---
_id: '1191'
abstract:
- lang: eng
text: Variation in genotypes may be responsible for differences in dispersal rates,
directional biases, and growth rates of individuals. These traits may favor certain
genotypes and enhance their spatiotemporal spreading into areas occupied by the
less advantageous genotypes. We study how these factors influence the speed of
spreading in the case of two competing genotypes under the assumption that spatial
variation of the total population is small compared to the spatial variation of
the frequencies of the genotypes in the population. In that case, the dynamics
of the frequency of one of the genotypes is approximately described by a generalized
Fisher–Kolmogorov–Petrovskii–Piskunov (F–KPP) equation. This generalized F–KPP
equation with (nonlinear) frequency-dependent diffusion and advection terms admits
traveling wave solutions that characterize the invasion of the dominant genotype.
Our existence results generalize the classical theory for traveling waves for
the F–KPP with constant coefficients. Moreover, in the particular case of the
quadratic (monostable) nonlinear growth–decay rate in the generalized F–KPP we
study in detail the influence of the variance in diffusion and mean displacement
rates of the two genotypes on the minimal wave propagation speed.
acknowledgement: "We thank Nick Barton, Katarína Bod’ová, and Sr\r\n-\r\ndan Sarikas
for constructive feed-\r\nback and support. Furthermore, we would like to express
our deep gratitude to the anonymous referees (one\r\nof whom, Jimmy Garnier, agreed
to reveal his identity) and the editor Max Souza, for very helpful and\r\ndetailed
comments and suggestions that significantly helped us to improve the manuscript.
This project has\r\nreceived funding from the European Union’s Seventh Framework
Programme for research, technological\r\ndevelopment and demonstration under Grant
Agreement 618091 Speed of Adaptation in Population Genet-\r\nics and Evolutionary
Computation (SAGE) and the European Research Council (ERC) Grant No. 250152\r\n(SN),
from the Scientific Grant Agency of the Slovak Republic under the Grant 1/0459/13
and by the Slovak\r\nResearch and Development Agency under the Contract No. APVV-14-0378
(RK). RK would also like to\r\nthank IST Austria for its hospitality during the
work on this project."
article_processing_charge: No
arxiv: 1
author:
- first_name: Richard
full_name: Kollár, Richard
last_name: Kollár
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
orcid: 0000-0002-2519-824X
citation:
ama: Kollár R, Novak S. Existence of traveling waves for the generalized F–KPP equation.
Bulletin of Mathematical Biology. 2017;79(3):525-559. doi:10.1007/s11538-016-0244-3
apa: Kollár, R., & Novak, S. (2017). Existence of traveling waves for the generalized
F–KPP equation. Bulletin of Mathematical Biology. Springer. https://doi.org/10.1007/s11538-016-0244-3
chicago: Kollár, Richard, and Sebastian Novak. “Existence of Traveling Waves for
the Generalized F–KPP Equation.” Bulletin of Mathematical Biology. Springer,
2017. https://doi.org/10.1007/s11538-016-0244-3.
ieee: R. Kollár and S. Novak, “Existence of traveling waves for the generalized
F–KPP equation,” Bulletin of Mathematical Biology, vol. 79, no. 3. Springer,
pp. 525–559, 2017.
ista: Kollár R, Novak S. 2017. Existence of traveling waves for the generalized
F–KPP equation. Bulletin of Mathematical Biology. 79(3), 525–559.
mla: Kollár, Richard, and Sebastian Novak. “Existence of Traveling Waves for the
Generalized F–KPP Equation.” Bulletin of Mathematical Biology, vol. 79,
no. 3, Springer, 2017, pp. 525–59, doi:10.1007/s11538-016-0244-3.
short: R. Kollár, S. Novak, Bulletin of Mathematical Biology 79 (2017) 525–559.
date_created: 2018-12-11T11:50:38Z
date_published: 2017-03-01T00:00:00Z
date_updated: 2025-09-22T09:44:54Z
day: '01'
department:
- _id: NiBa
doi: 10.1007/s11538-016-0244-3
ec_funded: 1
external_id:
arxiv:
- '1607.00944'
isi:
- '000395156200005'
intvolume: ' 79'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1607.00944
month: '03'
oa: 1
oa_version: Preprint
page: 525-559
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Bulletin of Mathematical Biology
publication_status: published
publisher: Springer
publist_id: '6160'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Existence of traveling waves for the generalized F–KPP equation
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 79
year: '2017'
...
