---
_id: '13221'
abstract:
- lang: eng
text: The safety-liveness dichotomy is a fundamental concept in formal languages
which plays a key role in verification. Recently, this dichotomy has been lifted
to quantitative properties, which are arbitrary functions from infinite words
to partially-ordered domains. We look into harnessing the dichotomy for the specific
classes of quantitative properties expressed by quantitative automata. These automata
contain finitely many states and rational-valued transition weights, and their
common value functions Inf, Sup, LimInf, LimSup, LimInfAvg, LimSupAvg, and DSum
map infinite words into the totallyordered domain of real numbers. In this automata-theoretic
setting, we establish a connection between quantitative safety and topological
continuity and provide an alternative characterization of quantitative safety
and liveness in terms of their boolean counterparts. For all common value functions,
we show how the safety closure of a quantitative automaton can be constructed
in PTime, and we provide PSpace-complete checks of whether a given quantitative
automaton is safe or live, with the exception of LimInfAvg and LimSupAvg automata,
for which the safety check is in ExpSpace. Moreover, for deterministic Sup, LimInf,
and LimSup automata, we give PTime decompositions into safe and live automata.
These decompositions enable the separation of techniques for safety and liveness
verification for quantitative specifications.
acknowledgement: We thank Christof Löding for pointing us to some results on PSpace-hardess
of universality problems and the anonymous reviewers for their helpful comments.
This work was supported in part by the ERC-2020-AdG 101020093 and the Israel Science
Foundation grant 2410/22.
alternative_title:
- LIPIcs
article_number: '17'
article_processing_charge: No
arxiv: 1
author:
- first_name: Udi
full_name: Boker, Udi
id: 31E297B6-F248-11E8-B48F-1D18A9856A87
last_name: Boker
- 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: Nicolas Adrien
full_name: Mazzocchi, Nicolas Adrien
id: b26baa86-3308-11ec-87b0-8990f34baa85
last_name: Mazzocchi
- first_name: Naci E
full_name: Sarac, Naci E
id: 8C6B42F8-C8E6-11E9-A03A-F2DCE5697425
last_name: Sarac
citation:
ama: 'Boker U, Henzinger TA, Mazzocchi NA, Sarac NE. Safety and liveness of quantitative
automata. In: 34th International Conference on Concurrency Theory. Vol
279. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.CONCUR.2023.17'
apa: 'Boker, U., Henzinger, T. A., Mazzocchi, N. A., & Sarac, N. E. (2023).
Safety and liveness of quantitative automata. In 34th International Conference
on Concurrency Theory (Vol. 279). Antwerp, Belgium: Schloss Dagstuhl - Leibniz-Zentrum
für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2023.17'
chicago: Boker, Udi, Thomas A Henzinger, Nicolas Adrien Mazzocchi, and Naci E Sarac.
“Safety and Liveness of Quantitative Automata.” In 34th International Conference
on Concurrency Theory, Vol. 279. Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2023. https://doi.org/10.4230/LIPIcs.CONCUR.2023.17.
ieee: U. Boker, T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “Safety and liveness
of quantitative automata,” in 34th International Conference on Concurrency
Theory, Antwerp, Belgium, 2023, vol. 279.
ista: 'Boker U, Henzinger TA, Mazzocchi NA, Sarac NE. 2023. Safety and liveness
of quantitative automata. 34th International Conference on Concurrency Theory.
CONCUR: Conference on Concurrency Theory, LIPIcs, vol. 279, 17.'
mla: Boker, Udi, et al. “Safety and Liveness of Quantitative Automata.” 34th
International Conference on Concurrency Theory, vol. 279, 17, Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.CONCUR.2023.17.
short: U. Boker, T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, in:, 34th International
Conference on Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2023.
conference:
end_date: 2023-09-23
location: Antwerp, Belgium
name: 'CONCUR: Conference on Concurrency Theory'
start_date: 2023-09-18
corr_author: '1'
date_created: 2023-07-14T10:00:15Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2026-08-12T08:46:04Z
day: '01'
ddc:
- '000'
department:
- _id: GradSch
- _id: ToHe
doi: 10.4230/LIPIcs.CONCUR.2023.17
ec_funded: 1
external_id:
arxiv:
- '2307.06016'
isi:
- '001570542500017'
file:
- access_level: open_access
checksum: d40e57a04448ea5c77d7e1cfb9590a81
content_type: application/pdf
creator: esarac
date_created: 2023-07-14T12:03:48Z
date_updated: 2023-07-14T12:03:48Z
file_id: '13224'
file_name: CONCUR23.pdf
file_size: 755529
relation: main_file
success: 1
file_date_updated: 2023-07-14T12:03:48Z
fulldoi: https://doi.org/10.4230/LIPIcs.CONCUR.2023.17
has_accepted_license: '1'
intvolume: ' 279'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: 34th International Conference on Concurrency Theory
publication_identifier:
eissn:
- 1868-8969
isbn:
- '9783959772990'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
related_material:
record:
- id: '20147'
relation: dissertation_contains
status: public
- id: '20342'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Safety and liveness of quantitative automata
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 279
year: '2023'
...
---
_id: '13965'
abstract:
- lang: eng
text: Many modes and mechanisms of epigenetic inheritance have been elucidated in
eukaryotes. Most of them are relatively short-term, generally not exceeding one
or a few organismal generations. However, emerging evidence indicates that one
mechanism, cytosine DNA methylation, can mediate epigenetic inheritance over much
longer timescales, which are mostly or completely inaccessible in the laboratory.
Here we discuss the evidence for, and mechanisms and implications of, such long-term
epigenetic inheritance. We argue that compelling evidence supports the long-term
epigenetic inheritance of gene body methylation, at least in the model angiosperm
Arabidopsis thaliana, and that variation in such methylation can therefore serve
as an epigenetic basis for phenotypic variation in natural populations.
article_number: '102087'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Elizabeth
full_name: Hollwey, Elizabeth
id: b8c4f54b-e484-11eb-8fdc-a54df64ef6dd
last_name: Hollwey
- first_name: Amy
full_name: Briffa, Amy
last_name: Briffa
- first_name: Martin
full_name: Howard, Martin
last_name: Howard
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Hollwey E, Briffa A, Howard M, Zilberman D. Concepts, mechanisms and implications
of long-term epigenetic inheritance. Current Opinion in Genetics & Development.
2023;81(8). doi:10.1016/j.gde.2023.102087
apa: Hollwey, E., Briffa, A., Howard, M., & Zilberman, D. (2023). Concepts,
mechanisms and implications of long-term epigenetic inheritance. Current Opinion
in Genetics & Development. Elsevier. https://doi.org/10.1016/j.gde.2023.102087
chicago: Hollwey, Elizabeth, Amy Briffa, Martin Howard, and Daniel Zilberman. “Concepts,
Mechanisms and Implications of Long-Term Epigenetic Inheritance.” Current Opinion
in Genetics & Development. Elsevier, 2023. https://doi.org/10.1016/j.gde.2023.102087.
ieee: E. Hollwey, A. Briffa, M. Howard, and D. Zilberman, “Concepts, mechanisms
and implications of long-term epigenetic inheritance,” Current Opinion in Genetics
& Development, vol. 81, no. 8. Elsevier, 2023.
ista: Hollwey E, Briffa A, Howard M, Zilberman D. 2023. Concepts, mechanisms and
implications of long-term epigenetic inheritance. Current Opinion in Genetics
& Development. 81(8), 102087.
mla: Hollwey, Elizabeth, et al. “Concepts, Mechanisms and Implications of Long-Term
Epigenetic Inheritance.” Current Opinion in Genetics & Development,
vol. 81, no. 8, 102087, Elsevier, 2023, doi:10.1016/j.gde.2023.102087.
short: E. Hollwey, A. Briffa, M. Howard, D. Zilberman, Current Opinion in Genetics
& Development 81 (2023).
corr_author: '1'
date_created: 2023-08-06T22:01:10Z
date_published: 2023-08-01T00:00:00Z
date_updated: 2026-08-12T09:55:32Z
day: '01'
ddc:
- '570'
department:
- _id: DaZi
doi: 10.1016/j.gde.2023.102087
external_id:
isi:
- '001047020200001'
pmid:
- '37441873'
file:
- access_level: open_access
checksum: a294cd9506b80ed6ef218ef44ed32765
content_type: application/pdf
creator: dernst
date_created: 2023-08-07T08:32:26Z
date_updated: 2023-08-07T08:32:26Z
file_id: '13980'
file_name: 2023_CurrentOpinionGenetics_Hollwey.pdf
file_size: 2568632
relation: main_file
success: 1
file_date_updated: 2023-08-07T08:32:26Z
fulldoi: https://doi.org/10.1016/j.gde.2023.102087
has_accepted_license: '1'
intvolume: ' 81'
isi: 1
issue: '8'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Current Opinion in Genetics & Development
publication_identifier:
eissn:
- 1879-0380
issn:
- 0959-437X
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Concepts, mechanisms and implications of long-term epigenetic inheritance
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 81
year: '2023'
...
---
_id: '14774'
abstract:
- lang: eng
text: Morphogen gradients impart positional information to cells in a homogenous
tissue field. Fgf8a, a highly conserved growth factor, has been proposed to act
as a morphogen during zebrafish gastrulation. However, technical limitations have
so far prevented direct visualization of the endogenous Fgf8a gradient and confirmation
of its morphogenic activity. Here, we monitor Fgf8a propagation in the developing
neural plate using a CRISPR/Cas9-mediated EGFP knock-in at the endogenous fgf8a
locus. By combining sensitive imaging with single-molecule fluorescence correlation
spectroscopy, we demonstrate that Fgf8a, which is produced at the embryonic margin,
propagates by diffusion through the extracellular space and forms a graded distribution
towards the animal pole. Overlaying the Fgf8a gradient curve with expression profiles
of its downstream targets determines the precise input-output relationship of
Fgf8a-mediated patterning. Manipulation of the extracellular Fgf8a levels alters
the signaling outcome, thus establishing Fgf8a as a bona fide morphogen during
zebrafish gastrulation. Furthermore, by hindering Fgf8a diffusion, we demonstrate
that extracellular diffusion of the protein from the source is crucial for it
to achieve its morphogenic potential.
acknowledgement: "We thank members of the Brand lab, as well as Justina Stark (Ivo
Sbalzarini group, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden,
Germany) for project-related discussions; Darren Gilmour (University of Zurich),
Karuna Sampath (University of Warwick) and Gokul Kesavan (Vowels Lifesciences Private
Limited, Bangalore) for comments on the manuscript; personnel of the CMCB technology
platform, TU Dresden for imaging and image analysis-related support; and Maurizio
Abbate (Technical support, Arivis) for help with image analysis. We are also grateful
to Stapornwongkul and Briscoe for commenting on a preprint version of our work (Stapornwongkul
and Briscoe, 2022).\r\nThis work was supported by the Deutsche Forschungsgemeinschaft
(BR 1746/6-2, BR 1746/11-1 and BR 1746/3 to M.B.), by a Cluster of Excellence ‘Physics
of Life’ seed grant and by institutional funds from Technische Universitat Dresden
(to M.B.). Open Access funding provided by Technische Universitat Dresden. Deposited
in PMC for immediate release."
article_number: dev201559
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Rohit K
full_name: Harish, Rohit K
id: 1bae78aa-ee0e-11ec-9b76-bc42990f409d
last_name: Harish
- first_name: Mansi
full_name: Gupta, Mansi
last_name: Gupta
- first_name: Daniela
full_name: Zöller, Daniela
last_name: Zöller
- first_name: Hella
full_name: Hartmann, Hella
last_name: Hartmann
- first_name: Ali
full_name: Gheisari, Ali
last_name: Gheisari
- first_name: Anja
full_name: Machate, Anja
last_name: Machate
- first_name: Stefan
full_name: Hans, Stefan
last_name: Hans
- first_name: Michael
full_name: Brand, Michael
last_name: Brand
citation:
ama: Harish RK, Gupta M, Zöller D, et al. Real-time monitoring of an endogenous
Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation.
Development. 2023;150(19). doi:10.1242/dev.201559
apa: Harish, R. K., Gupta, M., Zöller, D., Hartmann, H., Gheisari, A., Machate,
A., … Brand, M. (2023). Real-time monitoring of an endogenous Fgf8a gradient attests
to its role as a morphogen during zebrafish gastrulation. Development.
