---
_id: '4402'
alternative_title:
- LNCS
author:
- first_name: Rajeev
full_name: Alur, Rajeev
last_name: Alur
- first_name: Pavol
full_name: Pavol Cerny
id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87
last_name: Cerny
- first_name: Swarat
full_name: Chaudhuri,Swarat
last_name: Chaudhuri
citation:
ama: 'Alur R, Cerny P, Chaudhuri S. Model Checking on Trees with Path Equivalences.
In: Springer; 2007:664-678. doi:1544'
apa: 'Alur, R., Cerny, P., & Chaudhuri, S. (2007). Model Checking on Trees with
Path Equivalences (pp. 664–678). Presented at the TACAS: Tools and Algorithms
for the Construction and Analysis of Systems, Springer. https://doi.org/1544'
chicago: Alur, Rajeev, Pavol Cerny, and Swarat Chaudhuri. “Model Checking on Trees
with Path Equivalences,” 664–78. Springer, 2007. https://doi.org/1544.
ieee: 'R. Alur, P. Cerny, and S. Chaudhuri, “Model Checking on Trees with Path Equivalences,”
presented at the TACAS: Tools and Algorithms for the Construction and Analysis
of Systems, 2007, pp. 664–678.'
ista: 'Alur R, Cerny P, Chaudhuri S. 2007. Model Checking on Trees with Path Equivalences.
TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS,
, 664–678.'
mla: Alur, Rajeev, et al. Model Checking on Trees with Path Equivalences.
Springer, 2007, pp. 664–78, doi:1544.
short: R. Alur, P. Cerny, S. Chaudhuri, in:, Springer, 2007, pp. 664–678.
conference:
name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems'
date_created: 2018-12-11T12:08:40Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T07:56:43Z
day: '01'
doi: '1544'
extern: 1
month: '01'
page: 664 - 678
publication_status: published
publisher: Springer
publist_id: '1055'
quality_controlled: 0
status: public
title: Model Checking on Trees with Path Equivalences
type: conference
year: '2007'
...
---
_id: '4405'
abstract:
- lang: eng
text: |-
Background
A central goal of Systems Biology is to model and analyze biological signaling pathways that interact with one another to form complex networks. Here we introduce Qualitative networks, an extension of Boolean networks. With this framework, we use formal verification methods to check whether a model is consistent with the laboratory experimental observations on which it is based. If the model does not conform to the data, we suggest a revised model and the new hypotheses are tested in-silico.
Results
We consider networks in which elements range over a small finite domain allowing more flexibility than Boolean values, and add target functions that allow to model a rich set of behaviors. We propose a symbolic algorithm for analyzing the steady state of these networks, allowing us to scale up to a system consisting of 144 elements and state spaces of approximately 1086 states. We illustrate the usefulness of this approach through a model of the interaction between the Notch and the Wnt signaling pathways in mammalian skin, and its extensive analysis.
Conclusion
We introduce an approach for constructing computational models of biological systems that extends the framework of Boolean networks and uses formal verification methods for the analysis of the model. This approach can scale to multicellular models of complex pathways, and is therefore a useful tool for the analysis of complex biological systems. The hypotheses formulated during in-silico testing suggest new avenues to explore experimentally. Hence, this approach has the potential to efficiently complement experimental studies in biology.
author:
- first_name: Marc
full_name: Schaub, Marc A
last_name: Schaub
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Jasmin
full_name: Fisher, Jasmin
last_name: Fisher
citation:
ama: 'Schaub M, Henzinger TA, Fisher J. Qualitative networks: A symbolic approach
to analyze biological signaling networks. BMC Systems Biology. 2007;1(4).
doi:10.1186/1752-0509-1-4'
apa: 'Schaub, M., Henzinger, T. A., & Fisher, J. (2007). Qualitative networks:
A symbolic approach to analyze biological signaling networks. BMC Systems Biology.
BioMed Central. https://doi.org/10.1186/1752-0509-1-4'
chicago: 'Schaub, Marc, Thomas A Henzinger, and Jasmin Fisher. “Qualitative Networks:
A Symbolic Approach to Analyze Biological Signaling Networks.” BMC Systems
Biology. BioMed Central, 2007. https://doi.org/10.1186/1752-0509-1-4.'
ieee: 'M. Schaub, T. A. Henzinger, and J. Fisher, “Qualitative networks: A symbolic
approach to analyze biological signaling networks,” BMC Systems Biology,
vol. 1, no. 4. BioMed Central, 2007.'
ista: 'Schaub M, Henzinger TA, Fisher J. 2007. Qualitative networks: A symbolic
approach to analyze biological signaling networks. BMC Systems Biology. 1(4).'
mla: 'Schaub, Marc, et al. “Qualitative Networks: A Symbolic Approach to Analyze
Biological Signaling Networks.” BMC Systems Biology, vol. 1, no. 4, BioMed
Central, 2007, doi:10.1186/1752-0509-1-4.'
short: M. Schaub, T.A. Henzinger, J. Fisher, BMC Systems Biology 1 (2007).
date_created: 2018-12-11T12:08:41Z
date_published: 2007-01-08T00:00:00Z
date_updated: 2021-01-12T07:56:44Z
day: '08'
doi: 10.1186/1752-0509-1-4
extern: 1
intvolume: ' 1'
issue: '4'
main_file_link:
- open_access: '0'
url: http://www.biomedcentral.com/1752-0509/1/4
month: '01'
publication: BMC Systems Biology
publication_status: published
publisher: BioMed Central
publist_id: '325'
quality_controlled: 0
status: public
title: 'Qualitative networks: A symbolic approach to analyze biological signaling
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
volume: 1
year: '2007'
...
---
_id: '4417'
abstract:
- lang: eng
text: Counterexample-guided abstraction refinement (CEGAR) is a powerful technique
to scale automatic program analysis techniques to large programs. However, so
far it has been used primarily for model checking in the context of predicate
abstraction. We formalize CEGAR for general powerset domains. If a spurious abstract
counterexample needs to be removed through abstraction refinement, there are often
several choices, such as which program location(s) to refine, which abstract domain(s)
to use at different locations, and which abstract values to compute. We define
several plausible preference orderings on abstraction refinements, such as refining
as “late” as possible and as “coarse” as possible. We present generic algorithms
for finding refinements that are optimal with respect to the different preference
orderings. We also compare the different orderings with respect to desirable properties,
including the property if locally optimal refinements compose to a global optimum.
Finally, we point out some difficulties with CEGAR for non-powerset domains.
acknowledgement: This research is partially supported by the Clore Fellowship Programme.
Supported in part by the Swiss National Science Foundation.
alternative_title:
- LNCS
author:
- first_name: Roman
full_name: Manevich, Roman
last_name: Manevich
- first_name: John
full_name: Field, John
last_name: Field
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Ganesan
full_name: Ramalingam, Ganesan
last_name: Ramalingam
- first_name: Mooly
full_name: Sagiv, Mooly
last_name: Sagiv
citation:
ama: 'Manevich R, Field J, Henzinger TA, Ramalingam G, Sagiv M. Abstract counterexample-based
refinement for powerset domains. In: Program Analysis and Compilation, Theory
and Practice: Essays Dedicated to Reinhard Wilhelm on the Occasion of His 60th
Birthday. Vol 4444. Springer; 2007:273-292. doi:10.1007/978-3-540-71322-7_13'
apa: 'Manevich, R., Field, J., Henzinger, T. A., Ramalingam, G., & Sagiv, M.
(2007). Abstract counterexample-based refinement for powerset domains. In Program
Analysis and Compilation, Theory and Practice: Essays Dedicated to Reinhard Wilhelm
on the Occasion of His 60th Birthday (Vol. 4444, pp. 273–292). Springer. https://doi.org/10.1007/978-3-540-71322-7_13'
chicago: 'Manevich, Roman, John Field, Thomas A Henzinger, Ganesan Ramalingam, and
Mooly Sagiv. “Abstract Counterexample-Based Refinement for Powerset Domains.”
