---
_id: '4388'
abstract:
- lang: eng
text: GIST is a tool that (a) solves the qualitative analysis problem of turn-based
probabilistic games with ω-regular objectives; and (b) synthesizes reasonable
environment assumptions for synthesis of unrealizable specifications. Our tool
provides the first and efficient implementations of several reduction-based techniques
to solve turn-based probabilistic games, and uses the analysis of turn-based probabilistic
games for synthesizing environment assumptions for unrealizable specifications.
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- 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: Barbara
full_name: Jobstmann, Barbara
last_name: Jobstmann
- first_name: Arjun
full_name: Radhakrishna, Arjun
id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87
last_name: Radhakrishna
citation:
ama: 'Chatterjee K, Henzinger TA, Jobstmann B, Radhakrishna A. GIST: A solver for
probabilistic games. In: Vol 6174. Springer; 2010:665-669. doi:10.1007/978-3-642-14295-6_57'
apa: 'Chatterjee, K., Henzinger, T. A., Jobstmann, B., & Radhakrishna, A. (2010).
GIST: A solver for probabilistic games (Vol. 6174, pp. 665–669). Presented at
the CAV: Computer Aided Verification, Edinburgh, UK: Springer. https://doi.org/10.1007/978-3-642-14295-6_57'
chicago: 'Chatterjee, Krishnendu, Thomas A Henzinger, Barbara Jobstmann, and Arjun
Radhakrishna. “GIST: A Solver for Probabilistic Games,” 6174:665–69. Springer,
2010. https://doi.org/10.1007/978-3-642-14295-6_57.'
ieee: 'K. Chatterjee, T. A. Henzinger, B. Jobstmann, and A. Radhakrishna, “GIST:
A solver for probabilistic games,” presented at the CAV: Computer Aided Verification,
Edinburgh, UK, 2010, vol. 6174, pp. 665–669.'
ista: 'Chatterjee K, Henzinger TA, Jobstmann B, Radhakrishna A. 2010. GIST: A solver
for probabilistic games. CAV: Computer Aided Verification, LNCS, vol. 6174, 665–669.'
mla: 'Chatterjee, Krishnendu, et al. GIST: A Solver for Probabilistic Games.
Vol. 6174, Springer, 2010, pp. 665–69, doi:10.1007/978-3-642-14295-6_57.'
short: K. Chatterjee, T.A. Henzinger, B. Jobstmann, A. Radhakrishna, in:, Springer,
2010, pp. 665–669.
conference:
end_date: 2010-07-17
location: Edinburgh, UK
name: 'CAV: Computer Aided Verification'
start_date: 2010-07-15
corr_author: '1'
date_created: 2018-12-11T12:08:36Z
date_published: 2010-07-01T00:00:00Z
date_updated: 2024-10-09T20:54:00Z
day: '01'
ddc:
- '004'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1007/978-3-642-14295-6_57
ec_funded: 1
external_id:
arxiv:
- '1004.2367'
file:
- access_level: open_access
checksum: 0b2ef8c4037ffccc6902d93081af24f7
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:33Z
date_updated: 2020-07-14T12:46:28Z
file_id: '5221'
file_name: IST-2012-43-v1+1_GIST-_A_solver_for_probabilistic_games.pdf
file_size: 293605
relation: main_file
file_date_updated: 2020-07-14T12:46:28Z
has_accepted_license: '1'
intvolume: ' 6174'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 665 - 669
project:
- _id: 25EFB36C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '215543'
name: COMponent-Based Embedded Systems design Techniques
- _id: 25F1337C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '214373'
name: Design for Embedded Systems
publication_status: published
publisher: Springer
publist_id: '1068'
pubrep_id: '43'
quality_controlled: '1'
related_material:
record:
- id: '5393'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: 'GIST: A solver for probabilistic games'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6174
year: '2010'
...
---
_id: '4389'
abstract:
- lang: eng
text: 'Digital components play a central role in the design of complex embedded
systems. These components are interconnected with other, possibly analog, devices
and the physical environment. This environment cannot be entirely captured and
can provide inaccurate input data to the component. It is thus important for digital
components to have a robust behavior, i.e. the presence of a small change in the
input sequences should not result in a drastic change in the output sequences.
In this paper, we study a notion of robustness for sequential circuits. However,
since sequential circuits may have parts that are naturally discontinuous (e.g.,
digital controllers with switching behavior), we need a flexible framework that
accommodates this fact and leaves discontinuous parts of the circuit out from
the robustness analysis. As a consequence, we consider sequential circuits that
have their input variables partitioned into two disjoint sets: control and disturbance
variables. Our contributions are (1) a definition of robustness for sequential
circuits as a form of continuity with respect to disturbance variables, (2) the
characterization of the exact class of sequential circuits that are robust according
to our definition, (3) an algorithm to decide whether a sequential circuit is
robust or not.'
author:
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
- 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: Axel
full_name: Legay, Axel
last_name: Legay
- first_name: Dejan
full_name: Nickovic, Dejan
id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87
last_name: Nickovic
citation:
ama: 'Doyen L, Henzinger TA, Legay A, Nickovic D. Robustness of sequential circuits.
In: IEEE; 2010:77-84. doi:10.1109/ACSD.2010.26'
apa: 'Doyen, L., Henzinger, T. A., Legay, A., & Nickovic, D. (2010). Robustness
of sequential circuits (pp. 77–84). Presented at the ACSD: Application of Concurrency
to System Design, IEEE. https://doi.org/10.1109/ACSD.2010.26'
chicago: Doyen, Laurent, Thomas A Henzinger, Axel Legay, and Dejan Nickovic. “Robustness
of Sequential Circuits,” 77–84. IEEE, 2010. https://doi.org/10.1109/ACSD.2010.26.
ieee: 'L. Doyen, T. A. Henzinger, A. Legay, and D. Nickovic, “Robustness of sequential
circuits,” presented at the ACSD: Application of Concurrency to System Design,
2010, pp. 77–84.'
ista: 'Doyen L, Henzinger TA, Legay A, Nickovic D. 2010. Robustness of sequential
circuits. ACSD: Application of Concurrency to System Design, 77–84.'
mla: Doyen, Laurent, et al. Robustness of Sequential Circuits. IEEE, 2010,
pp. 77–84, doi:10.1109/ACSD.2010.26.
short: L. Doyen, T.A. Henzinger, A. Legay, D. Nickovic, in:, IEEE, 2010, pp. 77–84.
conference:
name: 'ACSD: Application of Concurrency to System Design'
date_created: 2018-12-11T12:08:36Z
date_published: 2010-08-23T00:00:00Z
date_updated: 2021-01-12T07:56:36Z
day: '23'
ddc:
- '004'
department:
- _id: ToHe
doi: 10.1109/ACSD.2010.26
file:
- access_level: open_access
checksum: 42b2952bfc6b6974617bd554842b904a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:10Z
date_updated: 2020-07-14T12:46:28Z
file_id: '4733'
file_name: IST-2012-44-v1+1_Robustness_of_sequential_circuits.pdf
file_size: 159920
relation: main_file
file_date_updated: 2020-07-14T12:46:28Z
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
page: 77 - 84
publication_status: published
publisher: IEEE
publist_id: '1069'
pubrep_id: '44'
quality_controlled: '1'
scopus_import: 1
status: public
title: Robustness of sequential circuits
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '4390'
abstract:
- lang: eng
text: Concurrent data structures with fine-grained synchronization are notoriously
difficult to implement correctly. The difficulty of reasoning about these implementations
does not stem from the number of variables or the program size, but rather from
the large number of possible interleavings. These implementations are therefore
prime candidates for model checking. We introduce an algorithm for verifying linearizability
of singly-linked heap-based concurrent data structures. We consider a model consisting
of an unbounded heap where each vertex stores an element from an unbounded data
domain, with a restricted set of operations for testing and updating pointers
and data elements. Our main result is that linearizability is decidable for programs
that invoke a fixed number of methods, possibly in parallel. This decidable fragment
covers many of the common implementation techniques — fine-grained locking, lazy
synchronization, and lock-free synchronization. We also show how the technique
can be used to verify optimistic implementations with the help of programmer annotations.
We developed a verification tool CoLT and evaluated it on a representative sample
of Java implementations of the concurrent set data structure. The tool verified
linearizability of a number of implementations, found a known error in a lock-free
implementation and proved that the corrected version is linearizable.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Pavol
full_name: Cerny, Pavol
id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87
last_name: Cerny
- first_name: Arjun
full_name: Radhakrishna, Arjun
id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87
last_name: Radhakrishna
- first_name: Damien
full_name: Zufferey, Damien
id: 4397AC76-F248-11E8-B48F-1D18A9856A87
last_name: Zufferey
orcid: 0000-0002-3197-8736
- first_name: Swarat
full_name: Chaudhuri, Swarat
last_name: Chaudhuri
- first_name: Rajeev
full_name: Alur, Rajeev
last_name: Alur
citation:
ama: 'Cerny P, Radhakrishna A, Zufferey D, Chaudhuri S, Alur R. Model checking of
linearizability of concurrent list implementations. In: Vol 6174. Springer; 2010:465-479.
doi:10.1007/978-3-642-14295-6_41'
apa: 'Cerny, P., Radhakrishna, A., Zufferey, D., Chaudhuri, S., & Alur, R. (2010).
