---
_id: '10588'
abstract:
- lang: eng
text: We prove the Sobolev-to-Lipschitz property for metric measure spaces satisfying
the quasi curvature-dimension condition recently introduced in Milman (Commun
Pure Appl Math, to appear). We provide several applications to properties of the
corresponding heat semigroup. In particular, under the additional assumption of
infinitesimal Hilbertianity, we show the Varadhan short-time asymptotics for the
heat semigroup with respect to the distance, and prove the irreducibility of the
heat semigroup. These results apply in particular to large classes of (ideal)
sub-Riemannian manifolds.
acknowledgement: "The authors are grateful to Dr. Bang-Xian Han for helpful discussions
on the Sobolev-to-Lipschitz property on metric measure spaces, and to Professor
Kazuhiro Kuwae, Professor Emanuel Milman, Dr. Giorgio Stefani, and Dr. Gioacchino
Antonelli for reading a preliminary version of this work and for their valuable
comments and suggestions. Finally, they wish to express their gratitude to two anonymous
Reviewers whose suggestions improved the presentation of this work.\r\n\r\nL.D.S.
gratefully acknowledges funding of his position by the Austrian Science Fund (FWF)
grant F65, and by the European Research Council (ERC, grant No. 716117, awarded
to Prof. Dr. Jan Maas).\r\n\r\nK.S. gratefully acknowledges funding by: the JSPS
Overseas Research Fellowships, Grant Nr. 290142; World Premier International Research
Center Initiative (WPI), MEXT, Japan; JSPS Grant-in-Aid for Scientific Research
on Innovative Areas “Discrete Geometric Analysis for Materials Design”, Grant Number
17H06465; and the Alexander von Humboldt Stiftung, Humboldt-Forschungsstipendium."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Lorenzo
full_name: Dello Schiavo, Lorenzo
id: ECEBF480-9E4F-11EA-B557-B0823DDC885E
last_name: Dello Schiavo
orcid: 0000-0002-9881-6870
- first_name: Kohei
full_name: Suzuki, Kohei
last_name: Suzuki
citation:
ama: Dello Schiavo L, Suzuki K. Sobolev-to-Lipschitz property on QCD- spaces and
applications. Mathematische Annalen. 2022;384:1815-1832. doi:10.1007/s00208-021-02331-2
apa: Dello Schiavo, L., & Suzuki, K. (2022). Sobolev-to-Lipschitz property on
QCD- spaces and applications. Mathematische Annalen. Springer Nature. https://doi.org/10.1007/s00208-021-02331-2
chicago: Dello Schiavo, Lorenzo, and Kohei Suzuki. “Sobolev-to-Lipschitz Property
on QCD- Spaces and Applications.” Mathematische Annalen. Springer Nature,
2022. https://doi.org/10.1007/s00208-021-02331-2.
ieee: L. Dello Schiavo and K. Suzuki, “Sobolev-to-Lipschitz property on QCD- spaces
and applications,” Mathematische Annalen, vol. 384. Springer Nature, pp.
1815–1832, 2022.
ista: Dello Schiavo L, Suzuki K. 2022. Sobolev-to-Lipschitz property on QCD- spaces
and applications. Mathematische Annalen. 384, 1815–1832.
mla: Dello Schiavo, Lorenzo, and Kohei Suzuki. “Sobolev-to-Lipschitz Property on
QCD- Spaces and Applications.” Mathematische Annalen, vol. 384, Springer
Nature, 2022, pp. 1815–32, doi:10.1007/s00208-021-02331-2.
short: L. Dello Schiavo, K. Suzuki, Mathematische Annalen 384 (2022) 1815–1832.
date_created: 2022-01-02T23:01:35Z
date_published: 2022-12-01T00:00:00Z
date_updated: 2023-08-02T13:39:05Z
day: '01'
ddc:
- '510'
department:
- _id: JaMa
doi: 10.1007/s00208-021-02331-2
ec_funded: 1
external_id:
arxiv:
- '2110.05137'
isi:
- '000734150200001'
file:
- access_level: open_access
checksum: 2593abbf195e38efa93b6006b1e90eb1
content_type: application/pdf
creator: alisjak
date_created: 2022-01-03T11:08:31Z
date_updated: 2022-01-03T11:08:31Z
file_id: '10596'
file_name: 2021_MathAnn_DelloSchiavo.pdf
file_size: 410090
relation: main_file
success: 1
file_date_updated: 2022-01-03T11:08:31Z
has_accepted_license: '1'
intvolume: ' 384'
isi: 1
keyword:
- quasi curvature-dimension condition
- sub-riemannian geometry
- Sobolev-to-Lipschitz property
- Varadhan short-time asymptotics
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '12'
oa: 1
oa_version: Published Version
page: 1815-1832
project:
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Mathematische Annalen
publication_identifier:
eissn:
- 1432-1807
issn:
- 0025-5831
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sobolev-to-Lipschitz property on QCD- spaces and applications
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: 384
year: '2022'
...