In Program Analysis and Compilation, Theory and Practice: Essays Dedicated
to Reinhard Wilhelm on the Occasion of His 60th Birthday, 4444:273–92. Springer,
2007. https://doi.org/10.1007/978-3-540-71322-7_13.'
ieee: 'R. Manevich, J. Field, T. A. Henzinger, G. Ramalingam, and M. Sagiv, “Abstract
counterexample-based refinement for powerset domains,” in Program Analysis
and Compilation, Theory and Practice: Essays Dedicated to Reinhard Wilhelm on
the Occasion of His 60th Birthday, vol. 4444, Springer, 2007, pp. 273–292.'
ista: 'Manevich R, Field J, Henzinger TA, Ramalingam G, Sagiv M. 2007.Abstract counterexample-based
refinement for powerset domains. In: Program Analysis and Compilation, Theory
and Practice: Essays Dedicated to Reinhard Wilhelm on the Occasion of His 60th
Birthday. LNCS, vol. 4444, 273–292.'
mla: 'Manevich, Roman, et al. “Abstract Counterexample-Based Refinement for Powerset
Domains.” Program Analysis and Compilation, Theory and Practice: Essays Dedicated
to Reinhard Wilhelm on the Occasion of His 60th Birthday, vol. 4444, Springer,
2007, pp. 273–92, doi:10.1007/978-3-540-71322-7_13.'
short: 'R. Manevich, J. Field, T.A. Henzinger, G. Ramalingam, M. Sagiv, in:, Program
Analysis and Compilation, Theory and Practice: Essays Dedicated to Reinhard Wilhelm
on the Occasion of His 60th Birthday, Springer, 2007, pp. 273–292.'
date_created: 2018-12-11T12:08:45Z
date_published: 2007-03-30T00:00:00Z
date_updated: 2021-01-12T07:56:49Z
day: '30'
doi: 10.1007/978-3-540-71322-7_13
extern: 1
intvolume: ' 4444'
month: '03'
page: 273 - 292
publication: 'Program Analysis and Compilation, Theory and Practice: Essays Dedicated
to Reinhard Wilhelm on the Occasion of His 60th Birthday'
publication_status: published
publisher: Springer
publist_id: '314'
quality_controlled: 0
status: public
title: Abstract counterexample-based refinement for powerset domains
type: book_chapter
volume: 4444
year: '2007'
...
---
_id: '4446'
abstract:
- lang: eng
text: The Embedded Machine is a virtual machine that mediates in real time the interaction
between software processes and physical processes. It separates the compilation
of embedded programs into two phases. The first phase, the platform-independent
compiler phase, generates E code (code executed by the Embedded Machine), which
supervises the timing, not the scheduling of, application tasks relative to external
events such as clock ticks and sensor interrupts. E code is portable and, given
an input behavior, exhibits predictable (i.e., deterministic) timing and output
behavior. The second phase, the platform-dependent compiler phase, checks the
time safety of the E code, that is, whether platform performance (determined by
the hardware) and platform utilization (determined by the scheduler of the operating
system) enable its timely execution. We have used the Embedded Machine to compile
and execute high-performance control applications written in Giotto, such as the
flight control system of an autonomous model helicopter.
author:
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Christoph
full_name: Kirsch, Christoph M
last_name: Kirsch
citation:
ama: 'Henzinger TA, Kirsch C. The embedded machine: Predictable, portable real-time
code. ACM Transactions on Programming Languages and Systems (TOPLAS). 2007;29(393).
doi:10.1145/1286821.1286824'
apa: 'Henzinger, T. A., & Kirsch, C. (2007). The embedded machine: Predictable,
portable real-time code. ACM Transactions on Programming Languages and Systems
(TOPLAS). ACM. https://doi.org/10.1145/1286821.1286824'
chicago: 'Henzinger, Thomas A, and Christoph Kirsch. “The Embedded Machine: Predictable,
Portable Real-Time Code.” ACM Transactions on Programming Languages and Systems
(TOPLAS). ACM, 2007. https://doi.org/10.1145/1286821.1286824.'
ieee: 'T. A. Henzinger and C. Kirsch, “The embedded machine: Predictable, portable
real-time code,” ACM Transactions on Programming Languages and Systems (TOPLAS),
vol. 29, no. 393. ACM, 2007.'
ista: 'Henzinger TA, Kirsch C. 2007. The embedded machine: Predictable, portable
real-time code. ACM Transactions on Programming Languages and Systems (TOPLAS).
29(393).'
mla: 'Henzinger, Thomas A., and Christoph Kirsch. “The Embedded Machine: Predictable,
Portable Real-Time Code.” ACM Transactions on Programming Languages and Systems
(TOPLAS), vol. 29, no. 393, ACM, 2007, doi:10.1145/1286821.1286824.'
short: T.A. Henzinger, C. Kirsch, ACM Transactions on Programming Languages and
Systems (TOPLAS) 29 (2007).
date_created: 2018-12-11T12:08:53Z
date_published: 2007-10-01T00:00:00Z
date_updated: 2021-01-12T07:57:01Z
day: '01'
doi: 10.1145/1286821.1286824
extern: 1
intvolume: ' 29'
issue: 393
month: '10'
publication: ACM Transactions on Programming Languages and Systems (TOPLAS)
publication_status: published
publisher: ACM
publist_id: '286'
quality_controlled: 0
status: public
title: 'The embedded machine: Predictable, portable real-time code'
type: journal_article
volume: 29
year: '2007'
...
---
_id: '4511'
abstract:
- lang: eng
text: 'In the traditional view, a language is a set of words, i.e., a function from
words to boolean values. We call this view “qualitative,” because each word either
belongs to or does not belong to a language. Let Σ be an alphabet, and let us
consider infinite words over Σ. Formally, a qualitative language over Σ is a function
A: B . There are many applications of qualitative languages. For example, qualitative
languages are used to specify the legal behaviors of systems, and zero-sum objectives
of games played on graphs. In the former case, each behavior of a system is either
legal or illegal; in the latter case, each outcome of a game is either winning
or losing. For defining languages, it is convenient to use finite acceptors (or
generators). In particular, qualitative languages are often defined using finite-state
machines (so-called ω-automata) whose transitions are labeled by letters from
Σ. For example, the states of an ω-automaton may represent states of a system,
and the transition labels may represent atomic observables of a behavior. There
is a rich and well-studied theory of finite-state acceptors of qualitative languages,
namely, the theory of theω-regular languages.'
acknowledgement: This research was supported in part by the Swiss National Science
Foundation and by the NSF grant CCR-0225610.
alternative_title:
- LNCS
author:
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Henzinger TA. Quantitative generalizations of languages. In: Vol 4588. Springer;
2007:20-22. doi:10.1007/978-3-540-73208-2_2'
apa: 'Henzinger, T. A. (2007). Quantitative generalizations of languages (Vol. 4588,
pp. 20–22). Presented at the DLT: Developments in Language Theory, Springer. https://doi.org/10.1007/978-3-540-73208-2_2'
chicago: Henzinger, Thomas A. “Quantitative Generalizations of Languages,” 4588:20–22.
Springer, 2007. https://doi.org/10.1007/978-3-540-73208-2_2.
ieee: 'T. A. Henzinger, “Quantitative generalizations of languages,” presented at
the DLT: Developments in Language Theory, 2007, vol. 4588, pp. 20–22.'
ista: 'Henzinger TA. 2007. Quantitative generalizations of languages. DLT: Developments
in Language Theory, LNCS, vol. 4588, 20–22.'
mla: Henzinger, Thomas A. Quantitative Generalizations of Languages. Vol.
4588, Springer, 2007, pp. 20–22, doi:10.1007/978-3-540-73208-2_2.
short: T.A. Henzinger, in:, Springer, 2007, pp. 20–22.
conference:
name: 'DLT: Developments in Language Theory'
date_created: 2018-12-11T12:09:14Z
date_published: 2007-06-21T00:00:00Z
date_updated: 2021-01-12T07:59:21Z
day: '21'
doi: 10.1007/978-3-540-73208-2_2
extern: 1
intvolume: ' 4588'
month: '06'
page: 20 - 22
publication_status: published
publisher: Springer
publist_id: '218'
quality_controlled: 0
status: public
title: Quantitative generalizations of languages
type: conference
volume: 4588
year: '2007'
...