Model checking of linearizability of concurrent list implementations (Vol. 6174,
pp. 465–479). Presented at the CAV: Computer Aided Verification, Edinburgh, UK:
Springer. https://doi.org/10.1007/978-3-642-14295-6_41'
chicago: Cerny, Pavol, Arjun Radhakrishna, Damien Zufferey, Swarat Chaudhuri, and
Rajeev Alur. “Model Checking of Linearizability of Concurrent List Implementations,”
6174:465–79. Springer, 2010. https://doi.org/10.1007/978-3-642-14295-6_41.
ieee: 'P. Cerny, A. Radhakrishna, D. Zufferey, S. Chaudhuri, and R. Alur, “Model
checking of linearizability of concurrent list implementations,” presented at
the CAV: Computer Aided Verification, Edinburgh, UK, 2010, vol. 6174, pp. 465–479.'
ista: 'Cerny P, Radhakrishna A, Zufferey D, Chaudhuri S, Alur R. 2010. Model checking
of linearizability of concurrent list implementations. CAV: Computer Aided Verification,
LNCS, vol. 6174, 465–479.'
mla: Cerny, Pavol, et al. Model Checking of Linearizability of Concurrent List
Implementations. Vol. 6174, Springer, 2010, pp. 465–79, doi:10.1007/978-3-642-14295-6_41.
short: P. Cerny, A. Radhakrishna, D. Zufferey, S. Chaudhuri, R. Alur, in:, Springer,
2010, pp. 465–479.
conference:
end_date: 2010-07-17
location: Edinburgh, UK
name: 'CAV: Computer Aided Verification'
start_date: 2010-07-15
corr_author: '1'
date_created: 2018-12-11T12:08:36Z
date_published: 2010-07-01T00:00:00Z
date_updated: 2024-10-21T06:03:05Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-642-14295-6_41
file:
- access_level: open_access
checksum: 2eb211ce40b3c4988bce3a3592980704
content_type: application/pdf
creator: dernst
date_created: 2020-05-19T16:31:56Z
date_updated: 2020-07-14T12:46:28Z
file_id: '7873'
file_name: 2010_CAV_Cerny.pdf
file_size: 3633276
relation: main_file
file_date_updated: 2020-07-14T12:46:28Z
has_accepted_license: '1'
intvolume: ' 6174'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 465 - 479
publication_status: published
publisher: Springer
publist_id: '1066'
pubrep_id: '27'
quality_controlled: '1'
related_material:
record:
- id: '5391'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Model checking of linearizability of concurrent list implementations
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6174
year: '2010'
...
---
_id: '4392'
abstract:
- lang: eng
text: 'While a boolean notion of correctness is given by a preorder on systems and
properties, a quantitative notion of correctness is defined by a distance function
on systems and properties, where the distance between a system and a property
provides a measure of “fit” or “desirability.” In this article, we explore several
ways how the simulation preorder can be generalized to a distance function. This
is done by equipping the classical simulation game between a system and a property
with quantitative objectives. In particular, for systems that satisfy a property,
a quantitative simulation game can measure the “robustness” of the satisfaction,
that is, how much the system can deviate from its nominal behavior while still
satisfying the property. For systems that violate a property, a quantitative simulation
game can measure the “seriousness” of the violation, that is, how much the property
has to be modified so that it is satisfied by the system. These distances can
be computed in polynomial time, since the computation reduces to the value problem
in limit average games with constant weights. Finally, we demonstrate how the
robustness distance can be used to measure how many transmission errors are tolerated
by error correcting codes. '
alternative_title:
- LNCS
author:
- first_name: Pavol
full_name: Cerny, Pavol
id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87
last_name: Cerny
- 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
citation:
ama: 'Cerny P, Henzinger TA, Radhakrishna A. Quantitative Simulation Games. In:
Manna Z, Peled D, eds. Time For Verification: Essays in Memory of Amir Pnueli.
Vol 6200. Essays in Memory of Amir Pnueli. Springer; 2010:42-60. doi:10.1007/978-3-642-13754-9_3'
apa: 'Cerny, P., Henzinger, T. A., & Radhakrishna, A. (2010). Quantitative Simulation
Games. In Z. Manna & D. Peled (Eds.), Time For Verification: Essays in
Memory of Amir Pnueli (Vol. 6200, pp. 42–60). Springer. https://doi.org/10.1007/978-3-642-13754-9_3'
chicago: 'Cerny, Pavol, Thomas A Henzinger, and Arjun Radhakrishna. “Quantitative
Simulation Games.” In Time For Verification: Essays in Memory of Amir Pnueli,
edited by Zohar Manna and Doron Peled, 6200:42–60. Essays in Memory of Amir Pnueli.
Springer, 2010. https://doi.org/10.1007/978-3-642-13754-9_3.'
ieee: 'P. Cerny, T. A. Henzinger, and A. Radhakrishna, “Quantitative Simulation
Games,” in Time For Verification: Essays in Memory of Amir Pnueli, vol.
6200, Z. Manna and D. Peled, Eds. Springer, 2010, pp. 42–60.'
ista: 'Cerny P, Henzinger TA, Radhakrishna A. 2010.Quantitative Simulation Games.
In: Time For Verification: Essays in Memory of Amir Pnueli. LNCS, vol. 6200, 42–60.'
mla: 'Cerny, Pavol, et al. “Quantitative Simulation Games.” Time For Verification:
Essays in Memory of Amir Pnueli, edited by Zohar Manna and Doron Peled, vol.
6200, Springer, 2010, pp. 42–60, doi:10.1007/978-3-642-13754-9_3.'
short: 'P. Cerny, T.A. Henzinger, A. Radhakrishna, in:, Z. Manna, D. Peled (Eds.),
Time For Verification: Essays in Memory of Amir Pnueli, Springer, 2010, pp. 42–60.'
corr_author: '1'
date_created: 2018-12-11T12:08:37Z
date_published: 2010-07-29T00:00:00Z
date_updated: 2024-10-09T20:53:58Z
day: '29'
department:
- _id: ToHe
doi: 10.1007/978-3-642-13754-9_3
ec_funded: 1
editor:
- first_name: Zohar
full_name: Manna, Zohar
last_name: Manna
- first_name: Doron
full_name: Peled, Doron
last_name: Peled
intvolume: ' 6200'
language:
- iso: eng
month: '07'
oa_version: None
page: 42 - 60
project:
- _id: 25EFB36C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '215543'
name: COMponent-Based Embedded Systems design Techniques
- _id: 25F1337C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '214373'
name: Design for Embedded Systems
publication: 'Time For Verification: Essays in Memory of Amir Pnueli'
publication_status: published
publisher: Springer
publist_id: '1064'
quality_controlled: '1'
scopus_import: 1
series_title: Essays in Memory of Amir Pnueli
status: public
title: Quantitative Simulation Games
type: book_chapter
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 6200
year: '2010'
...
---
_id: '4393'
abstract:
- lang: eng
text: Boolean notions of correctness are formalized by preorders on systems. Quantitative
measures of correctness can be formalized by real-valued distance functions between
systems, where the distance between implementation and specification provides
a measure of “fit” or “desirability.” We extend the simulation preorder to the
quantitative setting, by making each player of a simulation game pay a certain
price for her choices. We use the resulting games with quantitative objectives
to define three different simulation distances. The correctness distance measures
how much the specification must be changed in order to be satisfied by the implementation.
The coverage distance measures how much the implementation restricts the degrees
of freedom offered by the specification. The robustness distance measures how
much a system can deviate from the implementation description without violating
the specification. We consider these distances for safety as well as liveness
specifications. The distances can be computed in polynomial time for safety specifications,
and for liveness specifications given by weak fairness constraints. We show that
the distance functions satisfy the triangle inequality, that the distance between
two systems does not increase under parallel composition with a third system,
and that the distance between two systems can be bounded from above and below
by distances between abstractions of the two systems. These properties suggest
that our simulation distances provide an appropriate basis for a quantitative
theory of discrete systems. We also demonstrate how the robustness distance can
be used to measure how many transmission errors are tolerated by error correcting
codes.
acknowledgement: This work was partially supported by the European Union project COMBEST
and the European Network of Excellence ArtistDesign.
alternative_title:
- LNCS
author:
- first_name: Pavol
full_name: Cerny, Pavol
id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87
last_name: Cerny
- 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
citation:
ama: 'Cerny P, Henzinger TA, Radhakrishna A. Simulation distances. In: Vol 6269.
Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2010:235-268. doi:10.1007/978-3-642-15375-4_18'
apa: 'Cerny, P., Henzinger, T. A., & Radhakrishna, A. (2010). Simulation distances
(Vol. 6269, pp. 235–268). Presented at the CONCUR: Concurrency Theory, Paris,
France: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/978-3-642-15375-4_18'
chicago: Cerny, Pavol, Thomas A Henzinger, and Arjun Radhakrishna. “Simulation Distances,”
6269:235–68. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010. https://doi.org/10.1007/978-3-642-15375-4_18.
ieee: 'P. Cerny, T. A. Henzinger, and A. Radhakrishna, “Simulation distances,” presented
at the CONCUR: Concurrency Theory, Paris, France, 2010, vol. 6269, pp. 235–268.'
ista: 'Cerny P, Henzinger TA, Radhakrishna A. 2010. Simulation distances. CONCUR:
Concurrency Theory, LNCS, vol. 6269, 235–268.'
mla: Cerny, Pavol, et al. Simulation Distances. Vol. 6269, Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 2010, pp. 235–68, doi:10.1007/978-3-642-15375-4_18.
short: P. Cerny, T.A. Henzinger, A. Radhakrishna, in:, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2010, pp. 235–268.
conference:
end_date: 2010-09-03
location: Paris, France
name: 'CONCUR: Concurrency Theory'
start_date: 2010-08-31
corr_author: '1'
date_created: 2018-12-11T12:08:37Z
date_published: 2010-11-01T00:00:00Z
date_updated: 2026-06-18T18:41:23Z
day: '01'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1007/978-3-642-15375-4_18
ec_funded: 1
file:
- access_level: open_access
checksum: ea567903676ba8afe0507ee11313dce5
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:12Z
date_updated: 2020-07-14T12:46:28Z
file_id: '5130'
file_name: IST-2012-42-v1+1_Simulation_distances.pdf
file_size: 198913
relation: main_file
file_date_updated: 2020-07-14T12:46:28Z
has_accepted_license: '1'
intvolume: ' 6269'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 235 - 268
project:
- _id: 25EFB36C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '215543'
name: COMponent-Based Embedded Systems design Techniques
- _id: 25F1337C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '214373'
name: Design for Embedded Systems
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '1065'
pubrep_id: '42'
quality_controlled: '1'
related_material:
record:
- id: '5389'
relation: earlier_version
status: public
- id: '3249'
relation: later_version
status: public
scopus_import: 1
status: public
title: Simulation distances
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 6269
year: '2010'
...
