---
_id: '4388'
abstract:
- lang: eng
text: GIST is a tool that (a) solves the qualitative analysis problem of turn-based
probabilistic games with ω-regular objectives; and (b) synthesizes reasonable
environment assumptions for synthesis of unrealizable specifications. Our tool
provides the first and efficient implementations of several reduction-based techniques
to solve turn-based probabilistic games, and uses the analysis of turn-based probabilistic
games for synthesizing environment assumptions for unrealizable specifications.
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Barbara
full_name: Jobstmann, Barbara
last_name: Jobstmann
- first_name: Arjun
full_name: Radhakrishna, Arjun
id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87
last_name: Radhakrishna
citation:
ama: 'Chatterjee K, Henzinger TA, Jobstmann B, Radhakrishna A. GIST: A solver for
probabilistic games. In: Vol 6174. Springer; 2010:665-669. doi:10.1007/978-3-642-14295-6_57'
apa: 'Chatterjee, K., Henzinger, T. A., Jobstmann, B., & Radhakrishna, A. (2010).
GIST: A solver for probabilistic games (Vol. 6174, pp. 665–669). Presented at
the CAV: Computer Aided Verification, Edinburgh, UK: Springer. https://doi.org/10.1007/978-3-642-14295-6_57'
chicago: 'Chatterjee, Krishnendu, Thomas A Henzinger, Barbara Jobstmann, and Arjun
Radhakrishna. “GIST: A Solver for Probabilistic Games,” 6174:665–69. Springer,
2010. https://doi.org/10.1007/978-3-642-14295-6_57.'
ieee: 'K. Chatterjee, T. A. Henzinger, B. Jobstmann, and A. Radhakrishna, “GIST:
A solver for probabilistic games,” presented at the CAV: Computer Aided Verification,
Edinburgh, UK, 2010, vol. 6174, pp. 665–669.'
ista: 'Chatterjee K, Henzinger TA, Jobstmann B, Radhakrishna A. 2010. GIST: A solver
for probabilistic games. CAV: Computer Aided Verification, LNCS, vol. 6174, 665–669.'
mla: 'Chatterjee, Krishnendu, et al. GIST: A Solver for Probabilistic Games.
Vol. 6174, Springer, 2010, pp. 665–69, doi:10.1007/978-3-642-14295-6_57.'
short: K. Chatterjee, T.A. Henzinger, B. Jobstmann, A. Radhakrishna, in:, Springer,
2010, pp. 665–669.
conference:
end_date: 2010-07-17
location: Edinburgh, UK
name: 'CAV: Computer Aided Verification'
start_date: 2010-07-15
date_created: 2018-12-11T12:08:36Z
date_published: 2010-07-01T00:00:00Z
date_updated: 2023-02-23T12:24:17Z
day: '01'
ddc:
- '004'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1007/978-3-642-14295-6_57
ec_funded: 1
external_id:
arxiv:
- '1004.2367'
file:
- access_level: open_access
checksum: 0b2ef8c4037ffccc6902d93081af24f7
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:33Z
date_updated: 2020-07-14T12:46:28Z
file_id: '5221'
file_name: IST-2012-43-v1+1_GIST-_A_solver_for_probabilistic_games.pdf
file_size: 293605
relation: main_file
file_date_updated: 2020-07-14T12:46:28Z
has_accepted_license: '1'
intvolume: ' 6174'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 665 - 669
project:
- _id: 25EFB36C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '215543'
name: COMponent-Based Embedded Systems design Techniques
- _id: 25F1337C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '214373'
name: Design for Embedded Systems
publication_status: published
publisher: Springer
publist_id: '1068'
pubrep_id: '43'
quality_controlled: '1'
related_material:
record:
- id: '5393'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: 'GIST: A solver for probabilistic games'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6174
year: '2010'
...
---
_id: '4389'
abstract:
- lang: eng
text: 'Digital components play a central role in the design of complex embedded
systems. These components are interconnected with other, possibly analog, devices
and the physical environment. This environment cannot be entirely captured and
can provide inaccurate input data to the component. It is thus important for digital
components to have a robust behavior, i.e. the presence of a small change in the
input sequences should not result in a drastic change in the output sequences.
In this paper, we study a notion of robustness for sequential circuits. However,
since sequential circuits may have parts that are naturally discontinuous (e.g.,
digital controllers with switching behavior), we need a flexible framework that
accommodates this fact and leaves discontinuous parts of the circuit out from
the robustness analysis. As a consequence, we consider sequential circuits that
have their input variables partitioned into two disjoint sets: control and disturbance
variables. Our contributions are (1) a definition of robustness for sequential
circuits as a form of continuity with respect to disturbance variables, (2) the
characterization of the exact class of sequential circuits that are robust according
to our definition, (3) an algorithm to decide whether a sequential circuit is
robust or not.'
author:
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Axel
full_name: Legay, Axel
last_name: Legay
- first_name: Dejan
full_name: Nickovic, Dejan
id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87
last_name: Nickovic
citation:
ama: 'Doyen L, Henzinger TA, Legay A, Nickovic D. Robustness of sequential circuits.
In: IEEE; 2010:77-84. doi:10.1109/ACSD.2010.26'
apa: 'Doyen, L., Henzinger, T. A., Legay, A., & Nickovic, D. (2010). Robustness
of sequential circuits (pp. 77–84). Presented at the ACSD: Application of Concurrency
to System Design, IEEE. https://doi.org/10.1109/ACSD.2010.26'
chicago: Doyen, Laurent, Thomas A Henzinger, Axel Legay, and Dejan Nickovic. “Robustness
of Sequential Circuits,” 77–84. IEEE, 2010. https://doi.org/10.1109/ACSD.2010.26.
ieee: 'L. Doyen, T. A. Henzinger, A. Legay, and D. Nickovic, “Robustness of sequential
circuits,” presented at the ACSD: Application of Concurrency to System Design,
2010, pp. 77–84.'
ista: 'Doyen L, Henzinger TA, Legay A, Nickovic D. 2010. Robustness of sequential
circuits. ACSD: Application of Concurrency to System Design, 77–84.'
mla: Doyen, Laurent, et al. Robustness of Sequential Circuits. IEEE, 2010,
pp. 77–84, doi:10.1109/ACSD.2010.26.
short: L. Doyen, T.A. Henzinger, A. Legay, D. Nickovic, in:, IEEE, 2010, pp. 77–84.
conference:
name: 'ACSD: Application of Concurrency to System Design'
date_created: 2018-12-11T12:08:36Z
date_published: 2010-08-23T00:00:00Z
date_updated: 2021-01-12T07:56:36Z
day: '23'
ddc:
- '004'
department:
- _id: ToHe
doi: 10.1109/ACSD.2010.26
file:
- access_level: open_access
checksum: 42b2952bfc6b6974617bd554842b904a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:10Z
date_updated: 2020-07-14T12:46:28Z
file_id: '4733'
file_name: IST-2012-44-v1+1_Robustness_of_sequential_circuits.pdf
file_size: 159920
relation: main_file
file_date_updated: 2020-07-14T12:46:28Z
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
page: 77 - 84
publication_status: published
publisher: IEEE
publist_id: '1069'
pubrep_id: '44'
quality_controlled: '1'
scopus_import: 1
status: public
title: Robustness of sequential circuits
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '4390'
abstract:
- lang: eng
text: Concurrent data structures with fine-grained synchronization are notoriously
difficult to implement correctly. The difficulty of reasoning about these implementations
does not stem from the number of variables or the program size, but rather from
the large number of possible interleavings. These implementations are therefore
prime candidates for model checking. We introduce an algorithm for verifying linearizability
of singly-linked heap-based concurrent data structures. We consider a model consisting
of an unbounded heap where each vertex stores an element from an unbounded data
domain, with a restricted set of operations for testing and updating pointers
and data elements. Our main result is that linearizability is decidable for programs
that invoke a fixed number of methods, possibly in parallel. This decidable fragment
covers many of the common implementation techniques — fine-grained locking, lazy
synchronization, and lock-free synchronization. We also show how the technique
can be used to verify optimistic implementations with the help of programmer annotations.
We developed a verification tool CoLT and evaluated it on a representative sample
of Java implementations of the concurrent set data structure. The tool verified
linearizability of a number of implementations, found a known error in a lock-free
implementation and proved that the corrected version is linearizable.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Pavol
full_name: Cerny, Pavol
id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87
last_name: Cerny
- first_name: Arjun
full_name: Radhakrishna, Arjun
id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87
last_name: Radhakrishna
- first_name: Damien
full_name: Zufferey, Damien
id: 4397AC76-F248-11E8-B48F-1D18A9856A87
last_name: Zufferey
orcid: 0000-0002-3197-8736
- first_name: Swarat
full_name: Chaudhuri, Swarat
last_name: Chaudhuri
- first_name: Rajeev
full_name: Alur, Rajeev
last_name: Alur
citation:
ama: 'Cerny P, Radhakrishna A, Zufferey D, Chaudhuri S, Alur R. Model checking of
linearizability of concurrent list implementations. In: Vol 6174. Springer; 2010:465-479.
doi:10.1007/978-3-642-14295-6_41'
apa: 'Cerny, P., Radhakrishna, A., Zufferey, D., Chaudhuri, S., & Alur, R. (2010).