---
_id: '4514'
abstract:
- lang: eng
text: 'Digital technology is increasingly deployed in safety-critical situations.
This calls for systematic design and verification methodologies that can cope
with three major sources of system complexity: concurrency, real time, and uncertainty.
We advocate a two-step process: formal modeling followed by algorithmic analysis
(or, “model building” followed by “model checking”). We model the concurrent components
of a reactive system as potential collaborators or adversaries in a multi-player
game with temporal objectives, such as system safety. The real-time aspect of
embedded systems requires models that combine discrete state transitions and continuous
state evolutions. Uncertainty in the environment is naturally modeled by probabilistic
state changes. As a result, we obtain three orthogonal extensions of the basic
state-transition graph model for reactive systems —game graphs, timed graphs,
and stochastic graphs— as well as combinations thereof. In this short text, we
provide a uniform exposition of the underlying definitions. For verification algorithms,
we refer the reader to the literature.'
acknowledgement: This research was supported in part by the Swiss National Science
Foundation, and by the NSF ITR grant CCR-0225610.
alternative_title:
- LNCS
author:
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Henzinger TA. Games, time, and probability: Graph models for system design
and analysis. In: Vol 4362. Springer; 2007:103-110. doi:10.1007/978-3-540-69507-3_7'
apa: 'Henzinger, T. A. (2007). Games, time, and probability: Graph models for system
design and analysis (Vol. 4362, pp. 103–110). Presented at the SOFSEM: Current
Trends in Theory and Practice of Computer Science, Springer. https://doi.org/10.1007/978-3-540-69507-3_7'
chicago: 'Henzinger, Thomas A. “Games, Time, and Probability: Graph Models for System
Design and Analysis,” 4362:103–10. Springer, 2007. https://doi.org/10.1007/978-3-540-69507-3_7.'
ieee: 'T. A. Henzinger, “Games, time, and probability: Graph models for system design
and analysis,” presented at the SOFSEM: Current Trends in Theory and Practice
of Computer Science, 2007, vol. 4362, pp. 103–110.'
ista: 'Henzinger TA. 2007. Games, time, and probability: Graph models for system
design and analysis. SOFSEM: Current Trends in Theory and Practice of Computer
Science, LNCS, vol. 4362, 103–110.'
mla: 'Henzinger, Thomas A. Games, Time, and Probability: Graph Models for System
Design and Analysis. Vol. 4362, Springer, 2007, pp. 103–10, doi:10.1007/978-3-540-69507-3_7.'
short: T.A. Henzinger, in:, Springer, 2007, pp. 103–110.
conference:
name: 'SOFSEM: Current Trends in Theory and Practice of Computer Science'
date_created: 2018-12-11T12:09:15Z
date_published: 2007-01-04T00:00:00Z
date_updated: 2021-01-12T07:59:22Z
day: '04'
doi: 10.1007/978-3-540-69507-3_7
extern: 1
intvolume: ' 4362'
month: '01'
page: 103 - 110
publication_status: published
publisher: Springer
publist_id: '217'
quality_controlled: 0
status: public
title: 'Games, time, and probability: Graph models for system design and analysis'
type: conference
volume: 4362
year: '2007'
...
---
_id: '4529'
abstract:
- lang: eng
text: Computational modeling of biological systems is becoming increasingly important
in efforts to better understand complex biological behaviors. In this review,
we distinguish between two types of biological models—mathematical and computational—which
differ in their representations of biological phenomena. We call the approach
of constructing computational models of biological systems 'executable biology',
as it focuses on the design of executable computer algorithms that mimic biological
phenomena. We survey the main modeling efforts in this direction, emphasize the
applicability and benefits of executable models in biological research and highlight
some of the challenges that executable biology poses for biology and computer
science. We claim that for executable biology to reach its full potential as a
mainstream biological technique, formal and algorithmic approaches must be integrated
into biological research. This will drive biology toward a more precise engineering
discipline.
author:
- first_name: Jasmin
full_name: Fisher, Jasmin
last_name: Fisher
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: Fisher J, Henzinger TA. Executable cell biology. Nature Biotechnology.
2007;25:1239-1249. doi:10.1038/nbt1356
apa: Fisher, J., & Henzinger, T. A. (2007). Executable cell biology. Nature
Biotechnology. Nature Publishing Group. https://doi.org/10.1038/nbt1356
chicago: Fisher, Jasmin, and Thomas A Henzinger. “Executable Cell Biology.” Nature
Biotechnology. Nature Publishing Group, 2007. https://doi.org/10.1038/nbt1356.
ieee: J. Fisher and T. A. Henzinger, “Executable cell biology,” Nature Biotechnology,
vol. 25. Nature Publishing Group, pp. 1239–1249, 2007.
ista: Fisher J, Henzinger TA. 2007. Executable cell biology. Nature Biotechnology.
25, 1239–1249.
mla: Fisher, Jasmin, and Thomas A. Henzinger. “Executable Cell Biology.” Nature
Biotechnology, vol. 25, Nature Publishing Group, 2007, pp. 1239–49, doi:10.1038/nbt1356.
short: J. Fisher, T.A. Henzinger, Nature Biotechnology 25 (2007) 1239–1249.
date_created: 2018-12-11T12:09:19Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T07:59:28Z
day: '01'
doi: 10.1038/nbt1356
extern: 1
intvolume: ' 25'
month: '01'
page: 1239 - 1249
publication: Nature Biotechnology
publication_status: published
publisher: Nature Publishing Group
publist_id: '198'
quality_controlled: 0
status: public
title: Executable cell biology
type: journal_article
volume: 25
year: '2007'
...
---
_id: '4530'
abstract:
- lang: eng
text: This book constitutes the refereed proceedings of the 21st International Workshop
on Computer Science Logic, CSL 2007, held as the 16th Annual Conference of the
EACSL in Lausanne, Switzerland. The 36 revised full papers presented together
with the abstracts of six invited lectures are organized in topical sections on
logic and games, expressiveness, games and trees, logic and deduction, lambda
calculus, finite model theory, linear logic, proof theory, and game semantics.
alternative_title:
- LNCS
author:
- first_name: Jacques
full_name: Duparc, Jacques
last_name: Duparc
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Duparc J, Henzinger TA. CSL: Computer Science Logic . Vol 4646. Springer;
2007. doi:10.1007/978-3-540-74915-8'
apa: 'Duparc, J., & Henzinger, T. A. (2007). CSL: Computer Science Logic
. CSL: Computer Science Logic (Vol. 4646). Springer. https://doi.org/10.1007/978-3-540-74915-8'
chicago: 'Duparc, Jacques, and Thomas A Henzinger. CSL: Computer Science Logic
. CSL: Computer Science Logic. Vol. 4646. Springer, 2007. https://doi.org/10.1007/978-3-540-74915-8.'
ieee: 'J. Duparc and T. A. Henzinger, CSL: Computer Science Logic , vol.
4646. Springer, 2007.'
ista: 'Duparc J, Henzinger TA. 2007. CSL: Computer Science Logic , Springer,p.'
mla: 'Duparc, Jacques, and Thomas A. Henzinger. “CSL: Computer Science Logic .”
CSL: Computer Science Logic, vol. 4646, Springer, 2007, doi:10.1007/978-3-540-74915-8.'
short: 'J. Duparc, T.A. Henzinger, CSL: Computer Science Logic , Springer, 2007.'
date_created: 2018-12-11T12:09:20Z
date_published: 2007-09-01T00:00:00Z
date_updated: 2019-08-02T12:38:32Z
day: '01'
doi: 10.1007/978-3-540-74915-8
extern: 1
intvolume: ' 4646'
month: '09'
publication: 'CSL: Computer Science Logic'
publication_status: published
publisher: Springer
publist_id: '194'
quality_controlled: 0
status: public
title: 'CSL: Computer Science Logic '
type: conference_editor
volume: 4646
year: '2007'
...