---
_id: '4396'
abstract:
- lang: eng
text: 'Shape analysis is a promising technique to prove program properties about
recursive data structures. The challenge is to automatically determine the data-structure
type, and to supply the shape analysis with the necessary information about the
data structure. We present a stepwise approach to the selection of instrumentation
predicates for a TVLA-based shape analysis, which takes us a step closer towards
the fully automatic verification of data structures. The approach uses two techniques
to guide the refinement of shape abstractions: (1) during program exploration,
an explicit heap analysis collects sample instances of the heap structures, which
are used to identify the data structures that are manipulated by the program;
and (2) during abstraction refinement along an infeasible error path, we consider
different possible heap abstractions and choose the coarsest one that eliminates
the infeasible path. We have implemented this combined approach for automatic
shape refinement as an extension of the software model checker BLAST. Example
programs from a data-structure library that manipulate doubly-linked lists and
trees were successfully verified by our tool.'
alternative_title:
- LNCS
author:
- first_name: Dirk
full_name: Beyer, Dirk
last_name: Beyer
- 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: Grégory
full_name: Théoduloz, Grégory
last_name: Théoduloz
- first_name: Damien
full_name: Zufferey, Damien
id: 4397AC76-F248-11E8-B48F-1D18A9856A87
last_name: Zufferey
orcid: 0000-0002-3197-8736
citation:
ama: 'Beyer D, Henzinger TA, Théoduloz G, Zufferey D. Shape refinement through explicit
heap analysis. In: Rosenblum D, Taenzer G, eds. Vol 6013. Springer; 2010:263-277.
doi:10.1007/978-3-642-12029-9_19'
apa: 'Beyer, D., Henzinger, T. A., Théoduloz, G., & Zufferey, D. (2010). Shape
refinement through explicit heap analysis. In D. Rosenblum & G. Taenzer (Eds.)
(Vol. 6013, pp. 263–277). Presented at the FASE: Fundamental Approaches To Software
Engineering, Paphos, Cyprus: Springer. https://doi.org/10.1007/978-3-642-12029-9_19'
chicago: Beyer, Dirk, Thomas A Henzinger, Grégory Théoduloz, and Damien Zufferey.
“Shape Refinement through Explicit Heap Analysis.” edited by David Rosenblum and
Gabriele Taenzer, 6013:263–77. Springer, 2010. https://doi.org/10.1007/978-3-642-12029-9_19.
ieee: 'D. Beyer, T. A. Henzinger, G. Théoduloz, and D. Zufferey, “Shape refinement
through explicit heap analysis,” presented at the FASE: Fundamental Approaches
To Software Engineering, Paphos, Cyprus, 2010, vol. 6013, pp. 263–277.'
ista: 'Beyer D, Henzinger TA, Théoduloz G, Zufferey D. 2010. Shape refinement through
explicit heap analysis. FASE: Fundamental Approaches To Software Engineering,
LNCS, vol. 6013, 263–277.'
mla: Beyer, Dirk, et al. Shape Refinement through Explicit Heap Analysis.
Edited by David Rosenblum and Gabriele Taenzer, vol. 6013, Springer, 2010, pp.
263–77, doi:10.1007/978-3-642-12029-9_19.
short: D. Beyer, T.A. Henzinger, G. Théoduloz, D. Zufferey, in:, D. Rosenblum, G.
Taenzer (Eds.), Springer, 2010, pp. 263–277.
conference:
end_date: 2010-03-28
location: Paphos, Cyprus
name: 'FASE: Fundamental Approaches To Software Engineering'
start_date: 2010-03-20
date_created: 2018-12-11T12:08:38Z
date_published: 2010-04-21T00:00:00Z
date_updated: 2021-01-12T07:56:40Z
day: '21'
ddc:
- '004'
department:
- _id: ToHe
doi: 10.1007/978-3-642-12029-9_19
editor:
- first_name: David
full_name: Rosenblum, David
last_name: Rosenblum
- first_name: Gabriele
full_name: Taenzer, Gabriele
last_name: Taenzer
file:
- access_level: open_access
checksum: 7d26e59a9681487d7283eba337292b2c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:13Z
date_updated: 2020-07-14T12:46:29Z
file_id: '5332'
file_name: IST-2012-41-v1+1_Shape_refinement_through_explicit_heap_analysis.pdf
file_size: 312147
relation: main_file
file_date_updated: 2020-07-14T12:46:29Z
has_accepted_license: '1'
intvolume: ' 6013'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Submitted Version
page: 263 - 277
project:
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication_status: published
publisher: Springer
publist_id: '1061'
pubrep_id: '41'
quality_controlled: '1'
scopus_import: 1
status: public
title: Shape refinement through explicit heap analysis
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 6013
year: '2010'
...
---
_id: '488'
abstract:
- lang: eng
text: 'Streaming string transducers [1] define (partial) functions from input strings
to output strings. A streaming string transducer makes a single pass through the
input string and uses a finite set of variables that range over strings from the
output alphabet. At every step, the transducer processes an input symbol, and
updates all the variables in parallel using assignments whose right-hand-sides
are concatenations of output symbols and variables with the restriction that a
variable can be used at most once in a right-hand-side expression. It has been
shown that streaming string transducers operating on strings over infinite data
domains are of interest in algorithmic verification of list-processing programs,
as they lead to PSPACE decision procedures for checking pre/post conditions and
for checking semantic equivalence, for a well-defined class of heap-manipulating
programs. In order to understand the theoretical expressiveness of streaming transducers,
we focus on streaming transducers processing strings over finite alphabets, given
the existence of a robust and well-studied class of "regular" transductions
for this case. Such regular transductions can be defined either by two-way deterministic
finite-state transducers, or using a logical MSO-based characterization. Our main
result is that the expressiveness of streaming string transducers coincides exactly
with this class of regular transductions. '
alternative_title:
- LIPIcs
article_processing_charge: No
author:
- first_name: Rajeev
full_name: Alur, Rajeev
last_name: Alur
- first_name: Pavol
full_name: Cerny, Pavol
id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87
last_name: Cerny
citation:
ama: 'Alur R, Cerny P. Expressiveness of streaming string transducers. In: Vol 8.
Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2010:1-12. doi:10.4230/LIPIcs.FSTTCS.2010.1'
apa: 'Alur, R., & Cerny, P. (2010). Expressiveness of streaming string transducers
(Vol. 8, pp. 1–12). Presented at the FSTTCS: Foundations of Software Technology
and Theoretical Computer Science, Chennai, India: Schloss Dagstuhl - Leibniz-Zentrum
für Informatik. https://doi.org/10.4230/LIPIcs.FSTTCS.2010.1'
chicago: Alur, Rajeev, and Pavol Cerny. “Expressiveness of Streaming String Transducers,”
8:1–12. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010. https://doi.org/10.4230/LIPIcs.FSTTCS.2010.1.
ieee: 'R. Alur and P. Cerny, “Expressiveness of streaming string transducers,” presented
at the FSTTCS: Foundations of Software Technology and Theoretical Computer Science,
Chennai, India, 2010, vol. 8, pp. 1–12.'
ista: 'Alur R, Cerny P. 2010. Expressiveness of streaming string transducers. FSTTCS:
Foundations of Software Technology and Theoretical Computer Science, LIPIcs, vol.
8, 1–12.'
mla: Alur, Rajeev, and Pavol Cerny. Expressiveness of Streaming String Transducers.
Vol. 8, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010, pp. 1–12, doi:10.4230/LIPIcs.FSTTCS.2010.1.
short: R. Alur, P. Cerny, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2010, pp. 1–12.
conference:
end_date: 2010-12-18
location: Chennai, India
name: 'FSTTCS: Foundations of Software Technology and Theoretical Computer Science'
start_date: 2010-12-15
corr_author: '1'
date_created: 2018-12-11T11:46:45Z
date_published: 2010-01-01T00:00:00Z
date_updated: 2025-09-30T09:49:32Z
day: '01'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.4230/LIPIcs.FSTTCS.2010.1
external_id:
isi:
- '000310361000001'
file:
- access_level: open_access
checksum: 5845be5aa19791830f7407d8853f2df0
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:29Z
date_updated: 2020-07-14T12:46:35Z
file_id: '4690'
file_name: IST-2018-948-v1+1_2011_Cerny_Expressiveness_of.pdf
file_size: 492344
relation: main_file
file_date_updated: 2020-07-14T12:46:35Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '01'
oa: 1
oa_version: Published Version
page: 1 - 12
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '7331'
pubrep_id: '948'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Expressiveness of streaming string transducers
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 8
year: '2010'
...
---
_id: '533'
abstract:
- lang: eng
text: Any programming error that can be revealed before compiling a program saves
precious time for the programmer. While integrated development environments already
do a good job by detecting, e.g., data-flow abnormalities, current static analysis
tools suffer from false positives ("noise") or require strong user interaction.
We propose to avoid this deficiency by defining a new class of errors. A program
fragment is doomed if its execution will inevitably fail, regardless of which
state it is started in. We use a formal verification method to identify such errors
fully automatically and, most significantly, without producing noise. We report
on experiments with a prototype tool.
article_processing_charge: No
author:
- first_name: Jochen
full_name: Hoenicke, Jochen
last_name: Hoenicke
- first_name: Kari
full_name: Leino, Kari
last_name: Leino
- first_name: Andreas
full_name: Podelski, Andreas
last_name: Podelski
- first_name: Martin
full_name: Schäf, Martin
last_name: Schäf
- first_name: Thomas
full_name: Wies, Thomas
id: 447BFB88-F248-11E8-B48F-1D18A9856A87
last_name: Wies
citation:
ama: Hoenicke J, Leino K, Podelski A, Schäf M, Wies T. Doomed program points. Formal
Methods in System Design. 2010;37(2-3):171-199. doi:10.1007/s10703-010-0102-0
apa: Hoenicke, J., Leino, K., Podelski, A., Schäf, M., & Wies, T. (2010). Doomed
program points. Formal Methods in System Design. Springer. https://doi.org/10.1007/s10703-010-0102-0
chicago: Hoenicke, Jochen, Kari Leino, Andreas Podelski, Martin Schäf, and Thomas
Wies. “Doomed Program Points.” Formal Methods in System Design. Springer,
2010. https://doi.org/10.1007/s10703-010-0102-0.
ieee: J. Hoenicke, K. Leino, A. Podelski, M. Schäf, and T. Wies, “Doomed program
points,” Formal Methods in System Design, vol. 37, no. 2–3. Springer, pp.