---
_id: '1192'
abstract:
- lang: eng
text: The main result of this paper is a generalization of the classical blossom
algorithm for finding perfect matchings. Our algorithm can efficiently solve Boolean
CSPs where each variable appears in exactly two constraints (we call it edge CSP)
and all constraints are even Δ-matroid relations (represented by lists of tuples).
As a consequence of this, we settle the complexity classification of planar Boolean
CSPs started by Dvorak and Kupec. Knowing that edge CSP is tractable for even
Δ-matroid constraints allows us to extend the tractability result to a larger
class of Δ-matroids that includes many classes that were known to be tractable
before, namely co-independent, compact, local and binary.
article_processing_charge: No
arxiv: 1
author:
- first_name: Alexandr
full_name: Kazda, Alexandr
id: 3B32BAA8-F248-11E8-B48F-1D18A9856A87
last_name: Kazda
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Michal
full_name: Rolinek, Michal
id: 3CB3BC06-F248-11E8-B48F-1D18A9856A87
last_name: Rolinek
citation:
ama: 'Kazda A, Kolmogorov V, Rolinek M. Even delta-matroids and the complexity of
planar Boolean CSPs. In: SIAM; 2017:307-326. doi:10.1137/1.9781611974782.20'
apa: 'Kazda, A., Kolmogorov, V., & Rolinek, M. (2017). Even delta-matroids and
the complexity of planar Boolean CSPs (pp. 307–326). Presented at the SODA: Symposium
on Discrete Algorithms, Barcelona, Spain: SIAM. https://doi.org/10.1137/1.9781611974782.20'
chicago: Kazda, Alexandr, Vladimir Kolmogorov, and Michal Rolinek. “Even Delta-Matroids
and the Complexity of Planar Boolean CSPs,” 307–26. SIAM, 2017. https://doi.org/10.1137/1.9781611974782.20.
ieee: 'A. Kazda, V. Kolmogorov, and M. Rolinek, “Even delta-matroids and the complexity
of planar Boolean CSPs,” presented at the SODA: Symposium on Discrete Algorithms,
Barcelona, Spain, 2017, pp. 307–326.'
ista: 'Kazda A, Kolmogorov V, Rolinek M. 2017. Even delta-matroids and the complexity
of planar Boolean CSPs. SODA: Symposium on Discrete Algorithms, 307–326.'
mla: Kazda, Alexandr, et al. Even Delta-Matroids and the Complexity of Planar
Boolean CSPs. SIAM, 2017, pp. 307–26, doi:10.1137/1.9781611974782.20.
short: A. Kazda, V. Kolmogorov, M. Rolinek, in:, SIAM, 2017, pp. 307–326.
conference:
end_date: 2017-01019
location: Barcelona, Spain
name: 'SODA: Symposium on Discrete Algorithms'
start_date: 2017-01-16
date_created: 2018-12-11T11:50:38Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2025-06-04T08:46:59Z
day: '01'
department:
- _id: VlKo
doi: 10.1137/1.9781611974782.20
ec_funded: 1
external_id:
arxiv:
- '1602.03124'
isi:
- '000426965800020'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1602.03124
month: '01'
oa: 1
oa_version: Submitted Version
page: 307 - 326
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication_identifier:
isbn:
- 978-161197478-2
publication_status: published
publisher: SIAM
publist_id: '6159'
quality_controlled: '1'
related_material:
record:
- id: '6032'
relation: later_version
status: public
status: public
title: Even delta-matroids and the complexity of planar Boolean CSPs
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '1194'
abstract:
- lang: eng
text: 'Termination is one of the basic liveness properties, and we study the termination
problem for probabilistic programs with real-valued variables. Previous works
focused on the qualitative problem that asks whether an input program terminates
with probability~1 (almost-sure termination). A powerful approach for this qualitative
problem is the notion of ranking supermartingales with respect to a given set
of invariants. The quantitative problem (probabilistic termination) asks for bounds
on the termination probability. A fundamental and conceptual drawback of the existing
approaches to address probabilistic termination is that even though the supermartingales
consider the probabilistic behavior of the programs, the invariants are obtained
completely ignoring the probabilistic aspect. In this work we address the probabilistic
termination problem for linear-arithmetic probabilistic programs with nondeterminism.
