---
_id: '421'
abstract:
- lang: eng
text: Cell shape is determined by a balance of intrinsic properties of the cell
as well as its mechanochemical environment. Inhomogeneous shape changes underlie
many morphogenetic events and involve spatial gradients in active cellular forces
induced by complex chemical signaling. Here, we introduce a mechanochemical model
based on the notion that cell shape changes may be induced by external diffusible
biomolecules that influence cellular contractility (or equivalently, adhesions)
in a concentration-dependent manner—and whose spatial profile in turn is affected
by cell shape. We map out theoretically the possible interplay between chemical
concentration and cellular structure. Besides providing a direct route to spatial
gradients in cell shape profiles in tissues, we show that the dependence on cell
shape helps create robust mechanochemical gradients.
article_processing_charge: No
author:
- first_name: Kinjal
full_name: Dasbiswas, Kinjal
last_name: Dasbiswas
- first_name: Claude-Edouard B
full_name: Hannezo, Claude-Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Nir
full_name: Gov, Nir
last_name: Gov
citation:
ama: Dasbiswas K, Hannezo EB, Gov N. Theory of eppithelial cell shape transitions
induced by mechanoactive chemical gradients. Biophysical Journal. 2018;114(4):968-977.
doi:10.1016/j.bpj.2017.12.022
apa: Dasbiswas, K., Hannezo, E. B., & Gov, N. (2018). Theory of eppithelial
cell shape transitions induced by mechanoactive chemical gradients. Biophysical
Journal. Biophysical Society. https://doi.org/10.1016/j.bpj.2017.12.022
chicago: Dasbiswas, Kinjal, Edouard B Hannezo, and Nir Gov. “Theory of Eppithelial
Cell Shape Transitions Induced by Mechanoactive Chemical Gradients.” Biophysical
Journal. Biophysical Society, 2018. https://doi.org/10.1016/j.bpj.2017.12.022.
ieee: K. Dasbiswas, E. B. Hannezo, and N. Gov, “Theory of eppithelial cell shape
transitions induced by mechanoactive chemical gradients,” Biophysical Journal,
vol. 114, no. 4. Biophysical Society, pp. 968–977, 2018.
ista: Dasbiswas K, Hannezo EB, Gov N. 2018. Theory of eppithelial cell shape transitions
induced by mechanoactive chemical gradients. Biophysical Journal. 114(4), 968–977.
mla: Dasbiswas, Kinjal, et al. “Theory of Eppithelial Cell Shape Transitions Induced
by Mechanoactive Chemical Gradients.” Biophysical Journal, vol. 114, no.
4, Biophysical Society, 2018, pp. 968–77, doi:10.1016/j.bpj.2017.12.022.
short: K. Dasbiswas, E.B. Hannezo, N. Gov, Biophysical Journal 114 (2018) 968–977.
date_created: 2018-12-11T11:46:23Z
date_published: 2018-02-27T00:00:00Z
date_updated: 2023-09-19T10:13:55Z
day: '27'
department:
- _id: EdHa
doi: 10.1016/j.bpj.2017.12.022
external_id:
arxiv:
- '1709.01486'
isi:
- '000428016700021'
intvolume: ' 114'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1709.01486
month: '02'
oa: 1
oa_version: Submitted Version
page: 968 - 977
publication: Biophysical Journal
publication_status: published
publisher: Biophysical Society
publist_id: '7403'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Theory of eppithelial cell shape transitions induced by mechanoactive chemical
gradients
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 114
year: '2018'
...
---
_id: '63'
abstract:
- lang: eng
text: African cichlids display a remarkable assortment of jaw morphologies, pigmentation
patterns, and mating behaviors. In addition to this previously documented diversity,
recent studies have documented a rich diversity of sex chromosomes within these
fishes. Here we review the known sex-determination network within vertebrates,
and the extraordinary number of sex chromosomes systems segregating in African
cichlids. We also propose a model for understanding the unusual number of sex
chromosome systems within this clade.
acknowledgement: NSF DEB-1830753 and ISTPlus Fellowship
article_number: '480'
article_processing_charge: No
author:
- first_name: William J
full_name: Gammerdinger, William J
id: 3A7E01BC-F248-11E8-B48F-1D18A9856A87
last_name: Gammerdinger
orcid: 0000-0001-9638-1220
- first_name: Thomas
full_name: Kocher, Thomas
last_name: Kocher
citation:
ama: Gammerdinger WJ, Kocher T. Unusual diversity of sex chromosomes in African
cichlid fishes. Genes. 2018;9(10). doi:10.3390/genes9100480
apa: Gammerdinger, W. J., & Kocher, T. (2018). Unusual diversity of sex chromosomes
in African cichlid fishes. Genes. MDPI AG. https://doi.org/10.3390/genes9100480
chicago: Gammerdinger, William J, and Thomas Kocher. “Unusual Diversity of Sex Chromosomes
in African Cichlid Fishes.” Genes. MDPI AG, 2018. https://doi.org/10.3390/genes9100480.