171–199, 2010.
ista: Hoenicke J, Leino K, Podelski A, Schäf M, Wies T. 2010. Doomed program points.
Formal Methods in System Design. 37(2–3), 171–199.
mla: Hoenicke, Jochen, et al. “Doomed Program Points.” Formal Methods in System
Design, vol. 37, no. 2–3, Springer, 2010, pp. 171–99, doi:10.1007/s10703-010-0102-0.
short: J. Hoenicke, K. Leino, A. Podelski, M. Schäf, T. Wies, Formal Methods in
System Design 37 (2010) 171–199.
corr_author: '1'
date_created: 2018-12-11T11:47:01Z
date_published: 2010-12-01T00:00:00Z
date_updated: 2025-09-30T09:48:58Z
day: '01'
department:
- _id: ToHe
doi: 10.1007/s10703-010-0102-0
external_id:
isi:
- '000286631700004'
intvolume: ' 37'
isi: 1
issue: 2-3
language:
- iso: eng
month: '12'
oa_version: None
page: 171 - 199
publication: Formal Methods in System Design
publication_status: published
publisher: Springer
publist_id: '7284'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Doomed program points
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 37
year: '2010'
...
---
_id: '5388'
abstract:
- lang: eng
text: "We present an algorithmic method for the synthesis of concurrent programs
that are optimal with respect to quantitative performance measures. The input
consists of a sequential sketch, that is, a program that does not contain synchronization
constructs, and of a parametric performance model that assigns costs to actions
such as locking, context switching, and idling. The quantitative synthesis problem
is to automatically introduce synchronization constructs into the sequential sketch
so that both correctness is guaranteed and worst-case (or average-case) performance
is optimized. Correctness is formalized as race freedom or linearizability.\r\n\r\nWe
show that for worst-case performance, the problem can be modeled\r\nas a 2-player
graph game with quantitative (limit-average) objectives, and\r\nfor average-case
performance, as a 2 1/2 -player graph game (with probabilistic transitions). In
both cases, the optimal correct program is derived from an optimal strategy in
the corresponding quantitative game. We prove that the respective game problems
are computationally expensive (NP-complete), and present several techniques that
overcome the theoretical difficulty in cases of concurrent programs of practical
interest.\r\n\r\nWe have implemented a prototype tool and used it for the automatic
syn- thesis of programs that access a concurrent list. For certain parameter val-
ues, our method automatically synthesizes various classical synchronization schemes
for implementing a concurrent list, such as fine-grained locking or a lazy algorithm.
For other parameter values, a new, hybrid synchronization style is synthesized,
which uses both the lazy approach and coarse-grained locks (instead of standard
fine-grained locks). The trade-off occurs because while fine-grained locking tends
to decrease the cost that is due to waiting for locks, it increases cache size
requirements."
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Pavol
full_name: Cerny, Pavol
id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87
last_name: Cerny
- 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: Rohit
full_name: Singh, Rohit
last_name: Singh
citation:
ama: Chatterjee K, Cerny P, Henzinger TA, Radhakrishna A, Singh R. Quantitative
Synthesis for Concurrent Programs. IST Austria; 2010. doi:10.15479/AT:IST-2010-0004
apa: Chatterjee, K., Cerny, P., Henzinger, T. A., Radhakrishna, A., & Singh,
R. (2010). Quantitative synthesis for concurrent programs. IST Austria.
https://doi.org/10.15479/AT:IST-2010-0004
chicago: Chatterjee, Krishnendu, Pavol Cerny, Thomas A Henzinger, Arjun Radhakrishna,
and Rohit Singh. Quantitative Synthesis for Concurrent Programs. IST Austria,
2010. https://doi.org/10.15479/AT:IST-2010-0004.
ieee: K. Chatterjee, P. Cerny, T. A. Henzinger, A. Radhakrishna, and R. Singh, Quantitative
synthesis for concurrent programs. IST Austria, 2010.
ista: Chatterjee K, Cerny P, Henzinger TA, Radhakrishna A, Singh R. 2010. Quantitative
synthesis for concurrent programs, IST Austria, 17p.
mla: Chatterjee, Krishnendu, et al. Quantitative Synthesis for Concurrent Programs.
IST Austria, 2010, doi:10.15479/AT:IST-2010-0004.
short: K. Chatterjee, P. Cerny, T.A. Henzinger, A. Radhakrishna, R. Singh, Quantitative
Synthesis for Concurrent Programs, IST Austria, 2010.
date_created: 2018-12-12T11:39:03Z
date_published: 2010-10-07T00:00:00Z
date_updated: 2025-04-15T08:12:00Z
day: '07'
ddc:
- '000'
- '005'
department:
- _id: KrCh
- _id: ToHe
doi: 10.15479/AT:IST-2010-0004
file:
- access_level: open_access
checksum: da38782d2388a6fa32109d10bb9bad67
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:53Z
date_updated: 2020-07-14T12:46:42Z
file_id: '5515'
file_name: IST-2010-0004_IST-2010-0004.pdf
file_size: 429101
relation: main_file
file_date_updated: 2020-07-14T12:46:42Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '17'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '24'
related_material:
record:
- id: '3366'
relation: later_version
status: public
status: public
title: Quantitative synthesis for concurrent programs
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '5389'
abstract:
- lang: eng
text: Boolean notions of correctness are formalized by preorders on systems. Quantitative
measures of correctness can be formalized by real-valued distance functions between
systems, where the distance between implementation and specification provides
a measure of “fit” or “desirability.” We extend the simulation preorder to the
quantitative setting, by making each player of a simulation game pay a certain
price for her choices. We use the resulting games with quantitative objectives
to define three different simulation distances. The correctness distance measures
how much the specification must be changed in order to be satisfied by the implementation.
The coverage distance measures how much the im- plementation restricts the degrees
of freedom offered by the specification. The robustness distance measures how
much a system can deviate from the implementation description without violating
the specification. We consider these distances for safety as well as liveness
specifications. The distances can be computed in polynomial time for safety specifications,
and for liveness specifications given by weak fairness constraints. We show that
the distance functions satisfy the triangle inequality, that the distance between
two systems does not increase under parallel composition with a third system,
and that the distance between two systems can be bounded from above and below
by distances between abstractions of the two systems. These properties suggest
that our simulation distances provide an appropriate basis for a quantitative
theory of discrete systems. We also demonstrate how the robustness distance can
be used to measure how many transmission errors are tolerated by error correcting
codes.
alternative_title:
- IST Austria Technical Report
author:
- first_name: Pavol
full_name: Cerny, Pavol
id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87
last_name: Cerny
- 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
citation:
ama: Cerny P, Henzinger TA, Radhakrishna A. Simulation Distances. IST Austria;
2010. doi:10.15479/AT:IST-2010-0003
apa: Cerny, P., Henzinger, T. A., & Radhakrishna, A. (2010). Simulation distances.
IST Austria. https://doi.org/10.15479/AT:IST-2010-0003
chicago: Cerny, Pavol, Thomas A Henzinger, and Arjun Radhakrishna. Simulation
Distances. IST Austria, 2010. https://doi.org/10.15479/AT:IST-2010-0003.
ieee: P. Cerny, T. A. Henzinger, and A. Radhakrishna, Simulation distances.
IST Austria, 2010.
ista: Cerny P, Henzinger TA, Radhakrishna A. 2010. Simulation distances, IST Austria,
24p.
mla: Cerny, Pavol, et al. Simulation Distances. IST Austria, 2010, doi:10.15479/AT:IST-2010-0003.
short: P. Cerny, T.A. Henzinger, A. Radhakrishna, Simulation Distances, IST Austria,
2010.
date_created: 2018-12-12T11:39:03Z
date_published: 2010-06-04T00:00:00Z
date_updated: 2026-06-18T18:41:23Z
day: '04'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.15479/AT:IST-2010-0003
file:
- access_level: open_access
checksum: 284ded99764e32a583a8ea83fcea254b
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:54:25Z
date_updated: 2020-07-14T12:46:42Z
file_id: '5547'
file_name: IST-2010-0003_IST-2010-0003.pdf
file_size: 367246
relation: main_file
file_date_updated: 2020-07-14T12:46:42Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '24'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '25'
related_material:
record:
- id: '4393'
relation: later_version
status: public
- id: '3249'
relation: later_version
status: public
status: public
title: Simulation distances
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '5391'
abstract:
- lang: eng
text: Concurrent data structures with fine-grained synchronization are notoriously
difficult to implement correctly. The difficulty of reasoning about these implementations
does not stem from the number of variables or the program size, but rather from
the large number of possible interleavings. These implementations are therefore
prime candidates for model checking. We introduce an algorithm for verifying linearizability
of singly-linked heap-based concurrent data structures. We consider a model consisting
of an unbounded heap where each node consists an element from an unbounded data
domain, with a restricted set of operations for testing and updating pointers
and data elements. Our main result is that linearizability is decidable for programs
that invoke a fixed number of methods, possibly in parallel. This decidable fragment
covers many of the common implementation techniques — fine-grained locking, lazy
synchronization, and lock-free synchronization. We also show how the technique
can be used to verify optimistic implementations with the help of programmer annotations.