We define the notion of {\em stochastic invariants}, which are constraints along
with a probability bound that the constraints hold. We introduce a concept of
{\em repulsing supermartingales}. First, we show that repulsing supermartingales
can be used to obtain bounds on the probability of the stochastic invariants.
Second, we show the effectiveness of repulsing supermartingales in the following
three ways: (1)~With a combination of ranking and repulsing supermartingales we
can compute lower bounds on the probability of termination; (2)~repulsing supermartingales
provide witnesses for refutation of almost-sure termination; and (3)~with a combination
of ranking and repulsing supermartingales we can establish persistence properties
of probabilistic programs. We also present results on related computational problems
and an experimental evaluation of our approach on academic examples. '
alternative_title:
- ACM SIGPLAN Notices
article_processing_charge: No
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Petr
full_name: Novotny, Petr
id: 3CC3B868-F248-11E8-B48F-1D18A9856A87
last_name: Novotny
- first_name: Djordje
full_name: Zikelic, Djordje
last_name: Zikelic
citation:
ama: 'Chatterjee K, Novotný P, Zikelic D. Stochastic invariants for probabilistic
termination. In: Vol 52. ACM; 2017:145-160. doi:10.1145/3009837.3009873'
apa: 'Chatterjee, K., Novotný, P., & Zikelic, D. (2017). Stochastic invariants
for probabilistic termination (Vol. 52, pp. 145–160). Presented at the POPL: Principles
of Programming Languages, Paris, France: ACM. https://doi.org/10.1145/3009837.3009873'
chicago: Chatterjee, Krishnendu, Petr Novotný, and Djordje Zikelic. “Stochastic
Invariants for Probabilistic Termination,” 52:145–60. ACM, 2017. https://doi.org/10.1145/3009837.3009873.
ieee: 'K. Chatterjee, P. Novotný, and D. Zikelic, “Stochastic invariants for probabilistic
termination,” presented at the POPL: Principles of Programming Languages, Paris,
France, 2017, vol. 52, no. 1, pp. 145–160.'
ista: 'Chatterjee K, Novotný P, Zikelic D. 2017. Stochastic invariants for probabilistic
termination. POPL: Principles of Programming Languages, ACM SIGPLAN Notices, vol.
52, 145–160.'
mla: Chatterjee, Krishnendu, et al. Stochastic Invariants for Probabilistic Termination.
Vol. 52, no. 1, ACM, 2017, pp. 145–60, doi:10.1145/3009837.3009873.
short: K. Chatterjee, P. Novotný, D. Zikelic, in:, ACM, 2017, pp. 145–160.
conference:
end_date: 2017-01-21
location: Paris, France
name: 'POPL: Principles of Programming Languages'
start_date: 2017-01-15
date_created: 2018-12-11T11:50:39Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2026-04-07T13:27:56Z
day: '01'
department:
- _id: KrCh
doi: 10.1145/3009837.3009873
ec_funded: 1
external_id:
arxiv:
- '1611.01063'
isi:
- '000408311200013'
intvolume: ' 52'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1611.01063
month: '01'
oa: 1
oa_version: Submitted Version
page: 145 - 160
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_identifier:
issn:
- 0730-8566
publication_status: published
publisher: ACM
publist_id: '6157'
quality_controlled: '1'
related_material:
record:
- id: '14539'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Stochastic invariants for probabilistic termination
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 52
year: '2017'
...
---
_id: '1196'
abstract:
- lang: eng
text: 'We define the . model-measuring problem: given a model . M and specification
. ϕ, what is the maximal distance . ρ such that all models . M'' within distance
. ρ from . M satisfy (or violate) . ϕ. The model-measuring problem presupposes
a distance function on models. We concentrate on . automatic distance functions,
which are defined by weighted automata. The model-measuring problem subsumes several
generalizations of the classical model-checking problem, in particular, quantitative
model-checking problems that measure the degree of satisfaction of a specification;
robustness problems that measure how much a model can be perturbed without violating
the specification; and parameter synthesis for hybrid systems. We show that for
automatic distance functions, and (a) . ω-regular linear-time, (b) . ω-regular
branching-time, and (c) hybrid specifications, the model-measuring problem can
be solved.We use automata-theoretic model-checking methods for model measuring,
replacing the emptiness question for word, tree, and hybrid automata by the .