ieee: W. J. Gammerdinger and T. Kocher, “Unusual diversity of sex chromosomes in
African cichlid fishes,” Genes, vol. 9, no. 10. MDPI AG, 2018.
ista: Gammerdinger WJ, Kocher T. 2018. Unusual diversity of sex chromosomes in African
cichlid fishes. Genes. 9(10), 480.
mla: Gammerdinger, William J., and Thomas Kocher. “Unusual Diversity of Sex Chromosomes
in African Cichlid Fishes.” Genes, vol. 9, no. 10, 480, MDPI AG, 2018,
doi:10.3390/genes9100480.
short: W.J. Gammerdinger, T. Kocher, Genes 9 (2018).
date_created: 2018-12-11T11:44:26Z
date_published: 2018-10-04T00:00:00Z
date_updated: 2023-09-19T10:37:03Z
day: '04'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.3390/genes9100480
ec_funded: 1
external_id:
isi:
- '000448656700018'
file:
- access_level: open_access
checksum: bec527692e2c9b56919c0429634ff337
content_type: application/pdf
creator: dernst
date_created: 2018-12-18T09:54:46Z
date_updated: 2020-07-14T12:47:27Z
file_id: '5743'
file_name: 2018_Genes_Gammerdinger.pdf
file_size: 1415791
relation: main_file
file_date_updated: 2020-07-14T12:47:27Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Genes
publication_status: published
publisher: MDPI AG
publist_id: '7991'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Unusual diversity of sex chromosomes in African cichlid fishes
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 9
year: '2018'
...
---
_id: '296'
abstract:
- lang: eng
text: The thermodynamic description of many-particle systems rests on the assumption
of ergodicity, the ability of a system to explore all allowed configurations in
the phase space. Recent studies on many-body localization have revealed the existence
of systems that strongly violate ergodicity in the presence of quenched disorder.
Here, we demonstrate that ergodicity can be weakly broken by a different mechanism,
arising from the presence of special eigenstates in the many-body spectrum that
are reminiscent of quantum scars in chaotic non-interacting systems. In the single-particle
case, quantum scars correspond to wavefunctions that concentrate in the vicinity
of unstable periodic classical trajectories. We show that many-body scars appear
in the Fibonacci chain, a model with a constrained local Hilbert space that has
recently been experimentally realized in a Rydberg-atom quantum simulator. The
quantum scarred eigenstates are embedded throughout the otherwise thermalizing
many-body spectrum but lead to direct experimental signatures, as we show for
periodic recurrences that reproduce those observed in the experiment. Our results
suggest that scarred many-body bands give rise to a new universality class of
quantum dynamics, opening up opportunities for the creation of novel states with
long-lived coherence in systems that are now experimentally realizable.
acknowledgement: C.J.T., A.M. and Z.P. acknowledge support from EPSRC grants EP/P009409/1
and EP/M50807X/1, and Royal Society Research Grant RG160635. D.A. acknowledges support
from the Swiss National Science Foundation.
article_processing_charge: No
article_type: original
author:
- first_name: Christopher
full_name: Turner, Christopher
last_name: Turner
- first_name: Alexios
full_name: Michailidis, Alexios
id: 36EBAD38-F248-11E8-B48F-1D18A9856A87
last_name: Michailidis
orcid: 0000-0002-8443-1064
- first_name: Dmitry
full_name: Abanin, Dmitry
last_name: Abanin
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Zlatko
full_name: Papić, Zlatko
last_name: Papić
citation:
ama: Turner C, Michailidis A, Abanin D, Serbyn M, Papić Z. Weak ergodicity breaking
from quantum many-body scars. Nature Physics. 2018;14:745-749. doi:10.1038/s41567-018-0137-5
apa: Turner, C., Michailidis, A., Abanin, D., Serbyn, M., & Papić, Z. (2018).
Weak ergodicity breaking from quantum many-body scars. Nature Physics.