Model checking of linearizability of concurrent list implementations (Vol. 6174,
pp. 465–479). Presented at the CAV: Computer Aided Verification, Edinburgh, UK:
Springer. https://doi.org/10.1007/978-3-642-14295-6_41'
chicago: Cerny, Pavol, Arjun Radhakrishna, Damien Zufferey, Swarat Chaudhuri, and
Rajeev Alur. “Model Checking of Linearizability of Concurrent List Implementations,”
6174:465–79. Springer, 2010. https://doi.org/10.1007/978-3-642-14295-6_41.
ieee: 'P. Cerny, A. Radhakrishna, D. Zufferey, S. Chaudhuri, and R. Alur, “Model
checking of linearizability of concurrent list implementations,” presented at
the CAV: Computer Aided Verification, Edinburgh, UK, 2010, vol. 6174, pp. 465–479.'
ista: 'Cerny P, Radhakrishna A, Zufferey D, Chaudhuri S, Alur R. 2010. Model checking
of linearizability of concurrent list implementations. CAV: Computer Aided Verification,
LNCS, vol. 6174, 465–479.'
mla: Cerny, Pavol, et al. Model Checking of Linearizability of Concurrent List
Implementations. Vol. 6174, Springer, 2010, pp. 465–79, doi:10.1007/978-3-642-14295-6_41.
short: P. Cerny, A. Radhakrishna, D. Zufferey, S. Chaudhuri, R. Alur, in:, Springer,
2010, pp. 465–479.
conference:
end_date: 2010-07-17
location: Edinburgh, UK
name: 'CAV: Computer Aided Verification'
start_date: 2010-07-15
date_created: 2018-12-11T12:08:36Z
date_published: 2010-07-01T00:00:00Z
date_updated: 2023-02-23T12:24:12Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-642-14295-6_41
file:
- access_level: open_access
checksum: 2eb211ce40b3c4988bce3a3592980704
content_type: application/pdf
creator: dernst
date_created: 2020-05-19T16:31:56Z
date_updated: 2020-07-14T12:46:28Z
file_id: '7873'
file_name: 2010_CAV_Cerny.pdf
file_size: 3633276
relation: main_file
file_date_updated: 2020-07-14T12:46:28Z
has_accepted_license: '1'
intvolume: ' 6174'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 465 - 479
publication_status: published
publisher: Springer
publist_id: '1066'
pubrep_id: '27'
quality_controlled: '1'
related_material:
record:
- id: '5391'
relation: earlier_version
status: public
status: public
title: Model checking of linearizability of concurrent list implementations
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6174
year: '2010'
...
---
_id: '4392'
abstract:
- lang: eng
text: 'While a boolean notion of correctness is given by a preorder on systems and
properties, a quantitative notion of correctness is defined by a distance function
on systems and properties, where the distance between a system and a property
provides a measure of “fit” or “desirability.” In this article, we explore several
ways how the simulation preorder can be generalized to a distance function. This
is done by equipping the classical simulation game between a system and a property
with quantitative objectives. In particular, for systems that satisfy a property,
a quantitative simulation game can measure the “robustness” of the satisfaction,
that is, how much the system can deviate from its nominal behavior while still
satisfying the property. For systems that violate a property, a quantitative simulation
game can measure the “seriousness” of the violation, that is, how much the property
has to be modified so that it is satisfied by the system. These distances can
be computed in polynomial time, since the computation reduces to the value problem
in limit average games with constant weights. Finally, we demonstrate how the
robustness distance can be used to measure how many transmission errors are tolerated
by error correcting codes. '
alternative_title:
- LNCS
author:
- first_name: Pavol
full_name: Cerny, Pavol
id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87
last_name: Cerny
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Arjun
full_name: Radhakrishna, Arjun
id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87
last_name: Radhakrishna
citation:
ama: 'Cerny P, Henzinger TA, Radhakrishna A. Quantitative Simulation Games. In:
Manna Z, Peled D, eds. Time For Verification: Essays in Memory of Amir Pnueli.
Vol 6200. Essays in Memory of Amir Pnueli. Springer; 2010:42-60. doi:10.1007/978-3-642-13754-9_3'
apa: 'Cerny, P., Henzinger, T. A., & Radhakrishna, A. (2010). Quantitative Simulation
Games. In Z. Manna & D. Peled (Eds.), Time For Verification: Essays in
Memory of Amir Pnueli (Vol. 6200, pp. 42–60). Springer. https://doi.org/10.1007/978-3-642-13754-9_3'
chicago: 'Cerny, Pavol, Thomas A Henzinger, and Arjun Radhakrishna. “Quantitative
Simulation Games.” In Time For Verification: Essays in Memory of Amir Pnueli,
edited by Zohar Manna and Doron Peled, 6200:42–60. Essays in Memory of Amir Pnueli.
Springer, 2010. https://doi.org/10.1007/978-3-642-13754-9_3.'
ieee: 'P. Cerny, T. A. Henzinger, and A. Radhakrishna, “Quantitative Simulation
Games,” in Time For Verification: Essays in Memory of Amir Pnueli, vol.
6200, Z. Manna and D. Peled, Eds. Springer, 2010, pp. 42–60.'
ista: 'Cerny P, Henzinger TA, Radhakrishna A. 2010.Quantitative Simulation Games.
In: Time For Verification: Essays in Memory of Amir Pnueli. LNCS, vol. 6200, 42–60.'
mla: 'Cerny, Pavol, et al. “Quantitative Simulation Games.” Time For Verification:
Essays in Memory of Amir Pnueli, edited by Zohar Manna and Doron Peled, vol.
6200, Springer, 2010, pp. 42–60, doi:10.1007/978-3-642-13754-9_3.'
short: 'P. Cerny, T.A. Henzinger, A. Radhakrishna, in:, Z. Manna, D. Peled (Eds.),
Time For Verification: Essays in Memory of Amir Pnueli, Springer, 2010, pp. 42–60.'
date_created: 2018-12-11T12:08:37Z
date_published: 2010-07-29T00:00:00Z
date_updated: 2021-01-12T07:56:38Z
day: '29'
department:
- _id: ToHe
doi: 10.1007/978-3-642-13754-9_3
ec_funded: 1
editor:
- first_name: Zohar
full_name: Manna, Zohar
last_name: Manna
- first_name: Doron
full_name: Peled, Doron
last_name: Peled
intvolume: ' 6200'
language:
- iso: eng
month: '07'
oa_version: None
page: 42 - 60
project:
- _id: 25EFB36C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '215543'
name: COMponent-Based Embedded Systems design Techniques
- _id: 25F1337C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '214373'
name: Design for Embedded Systems
publication: 'Time For Verification: Essays in Memory of Amir Pnueli'
publication_status: published
publisher: Springer
publist_id: '1064'
quality_controlled: '1'
scopus_import: 1
series_title: Essays in Memory of Amir Pnueli
status: public
title: Quantitative Simulation Games
type: book_chapter
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 6200
year: '2010'
...
---
_id: '4393'
abstract:
- lang: eng
text: Boolean notions of correctness are formalized by preorders on systems. Quantitative
measures of correctness can be formalized by real-valued distance functions between
systems, where the distance between implementation and specification provides
a measure of “fit” or “desirability.” We extend the simulation preorder to the
quantitative setting, by making each player of a simulation game pay a certain
price for her choices. We use the resulting games with quantitative objectives
to define three different simulation distances. The correctness distance measures
how much the specification must be changed in order to be satisfied by the implementation.
The coverage distance measures how much the implementation restricts the degrees
of freedom offered by the specification. The robustness distance measures how
much a system can deviate from the implementation description without violating
the specification. We consider these distances for safety as well as liveness
specifications. The distances can be computed in polynomial time for safety specifications,
and for liveness specifications given by weak fairness constraints. We show that
the distance functions satisfy the triangle inequality, that the distance between
two systems does not increase under parallel composition with a third system,
and that the distance between two systems can be bounded from above and below
by distances between abstractions of the two systems. These properties suggest
that our simulation distances provide an appropriate basis for a quantitative
theory of discrete systems. We also demonstrate how the robustness distance can
be used to measure how many transmission errors are tolerated by error correcting
codes.
acknowledgement: This work was partially supported by the European Union project COMBEST
and the European Network of Excellence ArtistDesign.
alternative_title:
- LNCS
author:
- first_name: Pavol
full_name: Cerny, Pavol
id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87
last_name: Cerny
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Arjun
full_name: Radhakrishna, Arjun
id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87
last_name: Radhakrishna
citation:
ama: 'Cerny P, Henzinger TA, Radhakrishna A. Simulation distances. In: Vol 6269.
Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2010:235-268. doi:10.1007/978-3-642-15375-4_18'
apa: 'Cerny, P., Henzinger, T. A., & Radhakrishna, A. (2010). Simulation distances
(Vol. 6269, pp. 235–268). Presented at the CONCUR: Concurrency Theory, Paris,
France: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/978-3-642-15375-4_18'
chicago: Cerny, Pavol, Thomas A Henzinger, and Arjun Radhakrishna. “Simulation Distances,”
6269:235–68. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010. https://doi.org/10.1007/978-3-642-15375-4_18.
ieee: 'P. Cerny, T. A. Henzinger, and A. Radhakrishna, “Simulation distances,” presented
at the CONCUR: Concurrency Theory, Paris, France, 2010, vol. 6269, pp. 235–268.'
ista: 'Cerny P, Henzinger TA, Radhakrishna A. 2010. Simulation distances. CONCUR:
Concurrency Theory, LNCS, vol. 6269, 235–268.'
mla: Cerny, Pavol, et al. Simulation Distances. Vol. 6269, Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 2010, pp. 235–68, doi:10.1007/978-3-642-15375-4_18.
short: P. Cerny, T.A. Henzinger, A. Radhakrishna, in:, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2010, pp. 235–268.
conference:
end_date: 2010-09-03
location: Paris, France
name: 'CONCUR: Concurrency Theory'
start_date: 2010-08-31
date_created: 2018-12-11T12:08:37Z
date_published: 2010-11-01T00:00:00Z
date_updated: 2023-02-23T12:24:04Z
day: '01'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1007/978-3-642-15375-4_18
ec_funded: 1
file:
- access_level: open_access
checksum: ea567903676ba8afe0507ee11313dce5
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:12Z
date_updated: 2020-07-14T12:46:28Z
file_id: '5130'
file_name: IST-2012-42-v1+1_Simulation_distances.pdf
file_size: 198913
relation: main_file
file_date_updated: 2020-07-14T12:46:28Z
has_accepted_license: '1'
intvolume: ' 6269'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 235 - 268
project:
- _id: 25EFB36C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '215543'
name: COMponent-Based Embedded Systems design Techniques
- _id: 25F1337C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '214373'
name: Design for Embedded Systems
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '1065'
pubrep_id: '42'
quality_controlled: '1'
related_material:
record:
- id: '3249'
relation: later_version
status: public
- id: '5389'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Simulation distances
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 6269
year: '2010'
...
---
_id: '4396'
abstract:
- lang: eng
text: 'Shape analysis is a promising technique to prove program properties about
recursive data structures. The challenge is to automatically determine the data-structure
type, and to supply the shape analysis with the necessary information about the
data structure. We present a stepwise approach to the selection of instrumentation
predicates for a TVLA-based shape analysis, which takes us a step closer towards
the fully automatic verification of data structures. The approach uses two techniques
to guide the refinement of shape abstractions: (1) during program exploration,
an explicit heap analysis collects sample instances of the heap structures, which
are used to identify the data structures that are manipulated by the program;
and (2) during abstraction refinement along an infeasible error path, we consider
different possible heap abstractions and choose the coarsest one that eliminates
the infeasible path. We have implemented this combined approach for automatic
shape refinement as an extension of the software model checker BLAST. Example
programs from a data-structure library that manipulate doubly-linked lists and
trees were successfully verified by our tool.'
alternative_title:
- LNCS
author:
- first_name: Dirk
full_name: Beyer, Dirk
last_name: Beyer
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Grégory
full_name: Théoduloz, Grégory
last_name: Théoduloz
- first_name: Damien
full_name: Zufferey, Damien
id: 4397AC76-F248-11E8-B48F-1D18A9856A87
last_name: Zufferey
orcid: 0000-0002-3197-8736
citation:
ama: 'Beyer D, Henzinger TA, Théoduloz G, Zufferey D. Shape refinement through explicit
heap analysis. In: Rosenblum D, Taenzer G, eds. Vol 6013. Springer; 2010:263-277.
doi:10.1007/978-3-642-12029-9_19'
apa: 'Beyer, D., Henzinger, T. A., Théoduloz, G., & Zufferey, D. (2010). Shape
refinement through explicit heap analysis. In D. Rosenblum & G. Taenzer (Eds.)
(Vol. 6013, pp. 263–277). Presented at the FASE: Fundamental Approaches To Software
Engineering, Paphos, Cyprus: Springer. https://doi.org/10.1007/978-3-642-12029-9_19'
chicago: Beyer, Dirk, Thomas A Henzinger, Grégory Théoduloz, and Damien Zufferey.
“Shape Refinement through Explicit Heap Analysis.” edited by David Rosenblum and
Gabriele Taenzer, 6013:263–77. Springer, 2010. https://doi.org/10.1007/978-3-642-12029-9_19.
ieee: 'D. Beyer, T. A. Henzinger, G. Théoduloz, and D. Zufferey, “Shape refinement
through explicit heap analysis,” presented at the FASE: Fundamental Approaches
To Software Engineering, Paphos, Cyprus, 2010, vol. 6013, pp. 263–277.'
ista: 'Beyer D, Henzinger TA, Théoduloz G, Zufferey D. 2010. Shape refinement through
explicit heap analysis. FASE: Fundamental Approaches To Software Engineering,
LNCS, vol. 6013, 263–277.'
mla: Beyer, Dirk, et al. Shape Refinement through Explicit Heap Analysis.
Edited by David Rosenblum and Gabriele Taenzer, vol. 6013, Springer, 2010, pp.
263–77, doi:10.1007/978-3-642-12029-9_19.
short: D. Beyer, T.A. Henzinger, G. Théoduloz, D. Zufferey, in:, D. Rosenblum, G.
Taenzer (Eds.), Springer, 2010, pp. 263–277.
conference:
end_date: 2010-03-28
location: Paphos, Cyprus
name: 'FASE: Fundamental Approaches To Software Engineering'
start_date: 2010-03-20
date_created: 2018-12-11T12:08:38Z
date_published: 2010-04-21T00:00:00Z
date_updated: 2021-01-12T07:56:40Z
day: '21'
ddc:
- '004'
department:
- _id: ToHe
doi: 10.1007/978-3-642-12029-9_19
editor:
- first_name: David
full_name: Rosenblum, David
last_name: Rosenblum
- first_name: Gabriele
full_name: Taenzer, Gabriele
last_name: Taenzer
file:
- access_level: open_access
checksum: 7d26e59a9681487d7283eba337292b2c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:13Z
date_updated: 2020-07-14T12:46:29Z
file_id: '5332'
file_name: IST-2012-41-v1+1_Shape_refinement_through_explicit_heap_analysis.pdf
file_size: 312147
relation: main_file
file_date_updated: 2020-07-14T12:46:29Z
has_accepted_license: '1'
intvolume: ' 6013'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Submitted Version
page: 263 - 277
project:
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication_status: published
publisher: Springer
publist_id: '1061'
pubrep_id: '41'
quality_controlled: '1'
scopus_import: 1
status: public
title: Shape refinement through explicit heap analysis
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 6013
year: '2010'
...
---
_id: '474'
abstract:
- lang: eng
text: 'Classical models of gene flow fail in three ways: they cannot explain large-scale
patterns; they predict much more genetic diversity than is observed; and they
assume that loosely linked genetic loci evolve independently. We propose a new
model that deals with these problems. Extinction events kill some fraction of
individuals in a region. These are replaced by offspring from a small number of
parents, drawn from the preexisting population. This model of evolution forwards
in time corresponds to a backwards model, in which ancestral lineages jump to
a new location if they are hit by an event, and may coalesce with other lineages
that are hit by the same event. We derive an expression for the identity in allelic
state, and show that, over scales much larger than the largest event, this converges
to the classical value derived by Wright and Malécot. However, rare events that
cover large areas cause low genetic diversity, large-scale patterns, and correlations
in ancestry between unlinked loci.'
acknowledgement: This work has made use of the resources provided by the Edinburgh
Compute and Data Facility (ECDF). The ECDF is partially supported by the eDIKT initiative.
NHB is supported in part by EPSRC Grant EP/E066070/1; JK is supported by EPSRC Grant
EP/E066070/1; and AME is supported in part by EPSRC Grant EP/E065945/1.
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: Jerome
full_name: Kelleher, Jerome
last_name: Kelleher
- first_name: Alison
full_name: Etheridge, Alison
last_name: Etheridge
citation:
ama: 'Barton NH, Kelleher J, Etheridge A. A new model for extinction and recolonization
in two dimensions: Quantifying phylogeography. Evolution. 2010;64(9):2701-2715.
doi:10.1111/j.1558-5646.2010.01019.x'
apa: 'Barton, N. H., Kelleher, J., & Etheridge, A. (2010). A new model for extinction
and recolonization in two dimensions: Quantifying phylogeography. Evolution.
Wiley-Blackwell. https://doi.org/10.1111/j.1558-5646.2010.01019.x'
chicago: 'Barton, Nicholas H, Jerome Kelleher, and Alison Etheridge. “A New Model
for Extinction and Recolonization in Two Dimensions: Quantifying Phylogeography.”