---
_id: '4531'
abstract:
- lang: eng
text: Caenorhabditis elegans vulval development provides an important paradigm for
studying the process of cell fate determination and pattern formation during animal
development. Although many genes controlling vulval cell fate specification have
been identified, how they orchestrate themselves to generate a robust and invariant
pattern of cell fates is not yet completely understood. Here, we have developed
a dynamic computational model incorporating the current mechanistic understanding
of gene interactions during this patterning process. A key feature of our model
is the inclusion of multiple modes of crosstalk between the epidermal growth factor
receptor (EGFR) and LIN-12/Notch signaling pathways, which together determine
the fates of the six vulval precursor cells (VPCs). Computational analysis, using
the model-checking technique, provides new biological insights into the regulatory
network governing VPC fate specification and predicts novel negative feedback
loops. In addition, our analysis shows that most mutations affecting vulval development
lead to stable fate patterns in spite of variations in synchronicity between VPCs.
Computational searches for the basis of this robustness show that a sequential
activation of the EGFR-mediated inductive signaling and LIN-12 / Notch-mediated
lateral signaling pathways is key to achieve a stable cell fate pattern. We demonstrate
experimentally a time-delay between the activation of the inductive and lateral
signaling pathways in wild-type animals and the loss of sequential signaling in
mutants showing unstable fate patterns; thus, validating two key predictions provided
by our modeling work. The insights gained by our modeling study further substantiate
the usefulness of executing and analyzing mechanistic models to investigate complex
biological behaviors.
acknowledgement: This work was supported in part by the Swiss National Science Foundation
(grant 205321–111840).
author:
- first_name: Jasmin
full_name: Fisher, Jasmin
last_name: Fisher
- first_name: Nir
full_name: Piterman, Nir
last_name: Piterman
- first_name: Alex
full_name: Hajnal, Alex
last_name: Hajnal
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: Fisher J, Piterman N, Hajnal A, Henzinger TA. Predictive modeling of signaling
crosstalk during C. elegans vulval development. PLoS Computational Biology.
2007;3(5):e92. doi:10.1371/journal.pcbi.0030092
apa: Fisher, J., Piterman, N., Hajnal, A., & Henzinger, T. A. (2007). Predictive
modeling of signaling crosstalk during C. elegans vulval development. PLoS
Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.0030092
chicago: Fisher, Jasmin, Nir Piterman, Alex Hajnal, and Thomas A Henzinger. “Predictive
Modeling of Signaling Crosstalk during C. Elegans Vulval Development.” PLoS
Computational Biology. Public Library of Science, 2007. https://doi.org/10.1371/journal.pcbi.0030092.
ieee: J. Fisher, N. Piterman, A. Hajnal, and T. A. Henzinger, “Predictive modeling
of signaling crosstalk during C. elegans vulval development,” PLoS Computational
Biology, vol. 3(5):e92. Public Library of Science, 2007.
ista: Fisher J, Piterman N, Hajnal A, Henzinger TA. 2007. Predictive modeling of
signaling crosstalk during C. elegans vulval development. PLoS Computational Biology.
3(5):e92.
mla: Fisher, Jasmin, et al. “Predictive Modeling of Signaling Crosstalk during C.
Elegans Vulval Development.” PLoS Computational Biology, vol. 3(5):e92,
Public Library of Science, 2007, doi:10.1371/journal.pcbi.0030092.
short: J. Fisher, N. Piterman, A. Hajnal, T.A. Henzinger, PLoS Computational Biology
3(5):e92 (2007).
date_created: 2018-12-11T12:09:20Z
date_published: 2007-05-18T00:00:00Z
date_updated: 2021-01-12T07:59:29Z
day: '18'
doi: 10.1371/journal.pcbi.0030092
extern: 1
month: '05'
publication: PLoS Computational Biology
publication_status: published
publisher: Public Library of Science
publist_id: '195'
quality_controlled: 0
status: public
title: Predictive modeling of signaling crosstalk during C. elegans vulval development
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
volume: 3(5):e92
year: '2007'
...
---
_id: '4537'
abstract:
- lang: eng
text: The classical synthesis problem for reactive systems asks, given a proponent
process A and an opponent process B, to refine A so that the closed-loop system
A parallel to B satisfies a given specification Phi. The solution of this problem
requires the computation of a winning strategy for proponent A in a game against
opponent B. We define and study the co-synthesis problem, where the proponent
A consists itself of two independent processes, A = A(1)parallel to A(2), with
specifications Phi(1) and Phi(2), and the goal is to refine both A(1) and A(2)
so that A(1)parallel to A(2)parallel to B satisfies Phi(1) boolean AND Phi(2).
For example, if the opponent B is a fair scheduler for the two processes A(1)
and A(2), and Phi(i) specifies the requirements of mutual exclusion for A(i) (e.g.,
starvation freedom), then the co-synthesis problem asks for the automatic synthesis
of a mutual-exclusion protocol. We show that co-synthesis defined classically,
with the processes A(1) and A(2) either collaborating or competing, does not capture
desirable solutions. Instead, the proper formulation of co-synthesis is the one
where process A, competes with A(2) but not at the price of violating Phi(1),
and vice versa. We call this assume-guarantee synthesis and show that it can be
solved by computing secure-equilibrium strategies. In particular, from mutual-exclusion
requirements the assume-guarantee synthesis algorithm automatically computes Peterson's
protocol.
acknowledgement: This research was supported in part by the Swiss National Science
Foundation and by the NSF grants CCR-0225610 and CCR-0234690.
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Chatterjee K, Henzinger TA. Assume-guarantee synthesis. In: Vol 4424. Springer;
2007:261-275. doi:10.1007/978-3-540-71209-1_21'
apa: 'Chatterjee, K., & Henzinger, T. A. (2007). Assume-guarantee synthesis
(Vol. 4424, pp. 261–275). Presented at the TACAS: Tools and Algorithms for the
Construction and Analysis of Systems, Springer. https://doi.org/10.1007/978-3-540-71209-1_21'
chicago: Chatterjee, Krishnendu, and Thomas A Henzinger. “Assume-Guarantee Synthesis,”
4424:261–75. Springer, 2007. https://doi.org/10.1007/978-3-540-71209-1_21.
ieee: 'K. Chatterjee and T. A. Henzinger, “Assume-guarantee synthesis,” presented
at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems,
2007, vol. 4424, pp. 261–275.'
ista: 'Chatterjee K, Henzinger TA. 2007. Assume-guarantee synthesis. TACAS: Tools
and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 4424,
261–275.'
mla: Chatterjee, Krishnendu, and Thomas A. Henzinger. Assume-Guarantee Synthesis.
Vol. 4424, Springer, 2007, pp. 261–75, doi:10.1007/978-3-540-71209-1_21.
short: K. Chatterjee, T.A. Henzinger, in:, Springer, 2007, pp. 261–275.
conference:
name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems'
date_created: 2018-12-11T12:09:22Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T07:59:32Z
day: '01'
doi: 10.1007/978-3-540-71209-1_21
extern: 1
intvolume: ' 4424'
month: '01'
page: 261 - 275
publication_status: published
publisher: Springer
publist_id: '186'
quality_controlled: 0
status: public
title: Assume-guarantee synthesis
type: conference
volume: 4424
year: '2007'
...
---
_id: '4547'
abstract:
- lang: eng
text: We study observation-based strategies for two-player turn-based games on graphs
with omega-regular objectives. An observation-based strategy relies on imperfect
information about the history of a play, namely, on the past sequence of observations.
Such games occur in the synthesis of a controller that does not see the private
state of the plant. Our main results are twofold. First, we give a fixed-point
algorithm for computing the set of states from which a player can win with a deterministic
observation-based strategy for any omega-regular objective. The fixed point is
computed in the lattice of antichains of state sets. This algorithm has the advantages
of being directed by the objective and of avoiding an explicit subset construction
on the game graph. Second, we give an algorithm for computing the set of states
from which a player can win with probability 1 with a randomized observation-based
strategy for a Buechi objective. This set is of interest because in the absence
of perfect information, randomized strategies are more powerful than deterministic
ones. We show that our algorithms are optimal by proving matching lower bounds.
acknowledgement: This research was supported in part by the NSF grants CCR-0225610
and CCR-0234690 by the SNSF under the Indo-Swiss Joint Research Programme and by
the FRFC project “Centre Fédéré en Vérification” funded by the FNRS under grant
2.4530.02.
author:
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
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: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Jean
full_name: Raskin, Jean-François
last_name: Raskin
citation:
ama: Chatterjee K, Doyen L, Henzinger TA, Raskin J. Algorithms for omega-regular
games with imperfect information. Logical Methods in Computer Science.