Nature Publishing Group. https://doi.org/10.1038/s41567-018-0137-5
chicago: Turner, Christopher, Alexios Michailidis, Dmitry Abanin, Maksym Serbyn,
and Zlatko Papić. “Weak Ergodicity Breaking from Quantum Many-Body Scars.” Nature
Physics. Nature Publishing Group, 2018. https://doi.org/10.1038/s41567-018-0137-5.
ieee: C. Turner, A. Michailidis, D. Abanin, M. Serbyn, and Z. Papić, “Weak ergodicity
breaking from quantum many-body scars,” Nature Physics, vol. 14. Nature
Publishing Group, pp. 745–749, 2018.
ista: Turner C, Michailidis A, Abanin D, Serbyn M, Papić Z. 2018. Weak ergodicity
breaking from quantum many-body scars. Nature Physics. 14, 745–749.
mla: Turner, Christopher, et al. “Weak Ergodicity Breaking from Quantum Many-Body
Scars.” Nature Physics, vol. 14, Nature Publishing Group, 2018, pp. 745–49,
doi:10.1038/s41567-018-0137-5.
short: C. Turner, A. Michailidis, D. Abanin, M. Serbyn, Z. Papić, Nature Physics
14 (2018) 745–749.
date_created: 2018-12-11T11:45:40Z
date_published: 2018-05-14T00:00:00Z
date_updated: 2023-09-19T10:37:55Z
day: '14'
department:
- _id: MaSe
doi: 10.1038/s41567-018-0137-5
external_id:
isi:
- '000438253600028'
intvolume: ' 14'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://eprints.whiterose.ac.uk/130860/
month: '05'
oa: 1
oa_version: Submitted Version
page: 745 - 749
publication: Nature Physics
publication_status: published
publisher: Nature Publishing Group
publist_id: '7585'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Weak ergodicity breaking from quantum many-body scars
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 14
year: '2018'
...
---
_id: '607'
abstract:
- lang: eng
text: We study the Fokker-Planck equation derived in the large system limit of the
Markovian process describing the dynamics of quantitative traits. The Fokker-Planck
equation is posed on a bounded domain and its transport and diffusion coefficients
vanish on the domain's boundary. We first argue that, despite this degeneracy,
the standard no-flux boundary condition is valid. We derive the weak formulation
of the problem and prove the existence and uniqueness of its solutions by constructing
the corresponding contraction semigroup on a suitable function space. Then, we
prove that for the parameter regime with high enough mutation rate the problem
exhibits a positive spectral gap, which implies exponential convergence to equilibrium.Next,
we provide a simple derivation of the so-called Dynamic Maximum Entropy (DynMaxEnt)
method for approximation of observables (moments) of the Fokker-Planck solution,
which can be interpreted as a nonlinear Galerkin approximation. The limited applicability
of the DynMaxEnt method inspires us to introduce its modified version that is
valid for the whole range of admissible parameters. Finally, we present several
numerical experiments to demonstrate the performance of both the original and
modified DynMaxEnt methods. We observe that in the parameter regimes where both
methods are valid, the modified one exhibits slightly better approximation properties
compared to the original one.
acknowledgement: "JH and PM are funded by KAUST baseline funds and grant no. 1000000193
.\r\nWe thank Nicholas Barton (IST Austria) for his useful comments and suggestions.
\r\n\r\n"
article_processing_charge: No
author:
- first_name: Katarina
full_name: Bodova, Katarina
id: 2BA24EA0-F248-11E8-B48F-1D18A9856A87
last_name: Bodova
orcid: 0000-0002-7214-0171
- first_name: Jan
full_name: Haskovec, Jan
last_name: Haskovec
- first_name: Peter
full_name: Markowich, Peter
last_name: Markowich
citation:
ama: 'Bodova K, Haskovec J, Markowich P. Well posedness and maximum entropy approximation
for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena.
2018;376-377:108-120. doi:10.1016/j.physd.2017.10.015'
apa: 'Bodova, K., Haskovec, J., & Markowich, P. (2018). Well posedness and maximum
entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear
Phenomena. Elsevier. https://doi.org/10.1016/j.physd.2017.10.015'
chicago: 'Bodova, Katarina, Jan Haskovec, and Peter Markowich. “Well Posedness and
Maximum Entropy Approximation for the Dynamics of Quantitative Traits.” Physica
D: Nonlinear Phenomena. Elsevier, 2018. https://doi.org/10.1016/j.physd.2017.10.015.'
ieee: 'K. Bodova, J. Haskovec, and P. Markowich, “Well posedness and maximum entropy
approximation for the dynamics of quantitative traits,” Physica D: Nonlinear
Phenomena, vol. 376–377. Elsevier, pp. 108–120, 2018.'
ista: 'Bodova K, Haskovec J, Markowich P. 2018. Well posedness and maximum entropy
approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena.
376–377, 108–120.'
mla: 'Bodova, Katarina, et al. “Well Posedness and Maximum Entropy Approximation
for the Dynamics of Quantitative Traits.” Physica D: Nonlinear Phenomena,
vol. 376–377, Elsevier, 2018, pp. 108–20, doi:10.1016/j.physd.2017.10.015.'
short: 'K. Bodova, J. Haskovec, P. Markowich, Physica D: Nonlinear Phenomena 376–377
(2018) 108–120.'
date_created: 2018-12-11T11:47:28Z
date_published: 2018-08-01T00:00:00Z
date_updated: 2023-09-19T10:38:34Z
day: '01'
department:
- _id: NiBa
- _id: GaTk
doi: 10.1016/j.physd.2017.10.015
external_id:
arxiv:
- '1704.08757'
isi:
- '000437962900012'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1704.08757
month: '08'
oa: 1
oa_version: Submitted Version
page: 108-120
publication: 'Physica D: Nonlinear Phenomena'
publication_status: published
publisher: Elsevier
publist_id: '7198'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Well posedness and maximum entropy approximation for the dynamics of quantitative
traits
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 376-377
year: '2018'
...