---
_id: '10547'
abstract:
- lang: eng
text: "We establish global-in-time existence results for thermodynamically consistent
reaction-(cross-)diffusion systems coupled to an equation describing heat transfer.
Our main interest is to model species-dependent diffusivities,\r\nwhile at the
same time ensuring thermodynamic consistency. A key difficulty of the non-isothermal
case lies in the intrinsic presence of cross-diffusion type phenomena like the
Soret and the Dufour effect: due to the temperature/energy dependence of the thermodynamic
equilibria, a nonvanishing temperature gradient may drive a concentration flux
even in a situation with constant concentrations; likewise, a nonvanishing concentration
gradient may drive a heat flux even in a case of spatially constant temperature.
We use time discretisation and regularisation techniques and derive a priori estimates
based on a suitable entropy and the associated entropy production. Renormalised
solutions are used in cases where non-integrable diffusion fluxes or reaction
terms appear."
acknowledgement: M.K. gratefully acknowledges the hospitality of WIAS Berlin, where
a major part of the project was carried out. The research stay of M.K. at WIAS Berlin
was funded by the Austrian Federal Ministry of Education, Science and Research through
a research fellowship for graduates of a promotio sub auspiciis. The research of
A.M. has been partially supported by Deutsche Forschungsgemeinschaft (DFG) through
the Collaborative Research Center SFB 1114 “Scaling Cascades in Complex Systems”
(Project no. 235221301), Subproject C05 “Effective models for materials and interfaces
with multiple scales”. J.F. and A.M. are grateful for the hospitality of the Erwin
Schrödinger Institute in Vienna, where some ideas for this work have been developed.
The authors are grateful to two anonymous referees for several helpful comments,
in particular for the short proof of estimate (2.7).
article_processing_charge: No
article_type: original
author:
- first_name: Julian L
full_name: Fischer, Julian L
id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87
last_name: Fischer
orcid: 0000-0002-0479-558X
- first_name: Katharina
full_name: Hopf, Katharina
last_name: Hopf
- first_name: Michael
full_name: Kniely, Michael
id: 2CA2C08C-F248-11E8-B48F-1D18A9856A87
last_name: Kniely
orcid: 0000-0001-5645-4333
- first_name: Alexander
full_name: Mielke, Alexander
last_name: Mielke
citation:
ama: Fischer JL, Hopf K, Kniely M, Mielke A. Global existence analysis of energy-reaction-diffusion
systems. SIAM Journal on Mathematical Analysis. 2022;54(1):220-267. doi:10.1137/20M1387237
apa: Fischer, J. L., Hopf, K., Kniely, M., & Mielke, A. (2022). Global existence
analysis of energy-reaction-diffusion systems. SIAM Journal on Mathematical
Analysis. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/20M1387237
chicago: Fischer, Julian L, Katharina Hopf, Michael Kniely, and Alexander Mielke.
“Global Existence Analysis of Energy-Reaction-Diffusion Systems.” SIAM Journal
on Mathematical Analysis. Society for Industrial and Applied Mathematics,
2022. https://doi.org/10.1137/20M1387237.
ieee: J. L. Fischer, K. Hopf, M. Kniely, and A. Mielke, “Global existence analysis
of energy-reaction-diffusion systems,” SIAM Journal on Mathematical Analysis,
vol. 54, no. 1. Society for Industrial and Applied Mathematics, pp. 220–267, 2022.
ista: Fischer JL, Hopf K, Kniely M, Mielke A. 2022. Global existence analysis of
energy-reaction-diffusion systems. SIAM Journal on Mathematical Analysis. 54(1),
220–267.
mla: Fischer, Julian L., et al. “Global Existence Analysis of Energy-Reaction-Diffusion
Systems.” SIAM Journal on Mathematical Analysis, vol. 54, no. 1, Society
for Industrial and Applied Mathematics, 2022, pp. 220–67, doi:10.1137/20M1387237.
short: J.L. Fischer, K. Hopf, M. Kniely, A. Mielke, SIAM Journal on Mathematical
Analysis 54 (2022) 220–267.
date_created: 2021-12-16T12:08:56Z
date_published: 2022-01-04T00:00:00Z
date_updated: 2023-08-02T13:37:03Z
day: '04'
department:
- _id: JuFi
doi: 10.1137/20M1387237
external_id:
arxiv:
- '2012.03792 '
isi:
- '000762768000006'
intvolume: ' 54'
isi: 1
issue: '1'
keyword:
- Energy-Reaction-Diffusion Systems
- Cross Diffusion
- Global-In-Time Existence of Weak/Renormalised Solutions
- Entropy Method
- Onsager System
- Soret/Dufour Effect
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2012.03792
month: '01'
oa: 1
oa_version: Preprint
page: 220-267
publication: SIAM Journal on Mathematical Analysis
publication_identifier:
issn:
- 0036-1410
publication_status: published
publisher: Society for Industrial and Applied Mathematics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Global existence analysis of energy-reaction-diffusion systems
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 54
year: '2022'
...