optimal-value question for the weighted versions of these automata. For automata
over words and trees, we consider weighted automata that accumulate weights by
maximizing, summing, discounting, and limit averaging. For hybrid automata, we
consider monotonic (parametric) hybrid automata, a hybrid counterpart of (discrete)
weighted automata.We give several examples of using the model-measuring problem
to compute various notions of robustness and quantitative satisfaction for temporal
specifications. Further, we propose the modeling framework for model measuring
to ease the specification and reduce the likelihood of errors in modeling.Finally,
we present a variant of the model-measuring problem, called the . model-repair
problem. The model-repair problem applies to models that do not satisfy the specification;
it can be used to derive restrictions, under which the model satisfies the specification,
i.e., to repair the model.'
acknowledgement: "This research was supported in part by the European Research Council
(ERC) under grant 267989 (QUAREM), by the Austrian Science Fund1 (FWF) under grants
S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award), and by the National Science
Centre (NCN), Poland under grant 2014/15/D/ST6/04543.\r\nA Technical Report of this
article is available via: https://repository.ist.ac.at/171/"
article_processing_charge: No
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Jan
full_name: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
citation:
ama: 'Henzinger TA, Otop J. Model measuring for discrete and hybrid systems. Nonlinear
Analysis: Hybrid Systems. 2017;23:166-190. doi:10.1016/j.nahs.2016.09.001'
apa: 'Henzinger, T. A., & Otop, J. (2017). Model measuring for discrete and
hybrid systems. Nonlinear Analysis: Hybrid Systems. Elsevier. https://doi.org/10.1016/j.nahs.2016.09.001'
chicago: 'Henzinger, Thomas A, and Jan Otop. “Model Measuring for Discrete and Hybrid
Systems.” Nonlinear Analysis: Hybrid Systems. Elsevier, 2017. https://doi.org/10.1016/j.nahs.2016.09.001.'
ieee: 'T. A. Henzinger and J. Otop, “Model measuring for discrete and hybrid systems,”
Nonlinear Analysis: Hybrid Systems, vol. 23. Elsevier, pp. 166–190, 2017.'
ista: 'Henzinger TA, Otop J. 2017. Model measuring for discrete and hybrid systems.
Nonlinear Analysis: Hybrid Systems. 23, 166–190.'
mla: 'Henzinger, Thomas A., and Jan Otop. “Model Measuring for Discrete and Hybrid
Systems.” Nonlinear Analysis: Hybrid Systems, vol. 23, Elsevier, 2017,
pp. 166–90, doi:10.1016/j.nahs.2016.09.001.'
short: 'T.A. Henzinger, J. Otop, Nonlinear Analysis: Hybrid Systems 23 (2017) 166–190.'
date_created: 2018-12-11T11:50:39Z
date_published: 2017-02-01T00:00:00Z
date_updated: 2025-04-15T06:25:59Z
day: '01'
department:
- _id: ToHe
doi: 10.1016/j.nahs.2016.09.001
ec_funded: 1
external_id:
isi:
- '000390637000011'
intvolume: ' 23'
isi: 1
language:
- iso: eng
month: '02'
oa_version: None
page: 166 - 190
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _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: Formal methods for the design and analysis of complex systems
publication: 'Nonlinear Analysis: Hybrid Systems'
publication_status: published
publisher: Elsevier
publist_id: '6154'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Model measuring for discrete and hybrid systems
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 23
year: '2017'
...
---
_id: '1198'
abstract:
- lang: eng
text: We consider a model of fermions interacting via point interactions, defined
via a certain weighted Dirichlet form. While for two particles the interaction
corresponds to infinite scattering length, the presence of further particles effectively
decreases the interaction strength. We show that the model becomes trivial in
the thermodynamic limit, in the sense that the free energy density at any given
particle density and temperature agrees with the corresponding expression for
non-interacting particles.
acknowledgement: 'Open access funding provided by Institute of Science and Technology
(IST Austria). '
article_processing_charge: Yes (via OA deal)
author:
- first_name: Thomas
full_name: Moser, Thomas
id: 2B5FC9A4-F248-11E8-B48F-1D18A9856A87
last_name: Moser
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Moser T, Seiringer R. Triviality of a model of particles with point interactions
in the thermodynamic limit. Letters in Mathematical Physics. 2017;107(3):533-552.
doi:10.1007/s11005-016-0915-x
apa: Moser, T., & Seiringer, R. (2017). Triviality of a model of particles with
point interactions in the thermodynamic limit. Letters in Mathematical Physics.