---
_id: '294'
abstract:
- lang: eng
text: We developed a method to calculate two-photon processes in quantum mechanics
that replaces the infinite summation over the intermediate states by a perturbation
expansion. This latter consists of a series of commutators that involve position,
momentum, and Hamiltonian quantum operators. We analyzed several single- and many-particle
cases for which a closed-form solution to the perturbation expansion exists, as
well as more complicated cases for which a solution is found by convergence. Throughout
the article, Rayleigh and Raman scattering are taken as examples of two-photon
processes. The present method provides a clear distinction between the Thomson
scattering, regarded as classical scattering, and quantum contributions. Such
a distinction lets us derive general results concerning light scattering. Finally,
possible extensions to the developed formalism are discussed.
article_processing_charge: No
author:
- first_name: Filippo
full_name: Fratini, Filippo
last_name: Fratini
- first_name: Laleh
full_name: Safari, Laleh
id: 3C325E5E-F248-11E8-B48F-1D18A9856A87
last_name: Safari
- first_name: Pedro
full_name: Amaro, Pedro
last_name: Amaro
- first_name: José
full_name: Santos, José
last_name: Santos
citation:
ama: Fratini F, Safari L, Amaro P, Santos J. Two-photon processes based on quantum
commutators. Physical Review A - Atomic, Molecular, and Optical Physics.
2018;97(4). doi:10.1103/PhysRevA.97.043842
apa: Fratini, F., Safari, L., Amaro, P., & Santos, J. (2018). Two-photon processes
based on quantum commutators. Physical Review A - Atomic, Molecular, and Optical
Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.97.043842
chicago: Fratini, Filippo, Laleh Safari, Pedro Amaro, and José Santos. “Two-Photon
Processes Based on Quantum Commutators.” Physical Review A - Atomic, Molecular,
and Optical Physics. American Physical Society, 2018. https://doi.org/10.1103/PhysRevA.97.043842.
ieee: F. Fratini, L. Safari, P. Amaro, and J. Santos, “Two-photon processes based
on quantum commutators,” Physical Review A - Atomic, Molecular, and Optical
Physics, vol. 97, no. 4. American Physical Society, 2018.
ista: Fratini F, Safari L, Amaro P, Santos J. 2018. Two-photon processes based on
quantum commutators. Physical Review A - Atomic, Molecular, and Optical Physics.
97(4).
mla: Fratini, Filippo, et al. “Two-Photon Processes Based on Quantum Commutators.”
Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no.
4, American Physical Society, 2018, doi:10.1103/PhysRevA.97.043842.
short: F. Fratini, L. Safari, P. Amaro, J. Santos, Physical Review A - Atomic, Molecular,
and Optical Physics 97 (2018).
date_created: 2018-12-11T11:45:40Z
date_published: 2018-04-18T00:00:00Z
date_updated: 2023-09-19T10:17:56Z
day: '18'
department:
- _id: MiLe
doi: 10.1103/PhysRevA.97.043842
ec_funded: 1
external_id:
arxiv:
- '1801.06892'
isi:
- '000430296800008'
intvolume: ' 97'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1801.06892
month: '04'
oa: 1
oa_version: Submitted Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Physical Review A - Atomic, Molecular, and Optical Physics
publication_status: published
publisher: American Physical Society
publist_id: '7587'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Two-photon processes based on quantum commutators
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 97
year: '2018'
...
---
_id: '606'
abstract:
- lang: eng
text: We establish the existence of a global solution for a new family of fluid-like
equations, which are obtained in certain regimes in as the mean-field evolution
of the supercurrent density in a (2D section of a) type-II superconductor with
pinning and with imposed electric current. We also consider general vortex-sheet
initial data, and investigate the uniqueness and regularity properties of the
solution. For some choice of parameters, the equation under investigation coincides
with the so-called lake equation from 2D shallow water fluid dynamics, and our
analysis then leads to a new existence result for rough initial data.
acknowledgement: "The work of the author is supported by F.R.S.-FNRS ( Fonds de la
Recherche Scientifique - FNRS ) through a Research Fellowship.\r\n\r\n"
article_processing_charge: No
author:
- first_name: Mitia
full_name: Duerinckx, Mitia
last_name: Duerinckx
- first_name: Julian L
full_name: Fischer, Julian L
id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87
last_name: Fischer
orcid: 0000-0002-0479-558X
citation:
ama: Duerinckx M, Fischer JL. Well-posedness for mean-field evolutions arising in
superconductivity. Annales de l’Institut Henri Poincare (C) Non Linear Analysis.
