day: '01'
department:
- _id: ToHe
doi: 10.1007/978-3-319-13338-6_6
ec_funded: 1
editor:
- first_name: Eran
full_name: Yahav, Eran
last_name: Yahav
intvolume: ' 8855'
language:
- iso: eng
month: '01'
oa_version: None
page: 68 - 74
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
publication: HVC 2014
publication_status: published
publisher: Springer
publist_id: '5228'
quality_controlled: '1'
status: public
title: Suraq - a controller synthesis tool using uninterpreted functions
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 8855
year: '2014'
...
---
_id: '1872'
abstract:
- lang: eng
text: Extensionality axioms are common when reasoning about data collections, such
as arrays and functions in program analysis, or sets in mathematics. An extensionality
axiom asserts that two collections are equal if they consist of the same elements
at the same indices. Using extensionality is often required to show that two collections
are equal. A typical example is the set theory theorem (∀x)(∀y)x∪y = y ∪x. Interestingly,
while humans have no problem with proving such set identities using extensionality,
they are very hard for superposition theorem provers because of the calculi they
use. In this paper we show how addition of a new inference rule, called extensionality
resolution, allows first-order theorem provers to easily solve problems no modern
first-order theorem prover can solve. We illustrate this by running the VAMPIRE
theorem prover with extensionality resolution on a number of set theory and array
problems. Extensionality resolution helps VAMPIRE to solve problems from the TPTP
library of first-order problems that were never solved before by any prover.
acknowledgement: This research was supported in part by the Austrian National Research
Network RiSE (S11410-N23).
alternative_title:
- LNCS
author:
- first_name: Ashutosh
full_name: Gupta, Ashutosh
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
- first_name: Laura
full_name: Kovács, Laura
last_name: Kovács
- first_name: Bernhard
full_name: Kragl, Bernhard
id: 320FC952-F248-11E8-B48F-1D18A9856A87
last_name: Kragl
orcid: 0000-0001-7745-9117
- first_name: Andrei
full_name: Voronkov, Andrei
last_name: Voronkov
citation:
ama: 'Gupta A, Kovács L, Kragl B, Voronkov A. Extensional crisis and proving identity.
In: Cassez F, Raskin J-F, eds. ATVA 2014. Vol 8837. Springer; 2014:185-200.
doi:10.1007/978-3-319-11936-6_14'
apa: 'Gupta, A., Kovács, L., Kragl, B., & Voronkov, A. (2014). Extensional crisis
and proving identity. In F. Cassez & J.-F. Raskin (Eds.), ATVA 2014
(Vol. 8837, pp. 185–200). Sydney, Australia: Springer. https://doi.org/10.1007/978-3-319-11936-6_14'
chicago: Gupta, Ashutosh, Laura Kovács, Bernhard Kragl, and Andrei Voronkov. “Extensional
Crisis and Proving Identity.” In ATVA 2014, edited by Franck Cassez and
Jean-François Raskin, 8837:185–200. Springer, 2014. https://doi.org/10.1007/978-3-319-11936-6_14.
ieee: A. Gupta, L. Kovács, B. Kragl, and A. Voronkov, “Extensional crisis and proving
identity,” in ATVA 2014, Sydney, Australia, 2014, vol. 8837, pp. 185–200.
ista: 'Gupta A, Kovács L, Kragl B, Voronkov A. 2014. Extensional crisis and proving
identity. ATVA 2014. ATVA: Automated Technology for Verification and Analysis,
LNCS, vol. 8837, 185–200.'
mla: Gupta, Ashutosh, et al. “Extensional Crisis and Proving Identity.” ATVA
2014, edited by Franck Cassez and Jean-François Raskin, vol. 8837, Springer,
2014, pp. 185–200, doi:10.1007/978-3-319-11936-6_14.
short: A. Gupta, L. Kovács, B. Kragl, A. Voronkov, in:, F. Cassez, J.-F. Raskin
(Eds.), ATVA 2014, Springer, 2014, pp. 185–200.
