---
_id: '3837'
abstract:
- lang: eng
text: In this paper we extend the work of Alfaro, Henzinger et al. on interface
theories for component-based design. Existing interface theories often fail to
capture functional relations between the inputs and outputs of an interface. For
example, a simple synchronous interface that takes as input a number n ≥ 0 and
returns, at the same time, as output n + 1, cannot be expressed in existing theories.
In this paper we provide a theory of relational interfaces, where such input-output
relations can be captured. Our theory supports synchronous interfaces, both stateless
and stateful. It includes explicit notions of environments and pluggability, and
satisfies fundamental properties such as preservation of refinement by composition,
and characterization of pluggability by refinement. We achieve these properties
by making reasonable restrictions on feedback loops in interface compositions.
acknowledgement: 'This work is supported by the Center for Hybrid and Embedded Software
Systems (CHESS) at UC Berkeley, which receives support from the National Science
Foundation (NSF awards #0720882 (CSR-EHS: PRET) and #0720841 (CSR-CPS)), the U.S.
Army Research Office (ARO #W911NF-07-2-0019), the U.S. Air Force Office of Scientific
Research (MURI #FA9550-06-0312), the Air Force Research Lab (AFRL), the State of
California Micro Program, and the following companies: Agilent, Bosch, Lockheed-Martin,
National Instruments, Thales and Toyota. This work is also supported by the COMBEST
and ArtistDesign projects of the European Union, and the Swiss National Science
Foundation. '
author:
- first_name: Stavros
full_name: Tripakis, Stavros
last_name: Tripakis
- first_name: Ben
full_name: Lickly, Ben
last_name: Lickly
- 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: Edward
full_name: Lee, Edward
last_name: Lee
citation:
ama: 'Tripakis S, Lickly B, Henzinger TA, Lee E. On relational interfaces. In: EMSOFT
’09 Proceedings of the Seventh ACM International Conference on Embedded Software.
ACM; 2009:67-76. doi:10.1145/1629335.1629346'
apa: 'Tripakis, S., Lickly, B., Henzinger, T. A., & Lee, E. (2009). On relational
interfaces. In EMSOFT ’09 Proceedings of the seventh ACM international conference
on Embedded software (pp. 67–76). Grenoble, France: ACM. https://doi.org/10.1145/1629335.1629346'
chicago: Tripakis, Stavros, Ben Lickly, Thomas A Henzinger, and Edward Lee. “On
Relational Interfaces.” In EMSOFT ’09 Proceedings of the Seventh ACM International
Conference on Embedded Software, 67–76. ACM, 2009. https://doi.org/10.1145/1629335.1629346.
ieee: S. Tripakis, B. Lickly, T. A. Henzinger, and E. Lee, “On relational interfaces,”
in EMSOFT ’09 Proceedings of the seventh ACM international conference on Embedded
software, Grenoble, France, 2009, pp. 67–76.
ista: 'Tripakis S, Lickly B, Henzinger TA, Lee E. 2009. On relational interfaces.
EMSOFT ’09 Proceedings of the seventh ACM international conference on Embedded
software. EMSOFT: Embedded Software , 67–76.'
mla: Tripakis, Stavros, et al. “On Relational Interfaces.” EMSOFT ’09 Proceedings
of the Seventh ACM International Conference on Embedded Software, ACM, 2009,
pp. 67–76, doi:10.1145/1629335.1629346.
short: S. Tripakis, B. Lickly, T.A. Henzinger, E. Lee, in:, EMSOFT ’09 Proceedings
of the Seventh ACM International Conference on Embedded Software, ACM, 2009, pp.
67–76.
conference:
end_date: 2009-10-16
location: Grenoble, France
name: 'EMSOFT: Embedded Software '
start_date: 2009-10-12
date_created: 2018-12-11T12:05:26Z
date_published: 2009-01-01T00:00:00Z
date_updated: 2024-10-21T06:03:06Z
day: '01'
ddc:
- '004'
department:
- _id: ToHe
doi: 10.1145/1629335.1629346
ec_funded: 1
file:
- access_level: open_access
checksum: 3a70e21527dfaad2f198549ae5710786
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:57Z
date_updated: 2020-07-14T12:46:16Z
file_id: '5045'
file_name: IST-2012-70-v1+1_On_Relational_Interfaces.pdf
file_size: 310902
relation: main_file
file_date_updated: 2020-07-14T12:46:16Z
has_accepted_license: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 67 - 76
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: EMSOFT '09 Proceedings of the seventh ACM international conference on
Embedded software
publication_status: published
publisher: ACM
publist_id: '2360'
pubrep_id: '70'
quality_controlled: '1'
scopus_import: '1'
status: public
title: On relational interfaces
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2009'
...
---
_id: '3841'
abstract:
- lang: eng
text: 'We compare several languages for specifying Markovian population models such
as queuing networks and chemical reaction networks. These languages —matrix descriptions,
stochastic Petri nets, stoichiometric equations, stochastic process algebras,
and guarded command models— all describe continuous-time Markov chains, but they
differ according to important properties, such as compositionality, expressiveness
and succinctness, executability, ease of use, and the support they provide for
checking the well-formedness of a model and for analyzing a model. '
acknowledgement: This research was supported in part by the Excellence Cluster on
Multimodal Computing and Interaction and the Swiss National Science Foundation.