2018;35(5):1267-1319. doi:10.1016/j.anihpc.2017.11.004
apa: Duerinckx, M., & Fischer, J. L. (2018). Well-posedness for mean-field evolutions
arising in superconductivity. Annales de l’Institut Henri Poincare (C) Non
Linear Analysis. Elsevier. https://doi.org/10.1016/j.anihpc.2017.11.004
chicago: Duerinckx, Mitia, and Julian L Fischer. “Well-Posedness for Mean-Field
Evolutions Arising in Superconductivity.” Annales de l’Institut Henri Poincare
(C) Non Linear Analysis. Elsevier, 2018. https://doi.org/10.1016/j.anihpc.2017.11.004.
ieee: M. Duerinckx and J. L. Fischer, “Well-posedness for mean-field evolutions
arising in superconductivity,” Annales de l’Institut Henri Poincare (C) Non
Linear Analysis, vol. 35, no. 5. Elsevier, pp. 1267–1319, 2018.
ista: Duerinckx M, Fischer JL. 2018. Well-posedness for mean-field evolutions arising
in superconductivity. Annales de l’Institut Henri Poincare (C) Non Linear Analysis.
35(5), 1267–1319.
mla: Duerinckx, Mitia, and Julian L. Fischer. “Well-Posedness for Mean-Field Evolutions
Arising in Superconductivity.” Annales de l’Institut Henri Poincare (C) Non
Linear Analysis, vol. 35, no. 5, Elsevier, 2018, pp. 1267–319, doi:10.1016/j.anihpc.2017.11.004.
short: M. Duerinckx, J.L. Fischer, Annales de l’Institut Henri Poincare (C) Non
Linear Analysis 35 (2018) 1267–1319.
date_created: 2018-12-11T11:47:27Z
date_published: 2018-08-01T00:00:00Z
date_updated: 2023-09-19T10:39:09Z
day: '01'
department:
- _id: JuFi
doi: 10.1016/j.anihpc.2017.11.004
external_id:
arxiv:
- '1607.00268'
isi:
- '000437975500005'
intvolume: ' 35'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1607.00268
month: '08'
oa: 1
oa_version: Submitted Version
page: 1267-1319
publication: Annales de l'Institut Henri Poincare (C) Non Linear Analysis
publication_status: published
publisher: Elsevier
publist_id: '7199'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Well-posedness for mean-field evolutions arising in superconductivity
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 35
year: '2018'
...
---
_id: '5959'
abstract:
- lang: eng
text: Formalizing properties of systems with continuous dynamics is a challenging
task. In this paper, we propose a formal framework for specifying and monitoring
rich temporal properties of real-valued signals. We introduce signal first-order
logic (SFO) as a specification language that combines first-order logic with linear-real
arithmetic and unary function symbols interpreted as piecewise-linear signals.
We first show that while the satisfiability problem for SFO is undecidable, its
membership and monitoring problems are decidable. We develop an offline monitoring
procedure for SFO that has polynomial complexity in the size of the input trace
and the specification, for a fixed number of quantifiers and function symbols.
We show that the algorithm has computation time linear in the size of the input
trace for the important fragment of bounded-response specifications interpreted
over input traces with finite variability. We can use our results to extend signal
temporal logic with first-order quantifiers over time and value parameters, while
preserving its efficient monitoring. We finally demonstrate the practical appeal
of our logic through a case study in the micro-electronics domain.
article_processing_charge: No
author:
- first_name: Alexey
full_name: Bakhirkin, Alexey
last_name: Bakhirkin
- first_name: Thomas
full_name: Ferrere, Thomas
id: 40960E6E-F248-11E8-B48F-1D18A9856A87
last_name: Ferrere
orcid: 0000-0001-5199-3143
- 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: Deian
full_name: Nickovicl, Deian
last_name: Nickovicl
citation:
ama: 'Bakhirkin A, Ferrere T, Henzinger TA, Nickovicl D. Keynote: The first-order
logic of signals. In: 2018 International Conference on Embedded Software.
IEEE; 2018:1-10. doi:10.1109/emsoft.2018.8537203'
apa: 'Bakhirkin, A., Ferrere, T., Henzinger, T. A., & Nickovicl, D. (2018).
Keynote: The first-order logic of signals. In 2018 International Conference
on Embedded Software (pp. 1–10). Turin, Italy: IEEE. https://doi.org/10.1109/emsoft.2018.8537203'
chicago: 'Bakhirkin, Alexey, Thomas Ferrere, Thomas A Henzinger, and Deian Nickovicl.