---
_id: '10023'
abstract:
- lang: eng
text: We study the temporal dissipation of variance and relative entropy for ergodic
Markov Chains in continuous time, and compute explicitly the corresponding dissipation
rates. These are identified, as is well known, in the case of the variance in
terms of an appropriate Hilbertian norm; and in the case of the relative entropy,
in terms of a Dirichlet form which morphs into a version of the familiar Fisher
information under conditions of detailed balance. Here we obtain trajectorial
versions of these results, valid along almost every path of the random motion
and most transparent in the backwards direction of time. Martingale arguments
and time reversal play crucial roles, as in the recent work of Karatzas, Schachermayer
and Tschiderer for conservative diffusions. Extensions are developed to general
“convex divergences” and to countable state-spaces. The steepest descent and gradient
flow properties for the variance, the relative entropy, and appropriate generalizations,
are studied along with their respective geometries under conditions of detailed
balance, leading to a very direct proof for the HWI inequality of Otto and Villani
in the present context.
acknowledgement: I.K. acknowledges support from the U.S. National Science Foundation
under Grant NSF-DMS-20-04997. J.M. acknowledges support from the European Research
Council (ERC) under the European Union’s Horizon 2020 research and innovation programme
(grant agreement No 716117) and from the Austrian Science Fund (FWF) through project
F65. W.S. acknowledges support from the Austrian Science Fund (FWF) under grant
P28861 and by the Vienna Science and Technology Fund (WWTF) through projects MA14-008
and MA16-021.
article_processing_charge: No
article_type: original
author:
- first_name: Ioannis
full_name: Karatzas, Ioannis
last_name: Karatzas
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
- first_name: Walter
full_name: Schachermayer, Walter
last_name: Schachermayer
citation:
ama: Karatzas I, Maas J, Schachermayer W. Trajectorial dissipation and gradient
flow for the relative entropy in Markov chains. Communications in Information
and Systems. 2021;21(4):481-536. doi:10.4310/CIS.2021.v21.n4.a1
apa: Karatzas, I., Maas, J., & Schachermayer, W. (2021). Trajectorial dissipation
and gradient flow for the relative entropy in Markov chains. Communications
in Information and Systems. International Press. https://doi.org/10.4310/CIS.2021.v21.n4.a1
chicago: Karatzas, Ioannis, Jan Maas, and Walter Schachermayer. “Trajectorial Dissipation
and Gradient Flow for the Relative Entropy in Markov Chains.” Communications
in Information and Systems. International Press, 2021. https://doi.org/10.4310/CIS.2021.v21.n4.a1.
ieee: I. Karatzas, J. Maas, and W. Schachermayer, “Trajectorial dissipation and
gradient flow for the relative entropy in Markov chains,” Communications in
Information and Systems, vol. 21, no. 4. International Press, pp. 481–536,
2021.
ista: Karatzas I, Maas J, Schachermayer W. 2021. Trajectorial dissipation and gradient
flow for the relative entropy in Markov chains. Communications in Information
and Systems. 21(4), 481–536.
mla: Karatzas, Ioannis, et al. “Trajectorial Dissipation and Gradient Flow for the
Relative Entropy in Markov Chains.” Communications in Information and Systems,
vol. 21, no. 4, International Press, 2021, pp. 481–536, doi:10.4310/CIS.2021.v21.n4.a1.
short: I. Karatzas, J. Maas, W. Schachermayer, Communications in Information and
Systems 21 (2021) 481–536.
date_created: 2021-09-19T08:53:19Z
date_published: 2021-06-04T00:00:00Z
date_updated: 2021-09-20T12:51:18Z
day: '04'
department:
- _id: JaMa
doi: 10.4310/CIS.2021.v21.n4.a1
ec_funded: 1
external_id:
arxiv:
- '2005.14177'
intvolume: ' 21'
issue: '4'
keyword:
- Markov Chain
- relative entropy
- time reversal
- steepest descent
- gradient flow
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2005.14177
month: '06'
oa: 1
oa_version: Preprint
page: 481-536
project:
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
publication: Communications in Information and Systems
publication_identifier:
issn:
- 1526-7555
publication_status: published
publisher: International Press
quality_controlled: '1'
status: public
title: Trajectorial dissipation and gradient flow for the relative entropy in Markov
chains
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 21
year: '2021'
...