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: Barbara
full_name: Jobstmann, Barbara
last_name: Jobstmann
- first_name: Verena
full_name: Wolf, Verena
last_name: Wolf
citation:
ama: 'Henzinger TA, Jobstmann B, Wolf V. Formalisms for specifying Markovian population
models. In: Vol 5797. Springer; 2009:3-23. doi:10.1007/978-3-642-04420-5_2'
apa: 'Henzinger, T. A., Jobstmann, B., & Wolf, V. (2009). Formalisms for specifying
Markovian population models (Vol. 5797, pp. 3–23). Presented at the RP: Reachability
Problems, Palaiseau, France: Springer. https://doi.org/10.1007/978-3-642-04420-5_2'
chicago: Henzinger, Thomas A, Barbara Jobstmann, and Verena Wolf. “Formalisms for
Specifying Markovian Population Models,” 5797:3–23. Springer, 2009. https://doi.org/10.1007/978-3-642-04420-5_2.
ieee: 'T. A. Henzinger, B. Jobstmann, and V. Wolf, “Formalisms for specifying Markovian
population models,” presented at the RP: Reachability Problems, Palaiseau, France,
2009, vol. 5797, pp. 3–23.'
ista: 'Henzinger TA, Jobstmann B, Wolf V. 2009. Formalisms for specifying Markovian
population models. RP: Reachability Problems, LNCS, vol. 5797, 3–23.'
mla: Henzinger, Thomas A., et al. Formalisms for Specifying Markovian Population
Models. Vol. 5797, Springer, 2009, pp. 3–23, doi:10.1007/978-3-642-04420-5_2.
short: T.A. Henzinger, B. Jobstmann, V. Wolf, in:, Springer, 2009, pp. 3–23.
conference:
end_date: 2009-09-25
location: Palaiseau, France
name: 'RP: Reachability Problems'
start_date: 2009-09-23
date_created: 2018-12-11T12:05:28Z
date_published: 2009-09-07T00:00:00Z
date_updated: 2025-09-30T08:49:00Z
day: '07'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1007/978-3-642-04420-5_2
file:
- access_level: open_access
checksum: df88431872586c773fbcfea37d7b36a2
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:41Z
date_updated: 2020-07-14T12:46:16Z
file_id: '4702'
file_name: IST-2012-67-v1+1_Formalisms_for_specifying_Markovian_population_models.pdf
file_size: 222840
relation: main_file
file_date_updated: 2020-07-14T12:46:16Z
has_accepted_license: '1'
intvolume: ' 5797'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 3 - 23
publication_status: published
publisher: Springer
publist_id: '2352'
pubrep_id: '67'
quality_controlled: '1'
related_material:
record:
- id: '3381'
relation: later_version
status: public
scopus_import: 1
status: public
title: Formalisms for specifying Markovian population models
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5797
year: '2009'
...
---
_id: '3843'
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).\r\nStandard Uniformization (SU) is an efficient method for
the transient analysis of CTMCs. For systems with very different time scales,
such as biochemical reaction networks, SU is computationally expensive. In these
cases, a variant of SU, called adaptive uniformization (AU), is known to reduce
the large number of iterations needed by SU. The additional difficulty of AU is
that it requires the solution of a birth process.\r\nIn this paper we present
an on-the-fly variant of AU, where we improve the original algorithm for AU 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."
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: 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
id: 3B43276C-F248-11E8-B48F-1D18A9856A87
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. In: Vol 4. IEEE; 2009:118-127. doi:10.1109/HiBi.2009.23'
apa: 'Didier, F., Henzinger, T. A., Mateescu, M., & Wolf, V. (2009). Fast adaptive
uniformization of the chemical master equation (Vol. 4, pp. 118–127). Presented
at the HIBI: High-Performance Computational Systems Biology, Trento, Italy: IEEE.
https://doi.org/10.1109/HiBi.2009.23'
chicago: Didier, Frédéric, Thomas A Henzinger, Maria Mateescu, and Verena Wolf.
“Fast Adaptive Uniformization of the Chemical Master Equation,” 4:118–27. IEEE,
2009. https://doi.org/10.1109/HiBi.2009.23.
ieee: 'F. Didier, T. A. Henzinger, M. Mateescu, and V. Wolf, “Fast adaptive uniformization
of the chemical master equation,” presented at the HIBI: High-Performance Computational
Systems Biology, Trento, Italy, 2009, vol. 4, no. 6, pp. 118–127.'
ista: 'Didier F, Henzinger TA, Mateescu M, Wolf V. 2009. Fast adaptive uniformization
of the chemical master equation. HIBI: High-Performance Computational Systems
Biology vol. 4, 118–127.'
mla: Didier, Frédéric, et al. Fast Adaptive Uniformization of the Chemical Master
Equation. Vol. 4, no. 6, IEEE, 2009, pp. 118–27, doi:10.1109/HiBi.2009.23.
short: F. Didier, T.A. Henzinger, M. Mateescu, V. Wolf, in:, IEEE, 2009, pp. 118–127.