conference:
end_date: 2014-11-07
location: Sydney, Australia
name: 'ATVA: Automated Technology for Verification and Analysis'
start_date: 2014-11-03
date_created: 2018-12-11T11:54:28Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:53:45Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-319-11936-6_14
ec_funded: 1
editor:
- first_name: Franck
full_name: Cassez, Franck
last_name: Cassez
- first_name: Jean-François
full_name: Raskin, Jean-François
last_name: Raskin
file:
- access_level: open_access
checksum: af4bd3fc1f4c93075e4dc5cbf625fe7b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:15Z
date_updated: 2020-07-14T12:45:19Z
file_id: '4801'
file_name: IST-2016-641-v1+1_atva2014.pdf
file_size: 244294
relation: main_file
file_date_updated: 2020-07-14T12:45:19Z
has_accepted_license: '1'
intvolume: ' 8837'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 185 - 200
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
publication: ATVA 2014
publication_status: published
publisher: Springer
publist_id: '5226'
pubrep_id: '641'
quality_controlled: '1'
scopus_import: 1
status: public
title: Extensional crisis and proving identity
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 8837
year: '2014'
...
---
_id: '1385'
abstract:
- lang: eng
text: It is often difficult to correctly implement a Boolean controller for a complex
system, especially when concurrency is involved. Yet, it may be easy to formally
specify a controller. For instance, for a pipelined processor it suffices to state
that the visible behavior of the pipelined system should be identical to a non-pipelined
reference system (Burch-Dill paradigm). We present a novel procedure to efficiently
synthesize multiple Boolean control signals from a specification given as a quantified
first-order formula (with a specific quantifier structure). Our approach uses
uninterpreted functions to abstract details of the design. We construct an unsatisfiable
SMT formula from the given specification. Then, from just one proof of unsatisfiability,
we use a variant of Craig interpolation to compute multiple coordinated interpolants
that implement the Boolean control signals. Our method avoids iterative learning
and back-substitution of the control functions. We applied our approach to synthesize
a controller for a simple two-stage pipelined processor, and present first experimental
results.
acknowledgement: "This research was supported by the European Commission through project\r\nDIAMOND
\ (FP7-2009-IST-4-248613), and QUAINT (I774-N23), "
author:
- first_name: Georg
full_name: Hofferek, Georg
last_name: Hofferek
- first_name: Ashutosh
full_name: Gupta, Ashutosh
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
- first_name: Bettina
full_name: Könighofer, Bettina
last_name: Könighofer
- first_name: Jie
full_name: Jiang, Jie
last_name: Jiang
- first_name: Roderick
full_name: Bloem, Roderick
last_name: Bloem
citation:
ama: 'Hofferek G, Gupta A, Könighofer B, Jiang J, Bloem R. Synthesizing multiple
boolean functions using interpolation on a single proof. In: 2013 Formal Methods
in Computer-Aided Design. IEEE; 2013:77-84. doi:10.1109/FMCAD.2013.6679394'
apa: 'Hofferek, G., Gupta, A., Könighofer, B., Jiang, J., & Bloem, R. (2013).
Synthesizing multiple boolean functions using interpolation on a single proof.
In 2013 Formal Methods in Computer-Aided Design (pp. 77–84). Portland,
OR, United States: IEEE. https://doi.org/10.1109/FMCAD.2013.6679394'
chicago: Hofferek, Georg, Ashutosh Gupta, Bettina Könighofer, Jie Jiang, and Roderick
Bloem. “Synthesizing Multiple Boolean Functions Using Interpolation on a Single
Proof.” In 2013 Formal Methods in Computer-Aided Design, 77–84. IEEE, 2013.
https://doi.org/10.1109/FMCAD.2013.6679394.
ieee: G. Hofferek, A. Gupta, B. Könighofer, J. Jiang, and R. Bloem, “Synthesizing
multiple boolean functions using interpolation on a single proof,” in 2013
Formal Methods in Computer-Aided Design, Portland, OR, United States, 2013,
pp. 77–84.
ista: 'Hofferek G, Gupta A, Könighofer B, Jiang J, Bloem R. 2013. Synthesizing multiple
boolean functions using interpolation on a single proof. 2013 Formal Methods in
Computer-Aided Design. FMCAD: Formal Methods in Computer-Aided Design, 77–84.'
mla: Hofferek, Georg, et al. “Synthesizing Multiple Boolean Functions Using Interpolation
on a Single Proof.” 2013 Formal Methods in Computer-Aided Design, IEEE,
2013, pp. 77–84, doi:10.1109/FMCAD.2013.6679394.