Springer. https://doi.org/10.1007/s11005-016-0915-x
chicago: Moser, Thomas, and Robert Seiringer. “Triviality of a Model of Particles
with Point Interactions in the Thermodynamic Limit.” Letters in Mathematical
Physics. Springer, 2017. https://doi.org/10.1007/s11005-016-0915-x.
ieee: T. Moser and R. Seiringer, “Triviality of a model of particles with point
interactions in the thermodynamic limit,” Letters in Mathematical Physics,
vol. 107, no. 3. Springer, pp. 533–552, 2017.
ista: Moser T, Seiringer R. 2017. Triviality of a model of particles with point
interactions in the thermodynamic limit. Letters in Mathematical Physics. 107(3),
533–552.
mla: Moser, Thomas, and Robert Seiringer. “Triviality of a Model of Particles with
Point Interactions in the Thermodynamic Limit.” Letters in Mathematical Physics,
vol. 107, no. 3, Springer, 2017, pp. 533–52, doi:10.1007/s11005-016-0915-x.
short: T. Moser, R. Seiringer, Letters in Mathematical Physics 107 (2017) 533–552.
date_created: 2018-12-11T11:50:40Z
date_published: 2017-03-01T00:00:00Z
date_updated: 2026-04-16T10:06:46Z
day: '01'
ddc:
- '510'
- '539'
department:
- _id: RoSe
doi: 10.1007/s11005-016-0915-x
external_id:
isi:
- '000394280200007'
file:
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checksum: c0c835def162c1bc52f978fad26e3c2f
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date_updated: 2020-07-14T12:44:38Z
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file_name: IST-2016-723-v1+1_s11005-016-0915-x.pdf
file_size: 587207
relation: main_file
file_date_updated: 2020-07-14T12:44:38Z
has_accepted_license: '1'
intvolume: ' 107'
isi: 1
issue: '3'
language:
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month: '03'
oa: 1
oa_version: Published Version
page: ' 533 - 552'
project:
- _id: 25C878CE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27533_N27
name: Structure of the Excitation Spectrum for Many-Body Quantum Systems
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Letters in Mathematical Physics
publication_identifier:
issn:
- 0377-9017
publication_status: published
publisher: Springer
publist_id: '6152'
pubrep_id: '723'
quality_controlled: '1'
related_material:
record:
- id: '52'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Triviality of a model of particles with point interactions in the thermodynamic
limit
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 107
year: '2017'
...
---
_id: '1199'
abstract:
- lang: eng
text: Much of quantitative genetics is based on the ‘infinitesimal model’, under
which selection has a negligible effect on the genetic variance. This is typically
justified by assuming a very large number of loci with additive effects. However,
it applies even when genes interact, provided that the number of loci is large
enough that selection on each of them is weak relative to random drift. In the
long term, directional selection will change allele frequencies, but even then,
the effects of epistasis on the ultimate change in trait mean due to selection
may be modest. Stabilising selection can maintain many traits close to their optima,
even when the underlying alleles are weakly selected. However, the number of traits
that can be optimised is apparently limited to ~4Ne by the ‘drift load’, and this
is hard to reconcile with the apparent complexity of many organisms. Just as for
the mutation load, this limit can be evaded by a particular form of negative epistasis.
A more robust limit is set by the variance in reproductive success. This suggests
that selection accumulates information most efficiently in the infinitesimal regime,
when selection on individual alleles is weak, and comparable with random drift.
A review of evidence on selection strength suggests that although most variance
in fitness may be because of alleles with large Nes, substantial amounts of adaptation
may be because of alleles in the infinitesimal regime, in which epistasis has
modest effects.
article_processing_charge: No
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. How does epistasis influence the response to selection? Heredity.
2017;118:96-109. doi:10.1038/hdy.2016.109
apa: Barton, N. H. (2017). How does epistasis influence the response to selection?
Heredity. Nature Publishing Group. https://doi.org/10.1038/hdy.2016.109
chicago: Barton, Nicholas H. “How Does Epistasis Influence the Response to Selection?”
Heredity. Nature Publishing Group, 2017. https://doi.org/10.1038/hdy.2016.109.
ieee: N. H. Barton, “How does epistasis influence the response to selection?,” Heredity,
vol. 118. Nature Publishing Group, pp. 96–109, 2017.
ista: Barton NH. 2017. How does epistasis influence the response to selection? Heredity.
118, 96–109.
mla: Barton, Nicholas H. “How Does Epistasis Influence the Response to Selection?”