---
_id: '10108'
abstract:
- lang: eng
text: We argue that the time is ripe to investigate differential monitoring, in
which the specification of a program's behavior is implicitly given by a second
program implementing the same informal specification. Similar ideas have been
proposed before, and are currently implemented in restricted form for testing
and specialized run-time analyses, aspects of which we combine. We discuss the
challenges of implementing differential monitoring as a general-purpose, black-box
run-time monitoring framework, and present promising results of a preliminary
implementation, showing low monitoring overheads for diverse programs.
acknowledgement: The authors would like to thank Borzoo Bonakdarpour, Derek Dreyer,
Adrian Francalanza, Owolabi Legunsen, Mae Milano, Manuel Rigger, Cesar Sanchez,
and the members of the IST Verification Seminar for their helpful comments and insights
on various stages of this work, as well as the reviewers of RV’21 for their helpful
suggestions on the actual paper.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Fabian
full_name: Mühlböck, Fabian
id: 6395C5F6-89DF-11E9-9C97-6BDFE5697425
last_name: Mühlböck
orcid: 0000-0003-1548-0177
- 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: 'Mühlböck F, Henzinger TA. Differential monitoring. In: International Conference
on Runtime Verification. Vol 12974. Cham: Springer Nature; 2021:231-243. doi:10.1007/978-3-030-88494-9_12'
apa: 'Mühlböck, F., & Henzinger, T. A. (2021). Differential monitoring. In International
Conference on Runtime Verification (Vol. 12974, pp. 231–243). Cham: Springer
Nature. https://doi.org/10.1007/978-3-030-88494-9_12'
chicago: 'Mühlböck, Fabian, and Thomas A Henzinger. “Differential Monitoring.” In
International Conference on Runtime Verification, 12974:231–43. Cham: Springer
Nature, 2021. https://doi.org/10.1007/978-3-030-88494-9_12.'
ieee: F. Mühlböck and T. A. Henzinger, “Differential monitoring,” in International
Conference on Runtime Verification, Virtual, 2021, vol. 12974, pp. 231–243.
ista: 'Mühlböck F, Henzinger TA. 2021. Differential monitoring. International Conference
on Runtime Verification. RV: Runtime Verification, LNCS, vol. 12974, 231–243.'
mla: Mühlböck, Fabian, and Thomas A. Henzinger. “Differential Monitoring.” International
Conference on Runtime Verification, vol. 12974, Springer Nature, 2021, pp.
231–43, doi:10.1007/978-3-030-88494-9_12.
short: F. Mühlböck, T.A. Henzinger, in:, International Conference on Runtime Verification,
Springer Nature, Cham, 2021, pp. 231–243.
conference:
end_date: 2021-10-14
location: Virtual
name: 'RV: Runtime Verification'
start_date: 2021-10-11
date_created: 2021-10-07T23:30:10Z
date_published: 2021-10-06T00:00:00Z
date_updated: 2023-08-14T07:20:30Z
day: '06'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1007/978-3-030-88494-9_12
external_id:
isi:
- '000719383800012'
file:
- access_level: open_access
checksum: 554c7fdb259eda703a8b6328a6dad55a
content_type: application/pdf
creator: fmuehlbo
date_created: 2021-10-07T23:32:18Z
date_updated: 2021-10-07T23:32:18Z
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file_name: differentialmonitoring-cameraready-openaccess.pdf
file_size: 350632
relation: main_file
success: 1
file_date_updated: 2021-10-07T23:32:18Z
has_accepted_license: '1'
intvolume: ' 12974'
isi: 1
keyword:
- run-time verification
- software engineering
- implicit specification
language:
- iso: eng
month: '10'
oa: 1
oa_version: Preprint
page: 231-243
place: Cham
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: International Conference on Runtime Verification
publication_identifier:
eisbn:
- 978-3-030-88494-9
eissn:
- 1611-3349
isbn:
- 978-3-030-88493-2
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '9946'
relation: extended_version
status: public
scopus_import: '1'
status: public
title: Differential monitoring
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12974
year: '2021'
...