We developed a verification tool CoLT and evaluated it on a representative sample
of Java implementations of the concurrent set data structure. The tool verified
linearizability of a number of implementations, found a known error in a lock-free
imple- mentation and proved that the corrected version is linearizable.
alternative_title:
- IST Austria Technical Report
author:
- first_name: Pavol
full_name: Cerny, Pavol
id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87
last_name: Cerny
- first_name: Arjun
full_name: Radhakrishna, Arjun
id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87
last_name: Radhakrishna
- first_name: Damien
full_name: Zufferey, Damien
id: 4397AC76-F248-11E8-B48F-1D18A9856A87
last_name: Zufferey
orcid: 0000-0002-3197-8736
- first_name: Swarat
full_name: Chaudhuri, Swarat
last_name: Chaudhuri
- first_name: Rajeev
full_name: Alur, Rajeev
last_name: Alur
citation:
ama: Cerny P, Radhakrishna A, Zufferey D, Chaudhuri S, Alur R. Model Checking
of Linearizability of Concurrent List Implementations. IST Austria; 2010.
doi:10.15479/AT:IST-2010-0001
apa: Cerny, P., Radhakrishna, A., Zufferey, D., Chaudhuri, S., & Alur, R. (2010).
Model checking of linearizability of concurrent list implementations. IST
Austria. https://doi.org/10.15479/AT:IST-2010-0001
chicago: Cerny, Pavol, Arjun Radhakrishna, Damien Zufferey, Swarat Chaudhuri, and
Rajeev Alur. Model Checking of Linearizability of Concurrent List Implementations.
IST Austria, 2010. https://doi.org/10.15479/AT:IST-2010-0001.
ieee: P. Cerny, A. Radhakrishna, D. Zufferey, S. Chaudhuri, and R. Alur, Model
checking of linearizability of concurrent list implementations. IST Austria,
2010.
ista: Cerny P, Radhakrishna A, Zufferey D, Chaudhuri S, Alur R. 2010. Model checking
of linearizability of concurrent list implementations, IST Austria, 27p.
mla: Cerny, Pavol, et al. Model Checking of Linearizability of Concurrent List
Implementations. IST Austria, 2010, doi:10.15479/AT:IST-2010-0001.
short: P. Cerny, A. Radhakrishna, D. Zufferey, S. Chaudhuri, R. Alur, Model Checking
of Linearizability of Concurrent List Implementations, IST Austria, 2010.
date_created: 2018-12-12T11:39:04Z
date_published: 2010-04-19T00:00:00Z
date_updated: 2024-10-21T06:03:05Z
day: '19'
ddc:
- '004'
department:
- _id: ToHe
doi: 10.15479/AT:IST-2010-0001
file:
- access_level: open_access
checksum: 986645caad7dd85a6a091488f6c646dc
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:44Z
date_updated: 2020-07-14T12:46:43Z
file_id: '5505'
file_name: IST-2010-0001_IST-2010-0001.pdf
file_size: 372286
relation: main_file
file_date_updated: 2020-07-14T12:46:43Z
has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: '27'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '27'
related_material:
record:
- id: '4390'
relation: later_version
status: public
status: public
title: Model checking of linearizability of concurrent list implementations
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '3719'
abstract:
- lang: eng
text: The induction of a signaling pathway is characterized by transient complex
formation and mutual posttranslational modification of proteins. To faithfully
capture this combinatorial process in a math- ematical model is an important challenge
in systems biology. Exploiting the limited context on which most binding and modification
events are conditioned, attempts have been made to reduce the com- binatorial
complexity by quotienting the reachable set of molecular species, into species
aggregates while preserving the deterministic semantics of the thermodynamic limit.
Recently we proposed a quotienting that also preserves the stochastic semantics
and that is complete in the sense that the semantics of individual species can
be recovered from the aggregate semantics. In this paper we prove that this quotienting
yields a sufficient condition for weak lumpability and that it gives rise to a
backward Markov bisimulation between the original and aggregated transition system.
We illustrate the framework on a case study of the EGF/insulin receptor crosstalk.
acknowledgement: Jérôme Feret’s contribution was partially supported by the ABSTRACTCELL
ANR-Chair of Excellence. Heinz Koeppl acknowledges the support from the Swiss National
Science Foundation, grant no. 200020-117975/1. Tatjana Petrov acknowledges the support
from SystemsX.ch, the Swiss Initiative in Systems Biology.
alternative_title:
- EPTCS
arxiv: 1
author:
- first_name: Jérôme
full_name: Feret, Jérôme
last_name: Feret
- 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: Heinz
full_name: Koeppl, Heinz
last_name: Koeppl
- first_name: Tatjana
full_name: Petrov, Tatjana
id: 3D5811FC-F248-11E8-B48F-1D18A9856A87
last_name: Petrov
orcid: 0000-0002-9041-0905
citation:
ama: 'Feret J, Henzinger TA, Koeppl H, Petrov T. Lumpability abstractions of rule-based
systems. In: Vol 40. Open Publishing Association; 2010:142-161.'
apa: 'Feret, J., Henzinger, T. A., Koeppl, H., & Petrov, T. (2010). Lumpability
abstractions of rule-based systems (Vol. 40, pp. 142–161). Presented at the MECBIC:
Membrane Computing and Biologically Inspired Process Calculi, Jena, Germany: Open
Publishing Association.'
chicago: Feret, Jérôme, Thomas A Henzinger, Heinz Koeppl, and Tatjana Petrov. “Lumpability
Abstractions of Rule-Based Systems,” 40:142–61. Open Publishing Association, 2010.
ieee: 'J. Feret, T. A. Henzinger, H. Koeppl, and T. Petrov, “Lumpability abstractions
of rule-based systems,” presented at the MECBIC: Membrane Computing and Biologically
Inspired Process Calculi, Jena, Germany, 2010, vol. 40, pp. 142–161.'
ista: 'Feret J, Henzinger TA, Koeppl H, Petrov T. 2010. Lumpability abstractions
of rule-based systems. MECBIC: Membrane Computing and Biologically Inspired Process
Calculi, EPTCS, vol. 40, 142–161.'
mla: Feret, Jérôme, et al. Lumpability Abstractions of Rule-Based Systems.
Vol. 40, Open Publishing Association, 2010, pp. 142–61.
short: J. Feret, T.A. Henzinger, H. Koeppl, T. Petrov, in:, Open Publishing Association,
2010, pp. 142–161.
conference:
end_date: 2010-08-23
location: Jena, Germany
name: 'MECBIC: Membrane Computing and Biologically Inspired Process Calculi'
start_date: 2010-08-23
date_created: 2018-12-11T12:04:47Z
date_published: 2010-10-30T00:00:00Z
date_updated: 2026-06-18T18:39:27Z
day: '30'
ddc:
- '570'
department:
- _id: ToHe
- _id: CaGu
external_id:
arxiv:
- '1011.0496'
file:
- access_level: open_access
checksum: eaaba991a86fff37606b0eb5196878e8
content_type: application/pdf
creator: kschuh
date_created: 2019-01-31T12:09:09Z
date_updated: 2020-07-14T12:46:14Z
file_id: '5904'
file_name: Lumpability_abstractions_of_rule-based_systems.pdf
file_size: 907155
relation: main_file
file_date_updated: 2020-07-14T12:46:14Z
has_accepted_license: '1'
intvolume: ' 40'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 142-161
publication_status: published
publisher: Open Publishing Association
publist_id: '2511'
quality_controlled: '1'
related_material:
record:
- id: '3168'
relation: later_version
status: public
scopus_import: 1
status: public
title: Lumpability abstractions of rule-based systems
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 40
year: '2010'
...
---
_id: '3834'
abstract:
- lang: eng
text: "Background\r\n\r\nThe chemical master equation (CME) is a system of ordinary
differential equations that describes the evolution of a network of chemical reactions
as a stochastic process. Its solution yields the probability density vector of
the system at each point in time. Solving the CME numerically is in many cases
computationally expensive or even infeasible as the number of reachable states
can be very large or infinite. We introduce the sliding window method, which computes
an approximate solution of the CME by performing a sequence of local analysis
steps. In each step, only a manageable subset of states is considered, representing
a "window" into the state space. In subsequent steps, the window follows
the direction in which the probability mass moves, until the time period of interest
has elapsed. We construct the window based on a deterministic approximation of
the future behavior of the system by estimating upper and lower bounds on the
populations of the chemical species.\r\nResults\r\n\r\nIn order to show the effectiveness
of our approach, we apply it to several examples previously described in the literature.
The experimental results show that the proposed method speeds up the analysis
considerably, compared to a global analysis, while still providing high accuracy.\r\n\r\n\r\nConclusions\r\n\r\nThe
sliding window method is a novel approach to address the performance problems
of numerical algorithms for the solution of the chemical master equation. The
method efficiently approximates the probability distributions at the time points
of interest for a variety of chemically reacting systems, including systems for
which no upper bound on the population sizes of the chemical species is known
a priori."
acknowledgement: This research has been partially funded by the Swiss National Science
Foundation under grant 205321-111840 and by the Cluster of Excellence on Multimodal
Computing and Interaction at Saarland University.
article_processing_charge: No
author:
- first_name: Verena
full_name: Wolf, Verena
last_name: Wolf
- first_name: Rushil
full_name: Goel, Rushil
last_name: Goel
- first_name: Maria
full_name: Mateescu, Maria
id: 3B43276C-F248-11E8-B48F-1D18A9856A87
last_name: Mateescu
- 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: Wolf V, Goel R, Mateescu M, Henzinger TA. Solving the chemical master equation
using sliding windows. BMC Systems Biology. 2010;4(42):1-19. doi:10.1186/1752-0509-4-42
apa: Wolf, V., Goel, R., Mateescu, M., & Henzinger, T. A. (2010). Solving the
chemical master equation using sliding windows. BMC Systems Biology. BioMed
Central. https://doi.org/10.1186/1752-0509-4-42
chicago: Wolf, Verena, Rushil Goel, Maria Mateescu, and Thomas A Henzinger. “Solving
the Chemical Master Equation Using Sliding Windows.” BMC Systems Biology.