conference:
end_date: 2009-10-16
location: Trento, Italy
name: 'HIBI: High-Performance Computational Systems Biology'
start_date: 2009-10-14
date_created: 2018-12-11T12:05:28Z
date_published: 2009-10-30T00:00:00Z
date_updated: 2025-09-30T09:54:51Z
day: '30'
ddc:
- '000'
department:
- _id: ToHe
- _id: CaGu
doi: 10.1109/HiBi.2009.23
external_id:
isi:
- '000275038300017'
file:
- access_level: open_access
checksum: 9a3bde48f43203991a0b3c6a277c2f5b
content_type: application/pdf
creator: dernst
date_created: 2020-05-19T16:33:55Z
date_updated: 2020-07-14T12:46:17Z
file_id: '7874'
file_name: 2009_HIBI_Didier.pdf
file_size: 222890
relation: main_file
file_date_updated: 2020-07-14T12:46:17Z
has_accepted_license: '1'
intvolume: ' 4'
isi: 1
issue: '6'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 118 - 127
publication_status: published
publisher: IEEE
publist_id: '2348'
quality_controlled: '1'
related_material:
record:
- id: '3842'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Fast adaptive uniformization of the chemical master equation
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 4
year: '2009'
...
---
_id: '3844'
abstract:
- lang: eng
text: The Hierarchical Timing Language (HTL) is a real-time coordination language
for distributed control systems. HTL programs must be checked for well-formedness,
race freedom, transmission safety (schedulability of inter-host communication),
and time safety (schedulability of host computation). We present a modular abstract
syntax and semantics for HTL, modular checks of well-formedness, race freedom,
and transmission safety, and modular code distribution. Our contributions here
complement previous results on HTL time safety and modular code generation. Modularity
in HTL can be utilized in easy program composition as well as fast program analysis
and code generation, but also in so-called runtime patching, where program components
may be modified at runtime.
acknowledgement: Supported by the EU ArtistDesign Network of Excellence on Embedded
Systems Design, the EU project COMBEST, the Austrian Science Funds P18913-N15 and
V00125, and Fundacao para a Ciencia e Tecnologia funds SFRH/BD/29461/2006 and PTDC/EIA/71462/2006
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: Christoph
full_name: Kirsch, Christoph
last_name: Kirsch
- first_name: Eduardo
full_name: Marques, Eduardo
last_name: Marques
- first_name: Ana
full_name: Sokolova, Ana
last_name: Sokolova
citation:
ama: 'Henzinger TA, Kirsch C, Marques E, Sokolova A. Distributed, modular HTL. In:
IEEE; 2009:171-180. doi:10.1109/RTSS.2009.9'
apa: 'Henzinger, T. A., Kirsch, C., Marques, E., & Sokolova, A. (2009). Distributed,
modular HTL (pp. 171–180). Presented at the RTSS: Real-Time Systems Symposium,
Washington, DC, United States: IEEE. https://doi.org/10.1109/RTSS.2009.9'
chicago: Henzinger, Thomas A, Christoph Kirsch, Eduardo Marques, and Ana Sokolova.
“Distributed, Modular HTL,” 171–80. IEEE, 2009. https://doi.org/10.1109/RTSS.2009.9.
ieee: 'T. A. Henzinger, C. Kirsch, E. Marques, and A. Sokolova, “Distributed, modular
HTL,” presented at the RTSS: Real-Time Systems Symposium, Washington, DC, United
States, 2009, pp. 171–180.'
ista: 'Henzinger TA, Kirsch C, Marques E, Sokolova A. 2009. Distributed, modular
HTL. RTSS: Real-Time Systems Symposium, 171–180.'
mla: Henzinger, Thomas A., et al. Distributed, Modular HTL. IEEE, 2009, pp.
171–80, doi:10.1109/RTSS.2009.9.
short: T.A. Henzinger, C. Kirsch, E. Marques, A. Sokolova, in:, IEEE, 2009, pp.
171–180.
conference:
end_date: 2009-12-04
location: Washington, DC, United States
name: 'RTSS: Real-Time Systems Symposium'
start_date: 2009-12-01
date_created: 2018-12-11T12:05:28Z
date_published: 2009-01-01T00:00:00Z
date_updated: 2025-09-30T09:54:22Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1109/RTSS.2009.9
ec_funded: 1
external_id:
isi:
- '000277465500016'
file:
- access_level: open_access
checksum: b2b15a5ef71eb50d62eaa5aea7efd8c4
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:07:56Z
date_updated: 2020-07-14T12:46:17Z
file_id: '4655'
file_name: IST-2012-65-v1+1_Distributed_modular_Htl.pdf
file_size: 526458
relation: main_file
file_date_updated: 2020-07-14T12:46:17Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 171 - 180
project:
- _id: 25F1337C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '214373'
name: Design for Embedded Systems
- _id: 25EFB36C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '215543'
name: COMponent-Based Embedded Systems design Techniques
publication_status: published
publisher: IEEE
publist_id: '2346'
pubrep_id: '65'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Distributed, modular HTL
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2009'
...