Evolution. Wiley-Blackwell, 2010. https://doi.org/10.1111/j.1558-5646.2010.01019.x.'
ieee: 'N. H. Barton, J. Kelleher, and A. Etheridge, “A new model for extinction
and recolonization in two dimensions: Quantifying phylogeography,” Evolution,
vol. 64, no. 9. Wiley-Blackwell, pp. 2701–2715, 2010.'
ista: 'Barton NH, Kelleher J, Etheridge A. 2010. A new model for extinction and
recolonization in two dimensions: Quantifying phylogeography. Evolution. 64(9),
2701–2715.'
mla: 'Barton, Nicholas H., et al. “A New Model for Extinction and Recolonization
in Two Dimensions: Quantifying Phylogeography.” Evolution, vol. 64, no.
9, Wiley-Blackwell, 2010, pp. 2701–15, doi:10.1111/j.1558-5646.2010.01019.x.'
short: N.H. Barton, J. Kelleher, A. Etheridge, Evolution 64 (2010) 2701–2715.
date_created: 2018-12-11T11:46:40Z
date_published: 2010-09-01T00:00:00Z
date_updated: 2021-01-12T08:00:52Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/j.1558-5646.2010.01019.x
intvolume: ' 64'
issue: '9'
language:
- iso: eng
month: '09'
oa_version: None
page: 2701 - 2715
publication: Evolution
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2780'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'A new model for extinction and recolonization in two dimensions: Quantifying
phylogeography'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 64
year: '2010'
...
---
_id: '488'
abstract:
- lang: eng
text: 'Streaming string transducers [1] define (partial) functions from input strings
to output strings. A streaming string transducer makes a single pass through the
input string and uses a finite set of variables that range over strings from the
output alphabet. At every step, the transducer processes an input symbol, and
updates all the variables in parallel using assignments whose right-hand-sides
are concatenations of output symbols and variables with the restriction that a
variable can be used at most once in a right-hand-side expression. It has been
shown that streaming string transducers operating on strings over infinite data
domains are of interest in algorithmic verification of list-processing programs,
as they lead to PSPACE decision procedures for checking pre/post conditions and
for checking semantic equivalence, for a well-defined class of heap-manipulating
programs. In order to understand the theoretical expressiveness of streaming transducers,
we focus on streaming transducers processing strings over finite alphabets, given
the existence of a robust and well-studied class of "regular" transductions
for this case. Such regular transductions can be defined either by two-way deterministic
finite-state transducers, or using a logical MSO-based characterization. Our main
result is that the expressiveness of streaming string transducers coincides exactly
with this class of regular transductions. '
alternative_title:
- LIPIcs
author:
- first_name: Rajeev
full_name: Alur, Rajeev
last_name: Alur
- first_name: Pavol
full_name: Cerny, Pavol
id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87
last_name: Cerny
citation:
ama: 'Alur R, Cerny P. Expressiveness of streaming string transducers. In: Vol 8.
Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2010:1-12. doi:10.4230/LIPIcs.FSTTCS.2010.1'
apa: 'Alur, R., & Cerny, P. (2010). Expressiveness of streaming string transducers
(Vol. 8, pp. 1–12). Presented at the FSTTCS: Foundations of Software Technology
and Theoretical Computer Science, Chennai, India: Schloss Dagstuhl - Leibniz-Zentrum
für Informatik. https://doi.org/10.4230/LIPIcs.FSTTCS.2010.1'
chicago: Alur, Rajeev, and Pavol Cerny. “Expressiveness of Streaming String Transducers,”
8:1–12. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010. https://doi.org/10.4230/LIPIcs.FSTTCS.2010.1.
ieee: 'R. Alur and P. Cerny, “Expressiveness of streaming string transducers,” presented
at the FSTTCS: Foundations of Software Technology and Theoretical Computer Science,
Chennai, India, 2010, vol. 8, pp. 1–12.'
ista: 'Alur R, Cerny P. 2010. Expressiveness of streaming string transducers. FSTTCS:
Foundations of Software Technology and Theoretical Computer Science, LIPIcs, vol.
8, 1–12.'
mla: Alur, Rajeev, and Pavol Cerny. Expressiveness of Streaming String Transducers.
Vol. 8, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010, pp. 1–12, doi:10.4230/LIPIcs.FSTTCS.2010.1.
short: R. Alur, P. Cerny, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2010, pp. 1–12.
conference:
end_date: 2010-12-18
location: Chennai, India
name: 'FSTTCS: Foundations of Software Technology and Theoretical Computer Science'
start_date: 2010-12-15
date_created: 2018-12-11T11:46:45Z
date_published: 2010-01-01T00:00:00Z
date_updated: 2021-01-12T08:01:00Z
day: '01'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.4230/LIPIcs.FSTTCS.2010.1
file:
- access_level: open_access
checksum: 5845be5aa19791830f7407d8853f2df0
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:29Z
date_updated: 2020-07-14T12:46:35Z
file_id: '4690'
file_name: IST-2018-948-v1+1_2011_Cerny_Expressiveness_of.pdf
file_size: 492344
relation: main_file
file_date_updated: 2020-07-14T12:46:35Z
has_accepted_license: '1'
intvolume: ' 8'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '01'
oa: 1
oa_version: Published Version
page: 1 - 12
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '7331'
pubrep_id: '948'
quality_controlled: '1'
scopus_import: 1
status: public
title: Expressiveness of streaming string transducers
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2010'
...
---
_id: '489'
abstract:
- lang: eng
text: 'Graph games of infinite length are a natural model for open reactive processes:
one player represents the controller, trying to ensure a given specification,
and the other represents a hostile environment. The evolution of the system depends
on the decisions of both players, supplemented by chance. In this work, we focus
on the notion of randomised strategy. More specifically, we show that three natural
definitions may lead to very different results: in the most general cases, an
almost-surely winning situation may become almost-surely losing if the player
is only allowed to use a weaker notion of strategy. In more reasonable settings,
translations exist, but they require infinite memory, even in simple cases. Finally,
some traditional problems becomes undecidable for the strongest type of strategies.'
alternative_title:
- EPTCS
author:
- first_name: Julien
full_name: Cristau, Julien
last_name: Cristau
- first_name: Claire
full_name: David, Claire
last_name: David
- first_name: Florian
full_name: Horn, Florian
id: 37327ACE-F248-11E8-B48F-1D18A9856A87
last_name: Horn
citation:
ama: 'Cristau J, David C, Horn F. How do we remember the past in randomised strategies?
. In: Proceedings of GandALF 2010. Vol 25. Open Publishing Association;
2010:30-39. doi:10.4204/EPTCS.25.7'
apa: 'Cristau, J., David, C., & Horn, F. (2010). How do we remember the past
in randomised strategies? . In Proceedings of GandALF 2010 (Vol. 25, pp.
30–39). Minori, Amalfi Coast, Italy: Open Publishing Association. https://doi.org/10.4204/EPTCS.25.7'
chicago: Cristau, Julien, Claire David, and Florian Horn. “How Do We Remember the
Past in Randomised Strategies? .” In Proceedings of GandALF 2010, 25:30–39.
Open Publishing Association, 2010. https://doi.org/10.4204/EPTCS.25.7.
ieee: J. Cristau, C. David, and F. Horn, “How do we remember the past in randomised
strategies? ,” in Proceedings of GandALF 2010, Minori, Amalfi Coast, Italy,
2010, vol. 25, pp. 30–39.
ista: 'Cristau J, David C, Horn F. 2010. How do we remember the past in randomised
strategies? . Proceedings of GandALF 2010. GandALF: Games, Automata, Logic, and
Formal Verification, EPTCS, vol. 25, 30–39.'
mla: Cristau, Julien, et al. “How Do We Remember the Past in Randomised Strategies?
.” Proceedings of GandALF 2010, vol. 25, Open Publishing Association, 2010,
pp. 30–39, doi:10.4204/EPTCS.25.7.
short: J. Cristau, C. David, F. Horn, in:, Proceedings of GandALF 2010, Open Publishing
Association, 2010, pp. 30–39.
conference:
end_date: 2010-06-18
location: Minori, Amalfi Coast, Italy
name: 'GandALF: Games, Automata, Logic, and Formal Verification'
start_date: 2010-06-17
date_created: 2018-12-11T11:46:45Z
date_published: 2010-06-09T00:00:00Z
date_updated: 2021-01-12T08:01:01Z
day: '09'
department:
- _id: KrCh
doi: 10.4204/EPTCS.25.7
intvolume: ' 25'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1006.1404v1
month: '06'
oa: 1
oa_version: Published Version
page: 30 - 39
publication: Proceedings of GandALF 2010
publication_status: published
publisher: Open Publishing Association
publist_id: '7332'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'How do we remember the past in randomised strategies? '
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2010'
...
---
_id: '533'
abstract:
- lang: eng
text: Any programming error that can be revealed before compiling a program saves
precious time for the programmer. While integrated development environments already
do a good job by detecting, e.g., data-flow abnormalities, current static analysis
tools suffer from false positives ("noise") or require strong user interaction.