2007;3(184):1-23. doi:10.2168/LMCS-3(3:4)2007
apa: Chatterjee, K., Doyen, L., Henzinger, T. A., & Raskin, J. (2007). Algorithms
for omega-regular games with imperfect information. Logical Methods in Computer
Science. International Federation of Computational Logic. https://doi.org/10.2168/LMCS-3(3:4)2007
chicago: Chatterjee, Krishnendu, Laurent Doyen, Thomas A Henzinger, and Jean Raskin.
“Algorithms for Omega-Regular Games with Imperfect Information.” Logical Methods
in Computer Science. International Federation of Computational Logic, 2007.
https://doi.org/10.2168/LMCS-3(3:4)2007.
ieee: K. Chatterjee, L. Doyen, T. A. Henzinger, and J. Raskin, “Algorithms for omega-regular
games with imperfect information,” Logical Methods in Computer Science,
vol. 3, no. 184. International Federation of Computational Logic, pp. 1–23, 2007.
ista: Chatterjee K, Doyen L, Henzinger TA, Raskin J. 2007. Algorithms for omega-regular
games with imperfect information. Logical Methods in Computer Science. 3(184),
1–23.
mla: Chatterjee, Krishnendu, et al. “Algorithms for Omega-Regular Games with Imperfect
Information.” Logical Methods in Computer Science, vol. 3, no. 184, International
Federation of Computational Logic, 2007, pp. 1–23, doi:10.2168/LMCS-3(3:4)2007.
short: K. Chatterjee, L. Doyen, T.A. Henzinger, J. Raskin, Logical Methods in Computer
Science 3 (2007) 1–23.
date_created: 2018-12-11T12:09:25Z
date_published: 2007-07-27T00:00:00Z
date_updated: 2021-01-12T07:59:36Z
day: '27'
doi: 10.2168/LMCS-3(3:4)2007
extern: 1
intvolume: ' 3'
issue: 184
month: '07'
page: 1 - 23
publication: Logical Methods in Computer Science
publication_status: published
publisher: International Federation of Computational Logic
publist_id: '167'
quality_controlled: 0
status: public
title: Algorithms for omega-regular games with imperfect information
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
volume: 3
year: '2007'
...
---
_id: '4559'
abstract:
- lang: eng
text: |-
We study games played on graphs with omega-regular conditions specified as parity, Rabin, Streett or Muller conditions. These games have applications in the verification, synthesis, modeling, testing, and compatibility checking of reactive systems. Important distinctions between graph games are as follows: (a) turn-based vs. concurrent games, depending on whether at a state of the game only a single player makes a move, or players make moves simultaneously; (b) deterministic vs. stochastic, depending on whether the transition function is a deterministic or a probabilistic function over successor states; and (c) zero-sum vs. non-zero-sum, depending on whether the objectives of the players are strictly conflicting or not.
We establish that the decision problem for turn-based stochastic zero-sum games with Rabin, Streett, and Muller objectives are NP-complete, coNP-complete, and PSPACE-complete, respectively, substantially improving the previously known 3EXPTIME bound. We also present strategy improvement style algorithms for turn-based stochastic Rabin and Streett games. In the case of concurrent stochastic zero-sum games with parity objectives we obtain a PSPACE bound, again improving the previously known 3EXPTIME bound. As a consequence, concurrent stochastic zero-sum games with Rabin, Streett, and Muller objectives can be solved in EXPSPACE, improving the previously known 4EXPTIME bound. We also present an elementary and combinatorial proof of the existence of memoryless \epsilon-optimal strategies in concurrent stochastic games with reachability objectives, for all real \epsilon>0, where an \epsilon-optimal strategy achieves the value of the game with in \epsilon against all strategies of the opponent. We also use the proof techniques to present a strategy improvement style algorithm for concurrent stochastic reachability games.
We then go beyond \omega-regular objectives and study the complexity of an important class of quantitative objectives, namely, limit-average objectives. In the case of limit-average games, the states of the graph is labeled with rewards and the goal is to maximize the long-run average of the rewards. We show that concurrent stochastic zero-sum games with limit-average objectives can be solved in EXPTIME.
Finally, we introduce a new notion of equilibrium, called secure equilibrium, in non-zero-sum games which captures the notion of conditional competitiveness. We prove the existence of unique maximal secure equilibrium payoff profiles in turn-based deterministic games, and present algorithms to compute such payoff profiles. We also show how the notion of secure equilibrium extends the assume-guarantee style of reasoning in the game theoretic framework.
acknowledgement: Technical Report No. UCB/EECS-2007-122
author:
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: Chatterjee K. Stochastic ω-Regular Games. 2007:1-247.
apa: Chatterjee, K. (2007). Stochastic ω-Regular Games. University of California,
Berkeley.
chicago: Chatterjee, Krishnendu. “Stochastic ω-Regular Games.” University of California,
Berkeley, 2007.
ieee: K. Chatterjee, “Stochastic ω-Regular Games,” University of California, Berkeley,
2007.
ista: Chatterjee K. 2007. Stochastic ω-Regular Games. University of California,
Berkeley.
mla: Chatterjee, Krishnendu. Stochastic ω-Regular Games. University of California,
Berkeley, 2007, pp. 1–247.
short: K. Chatterjee, Stochastic ω-Regular Games, University of California, Berkeley,
2007.
date_created: 2018-12-11T12:09:29Z
date_published: 2007-10-08T00:00:00Z
date_updated: 2021-01-12T07:59:42Z
day: '08'
extern: 1
main_file_link:
- open_access: '0'
url: http://chess.eecs.berkeley.edu/pubs/462.html
month: '10'
page: 1 - 247
publication_status: published
publisher: University of California, Berkeley
publist_id: '150'
quality_controlled: 0
status: public
title: Stochastic ω-Regular Games
type: dissertation
year: '2007'
...
---
_id: '4566'
abstract:
- lang: eng
text: "Complex system design today calls for compositional design and implementation.
However each component is designed with certain assumptions about the environment
it is meant to operate in, and delivering certain guarantees if those assumptions
are satisfied; numerous inter-component interaction errors are introduced in the
manual and error-prone integration process as there is little support in design
environments for machine-readably representing these assumptions and guarantees
and automatically checking consistency during integration.\r\n\r\nBased on Interface
Automata we propose a framework for compositional design and analysis of systems:
a set of domain-specific automata-theoretic type systems for compositional system
specification and analysis by behavioral specification of open systems. We focus
on three different domains: component-based hardware systems communicating on
bidirectional wires. concurrent distributed recursive message-passing software
systems, and embedded software system components operating in resource-constrained
environments. For these domains we present approaches to formally represent the
assumptions and conditional guarantees between interacting open system components.
Composition of such components produces new components with the appropriate assumptions
and guarantees. We check satisfaction of temporal logic specifications by such
components, and the substitutability of one component with another in an arbitrary
context. Using this framework one can analyze large systems incrementally without
needing extensive summary information to close the system at each stage. Furthermore,
we focus only on the inter-component interaction behavior without dealing with
the full implementation details of each component. Many of the merits of automata-theoretic
model-checking are combined with the compositionality afforded by type-system
based techniques. We also present an integer-based extension of the conventional
boolean verification framework motivated by our interface formalism for embedded
software components.\r\n\r\nOur algorithms for checking the behavioral compatibility
of component interfaces are available in our tool Chic, which can be used as a
plug-in for the Java IDE JBuilder and the heterogenous modeling and design environment
Ptolemy II.\r\n\r\nFinally, we address the complementary problem of partitioning
a large system into meaningful coherent components by analyzing the interaction
patterns between its basic elements. We demonstrate the usefulness of our partitioning
approach by evaluating its efficacy in improving unit-test branch coverage for
a large software system implemented in C."
article_processing_charge: No
author:
- first_name: Arindam
full_name: Chakrabarti, Arindam
last_name: Chakrabarti
citation:
ama: Chakrabarti A. A framework for compositional design and analysis of systems.