---
_id: '3871'
abstract:
- lang: eng
text: 'Nondeterministic weighted automata are finite automata with numerical weights
oil transitions. They define quantitative languages 1, that assign to each word
v; a real number L(w). The value of ail infinite word w is computed as the maximal
value of all runs over w, and the value of a run as the supremum, limsup liminf,
limit average, or discounted sum of the transition weights. We introduce probabilistic
weighted antomata, in which the transitions are chosen in a randomized (rather
than nondeterministic) fashion. Under almost-sure semantics (resp. positive semantics),
the value of a word v) is the largest real v such that the runs over w have value
at least v with probability I (resp. positive probability). We study the classical
questions of automata theory for probabilistic weighted automata: emptiness and
universality, expressiveness, and closure under various operations oil languages.
For quantitative languages, emptiness university axe defined as whether the value
of some (resp. every) word exceeds a given threshold. We prove some, of these
questions to he decidable, and others undecidable. Regarding expressive power,
we show that probabilities allow its to define a wide variety of new classes of
quantitative languages except for discounted-sum automata, where probabilistic
choice is no more expressive than nondeterminism. Finally we live ail almost complete
picture of the closure of various classes of probabilistic weighted automata for
the following, provide, is operations oil quantitative languages: maximum, sum.
and numerical complement.'
acknowledgement: This research was supported in part by the Swiss National Science
Foundation under the Indo-Swiss Joint Research Programme, by the European Network
of Excellence on Embedded Systems Design (ArtistDesign), by the European projects
Combest, Quasimodo, and Gasics, by the PAI program Moves funded by the Belgian Federal
Government, and by the CFV (Federated Center in Verification ) funded by the F.R.S.-FNRS.
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: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Chatterjee K, Doyen L, Henzinger TA. Probabilistic weighted automata. In:
Vol 5710. Springer; 2009:244-258. doi:10.1007/978-3-642-04081-8_17'
apa: 'Chatterjee, K., Doyen, L., & Henzinger, T. A. (2009). Probabilistic weighted
automata (Vol. 5710, pp. 244–258). Presented at the CONCUR: Concurrency Theory,
Bologna, Italy: Springer. https://doi.org/10.1007/978-3-642-04081-8_17'
chicago: Chatterjee, Krishnendu, Laurent Doyen, and Thomas A Henzinger. “Probabilistic
Weighted Automata,” 5710:244–58. Springer, 2009. https://doi.org/10.1007/978-3-642-04081-8_17.
ieee: 'K. Chatterjee, L. Doyen, and T. A. Henzinger, “Probabilistic weighted automata,”
presented at the CONCUR: Concurrency Theory, Bologna, Italy, 2009, vol. 5710,
pp. 244–258.'
ista: 'Chatterjee K, Doyen L, Henzinger TA. 2009. Probabilistic weighted automata.
CONCUR: Concurrency Theory, LNCS, vol. 5710, 244–258.'
mla: Chatterjee, Krishnendu, et al. Probabilistic Weighted Automata. Vol.
5710, Springer, 2009, pp. 244–58, doi:10.1007/978-3-642-04081-8_17.
short: K. Chatterjee, L. Doyen, T.A. Henzinger, in:, Springer, 2009, pp. 244–258.
conference:
end_date: 2009-09-04
location: Bologna, Italy
name: 'CONCUR: Concurrency Theory'
start_date: 2009-09-01
corr_author: '1'
date_created: 2018-12-11T12:05:37Z
date_published: 2009-09-01T00:00:00Z
date_updated: 2024-10-09T20:53:56Z
day: '01'
ddc:
- '000'
- '005'
department:
- _id: KrCh
doi: 10.1007/978-3-642-04081-8_17
ec_funded: 1
file:
- access_level: open_access
checksum: af973ddbcf131b8810c6bff2c055ff56
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:46Z
date_updated: 2020-07-14T12:46:20Z
file_id: '4771'
file_name: IST-2012-52-v1+1_Probabilistic_Weighted_Automata.pdf
file_size: 200161
relation: main_file
file_date_updated: 2020-07-14T12:46:20Z
has_accepted_license: '1'
intvolume: ' 5710'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 244 - 258
project:
- _id: 25F1337C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '214373'
name: Design for Embedded Systems
- _id: 25EFB36C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '215543'
name: COMponent-Based Embedded Systems design Techniques
publication_status: published
publisher: Springer
publist_id: '2304'
pubrep_id: '52'
quality_controlled: '1'
scopus_import: 1
status: public
title: Probabilistic weighted automata
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5710
year: '2009'
...
---
_id: '3968'
abstract:
- lang: eng
text: We describe an algorithm for segmenting three-dimensional medical imaging
data modeled as a continuous function on a 3-manifold. It is related to watershed
algorithms developed in image processing but is closer to its mathematical roots,
which are Morse theory and homological algebra. It allows for the implicit treatment
of an underlying mesh, thus combining the structural integrity of its mathematical
foundations with the computational efficiency of image processing.
acknowledgement: This research was partially supported by Geomagic, Inc., and by the
Defense Advanced Research Projects Agency (DARPA) under grants HR0011-05-1-0007
and HR0011-05-1-0057.
alternative_title:
- LNCS
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: John
full_name: Harer, John
last_name: Harer
citation:
ama: 'Edelsbrunner H, Harer J. The persistent Morse complex segmentation of a 3-manifold.