short: G. Hofferek, A. Gupta, B. Könighofer, J. Jiang, R. Bloem, in:, 2013 Formal
Methods in Computer-Aided Design, IEEE, 2013, pp. 77–84.
conference:
end_date: 2013-10-23
location: Portland, OR, United States
name: 'FMCAD: Formal Methods in Computer-Aided Design'
start_date: 2013-10-20
date_created: 2018-12-11T11:51:43Z
date_published: 2013-12-11T00:00:00Z
date_updated: 2021-01-12T06:50:19Z
day: '11'
department:
- _id: ToHe
doi: 10.1109/FMCAD.2013.6679394
ec_funded: 1
external_id:
arxiv:
- '1308.4767'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1308.4767
month: '12'
oa: 1
oa_version: Preprint
page: 77 - 84
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
publication: 2013 Formal Methods in Computer-Aided Design
publication_status: published
publisher: IEEE
publist_id: '5825'
quality_controlled: '1'
status: public
title: Synthesizing multiple boolean functions using interpolation on a single proof
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '2237'
abstract:
- lang: eng
text: We describe new extensions of the Vampire theorem prover for computing tree
interpolants. These extensions generalize Craig interpolation in Vampire, and
can also be used to derive sequence interpolants. We evaluated our implementation
on a large number of examples over the theory of linear integer arithmetic and
integer-indexed arrays, with and without quantifiers. When compared to other methods,
our experiments show that some examples could only be solved by our implementation.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Régis
full_name: Blanc, Régis
last_name: Blanc
- first_name: Ashutosh
full_name: Gupta, Ashutosh
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
- first_name: Laura
full_name: Kovács, Laura
last_name: Kovács
- first_name: Bernhard
full_name: Kragl, Bernhard
id: 320FC952-F248-11E8-B48F-1D18A9856A87
last_name: Kragl
orcid: 0000-0001-7745-9117
citation:
ama: Blanc R, Gupta A, Kovács L, Kragl B. Tree interpolation in Vampire. 2013;8312:173-181.
doi:10.1007/978-3-642-45221-5_13
apa: 'Blanc, R., Gupta, A., Kovács, L., & Kragl, B. (2013). Tree interpolation
in Vampire. Presented at the LPAR: Logic for Programming, Artificial Intelligence,
and Reasoning, Stellenbosch, South Africa: Springer. https://doi.org/10.1007/978-3-642-45221-5_13'
chicago: Blanc, Régis, Ashutosh Gupta, Laura Kovács, and Bernhard Kragl. “Tree Interpolation
in Vampire.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-45221-5_13.
ieee: R. Blanc, A. Gupta, L. Kovács, and B. Kragl, “Tree interpolation in Vampire,”
vol. 8312. Springer, pp. 173–181, 2013.
ista: Blanc R, Gupta A, Kovács L, Kragl B. 2013. Tree interpolation in Vampire.
8312, 173–181.
mla: Blanc, Régis, et al. Tree Interpolation in Vampire. Vol. 8312, Springer,
2013, pp. 173–81, doi:10.1007/978-3-642-45221-5_13.
short: R. Blanc, A. Gupta, L. Kovács, B. Kragl, 8312 (2013) 173–181.
conference:
end_date: 2013-12-19
location: Stellenbosch, South Africa
name: 'LPAR: Logic for Programming, Artificial Intelligence, and Reasoning'
start_date: 2013-12-14
date_created: 2018-12-11T11:56:29Z
date_published: 2013-01-14T00:00:00Z
date_updated: 2020-08-11T10:09:42Z
day: '14'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-642-45221-5_13
file:
- access_level: open_access
checksum: 9cebaafca032e6769d273f393305c705
content_type: application/pdf
creator: dernst
date_created: 2020-05-15T11:10:40Z
date_updated: 2020-07-14T12:45:34Z
file_id: '7858'
file_name: 2013_LPAR_Blanc.pdf
file_size: 279206
relation: main_file
file_date_updated: 2020-07-14T12:45:34Z
has_accepted_license: '1'
intvolume: ' 8312'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 173 - 181
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication_status: published
publisher: Springer
publist_id: '4724'
quality_controlled: '1'
scopus_import: 1
series_title: Lecture Notes in Computer Science
status: public
title: Tree interpolation in Vampire
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8312
year: '2013'
...