Company of Biologists. https://doi.org/10.1242/dev.201559
chicago: Harish, Rohit K, Mansi Gupta, Daniela Zöller, Hella Hartmann, Ali Gheisari,
Anja Machate, Stefan Hans, and Michael Brand. “Real-Time Monitoring of an Endogenous
Fgf8a Gradient Attests to Its Role as a Morphogen during Zebrafish Gastrulation.”
Development. Company of Biologists, 2023. https://doi.org/10.1242/dev.201559.
ieee: R. K. Harish et al., “Real-time monitoring of an endogenous Fgf8a gradient
attests to its role as a morphogen during zebrafish gastrulation,” Development,
vol. 150, no. 19. Company of Biologists, 2023.
ista: Harish RK, Gupta M, Zöller D, Hartmann H, Gheisari A, Machate A, Hans S, Brand
M. 2023. Real-time monitoring of an endogenous Fgf8a gradient attests to its role
as a morphogen during zebrafish gastrulation. Development. 150(19), dev201559.
mla: Harish, Rohit K., et al. “Real-Time Monitoring of an Endogenous Fgf8a Gradient
Attests to Its Role as a Morphogen during Zebrafish Gastrulation.” Development,
vol. 150, no. 19, dev201559, Company of Biologists, 2023, doi:10.1242/dev.201559.
short: R.K. Harish, M. Gupta, D. Zöller, H. Hartmann, A. Gheisari, A. Machate, S.
Hans, M. Brand, Development 150 (2023).
date_created: 2024-01-10T09:18:54Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2026-08-12T09:59:59Z
day: '01'
ddc:
- '570'
department:
- _id: AnKi
doi: 10.1242/dev.201559
external_id:
isi:
- '001097449100002'
pmid:
- '37665167'
file:
- access_level: open_access
checksum: 2d6f52dc33260a9b2352b8f28374ba5f
content_type: application/pdf
creator: dernst
date_created: 2024-01-10T12:41:13Z
date_updated: 2024-01-10T12:41:13Z
file_id: '14790'
file_name: 2023_Development_Harish.pdf
file_size: 12836306
relation: main_file
success: 1
file_date_updated: 2024-01-10T12:41:13Z
fulldoi: https://doi.org/10.1242/dev.201559
has_accepted_license: '1'
intvolume: ' 150'
isi: 1
issue: '19'
keyword:
- Developmental Biology
- Molecular Biology
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: Development
publication_identifier:
eissn:
- 1477-9129
issn:
- 0950-1991
publication_status: published
publisher: Company of Biologists
quality_controlled: '1'
status: public
title: Real-time monitoring of an endogenous Fgf8a gradient attests to its role as
a morphogen during zebrafish gastrulation
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 150
year: '2023'
...
---
OA_place: publisher
OA_type: closed access
_id: '22530'
abstract:
- lang: eng
text: Water Use Efficiency (WUE) expresses the trade-off between carbon assimilation
(or subsequent carbon storage) and water release, two concurrent gas fluxes essential
for plant functioning. Here, we review metrics that have been introduced to quantify
WUE across spatial and temporal scales and corresponding observational methods.
The physiological and environmental dependencies of WUE for crops and unmanaged
ecosystems are discussed with a quantitative examination of observed and simulated
WUE values. A constrained range of WUE across ecosystems and climates is highlighted.
However, WUE increased considerably in the past century in response to growing
atmospheric CO2 concentration and it will likely continue along the same trajectory
in the near future.
article_processing_charge: No
author:
- first_name: Simone
full_name: Fatichi, Simone
id: cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6
last_name: Fatichi
- first_name: Athanasios
full_name: Paschalis, Athanasios
last_name: Paschalis
- first_name: Sara
full_name: Bonetti, Sara
last_name: Bonetti
- first_name: Gabriele
full_name: Manoli, Gabriele
last_name: Manoli
- first_name: Christoforos
full_name: Pappas, Christoforos
last_name: Pappas
citation:
ama: 'Fatichi S, Paschalis A, Bonetti S, Manoli G, Pappas C. Water use efficiency:
A review of spatial and temporal variability. In: Goss MJ, Oliver M, eds. Encyclopedia
of Soils in the Environment. Vol 5. 2nd ed. Elsevier; 2023:527-542. doi:10.1016/b978-0-12-822974-3.00166-x'
apa: 'Fatichi, S., Paschalis, A., Bonetti, S., Manoli, G., & Pappas, C. (2023).
Water use efficiency: A review of spatial and temporal variability. In M. J. Goss
& M. Oliver (Eds.), Encyclopedia of Soils in the Environment (2nd ed.,
Vol. 5, pp. 527–542). Elsevier. https://doi.org/10.1016/b978-0-12-822974-3.00166-x'
chicago: 'Fatichi, Simone, Athanasios Paschalis, Sara Bonetti, Gabriele Manoli,
and Christoforos Pappas. “Water Use Efficiency: A Review of Spatial and Temporal
Variability.” In Encyclopedia of Soils in the Environment, edited by Michael
J. Goss and Margaret Oliver, 2nd ed., 5:527–42. Elsevier, 2023. https://doi.org/10.1016/b978-0-12-822974-3.00166-x.'
ieee: 'S. Fatichi, A. Paschalis, S. Bonetti, G. Manoli, and C. Pappas, “Water use
efficiency: A review of spatial and temporal variability,” in Encyclopedia
of Soils in the Environment, 2nd ed., vol. 5, M. J. Goss and M. Oliver, Eds.
Elsevier, 2023, pp. 527–542.'
ista: 'Fatichi S, Paschalis A, Bonetti S, Manoli G, Pappas C. 2023.Water use efficiency:
A review of spatial and temporal variability. In: Encyclopedia of Soils in the
Environment. vol. 5, 527–542.'
mla: 'Fatichi, Simone, et al. “Water Use Efficiency: A Review of Spatial and Temporal
Variability.” Encyclopedia of Soils in the Environment, edited by Michael
J. Goss and Margaret Oliver, 2nd ed., vol. 5, Elsevier, 2023, pp. 527–42, doi:10.1016/b978-0-12-822974-3.00166-x.'
short: S. Fatichi, A. Paschalis, S. Bonetti, G. Manoli, C. Pappas, in:, M.J. Goss,
M. Oliver (Eds.), Encyclopedia of Soils in the Environment, 2nd ed., Elsevier,
2023, pp. 527–542.
das_tickbox: '1'
date_created: 2026-07-27T12:30:24Z
date_published: 2023-08-14T00:00:00Z
date_updated: 2026-08-12T11:52:58Z
day: '14'
doi: 10.1016/b978-0-12-822974-3.00166-x
edition: '2'
editor:
- first_name: Michael J.
full_name: Goss, Michael J.
last_name: Goss
- first_name: Margaret
full_name: Oliver, Margaret
last_name: Oliver
extern: '1'
fulldoi: https://doi.org/10.1016/b978-0-12-822974-3.00166-x
intvolume: ' 5'
language:
- iso: eng
month: '08'
oa_version: None
page: 527-542
publication: Encyclopedia of Soils in the Environment
publication_identifier:
isbn:
- '9780323951333'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Water use efficiency: A review of spatial and temporal variability'
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2023'
...
---
_id: '14657'
abstract:
- lang: eng
text: 'Natural selection is usually studied between mutants that differ in reproductive
rate, but are subject to the same population structure. Here we explore how natural
selection acts on mutants that have the same reproductive rate, but different
population structures. In our framework, population structure is given by a graph
that specifies where offspring can disperse. The invading mutant disperses offspring
on a different graph than the resident wild-type. We find that more densely connected
dispersal graphs tend to increase the invader’s fixation probability, but the
exact relationship between structure and fixation probability is subtle. We present
three main results. First, we prove that if both invader and resident are on complete
dispersal graphs, then removing a single edge in the invader’s dispersal graph
reduces its fixation probability. Second, we show that for certain island models
higher invader’s connectivity increases its fixation probability, but the magnitude
of the effect depends on the exact layout of the connections. Third, we show that
for lattices the effect of different connectivity is comparable to that of different
fitness: for large population size, the invader’s fixation probability is either
constant or exponentially small, depending on whether it is more or less connected
than the resident.'
acknowledgement: K.C. acknowledges support from the ERC CoG 863818(ForM-SMArt). J.T.
is supported by Center for Foundations ofModern Computer Science (Charles Univ.
project UNCE/SCI/004).
article_number: '20230355'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
- first_name: Kamran
full_name: Kaveh, Kamran
last_name: Kaveh
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin A.
full_name: Nowak, Martin A.
last_name: Nowak
citation:
ama: Tkadlec J, Kaveh K, Chatterjee K, Nowak MA. Evolutionary dynamics of mutants
that modify population structure. Journal of the Royal Society Interface.
2023;20(208). doi:10.1098/rsif.2023.0355
apa: Tkadlec, J., Kaveh, K., Chatterjee, K., & Nowak, M. A. (2023). Evolutionary
dynamics of mutants that modify population structure. Journal of the Royal
Society Interface. Royal Society. https://doi.org/10.1098/rsif.2023.0355
chicago: Tkadlec, Josef, Kamran Kaveh, Krishnendu Chatterjee, and Martin A. Nowak.
“Evolutionary Dynamics of Mutants That Modify Population Structure.” Journal
of the Royal Society Interface. Royal Society, 2023. https://doi.org/10.1098/rsif.2023.0355.
ieee: J. Tkadlec, K. Kaveh, K. Chatterjee, and M. A. Nowak, “Evolutionary dynamics
of mutants that modify population structure,” Journal of the Royal Society
Interface, vol. 20, no. 208. Royal Society, 2023.
ista: Tkadlec J, Kaveh K, Chatterjee K, Nowak MA. 2023. Evolutionary dynamics of
mutants that modify population structure. Journal of the Royal Society Interface.
20(208), 20230355.
mla: Tkadlec, Josef, et al. “Evolutionary Dynamics of Mutants That Modify Population
Structure.” Journal of the Royal Society Interface, vol. 20, no. 208, 20230355,
Royal Society, 2023, doi:10.1098/rsif.2023.0355.
short: J. Tkadlec, K. Kaveh, K. Chatterjee, M.A. Nowak, Journal of the Royal Society
Interface 20 (2023).
date_created: 2023-12-10T23:00:58Z
date_published: 2023-11-29T00:00:00Z
date_updated: 2026-08-12T14:05:25Z
day: '29'
ddc:
- '000'
- '570'
department:
- _id: KrCh
doi: 10.1098/rsif.2023.0355
ec_funded: 1
external_id:
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- '001124419300002'
pmid:
- '38016637'
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file_size: 1720243
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issue: '208'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
project:
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call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: Journal of the Royal Society Interface
publication_identifier:
eissn:
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publication_status: published
publisher: Royal Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evolutionary dynamics of mutants that modify population structure
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 20
year: '2023'
...