In: Vol 5903. Springer; 2009:36-50. doi:10.1007/978-3-642-10470-1_4'
apa: 'Edelsbrunner, H., & Harer, J. (2009). The persistent Morse complex segmentation
of a 3-manifold (Vol. 5903, pp. 36–50). Presented at the 3DPH: Modelling the Physiological
Human, Zermatt, Switzerland: Springer. https://doi.org/10.1007/978-3-642-10470-1_4'
chicago: Edelsbrunner, Herbert, and John Harer. “The Persistent Morse Complex Segmentation
of a 3-Manifold,” 5903:36–50. Springer, 2009. https://doi.org/10.1007/978-3-642-10470-1_4.
ieee: 'H. Edelsbrunner and J. Harer, “The persistent Morse complex segmentation
of a 3-manifold,” presented at the 3DPH: Modelling the Physiological Human, Zermatt,
Switzerland, 2009, vol. 5903, pp. 36–50.'
ista: 'Edelsbrunner H, Harer J. 2009. The persistent Morse complex segmentation
of a 3-manifold. 3DPH: Modelling the Physiological Human, LNCS, vol. 5903, 36–50.'
mla: Edelsbrunner, Herbert, and John Harer. The Persistent Morse Complex Segmentation
of a 3-Manifold. Vol. 5903, Springer, 2009, pp. 36–50, doi:10.1007/978-3-642-10470-1_4.
short: H. Edelsbrunner, J. Harer, in:, Springer, 2009, pp. 36–50.
conference:
end_date: 2009-12-02
location: Zermatt, Switzerland
name: '3DPH: Modelling the Physiological Human'
start_date: 2009-11-29
corr_author: '1'
date_created: 2018-12-11T12:06:10Z
date_published: 2009-11-17T00:00:00Z
date_updated: 2024-10-09T20:53:56Z
day: '17'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.1007/978-3-642-10470-1_4
file:
- access_level: open_access
checksum: 11fc85bcc19bab1f020e706a4b8a4660
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:33Z
date_updated: 2020-07-14T12:46:21Z
file_id: '4694'
file_name: IST-2016-535-v1+1_2009-P-04-3ManifoldSegmentation.pdf
file_size: 165090
relation: main_file
file_date_updated: 2020-07-14T12:46:21Z
has_accepted_license: '1'
intvolume: ' 5903'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 36 - 50
publication_status: published
publisher: Springer
publist_id: '2160'
pubrep_id: '535'
quality_controlled: '1'
scopus_import: 1
status: public
title: The persistent Morse complex segmentation of a 3-manifold
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5903
year: '2009'
...
---
_id: '4136'
abstract:
- lang: eng
text: 'Populations living in a spatially and temporally changing environment can
adapt to the changing optimum and/or migrate toward favorable habitats. Here we
extend previous analyses with a static optimum to allow the environment to vary
in time as well as in space. The model follows both population dynamics and the
trait mean under stabilizing selection, and the outcomes can be understood by
comparing the loads due to genetic variance, dispersal, and temporal change. With
fixed genetic variance, we obtain two regimes: (1) adaptation that is uniform
along the environmental gradient and that responds to the moving optimum as expected
for panmictic populations and when the spatial gradient is sufficiently steep,
and (2) a population with limited range that adapts more slowly than the environmental
optimum changes in both time and space; the population therefore becomes locally
extinct and migrates toward suitable habitat. We also use a population‐genetic
model with many loci to allow genetic variance to evolve, and we show that the
only solution now has uniform adaptation.'
article_processing_charge: No
article_type: original
author:
- first_name: Jitka
full_name: Polechova, Jitka
id: 3BBFB084-F248-11E8-B48F-1D18A9856A87
last_name: Polechova
orcid: 0000-0003-0951-3112
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Glenn
full_name: Marion, Glenn
last_name: Marion
citation:
ama: 'Polechova J, Barton NH, Marion G. Species’ range: Adaptation in space and
time. American Naturalist. 2009;174(5):E186-E204. doi:10.1086/605958'
apa: 'Polechova, J., Barton, N. H., & Marion, G. (2009). Species’ range: Adaptation
in space and time. American Naturalist. University of Chicago Press. https://doi.org/10.1086/605958'
chicago: 'Polechova, Jitka, Nicholas H Barton, and Glenn Marion. “Species’ Range:
Adaptation in Space and Time.” American Naturalist. University of Chicago
Press, 2009. https://doi.org/10.1086/605958.'
ieee: 'J. Polechova, N. H. Barton, and G. Marion, “Species’ range: Adaptation in
space and time,” American Naturalist, vol. 174, no. 5. University of Chicago
Press, pp. E186–E204, 2009.'
ista: 'Polechova J, Barton NH, Marion G. 2009. Species’ range: Adaptation in space
and time. American Naturalist. 174(5), E186–E204.'
mla: 'Polechova, Jitka, et al. “Species’ Range: Adaptation in Space and Time.” American
Naturalist, vol. 174, no. 5, University of Chicago Press, 2009, pp. E186–204,
doi:10.1086/605958.'