“Keynote: The First-Order Logic of Signals.” In 2018 International Conference
on Embedded Software, 1–10. IEEE, 2018. https://doi.org/10.1109/emsoft.2018.8537203.'
ieee: 'A. Bakhirkin, T. Ferrere, T. A. Henzinger, and D. Nickovicl, “Keynote: The
first-order logic of signals,” in 2018 International Conference on Embedded
Software, Turin, Italy, 2018, pp. 1–10.'
ista: 'Bakhirkin A, Ferrere T, Henzinger TA, Nickovicl D. 2018. Keynote: The first-order
logic of signals. 2018 International Conference on Embedded Software. EMSOFT:
International Conference on Embedded Software, 1–10.'
mla: 'Bakhirkin, Alexey, et al. “Keynote: The First-Order Logic of Signals.” 2018
International Conference on Embedded Software, IEEE, 2018, pp. 1–10, doi:10.1109/emsoft.2018.8537203.'
short: A. Bakhirkin, T. Ferrere, T.A. Henzinger, D. Nickovicl, in:, 2018 International
Conference on Embedded Software, IEEE, 2018, pp. 1–10.
conference:
end_date: 2018-10-05
location: Turin, Italy
name: 'EMSOFT: International Conference on Embedded Software'
start_date: 2018-09-30
date_created: 2019-02-13T09:19:28Z
date_published: 2018-09-30T00:00:00Z
date_updated: 2023-09-19T10:41:29Z
day: '30'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1109/emsoft.2018.8537203
external_id:
isi:
- '000492828500005'
file:
- access_level: open_access
checksum: 234a33ad9055b3458fcdda6af251b33a
content_type: application/pdf
creator: dernst
date_created: 2020-05-14T16:01:29Z
date_updated: 2020-07-14T12:47:13Z
file_id: '7839'
file_name: 2018_EMSOFT_Bakhirkin.pdf
file_size: 338006
relation: main_file
file_date_updated: 2020-07-14T12:47:13Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 1-10
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: 2018 International Conference on Embedded Software
publication_identifier:
isbn:
- '9781538655603'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Keynote: The first-order logic of signals'
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '5962'
abstract:
- lang: eng
text: Stochastic Gradient Descent (SGD) is a fundamental algorithm in machine learning,
representing the optimization backbone for training several classic models, from
regression to neural networks. Given the recent practical focus on distributed
machine learning, significant work has been dedicated to the convergence properties
of this algorithm under the inconsistent and noisy updates arising from execution
in a distributed environment. However, surprisingly, the convergence properties
of this classic algorithm in the standard shared-memory model are still not well-understood.
In this work, we address this gap, and provide new convergence bounds for lock-free
concurrent stochastic gradient descent, executing in the classic asynchronous
shared memory model, against a strong adaptive adversary. Our results give improved
upper and lower bounds on the "price of asynchrony'' when executing the fundamental
SGD algorithm in a concurrent setting. They show that this classic optimization
tool can converge faster and with a wider range of parameters than previously
known under asynchronous iterations. At the same time, we exhibit a fundamental
trade-off between the maximum delay in the system and the rate at which SGD can
converge, which governs the set of parameters under which this algorithm can still
work efficiently.
article_processing_charge: No
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Christopher
full_name: De Sa, Christopher
last_name: De Sa
- first_name: Nikola H
full_name: Konstantinov, Nikola H
id: 4B9D76E4-F248-11E8-B48F-1D18A9856A87
last_name: Konstantinov
citation:
ama: 'Alistarh D-A, De Sa C, Konstantinov NH. The convergence of stochastic gradient
descent in asynchronous shared memory. In: Proceedings of the 2018 ACM Symposium
on Principles of Distributed Computing - PODC ’18. ACM Press; 2018:169-178.
doi:10.1145/3212734.3212763'
apa: 'Alistarh, D.-A., De Sa, C., & Konstantinov, N. H. (2018). The convergence
of stochastic gradient descent in asynchronous shared memory. In Proceedings
of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18
(pp. 169–178). Egham, United Kingdom: ACM Press. https://doi.org/10.1145/3212734.3212763'
chicago: Alistarh, Dan-Adrian, Christopher De Sa, and Nikola H Konstantinov. “The
Convergence of Stochastic Gradient Descent in Asynchronous Shared Memory.” In
Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing
- PODC ’18, 169–78. ACM Press, 2018. https://doi.org/10.1145/3212734.3212763.
ieee: D.-A. Alistarh, C. De Sa, and N. H. Konstantinov, “The convergence of stochastic
gradient descent in asynchronous shared memory,” in Proceedings of the 2018
ACM Symposium on Principles of Distributed Computing - PODC ’18, Egham, United
Kingdom, 2018, pp. 169–178.