---
_id: '14036'
abstract:
- lang: eng
text: Magic-angle spinning (MAS) nuclear magnetic resonance (NMR) is establishing
itself as a powerful method for the characterization of protein dynamics at the
atomic scale. We discuss here how R1ρ MAS relaxation dispersion NMR can explore
microsecond-to-millisecond motions. Progress in instrumentation, isotope labeling,
and pulse sequence design has paved the way for quantitative analyses of even
rare structural fluctuations. In addition to isotropic chemical-shift fluctuations
exploited in solution-state NMR relaxation dispersion experiments, MAS NMR has
a wider arsenal of observables, allowing to see motions even if the exchanging
states do not differ in their chemical shifts. We demonstrate the potential of
the technique for probing motions in challenging large enzymes, membrane proteins,
and protein assemblies.
acknowledgement: We thank Petra Rovó for critical reading of this manuscript. We acknowledge
the Austrian Science Foundation FWF (project AlloSpace, number I5812–B) and funding
by the Institute of Science and Technology Austria.
article_number: '102660'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Federico
full_name: Napoli, Federico
id: d42e08e7-f4fc-11eb-af0a-d71e26138f1b
last_name: Napoli
orcid: 0000-0002-9043-136X
- first_name: Lea Marie
full_name: Becker, Lea Marie
id: 36336939-eb97-11eb-a6c2-c83f1214ca79
last_name: Becker
orcid: 0000-0002-6401-5151
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Napoli F, Becker LM, Schanda P. Protein dynamics detected by magic-angle spinning
relaxation dispersion NMR. Current Opinion in Structural Biology. 2023;82(10).
doi:10.1016/j.sbi.2023.102660
apa: Napoli, F., Becker, L. M., & Schanda, P. (2023). Protein dynamics detected
by magic-angle spinning relaxation dispersion NMR. Current Opinion in Structural
Biology. Elsevier. https://doi.org/10.1016/j.sbi.2023.102660
chicago: Napoli, Federico, Lea Marie Becker, and Paul Schanda. “Protein Dynamics
Detected by Magic-Angle Spinning Relaxation Dispersion NMR.” Current Opinion
in Structural Biology. Elsevier, 2023. https://doi.org/10.1016/j.sbi.2023.102660.
ieee: F. Napoli, L. M. Becker, and P. Schanda, “Protein dynamics detected by magic-angle
spinning relaxation dispersion NMR,” Current Opinion in Structural Biology,
vol. 82, no. 10. Elsevier, 2023.
ista: Napoli F, Becker LM, Schanda P. 2023. Protein dynamics detected by magic-angle
spinning relaxation dispersion NMR. Current Opinion in Structural Biology. 82(10),
102660.
mla: Napoli, Federico, et al. “Protein Dynamics Detected by Magic-Angle Spinning
Relaxation Dispersion NMR.” Current Opinion in Structural Biology, vol.
82, no. 10, 102660, Elsevier, 2023, doi:10.1016/j.sbi.2023.102660.
short: F. Napoli, L.M. Becker, P. Schanda, Current Opinion in Structural Biology
82 (2023).
corr_author: '1'
date_created: 2023-08-13T22:01:11Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2025-04-14T09:10:17Z
day: '01'
ddc:
- '570'
department:
- _id: PaSc
doi: 10.1016/j.sbi.2023.102660
external_id:
isi:
- '001053616200001'
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- '37536064'
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- iso: eng
month: '10'
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oa_version: Published Version
pmid: 1
project:
- _id: eb9c82eb-77a9-11ec-83b8-aadd536561cf
grant_number: I05812
name: AlloSpace. The emergence and mechanisms of allostery
publication: Current Opinion in Structural Biology
publication_identifier:
eissn:
- 1879-033X
issn:
- 0959-440X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Protein dynamics detected by magic-angle spinning relaxation dispersion NMR
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 82
year: '2023'
...
---
_id: '14042'
abstract:
- lang: eng
text: Long-time and large-data existence of weak solutions for initial- and boundary-value
problems concerning three-dimensional flows of incompressible fluids is nowadays
available not only for Navier–Stokes fluids but also for various fluid models
where the relation between the Cauchy stress tensor and the symmetric part of
the velocity gradient is nonlinear. The majority of such studies however concerns
models where such a dependence is explicit (the stress is a function of the velocity
gradient), which makes the class of studied models unduly restrictive. The same
concerns boundary conditions, or more precisely the slipping mechanisms on the
boundary, where the no-slip is still the most preferred condition considered in
the literature. Our main objective is to develop a robust mathematical theory
for unsteady internal flows of implicitly constituted incompressible fluids with
implicit relations between the tangential projections of the velocity and the
normal traction on the boundary. The theory covers numerous rheological models
used in chemistry, biorheology, polymer and food industry as well as in geomechanics.
It also includes, as special cases, nonlinear slip as well as stick–slip boundary
conditions. Unlike earlier studies, the conditions characterizing admissible classes
of constitutive equations are expressed by means of tools of elementary calculus.
In addition, a fully constructive proof (approximation scheme) is incorporated.
Finally, we focus on the question of uniqueness of such weak solutions.
acknowledgement: "M. Bulíček and J. Málek acknowledge the support of the project No.
20-11027X financed by the Czech Science foundation (GAČR). M. Bulíček and J. Málek
are members of the Nečas Center for Mathematical Modelling.\r\nOpen access publishing
supported by the National Technical Library in Prague."
article_number: '72'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Miroslav
full_name: Bulíček, Miroslav
last_name: Bulíček
- first_name: Josef
full_name: Málek, Josef
last_name: Málek
- first_name: Erika
full_name: Maringová, Erika
id: dbabca31-66eb-11eb-963a-fb9c22c880b4
last_name: Maringová
citation:
ama: Bulíček M, Málek J, Maringová E. On unsteady internal flows of incompressible
fluids characterized by implicit constitutive equations in the bulk and on the
boundary. Journal of Mathematical Fluid Mechanics. 2023;25(3). doi:10.1007/s00021-023-00803-w
apa: Bulíček, M., Málek, J., & Maringová, E. (2023). On unsteady internal flows
of incompressible fluids characterized by implicit constitutive equations in the
bulk and on the boundary. Journal of Mathematical Fluid Mechanics. Springer
Nature. https://doi.org/10.1007/s00021-023-00803-w
chicago: Bulíček, Miroslav, Josef Málek, and Erika Maringová. “On Unsteady Internal
Flows of Incompressible Fluids Characterized by Implicit Constitutive Equations
in the Bulk and on the Boundary.” Journal of Mathematical Fluid Mechanics.
Springer Nature, 2023. https://doi.org/10.1007/s00021-023-00803-w.
ieee: M. Bulíček, J. Málek, and E. Maringová, “On unsteady internal flows of incompressible
fluids characterized by implicit constitutive equations in the bulk and on the
boundary,” Journal of Mathematical Fluid Mechanics, vol. 25, no. 3. Springer
Nature, 2023.
ista: Bulíček M, Málek J, Maringová E. 2023. On unsteady internal flows of incompressible
fluids characterized by implicit constitutive equations in the bulk and on the
boundary. Journal of Mathematical Fluid Mechanics. 25(3), 72.
mla: Bulíček, Miroslav, et al. “On Unsteady Internal Flows of Incompressible Fluids
Characterized by Implicit Constitutive Equations in the Bulk and on the Boundary.”
Journal of Mathematical Fluid Mechanics, vol. 25, no. 3, 72, Springer Nature,
2023, doi:10.1007/s00021-023-00803-w.
short: M. Bulíček, J. Málek, E. Maringová, Journal of Mathematical Fluid Mechanics
25 (2023).
date_created: 2023-08-13T22:01:13Z
date_published: 2023-08-01T00:00:00Z
date_updated: 2026-08-18T07:47:38Z
day: '01'
ddc:
- '510'
department:
- _id: JuFi
doi: 10.1007/s00021-023-00803-w
external_id:
arxiv:
- '2301.12834'
isi:
- '001040354900001'
file:
- access_level: open_access
checksum: c549cd8f0dd02ed60477a05ca045f481
content_type: application/pdf
creator: dernst
date_created: 2023-08-14T07:24:17Z
date_updated: 2023-08-14T07:24:17Z
file_id: '14046'
file_name: 2023_JourMathFluidMech_Bulicek.pdf
file_size: 845748
relation: main_file
success: 1
file_date_updated: 2023-08-14T07:24:17Z
fulldoi: https://doi.org/10.1007/s00021-023-00803-w
has_accepted_license: '1'
intvolume: ' 25'
isi: 1
issue: '3'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: Journal of Mathematical Fluid Mechanics
publication_identifier:
eissn:
- 1422-6952
issn:
- 1422-6928
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: On unsteady internal flows of incompressible fluids characterized by implicit
constitutive equations in the bulk and on the boundary
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2023'
...
---
_id: '14466'
abstract:
- lang: eng
text: The first long-lived turbulent structures observable in planar shear flows
take the form of localized stripes, inclined with respect to the mean flow direction.
The dynamics of these stripes is central to transition, and recent studies proposed
an analogy to directed percolation where the stripes’ proliferation is ultimately
responsible for the turbulence becoming sustained. In the present study we focus
on the internal stripe dynamics as well as on the eventual stripe expansion, and
we compare the underlying mechanisms in pressure- and shear-driven planar flows,
respectively, plane-Poiseuille and plane-Couette flow. Despite the similarities
of the overall laminar–turbulence patterns, the stripe proliferation processes
in the two cases are fundamentally different. Starting from the growth and sustenance
of individual stripes, we find that in plane-Couette flow new streaks are created
stochastically throughout the stripe whereas in plane-Poiseuille flow streak creation
is deterministic and occurs locally at the downstream tip. Because of the up/downstream
symmetry, Couette stripes, in contrast to Poiseuille stripes, have two weak and
two strong laminar turbulent interfaces. These differences in symmetry as well
as in internal growth give rise to two fundamentally different stripe splitting
mechanisms. In plane-Poiseuille flow splitting is connected to the elongational
growth of the original stripe, and it results from a break-off/shedding of the
stripe's tail. In plane-Couette flow splitting follows from a broadening of the
original stripe and a division along the stripe into two slimmer stripes.
acknowledgement: E.M. acknowledges funding from the ISTplus fellowship programme.
G.Y. and B.H. acknowledge a grant from the Simons Foundation (662960, BH).
article_number: A21
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Elena
full_name: Marensi, Elena
id: 0BE7553A-1004-11EA-B805-18983DDC885E
last_name: Marensi
orcid: 0000-0001-7173-4923
- first_name: Gökhan
full_name: Yalniz, Gökhan
id: 66E74FA2-D8BF-11E9-8249-8DE2E5697425
last_name: Yalniz
orcid: 0000-0002-8490-9312
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Marensi E, Yalniz G, Hof B. Dynamics and proliferation of turbulent stripes
in plane-Poiseuille and plane-Couette flows. Journal of Fluid Mechanics.
2023;974. doi:10.1017/jfm.2023.780
apa: Marensi, E., Yalniz, G., & Hof, B. (2023). Dynamics and proliferation of
turbulent stripes in plane-Poiseuille and plane-Couette flows. Journal of Fluid
Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2023.780
chicago: Marensi, Elena, Gökhan Yalniz, and Björn Hof. “Dynamics and Proliferation
of Turbulent Stripes in Plane-Poiseuille and Plane-Couette Flows.” Journal
of Fluid Mechanics. Cambridge University Press, 2023. https://doi.org/10.1017/jfm.2023.780.
ieee: E. Marensi, G. Yalniz, and B. Hof, “Dynamics and proliferation of turbulent
stripes in plane-Poiseuille and plane-Couette flows,” Journal of Fluid Mechanics,
vol. 974. Cambridge University Press, 2023.
ista: Marensi E, Yalniz G, Hof B. 2023. Dynamics and proliferation of turbulent
stripes in plane-Poiseuille and plane-Couette flows. Journal of Fluid Mechanics.
974, A21.
mla: Marensi, Elena, et al. “Dynamics and Proliferation of Turbulent Stripes in
Plane-Poiseuille and Plane-Couette Flows.” Journal of Fluid Mechanics,
vol. 974, A21, Cambridge University Press, 2023, doi:10.1017/jfm.2023.780.
short: E. Marensi, G. Yalniz, B. Hof, Journal of Fluid Mechanics 974 (2023).
corr_author: '1'
date_created: 2023-10-30T09:32:28Z
date_published: 2023-11-10T00:00:00Z
date_updated: 2026-09-02T08:16:31Z
day: '10'
ddc:
- '530'
department:
- _id: GradSch
- _id: BjHo
doi: 10.1017/jfm.2023.780
external_id:
arxiv:
- '2212.12406'
isi:
- '001088363700001'
file:
- access_level: open_access
checksum: 17c64c1fb0d5f73252364bf98b0b9e1a
content_type: application/pdf
creator: dernst
date_created: 2024-02-15T09:05:21Z
date_updated: 2024-02-15T09:05:21Z
file_id: '14996'
file_name: 2023_JourFluidMechanics_Marensi.pdf
file_size: 2804641
relation: main_file
success: 1
file_date_updated: 2024-02-15T09:05:21Z
fulldoi: https://doi.org/10.1017/jfm.2023.780
has_accepted_license: '1'
intvolume: ' 974'
isi: 1
keyword:
- turbulence
- transition to turbulence
- patterns
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 238598C6-32DE-11EA-91FC-C7463DDC885E
grant_number: '662960'
name: Revisiting the Turbulence Problem Using Statistical Mechanics
publication: Journal of Fluid Mechanics
publication_identifier:
eissn:
- 1469-7645
issn:
- 0022-1120
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
related_material:
record:
- id: '19684'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Dynamics and proliferation of turbulent stripes in plane-Poiseuille and plane-Couette
flows
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 974
year: '2023'
...