---
_id: '2288'
abstract:
- lang: eng
text: This book constitutes the proceedings of the 11th International Conference
on Computational Methods in Systems Biology, CMSB 2013, held in Klosterneuburg,
Austria, in September 2013. The 15 regular papers included in this volume were
carefully reviewed and selected from 27 submissions. They deal with computational
models for all levels, from molecular and cellular, to organs and entire organisms.
alternative_title:
- LNCS
citation:
ama: Gupta A, Henzinger TA, eds. Computational Methods in Systems Biology.
Vol 8130. Springer; 2013. doi:10.1007/978-3-642-40708-6
apa: 'Gupta, A., & Henzinger, T. A. (Eds.). (2013). Computational Methods
in Systems Biology (Vol. 8130). Presented at the CMSB: Computational Methods
in Systems Biology, Klosterneuburg, Austria: Springer. https://doi.org/10.1007/978-3-642-40708-6'
chicago: Gupta, Ashutosh, and Thomas A Henzinger, eds. Computational Methods
in Systems Biology. Vol. 8130. Springer, 2013. https://doi.org/10.1007/978-3-642-40708-6.
ieee: A. Gupta and T. A. Henzinger, Eds., Computational Methods in Systems Biology,
vol. 8130. Springer, 2013.
ista: Gupta A, Henzinger TA eds. 2013. Computational Methods in Systems Biology,
Springer,p.
mla: Gupta, Ashutosh, and Thomas A. Henzinger, editors. Computational Methods
in Systems Biology. Vol. 8130, Springer, 2013, doi:10.1007/978-3-642-40708-6.
short: A. Gupta, T.A. Henzinger, eds., Computational Methods in Systems Biology,
Springer, 2013.
conference:
end_date: 2013-09-24
location: Klosterneuburg, Austria
name: 'CMSB: Computational Methods in Systems Biology'
start_date: 2013-09-22
date_created: 2018-12-11T11:56:47Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2019-08-02T12:37:44Z
day: '01'
department:
- _id: ToHe
doi: 10.1007/978-3-642-40708-6
editor:
- 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
intvolume: ' 8130'
language:
- iso: eng
month: '07'
oa_version: None
publication_identifier:
isbn:
- 978-3-642-40707-9
publication_status: published
publisher: Springer
publist_id: '4643'
quality_controlled: '1'
status: public
title: Computational Methods in Systems Biology
type: conference_editor
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8130
year: '2013'
...
---
_id: '5747'
article_processing_charge: No
author:
- first_name: Cezara
full_name: Dragoi, Cezara
id: 2B2B5ED0-F248-11E8-B48F-1D18A9856A87
last_name: Dragoi
- 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
citation:
ama: 'Dragoi C, Gupta A, Henzinger TA. Automatic Linearizability Proofs of Concurrent
Objects with Cooperating Updates. In: Computer Aided Verification. Vol
8044. CAV. Berlin, Heidelberg: Springer Berlin Heidelberg; 2013:174-190. doi:10.1007/978-3-642-39799-8_11'
apa: 'Dragoi, C., Gupta, A., & Henzinger, T. A. (2013). Automatic Linearizability
Proofs of Concurrent Objects with Cooperating Updates. In Computer Aided Verification
(Vol. 8044, pp. 174–190). Berlin, Heidelberg: Springer Berlin Heidelberg. https://doi.org/10.1007/978-3-642-39799-8_11'
chicago: 'Dragoi, Cezara, Ashutosh Gupta, and Thomas A Henzinger. “Automatic Linearizability
Proofs of Concurrent Objects with Cooperating Updates.” In Computer Aided Verification,
8044:174–90. CAV. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. https://doi.org/10.1007/978-3-642-39799-8_11.'
ieee: 'C. Dragoi, A. Gupta, and T. A. Henzinger, “Automatic Linearizability Proofs
of Concurrent Objects with Cooperating Updates,” in Computer Aided Verification,
vol. 8044, Berlin, Heidelberg: Springer Berlin Heidelberg, 2013, pp. 174–190.'
ista: 'Dragoi C, Gupta A, Henzinger TA. 2013.Automatic Linearizability Proofs of
Concurrent Objects with Cooperating Updates. In: Computer Aided Verification.
vol. 8044, 174–190.'
mla: Dragoi, Cezara, et al. “Automatic Linearizability Proofs of Concurrent Objects
with Cooperating Updates.” Computer Aided Verification, vol. 8044, Springer
Berlin Heidelberg, 2013, pp. 174–90, doi:10.1007/978-3-642-39799-8_11.