2007:1-244.
apa: Chakrabarti, A. (2007). A framework for compositional design and analysis
of systems. University of California, Berkeley.
chicago: Chakrabarti, Arindam. “A Framework for Compositional Design and Analysis
of Systems.” University of California, Berkeley, 2007.
ieee: A. Chakrabarti, “A framework for compositional design and analysis of systems,”
University of California, Berkeley, 2007.
ista: Chakrabarti A. 2007. A framework for compositional design and analysis of
systems. University of California, Berkeley.
mla: Chakrabarti, Arindam. A Framework for Compositional Design and Analysis
of Systems. University of California, Berkeley, 2007, pp. 1–244.
short: A. Chakrabarti, A Framework for Compositional Design and Analysis of Systems,
University of California, Berkeley, 2007.
date_created: 2018-12-11T12:09:31Z
date_published: 2007-12-20T00:00:00Z
date_updated: 2021-01-12T07:59:45Z
day: '20'
extern: '1'
language:
- iso: eng
month: '12'
oa_version: None
page: 1 - 244
publication_status: published
publisher: University of California, Berkeley
publist_id: '145'
status: public
supervisor:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: George
full_name: Necula, George
last_name: Necula
- first_name: Edward
full_name: Lee, Edward
last_name: Lee
- first_name: Jack
full_name: Silver, Jack
last_name: Silver
title: A framework for compositional design and analysis of systems
type: dissertation
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2007'
...
---
_id: '4567'
abstract:
- lang: eng
text: BLAST is an automatic verification tool for checking temporal safety properties
of C programs. Given a C program and a temporal safety property, BLAST either
statically proves that the program satisfies the safety property, or provides
an execution path that exhibits a violation of the property (or, since the problem
is undecidable, does not terminate). BLAST constructs, explores, and refines abstractions
of the program state space based on lazy predicate abstraction and interpolation-based
predicate discovery. This paper gives an introduction to BLAST and demonstrates,
through two case studies, how it can be applied to program verification and test-case
generation. In the first case study, we use BLAST to statically prove memory safety
for C programs. We use CCured, a type-based memory-safety analyzer, to annotate
a program with run-time assertions that check for safe memory operations. Then,
we use BLAST to remove as many of the run-time checks as possible (by proving
that these checks never fail), and to generate execution scenarios that violate
the assertions for the remaining run-time checks. In our second case study, we
use BLAST to automatically generate test suites that guarantee full coverage with
respect to a given predicate. Given a C program and a target predicate p, BLAST
determines the program locations q for which there exists a program execution
that reaches q with p true, and automatically generates a set of test vectors
that cause such executions. Our experiments show that BLAST can provide automated,
precise, and scalable analysis for C programs.
author:
- first_name: Dirk
full_name: Beyer, Dirk
last_name: Beyer
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Ranjit
full_name: Jhala, Ranjit
last_name: Jhala
- first_name: Ritankar
full_name: Majumdar, Ritankar S
last_name: Majumdar
citation:
ama: 'Beyer D, Henzinger TA, Jhala R, Majumdar R. The software model checker BLAST:
Applications to software engineering. International Journal on Software Tools
for Technology Transfer. 2007;9(5):505-525. doi:10.1007/s10009-007-0044-z'
apa: 'Beyer, D., Henzinger, T. A., Jhala, R., & Majumdar, R. (2007). The software
model checker BLAST: Applications to software engineering. International Journal
on Software Tools for Technology Transfer. Springer. https://doi.org/10.1007/s10009-007-0044-z'
chicago: 'Beyer, Dirk, Thomas A Henzinger, Ranjit Jhala, and Ritankar Majumdar.
“The Software Model Checker BLAST: Applications to Software Engineering.” International
Journal on Software Tools for Technology Transfer. Springer, 2007. https://doi.org/10.1007/s10009-007-0044-z.'
ieee: 'D. Beyer, T. A. Henzinger, R. Jhala, and R. Majumdar, “The software model
checker BLAST: Applications to software engineering,” International Journal
on Software Tools for Technology Transfer, vol. 9, no. 5. Springer, pp. 505–525,
2007.'
ista: 'Beyer D, Henzinger TA, Jhala R, Majumdar R. 2007. The software model checker
BLAST: Applications to software engineering. International Journal on Software
Tools for Technology Transfer. 9(5), 505–525.'
mla: 'Beyer, Dirk, et al. “The Software Model Checker BLAST: Applications to Software
Engineering.” International Journal on Software Tools for Technology Transfer,
vol. 9, no. 5, Springer, 2007, pp. 505–25, doi:10.1007/s10009-007-0044-z.'
short: D. Beyer, T.A. Henzinger, R. Jhala, R. Majumdar, International Journal on
Software Tools for Technology Transfer 9 (2007) 505–525.
date_created: 2018-12-11T12:09:31Z
date_published: 2007-10-01T00:00:00Z
date_updated: 2021-01-12T07:59:45Z
day: '01'
doi: 10.1007/s10009-007-0044-z
extern: 1
intvolume: ' 9'
issue: '5'
month: '10'
page: 505 - 525
publication: International Journal on Software Tools for Technology Transfer
publication_status: published
publisher: Springer
publist_id: '139'
quality_controlled: 0
status: public
title: 'The software model checker BLAST: Applications to software engineering'
type: journal_article
volume: 9
year: '2007'
...
---
_id: '4570'
abstract:
- lang: eng
text: We consider the minimum-time reachability problem in concurrent two-player
timed automaton game structures. We show how to compute the minimum time needed
by a player to reach a target location against all possible choices of the opponent.
We do not put any syntactic restriction on the game structure, nor do we require
any player to guarantee time divergence. We only require players to use receptive
strategies which do not block time. The minimal time is computed in part using
a fixpoint expression, which we show can be evaluated on equivalence classes of
a non-trivial extension of the clock-region equivalence relation for timed automata.
acknowledgement: This research was supported in part by the NSF grant CCR-0225610
and by the Swiss National Science Foundation.
alternative_title:
- LNCS
author:
- first_name: Thomas
full_name: Brihaye, Thomas
last_name: Brihaye
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Vinayak
full_name: Prabhu, Vinayak S
last_name: Prabhu
- first_name: Jean
full_name: Raskin, Jean-François
last_name: Raskin
citation:
ama: 'Brihaye T, Henzinger TA, Prabhu V, Raskin J. Minimum-time reachability in
timed games. In: Vol 4596. Springer; 2007:825-837. doi:10.1007/978-3-540-73420-8_71'
apa: 'Brihaye, T., Henzinger, T. A., Prabhu, V., & Raskin, J. (2007). Minimum-time
reachability in timed games (Vol. 4596, pp. 825–837). Presented at the ICALP:
Automata, Languages and Programming, Springer. https://doi.org/10.1007/978-3-540-73420-8_71'
chicago: Brihaye, Thomas, Thomas A Henzinger, Vinayak Prabhu, and Jean Raskin. “Minimum-Time
Reachability in Timed Games,” 4596:825–37. Springer, 2007. https://doi.org/10.1007/978-3-540-73420-8_71.
ieee: 'T. Brihaye, T. A. Henzinger, V. Prabhu, and J. Raskin, “Minimum-time reachability
in timed games,” presented at the ICALP: Automata, Languages and Programming,
2007, vol. 4596, pp. 825–837.'
ista: 'Brihaye T, Henzinger TA, Prabhu V, Raskin J. 2007. Minimum-time reachability
in timed games. ICALP: Automata, Languages and Programming, LNCS, vol. 4596, 825–837.'
mla: Brihaye, Thomas, et al. Minimum-Time Reachability in Timed Games. Vol.
4596, Springer, 2007, pp. 825–37, doi:10.1007/978-3-540-73420-8_71.
short: T. Brihaye, T.A. Henzinger, V. Prabhu, J. Raskin, in:, Springer, 2007, pp.