---
_id: '12105'
abstract:
- lang: eng
text: Data-driven dimensionality reduction methods such as proper orthogonal decomposition
and dynamic mode decomposition have proven to be useful for exploring complex
phenomena within fluid dynamics and beyond. A well-known challenge for these techniques
is posed by the continuous symmetries, e.g. translations and rotations, of the
system under consideration, as drifts in the data dominate the modal expansions
without providing an insight into the dynamics of the problem. In the present
study, we address this issue for fluid flows in rectangular channels by formulating
a continuous symmetry reduction method that eliminates the translations in the
streamwise and spanwise directions simultaneously. We demonstrate our method by
computing the symmetry-reduced dynamic mode decomposition (SRDMD) of sliding windows
of data obtained from the transitional plane-Couette and turbulent plane-Poiseuille
flow simulations. In the former setting, SRDMD captures the dynamics in the vicinity
of the invariant solutions with translation symmetries, i.e. travelling waves
and relative periodic orbits, whereas in the latter, our calculations reveal episodes
of turbulent time evolution that can be approximated by a low-dimensional linear
expansion.
acknowledgement: "E.M. acknowledges funding from the ISTplus fellowship programme.
G.Y. and B.H. acknowledge\r\na grant from the Simons Foundation (662960, BH)."
article_number: A10
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Elena
full_name: Marensi, Elena
id: 0BE7553A-1004-11EA-B805-18983DDC885E
last_name: Marensi
orcid: 0000-0001-7173-4923
- first_name: Gökhan
full_name: Yalniz, Gökhan
id: 66E74FA2-D8BF-11E9-8249-8DE2E5697425
last_name: Yalniz
orcid: 0000-0002-8490-9312
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
- first_name: Nazmi B
full_name: Budanur, Nazmi B
id: 3EA1010E-F248-11E8-B48F-1D18A9856A87
last_name: Budanur
orcid: 0000-0003-0423-5010
citation:
ama: Marensi E, Yalniz G, Hof B, Budanur NB. Symmetry-reduced dynamic mode decomposition
of near-wall turbulence. Journal of Fluid Mechanics. 2023;954. doi:10.1017/jfm.2022.1001
apa: Marensi, E., Yalniz, G., Hof, B., & Budanur, N. B. (2023). Symmetry-reduced
dynamic mode decomposition of near-wall turbulence. Journal of Fluid Mechanics.
Cambridge University Press. https://doi.org/10.1017/jfm.2022.1001
chicago: Marensi, Elena, Gökhan Yalniz, Björn Hof, and Nazmi B Budanur. “Symmetry-Reduced
Dynamic Mode Decomposition of near-Wall Turbulence.” Journal of Fluid Mechanics.
Cambridge University Press, 2023. https://doi.org/10.1017/jfm.2022.1001.
ieee: E. Marensi, G. Yalniz, B. Hof, and N. B. Budanur, “Symmetry-reduced dynamic
mode decomposition of near-wall turbulence,” Journal of Fluid Mechanics,
vol. 954. Cambridge University Press, 2023.
ista: Marensi E, Yalniz G, Hof B, Budanur NB. 2023. Symmetry-reduced dynamic mode
decomposition of near-wall turbulence. Journal of Fluid Mechanics. 954, A10.
mla: Marensi, Elena, et al. “Symmetry-Reduced Dynamic Mode Decomposition of near-Wall
Turbulence.” Journal of Fluid Mechanics, vol. 954, A10, Cambridge University
Press, 2023, doi:10.1017/jfm.2022.1001.
short: E. Marensi, G. Yalniz, B. Hof, N.B. Budanur, Journal of Fluid Mechanics 954
(2023).
corr_author: '1'
date_created: 2023-01-08T23:00:53Z
date_published: 2023-01-10T00:00:00Z
date_updated: 2026-09-02T08:16:31Z
day: '10'
ddc:
- '530'
department:
- _id: BjHo
doi: 10.1017/jfm.2022.1001
external_id:
arxiv:
- '2101.07516'
isi:
- '000903336600001'
file:
- access_level: open_access
checksum: 9224f987caefe5dd85a70814d3cce65c
content_type: application/pdf
creator: dernst
date_created: 2023-02-02T12:34:54Z
date_updated: 2023-02-02T12:34:54Z
file_id: '12489'
file_name: 2023_JourFluidMechanics_Marensi.pdf
file_size: 1931647
relation: main_file
success: 1
file_date_updated: 2023-02-02T12:34:54Z
fulldoi: https://doi.org/10.1017/jfm.2022.1001
has_accepted_license: '1'
intvolume: ' 954'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 238598C6-32DE-11EA-91FC-C7463DDC885E
grant_number: '662960'
name: Revisiting the Turbulence Problem Using Statistical Mechanics
publication: Journal of Fluid Mechanics
publication_identifier:
eissn:
- 1469-7645
issn:
- 0022-1120
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
related_material:
record:
- id: '19684'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Symmetry-reduced dynamic mode decomposition of near-wall turbulence
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 954
year: '2023'
...
---
_id: '13274'
abstract:
- lang: eng
text: Viscous flows through pipes and channels are steady and ordered until, with
increasing velocity, the laminar motion catastrophically breaks down and gives
way to turbulence. How this apparently discontinuous change from low- to high-dimensional
motion can be rationalized within the framework of the Navier-Stokes equations
is not well understood. Exploiting geometrical properties of transitional channel
flow we trace turbulence to far lower Reynolds numbers (Re) than previously possible
and identify the complete path that reversibly links fully turbulent motion to
an invariant solution. This precursor of turbulence destabilizes rapidly with
Re, and the accompanying explosive increase in attractor dimension effectively
marks the transition between deterministic and de facto stochastic dynamics.
acknowledgement: We thank Baofang Song as well as the developers of Channelflow for
sharing their numerical codes, and Mukund Vasudevan and Holger Kantz for fruitful
discussions. This work was supported by a grant from the Simons Foundation (662960,
B. H.).
article_number: '034002'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Chaitanya S
full_name: Paranjape, Chaitanya S
id: 3D85B7C4-F248-11E8-B48F-1D18A9856A87
last_name: Paranjape
- first_name: Gökhan
full_name: Yalniz, Gökhan
id: 66E74FA2-D8BF-11E9-8249-8DE2E5697425
last_name: Yalniz
orcid: 0000-0002-8490-9312
- first_name: Yohann
full_name: Duguet, Yohann
last_name: Duguet
- first_name: Nazmi B
full_name: Budanur, Nazmi B
id: 3EA1010E-F248-11E8-B48F-1D18A9856A87
last_name: Budanur
orcid: 0000-0003-0423-5010
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Paranjape CS, Yalniz G, Duguet Y, Budanur NB, Hof B. Direct path from turbulence
to time-periodic solutions. Physical Review Letters. 2023;131(3). doi:10.1103/physrevlett.131.034002
apa: Paranjape, C. S., Yalniz, G., Duguet, Y., Budanur, N. B., & Hof, B. (2023).
Direct path from turbulence to time-periodic solutions. Physical Review Letters.
American Physical Society. https://doi.org/10.1103/physrevlett.131.034002
chicago: Paranjape, Chaitanya S, Gökhan Yalniz, Yohann Duguet, Nazmi B Budanur,
and Björn Hof. “Direct Path from Turbulence to Time-Periodic Solutions.” Physical
Review Letters. American Physical Society, 2023. https://doi.org/10.1103/physrevlett.131.034002.
ieee: C. S. Paranjape, G. Yalniz, Y. Duguet, N. B. Budanur, and B. Hof, “Direct
path from turbulence to time-periodic solutions,” Physical Review Letters,
vol. 131, no. 3. American Physical Society, 2023.
ista: Paranjape CS, Yalniz G, Duguet Y, Budanur NB, Hof B. 2023. Direct path from
turbulence to time-periodic solutions. Physical Review Letters. 131(3), 034002.
mla: Paranjape, Chaitanya S., et al. “Direct Path from Turbulence to Time-Periodic
Solutions.” Physical Review Letters, vol. 131, no. 3, 034002, American
Physical Society, 2023, doi:10.1103/physrevlett.131.034002.
short: C.S. Paranjape, G. Yalniz, Y. Duguet, N.B. Budanur, B. Hof, Physical Review
Letters 131 (2023).
corr_author: '1'
date_created: 2023-07-24T09:43:59Z
date_published: 2023-07-21T00:00:00Z
date_updated: 2026-09-02T08:16:31Z
day: '21'
department:
- _id: GradSch
- _id: BjHo
doi: 10.1103/physrevlett.131.034002
external_id:
arxiv:
- '2306.05098'
isi:
- '001052929900004'
pmid:
- '37540883'
fulldoi: https://doi.org/10.1103/physrevlett.131.034002
intvolume: ' 131'
isi: 1
issue: '3'
keyword:
- General Physics and Astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2306.05098
month: '07'
oa: 1
oa_version: Preprint
pmid: 1
project:
- _id: 238598C6-32DE-11EA-91FC-C7463DDC885E
grant_number: '662960'
name: Revisiting the Turbulence Problem Using Statistical Mechanics
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
record:
- id: '19684'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Direct path from turbulence to time-periodic solutions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 131
year: '2023'
...
---
_id: '12421'
abstract:
- lang: eng
text: The actin cytoskeleton plays a key role in cell migration and cellular morphodynamics
in most eukaryotes. The ability of the actin cytoskeleton to assemble and disassemble
in a spatiotemporally controlled manner allows it to form higher-order structures,
which can generate forces required for a cell to explore and navigate through
its environment. It is regulated not only via a complex synergistic and competitive
interplay between actin-binding proteins (ABP), but also by filament biochemistry
and filament geometry. The lack of structural insights into how geometry and ABPs
regulate the actin cytoskeleton limits our understanding of the molecular mechanisms
that define actin cytoskeleton remodeling and, in turn, impact emerging cell migration
characteristics. With the advent of cryo-electron microscopy (cryo-EM) and advanced
computational methods, it is now possible to define these molecular mechanisms
involving actin and its interactors at both atomic and ultra-structural levels
in vitro and in cellulo. In this review, we will provide an overview of the available
cryo-EM methods, applicable to further our understanding of the actin cytoskeleton,
specifically in the context of cell migration. We will discuss how these methods
have been employed to elucidate ABP- and geometry-defined regulatory mechanisms
in initiating, maintaining, and disassembling cellular actin networks in migratory
protrusions.
acknowledgement: 'We apologize for not being able to mention and cite additional excellent
work that would have fit the scope of this review, due to space restraints. We thank
Jesse Hansen for comments on the manuscript. We acknowledge support from the Austrian
Science Fund (FWF): P33367 and the Institute of Science and Technology Austria.'
article_processing_charge: No
article_type: original
author:
- first_name: Florian
full_name: Fäßler, Florian
id: 404F5528-F248-11E8-B48F-1D18A9856A87
last_name: Fäßler
orcid: 0000-0001-7149-769X
- first_name: Manjunath
full_name: Javoor, Manjunath
id: 305ab18b-dc7d-11ea-9b2f-b58195228ea2
last_name: Javoor
orcid: 0000-0003-2311-2112
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
citation:
ama: Fäßler F, Javoor M, Schur FK. Deciphering the molecular mechanisms of actin
cytoskeleton regulation in cell migration using cryo-EM. Biochemical Society
Transactions. 2023;51(1):87-99. doi:10.1042/bst20220221
apa: Fäßler, F., Javoor, M., & Schur, F. K. (2023). Deciphering the molecular
mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM. Biochemical
Society Transactions. Portland Press. https://doi.org/10.1042/bst20220221
chicago: Fäßler, Florian, Manjunath Javoor, and Florian KM Schur. “Deciphering the
Molecular Mechanisms of Actin Cytoskeleton Regulation in Cell Migration Using
Cryo-EM.” Biochemical Society Transactions. Portland Press, 2023. https://doi.org/10.1042/bst20220221.