short: C. Dragoi, A. Gupta, T.A. Henzinger, in:, Computer Aided Verification, Springer
Berlin Heidelberg, Berlin, Heidelberg, 2013, pp. 174–190.
conference:
end_date: 2013-07-19
location: Saint Petersburg, Russia
name: CAV 2013
start_date: 2013-07-13
date_created: 2018-12-18T13:10:21Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2023-09-05T14:16:07Z
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1007/978-3-642-39799-8_11
ec_funded: 1
file:
- access_level: open_access
checksum: a901cc6b71db08b61c0d4c0cbacc6287
content_type: application/pdf
creator: dernst
date_created: 2018-12-18T13:13:33Z
date_updated: 2020-07-14T12:47:10Z
file_id: '5748'
file_name: 2013_CAV_Dragoi.pdf
file_size: 236480
relation: main_file
file_date_updated: 2020-07-14T12:47:10Z
has_accepted_license: '1'
intvolume: ' 8044'
language:
- iso: eng
oa: 1
oa_version: None
page: 174-190
place: Berlin, Heidelberg
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
publication: Computer Aided Verification
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783642397981'
- '9783642397998'
issn:
- 0302-9743
publication_status: published
publisher: Springer Berlin Heidelberg
pubrep_id: '195'
quality_controlled: '1'
scopus_import: '1'
series_title: CAV
status: public
title: Automatic Linearizability Proofs of Concurrent Objects with Cooperating Updates
type: book_chapter
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 8044
year: '2013'
...
---
_id: '3136'
abstract:
- lang: eng
text: 'Continuous-time Markov chains (CTMC) with their rich theory and efficient
simulation algorithms have been successfully used in modeling stochastic processes
in diverse areas such as computer science, physics, and biology. However, systems
that comprise non-instantaneous events cannot be accurately and efficiently modeled
with CTMCs. In this paper we define delayed CTMCs, an extension of CTMCs that
allows for the specification of a lower bound on the time interval between an
event''s initiation and its completion, and we propose an algorithm for the computation
of their behavior. Our algorithm effectively decomposes the computation into two
stages: a pure CTMC governs event initiations while a deterministic process guarantees
lower bounds on event completion times. Furthermore, from the nature of delayed
CTMCs, we obtain a parallelized version of our algorithm. We use our formalism
to model genetic regulatory circuits (biological systems where delayed events
are common) and report on the results of our numerical algorithm as run on a cluster.
We compare performance and accuracy of our results with results obtained by using
pure CTMCs. © 2012 Springer-Verlag.'
acknowledgement: This work was supported by the ERC Advanced Investigator grant on
Quantitative Reactive Modeling (QUAREM) and by the Swiss National Science Foundation.
alternative_title:
- LNCS
author:
- 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: Maria
full_name: Mateescu, Maria
id: 3B43276C-F248-11E8-B48F-1D18A9856A87
last_name: Mateescu
- first_name: Ali
full_name: Sezgin, Ali
id: 4C7638DA-F248-11E8-B48F-1D18A9856A87
last_name: Sezgin
citation:
ama: 'Guet CC, Gupta A, Henzinger TA, Mateescu M, Sezgin A. Delayed continuous time
Markov chains for genetic regulatory circuits. In: Vol 7358. Springer; 2012:294-309.
doi:10.1007/978-3-642-31424-7_24'
apa: 'Guet, C. C., Gupta, A., Henzinger, T. A., Mateescu, M., & Sezgin, A. (2012).
Delayed continuous time Markov chains for genetic regulatory circuits (Vol. 7358,
pp. 294–309). Presented at the CAV: Computer Aided Verification, Berkeley, CA,
USA: Springer. https://doi.org/10.1007/978-3-642-31424-7_24'
chicago: Guet, Calin C, Ashutosh Gupta, Thomas A Henzinger, Maria Mateescu, and
Ali Sezgin. “Delayed Continuous Time Markov Chains for Genetic Regulatory Circuits,”
7358:294–309. Springer, 2012. https://doi.org/10.1007/978-3-642-31424-7_24.