ista: 'Alistarh D-A, De Sa C, Konstantinov NH. 2018. The convergence of stochastic
gradient descent in asynchronous shared memory. Proceedings of the 2018 ACM Symposium
on Principles of Distributed Computing - PODC ’18. PODC: Principles of Distributed
Computing, 169–178.'
mla: Alistarh, Dan-Adrian, et al. “The Convergence of Stochastic Gradient Descent
in Asynchronous Shared Memory.” Proceedings of the 2018 ACM Symposium on Principles
of Distributed Computing - PODC ’18, ACM Press, 2018, pp. 169–78, doi:10.1145/3212734.3212763.
short: D.-A. Alistarh, C. De Sa, N.H. Konstantinov, in:, Proceedings of the 2018
ACM Symposium on Principles of Distributed Computing - PODC ’18, ACM Press, 2018,
pp. 169–178.
conference:
end_date: 2018-07-27
location: Egham, United Kingdom
name: 'PODC: Principles of Distributed Computing'
start_date: 2018-07-23
date_created: 2019-02-13T09:58:58Z
date_published: 2018-07-23T00:00:00Z
date_updated: 2023-09-19T10:42:53Z
day: '23'
department:
- _id: DaAl
doi: 10.1145/3212734.3212763
external_id:
arxiv:
- '1803.08841'
isi:
- '000458186900022'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1803.08841
month: '07'
oa: 1
oa_version: Preprint
page: 169-178
publication: Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing -
PODC '18
publication_identifier:
isbn:
- '9781450357951'
publication_status: published
publisher: ACM Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: The convergence of stochastic gradient descent in asynchronous shared memory
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '5860'
abstract:
- lang: eng
text: 'A major problem for evolutionary theory is understanding the so-called open-ended
nature of evolutionary change, from its definition to its origins. Open-ended
evolution (OEE) refers to the unbounded increase in complexity that seems to characterize
evolution on multiple scales. This property seems to be a characteristic feature
of biological and technological evolution and is strongly tied to the generative
potential associated with combinatorics, which allows the system to grow and expand
their available state spaces. Interestingly, many complex systems presumably displaying
OEE, from language to proteins, share a common statistical property: the presence
of Zipf''s Law. Given an inventory of basic items (such as words or protein domains)
required to build more complex structures (sentences or proteins) Zipf''s Law
tells us that most of these elements are rare whereas a few of them are extremely
common. Using algorithmic information theory, in this paper we provide a fundamental
definition for open-endedness, which can be understood as postulates. Its statistical
counterpart, based on standard Shannon information theory, has the structure of
a variational problem which is shown to lead to Zipf''s Law as the expected consequence
of an evolutionary process displaying OEE. We further explore the problem of information
conservation through an OEE process and we conclude that statistical information
(standard Shannon information) is not conserved, resulting in the paradoxical
situation in which the increase of information content has the effect of erasing
itself. We prove that this paradox is solved if we consider non-statistical forms
of information. This last result implies that standard information theory may
not be a suitable theoretical framework to explore the persistence and increase
of the information content in OEE systems.'
article_number: '20180395'
article_processing_charge: No
author:
- first_name: Bernat
full_name: Corominas-Murtra, Bernat
id: 43BE2298-F248-11E8-B48F-1D18A9856A87
last_name: Corominas-Murtra
orcid: 0000-0001-9806-5643
- first_name: Luís F.
full_name: Seoane, Luís F.
last_name: Seoane
- first_name: Ricard
full_name: Solé, Ricard
last_name: Solé
citation:
ama: Corominas-Murtra B, Seoane LF, Solé R. Zipf’s Law, unbounded complexity and
open-ended evolution. Journal of the Royal Society Interface. 2018;15(149).
doi:10.1098/rsif.2018.0395
apa: Corominas-Murtra, B., Seoane, L. F., & Solé, R. (2018). Zipf’s Law, unbounded
complexity and open-ended evolution. Journal of the Royal Society Interface.
Royal Society Publishing. https://doi.org/10.1098/rsif.2018.0395
chicago: Corominas-Murtra, Bernat, Luís F. Seoane, and Ricard Solé. “Zipf’s Law,
Unbounded Complexity and Open-Ended Evolution.” Journal of the Royal Society
Interface. Royal Society Publishing, 2018. https://doi.org/10.1098/rsif.2018.0395.
ieee: B. Corominas-Murtra, L. F. Seoane, and R. Solé, “Zipf’s Law, unbounded complexity
and open-ended evolution,” Journal of the Royal Society Interface, vol.