ieee: F. Fäßler, M. Javoor, and F. K. Schur, “Deciphering the molecular mechanisms
of actin cytoskeleton regulation in cell migration using cryo-EM,” Biochemical
Society Transactions, vol. 51, no. 1. Portland Press, pp. 87–99, 2023.
ista: Fäßler F, Javoor M, Schur FK. 2023. Deciphering the molecular mechanisms of
actin cytoskeleton regulation in cell migration using cryo-EM. Biochemical Society
Transactions. 51(1), 87–99.
mla: Fäßler, Florian, et al. “Deciphering the Molecular Mechanisms of Actin Cytoskeleton
Regulation in Cell Migration Using Cryo-EM.” Biochemical Society Transactions,
vol. 51, no. 1, Portland Press, 2023, pp. 87–99, doi:10.1042/bst20220221.
short: F. Fäßler, M. Javoor, F.K. Schur, Biochemical Society Transactions 51 (2023)
87–99.
corr_author: '1'
date_created: 2023-01-27T10:08:19Z
date_published: 2023-02-01T00:00:00Z
date_updated: 2026-09-03T09:36:24Z
day: '01'
ddc:
- '570'
department:
- _id: FlSc
doi: 10.1042/bst20220221
external_id:
isi:
- '000926043100001'
pmid:
- '36695514'
file:
- access_level: open_access
checksum: 4e7069845e3dad22bb44fb71ec624c60
content_type: application/pdf
creator: dernst
date_created: 2023-03-16T07:58:16Z
date_updated: 2023-03-16T07:58:16Z
file_id: '12728'
file_name: 2023_BioChemicalSocietyTransactions_Faessler.pdf
file_size: 10045006
relation: main_file
success: 1
file_date_updated: 2023-03-16T07:58:16Z
fulldoi: https://doi.org/10.1042/bst20220221
has_accepted_license: '1'
intvolume: ' 51'
isi: 1
issue: '1'
keyword:
- Biochemistry
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 87-99
pmid: 1
project:
- _id: 9B954C5C-BA93-11EA-9121-9846C619BF3A
grant_number: P33367
name: Structure and isoform diversity of the Arp2/3 complex
publication: Biochemical Society Transactions
publication_identifier:
eissn:
- 1470-8752
issn:
- 0300-5127
publication_status: published
publisher: Portland Press
quality_controlled: '1'
related_material:
record:
- id: '22744'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell
migration using cryo-EM
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 51
year: '2023'
...
---
_id: '14692'
abstract:
- lang: eng
text: "The generic-group model (GGM) aims to capture algorithms working over groups
of prime order that only rely on the group operation, but do not exploit any additional
structure given by the concrete implementation of the group. In it, it is possible
to prove information-theoretic lower bounds on the hardness of problems like the
discrete logarithm (DL) or computational Diffie-Hellman (CDH). Thus, since its
introduction, it has served as a valuable tool to assess the concrete security
provided by cryptographic schemes based on such problems. A work on the related
algebraic-group model (AGM) introduced a method, used by many subsequent works,
to adapt GGM lower bounds for one problem to another, by means of conceptually
simple reductions.\r\nIn this work, we propose an alternative approach to extend
GGM bounds from one problem to another. Following an idea by Yun [EC15], we show
that, in the GGM, the security of a large class of problems can be reduced to
that of geometric search-problems. By reducing the security of the resulting geometric-search
problems to variants of the search-by-hypersurface problem, for which information
theoretic lower bounds exist, we give alternative proofs of several results that
used the AGM approach.\r\nThe main advantage of our approach is that our reduction
from geometric search-problems works, as well, for the GGM with preprocessing
(more precisely the bit-fixing GGM introduced by Coretti, Dodis and Guo [Crypto18]).
As a consequence, this opens up the possibility of transferring preprocessing
GGM bounds from one problem to another, also by means of simple reductions. Concretely,
we prove novel preprocessing bounds on the hardness of the d-strong discrete logarithm,
the d-strong Diffie-Hellman inversion, and multi-instance CDH problems, as well
as a large class of Uber assumptions. Additionally, our approach applies to Shoup’s
GGM without additional restrictions on the query behavior of the adversary, while
the recent works of Zhang, Zhou, and Katz [AC22] and Zhandry [Crypto22] highlight
that this is not the case for the AGM approach."
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Benedikt
full_name: Auerbach, Benedikt
id: D33D2B18-E445-11E9-ABB7-15F4E5697425
last_name: Auerbach
orcid: 0000-0002-7553-6606
- first_name: Charlotte
full_name: Hoffmann, Charlotte
id: 0f78d746-dc7d-11ea-9b2f-83f92091afe7
last_name: Hoffmann
orcid: 0000-0003-2027-5549
- first_name: Guillermo
full_name: Pascual Perez, Guillermo
id: 2D7ABD02-F248-11E8-B48F-1D18A9856A87
last_name: Pascual Perez
orcid: 0000-0001-8630-415X
citation:
ama: 'Auerbach B, Hoffmann C, Pascual Perez G. Generic-group lower bounds via reductions
between geometric-search problems: With and without preprocessing. In: 21st
International Conference on Theory of Cryptography. Vol 14371. Springer Nature;
2023:301-330. doi:10.1007/978-3-031-48621-0_11'
apa: 'Auerbach, B., Hoffmann, C., & Pascual Perez, G. (2023). Generic-group
lower bounds via reductions between geometric-search problems: With and without
preprocessing. In 21st International Conference on Theory of Cryptography
(Vol. 14371, pp. 301–330). Springer Nature. https://doi.org/10.1007/978-3-031-48621-0_11'
chicago: 'Auerbach, Benedikt, Charlotte Hoffmann, and Guillermo Pascual Perez. “Generic-Group
Lower Bounds via Reductions between Geometric-Search Problems: With and without
Preprocessing.” In 21st International Conference on Theory of Cryptography,
14371:301–30. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-48621-0_11.'
ieee: 'B. Auerbach, C. Hoffmann, and G. Pascual Perez, “Generic-group lower bounds
via reductions between geometric-search problems: With and without preprocessing,”
in 21st International Conference on Theory of Cryptography, 2023, vol.
14371, pp. 301–330.'
ista: 'Auerbach B, Hoffmann C, Pascual Perez G. 2023. Generic-group lower bounds
via reductions between geometric-search problems: With and without preprocessing.
21st International Conference on Theory of Cryptography. , LNCS, vol. 14371, 301–330.'
mla: 'Auerbach, Benedikt, et al. “Generic-Group Lower Bounds via Reductions between
Geometric-Search Problems: With and without Preprocessing.” 21st International
Conference on Theory of Cryptography, vol. 14371, Springer Nature, 2023, pp.
301–30, doi:10.1007/978-3-031-48621-0_11.'
short: B. Auerbach, C. Hoffmann, G. Pascual Perez, in:, 21st International Conference
on Theory of Cryptography, Springer Nature, 2023, pp. 301–330.
corr_author: '1'
date_created: 2023-12-17T23:00:54Z
date_published: 2023-11-27T00:00:00Z
date_updated: 2026-09-07T11:37:53Z
day: '27'
department:
- _id: KrPi
doi: 10.1007/978-3-031-48621-0_11
external_id:
isi:
- '001160724400011'
fulldoi: https://doi.org/10.1007/978-3-031-48621-0_11
intvolume: ' 14371'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2023/808
month: '11'
oa: 1
oa_version: Preprint
page: 301-330
publication: 21st International Conference on Theory of Cryptography
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031486203'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Generic-group lower bounds via reductions between geometric-search problems:
With and without preprocessing'
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 14371
year: '2023'
...
---
_id: '14691'
abstract:
- lang: eng
text: "Continuous Group-Key Agreement (CGKA) allows a group of users to maintain
a shared key. It is the fundamental cryptographic primitive underlying group messaging
schemes and related protocols, most notably TreeKEM, the underlying key agreement
protocol of the Messaging Layer Security (MLS) protocol, a standard for group
messaging by the IETF. CKGA works in an asynchronous setting where parties only
occasionally must come online, and their messages are relayed by an untrusted
server. The most expensive operation provided by CKGA is that which allows for
a user to refresh their key material in order to achieve forward secrecy (old
messages are secure when a user is compromised) and post-compromise security (users
can heal from compromise). One caveat of early CGKA protocols is that these update
operations had to be performed sequentially, with any user wanting to update their
key material having had to receive and process all previous updates. Late versions
of TreeKEM do allow for concurrent updates at the cost of a communication overhead
per update message that is linear in the number of updating parties. This was
shown to be indeed necessary when achieving PCS in just two rounds of communication
by [Bienstock et al. TCC’20].\r\nThe recently proposed protocol CoCoA [Alwen et
al. Eurocrypt’22], however, shows that this overhead can be reduced if PCS requirements
are relaxed, and only a logarithmic number of rounds is required. The natural
question, thus, is whether CoCoA is optimal in this setting.\r\nIn this work we
answer this question, providing a lower bound on the cost (concretely, the amount
of data to be uploaded to the server) for CGKA protocols that heal in an arbitrary
k number of rounds, that shows that CoCoA is very close to optimal. Additionally,
we extend CoCoA to heal in an arbitrary number of rounds, and propose a modification
of it, with a reduced communication cost for certain k.\r\nWe prove our bound
in a combinatorial setting where the state of the protocol progresses in rounds,
and the state of the protocol in each round is captured by a set system, each
set specifying a set of users who share a secret key. We show this combinatorial
model is equivalent to a symbolic model capturing building blocks including PRFs
and public-key encryption, related to the one used by Bienstock et al.\r\nOur
lower bound is of order k•n1+1/(k-1)/log(k), where 2≤k≤log(n) is the number of
updates per user the protocol requires to heal. This generalizes the n2 bound
for k=2 from Bienstock et al.. This bound almost matches the k⋅n1+2/(k-1) or k2⋅n1+1/(k-1)
efficiency we get for the variants of the CoCoA protocol also introduced in this
paper."
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Benedikt
full_name: Auerbach, Benedikt
id: D33D2B18-E445-11E9-ABB7-15F4E5697425
last_name: Auerbach
orcid: 0000-0002-7553-6606
- first_name: Miguel
full_name: Cueto Noval, Miguel
id: ffc563a3-f6e0-11ea-865d-e3cce03d17cc
last_name: Cueto Noval
orcid: 0000-0002-2505-4246
- first_name: Guillermo
full_name: Pascual Perez, Guillermo
id: 2D7ABD02-F248-11E8-B48F-1D18A9856A87
last_name: Pascual Perez
orcid: 0000-0001-8630-415X
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Auerbach B, Cueto Noval M, Pascual Perez G, Pietrzak KZ. On the cost of post-compromise
security in concurrent Continuous Group-Key Agreement. In: 21st International
Conference on Theory of Cryptography. Vol 14371. Springer Nature; 2023:271-300.
doi:10.1007/978-3-031-48621-0_10'
apa: 'Auerbach, B., Cueto Noval, M., Pascual Perez, G., & Pietrzak, K. Z. (2023).
On the cost of post-compromise security in concurrent Continuous Group-Key Agreement.