825–837.
conference:
name: 'ICALP: Automata, Languages and Programming'
date_created: 2018-12-11T12:09:32Z
date_published: 2007-06-29T00:00:00Z
date_updated: 2021-01-12T07:59:47Z
day: '29'
doi: 10.1007/978-3-540-73420-8_71
extern: 1
intvolume: ' 4596'
month: '06'
page: 825 - 837
publication_status: published
publisher: Springer
publist_id: '142'
quality_controlled: 0
status: public
title: Minimum-time reachability in timed games
type: conference
volume: 4596
year: '2007'
...
---
_id: '4571'
abstract:
- lang: eng
text: The success of software verification depends on the ability to find a suitable
abstraction of a program automatically. We propose a method for automated abstraction
refinement which overcomes some limitations of current predicate discovery schemes.
In current schemes, the cause of a false alarm is identified as an infeasible
error path, and the abstraction is refined in order to remove that path. By contrast,
we view the cause of a false alarm -the spurious counterexample- as a full-fledged
program, namely, a fragment of the original program whose control-flow graph may
contain loops and represent unbounded computations. There are two advantages to
using such path programs as counterexamples for abstraction refinement. First,
we can bring the whole machinery of program analysis to bear on path programs,
which are typically small compared to the original program. Specifically, we use
constraint-based invariant generation to automatically infer invariants of path
programs-so-called path invariants. Second, we use path invariants for abstraction
refinement in order to remove not one infeasibility at a time, but at once all
(possibly infinitely many) infeasible error computations that are represented
by a path program. Unlike previous predicate discovery schemes, our method handles
loops without unrolling them; it infers abstractions that involve universal quantification
and naturally incorporates disjunctive reasoning.
author:
- first_name: Dirk
full_name: Beyer, Dirk
last_name: Beyer
- 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
citation:
ama: 'Beyer D, Henzinger TA, Majumdar R, Rybalchenko A. Path invariants. In: ACM;
2007:300-309. doi:10.1145/1250734.1250769'
apa: 'Beyer, D., Henzinger, T. A., Majumdar, R., & Rybalchenko, A. (2007). Path
invariants (pp. 300–309). Presented at the PLDI: Programming Languages Design
and Implementation, ACM. https://doi.org/10.1145/1250734.1250769'
chicago: Beyer, Dirk, Thomas A Henzinger, Ritankar Majumdar, and Andrey Rybalchenko.
“Path Invariants,” 300–309. ACM, 2007. https://doi.org/10.1145/1250734.1250769.
ieee: 'D. Beyer, T. A. Henzinger, R. Majumdar, and A. Rybalchenko, “Path invariants,”
presented at the PLDI: Programming Languages Design and Implementation, 2007,
pp. 300–309.'
ista: 'Beyer D, Henzinger TA, Majumdar R, Rybalchenko A. 2007. Path invariants.
PLDI: Programming Languages Design and Implementation, 300–309.'
mla: Beyer, Dirk, et al. Path Invariants. ACM, 2007, pp. 300–09, doi:10.1145/1250734.1250769.
short: D. Beyer, T.A. Henzinger, R. Majumdar, A. Rybalchenko, in:, ACM, 2007, pp.
300–309.
conference:
name: 'PLDI: Programming Languages Design and Implementation'
date_created: 2018-12-11T12:09:32Z
date_published: 2007-06-01T00:00:00Z
date_updated: 2021-01-12T07:59:48Z
day: '01'
doi: 10.1145/1250734.1250769
extern: 1
month: '06'
page: 300 - 309
publication_status: published
publisher: ACM
publist_id: '137'
quality_controlled: 0
status: public
title: Path invariants
type: conference
year: '2007'
...
---
_id: '4572'
abstract:
- lang: eng
text: We present a constraint-based algorithm for the synthesis of invariants expressed
in the combined theory of linear arithmetic and uninterpreted function symbols.
Given a set of programmer-specified invariant templates, our algorithm reduces
the invariant synthesis problem to a sequence of arithmetic constraint satisfaction
queries. Since the combination of linear arithmetic and uninterpreted functions
is a widely applied predicate domain for program verification, our algorithm provides
a powerful tool to statically and automatically reason about program correctness.
The algorithm can also be used for the synthesis of invariants over arrays and
set data structures, because satisfiability questions for the theories of sets
and arrays can be reduced to the theory of linear arithmetic with uninterpreted
functions. We have implemented our algorithm and used it to find invariants for
a low-level memory allocator written in C.
acknowledgement: This research was sponsored in part by the grants NSF-CCF-0427202
and NSF-CCF-0546170.
alternative_title:
- LNCS
author:
- first_name: Dirk
full_name: Beyer, Dirk
last_name: Beyer
- 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
citation:
ama: 'Beyer D, Henzinger TA, Majumdar R, Rybalchenko A. Invariant synthesis for
combined theories. In: Vol 4349. Springer; 2007:378-394. doi:10.1007/978-3-540-69738-1_27'
apa: 'Beyer, D., Henzinger, T. A., Majumdar, R., & Rybalchenko, A. (2007). Invariant
synthesis for combined theories (Vol. 4349, pp. 378–394). Presented at the VMCAI:
Verification, Model Checking and Abstract Interpretation, Springer. https://doi.org/10.1007/978-3-540-69738-1_27'
chicago: Beyer, Dirk, Thomas A Henzinger, Ritankar Majumdar, and Andrey Rybalchenko.
“Invariant Synthesis for Combined Theories,” 4349:378–94. Springer, 2007. https://doi.org/10.1007/978-3-540-69738-1_27.
ieee: 'D. Beyer, T. A. Henzinger, R. Majumdar, and A. Rybalchenko, “Invariant synthesis
for combined theories,” presented at the VMCAI: Verification, Model Checking and
Abstract Interpretation, 2007, vol. 4349, pp. 378–394.'
ista: 'Beyer D, Henzinger TA, Majumdar R, Rybalchenko A. 2007. Invariant synthesis
for combined theories. VMCAI: Verification, Model Checking and Abstract Interpretation,
LNCS, vol. 4349, 378–394.'
mla: Beyer, Dirk, et al. Invariant Synthesis for Combined Theories. Vol.
4349, Springer, 2007, pp. 378–94, doi:10.1007/978-3-540-69738-1_27.
short: D. Beyer, T.A. Henzinger, R. Majumdar, A. Rybalchenko, in:, Springer, 2007,
pp. 378–394.
conference:
name: 'VMCAI: Verification, Model Checking and Abstract Interpretation'
date_created: 2018-12-11T12:09:32Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T07:59:48Z
day: '01'
doi: 10.1007/978-3-540-69738-1_27
extern: 1
intvolume: ' 4349'
month: '01'
page: 378 - 394
publication_status: published
publisher: Springer
publist_id: '138'
quality_controlled: 0
status: public
title: Invariant synthesis for combined theories
type: conference
volume: 4349
year: '2007'
...
---
_id: '4573'
abstract:
- lang: eng
text: In automatic software verification, we have observed a theoretical convergence
of model checking and program analysis. In practice, however, model checkers are
still mostly concerned with precision, e.g., the removal of spurious counterexamples;
for this purpose they build and refine reachability trees. Lattice-based program
analyzers, on the other hand, are primarily concerned with efficiency. We designed
an algorithm and built a tool that can be configured to perform not only a purely
tree-based or a purely lattice-based analysis, but offers many intermediate settings
that have not been evaluated before. The algorithm and tool take one or more abstract
interpreters, such as a predicate abstraction and a shape analysis, and configure
their execution and interaction using several parameters. Our experiments show
that such customization may lead to dramatic improvements in the precision-efficiency
spectrum.
acknowledgement: This research was supported in part by the grant SFU/PRG 06-3, and
by the Swiss National Science Foundation.
alternative_title:
- LNCS
author:
- first_name: Dirk
full_name: Beyer, Dirk
last_name: Beyer
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Grégory
full_name: Théoduloz, Grégory
last_name: Théoduloz
citation:
ama: 'Beyer D, Henzinger TA, Théoduloz G. Configurable software verification: Concretizing
the convergence of model checking and program analysis. In: Vol 4590. Springer;
2007:504-518. doi:10.1007/978-3-540-73368-3_51'
apa: 'Beyer, D., Henzinger, T. A., & Théoduloz, G. (2007). Configurable software
verification: Concretizing the convergence of model checking and program analysis
(Vol. 4590, pp. 504–518). Presented at the CAV: Computer Aided Verification, Springer.