---
_id: '9946'
abstract:
- lang: eng
text: We argue that the time is ripe to investigate differential monitoring, in
which the specification of a program's behavior is implicitly given by a second
program implementing the same informal specification. Similar ideas have been
proposed before, and are currently implemented in restricted form for testing
and specialized run-time analyses, aspects of which we combine. We discuss the
challenges of implementing differential monitoring as a general-purpose, black-box
run-time monitoring framework, and present promising results of a preliminary
implementation, showing low monitoring overheads for diverse programs.
acknowledgement: The authors would like to thank Borzoo Bonakdarpour, Derek Dreyer,
Adrian Francalanza, Owolabi Legunsen, Matthew Milano, Manuel Rigger, Cesar Sanchez,
and the members of the IST Verification Seminar for their helpful comments and insights
on various stages of this work, as well as the reviewers of RV’21 for their helpful
suggestions on the actual paper.
alternative_title:
- IST Austria Technical Report
article_processing_charge: No
author:
- first_name: Fabian
full_name: Mühlböck, Fabian
id: 6395C5F6-89DF-11E9-9C97-6BDFE5697425
last_name: Mühlböck
orcid: 0000-0003-1548-0177
- 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: Mühlböck F, Henzinger TA. Differential Monitoring. IST Austria; 2021.
doi:10.15479/AT:ISTA:9946
apa: Mühlböck, F., & Henzinger, T. A. (2021). Differential monitoring.
IST Austria. https://doi.org/10.15479/AT:ISTA:9946
chicago: Mühlböck, Fabian, and Thomas A Henzinger. Differential Monitoring.
IST Austria, 2021. https://doi.org/10.15479/AT:ISTA:9946.
ieee: F. Mühlböck and T. A. Henzinger, Differential monitoring. IST Austria,
2021.
ista: Mühlböck F, Henzinger TA. 2021. Differential monitoring, IST Austria, 17p.
mla: Mühlböck, Fabian, and Thomas A. Henzinger. Differential Monitoring.
IST Austria, 2021, doi:10.15479/AT:ISTA:9946.
short: F. Mühlböck, T.A. Henzinger, Differential Monitoring, IST Austria, 2021.
date_created: 2021-08-20T20:00:37Z
date_published: 2021-09-01T00:00:00Z
date_updated: 2023-08-14T07:20:29Z
day: '01'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.15479/AT:ISTA:9946
file:
- access_level: open_access
checksum: 0f9aafd59444cb6bdca6925d163ab946
content_type: application/pdf
creator: fmuehlbo
date_created: 2021-08-20T19:59:44Z
date_updated: 2021-09-03T12:34:28Z
file_id: '9948'
file_name: differentialmonitoring-techreport.pdf
file_size: '320453'
relation: main_file
file_date_updated: 2021-09-03T12:34:28Z
has_accepted_license: '1'
keyword:
- run-time verification
- software engineering
- implicit specification
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '17'
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
related_material:
record:
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relation: other
status: public
- id: '10108'
relation: shorter_version
status: public
status: public
title: Differential monitoring
type: technical_report
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2021'
...
---
_id: '7369'
abstract:
- lang: eng
text: Neuronal responses to complex stimuli and tasks can encompass a wide range
of time scales. Understanding these responses requires measures that characterize
how the information on these response patterns are represented across multiple
temporal resolutions. In this paper we propose a metric – which we call multiscale
relevance (MSR) – to capture the dynamical variability of the activity of single
neurons across different time scales. The MSR is a non-parametric, fully featureless
indicator in that it uses only the time stamps of the firing activity without
resorting to any a priori covariate or invoking any specific structure in the
tuning curve for neural activity. When applied to neural data from the mEC and
from the ADn and PoS regions of freely-behaving rodents, we found that neurons
having low MSR tend to have low mutual information and low firing sparsity across
the correlates that are believed to be encoded by the region of the brain where
the recordings were made. In addition, neurons with high MSR contain significant
information on spatial navigation and allow to decode spatial position or head
direction as efficiently as those neurons whose firing activity has high mutual
information with the covariate to be decoded and significantly better than the
set of neurons with high local variations in their interspike intervals. Given
these results, we propose that the MSR can be used as a measure to rank and select
neurons for their information content without the need to appeal to any a priori
covariate.
acknowledgement: This research was supported by the Kavli Foundation and the Centre
of Excellence scheme of the Research Council of Norway (Centre for Neural Computation).
RJC is currently receiving funding from the European Union’s Horizon 2020 research
and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Ryan J
full_name: Cubero, Ryan J
id: 850B2E12-9CD4-11E9-837F-E719E6697425
last_name: Cubero
orcid: 0000-0003-0002-1867
- first_name: Matteo
full_name: Marsili, Matteo
last_name: Marsili
- first_name: Yasser
full_name: Roudi, Yasser
last_name: Roudi
citation:
ama: Cubero RJ, Marsili M, Roudi Y. Multiscale relevance and informative encoding
in neuronal spike trains. Journal of Computational Neuroscience. 2020;48:85-102.
doi:10.1007/s10827-020-00740-x
apa: Cubero, R. J., Marsili, M., & Roudi, Y. (2020). Multiscale relevance and
informative encoding in neuronal spike trains. Journal of Computational Neuroscience.