BioMed Central, 2010. https://doi.org/10.1186/1752-0509-4-42.
ieee: V. Wolf, R. Goel, M. Mateescu, and T. A. Henzinger, “Solving the chemical
master equation using sliding windows,” BMC Systems Biology, vol. 4, no.
42. BioMed Central, pp. 1–19, 2010.
ista: Wolf V, Goel R, Mateescu M, Henzinger TA. 2010. Solving the chemical master
equation using sliding windows. BMC Systems Biology. 4(42), 1–19.
mla: Wolf, Verena, et al. “Solving the Chemical Master Equation Using Sliding Windows.”
BMC Systems Biology, vol. 4, no. 42, BioMed Central, 2010, pp. 1–19, doi:10.1186/1752-0509-4-42.
short: V. Wolf, R. Goel, M. Mateescu, T.A. Henzinger, BMC Systems Biology 4 (2010)
1–19.
corr_author: '1'
date_created: 2018-12-11T12:05:25Z
date_published: 2010-04-08T00:00:00Z
date_updated: 2025-09-30T09:37:27Z
day: '08'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1186/1752-0509-4-42
external_id:
isi:
- '000277612700001'
file:
- access_level: open_access
checksum: 220239fae76f7b03c4d7f05d74ef426f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:29Z
date_updated: 2020-07-14T12:46:16Z
file_id: '5217'
file_name: IST-2012-72-v1+1_Solving_the_chemical_master_equation_using_sliding_windows.pdf
file_size: 1919130
relation: main_file
file_date_updated: 2020-07-14T12:46:16Z
has_accepted_license: '1'
intvolume: ' 4'
isi: 1
issue: '42'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '04'
oa: 1
oa_version: Published Version
page: 1 - 19
publication: BMC Systems Biology
publication_status: published
publisher: BioMed Central
publist_id: '2374'
pubrep_id: '72'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Solving the chemical master equation using sliding windows
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 4
year: '2010'
...
---
_id: '3838'
abstract:
- lang: eng
text: We present a numerical approximation technique for the analysis of continuous-time
Markov chains that describe net- works of biochemical reactions and play an important
role in the stochastic modeling of biological systems. Our approach is based on
the construction of a stochastic hybrid model in which certain discrete random
variables of the original Markov chain are approximated by continuous deterministic
variables. We compute the solution of the stochastic hybrid model using a numerical
algorithm that discretizes time and in each step performs a mutual update of the
transient prob- ability distribution of the discrete stochastic variables and
the values of the continuous deterministic variables. We im- plemented the algorithm
and we demonstrate its usefulness and efficiency on several case studies from
systems biology.
author:
- 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
last_name: Mateescu
- first_name: Linar
full_name: Mikeev, Linar
last_name: Mikeev
- first_name: Verena
full_name: Wolf, Verena
last_name: Wolf
citation:
ama: 'Henzinger TA, Mateescu M, Mikeev L, Wolf V. Hybrid numerical solution of the
chemical master equation. In: Springer; 2010:55-65. doi:10.1145/1839764.1839772'
apa: 'Henzinger, T. A., Mateescu, M., Mikeev, L., & Wolf, V. (2010). Hybrid
numerical solution of the chemical master equation (pp. 55–65). Presented at the
CMSB: Computational Methods in Systems Biology, Trento, Italy: Springer. https://doi.org/10.1145/1839764.1839772'
chicago: Henzinger, Thomas A, Maria Mateescu, Linar Mikeev, and Verena Wolf. “Hybrid
Numerical Solution of the Chemical Master Equation,” 55–65. Springer, 2010. https://doi.org/10.1145/1839764.1839772.
ieee: 'T. A. Henzinger, M. Mateescu, L. Mikeev, and V. Wolf, “Hybrid numerical solution
of the chemical master equation,” presented at the CMSB: Computational Methods
in Systems Biology, Trento, Italy, 2010, pp. 55–65.'
ista: 'Henzinger TA, Mateescu M, Mikeev L, Wolf V. 2010. Hybrid numerical solution
of the chemical master equation. CMSB: Computational Methods in Systems Biology,
55–65.'
mla: Henzinger, Thomas A., et al. Hybrid Numerical Solution of the Chemical Master
Equation. Springer, 2010, pp. 55–65, doi:10.1145/1839764.1839772.
short: T.A. Henzinger, M. Mateescu, L. Mikeev, V. Wolf, in:, Springer, 2010, pp.
55–65.
conference:
end_date: 2010-10-01
location: Trento, Italy
name: 'CMSB: Computational Methods in Systems Biology'
start_date: 2010-09-29
date_created: 2018-12-11T12:05:27Z
date_published: 2010-09-29T00:00:00Z
date_updated: 2021-01-12T07:52:33Z
day: '29'
ddc:
- '004'
department:
- _id: ToHe
doi: 10.1145/1839764.1839772
file:
- access_level: open_access
checksum: 81cb6f0babd97151b171d1ce86582831
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:55Z
date_updated: 2020-07-14T12:46:16Z
file_id: '5179'
file_name: IST-2012-68-v1+1_Hybrid_Numerical_Solution_of_the_Chemical_Master_Equation.pdf
file_size: 671790
relation: main_file
file_date_updated: 2020-07-14T12:46:16Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 55 - 65
publication_status: published
publisher: Springer
publist_id: '2356'
pubrep_id: '68'
quality_controlled: '1'
scopus_import: 1
status: public
title: Hybrid numerical solution of the chemical master equation
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '3839'
abstract:
- lang: eng
text: We present a loop property generation method for loops iterating over multi-dimensional
arrays. When used on matrices, our method is able to infer their shapes (also
called types), such as upper-triangular, diagonal, etc. To gen- erate loop properties,
we first transform a nested loop iterating over a multi- dimensional array into
an equivalent collection of unnested loops. Then, we in- fer quantified loop invariants
for each unnested loop using a generalization of a recurrence-based invariant
generation technique. These loop invariants give us conditions on matrices from
which we can derive matrix types automatically us- ing theorem provers. Invariant
generation is implemented in the software package Aligator and types are derived
by theorem provers and SMT solvers, including Vampire and Z3. When run on the
Java matrix package JAMA, our tool was able to infer automatically all matrix
types describing the matrix shapes guaranteed by JAMA’s API.
acknowledgement: The research was supported by the Swiss NSF.
alternative_title:
- LNCS
author:
- 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: Thibaud
full_name: Hottelier, Thibaud
last_name: Hottelier
- first_name: Laura
full_name: Kovács, Laura
last_name: Kovács
- first_name: Andrei
full_name: Voronkov, Andrei
last_name: Voronkov
citation:
ama: 'Henzinger TA, Hottelier T, Kovács L, Voronkov A. Invariant and type inference
for matrices. In: Vol 5944. Springer; 2010:163-179. doi:10.1007/978-3-642-11319-2_14'
apa: 'Henzinger, T. A., Hottelier, T., Kovács, L., & Voronkov, A. (2010). Invariant
and type inference for matrices (Vol. 5944, pp. 163–179). Presented at the VMCAI:
Verification, Model Checking and Abstract Interpretation, Madrid, Spain: Springer.
https://doi.org/10.1007/978-3-642-11319-2_14'
chicago: Henzinger, Thomas A, Thibaud Hottelier, Laura Kovács, and Andrei Voronkov.
“Invariant and Type Inference for Matrices,” 5944:163–79. Springer, 2010. https://doi.org/10.1007/978-3-642-11319-2_14.
ieee: 'T. A. Henzinger, T. Hottelier, L. Kovács, and A. Voronkov, “Invariant and
type inference for matrices,” presented at the VMCAI: Verification, Model Checking
and Abstract Interpretation, Madrid, Spain, 2010, vol. 5944, pp. 163–179.'
ista: 'Henzinger TA, Hottelier T, Kovács L, Voronkov A. 2010. Invariant and type
inference for matrices. VMCAI: Verification, Model Checking and Abstract Interpretation,
LNCS, vol. 5944, 163–179.'
mla: Henzinger, Thomas A., et al. Invariant and Type Inference for Matrices.
Vol. 5944, Springer, 2010, pp. 163–79, doi:10.1007/978-3-642-11319-2_14.
short: T.A. Henzinger, T. Hottelier, L. Kovács, A. Voronkov, in:, Springer, 2010,
pp. 163–179.
conference:
end_date: 2010-01-19
location: Madrid, Spain
name: 'VMCAI: Verification, Model Checking and Abstract Interpretation'
start_date: 2010-01-17
date_created: 2018-12-11T12:05:27Z
date_published: 2010-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:33Z
day: '01'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1007/978-3-642-11319-2_14
file:
- access_level: open_access
checksum: da69b13a2d9a7a316c909e09c1090cef
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:09Z
date_updated: 2020-07-14T12:46:16Z
file_id: '4989'
file_name: IST-2012-69-v1+1_Invariant_and_type_inference_for_matrices.pdf
file_size: 251265
relation: main_file
file_date_updated: 2020-07-14T12:46:16Z
has_accepted_license: '1'
intvolume: ' 5944'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 163 - 179
publication_status: published
publisher: Springer
publist_id: '2357'
pubrep_id: '69'
quality_controlled: '1'
scopus_import: 1
status: public
title: Invariant and type inference for matrices
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 5944
year: '2010'
...