We propose to avoid this deficiency by defining a new class of errors. A program
fragment is doomed if its execution will inevitably fail, regardless of which
state it is started in. We use a formal verification method to identify such errors
fully automatically and, most significantly, without producing noise. We report
on experiments with a prototype tool.
author:
- first_name: Jochen
full_name: Hoenicke, Jochen
last_name: Hoenicke
- first_name: Kari
full_name: Leino, Kari
last_name: Leino
- first_name: Andreas
full_name: Podelski, Andreas
last_name: Podelski
- first_name: Martin
full_name: Schäf, Martin
last_name: Schäf
- first_name: Thomas
full_name: Wies, Thomas
id: 447BFB88-F248-11E8-B48F-1D18A9856A87
last_name: Wies
citation:
ama: Hoenicke J, Leino K, Podelski A, Schäf M, Wies T. Doomed program points. Formal
Methods in System Design. 2010;37(2-3):171-199. doi:10.1007/s10703-010-0102-0
apa: Hoenicke, J., Leino, K., Podelski, A., Schäf, M., & Wies, T. (2010). Doomed
program points. Formal Methods in System Design. Springer. https://doi.org/10.1007/s10703-010-0102-0
chicago: Hoenicke, Jochen, Kari Leino, Andreas Podelski, Martin Schäf, and Thomas
Wies. “Doomed Program Points.” Formal Methods in System Design. Springer,
2010. https://doi.org/10.1007/s10703-010-0102-0.
ieee: J. Hoenicke, K. Leino, A. Podelski, M. Schäf, and T. Wies, “Doomed program
points,” Formal Methods in System Design, vol. 37, no. 2–3. Springer, pp.
171–199, 2010.
ista: Hoenicke J, Leino K, Podelski A, Schäf M, Wies T. 2010. Doomed program points.
Formal Methods in System Design. 37(2–3), 171–199.
mla: Hoenicke, Jochen, et al. “Doomed Program Points.” Formal Methods in System
Design, vol. 37, no. 2–3, Springer, 2010, pp. 171–99, doi:10.1007/s10703-010-0102-0.
short: J. Hoenicke, K. Leino, A. Podelski, M. Schäf, T. Wies, Formal Methods in
System Design 37 (2010) 171–199.
date_created: 2018-12-11T11:47:01Z
date_published: 2010-12-01T00:00:00Z
date_updated: 2021-01-12T08:01:28Z
day: '01'
department:
- _id: ToHe
doi: 10.1007/s10703-010-0102-0
intvolume: ' 37'
issue: 2-3
language:
- iso: eng
month: '12'
oa_version: None
page: 171 - 199
publication: Formal Methods in System Design
publication_status: published
publisher: Springer
publist_id: '7284'
quality_controlled: '1'
scopus_import: 1
status: public
title: Doomed program points
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 37
year: '2010'
...
---
_id: '5388'
abstract:
- lang: eng
text: "We present an algorithmic method for the synthesis of concurrent programs
that are optimal with respect to quantitative performance measures. The input
consists of a sequential sketch, that is, a program that does not contain synchronization
constructs, and of a parametric performance model that assigns costs to actions
such as locking, context switching, and idling. The quantitative synthesis problem
is to automatically introduce synchronization constructs into the sequential sketch
so that both correctness is guaranteed and worst-case (or average-case) performance
is optimized. Correctness is formalized as race freedom or linearizability.\r\n\r\nWe
show that for worst-case performance, the problem can be modeled\r\nas a 2-player
graph game with quantitative (limit-average) objectives, and\r\nfor average-case
performance, as a 2 1/2 -player graph game (with probabilistic transitions). In
both cases, the optimal correct program is derived from an optimal strategy in
the corresponding quantitative game. We prove that the respective game problems
are computationally expensive (NP-complete), and present several techniques that
overcome the theoretical difficulty in cases of concurrent programs of practical
interest.\r\n\r\nWe have implemented a prototype tool and used it for the automatic
syn- thesis of programs that access a concurrent list. For certain parameter val-
ues, our method automatically synthesizes various classical synchronization schemes
for implementing a concurrent list, such as fine-grained locking or a lazy algorithm.
For other parameter values, a new, hybrid synchronization style is synthesized,
which uses both the lazy approach and coarse-grained locks (instead of standard
fine-grained locks). The trade-off occurs because while fine-grained locking tends
to decrease the cost that is due to waiting for locks, it increases cache size
requirements."
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Pavol
full_name: Cerny, Pavol
id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87
last_name: Cerny
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Arjun
full_name: Radhakrishna, Arjun
id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87
last_name: Radhakrishna
- first_name: Rohit
full_name: Singh, Rohit
last_name: Singh
citation:
ama: Chatterjee K, Cerny P, Henzinger TA, Radhakrishna A, Singh R. Quantitative
Synthesis for Concurrent Programs. IST Austria; 2010. doi:10.15479/AT:IST-2010-0004
apa: Chatterjee, K., Cerny, P., Henzinger, T. A., Radhakrishna, A., & Singh,
R. (2010). Quantitative synthesis for concurrent programs. IST Austria.
https://doi.org/10.15479/AT:IST-2010-0004
chicago: Chatterjee, Krishnendu, Pavol Cerny, Thomas A Henzinger, Arjun Radhakrishna,
and Rohit Singh. Quantitative Synthesis for Concurrent Programs. IST Austria,
2010. https://doi.org/10.15479/AT:IST-2010-0004.
ieee: K. Chatterjee, P. Cerny, T. A. Henzinger, A. Radhakrishna, and R. Singh, Quantitative
synthesis for concurrent programs. IST Austria, 2010.
ista: Chatterjee K, Cerny P, Henzinger TA, Radhakrishna A, Singh R. 2010. Quantitative
synthesis for concurrent programs, IST Austria, 17p.
mla: Chatterjee, Krishnendu, et al. Quantitative Synthesis for Concurrent Programs.
IST Austria, 2010, doi:10.15479/AT:IST-2010-0004.
short: K. Chatterjee, P. Cerny, T.A. Henzinger, A. Radhakrishna, R. Singh, Quantitative
Synthesis for Concurrent Programs, IST Austria, 2010.
date_created: 2018-12-12T11:39:03Z
date_published: 2010-10-07T00:00:00Z
date_updated: 2023-02-23T11:24:08Z
day: '07'
ddc:
- '000'
- '005'
department:
- _id: KrCh
- _id: ToHe
doi: 10.15479/AT:IST-2010-0004
file:
- access_level: open_access
checksum: da38782d2388a6fa32109d10bb9bad67
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:53Z
date_updated: 2020-07-14T12:46:42Z
file_id: '5515'
file_name: IST-2010-0004_IST-2010-0004.pdf
file_size: 429101
relation: main_file
file_date_updated: 2020-07-14T12:46:42Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '17'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '24'
related_material:
record:
- id: '3366'
relation: later_version
status: public
status: public
title: Quantitative synthesis for concurrent programs
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '5389'
abstract:
- lang: eng
text: Boolean notions of correctness are formalized by preorders on systems. Quantitative
measures of correctness can be formalized by real-valued distance functions between
systems, where the distance between implementation and specification provides
a measure of “fit” or “desirability.” We extend the simulation preorder to the
quantitative setting, by making each player of a simulation game pay a certain
price for her choices. We use the resulting games with quantitative objectives
to define three different simulation distances. The correctness distance measures
how much the specification must be changed in order to be satisfied by the implementation.
The coverage distance measures how much the im- plementation restricts the degrees
of freedom offered by the specification. The robustness distance measures how
much a system can deviate from the implementation description without violating
the specification. We consider these distances for safety as well as liveness
specifications. The distances can be computed in polynomial time for safety specifications,
and for liveness specifications given by weak fairness constraints. We show that
the distance functions satisfy the triangle inequality, that the distance between
two systems does not increase under parallel composition with a third system,
and that the distance between two systems can be bounded from above and below
by distances between abstractions of the two systems. These properties suggest
that our simulation distances provide an appropriate basis for a quantitative
theory of discrete systems. We also demonstrate how the robustness distance can
be used to measure how many transmission errors are tolerated by error correcting
codes.
alternative_title:
- IST Austria Technical Report
author:
- first_name: Pavol
full_name: Cerny, Pavol
id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87
last_name: Cerny
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Arjun
full_name: Radhakrishna, Arjun
id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87
last_name: Radhakrishna
citation:
ama: Cerny P, Henzinger TA, Radhakrishna A. Simulation Distances. IST Austria;
2010. doi:10.15479/AT:IST-2010-0003
apa: Cerny, P., Henzinger, T. A., & Radhakrishna, A. (2010). Simulation distances.
IST Austria. https://doi.org/10.15479/AT:IST-2010-0003
chicago: Cerny, Pavol, Thomas A Henzinger, and Arjun Radhakrishna. Simulation
Distances. IST Austria, 2010. https://doi.org/10.15479/AT:IST-2010-0003.
ieee: P. Cerny, T. A. Henzinger, and A. Radhakrishna, Simulation distances.