short: J. Polechova, N.H. Barton, G. Marion, American Naturalist 174 (2009) E186–E204.
corr_author: '1'
date_created: 2018-12-11T12:07:09Z
date_published: 2009-11-05T00:00:00Z
date_updated: 2025-09-30T09:53:09Z
day: '05'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1086/605958
external_id:
isi:
- '000271021900002'
pmid:
- ' 19788353'
intvolume: ' 174'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.doi.org/10.1086/605958
month: '11'
oa: 1
oa_version: Published Version
page: E186 - E204
pmid: 1
publication: American Naturalist
publication_status: published
publisher: University of Chicago Press
publist_id: '1986'
pubrep_id: '552'
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1086/659642
scopus_import: '1'
status: public
title: 'Species'' range: Adaptation in space and time'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 174
year: '2009'
...
---
_id: '4231'
abstract:
- lang: eng
text: The evolution of quantitative characters depends on the frequencies of the
alleles involved, yet these frequencies cannot usually be measured. Previous groups
have proposed an approximation to the dynamics of quantitative traits, based on
an analogy with statistical mechanics. We present a modified version of that approach,
which makes the analogy more precise and applies quite generally to describe the
evolution of allele frequencies. We calculate explicitly how the macroscopic quantities
(i.e., quantities that depend on the quantitative trait) depend on evolutionary
forces, in a way that is independent of the microscopic details. We first show
that the stationary distribution of allele frequencies under drift, selection,
and mutation maximizes a certain measure of entropy, subject to constraints on
the expectation of observable quantities. We then approximate the dynamical changes
in these expectations, assuming that the distribution of allele frequencies always
maximizes entropy, conditional on the expected values. When applied to directional
selection on an additive trait, this gives a very good approximation to the evolution
of the trait mean and the genetic variance, when the number of mutations per generation
is sufficiently high (4Nμ > 1). We show how the method can be modified for
small mutation rates (4Nμ → 0). We outline how this method describes epistatic
interactions as, for example, with stabilizing selection.
acknowledgement: "N.B. was supported by the Engineering and Physical Sciences Research
Council (GR/T11753 and GR/T19537) and by the Royal Society.\r\nWe are grateful to
Ellen Baake for helping to initiate this project and for her comments on this manuscript.
We also thank Michael Turelli for his comments on the manuscript and I. Pen for
discussions and support in this project. This project was a result of a collaboration
supported by the European Science Foundation grant “Integrating population genetics
and conservation biology.” "
article_processing_charge: No
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Harold
full_name: De Vladar, Harold
last_name: De Vladar
citation:
ama: Barton NH, De Vladar H. Statistical mechanics and the evolution of polygenic
quantitative traits. Genetics. 2009;181(3):997-1011. doi:10.1534/genetics.108.099309
apa: Barton, N. H., & De Vladar, H. (2009). Statistical mechanics and the evolution
of polygenic quantitative traits. Genetics. Genetics Society of America.
https://doi.org/10.1534/genetics.108.099309
chicago: Barton, Nicholas H, and Harold De Vladar. “Statistical Mechanics and the
Evolution of Polygenic Quantitative Traits.” Genetics. Genetics Society
of America, 2009. https://doi.org/10.1534/genetics.108.099309.
ieee: N. H. Barton and H. De Vladar, “Statistical mechanics and the evolution of
polygenic quantitative traits,” Genetics, vol. 181, no. 3. Genetics Society
of America, pp. 997–1011, 2009.
ista: Barton NH, De Vladar H. 2009. Statistical mechanics and the evolution of polygenic
quantitative traits. Genetics. 181(3), 997–1011.
mla: Barton, Nicholas H., and Harold De Vladar. “Statistical Mechanics and the Evolution
of Polygenic Quantitative Traits.” Genetics, vol. 181, no. 3, Genetics
Society of America, 2009, pp. 997–1011, doi:10.1534/genetics.108.099309.
short: N.H. Barton, H. De Vladar, Genetics 181 (2009) 997–1011.
corr_author: '1'
date_created: 2018-12-11T12:07:44Z
date_published: 2009-03-01T00:00:00Z
date_updated: 2025-09-30T09:52:35Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.108.099309
external_id:
isi:
- '000270213500018'
intvolume: ' 181'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa_version: None
page: 997 - 1011
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '1882'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Statistical mechanics and the evolution of polygenic quantitative traits
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 181
year: '2009'
...
---
_id: '4242'
abstract:
- lang: eng
text: 'Felsenstein distinguished two ways by which selection can directly strengthen
isolation. First, a modifier that strengthens prezygotic isolation can be favored
everywhere. This fits with the traditional view of reinforcement as an adaptation
to reduce deleterious hybridization by strengthening assortative mating. Second,
selection can favor association between different incompatibilities, despite recombination.
We generalize this “two allele” model to follow associations among any number
of incompatibilities, which may include both assortment and hybrid inviability.