ieee: 'C. C. Guet, A. Gupta, T. A. Henzinger, M. Mateescu, and A. Sezgin, “Delayed
continuous time Markov chains for genetic regulatory circuits,” presented at the
CAV: Computer Aided Verification, Berkeley, CA, USA, 2012, vol. 7358, pp. 294–309.'
ista: 'Guet CC, Gupta A, Henzinger TA, Mateescu M, Sezgin A. 2012. Delayed continuous
time Markov chains for genetic regulatory circuits. CAV: Computer Aided Verification,
LNCS, vol. 7358, 294–309.'
mla: Guet, Calin C., et al. Delayed Continuous Time Markov Chains for Genetic
Regulatory Circuits. Vol. 7358, Springer, 2012, pp. 294–309, doi:10.1007/978-3-642-31424-7_24.
short: C.C. Guet, A. Gupta, T.A. Henzinger, M. Mateescu, A. Sezgin, in:, Springer,
2012, pp. 294–309.
conference:
end_date: 2012-07-13
location: Berkeley, CA, USA
name: 'CAV: Computer Aided Verification'
start_date: 2012-07-07
date_created: 2018-12-11T12:01:36Z
date_published: 2012-07-01T00:00:00Z
date_updated: 2021-01-12T07:41:18Z
day: '01'
department:
- _id: CaGu
- _id: ToHe
doi: 10.1007/978-3-642-31424-7_24
ec_funded: 1
language:
- iso: eng
month: '07'
oa_version: None
page: 294 - 309
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
publication_status: published
publisher: Springer
publist_id: '3561'
quality_controlled: '1'
scopus_import: 1
status: public
title: Delayed continuous time Markov chains for genetic regulatory circuits
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: '7358 '
year: '2012'
...
---
_id: '10906'
abstract:
- lang: eng
text: HSF(C) is a tool that automates verification of safety and liveness properties
for C programs. This paper describes the verification approach taken by HSF(C)
and provides instructions on how to install and use the tool.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Sergey
full_name: Grebenshchikov, Sergey
last_name: Grebenshchikov
- first_name: Ashutosh
full_name: Gupta, Ashutosh
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
- first_name: Nuno P.
full_name: Lopes, Nuno P.
last_name: Lopes
- first_name: Corneliu
full_name: Popeea, Corneliu
last_name: Popeea
- first_name: Andrey
full_name: Rybalchenko, Andrey
last_name: Rybalchenko
citation:
ama: 'Grebenshchikov S, Gupta A, Lopes NP, Popeea C, Rybalchenko A. HSF(C): A software
verifier based on Horn clauses. In: Flanagan C, König B, eds. Tools and Algorithms
for the Construction and Analysis of Systems. Vol 7214. LNCS. Berlin, Heidelberg:
Springer; 2012:549-551. doi:10.1007/978-3-642-28756-5_46'
apa: 'Grebenshchikov, S., Gupta, A., Lopes, N. P., Popeea, C., & Rybalchenko,
A. (2012). HSF(C): A software verifier based on Horn clauses. In C. Flanagan &
B. König (Eds.), Tools and Algorithms for the Construction and Analysis of
Systems (Vol. 7214, pp. 549–551). Berlin, Heidelberg: Springer. https://doi.org/10.1007/978-3-642-28756-5_46'
chicago: 'Grebenshchikov, Sergey, Ashutosh Gupta, Nuno P. Lopes, Corneliu Popeea,
and Andrey Rybalchenko. “HSF(C): A Software Verifier Based on Horn Clauses.” In
Tools and Algorithms for the Construction and Analysis of Systems, edited
by Cormac Flanagan and Barbara König, 7214:549–51. LNCS. Berlin, Heidelberg: Springer,
2012. https://doi.org/10.1007/978-3-642-28756-5_46.'
ieee: 'S. Grebenshchikov, A. Gupta, N. P. Lopes, C. Popeea, and A. Rybalchenko,
“HSF(C): A software verifier based on Horn clauses,” in Tools and Algorithms
for the Construction and Analysis of Systems, Tallinn, Estonia, 2012, vol.