IST Austria, 2010.
ista: Cerny P, Henzinger TA, Radhakrishna A. 2010. Simulation distances, IST Austria,
24p.
mla: Cerny, Pavol, et al. Simulation Distances. IST Austria, 2010, doi:10.15479/AT:IST-2010-0003.
short: P. Cerny, T.A. Henzinger, A. Radhakrishna, Simulation Distances, IST Austria,
2010.
date_created: 2018-12-12T11:39:03Z
date_published: 2010-06-04T00:00:00Z
date_updated: 2023-02-23T12:09:16Z
day: '04'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.15479/AT:IST-2010-0003
file:
- access_level: open_access
checksum: 284ded99764e32a583a8ea83fcea254b
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:54:25Z
date_updated: 2020-07-14T12:46:42Z
file_id: '5547'
file_name: IST-2010-0003_IST-2010-0003.pdf
file_size: 367246
relation: main_file
file_date_updated: 2020-07-14T12:46:42Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '24'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '25'
related_material:
record:
- id: '3249'
relation: later_version
status: public
- id: '4393'
relation: later_version
status: public
status: public
title: Simulation distances
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '5390'
abstract:
- lang: eng
text: The class of ω regular languages provide a robust specification language in
verification. Every ω-regular condition 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. In this work we consider the finitary parity and Streett (fairness)
conditions. We present the topological, automata-theoretic and logical characterization
of finitary languages defined by finitary parity and Streett conditions. We (a)
show that the finitary parity and Streett languages are Σ2-complete; (b) present
a complete characterization of the expressive power of various classes of automata
with finitary and infinitary conditions (in particular we show that non-deterministic
finitary parity and Streett automata cannot be determinized to deterministic finitary
parity or Streett automata); and (c) show that the languages defined by non-deterministic
finitary parity automata exactly characterize the star-free fragment of ωB-regular
languages.
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Nathanaël
full_name: Fijalkow, Nathanaël
last_name: Fijalkow
citation:
ama: Chatterjee K, Fijalkow N. Topological, Automata-Theoretic and Logical Characterization
of Finitary Languages. IST Austria; 2010. doi:10.15479/AT:IST-2010-0002
apa: Chatterjee, K., & Fijalkow, N. (2010). Topological, automata-theoretic
and logical characterization of finitary languages. IST Austria. https://doi.org/10.15479/AT:IST-2010-0002
chicago: Chatterjee, Krishnendu, and Nathanaël Fijalkow. Topological, Automata-Theoretic
and Logical Characterization of Finitary Languages. IST Austria, 2010. https://doi.org/10.15479/AT:IST-2010-0002.
ieee: K. Chatterjee and N. Fijalkow, Topological, automata-theoretic and logical
characterization of finitary languages. IST Austria, 2010.
ista: Chatterjee K, Fijalkow N. 2010. Topological, automata-theoretic and logical
characterization of finitary languages, IST Austria, 21p.
mla: Chatterjee, Krishnendu, and Nathanaël Fijalkow. Topological, Automata-Theoretic
and Logical Characterization of Finitary Languages. IST Austria, 2010, doi:10.15479/AT:IST-2010-0002.
short: K. Chatterjee, N. Fijalkow, Topological, Automata-Theoretic and Logical Characterization
of Finitary Languages, IST Austria, 2010.
date_created: 2018-12-12T11:39:03Z
date_published: 2010-06-04T00:00:00Z
date_updated: 2020-07-14T23:04:41Z
day: '04'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2010-0002
file:
- access_level: open_access
checksum: 283d3604d76dd4d5161585d4c8625fbe
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:54:10Z
date_updated: 2020-07-14T12:46:43Z
file_id: '5532'
file_name: IST-2010-0002_IST-2010-0002.pdf
file_size: 395662
relation: main_file
file_date_updated: 2020-07-14T12:46:43Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '21'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '26'
status: public
title: Topological, automata-theoretic and logical characterization of finitary languages
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '5391'
abstract:
- lang: eng
text: Concurrent data structures with fine-grained synchronization are notoriously
difficult to implement correctly. The difficulty of reasoning about these implementations
does not stem from the number of variables or the program size, but rather from
the large number of possible interleavings. These implementations are therefore
prime candidates for model checking. We introduce an algorithm for verifying linearizability
of singly-linked heap-based concurrent data structures. We consider a model consisting
of an unbounded heap where each node consists an element from an unbounded data
domain, with a restricted set of operations for testing and updating pointers
and data elements. Our main result is that linearizability is decidable for programs
that invoke a fixed number of methods, possibly in parallel. This decidable fragment
covers many of the common implementation techniques — fine-grained locking, lazy
synchronization, and lock-free synchronization. We also show how the technique
can be used to verify optimistic implementations with the help of programmer annotations.
We developed a verification tool CoLT and evaluated it on a representative sample
of Java implementations of the concurrent set data structure. The tool verified
linearizability of a number of implementations, found a known error in a lock-free
imple- mentation and proved that the corrected version is linearizable.
alternative_title:
- IST Austria Technical Report
author:
- first_name: Pavol
full_name: Cerny, Pavol
id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87
last_name: Cerny
- first_name: Arjun
full_name: Radhakrishna, Arjun
id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87
last_name: Radhakrishna
- first_name: Damien
full_name: Zufferey, Damien
id: 4397AC76-F248-11E8-B48F-1D18A9856A87
last_name: Zufferey
orcid: 0000-0002-3197-8736
- first_name: Swarat
full_name: Chaudhuri, Swarat
last_name: Chaudhuri
- first_name: Rajeev
full_name: Alur, Rajeev
last_name: Alur
citation:
ama: Cerny P, Radhakrishna A, Zufferey D, Chaudhuri S, Alur R. Model Checking
of Linearizability of Concurrent List Implementations. IST Austria; 2010.
doi:10.15479/AT:IST-2010-0001
apa: Cerny, P., Radhakrishna, A., Zufferey, D., Chaudhuri, S., & Alur, R. (2010).
Model checking of linearizability of concurrent list implementations. IST
Austria. https://doi.org/10.15479/AT:IST-2010-0001
chicago: Cerny, Pavol, Arjun Radhakrishna, Damien Zufferey, Swarat Chaudhuri, and
Rajeev Alur. Model Checking of Linearizability of Concurrent List Implementations.
IST Austria, 2010. https://doi.org/10.15479/AT:IST-2010-0001.
ieee: P. Cerny, A. Radhakrishna, D. Zufferey, S. Chaudhuri, and R. Alur, Model
checking of linearizability of concurrent list implementations. IST Austria,
2010.
ista: Cerny P, Radhakrishna A, Zufferey D, Chaudhuri S, Alur R. 2010. Model checking
of linearizability of concurrent list implementations, IST Austria, 27p.
mla: Cerny, Pavol, et al. Model Checking of Linearizability of Concurrent List
Implementations. IST Austria, 2010, doi:10.15479/AT:IST-2010-0001.
short: P. Cerny, A. Radhakrishna, D. Zufferey, S. Chaudhuri, R. Alur, Model Checking
of Linearizability of Concurrent List Implementations, IST Austria, 2010.
date_created: 2018-12-12T11:39:04Z
date_published: 2010-04-19T00:00:00Z
date_updated: 2023-02-23T12:09:09Z
day: '19'
ddc:
- '004'
department:
- _id: ToHe
doi: 10.15479/AT:IST-2010-0001
file:
- access_level: open_access
checksum: 986645caad7dd85a6a091488f6c646dc
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:44Z
date_updated: 2020-07-14T12:46:43Z
file_id: '5505'
file_name: IST-2010-0001_IST-2010-0001.pdf
file_size: 372286
relation: main_file
file_date_updated: 2020-07-14T12:46:43Z
has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: '27'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '27'
related_material:
record:
- id: '4390'
relation: later_version
status: public
status: public
title: Model checking of linearizability of concurrent list implementations
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '9452'
abstract:
- lang: eng
text: Eukaryotic cytosine methylation represses transcription but also occurs in
the bodies of active genes, and the extent of methylation biology conservation
is unclear. We quantified DNA methylation in 17 eukaryotic genomes and found that
gene body methylation is conserved between plants and animals, whereas selective
methylation of transposons is not. We show that methylation of plant transposons
in the CHG context extends to green algae and that exclusion of histone H2A.Z
from methylated DNA is conserved between plants and animals, and we present evidence
for RNA-directed DNA methylation of fungal genes. Our data demonstrate that extant
DNA methylation systems are mosaics of conserved and derived features, and indicate
that gene body methylation is an ancient property of eukaryotic genomes.
article_processing_charge: No
article_type: original
author:
- first_name: 'Assaf '
full_name: 'Zemach, Assaf '
last_name: Zemach
- first_name: Ivy E.
full_name: McDaniel, Ivy E.