https://doi.org/10.1007/978-3-540-73368-3_51'
chicago: 'Beyer, Dirk, Thomas A Henzinger, and Grégory Théoduloz. “Configurable
Software Verification: Concretizing the Convergence of Model Checking and Program
Analysis,” 4590:504–18. Springer, 2007. https://doi.org/10.1007/978-3-540-73368-3_51.'
ieee: 'D. Beyer, T. A. Henzinger, and G. Théoduloz, “Configurable software verification:
Concretizing the convergence of model checking and program analysis,” presented
at the CAV: Computer Aided Verification, 2007, vol. 4590, pp. 504–518.'
ista: 'Beyer D, Henzinger TA, Théoduloz G. 2007. Configurable software verification:
Concretizing the convergence of model checking and program analysis. CAV: Computer
Aided Verification, LNCS, vol. 4590, 504–518.'
mla: 'Beyer, Dirk, et al. Configurable Software Verification: Concretizing the
Convergence of Model Checking and Program Analysis. Vol. 4590, Springer, 2007,
pp. 504–18, doi:10.1007/978-3-540-73368-3_51.'
short: D. Beyer, T.A. Henzinger, G. Théoduloz, in:, Springer, 2007, pp. 504–518.
conference:
name: 'CAV: Computer Aided Verification'
date_created: 2018-12-11T12:09:33Z
date_published: 2007-07-02T00:00:00Z
date_updated: 2021-01-12T07:59:48Z
day: '02'
doi: 10.1007/978-3-540-73368-3_51
extern: 1
intvolume: ' 4590'
month: '07'
page: 504 - 518
publication_status: published
publisher: Springer
publist_id: '135'
quality_controlled: 0
status: public
title: 'Configurable software verification: Concretizing the convergence of model
checking and program analysis'
type: conference
volume: 4590
year: '2007'
...
---
_id: '4575'
abstract:
- lang: eng
text: 'We present a case study to illustrate our formalism for the specification
and verification of the method-invocation behavior of web-service applications
constructed from asynchronously interacting multi-threaded distributed components.
Our model is expressive enough to allow the representation of recursion and dynamic
thread creation, and yet permits the algorithmic analysis of the following two
questions: (1) Does a given service satisfy a safety specification? (2) Can a
given service be substituted by a another service in an arbitrary context? Our
case study is based on the Amazon.com E-Commerce Services (ECS) platform.'
acknowledgement: This research was supported in part by the NSF grant CCR-0225610
and by the Swiss National Science Foundation.
author:
- first_name: Dirk
full_name: Beyer, Dirk
last_name: Beyer
- first_name: Arindam
full_name: Chakrabarti, Arindam
last_name: Chakrabarti
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Sanjit
full_name: Seshia, Sanjit A
last_name: Seshia
citation:
ama: 'Beyer D, Chakrabarti A, Henzinger TA, Seshia S. An application of web-service
interfaces. In: IEEE; 2007:831-838. doi:10.1109/ICWS.2007.32 '
apa: 'Beyer, D., Chakrabarti, A., Henzinger, T. A., & Seshia, S. (2007). An
application of web-service interfaces (pp. 831–838). Presented at the ICWS: International
Conference on Web Service, IEEE. https://doi.org/10.1109/ICWS.2007.32 '
chicago: Beyer, Dirk, Arindam Chakrabarti, Thomas A Henzinger, and Sanjit Seshia.
“An Application of Web-Service Interfaces,” 831–38. IEEE, 2007. https://doi.org/10.1109/ICWS.2007.32 .
ieee: 'D. Beyer, A. Chakrabarti, T. A. Henzinger, and S. Seshia, “An application
of web-service interfaces,” presented at the ICWS: International Conference on
Web Service, 2007, pp. 831–838.'
ista: 'Beyer D, Chakrabarti A, Henzinger TA, Seshia S. 2007. An application of web-service
interfaces. ICWS: International Conference on Web Service, 831–838.'
mla: Beyer, Dirk, et al. An Application of Web-Service Interfaces. IEEE,
2007, pp. 831–38, doi:10.1109/ICWS.2007.32
.
short: D. Beyer, A. Chakrabarti, T.A. Henzinger, S. Seshia, in:, IEEE, 2007, pp.
831–838.
conference:
name: 'ICWS: International Conference on Web Service'
date_created: 2018-12-11T12:09:33Z
date_published: 2007-07-30T00:00:00Z
date_updated: 2021-01-12T07:59:49Z
day: '30'
doi: '10.1109/ICWS.2007.32 '
extern: 1
month: '07'
page: 831 - 838
publication_status: published
publisher: IEEE
publist_id: '134'
quality_controlled: 0
status: public
title: An application of web-service interfaces
type: conference
year: '2007'
...
---
_id: '4626'
abstract:
- lang: eng
text: 'We consider concurrent two-player games with reachability objectives. In
such games, at each round, player 1 and player 2 independently and simultaneously
choose moves, and the two choices determine the next state of the game. The objective
of player 1 is to reach a set of target states; the objective of player 2 is to
prevent this. These are zero-sum games, and the reachability objective is one
of the most basic objectives: determining the set of states from which player
1 can win the game is a fundamental problem in control theory and system verification.
There are three types of winning states, according to the degree of certainty
with which player 1 can reach the target. From type-1 states, player 1 has a deterministic
strategy to always reach the target. From type-2 states, player 1 has a randomized
strategy to reach the target with probability 1. From type-3 states, player 1
has for every real ε>0 a randomized strategy to reach the target with probability
greater than 1−ε. We show that for finite state spaces, all three sets of winning
states can be computed in polynomial time: type-1 states in linear time, and type-2
and type-3 states in quadratic time. The algorithms to compute the three sets
of winning states also enable the construction of the winning and spoiling strategies.'
author:
- first_name: Luca
full_name: de Alfaro, Luca
last_name: De Alfaro
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Orna
full_name: Kupferman, Orna
last_name: Kupferman
citation:
ama: De Alfaro L, Henzinger TA, Kupferman O. Concurrent reachability games. Theoretical
Computer Science. 2007;386(3):188-217. doi:10.1016/j.tcs.2007.07.008
apa: De Alfaro, L., Henzinger, T. A., & Kupferman, O. (2007). Concurrent reachability
games. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2007.07.008
chicago: De Alfaro, Luca, Thomas A Henzinger, and Orna Kupferman. “Concurrent Reachability
Games.” Theoretical Computer Science. Elsevier, 2007. https://doi.org/10.1016/j.tcs.2007.07.008.
ieee: L. De Alfaro, T. A. Henzinger, and O. Kupferman, “Concurrent reachability
games,” Theoretical Computer Science, vol. 386, no. 3. Elsevier, pp. 188–217,
2007.
ista: De Alfaro L, Henzinger TA, Kupferman O. 2007. Concurrent reachability games.
Theoretical Computer Science. 386(3), 188–217.
mla: De Alfaro, Luca, et al. “Concurrent Reachability Games.” Theoretical Computer
Science, vol. 386, no. 3, Elsevier, 2007, pp. 188–217, doi:10.1016/j.tcs.2007.07.008.
short: L. De Alfaro, T.A. Henzinger, O. Kupferman, Theoretical Computer Science
386 (2007) 188–217.
date_created: 2018-12-11T12:09:49Z
date_published: 2007-11-01T00:00:00Z
date_updated: 2021-01-12T08:00:37Z
day: '01'
doi: 10.1016/j.tcs.2007.07.008
extern: 1
intvolume: ' 386'
issue: '3'
month: '11'
page: 188 - 217
publication: Theoretical Computer Science
publication_status: published
publisher: Elsevier
publist_id: '81'
quality_controlled: 0
status: public
title: Concurrent reachability games
type: journal_article
volume: 386
year: '2007'
...