7214, pp. 549–551.'
ista: 'Grebenshchikov S, Gupta A, Lopes NP, Popeea C, Rybalchenko A. 2012. HSF(C):
A software verifier based on Horn clauses. Tools and Algorithms for the Construction
and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and
Analysis of SystemsLNCS, LNCS, vol. 7214, 549–551.'
mla: 'Grebenshchikov, Sergey, et al. “HSF(C): A Software Verifier Based on Horn
Clauses.” Tools and Algorithms for the Construction and Analysis of Systems,
edited by Cormac Flanagan and Barbara König, vol. 7214, Springer, 2012, pp. 549–51,
doi:10.1007/978-3-642-28756-5_46.'
short: S. Grebenshchikov, A. Gupta, N.P. Lopes, C. Popeea, A. Rybalchenko, in:,
C. Flanagan, B. König (Eds.), Tools and Algorithms for the Construction and Analysis
of Systems, Springer, Berlin, Heidelberg, 2012, pp. 549–551.
conference:
end_date: 2012-04-01
location: Tallinn, Estonia
name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems'
start_date: 2012-03-24
date_created: 2022-03-21T08:03:30Z
date_published: 2012-04-01T00:00:00Z
date_updated: 2023-09-05T14:09:54Z
day: '01'
department:
- _id: ToHe
doi: 10.1007/978-3-642-28756-5_46
editor:
- first_name: Cormac
full_name: Flanagan, Cormac
last_name: Flanagan
- first_name: Barbara
full_name: König, Barbara
last_name: König
intvolume: ' 7214'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1007/978-3-642-28756-5_46
month: '04'
oa: 1
oa_version: Published Version
page: 549-551
place: Berlin, Heidelberg
publication: Tools and Algorithms for the Construction and Analysis of Systems
publication_identifier:
eisbn:
- '9783642287565'
eissn:
- 1611-3349
isbn:
- '9783642287558'
issn:
- 0302-9743
publication_status: published
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
series_title: LNCS
status: public
title: 'HSF(C): A software verifier based on Horn clauses'
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 7214
year: '2012'
...
---
_id: '3264'
abstract:
- lang: eng
text: Verification of programs with procedures, multi-threaded programs, and higher-order
functional programs can be effectively au- tomated using abstraction and refinement
schemes that rely on spurious counterexamples for abstraction discovery. The analysis
of counterexam- ples can be automated by a series of interpolation queries, or,
alterna- tively, as a constraint solving query expressed by a set of recursion
free Horn clauses. (A set of interpolation queries can be formulated as a single
constraint over Horn clauses with linear dependency structure between the unknown
relations.) In this paper we present an algorithm for solving recursion free Horn
clauses over a combined theory of linear real/rational arithmetic and uninterpreted
functions. Our algorithm performs resolu- tion to deal with the clausal structure
and relies on partial solutions to deal with (non-local) instances of functionality
axioms.
alternative_title:
- LNCS
author:
- first_name: Ashutosh
full_name: Gupta, Ashutosh
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
- first_name: Corneliu
full_name: Popeea, Corneliu
last_name: Popeea
- first_name: Andrey
full_name: Rybalchenko, Andrey
last_name: Rybalchenko
citation:
ama: 'Gupta A, Popeea C, Rybalchenko A. Solving recursion-free Horn clauses over
LI+UIF. In: Yang H, ed. Vol 7078. Springer; 2011:188-203. doi:10.1007/978-3-642-25318-8_16'
apa: 'Gupta, A., Popeea, C., & Rybalchenko, A. (2011). Solving recursion-free
Horn clauses over LI+UIF. In H. Yang (Ed.) (Vol. 7078, pp. 188–203). Presented
at the APLAS: Asian Symposium on Programming Languages and Systems, Kenting, Taiwan:
Springer. https://doi.org/10.1007/978-3-642-25318-8_16'
chicago: Gupta, Ashutosh, Corneliu Popeea, and Andrey Rybalchenko. “Solving Recursion-Free
Horn Clauses over LI+UIF.” edited by Hongseok Yang, 7078:188–203. Springer, 2011.
https://doi.org/10.1007/978-3-642-25318-8_16.
ieee: 'A. Gupta, C. Popeea, and A. Rybalchenko, “Solving recursion-free Horn clauses
over LI+UIF,” presented at the APLAS: Asian Symposium on Programming Languages
and Systems, Kenting, Taiwan, 2011, vol. 7078, pp. 188–203.'
ista: 'Gupta A, Popeea C, Rybalchenko A. 2011. Solving recursion-free Horn clauses
over LI+UIF. APLAS: Asian Symposium on Programming Languages and Systems, LNCS,
vol. 7078, 188–203.'
mla: Gupta, Ashutosh, et al. Solving Recursion-Free Horn Clauses over LI+UIF.