last_name: McDaniel
- first_name: Pedro
full_name: Silva, Pedro
last_name: Silva
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Zemach A, McDaniel IE, Silva P, Zilberman D. Genome-wide evolutionary analysis
of eukaryotic DNA methylation. Science. 2010;328(5980):916-919. doi:10.1126/science.1186366
apa: Zemach, A., McDaniel, I. E., Silva, P., & Zilberman, D. (2010). Genome-wide
evolutionary analysis of eukaryotic DNA methylation. Science. American
Association for the Advancement of Science. https://doi.org/10.1126/science.1186366
chicago: Zemach, Assaf , Ivy E. McDaniel, Pedro Silva, and Daniel Zilberman. “Genome-Wide
Evolutionary Analysis of Eukaryotic DNA Methylation.” Science. American
Association for the Advancement of Science, 2010. https://doi.org/10.1126/science.1186366.
ieee: A. Zemach, I. E. McDaniel, P. Silva, and D. Zilberman, “Genome-wide evolutionary
analysis of eukaryotic DNA methylation,” Science, vol. 328, no. 5980. American
Association for the Advancement of Science, pp. 916–919, 2010.
ista: Zemach A, McDaniel IE, Silva P, Zilberman D. 2010. Genome-wide evolutionary
analysis of eukaryotic DNA methylation. Science. 328(5980), 916–919.
mla: Zemach, Assaf, et al. “Genome-Wide Evolutionary Analysis of Eukaryotic DNA
Methylation.” Science, vol. 328, no. 5980, American Association for the
Advancement of Science, 2010, pp. 916–19, doi:10.1126/science.1186366.
short: A. Zemach, I.E. McDaniel, P. Silva, D. Zilberman, Science 328 (2010) 916–919.
date_created: 2021-06-04T08:26:08Z
date_published: 2010-05-14T00:00:00Z
date_updated: 2021-12-14T08:35:37Z
day: '14'
department:
- _id: DaZi
doi: 10.1126/science.1186366
extern: '1'
external_id:
pmid:
- '20395474 '
intvolume: ' 328'
issue: '5980'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '05'
oa_version: None
page: 916-919
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genome-wide evolutionary analysis of eukaryotic DNA methylation
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 328
year: '2010'
...
---
_id: '9485'
abstract:
- lang: eng
text: 'Cytosine methylation silences transposable elements in plants, vertebrates,
and fungi but also regulates gene expression. Plant methylation is catalyzed by
three families of enzymes, each with a preferred sequence context: CG, CHG (H
= A, C, or T), and CHH, with CHH methylation targeted by the RNAi pathway. Arabidopsis
thaliana endosperm, a placenta-like tissue that nourishes the embryo, is globally
hypomethylated in the CG context while retaining high non-CG methylation. Global
methylation dynamics in seeds of cereal crops that provide the bulk of human nutrition
remain unknown. Here, we show that rice endosperm DNA is hypomethylated in all
sequence contexts. Non-CG methylation is reduced evenly across the genome, whereas
CG hypomethylation is localized. CHH methylation of small transposable elements
is increased in embryos, suggesting that endosperm demethylation enhances transposon
silencing. Genes preferentially expressed in endosperm, including those coding
for major storage proteins and starch synthesizing enzymes, are frequently hypomethylated
in endosperm, indicating that DNA methylation is a crucial regulator of rice endosperm
biogenesis. Our data show that genome-wide reshaping of seed DNA methylation is
conserved among angiosperms and has a profound effect on gene expression in cereal
crops.'
article_processing_charge: No
article_type: original
author:
- first_name: Assaf
full_name: Zemach, Assaf
last_name: Zemach
- first_name: M. Yvonne
full_name: Kim, M. Yvonne
last_name: Kim
- first_name: Pedro
full_name: Silva, Pedro
last_name: Silva
- first_name: Jessica A.
full_name: Rodrigues, Jessica A.
last_name: Rodrigues
- first_name: Bradley
full_name: Dotson, Bradley
last_name: Dotson
- first_name: Matthew D.
full_name: Brooks, Matthew D.
last_name: Brooks
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Zemach A, Kim MY, Silva P, et al. Local DNA hypomethylation activates genes
in rice endosperm. Proceedings of the National Academy of Sciences. 2010;107(43):18729-18734.
doi:10.1073/pnas.1009695107
apa: Zemach, A., Kim, M. Y., Silva, P., Rodrigues, J. A., Dotson, B., Brooks, M.
D., & Zilberman, D. (2010). Local DNA hypomethylation activates genes in rice
endosperm. Proceedings of the National Academy of Sciences. National Academy
of Sciences. https://doi.org/10.1073/pnas.1009695107
chicago: Zemach, Assaf, M. Yvonne Kim, Pedro Silva, Jessica A. Rodrigues, Bradley
Dotson, Matthew D. Brooks, and Daniel Zilberman. “Local DNA Hypomethylation Activates
Genes in Rice Endosperm.” Proceedings of the National Academy of Sciences.
National Academy of Sciences, 2010. https://doi.org/10.1073/pnas.1009695107.
ieee: A. Zemach et al., “Local DNA hypomethylation activates genes in rice
endosperm,” Proceedings of the National Academy of Sciences, vol. 107,
no. 43. National Academy of Sciences, pp. 18729–18734, 2010.
ista: Zemach A, Kim MY, Silva P, Rodrigues JA, Dotson B, Brooks MD, Zilberman D.
2010. Local DNA hypomethylation activates genes in rice endosperm. Proceedings
of the National Academy of Sciences. 107(43), 18729–18734.
mla: Zemach, Assaf, et al. “Local DNA Hypomethylation Activates Genes in Rice Endosperm.”
Proceedings of the National Academy of Sciences, vol. 107, no. 43, National
Academy of Sciences, 2010, pp. 18729–34, doi:10.1073/pnas.1009695107.
short: A. Zemach, M.Y. Kim, P. Silva, J.A. Rodrigues, B. Dotson, M.D. Brooks, D.
Zilberman, Proceedings of the National Academy of Sciences 107 (2010) 18729–18734.
date_created: 2021-06-07T09:31:01Z
date_published: 2010-10-26T00:00:00Z
date_updated: 2021-12-14T08:40:02Z
day: '26'
department:
- _id: DaZi
doi: 10.1073/pnas.1009695107
extern: '1'
external_id:
pmid:
- '20937895'
intvolume: ' 107'
issue: '43'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1009695107
month: '10'
oa: 1
oa_version: Published Version
page: 18729-18734
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Local DNA hypomethylation activates genes in rice endosperm
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 107
year: '2010'
...
---
_id: '9489'
abstract:
- lang: eng
text: Cytosine methylation is an ancient process with conserved enzymology but diverse
biological functions that include defense against transposable elements and regulation
of gene expression. Here we will discuss the evolution and biological significance
of eukaryotic DNA methylation, the likely drivers of that evolution, and major
remaining mysteries.
article_processing_charge: No
article_type: review
author:
- first_name: Assaf
full_name: Zemach, Assaf
last_name: Zemach
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Zemach A, Zilberman D. Evolution of eukaryotic DNA methylation and the pursuit
of safer sex. Current Biology. 2010;20(17):R780-R785. doi:10.1016/j.cub.2010.07.007
apa: Zemach, A., & Zilberman, D. (2010). Evolution of eukaryotic DNA methylation
and the pursuit of safer sex. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2010.07.007
chicago: Zemach, Assaf, and Daniel Zilberman. “Evolution of Eukaryotic DNA Methylation
and the Pursuit of Safer Sex.” Current Biology. Elsevier, 2010. https://doi.org/10.1016/j.cub.2010.07.007.
ieee: A. Zemach and D. Zilberman, “Evolution of eukaryotic DNA methylation and the
pursuit of safer sex,” Current Biology, vol. 20, no. 17. Elsevier, pp.
R780–R785, 2010.
ista: Zemach A, Zilberman D. 2010. Evolution of eukaryotic DNA methylation and the
pursuit of safer sex. Current Biology. 20(17), R780–R785.
mla: Zemach, Assaf, and Daniel Zilberman. “Evolution of Eukaryotic DNA Methylation
and the Pursuit of Safer Sex.” Current Biology, vol. 20, no. 17, Elsevier,
2010, pp. R780–85, doi:10.1016/j.cub.2010.07.007.
short: A. Zemach, D. Zilberman, Current Biology 20 (2010) R780–R785.
date_created: 2021-06-07T09:45:27Z
date_published: 2010-09-14T00:00:00Z
date_updated: 2021-12-14T08:52:34Z
day: '14'
department:
- _id: DaZi
doi: 10.1016/j.cub.2010.07.007
extern: '1'
external_id:
pmid:
- '20833323'
intvolume: ' 20'
issue: '17'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cub.2010.07.007
month: '09'
oa: 1
oa_version: Published Version
page: R780-R785
pmid: 1
publication: Current Biology
publication_identifier:
eissn:
- 1879-0445
issn:
- 0960-9822
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evolution of eukaryotic DNA methylation and the pursuit of safer sex
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 20
year: '2010'
...
---
_id: '9764'
article_processing_charge: No
author:
- first_name: Ulises
full_name: Rosas, Ulises
last_name: Rosas
- 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: Lucy
full_name: Copsey, Lucy
last_name: Copsey
- first_name: Pierre
full_name: Barbier De Reuille, Pierre
last_name: Barbier De Reuille
- first_name: Enrico
full_name: Coen, Enrico
last_name: Coen
citation:
ama: Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. Heterosis and the
drift load. 2010. doi:10.1371/journal.pbio.1000429.s003
apa: Rosas, U., Barton, N. H., Copsey, L., Barbier De Reuille, P., & Coen, E.