15, no. 149. Royal Society Publishing, 2018.
ista: Corominas-Murtra B, Seoane LF, Solé R. 2018. Zipf’s Law, unbounded complexity
and open-ended evolution. Journal of the Royal Society Interface. 15(149), 20180395.
mla: Corominas-Murtra, Bernat, et al. “Zipf’s Law, Unbounded Complexity and Open-Ended
Evolution.” Journal of the Royal Society Interface, vol. 15, no. 149, 20180395,
Royal Society Publishing, 2018, doi:10.1098/rsif.2018.0395.
short: B. Corominas-Murtra, L.F. Seoane, R. Solé, Journal of the Royal Society Interface
15 (2018).
date_created: 2019-01-20T22:59:19Z
date_published: 2018-12-12T00:00:00Z
date_updated: 2023-09-19T10:40:38Z
day: '12'
department:
- _id: EdHa
doi: 10.1098/rsif.2018.0395
external_id:
arxiv:
- '1612.01605'
isi:
- '000456783800002'
intvolume: ' 15'
isi: 1
issue: '149'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1612.01605
month: '12'
oa: 1
oa_version: Preprint
publication: Journal of the Royal Society Interface
publication_identifier:
issn:
- '17425689'
publication_status: published
publisher: Royal Society Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Zipf's Law, unbounded complexity and open-ended evolution
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 15
year: '2018'
...
---
_id: '5960'
abstract:
- lang: eng
text: In this paper we present a reliable method to verify the existence of loops
along the uncertain trajectory of a robot, based on proprioceptive measurements
only, within a bounded-error context. The loop closure detection is one of the
key points in simultaneous localization and mapping (SLAM) methods, especially
in homogeneous environments with difficult scenes recognitions. The proposed approach
is generic and could be coupled with conventional SLAM algorithms to reliably
reduce their computing burden, thus improving the localization and mapping processes
in the most challenging environments such as unexplored underwater extents. To
prove that a robot performed a loop whatever the uncertainties in its evolution,
we employ the notion of topological degree that originates in the field of differential
topology. We show that a verification tool based on the topological degree is
an optimal method for proving robot loops. This is demonstrated both on datasets
from real missions involving autonomous underwater vehicles and by a mathematical
discussion.
article_processing_charge: No
author:
- first_name: Simon
full_name: Rohou, Simon
last_name: Rohou
- first_name: Peter
full_name: Franek, Peter
id: 473294AE-F248-11E8-B48F-1D18A9856A87
last_name: Franek
orcid: 0000-0001-8878-8397
- first_name: Clément
full_name: Aubry, Clément
last_name: Aubry
- first_name: Luc
full_name: Jaulin, Luc
last_name: Jaulin
citation:
ama: Rohou S, Franek P, Aubry C, Jaulin L. Proving the existence of loops in robot
trajectories. The International Journal of Robotics Research. 2018;37(12):1500-1516.
doi:10.1177/0278364918808367
apa: Rohou, S., Franek, P., Aubry, C., & Jaulin, L. (2018). Proving the existence
of loops in robot trajectories. The International Journal of Robotics Research.
SAGE Publications. https://doi.org/10.1177/0278364918808367
chicago: Rohou, Simon, Peter Franek, Clément Aubry, and Luc Jaulin. “Proving the
Existence of Loops in Robot Trajectories.” The International Journal of Robotics
Research. SAGE Publications, 2018. https://doi.org/10.1177/0278364918808367.
ieee: S. Rohou, P. Franek, C. Aubry, and L. Jaulin, “Proving the existence of loops
in robot trajectories,” The International Journal of Robotics Research,
vol. 37, no. 12. SAGE Publications, pp. 1500–1516, 2018.
ista: Rohou S, Franek P, Aubry C, Jaulin L. 2018. Proving the existence of loops
in robot trajectories. The International Journal of Robotics Research. 37(12),
1500–1516.
mla: Rohou, Simon, et al. “Proving the Existence of Loops in Robot Trajectories.”
The International Journal of Robotics Research, vol. 37, no. 12, SAGE Publications,
2018, pp. 1500–16, doi:10.1177/0278364918808367.
short: S. Rohou, P. Franek, C. Aubry, L. Jaulin, The International Journal of Robotics
Research 37 (2018) 1500–1516.
date_created: 2019-02-13T09:36:20Z
date_published: 2018-10-24T00:00:00Z
date_updated: 2023-09-19T10:41:59Z
day: '24'
department:
- _id: UlWa
doi: 10.1177/0278364918808367
external_id:
arxiv:
- '1712.01341'
isi:
- '000456881100004'
intvolume: ' 37'
isi: 1
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1712.01341
month: '10'
oa: 1
oa_version: Preprint
page: 1500-1516
publication: The International Journal of Robotics Research
publication_identifier:
eissn:
- 1741-3176
issn:
- 0278-3649
publication_status: published
publisher: SAGE Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Proving the existence of loops in robot trajectories
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 37
year: '2018'
...