In 21st International Conference on Theory of Cryptography (Vol. 14371,
pp. 271–300). Taipei, Taiwan: Springer Nature. https://doi.org/10.1007/978-3-031-48621-0_10'
chicago: Auerbach, Benedikt, Miguel Cueto Noval, Guillermo Pascual Perez, and Krzysztof
Z Pietrzak. “On the Cost of Post-Compromise Security in Concurrent Continuous
Group-Key Agreement.” In 21st International Conference on Theory of Cryptography,
14371:271–300. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-48621-0_10.
ieee: B. Auerbach, M. Cueto Noval, G. Pascual Perez, and K. Z. Pietrzak, “On the cost
of post-compromise security in concurrent Continuous Group-Key Agreement,” in
21st International Conference on Theory of Cryptography, Taipei, Taiwan,
2023, vol. 14371, pp. 271–300.
ista: 'Auerbach B, Cueto Noval M, Pascual Perez G, Pietrzak KZ. 2023. On the cost
of post-compromise security in concurrent Continuous Group-Key Agreement. 21st
International Conference on Theory of Cryptography. TCC: Theory of Cryptography,
LNCS, vol. 14371, 271–300.'
mla: Auerbach, Benedikt, et al. “On the Cost of Post-Compromise Security in Concurrent
Continuous Group-Key Agreement.” 21st International Conference on Theory of
Cryptography, vol. 14371, Springer Nature, 2023, pp. 271–300, doi:10.1007/978-3-031-48621-0_10.
short: B. Auerbach, M. Cueto Noval, G. Pascual Perez, K.Z. Pietrzak, in:, 21st International
Conference on Theory of Cryptography, Springer Nature, 2023, pp. 271–300.
conference:
end_date: 2023-12-02
location: Taipei, Taiwan
name: 'TCC: Theory of Cryptography'
start_date: 2023-11-29
corr_author: '1'
date_created: 2023-12-17T23:00:53Z
date_published: 2023-11-27T00:00:00Z
date_updated: 2026-09-07T11:37:56Z
day: '27'
department:
- _id: KrPi
doi: 10.1007/978-3-031-48621-0_10
external_id:
isi:
- '001160724400010'
fulldoi: https://doi.org/10.1007/978-3-031-48621-0_10
intvolume: ' 14371'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2023/1123
month: '11'
oa: 1
oa_version: Preprint
page: 271-300
publication: 21st International Conference on Theory of Cryptography
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031486203'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '22664'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: On the cost of post-compromise security in concurrent Continuous Group-Key
Agreement
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 14371
year: '2023'
...
---
_id: '12787'
abstract:
- lang: eng
text: "Populations evolve in spatially heterogeneous environments. While a certain
trait might bring a fitness advantage in some patch of the environment, a different
trait might be advantageous in another patch. Here, we study the Moran birth–death
process with two types of individuals in a population stretched across two patches
of size N, each patch favouring one of the two types. We show that the long-term
fate of such populations crucially depends on the migration rate μ\r\n between
the patches. To classify the possible fates, we use the distinction between polynomial
(short) and exponential (long) timescales. We show that when μ is high then one
of the two types fixates on the whole population after a number of steps that
is only polynomial in N. By contrast, when μ is low then each type holds majority
in the patch where it is favoured for a number of steps that is at least exponential
in N. Moreover, we precisely identify the threshold migration rate μ⋆ that separates
those two scenarios, thereby exactly delineating the situations that support long-term
coexistence of the two types. We also discuss the case of various cycle graphs
and we present computer simulations that perfectly match our analytical results."
acknowledgement: J.S. and K.C. acknowledge support from the ERC CoG 863818 (ForM-SMArt)
article_number: '20220685'
article_processing_charge: No
article_type: original
author:
- first_name: Jakub
full_name: Svoboda, Jakub
id: 130759D2-D7DD-11E9-87D2-DE0DE6697425
last_name: Svoboda
orcid: 0000-0002-1419-3267
- first_name: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
- first_name: Kamran
full_name: Kaveh, Kamran
last_name: Kaveh
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: 'Svoboda J, Tkadlec J, Kaveh K, Chatterjee K. Coexistence times in the Moran
process with environmental heterogeneity. Proceedings of the Royal Society
A: Mathematical, Physical and Engineering Sciences. 2023;479(2271). doi:10.1098/rspa.2022.0685'
apa: 'Svoboda, J., Tkadlec, J., Kaveh, K., & Chatterjee, K. (2023). Coexistence
times in the Moran process with environmental heterogeneity. Proceedings of
the Royal Society A: Mathematical, Physical and Engineering Sciences. The
Royal Society. https://doi.org/10.1098/rspa.2022.0685'
chicago: 'Svoboda, Jakub, Josef Tkadlec, Kamran Kaveh, and Krishnendu Chatterjee.
“Coexistence Times in the Moran Process with Environmental Heterogeneity.” Proceedings
of the Royal Society A: Mathematical, Physical and Engineering Sciences. The
Royal Society, 2023. https://doi.org/10.1098/rspa.2022.0685.'
ieee: 'J. Svoboda, J. Tkadlec, K. Kaveh, and K. Chatterjee, “Coexistence times in
the Moran process with environmental heterogeneity,” Proceedings of the Royal
Society A: Mathematical, Physical and Engineering Sciences, vol. 479, no.
2271. The Royal Society, 2023.'
ista: 'Svoboda J, Tkadlec J, Kaveh K, Chatterjee K. 2023. Coexistence times in the
Moran process with environmental heterogeneity. Proceedings of the Royal Society
A: Mathematical, Physical and Engineering Sciences. 479(2271), 20220685.'
mla: 'Svoboda, Jakub, et al. “Coexistence Times in the Moran Process with Environmental
Heterogeneity.” Proceedings of the Royal Society A: Mathematical, Physical
and Engineering Sciences, vol. 479, no. 2271, 20220685, The Royal Society,
2023, doi:10.1098/rspa.2022.0685.'
short: 'J. Svoboda, J. Tkadlec, K. Kaveh, K. Chatterjee, Proceedings of the Royal
Society A: Mathematical, Physical and Engineering Sciences 479 (2023).'
date_created: 2023-04-02T22:01:09Z
date_published: 2023-03-29T00:00:00Z
date_updated: 2026-09-16T06:59:32Z
day: '29'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1098/rspa.2022.0685
ec_funded: 1
external_id:
isi:
- '000957125500002'
file:
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checksum: 13953d349fbefcb5d21ccc6b303297eb
content_type: application/pdf
creator: dernst
date_created: 2023-04-03T06:25:29Z
date_updated: 2023-04-03T06:25:29Z
file_id: '12796'
file_name: 2023_ProceedingsRoyalSocietyA_Svoboda.pdf
file_size: 827784
relation: main_file
success: 1
file_date_updated: 2023-04-03T06:25:29Z
fulldoi: https://doi.org/10.1098/rspa.2022.0685
has_accepted_license: '1'
intvolume: ' 479'
isi: 1
issue: '2271'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: 'Proceedings of the Royal Society A: Mathematical, Physical and Engineering
Sciences'
publication_identifier:
eissn:
- 1471-2946
issn:
- 1364-5021
publication_status: published
publisher: The Royal Society
quality_controlled: '1'
related_material:
link:
- relation: research_data
url: https://doi.org/10.6084/m9.figshare.21261771.v1
record:
- id: '20138'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Coexistence times in the Moran process with environmental heterogeneity
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 479
year: '2023'
...
---
OA_place: publisher
OA_type: gold
_id: '14954'
abstract:
- lang: eng
text: "When domain knowledge is limited and experimentation is restricted by ethical,\r\nfinancial,
or time constraints, practitioners turn to observational causal discovery\r\nmethods
to recover the causal structure, exploiting the statistical properties of their\r\ndata.
Because causal discovery without further assumptions is an ill-posed problem,\r\neach
algorithm comes with its own set of usually untestable assumptions, some\r\nof
which are hard to meet in real datasets. Motivated by these considerations, this\r\npaper
extensively benchmarks the empirical performance of recent causal discovery\r\nmethods
on observational iid data generated under different background conditions,\r\nallowing
for violations of the critical assumptions required by each selected approach.
Our experimental findings show that score matching-based methods demonstrate surprising
performance in the false positive and false negative rate of the\r\ninferred graph
in these challenging scenarios, and we provide theoretical insights\r\ninto their
performance. This work is also the first effort to benchmark the stability of\r\ncausal
discovery algorithms with respect to the values of their hyperparameters. Finally,
we hope this paper will set a new standard for the evaluation of causal discovery
methods and can serve as an accessible entry point for practitioners interested\r\nin
the field, highlighting the empirical implications of different algorithm choices."
acknowledgement: "We thank Kun Zhang and Carl-Johann Simon-Gabriel for the insightful
discussions. This work\r\nhas been supported by AFOSR, grant n. FA8655-20-1-7035.
FM is supported by Programma\r\nOperativo Nazionale ricerca e innovazione 2014-2020.
FM partially contributed to this work during an internship at Amazon Web Services
with FL. FL partially contributed while at AWS."
alternative_title:
- Advances in Neural Information Processing Systems
article_processing_charge: No
arxiv: 1
author:
- first_name: Francesco
full_name: Montagna, Francesco
last_name: Montagna
- first_name: Atalanti A.
full_name: Mastakouri, Atalanti A.
last_name: Mastakouri
- first_name: Elias
full_name: Eulig, Elias
last_name: Eulig
- first_name: Nicoletta
full_name: Noceti, Nicoletta
last_name: Noceti
- first_name: Lorenzo
full_name: Rosasco, Lorenzo
last_name: Rosasco
- first_name: Dominik
full_name: Janzing, Dominik
last_name: Janzing
- first_name: Bryon
full_name: Aragam, Bryon
last_name: Aragam
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
citation:
ama: 'Montagna F, Mastakouri AA, Eulig E, et al. Assumption violations in causal
discovery and the robustness of score matching. In: 37th Conference on Neural
Information Processing Systems. Vol 36. Neural Information Processing Systems
Foundation; 2023. doi:10.52202/075280-2050'
apa: 'Montagna, F., Mastakouri, A. A., Eulig, E., Noceti, N., Rosasco, L., Janzing,
D., … Locatello, F. (2023). Assumption violations in causal discovery and the
robustness of score matching. In 37th Conference on Neural Information Processing
Systems (Vol. 36). New Orleans, LA, United States: Neural Information Processing
Systems Foundation. https://doi.org/10.52202/075280-2050'
chicago: Montagna, Francesco, Atalanti A. Mastakouri, Elias Eulig, Nicoletta Noceti,
Lorenzo Rosasco, Dominik Janzing, Bryon Aragam, and Francesco Locatello. “Assumption
Violations in Causal Discovery and the Robustness of Score Matching.” In 37th
Conference on Neural Information Processing Systems, Vol. 36. Neural Information
Processing Systems Foundation, 2023. https://doi.org/10.52202/075280-2050.
ieee: F. Montagna et al., “Assumption violations in causal discovery and
the robustness of score matching,” in 37th Conference on Neural Information
Processing Systems, New Orleans, LA, United States, 2023, vol. 36.
ista: 'Montagna F, Mastakouri AA, Eulig E, Noceti N, Rosasco L, Janzing D, Aragam
B, Locatello F. 2023. Assumption violations in causal discovery and the robustness
of score matching. 37th Conference on Neural Information Processing Systems. NeurIPS:
Neural Information Processing Systems, Advances in Neural Information Processing
Systems, vol. 36.'
mla: Montagna, Francesco, et al. “Assumption Violations in Causal Discovery and
the Robustness of Score Matching.” 37th Conference on Neural Information Processing
Systems, vol. 36, Neural Information Processing Systems Foundation, 2023,
doi:10.52202/075280-2050.
short: F. Montagna, A.A. Mastakouri, E. Eulig, N. Noceti, L. Rosasco, D. Janzing,
B. Aragam, F. Locatello, in:, 37th Conference on Neural Information Processing
Systems, Neural Information Processing Systems Foundation, 2023.
conference:
end_date: 2023-12-16
location: New Orleans, LA, United States
name: 'NeurIPS: Neural Information Processing Systems'
start_date: 2023-12-12
das_tickbox: '0'
date_created: 2024-02-07T15:11:56Z
date_published: 2023-12-20T00:00:00Z
date_updated: 2026-09-17T12:59:55Z
day: '20'
ddc:
- '000'
department:
- _id: FrLo
doi: 10.52202/075280-2050
external_id:
arxiv:
- '2310.13387'
file:
- access_level: open_access
checksum: 71d38402b4edef4c084b39f3e2f04526
content_type: application/pdf
creator: dernst
date_created: 2026-08-13T07:49:38Z
date_updated: 2026-08-13T07:49:38Z
file_id: '22701'
file_name: 2023_Neurips_Montagna.pdf
file_size: 7640984
relation: main_file
success: 1
file_date_updated: 2026-08-13T07:49:38Z
fulldoi: https://doi.org/10.52202/075280-2050
has_accepted_license: '1'
intvolume: ' 36'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: 37th Conference on Neural Information Processing Systems
publication_identifier:
eissn:
- 1049-5258
publication_status: published
publisher: Neural Information Processing Systems Foundation
quality_controlled: '1'
researchdata_availability: no
status: public
supplementarymaterial: yes
title: Assumption violations in causal discovery and the robustness of score matching
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 36
year: '2023'
...