Edited by Hongseok Yang, vol. 7078, Springer, 2011, pp. 188–203, doi:10.1007/978-3-642-25318-8_16.
short: A. Gupta, C. Popeea, A. Rybalchenko, in:, H. Yang (Ed.), Springer, 2011,
pp. 188–203.
conference:
end_date: 2011-12-07
location: Kenting, Taiwan
name: 'APLAS: Asian Symposium on Programming Languages and Systems'
start_date: 2011-12-05
date_created: 2018-12-11T12:02:20Z
date_published: 2011-12-05T00:00:00Z
date_updated: 2021-01-12T07:42:15Z
day: '05'
department:
- _id: ToHe
doi: 10.1007/978-3-642-25318-8_16
ec_funded: 1
editor:
- first_name: Hongseok
full_name: Yang, Hongseok
last_name: Yang
intvolume: ' 7078'
language:
- iso: eng
month: '12'
oa_version: None
page: 188 - 203
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
publication_status: published
publisher: Springer
publist_id: '3383'
quality_controlled: '1'
status: public
title: Solving recursion-free Horn clauses over LI+UIF
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 7078
year: '2011'
...
---
_id: '4521'
abstract:
- lang: eng
text: The search for proof and the search for counterexamples (bugs) are complementary
activities that need to be pursued concurrently in order to maximize the practical
success rate of verification tools.While this is well-understood in safety verification,
the current focus of liveness verification has been almost exclusively on the
search for termination proofs. A counterexample to termination is an infinite
programexecution. In this paper, we propose a method to search for such counterexamples.
The search proceeds in two phases. We first dynamically enumerate lasso-shaped
candidate paths for counterexamples, and then statically prove their feasibility.
We illustrate the utility of our nontermination prover, called TNT, on several
nontrivial examples, some of which require bit-level reasoning about integer representations.
author:
- first_name: Ashutosh
full_name: Ashutosh Gupta
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Ritankar
full_name: Majumdar, Ritankar S
last_name: Majumdar
- first_name: Andrey
full_name: Rybalchenko, Andrey
last_name: Rybalchenko
- first_name: Ru
full_name: Xu, Ru-Gang
last_name: Xu
citation:
ama: 'Gupta A, Henzinger TA, Majumdar R, Rybalchenko A, Xu R. Proving non-termination.
In: ACM; 2008:147-158. doi:10.1145/1328438.1328459'
apa: 'Gupta, A., Henzinger, T. A., Majumdar, R., Rybalchenko, A., & Xu, R. (2008).
Proving non-termination (pp. 147–158). Presented at the POPL: Principles of Programming
Languages, ACM. https://doi.org/10.1145/1328438.1328459'
chicago: Gupta, Ashutosh, Thomas A Henzinger, Ritankar Majumdar, Andrey Rybalchenko,
and Ru Xu. “Proving Non-Termination,” 147–58. ACM, 2008. https://doi.org/10.1145/1328438.1328459.
ieee: 'A. Gupta, T. A. Henzinger, R. Majumdar, A. Rybalchenko, and R. Xu, “Proving
non-termination,” presented at the POPL: Principles of Programming Languages,
2008, pp. 147–158.'
ista: 'Gupta A, Henzinger TA, Majumdar R, Rybalchenko A, Xu R. 2008. Proving non-termination.
POPL: Principles of Programming Languages, 147–158.'
mla: Gupta, Ashutosh, et al. Proving Non-Termination. ACM, 2008, pp. 147–58,
doi:10.1145/1328438.1328459.
short: A. Gupta, T.A. Henzinger, R. Majumdar, A. Rybalchenko, R. Xu, in:, ACM, 2008,
pp. 147–158.
conference:
name: 'POPL: Principles of Programming Languages'
date_created: 2018-12-11T12:09:17Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:59:25Z
day: '01'
doi: 10.1145/1328438.1328459
extern: 1
main_file_link:
- open_access: '0'
url: http://pub.ist.ac.at/%7Etah/Publications/proving_non-termination.pdf
month: '01'
page: 147 - 158
publication_status: published
publisher: ACM
publist_id: '208'
quality_controlled: 0
status: public
title: Proving non-termination
type: conference
year: '2008'
...