Springer Nature. https://doi.org/10.1007/s10827-020-00740-x
chicago: Cubero, Ryan J, Matteo Marsili, and Yasser Roudi. “Multiscale Relevance
and Informative Encoding in Neuronal Spike Trains.” Journal of Computational
Neuroscience. Springer Nature, 2020. https://doi.org/10.1007/s10827-020-00740-x.
ieee: R. J. Cubero, M. Marsili, and Y. Roudi, “Multiscale relevance and informative
encoding in neuronal spike trains,” Journal of Computational Neuroscience,
vol. 48. Springer Nature, pp. 85–102, 2020.
ista: Cubero RJ, Marsili M, Roudi Y. 2020. Multiscale relevance and informative
encoding in neuronal spike trains. Journal of Computational Neuroscience. 48,
85–102.
mla: Cubero, Ryan J., et al. “Multiscale Relevance and Informative Encoding in Neuronal
Spike Trains.” Journal of Computational Neuroscience, vol. 48, Springer
Nature, 2020, pp. 85–102, doi:10.1007/s10827-020-00740-x.
short: R.J. Cubero, M. Marsili, Y. Roudi, Journal of Computational Neuroscience
48 (2020) 85–102.
date_created: 2020-01-28T10:34:00Z
date_published: 2020-02-01T00:00:00Z
date_updated: 2023-08-17T14:35:22Z
day: '01'
ddc:
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doi: 10.1007/s10827-020-00740-x
ec_funded: 1
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file_size: 3257880
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isi: 1
keyword:
- Time series analysis
- Multiple time scale analysis
- Spike train data
- Information theory
- Bayesian decoding
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 85-102
project:
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call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Journal of Computational Neuroscience
publication_identifier:
eissn:
- 1573-6873
issn:
- 0929-5313
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Multiscale relevance and informative encoding in neuronal spike trains
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: 48
year: '2020'
...
---
_id: '6473'
abstract:
- lang: eng
text: "Single cells are constantly interacting with their environment and each other,
more importantly, the accurate perception of environmental cues is crucial for
growth, survival, and reproduction. This communication between cells and their
environment can be formalized in mathematical terms and be quantified as the information
flow between them, as prescribed by information theory. \r\nThe recent availability
of real–time dynamical patterns of signaling molecules in single cells has allowed
us to identify encoding about the identity of the environment in the time–series.
However, efficient estimation of the information transmitted by these signals
has been a data–analysis challenge due to the high dimensionality of the trajectories
and the limited number of samples. In the first part of this thesis, we develop
and evaluate decoding–based estimation methods to lower bound the mutual information
and derive model–based precise information estimates for biological reaction networks
governed by the chemical master equation. This is followed by applying the decoding-based
methods to study the intracellular representation of extracellular changes in
budding yeast, by observing the transient dynamics of nuclear translocation of
10 transcription factors in response to 3 stress conditions. Additionally, we
apply these estimators to previously published data on ERK and Ca2+ signaling
and yeast stress response. We argue that this single cell decoding-based measure
of information provides an unbiased, quantitative and interpretable measure for
the fidelity of biological signaling processes. \r\nFinally, in the last section,
we deal with gene regulation which is primarily controlled by transcription factors
(TFs) that bind to the DNA to activate gene expression. The possibility that non-cognate
TFs activate transcription diminishes the accuracy of regulation with potentially
disastrous effects for the cell. This ’crosstalk’ acts as a previously unexplored
source of noise in biochemical networks and puts a strong constraint on their
performance. To mitigate erroneous initiation we propose an out of equilibrium
scheme that implements kinetic proofreading. We show that such architectures are
favored over their equilibrium counterparts for complex organisms despite introducing
noise in gene expression. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Sarah A
full_name: Cepeda Humerez, Sarah A
id: 3DEE19A4-F248-11E8-B48F-1D18A9856A87
last_name: Cepeda Humerez
citation:
ama: Cepeda Humerez SA. Estimating information flow in single cells. 2019. doi:10.15479/AT:ISTA:6473
apa: Cepeda Humerez, S. A. (2019). Estimating information flow in single cells.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6473
chicago: Cepeda Humerez, Sarah A. “Estimating Information Flow in Single Cells.”
Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6473.
ieee: S. A. Cepeda Humerez, “Estimating information flow in single cells,” Institute
of Science and Technology Austria, 2019.
ista: Cepeda Humerez SA. 2019. Estimating information flow in single cells. Institute
of Science and Technology Austria.
mla: Cepeda Humerez, Sarah A. Estimating Information Flow in Single Cells.
Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6473.
short: S.A. Cepeda Humerez, Estimating Information Flow in Single Cells, Institute
of Science and Technology Austria, 2019.
date_created: 2019-05-21T00:11:23Z
date_published: 2019-05-23T00:00:00Z
date_updated: 2023-09-19T15:13:26Z
day: '23'
ddc:
- '004'
degree_awarded: PhD
department:
- _id: GaTk
doi: 10.15479/AT:ISTA:6473
file:
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creator: scepeda
date_created: 2019-05-23T11:18:16Z
date_updated: 2020-07-14T12:47:31Z
file_id: '6480'
file_name: Thesis_Cepeda.zip
file_size: 23937464
relation: source_file
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content_type: application/pdf
creator: scepeda
date_created: 2019-05-23T11:18:13Z
date_updated: 2020-07-14T12:47:31Z
file_id: '6481'
file_name: CepedaThesis.pdf
file_size: 16646985
relation: main_file
file_date_updated: 2020-07-14T12:47:31Z
has_accepted_license: '1'
keyword:
- Information estimation
- Time-series
- data analysis
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '135'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '1576'
relation: dissertation_contains
status: public
- id: '6900'
relation: dissertation_contains
status: public
- id: '281'
relation: dissertation_contains
status: public
- id: '2016'
relation: dissertation_contains
status: public
status: public
supervisor:
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
title: Estimating information flow in single cells
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: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '11691'
abstract:
- lang: eng
text: In this paper we consider the online ftp problem. The goal is to service a
sequence of file transfer requests given bandwidth constraints of the underlying
communication network. The main result of the paper is a technique that leads
to algorithms that optimize several natural metrics, such as max-stretch, total
flow time, max flow time, and total completion time. In particular, we show how
to achieve optimum total flow time and optimum max-stretch if we increase the
capacity of the underlying network by a logarithmic factor. We show that the resource
augmentation is necessary by proving polynomial lower bounds on the max-stretch
and total flow time for the case where online and offline algorithms are using
same-capacity edges. Moreover, we also give polylogarithmic lower bounds on the
resource augmentation factor necessary in order to keep the total flow time and
max-stretch within a constant factor of optimum.
article_processing_charge: No
author:
- first_name: Ashish
full_name: Goel, Ashish
last_name: Goel
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Serge
full_name: Plotkin, Serge
last_name: Plotkin
- first_name: Eva
full_name: Tardos, Eva
last_name: Tardos
citation:
ama: 'Goel A, Henzinger MH, Plotkin S, Tardos E. Scheduling data transfers in a
network and the set scheduling problem. In: Proceedings of the 31st Annual
ACM Symposium on Theory of Computing. Association for Computing Machinery;
1999:189-197. doi:10.1145/301250.301300'
apa: 'Goel, A., Henzinger, M. H., Plotkin, S., & Tardos, E. (1999). Scheduling
data transfers in a network and the set scheduling problem. In Proceedings
of the 31st annual ACM symposium on Theory of computing (pp. 189–197). Atlanta,
GA, United States: Association for Computing Machinery. https://doi.org/10.1145/301250.301300'
chicago: Goel, Ashish, Monika H Henzinger, Serge Plotkin, and Eva Tardos. “Scheduling
Data Transfers in a Network and the Set Scheduling Problem.” In Proceedings
of the 31st Annual ACM Symposium on Theory of Computing, 189–97. Association
for Computing Machinery, 1999. https://doi.org/10.1145/301250.301300.
ieee: A. Goel, M. H. Henzinger, S. Plotkin, and E. Tardos, “Scheduling data transfers
in a network and the set scheduling problem,” in Proceedings of the 31st annual
ACM symposium on Theory of computing, Atlanta, GA, United States, 1999, pp.