(2010). Heterosis and the drift load. Public Library of Science. https://doi.org/10.1371/journal.pbio.1000429.s003
chicago: Rosas, Ulises, Nicholas H Barton, Lucy Copsey, Pierre Barbier De Reuille,
and Enrico Coen. “Heterosis and the Drift Load.” Public Library of Science, 2010.
https://doi.org/10.1371/journal.pbio.1000429.s003.
ieee: U. Rosas, N. H. Barton, L. Copsey, P. Barbier De Reuille, and E. Coen, “Heterosis
and the drift load.” Public Library of Science, 2010.
ista: Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. 2010. Heterosis
and the drift load, Public Library of Science, 10.1371/journal.pbio.1000429.s003.
mla: Rosas, Ulises, et al. Heterosis and the Drift Load. Public Library of
Science, 2010, doi:10.1371/journal.pbio.1000429.s003.
short: U. Rosas, N.H. Barton, L. Copsey, P. Barbier De Reuille, E. Coen, (2010).
date_created: 2021-08-02T09:45:39Z
date_published: 2010-07-20T00:00:00Z
date_updated: 2023-02-23T11:42:17Z
day: '20'
department:
- _id: NiBa
doi: 10.1371/journal.pbio.1000429.s003
month: '07'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '3779'
relation: used_in_publication
status: public
status: public
title: Heterosis and the drift load
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2010'
...
---
_id: '3675'
abstract:
- lang: eng
text: "Sex and recombination have long been seen as adaptations that facilitate
natural selection by generating favorable variations. If recombination is to aid
selection, there must be negative linkage disequilibria—favorable alleles must
be found together less often than expected by chance. These negative linkage disequilibria
can be generated directly by selection, but this must involve negative epistasis
of just the right strength, which is not expected, from either experiment or theory.
Random drift provides a more general source of negative associations: Favorable
mutations almost always arise on different genomes, and negative associations
tend to persist, precisely because they shield variation from selection.\r\n\r\nWe
can understand how recombination aids adaptation by determining the maximum possible
rate of adaptation. With unlinked loci, this rate increases only logarithmically
with the influx of favorable mutations. With a linear genome, a scaling argument
shows that in a large population, the rate of adaptive substitution depends only
on the expected rate in the absence of interference, divided by the total rate
of recombination. A two-locus approximation predicts an upper bound on the rate
of substitution, proportional to recombination rate.\r\n\r\nIf associations between
linked loci do impede adaptation, there can be substantial selection for modifiers
that increase recombination. Whether this can account for the maintenance of high
rates of sex and recombination depends on the extent of selection. It is clear
that the rate of species-wide substitutions is typically far too low to generate
appreciable selection for recombination. However, local sweeps within a subdivided
population may be effective."
acknowledgement: Royal Society and the Engineering and Physical Sciences for support
(GR/ T11753/01)
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. Why sex and recombination? . In: Cold Spring Harbor Symposia
on Quantitative Biology. Vol 74. Cold Spring Harbor Laboratory Press; 2009:187-195.
doi:10.1101/sqb.2009.74.030'
apa: Barton, N. H. (2009). Why sex and recombination? . In Cold Spring Harbor
Symposia on Quantitative Biology (Vol. 74, pp. 187–195). Cold Spring Harbor
Laboratory Press. https://doi.org/10.1101/sqb.2009.74.030
chicago: Barton, Nicholas H. “Why Sex and Recombination? .” In Cold Spring Harbor
Symposia on Quantitative Biology, 74:187–95. Cold Spring Harbor Laboratory
Press, 2009. https://doi.org/10.1101/sqb.2009.74.030.
ieee: N. H. Barton, “Why sex and recombination? ,” in Cold Spring Harbor Symposia
on Quantitative Biology, vol. 74, Cold Spring Harbor Laboratory Press, 2009,
pp. 187–195.
ista: 'Barton NH. 2009.Why sex and recombination? . In: Cold Spring Harbor Symposia
on Quantitative Biology. vol. 74, 187–195.'
mla: Barton, Nicholas H. “Why Sex and Recombination? .” Cold Spring Harbor Symposia
on Quantitative Biology, vol. 74, Cold Spring Harbor Laboratory Press, 2009,
pp. 187–95, doi:10.1101/sqb.2009.74.030.
short: N.H. Barton, in:, Cold Spring Harbor Symposia on Quantitative Biology, Cold
Spring Harbor Laboratory Press, 2009, pp. 187–195.
date_created: 2018-12-11T12:04:33Z
date_published: 2009-11-10T00:00:00Z
date_updated: 2021-01-12T07:45:04Z
day: '10'
department:
- _id: NiBa
doi: 10.1101/sqb.2009.74.030
intvolume: ' 74'
language:
- iso: eng
month: '11'
oa_version: None
page: 187 - 195
publication: Cold Spring Harbor Symposia on Quantitative Biology
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
publist_id: '2708'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Why sex and recombination? '
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 74
year: '2009'
...
---
_id: '3775'
abstract:
- lang: eng
text: There is a close analogy between statistical thermodynamics and the evolution
of allele frequencies under mutation, selection and random drift. Wright's formula
for the stationary distribution of allele frequencies is analogous to the Boltzmann
distribution in statistical physics. Population size, 2N, plays the role of the
inverse temperature, 1/kT, and determines the magnitude of random fluctuations.
Log mean fitness, View the MathML source, tends to increase under selection, and
is analogous to a (negative) energy; a potential function, U, increases under
mutation in a similar way. An entropy, SH, can be defined which measures the deviation
from the distribution of allele frequencies expected under random drift alone;
the sum View the MathML source gives a free fitness that increases as the population
evolves towards its stationary distribution. Usually, we observe the distribution
of a few quantitative traits that depend on the frequencies of very many alleles.
The mean and variance of such traits are analogous to observable quantities in
statistical thermodynamics. Thus, we can define an entropy, SΩ, which measures
the volume of allele frequency space that is consistent with the observed trait
distribution. The stationary distribution of the traits is View the MathML source;
this applies with arbitrary epistasis and dominance. The entropies SΩ, SH are
distinct, but converge when there are so many alleles that traits fluctuate close
to their expectations. Populations tend to evolve towards states that can be realised
in many ways (i.e., large SΩ), which may lead to a substantial drop below the
adaptive peak; we illustrate this point with a simple model of genetic redundancy.
This analogy with statistical thermodynamics brings together previous ideas in
a general framework, and justifies a maximum entropy approximation to the dynamics
of quantitative traits.
acknowledgement: "This work was supported by a Royal Society/Wolfson Award, and by
grants EP/T11753/01, EP/C546318/01 from the EPSRC.\r\nWe are grateful to M. Cates,
H.P. de Vladar and G. Sella, and to two anonymous referees, for their helpful comments."
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: Jason
full_name: Coe, Jason
last_name: Coe
citation:
ama: Barton NH, Coe J. On the application of statistical physics to evolutionary
biology. Journal of Theoretical Biology. 2009;259(2):317-324. doi:10.1016/j.jtbi.2009.03.019
apa: Barton, N. H., & Coe, J. (2009). On the application of statistical physics
to evolutionary biology. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2009.03.019
chicago: Barton, Nicholas H, and Jason Coe. “On the Application of Statistical Physics
to Evolutionary Biology.” Journal of Theoretical Biology. Elsevier, 2009.
https://doi.org/10.1016/j.jtbi.2009.03.019.
ieee: N. H. Barton and J. Coe, “On the application of statistical physics to evolutionary
biology,” Journal of Theoretical Biology, vol. 259, no. 2. Elsevier, pp.
317–324, 2009.
ista: Barton NH, Coe J. 2009. On the application of statistical physics to evolutionary
biology. Journal of Theoretical Biology. 259(2), 317–324.
mla: Barton, Nicholas H., and Jason Coe. “On the Application of Statistical Physics
to Evolutionary Biology.” Journal of Theoretical Biology, vol. 259, no.
2, Elsevier, 2009, pp. 317–24, doi:10.1016/j.jtbi.2009.03.019.
short: N.H. Barton, J. Coe, Journal of Theoretical Biology 259 (2009) 317–324.
date_created: 2018-12-11T12:05:06Z
date_published: 2009-07-21T00:00:00Z
date_updated: 2021-01-12T07:52:06Z
day: '21'
department:
- _id: NiBa
doi: 10.1016/j.jtbi.2009.03.019
intvolume: ' 259'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://hal.archives-ouvertes.fr/hal-00554594/document
month: '07'
oa: 1
oa_version: Submitted Version
page: 317 - 324
publication: Journal of Theoretical Biology
publication_status: published
publisher: Elsevier
publist_id: '2452'
quality_controlled: '1'
scopus_import: 1
status: public
title: On the application of statistical physics to evolutionary biology
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 259
year: '2009'
...