---
_id: '15023'
abstract:
- lang: eng
text: Reinforcement learning has shown promising results in learning neural network
policies for complicated control tasks. However, the lack of formal guarantees
about the behavior of such policies remains an impediment to their deployment.
We propose a novel method for learning a composition of neural network policies
in stochastic environments, along with a formal certificate which guarantees that
a specification over the policy's behavior is satisfied with the desired probability.
Unlike prior work on verifiable RL, our approach leverages the compositional nature
of logical specifications provided in SpectRL, to learn over graphs of probabilistic
reach-avoid specifications. The formal guarantees are provided by learning neural
network policies together with reach-avoid supermartingales (RASM) for the graph’s
sub-tasks and then composing them into a global policy. We also derive a tighter
lower bound compared to previous work on the probability of reach-avoidance implied
by a RASM, which is required to find a compositional policy with an acceptable
probabilistic threshold for complex tasks with multiple edge policies. We implement
a prototype of our approach and evaluate it on a Stochastic Nine Rooms environment.
acknowledgement: "This work was supported in part by the ERC-2020-AdG 101020093 (VAMOS)
and the ERC-2020-\r\nCoG 863818 (FoRM-SMArt)."
alternative_title:
- Advances in Neural Information Processing Systems
article_processing_charge: No
arxiv: 1
author:
- first_name: Dorde
full_name: Zikelic, Dorde
id: 294AA7A6-F248-11E8-B48F-1D18A9856A87
last_name: Zikelic
orcid: 0000-0002-4681-1699
- first_name: Mathias
full_name: Lechner, Mathias
id: 3DC22916-F248-11E8-B48F-1D18A9856A87
last_name: Lechner
- first_name: Abhinav
full_name: Verma, Abhinav
id: a235593c-d7fa-11eb-a0c5-b22ca3c66ee6
last_name: Verma
- 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
citation:
ama: 'Zikelic D, Lechner M, Verma A, Chatterjee K, Henzinger TA. Compositional policy
learning in stochastic control systems with formal guarantees. In: 37th Conference
on Neural Information Processing Systems. Neural Information Processing Systems
Foundation; 2023.'
apa: 'Zikelic, D., Lechner, M., Verma, A., Chatterjee, K., & Henzinger, T. A.
(2023). Compositional policy learning in stochastic control systems with formal
guarantees. In 37th Conference on Neural Information Processing Systems.
New Orleans, LA, United States: Neural Information Processing Systems Foundation.'
chicago: Zikelic, Dorde, Mathias Lechner, Abhinav Verma, Krishnendu Chatterjee,
and Thomas A Henzinger. “Compositional Policy Learning in Stochastic Control Systems
with Formal Guarantees.” In 37th Conference on Neural Information Processing
Systems. Neural Information Processing Systems Foundation, 2023.
ieee: D. Zikelic, M. Lechner, A. Verma, K. Chatterjee, and T. A. Henzinger, “Compositional
policy learning in stochastic control systems with formal guarantees,” in 37th
Conference on Neural Information Processing Systems, New Orleans, LA, United
States, 2023.
ista: 'Zikelic D, Lechner M, Verma A, Chatterjee K, Henzinger TA. 2023. Compositional
policy learning in stochastic control systems with formal guarantees. 37th Conference
on Neural Information Processing Systems. NeurIPS: Neural Information Processing
Systems, Advances in Neural Information Processing Systems, .'
mla: Zikelic, Dorde, et al. “Compositional Policy Learning in Stochastic Control
Systems with Formal Guarantees.” 37th Conference on Neural Information Processing
Systems, Neural Information Processing Systems Foundation, 2023.
short: D. Zikelic, M. Lechner, A. Verma, K. Chatterjee, T.A. Henzinger, in:, 37th
Conference on Neural Information Processing Systems, Neural Information Processing
Systems Foundation, 2023.
conference:
end_date: 2023-12-16
location: New Orleans, LA, United States
name: 'NeurIPS: Neural Information Processing Systems'
start_date: 2023-12-10
corr_author: '1'
das_tickbox: '1'
date_created: 2024-02-25T09:23:24Z
date_published: 2023-12-15T00:00:00Z
date_updated: 2026-09-17T12:59:12Z
day: '15'
ddc:
- '000'
department:
- _id: ToHe
- _id: KrCh
ec_funded: 1
external_id:
arxiv:
- '2312.01456'
file:
- access_level: open_access
checksum: 739c6d72506b778302d4e708723bf12c
content_type: application/pdf
creator: dernst
date_created: 2024-07-22T11:45:17Z
date_updated: 2024-07-22T11:45:17Z
file_id: '17309'
file_name: 2023_NeurIPS_Zikelic.pdf
file_size: 562008
relation: main_file
success: 1
file_date_updated: 2024-07-22T11:45:17Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: 37th Conference on Neural Information Processing Systems
publication_identifier:
eissn:
- 1049-5258
publication_status: published
publisher: Neural Information Processing Systems Foundation
quality_controlled: '1'
status: public
title: Compositional policy learning in stochastic control systems with formal guarantees
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
OA_place: publisher
OA_type: gold
_id: '14953'
abstract:
- lang: eng
text: "This paper provides statistical sample complexity bounds for score-matching
and\r\nits applications in causal discovery. We demonstrate that accurate estimation
of the\r\nscore function is achievable by training a standard deep ReLU neural
network using\r\nstochastic gradient descent. We establish bounds on the error
rate of recovering\r\ncausal relationships using the score-matching-based causal
discovery method of\r\nRolland et al. [2022], assuming a sufficiently good estimation
of the score function.\r\nFinally, we analyze the upper bound of score-matching
estimation within the scorebased generative modeling, which has been applied for
causal discovery but is also\r\nof independent interest within the domain of generative
models.y"
acknowledgement: "We are thankful to the reviewers for providing constructive feedback
and Kun Zhang and Dominik\r\nJanzing for helpful discussion on the special case
of deterministic children. This work was supported\r\nby Hasler Foundation Program:
Hasler Responsible AI (project number 21043). This work was\r\nsupported by the
Swiss National Science Foundation (SNSF) under grant number 200021_205011.\r\nFrancesco
Locatello did not contribute to this work at Amazon. "
alternative_title:
- Advances in Neural Information Processing Systems
article_processing_charge: No
arxiv: 1
author:
- first_name: Zhenyu
full_name: Zhu, Zhenyu
last_name: Zhu
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Volkan
full_name: Cevher, Volkan
last_name: Cevher
citation:
ama: 'Zhu Z, Locatello F, Cevher V. Sample complexity bounds for score-matching:
Causal discovery and generative modeling. In: 37th Conference on Neural Information
Processing Systems. Vol 36. Neural Information Processing Systems Foundation;
2023:3325-3337. doi:10.52202/075280-0147'
apa: 'Zhu, Z., Locatello, F., & Cevher, V. (2023). Sample complexity bounds
for score-matching: Causal discovery and generative modeling. In 37th Conference
on Neural Information Processing Systems (Vol. 36, pp. 3325–3337). New Orleans,
LA, United States: Neural Information Processing Systems Foundation. https://doi.org/10.52202/075280-0147'
chicago: 'Zhu, Zhenyu, Francesco Locatello, and Volkan Cevher. “Sample Complexity
Bounds for Score-Matching: Causal Discovery and Generative Modeling.” In 37th
Conference on Neural Information Processing Systems, 36:3325–37. Neural Information
Processing Systems Foundation, 2023. https://doi.org/10.52202/075280-0147.'
ieee: 'Z. Zhu, F. Locatello, and V. Cevher, “Sample complexity bounds for score-matching:
Causal discovery and generative modeling,” in 37th Conference on Neural Information
Processing Systems, New Orleans, LA, United States, 2023, vol. 36, pp. 3325–3337.'
ista: 'Zhu Z, Locatello F, Cevher V. 2023. Sample complexity bounds for score-matching:
Causal discovery and generative modeling. 37th Conference on Neural Information
Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in
Neural Information Processing Systems, vol. 36, 3325–3337.'
mla: 'Zhu, Zhenyu, et al. “Sample Complexity Bounds for Score-Matching: Causal Discovery
and Generative Modeling.” 37th Conference on Neural Information Processing
Systems, vol. 36, Neural Information Processing Systems Foundation, 2023,
pp. 3325–37, doi:10.52202/075280-0147.'
short: Z. Zhu, F. Locatello, V. Cevher, in:, 37th Conference on Neural Information
Processing Systems, Neural Information Processing Systems Foundation, 2023, pp.
3325–3337.
conference:
end_date: 2023-12-16
location: New Orleans, LA, United States
name: 'NeurIPS: Neural Information Processing Systems'
start_date: 2023-12-12
corr_author: '1'
das_tickbox: '0'
date_created: 2024-02-07T15:11:11Z
date_published: 2023-10-27T00:00:00Z
date_updated: 2026-09-17T12:59:35Z
day: '27'
ddc:
- '000'
department:
- _id: FrLo
doi: 10.52202/075280-0147
external_id:
arxiv:
- '2310.18123'
file:
- access_level: open_access
checksum: 6f10adadefceb3bb50ad0b2637493381
content_type: application/pdf
creator: dernst
date_created: 2026-08-13T07:02:51Z
date_updated: 2026-08-13T07:02:51Z
file_id: '22700'
file_name: 2023_Neurips_Zhu.pdf
file_size: 305362
relation: main_file
success: 1
file_date_updated: 2026-08-13T07:02:51Z
fulldoi: https://doi.org/10.52202/075280-0147
has_accepted_license: '1'
intvolume: ' 36'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 3325-3337
publication: 37th Conference on Neural Information Processing Systems
publication_identifier:
eissn:
- 1049-5258
isbn:
- '9781713899921'
publication_status: published
publisher: Neural Information Processing Systems Foundation
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: yes
title: 'Sample complexity bounds for score-matching: Causal discovery and generative
modeling'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 36
year: '2023'
...
---
_id: '13310'
abstract:
- lang: eng
text: Machine-learned systems are in widespread use for making decisions about humans,
and it is important that they are fair, i.e., not biased against individuals based
on sensitive attributes. We present runtime verification of algorithmic fairness
for systems whose models are unknown, but are assumed to have a Markov chain structure.
We introduce a specification language that can model many common algorithmic fairness
properties, such as demographic parity, equal opportunity, and social burden.
We build monitors that observe a long sequence of events as generated by a given
system, and output, after each observation, a quantitative estimate of how fair
or biased the system was on that run until that point in time. The estimate is
proven to be correct modulo a variable error bound and a given confidence level,
where the error bound gets tighter as the observed sequence gets longer. Our monitors
are of two types, and use, respectively, frequentist and Bayesian statistical
inference techniques. While the frequentist monitors compute estimates that are
objectively correct with respect to the ground truth, the Bayesian monitors compute
estimates that are correct subject to a given prior belief about the system’s
model. Using a prototype implementation, we show how we can monitor if a bank
is fair in giving loans to applicants from different social backgrounds, and if
a college is fair in admitting students while maintaining a reasonable financial
burden on the society. Although they exhibit different theoretical complexities
in certain cases, in our experiments, both frequentist and Bayesian monitors took
less than a millisecond to update their verdicts after each observation.
acknowledgement: 'This work is supported by the European Research Council under Grant
No.: ERC-2020-AdG101020093.'
alternative_title:
- LNCS
article_processing_charge: Yes (in subscription journal)
arxiv: 1
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: Mahyar
full_name: Karimi, Mahyar
id: 6e5417ba-5355-11ee-ae5a-94c2e510b26b
last_name: Karimi
orcid: 0009-0005-0820-1696
- first_name: Konstantin
full_name: Kueffner, Konstantin
id: 8121a2d0-dc85-11ea-9058-af578f3b4515
last_name: Kueffner
orcid: 0000-0001-8974-2542
- first_name: Kaushik
full_name: Mallik, Kaushik
id: 0834ff3c-6d72-11ec-94e0-b5b0a4fb8598
last_name: Mallik
orcid: 0000-0001-9864-7475
citation:
ama: 'Henzinger TA, Karimi M, Kueffner K, Mallik K. Monitoring algorithmic fairness.