---
_id: '3840'
abstract:
- lang: eng
text: 'Classical formalizations of systems and properties are boolean: given a system
and a property, the property is either true or false of the system. Correspondingly,
classical methods for system analysis determine the truth value of a property,
preferably giving a proof if the property is true, and a counterexample if the
property is false; classical methods for system synthesis construct a system for
which a property is true; classical methods for system transformation, composition,
and abstraction aim to preserve the truth of properties. The boolean view is prevalent
even if the system, the property, or both refer to numerical quantities, such
as the times or probabilities of events. For example, a timed automaton either
satisfies or violates a formula of a real-time logic; a stochastic process either
satisfies or violates a formula of a probabilistic logic. The classical black-and-white
view partitions the world into "correct" and "incorrect" systems, offering few
nuances. In reality, of several systems that satisfy a property in the boolean
sense, often some are more desirable than others, and of the many systems that
violate a property, usually some are less objectionable than others. For instance,
among the systems that satisfy the response property that every request be granted,
we may prefer systems that grant requests quickly (the quicker, the better), or
we may prefer systems that issue few unnecessary grants (the fewer, the better);
and among the systems that violate the response property, we may prefer systems
that serve many initial requests (the more, the better), or we may prefer systems
that serve many requests in the long run (the greater the fraction of served to
unserved requests, the better). Formally, while a boolean notion of correctness
is given by a preorder on systems and properties, a quantitative notion of correctness
is defined by a directed metric on systems and properties, where the distance
between a system and a property provides a measure of "fit" or "desirability."
There are many ways how such distances can be defined. In a linear-time framework,
one assigns numerical values to individual behaviors before assigning values to
systems and properties, which are sets of behaviors. For example, the value of
a single behavior may be a discounted value, which is largely determined by a
prefix of the behavior, e.g., by the number of requests that are granted before
the first request that is not granted; or a limit value, which is independent
of any finite prefix. A limit value may be an average, such as the average response
time over an infinite sequence of requests and grants, or a supremum, such as
the worst-case response time. Similarly, the value of a set of behaviors may be
an extremum or an average across the values of all behaviors in the set: in this
way one can measure the worst of all possible average-case response times, or
the average of all possible worst-case response times, etc. Accordingly, the distance
between two sets of behaviors may be defined as the worst or average difference
between the values of corresponding behaviors. In summary, we propagate replacing
boolean specifications for the correctness of systems with quantitative measures
for the desirability of systems. In quantitative analysis, the aim is to compute
the distance between a system and a property (or between two systems, or two properties);
in quantitative synthesis, the objective is to construct a system that has minimal
distance from a given property. Multiple quantitative measures can be prioritized
(e.g., combined lexicographically into a single measure) or studied along the
Pareto curve. Quantitative transformations, compositions, and abstractions of
systems are useful if they allow us to bound the induced change in distance from
a property. We present some initial results in some of these directions. We also
give some potential applications, which not only generalize tradiditional correctness
concerns in the functional, timed, and probabilistic domains, but also capture
such system measures as resource use, performance, cost, reliability, and robustness.'
acknowledgement: This talk surveys joint work with Roderick Bloem, Krishnendu Chatterjee,
Laurent Doyen, and Barbara Jobstmann.
article_processing_charge: No
author:
- 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: 'Henzinger TA. From boolean to quantitative notions of correctness. In: Vol
45. ACM; 2010:157-158. doi:10.1145/1706299.1706319'
apa: 'Henzinger, T. A. (2010). From boolean to quantitative notions of correctness
(Vol. 45, pp. 157–158). Presented at the POPL: Principles of Programming Languages,
Madrid, Spain: ACM. https://doi.org/10.1145/1706299.1706319'
chicago: Henzinger, Thomas A. “From Boolean to Quantitative Notions of Correctness,”
45:157–58. ACM, 2010. https://doi.org/10.1145/1706299.1706319.
ieee: 'T. A. Henzinger, “From boolean to quantitative notions of correctness,” presented
at the POPL: Principles of Programming Languages, Madrid, Spain, 2010, vol. 45,
no. 1, pp. 157–158.'
ista: 'Henzinger TA. 2010. From boolean to quantitative notions of correctness.
POPL: Principles of Programming Languages vol. 45, 157–158.'
mla: Henzinger, Thomas A. From Boolean to Quantitative Notions of Correctness.
Vol. 45, no. 1, ACM, 2010, pp. 157–58, doi:10.1145/1706299.1706319.
short: T.A. Henzinger, in:, ACM, 2010, pp. 157–158.
conference:
end_date: 2010-01-23
location: Madrid, Spain
name: 'POPL: Principles of Programming Languages'
start_date: 2010-01-17
corr_author: '1'
date_created: 2018-12-11T12:05:27Z
date_published: 2010-01-17T00:00:00Z
date_updated: 2025-09-30T09:36:44Z
day: '17'
department:
- _id: ToHe
doi: 10.1145/1706299.1706319
external_id:
isi:
- '000281053800014'
intvolume: ' 45'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 157 - 158
publication_status: published
publisher: ACM
publist_id: '2354'
quality_controlled: '1'
scopus_import: '1'
status: public
title: From boolean to quantitative notions of correctness
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 45
year: '2010'
...
---
_id: '3842'
abstract:
- lang: eng
text: Within systems biology there is an increasing interest in the stochastic behavior
of biochemical reaction networks. An appropriate stochastic description is provided
by the chemical master equation, which represents a continuous-time Markov chain
(CTMC). The uniformization technique is an efficient method to compute probability
distributions of a CTMC if the number of states is manageable. However, the size
of a CTMC that represents a biochemical reaction network is usually far beyond
what is feasible. In this paper we present an on-the-fly variant of uniformization,
where we improve the original algorithm at the cost of a small approximation error.
By means of several examples, we show that our approach is particularly well-suited
for biochemical reaction networks.
article_processing_charge: No
author:
- first_name: Frédéric
full_name: Didier, Frédéric
last_name: Didier
- 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
last_name: Mateescu
- first_name: Verena
full_name: Wolf, Verena
last_name: Wolf
citation:
ama: Didier F, Henzinger TA, Mateescu M, Wolf V. Fast adaptive uniformization of
the chemical master equation. IET Systems Biology. 2010;4(6):441-452. doi:10.1049/iet-syb.2010.0005
apa: Didier, F., Henzinger, T. A., Mateescu, M., & Wolf, V. (2010). Fast adaptive
uniformization of the chemical master equation. IET Systems Biology. Institution
of Engineering and Technology. https://doi.org/10.1049/iet-syb.2010.0005
chicago: Didier, Frédéric, Thomas A Henzinger, Maria Mateescu, and Verena Wolf.
“Fast Adaptive Uniformization of the Chemical Master Equation.” IET Systems
Biology. Institution of Engineering and Technology, 2010. https://doi.org/10.1049/iet-syb.2010.0005.
ieee: F. Didier, T. A. Henzinger, M. Mateescu, and V. Wolf, “Fast adaptive uniformization
of the chemical master equation,” IET Systems Biology, vol. 4, no. 6. Institution
of Engineering and Technology, pp. 441–452, 2010.
ista: Didier F, Henzinger TA, Mateescu M, Wolf V. 2010. Fast adaptive uniformization
of the chemical master equation. IET Systems Biology. 4(6), 441–452.
mla: Didier, Frédéric, et al. “Fast Adaptive Uniformization of the Chemical Master
Equation.” IET Systems Biology, vol. 4, no. 6, Institution of Engineering
and Technology, 2010, pp. 441–52, doi:10.1049/iet-syb.2010.0005.
short: F. Didier, T.A. Henzinger, M. Mateescu, V. Wolf, IET Systems Biology 4 (2010)
441–452.
date_created: 2018-12-11T12:05:28Z
date_published: 2010-11-15T00:00:00Z
date_updated: 2025-09-30T09:54:51Z
day: '15'
ddc:
- '570'
department:
- _id: ToHe
doi: 10.1049/iet-syb.2010.0005
external_id:
isi:
- '000284108800011'
file:
- access_level: open_access
checksum: 9a3bde48f43203991a0b3c6a277c2f5b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:02Z
date_updated: 2020-07-14T12:46:16Z
file_id: '5254'
file_name: IST-2012-66-v1+1_Fast_adaptive_uniformization_of_the_chemical_master_equation.pdf
file_size: 222890
relation: main_file
file_date_updated: 2020-07-14T12:46:16Z
has_accepted_license: '1'
intvolume: ' 4'
isi: 1
issue: '6'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 441 - 452
publication: IET Systems Biology
publication_status: published
publisher: Institution of Engineering and Technology
publist_id: '2349'
pubrep_id: '66'
quality_controlled: '1'
related_material:
record:
- id: '3843'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Fast adaptive uniformization of the chemical master equation
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 4
year: '2010'
...
---
_id: '3845'
abstract:
- lang: eng
text: This paper presents Aligators, a tool for the generation of universally quantified
array invariants. Aligators leverages recurrence solving and algebraic techniques
to carry out inductive reasoning over array content. The Aligators’ loop extraction
module allows treatment of multi-path loops by exploiting their commutativity
and serializability properties. Our experience in applying Aligators on a collection
of loops from open source software projects indicates the applicability of recurrence
and algebraic solving techniques for reasoning about arrays.
alternative_title:
- LNCS
article_processing_charge: No
author:
- 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: Thibaud
full_name: Hottelier, Thibaud
last_name: Hottelier
- first_name: Laura
full_name: Kovács, Laura
last_name: Kovács
- first_name: Andrey
full_name: Rybalchenko, Andrey
last_name: Rybalchenko
citation:
ama: 'Henzinger TA, Hottelier T, Kovács L, Rybalchenko A. Aligators for arrays.
In: Vol 6397. Springer; 2010:348-356. doi:10.1007/978-3-642-16242-8_25'
apa: 'Henzinger, T. A., Hottelier, T., Kovács, L., & Rybalchenko, A. (2010).
Aligators for arrays (Vol. 6397, pp. 348–356). Presented at the LPAR: Logic for
Programming, Artificial Intelligence, and Reasoning, Yogyakarta, Indonesia: Springer.
https://doi.org/10.1007/978-3-642-16242-8_25'
chicago: Henzinger, Thomas A, Thibaud Hottelier, Laura Kovács, and Andrey Rybalchenko.