189–197.
ista: 'Goel A, Henzinger MH, Plotkin S, Tardos E. 1999. Scheduling data transfers
in a network and the set scheduling problem. Proceedings of the 31st annual ACM
symposium on Theory of computing. STOC: Symposium on Theory of Computing, 189–197.'
mla: Goel, Ashish, et al. “Scheduling Data Transfers in a Network and the Set Scheduling
Problem.” Proceedings of the 31st Annual ACM Symposium on Theory of Computing,
Association for Computing Machinery, 1999, pp. 189–97, doi:10.1145/301250.301300.
short: A. Goel, M.H. Henzinger, S. Plotkin, E. Tardos, in:, Proceedings of the 31st
Annual ACM Symposium on Theory of Computing, Association for Computing Machinery,
1999, pp. 189–197.
conference:
end_date: 1999-05-04
location: ' Atlanta, GA, United States'
name: 'STOC: Symposium on Theory of Computing'
start_date: 1999-05-01
date_created: 2022-07-29T07:43:00Z
date_published: 1999-05-01T00:00:00Z
date_updated: 2023-02-09T11:47:09Z
day: '01'
doi: 10.1145/301250.301300
extern: '1'
keyword:
- Scheduling
- Flow time
language:
- iso: eng
month: '05'
oa_version: None
page: 189-197
publication: Proceedings of the 31st annual ACM symposium on Theory of computing
publication_identifier:
issn:
- 0196-6774
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Scheduling data transfers in a network and the set scheduling problem
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '1999'
...
---
_id: '4590'
abstract:
- lang: eng
text: 'We introduce a temporal logic for the specification of real-time systems.
Our logic, TPTL, employs a novel quantifier construct for referencing time: the
"freeze" quantifier binds a variable to the time of the local temporal
context. TPTL is both a natural language for specification and a suitable formalism
for verification. We present a tableau-based decision procedure and a model-checking
algorithm for TPTL. Several generalizations of TPTL are shown to be highly undecidable.'
acknowledgement: The authors thank Rance Cleaveland, Limor Fix, David Karr, Peter
Kopke, Fred Schneider, and Bernhard Steffen for helpful comments.
alternative_title:
- AMAST Series in Computing
article_processing_charge: No
author:
- first_name: Rajeev
full_name: Alur, Rajeev
last_name: Alur
- 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: 'Alur R, Henzinger TA. Real-time system = discrete system + clock variables.
In: Rus T, Rattray C, eds. Theories and Experiences for Real-Time System Development.
Vol 2. AMAST Series in Computing. World Scientific Publishing; 1994:1-29. doi:10.1142/9789812831583_0001'
apa: Alur, R., & Henzinger, T. A. (1994). Real-time system = discrete system
+ clock variables. In T. Rus & C. Rattray (Eds.), Theories and Experiences
for Real-Time System Development (Vol. 2, pp. 1–29). World Scientific Publishing.
https://doi.org/10.1142/9789812831583_0001
chicago: Alur, Rajeev, and Thomas A Henzinger. “Real-Time System = Discrete System
+ Clock Variables.” In Theories and Experiences for Real-Time System Development,
edited by Teodor Rus and Charles Rattray, 2:1–29. AMAST Series in Computing. World
Scientific Publishing, 1994. https://doi.org/10.1142/9789812831583_0001.
ieee: R. Alur and T. A. Henzinger, “Real-time system = discrete system + clock variables,”
in Theories and Experiences for Real-Time System Development, vol. 2, T.
Rus and C. Rattray, Eds. World Scientific Publishing, 1994, pp. 1–29.
ista: 'Alur R, Henzinger TA. 1994.Real-time system = discrete system + clock variables.
In: Theories and Experiences for Real-Time System Development. AMAST Series in
Computing, vol. 2, 1–29.'
mla: Alur, Rajeev, and Thomas A. Henzinger. “Real-Time System = Discrete System
+ Clock Variables.” Theories and Experiences for Real-Time System Development,
edited by Teodor Rus and Charles Rattray, vol. 2, World Scientific Publishing,
1994, pp. 1–29, doi:10.1142/9789812831583_0001.
short: R. Alur, T.A. Henzinger, in:, T. Rus, C. Rattray (Eds.), Theories and Experiences
for Real-Time System Development, World Scientific Publishing, 1994, pp. 1–29.
date_created: 2018-12-11T12:09:38Z
date_published: 1994-01-01T00:00:00Z
date_updated: 2022-06-02T08:07:57Z
day: '01'
doi: 10.1142/9789812831583_0001
editor:
- first_name: Teodor
full_name: Rus, Teodor
last_name: Rus
- first_name: Charles
full_name: Rattray, Charles
last_name: Rattray
extern: '1'
intvolume: ' 2'
keyword:
- real-time systems
- clock variables
language:
- iso: eng
main_file_link:
- url: https://link.springer.com/article/10.1007/s100090050007
month: '01'
oa_version: None
page: 1 - 29
publication: Theories and Experiences for Real-Time System Development
publication_identifier:
isbn:
- ' 9789810219239'
publication_status: published
publisher: World Scientific Publishing
publist_id: '117'
quality_controlled: '1'
series_title: AMAST Series in Computing
status: public
title: Real-time system = discrete system + clock variables
type: book_chapter
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 2
year: '1994'
...