In: Computer Aided Verification. Vol 13965. Springer Nature; 2023:358–382.
doi:10.1007/978-3-031-37703-7_17'
apa: 'Henzinger, T. A., Karimi, M., Kueffner, K., & Mallik, K. (2023). Monitoring
algorithmic fairness. In Computer Aided Verification (Vol. 13965, pp. 358–382).
Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37703-7_17'
chicago: Henzinger, Thomas A, Mahyar Karimi, Konstantin Kueffner, and Kaushik Mallik.
“Monitoring Algorithmic Fairness.” In Computer Aided Verification, 13965:358–382.
Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37703-7_17.
ieee: T. A. Henzinger, M. Karimi, K. Kueffner, and K. Mallik, “Monitoring algorithmic
fairness,” in Computer Aided Verification, Paris, France, 2023, vol. 13965,
pp. 358–382.
ista: 'Henzinger TA, Karimi M, Kueffner K, Mallik K. 2023. Monitoring algorithmic
fairness. Computer Aided Verification. CAV: Computer Aided Verification, LNCS,
vol. 13965, 358–382.'
mla: Henzinger, Thomas A., et al. “Monitoring Algorithmic Fairness.” Computer
Aided Verification, vol. 13965, Springer Nature, 2023, pp. 358–382, doi:10.1007/978-3-031-37703-7_17.
short: T.A. Henzinger, M. Karimi, K. Kueffner, K. Mallik, in:, Computer Aided Verification,
Springer Nature, 2023, pp. 358–382.
conference:
end_date: 2023-07-22
location: Paris, France
name: 'CAV: Computer Aided Verification'
start_date: 2023-07-17
corr_author: '1'
date_created: 2023-07-25T18:32:40Z
date_published: 2023-07-18T00:00:00Z
date_updated: 2026-09-18T07:41:29Z
day: '18'
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- _id: ToHe
doi: 10.1007/978-3-031-37703-7_17
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arxiv:
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month: '07'
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oa_version: Published Version
page: 358–382
project:
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call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: Computer Aided Verification
publication_identifier:
eisbn:
- '9783031377037'
eissn:
- 1611-3349
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issn:
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publisher: Springer Nature
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relation: dissertation_contains
status: public
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status: public
title: Monitoring algorithmic fairness
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13965
year: '2023'
...
---
_id: '13228'
abstract:
- lang: eng
text: A machine-learned system that is fair in static decision-making tasks may
have biased societal impacts in the long-run. This may happen when the system
interacts with humans and feedback patterns emerge, reinforcing old biases in
the system and creating new biases. While existing works try to identify and mitigate
long-run biases through smart system design, we introduce techniques for monitoring
fairness in real time. Our goal is to build and deploy a monitor that will continuously
observe a long sequence of events generated by the system in the wild, and will
output, with each event, a verdict on how fair the system is at the current point
in time. The advantages of monitoring are two-fold. Firstly, fairness is evaluated
at run-time, which is important because unfair behaviors may not be eliminated
a priori, at design-time, due to partial knowledge about the system and the environment,
as well as uncertainties and dynamic changes in the system and the environment,
such as the unpredictability of human behavior. Secondly, monitors are by design
oblivious to how the monitored system is constructed, which makes them suitable
to be used as trusted third-party fairness watchdogs. They function as computationally
lightweight statistical estimators, and their correctness proofs rely on the rigorous
analysis of the stochastic process that models the assumptions about the underlying
dynamics of the system. We show, both in theory and experiments, how monitors
can warn us (1) if a bank’s credit policy over time has created an unfair distribution
of credit scores among the population, and (2) if a resource allocator’s allocation
policy over time has made unfair allocations. Our experiments demonstrate that
the monitors introduce very low overhead. We believe that runtime monitoring is
an important and mathematically rigorous new addition to the fairness toolbox.
acknowledgement: 'The authors would like to thank the anonymous reviewers for their
valuable comments and helpful suggestions. This work is supported by the European
Research Council under Grant No.: ERC-2020-AdG 101020093.'
article_processing_charge: Yes (via OA deal)
arxiv: 1
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: Mahyar
full_name: Karimi, Mahyar
id: 6e5417ba-5355-11ee-ae5a-94c2e510b26b
last_name: Karimi
orcid: 0009-0005-0820-1696
- first_name: Konstantin
full_name: Kueffner, Konstantin
id: 8121a2d0-dc85-11ea-9058-af578f3b4515
last_name: Kueffner
orcid: 0000-0001-8974-2542
- first_name: Kaushik
full_name: Mallik, Kaushik
id: 0834ff3c-6d72-11ec-94e0-b5b0a4fb8598
last_name: Mallik
orcid: 0000-0001-9864-7475
citation:
ama: 'Henzinger TA, Karimi M, Kueffner K, Mallik K. Runtime monitoring of dynamic
fairness properties. In: FAccT ’23: Proceedings of the 2023 ACM Conference
on Fairness, Accountability, and Transparency. Association for Computing Machinery;
2023:604-614. doi:10.1145/3593013.3594028'
apa: 'Henzinger, T. A., Karimi, M., Kueffner, K., & Mallik, K. (2023). Runtime
monitoring of dynamic fairness properties. In FAccT ’23: Proceedings of the
2023 ACM Conference on Fairness, Accountability, and Transparency (pp. 604–614).
Chicago, IL, United States: Association for Computing Machinery. https://doi.org/10.1145/3593013.3594028'
chicago: 'Henzinger, Thomas A, Mahyar Karimi, Konstantin Kueffner, and Kaushik Mallik.
“Runtime Monitoring of Dynamic Fairness Properties.” In FAccT ’23: Proceedings
of the 2023 ACM Conference on Fairness, Accountability, and Transparency,
604–14. Association for Computing Machinery, 2023. https://doi.org/10.1145/3593013.3594028.'
ieee: 'T. A. Henzinger, M. Karimi, K. Kueffner, and K. Mallik, “Runtime monitoring
of dynamic fairness properties,” in FAccT ’23: Proceedings of the 2023 ACM
Conference on Fairness, Accountability, and Transparency, Chicago, IL, United
States, 2023, pp. 604–614.'
ista: 'Henzinger TA, Karimi M, Kueffner K, Mallik K. 2023. Runtime monitoring of
dynamic fairness properties. FAccT ’23: Proceedings of the 2023 ACM Conference
on Fairness, Accountability, and Transparency. FAccT: Conference on Fairness,
Accountability and Transparency, 604–614.'
mla: 'Henzinger, Thomas A., et al. “Runtime Monitoring of Dynamic Fairness Properties.”
FAccT ’23: Proceedings of the 2023 ACM Conference on Fairness, Accountability,
and Transparency, Association for Computing Machinery, 2023, pp. 604–14, doi:10.1145/3593013.3594028.'
short: 'T.A. Henzinger, M. Karimi, K. Kueffner, K. Mallik, in:, FAccT ’23: Proceedings
of the 2023 ACM Conference on Fairness, Accountability, and Transparency, Association
for Computing Machinery, 2023, pp. 604–614.'
conference:
end_date: 2023-06-15
location: Chicago, IL, United States
name: 'FAccT: Conference on Fairness, Accountability and Transparency'
start_date: 2023-06-12
corr_author: '1'
date_created: 2023-07-16T22:01:09Z
date_published: 2023-06-12T00:00:00Z
date_updated: 2026-09-18T07:41:29Z
day: '12'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1145/3593013.3594028
ec_funded: 1
external_id:
arxiv:
- '2305.04699'
isi:
- '001062819300057'
file:
- access_level: open_access
checksum: 96c759db9cdf94b81e37871a66a6ff48
content_type: application/pdf
creator: dernst
date_created: 2023-07-18T07:43:10Z
date_updated: 2023-07-18T07:43:10Z
file_id: '13245'
file_name: 2023_ACM_HenzingerT.pdf
file_size: 4100596
relation: main_file
success: 1
file_date_updated: 2023-07-18T07:43:10Z
fulldoi: https://doi.org/10.1145/3593013.3594028
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 604-614
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: 'FAccT ''23: Proceedings of the 2023 ACM Conference on Fairness, Accountability,
and Transparency'
publication_identifier:
isbn:
- '9781450372527'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
record:
- id: '22808'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Runtime monitoring of dynamic fairness properties
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14454'
abstract:
- lang: eng
text: As AI and machine-learned software are used increasingly for making decisions
that affect humans, it is imperative that they remain fair and unbiased in their
decisions. To complement design-time bias mitigation measures, runtime verification
techniques have been introduced recently to monitor the algorithmic fairness of
deployed systems. Previous monitoring techniques assume full observability of
the states of the (unknown) monitored system. Moreover, they can monitor only
fairness properties that are specified as arithmetic expressions over the probabilities
of different events. In this work, we extend fairness monitoring to systems modeled
as partially observed Markov chains (POMC), and to specifications containing arithmetic
expressions over the expected values of numerical functions on event sequences.
The only assumptions we make are that the underlying POMC is aperiodic and starts
in the stationary distribution, with a bound on its mixing time being known. These
assumptions enable us to estimate a given property for the entire distribution
of possible executions of the monitored POMC, by observing only a single execution.
Our monitors observe a long run of the system and, after each new observation,
output updated PAC-estimates of how fair or biased the system is. The monitors
are computationally lightweight and, using a prototype implementation, we demonstrate
their effectiveness on several real-world examples.
acknowledgement: 'This work is supported by the European Research Council under Grant
No.: ERC-2020-AdG 101020093.'
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
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: Konstantin
full_name: Kueffner, Konstantin
id: 8121a2d0-dc85-11ea-9058-af578f3b4515
last_name: Kueffner
orcid: 0000-0001-8974-2542
- first_name: Kaushik
full_name: Mallik, Kaushik
id: 0834ff3c-6d72-11ec-94e0-b5b0a4fb8598
last_name: Mallik
orcid: 0000-0001-9864-7475
citation:
ama: 'Henzinger TA, Kueffner K, Mallik K. Monitoring algorithmic fairness under
partial observations. In: 23rd International Conference on Runtime Verification.
Vol 14245. Springer Nature; 2023:291-311. doi:10.1007/978-3-031-44267-4_15'
apa: 'Henzinger, T. A., Kueffner, K., & Mallik, K. (2023). Monitoring algorithmic
fairness under partial observations. In 23rd International Conference on Runtime
Verification (Vol. 14245, pp. 291–311). Thessaloniki, Greece: Springer Nature.
https://doi.org/10.1007/978-3-031-44267-4_15'
chicago: Henzinger, Thomas A, Konstantin Kueffner, and Kaushik Mallik. “Monitoring
Algorithmic Fairness under Partial Observations.” In 23rd International Conference
on Runtime Verification, 14245:291–311. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-44267-4_15.
ieee: T. A. Henzinger, K. Kueffner, and K. Mallik, “Monitoring algorithmic fairness
under partial observations,” in 23rd International Conference on Runtime Verification,
Thessaloniki, Greece, 2023, vol. 14245, pp. 291–311.
ista: 'Henzinger TA, Kueffner K, Mallik K. 2023. Monitoring algorithmic fairness
under partial observations. 23rd International Conference on Runtime Verification.
RV: Conference on Runtime Verification, LNCS, vol. 14245, 291–311.'
mla: Henzinger, Thomas A., et al. “Monitoring Algorithmic Fairness under Partial
Observations.” 23rd International Conference on Runtime Verification, vol.
14245, Springer Nature, 2023, pp. 291–311, doi:10.1007/978-3-031-44267-4_15.
short: T.A. Henzinger, K. Kueffner, K. Mallik, in:, 23rd International Conference
on Runtime Verification, Springer Nature, 2023, pp. 291–311.
conference:
end_date: 2023-10-06
location: Thessaloniki, Greece
name: 'RV: Conference on Runtime Verification'
start_date: 2023-10-03
corr_author: '1'
date_created: 2023-10-29T23:01:15Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2026-09-18T07:41:29Z
day: '01'
department:
- _id: ToHe
doi: 10.1007/978-3-031-44267-4_15
ec_funded: 1
external_id:
arxiv:
- '2308.00341'
fulldoi: https://doi.org/10.1007/978-3-031-44267-4_15
intvolume: ' 14245'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2308.00341
month: '10'
oa: 1
oa_version: Preprint
page: 291-311
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: 23rd International Conference on Runtime Verification
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031442667'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '22808'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Monitoring algorithmic fairness under partial observations
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14245
year: '2023'
...