Our key argument is that this process, of coupling between incompatibilities,
may be quite different from the usual view of reinforcement: strong isolation
can evolve through the coupling of any kind of incompatibility, whether prezygotic
or postzygotic. Single locus incompatibilities become coupled because associations
between them increase the variance in compatibility, which in turn increases mean
fitness if there is positive epistasis. Multiple incompatibilities, each maintained
by epistasis, can become coupled in the same way. In contrast, a single-locus
incompatibility can become coupled with loci that reduce the viability of haploid
hybrids because this reduces harmful recombination. We obtain simple approximations
for the limits of tight linkage, and strong assortment, and show how assortment
alleles can invade through associations with other components of reproductive
isolation.'
acknowledgement: "This work was supported by a Royal Society/Wolfson Research Merit
award, and by a grant from the Natural Environment Research Council.\r\nWe are very
grateful for insightful comments from S. P. Otto, and for helpful suggestions from
the referees and the Associate Editor, Maria Servedio."
article_processing_charge: No
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Maria
full_name: De Cara, Maria
last_name: De Cara
citation:
ama: Barton NH, De Cara M. The evolution of strong reproductive isolation. Evolution;
International Journal of Organic Evolution. 2009;63(5):1171-1190. doi:10.1111/j.1558-5646.2009.00622.x
apa: Barton, N. H., & De Cara, M. (2009). The evolution of strong reproductive
isolation. Evolution; International Journal of Organic Evolution. Wiley.
https://doi.org/10.1111/j.1558-5646.2009.00622.x
chicago: Barton, Nicholas H, and Maria De Cara. “The Evolution of Strong Reproductive
Isolation.” Evolution; International Journal of Organic Evolution. Wiley,
2009. https://doi.org/10.1111/j.1558-5646.2009.00622.x.
ieee: N. H. Barton and M. De Cara, “The evolution of strong reproductive isolation,”
Evolution; International Journal of Organic Evolution, vol. 63, no. 5.
Wiley, pp. 1171–1190, 2009.
ista: Barton NH, De Cara M. 2009. The evolution of strong reproductive isolation.
Evolution; International Journal of Organic Evolution. 63(5), 1171–1190.
mla: Barton, Nicholas H., and Maria De Cara. “The Evolution of Strong Reproductive
Isolation.” Evolution; International Journal of Organic Evolution, vol.
63, no. 5, Wiley, 2009, pp. 1171–90, doi:10.1111/j.1558-5646.2009.00622.x.
short: N.H. Barton, M. De Cara, Evolution; International Journal of Organic Evolution
63 (2009) 1171–1190.
corr_author: '1'
date_created: 2018-12-11T12:07:48Z
date_published: 2009-05-01T00:00:00Z
date_updated: 2025-09-30T09:52:11Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/j.1558-5646.2009.00622.x
external_id:
isi:
- '000265145800006'
file:
- access_level: open_access
checksum: 1920d2e25ef335833764256c1a47bbfb
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:46Z
date_updated: 2020-07-14T12:46:25Z
file_id: '4903'
file_name: IST-2016-551-v1+1_BartonDeCaraRevNew.pdf
file_size: 720913
relation: main_file
- access_level: open_access
checksum: c1c51bbc10d4f328fc96fc5b0e5dc25d
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:47Z
date_updated: 2020-07-14T12:46:25Z
file_id: '4904'
file_name: IST-2016-551-v1+2_BartonDeCaraRevNewSI.pdf
file_size: 290160
relation: main_file
file_date_updated: 2020-07-14T12:46:25Z
has_accepted_license: '1'
intvolume: ' 63'
isi: 1
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Submitted Version
page: 1171 - 1190
publication: Evolution; International Journal of Organic Evolution
publication_status: published
publisher: Wiley
publist_id: '1866'
pubrep_id: '551'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The evolution of strong reproductive isolation
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 63
year: '2009'
...
---
_id: '3870'
abstract:
- lang: eng
text: Games on graphs with omega-regular objectives provide a model for the control
and synthesis of reactive systems. Every omega-regular objective can be decomposed
into a safety part and a liveness part. The liveness part ensures that something
good happens “eventually.” Two main strengths of the classical, infinite-limit
formulation of liveness are robustness (independence from the granularity of transitions)
and simplicity (abstraction of complicated time bounds). However, the classical
liveness formulation suffers from the drawback that the time until something good
happens may be unbounded. A stronger formulation of liveness, so-called finitary
liveness, overcomes this drawback, while still retaining robustness and simplicity.
Finitary liveness requires that there exists an unknown, fixed bound b such that
something good happens within b transitions. While for one-shot liveness (reachability)
objectives, classical and finitary liveness coincide, for repeated liveness (Buchi)
objectives, the finitary formulation is strictly stronger. In this work we study
games with finitary parity and Streett objectives. We prove the determinacy of
these games, present algorithms for solving these games, and characterize the
memory requirements of winning strategies. We show that finitary parity games
can be solved in polynomial time, which is not known for infinitary parity games.