“Aligators for Arrays,” 6397:348–56. Springer, 2010. https://doi.org/10.1007/978-3-642-16242-8_25.
ieee: 'T. A. Henzinger, T. Hottelier, L. Kovács, and A. Rybalchenko, “Aligators
for arrays,” presented at the LPAR: Logic for Programming, Artificial Intelligence,
and Reasoning, Yogyakarta, Indonesia, 2010, vol. 6397, pp. 348–356.'
ista: 'Henzinger TA, Hottelier T, Kovács L, Rybalchenko A. 2010. Aligators for arrays.
LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, LNCS, vol.
6397, 348–356.'
mla: Henzinger, Thomas A., et al. Aligators for Arrays. Vol. 6397, Springer,
2010, pp. 348–56, doi:10.1007/978-3-642-16242-8_25.
short: T.A. Henzinger, T. Hottelier, L. Kovács, A. Rybalchenko, in:, Springer, 2010,
pp. 348–356.
conference:
end_date: 2010-10-15
location: Yogyakarta, Indonesia
name: 'LPAR: Logic for Programming, Artificial Intelligence, and Reasoning'
start_date: 2010-10-10
corr_author: '1'
date_created: 2018-12-11T12:05:29Z
date_published: 2010-10-01T00:00:00Z
date_updated: 2025-09-30T09:35:47Z
day: '01'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1007/978-3-642-16242-8_25
external_id:
isi:
- '000288062700025'
file:
- access_level: open_access
checksum: 913af269da6710f2174f470b48ab7a82
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:05Z
date_updated: 2020-07-14T12:46:17Z
file_id: '4790'
file_name: IST-2012-64-v1+1_Aligators_for_arrays.pdf
file_size: 186143
relation: main_file
file_date_updated: 2020-07-14T12:46:17Z
has_accepted_license: '1'
intvolume: ' 6397'
isi: 1
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 348 - 356
publication_status: published
publisher: Springer
publist_id: '2342'
pubrep_id: '64'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Aligators for arrays
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 6397
year: '2010'
...
---
_id: '3847'
abstract:
- lang: eng
text: The importance of stochasticity within biological systems has been shown repeatedly
during the last years and has raised the need for efficient stochastic tools.
We present SABRE, a tool for stochastic analysis of biochemical reaction networks.
SABRE implements fast adaptive uniformization (FAU), a direct numerical approximation
algorithm for computing transient solutions of biochemical reaction networks.
Biochemical reactions networks represent biological systems studied at a molecular
level and these reactions can be modeled as transitions of a Markov chain. SABRE
accepts as input the formalism of guarded commands, which it interprets either
as continuous-time or as discrete-time Markov chains. Besides operating in a stochastic
mode, SABRE may also perform a deterministic analysis by directly computing a
mean-field approximation of the system under study. We illustrate the different
functionalities of SABRE by means of biological case studies.
author:
- first_name: Frédéric
full_name: Didier, Frédéric
last_name: Didier
- 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
last_name: Mateescu
- first_name: Verena
full_name: Wolf, Verena
last_name: Wolf
citation:
ama: 'Didier F, Henzinger TA, Mateescu M, Wolf V. SABRE: A tool for the stochastic
analysis of biochemical reaction networks. In: IEEE; 2010:193-194. doi:10.1109/QEST.2010.33'
apa: 'Didier, F., Henzinger, T. A., Mateescu, M., & Wolf, V. (2010). SABRE:
A tool for the stochastic analysis of biochemical reaction networks (pp. 193–194).
Presented at the QEST: Quantitative Evaluation of Systems, Williamsburg, USA:
IEEE. https://doi.org/10.1109/QEST.2010.33'
chicago: 'Didier, Frédéric, Thomas A Henzinger, Maria Mateescu, and Verena Wolf.
“SABRE: A Tool for the Stochastic Analysis of Biochemical Reaction Networks,”
193–94. IEEE, 2010. https://doi.org/10.1109/QEST.2010.33.'
ieee: 'F. Didier, T. A. Henzinger, M. Mateescu, and V. Wolf, “SABRE: A tool for
the stochastic analysis of biochemical reaction networks,” presented at the QEST:
Quantitative Evaluation of Systems, Williamsburg, USA, 2010, pp. 193–194.'
ista: 'Didier F, Henzinger TA, Mateescu M, Wolf V. 2010. SABRE: A tool for the stochastic
analysis of biochemical reaction networks. QEST: Quantitative Evaluation of Systems,
193–194.'
mla: 'Didier, Frédéric, et al. SABRE: A Tool for the Stochastic Analysis of Biochemical
Reaction Networks. IEEE, 2010, pp. 193–94, doi:10.1109/QEST.2010.33.'
short: F. Didier, T.A. Henzinger, M. Mateescu, V. Wolf, in:, IEEE, 2010, pp. 193–194.
conference:
end_date: 2010-09-18
location: Williamsburg, USA
name: 'QEST: Quantitative Evaluation of Systems'
start_date: 2010-09-15
date_created: 2018-12-11T12:05:29Z
date_published: 2010-10-14T00:00:00Z
date_updated: 2021-01-12T07:52:37Z
day: '14'
ddc:
- '004'
department:
- _id: ToHe
- _id: CaGu
doi: 10.1109/QEST.2010.33
file:
- access_level: open_access
checksum: 38707b149d2174f01be406e794ffa849
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:03Z
date_updated: 2020-07-14T12:46:17Z
file_id: '4726'
file_name: IST-2012-63-v1+1_SABRE-A_tool_for_the_stochastic_analysis_of_biochemical_reaction_networks.pdf
file_size: 433824
relation: main_file
file_date_updated: 2020-07-14T12:46:17Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 193 - 194
publication_status: published
publisher: IEEE
publist_id: '2339'
pubrep_id: '63'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'SABRE: A tool for the stochastic analysis of biochemical reaction networks'
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '3853'
abstract:
- lang: eng
text: 'Quantitative languages are an extension of boolean languages that assign
to each word a real number. Mean-payoff automata are finite automata with numerical
weights on transitions that assign to each infinite path the long-run average
of the transition weights. When the mode of branching of the automaton is deterministic,
nondeterministic, or alternating, the corresponding class of quantitative languages
is not robust as it is not closed under the pointwise operations of max, min,
sum, and numerical complement. Nondeterministic and alternating mean-payoff automata
are not decidable either, as the quantitative generalization of the problems of
universality and language inclusion is undecidable. We introduce a new class of
quantitative languages, defined by mean-payoff automaton expressions, which is
robust and decidable: it is closed under the four pointwise operations, and we
show that all decision problems are decidable for this class. Mean-payoff automaton
expressions subsume deterministic meanpayoff automata, and we show that they have
expressive power incomparable to nondeterministic and alternating mean-payoff
automata. We also present for the first time an algorithm to compute distance
between two quantitative languages, and in our case the quantitative languages
are given as mean-payoff automaton expressions.'
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- 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: Philippe
full_name: Rannou, Philippe
last_name: Rannou
citation:
ama: 'Chatterjee K, Doyen L, Edelsbrunner H, Henzinger TA, Rannou P. Mean-payoff
automaton expressions. In: Vol 6269. Schloss Dagstuhl - Leibniz-Zentrum für Informatik;
2010:269-283. doi:10.1007/978-3-642-15375-4_19'
apa: 'Chatterjee, K., Doyen, L., Edelsbrunner, H., Henzinger, T. A., & Rannou,
P. (2010). Mean-payoff automaton expressions (Vol. 6269, pp. 269–283). Presented
at the CONCUR: Concurrency Theory, Paris, France: Schloss Dagstuhl - Leibniz-Zentrum
für Informatik. https://doi.org/10.1007/978-3-642-15375-4_19'
chicago: Chatterjee, Krishnendu, Laurent Doyen, Herbert Edelsbrunner, Thomas A Henzinger,
and Philippe Rannou. “Mean-Payoff Automaton Expressions,” 6269:269–83. Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2010. https://doi.org/10.1007/978-3-642-15375-4_19.
ieee: 'K. Chatterjee, L. Doyen, H. Edelsbrunner, T. A. Henzinger, and P. Rannou,
“Mean-payoff automaton expressions,” presented at the CONCUR: Concurrency Theory,
Paris, France, 2010, vol. 6269, pp. 269–283.'
ista: 'Chatterjee K, Doyen L, Edelsbrunner H, Henzinger TA, Rannou P. 2010. Mean-payoff
automaton expressions. CONCUR: Concurrency Theory, LNCS, vol. 6269, 269–283.'
mla: Chatterjee, Krishnendu, et al. Mean-Payoff Automaton Expressions. Vol.
6269, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010, pp. 269–83, doi:10.1007/978-3-642-15375-4_19.
short: K. Chatterjee, L. Doyen, H. Edelsbrunner, T.A. Henzinger, P. Rannou, in:,
Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010, pp. 269–283.
conference:
end_date: 2010-09-03
location: Paris, France
name: 'CONCUR: Concurrency Theory'
start_date: 2010-08-31
corr_author: '1'
date_created: 2018-12-11T12:05:31Z
date_published: 2010-11-18T00:00:00Z
date_updated: 2024-10-09T20:54:08Z
day: '18'
ddc:
- '000'
- '005'
department:
- _id: KrCh
- _id: HeEd
- _id: ToHe
doi: 10.1007/978-3-642-15375-4_19
ec_funded: 1
file:
- access_level: open_access
checksum: 4f753ae99d076553fb8733e2c8b390e2
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:41Z
date_updated: 2020-07-14T12:46:17Z
file_id: '5163'
file_name: IST-2012-62-v1+1_Mean-payoff_automaton_expressions.pdf
file_size: 233260
relation: main_file
file_date_updated: 2020-07-14T12:46:17Z
has_accepted_license: '1'
intvolume: ' 6269'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 269 - 283
project:
- _id: 25EFB36C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '215543'
name: COMponent-Based Embedded Systems design Techniques
- _id: 25F1337C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '214373'
name: Design for Embedded Systems
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '2328'
pubrep_id: '62'
quality_controlled: '1'
scopus_import: 1
status: public
title: Mean-payoff automaton expressions
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 6269
year: '2010'
...