For finitary Streett games, we give an EXPTIME algorithm and show that the problem
is NP-hard. Our algorithms can be used, for example, for synthesizing controllers
that do not let the response time of a system increase without bound.
acknowledgement: "This research was supported in part by the AFOSR MURI grant F49620-00-1-0327,
the NSF grants CCR-0132780, CNS-0720884, and CCR- 225610, by the Swiss National
Science Foundation, by the COMBEST project of the European Union, and EU-TMR network
Games.\r\nWe thank anonymous reviewers for useful comments."
article_number: '1'
article_processing_charge: No
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: Florian
full_name: Horn, Florian
id: 37327ACE-F248-11E8-B48F-1D18A9856A87
last_name: Horn
citation:
ama: Chatterjee K, Henzinger TA, Horn F. Finitary winning in omega-regular games.
ACM Transactions on Computational Logic. 2009;11(1). doi:10.1145/1614431.1614432
apa: Chatterjee, K., Henzinger, T. A., & Horn, F. (2009). Finitary winning in
omega-regular games. ACM Transactions on Computational Logic. ACM. https://doi.org/10.1145/1614431.1614432
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Florian Horn. “Finitary
Winning in Omega-Regular Games.” ACM Transactions on Computational Logic.
ACM, 2009. https://doi.org/10.1145/1614431.1614432.
ieee: K. Chatterjee, T. A. Henzinger, and F. Horn, “Finitary winning in omega-regular
games,” ACM Transactions on Computational Logic, vol. 11, no. 1. ACM, 2009.
ista: Chatterjee K, Henzinger TA, Horn F. 2009. Finitary winning in omega-regular
games. ACM Transactions on Computational Logic. 11(1), 1.
mla: Chatterjee, Krishnendu, et al. “Finitary Winning in Omega-Regular Games.” ACM
Transactions on Computational Logic, vol. 11, no. 1, 1, ACM, 2009, doi:10.1145/1614431.1614432.
short: K. Chatterjee, T.A. Henzinger, F. Horn, ACM Transactions on Computational
Logic 11 (2009).
corr_author: '1'
das_tickbox: '1'
date_created: 2018-12-11T12:05:37Z
date_published: 2009-10-01T00:00:00Z
date_updated: 2026-07-07T14:02:53Z
day: '01'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.1145/1614431.1614432
ec_funded: 1
external_id:
isi:
- '000272039900001'
file:
- access_level: open_access
checksum: 139c4586d24f11e5da31fb3a0cf96ef4
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:08Z
date_updated: 2020-07-14T12:46:20Z
file_id: '5125'
file_name: IST-2012-53-v1+1_Finitary_winning_in_omega-regular_games.pdf
file_size: 180082
relation: main_file
file_date_updated: 2020-07-14T12:46:20Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
issue: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
project:
- _id: 25EFB36C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '215543'
name: COMponent-Based Embedded Systems design Techniques
publication: ACM Transactions on Computational Logic
publication_status: published
publisher: ACM
publist_id: '2309'
pubrep_id: '53'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Finitary winning in omega-regular games
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2009'
...
---
_id: '517'
article_processing_charge: No
article_type: comment
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Barton NH. Identity and coalescence in structured populations: A commentary
on “Inbreeding coefficients and coalescence times” by Montgomery Slatkin. Genetics
Research. 2008;89(5-6):475-477. doi:10.1017/S0016672308009683'
apa: 'Barton, N. H. (2008). Identity and coalescence in structured populations:
A commentary on “Inbreeding coefficients and coalescence times” by Montgomery
Slatkin. Genetics Research. Cambridge University Press. https://doi.org/10.1017/S0016672308009683'
chicago: 'Barton, Nicholas H. “Identity and Coalescence in Structured Populations:
A Commentary on ‘Inbreeding Coefficients and Coalescence Times’ by Montgomery
Slatkin.” Genetics Research. Cambridge University Press, 2008. https://doi.org/10.1017/S0016672308009683.'
ieee: 'N. H. Barton, “Identity and coalescence in structured populations: A commentary
on ‘Inbreeding coefficients and coalescence times’ by Montgomery Slatkin,” Genetics
Research, vol. 89, no. 5–6. Cambridge University Press, pp. 475–477, 2008.'
ista: 'Barton NH. 2008. Identity and coalescence in structured populations: A commentary
on ‘Inbreeding coefficients and coalescence times’ by Montgomery Slatkin. Genetics
Research. 89(5–6), 475–477.'
mla: 'Barton, Nicholas H. “Identity and Coalescence in Structured Populations: A
Commentary on ‘Inbreeding Coefficients and Coalescence Times’ by Montgomery Slatkin.”
Genetics Research, vol. 89, no. 5–6, Cambridge University Press, 2008,
pp. 475–77, doi:10.1017/S0016672308009683.'
short: N.H. Barton, Genetics Research 89 (2008) 475–477.
date_created: 2018-12-11T11:46:55Z
date_published: 2008-10-29T00:00:00Z
date_updated: 2026-04-29T07:15:43Z
day: '29'
department:
- _id: NiBa
doi: 10.1017/S0016672308009683
external_id:
isi:
- '000207048900023'
intvolume: ' 89'
isi: 1
issue: 5-6
language:
- iso: eng
month: '10'
oa_version: None
page: 475 - 477
publication: Genetics Research
publication_status: published
publisher: Cambridge University Press
publist_id: '7302'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Identity and coalescence in structured populations: A commentary on ''Inbreeding
coefficients and coalescence times'' by Montgomery Slatkin'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 89
year: '2008'
...