Heredity, vol. 118, Nature Publishing Group, 2017, pp. 96–109, doi:10.1038/hdy.2016.109.
short: N.H. Barton, Heredity 118 (2017) 96–109.
date_created: 2018-12-11T11:50:40Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2025-04-15T07:11:02Z
day: '01'
department:
- _id: NiBa
doi: 10.1038/hdy.2016.109
ec_funded: 1
external_id:
isi:
- '000392229100011'
intvolume: ' 118'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5176114/
month: '01'
oa: 1
oa_version: Submitted Version
page: 96 - 109
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Heredity
publication_status: published
publisher: Nature Publishing Group
publist_id: '6151'
quality_controlled: '1'
related_material:
record:
- id: '9710'
relation: research_data
status: public
scopus_import: '1'
status: public
title: How does epistasis influence the response to selection?
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 118
year: '2017'
...
---
_id: '1207'
abstract:
- lang: eng
text: The eigenvalue distribution of the sum of two large Hermitian matrices, when
one of them is conjugated by a Haar distributed unitary matrix, is asymptotically
given by the free convolution of their spectral distributions. We prove that this
convergence also holds locally in the bulk of the spectrum, down to the optimal
scales larger than the eigenvalue spacing. The corresponding eigenvectors are
fully delocalized. Similar results hold for the sum of two real symmetric matrices,
when one is conjugated by Haar orthogonal matrix.
article_processing_charge: Yes (via OA deal)
author:
- first_name: Zhigang
full_name: Bao, Zhigang
id: 442E6A6C-F248-11E8-B48F-1D18A9856A87
last_name: Bao
orcid: 0000-0003-3036-1475
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Kevin
full_name: Schnelli, Kevin
id: 434AD0AE-F248-11E8-B48F-1D18A9856A87
last_name: Schnelli
orcid: 0000-0003-0954-3231
citation:
ama: Bao Z, Erdös L, Schnelli K. Local law of addition of random matrices on optimal
scale. Communications in Mathematical Physics. 2017;349(3):947-990. doi:10.1007/s00220-016-2805-6
apa: Bao, Z., Erdös, L., & Schnelli, K. (2017). Local law of addition of random
matrices on optimal scale. Communications in Mathematical Physics. Springer.
https://doi.org/10.1007/s00220-016-2805-6
chicago: Bao, Zhigang, László Erdös, and Kevin Schnelli. “Local Law of Addition
of Random Matrices on Optimal Scale.” Communications in Mathematical Physics.
Springer, 2017. https://doi.org/10.1007/s00220-016-2805-6.
ieee: Z. Bao, L. Erdös, and K. Schnelli, “Local law of addition of random matrices
on optimal scale,” Communications in Mathematical Physics, vol. 349, no.
3. Springer, pp. 947–990, 2017.
ista: Bao Z, Erdös L, Schnelli K. 2017. Local law of addition of random matrices
on optimal scale. Communications in Mathematical Physics. 349(3), 947–990.
mla: Bao, Zhigang, et al. “Local Law of Addition of Random Matrices on Optimal Scale.”
Communications in Mathematical Physics, vol. 349, no. 3, Springer, 2017,
pp. 947–90, doi:10.1007/s00220-016-2805-6.
short: Z. Bao, L. Erdös, K. Schnelli, Communications in Mathematical Physics 349
(2017) 947–990.
date_created: 2018-12-11T11:50:43Z
date_published: 2017-02-01T00:00:00Z
date_updated: 2025-07-10T11:50:22Z
day: '01'
ddc:
- '530'
department:
- _id: LaEr
doi: 10.1007/s00220-016-2805-6
ec_funded: 1
external_id:
isi:
- '000393696700005'
file:
- access_level: open_access
checksum: ddff79154c3daf27237de5383b1264a9
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:47Z
date_updated: 2020-07-14T12:44:39Z
file_id: '5102'
file_name: IST-2016-722-v1+1_s00220-016-2805-6.pdf
file_size: 1033743
relation: main_file
file_date_updated: 2020-07-14T12:44:39Z
has_accepted_license: '1'
intvolume: ' 349'
isi: 1
issue: '3'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 947 - 990
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Communications in Mathematical Physics
publication_identifier:
issn:
- 0010-3616
publication_status: published
publisher: Springer
publist_id: '6141'
pubrep_id: '722'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Local law of addition of random matrices on optimal scale
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: 349
year: '2017'
...
---
_id: '1208'
abstract:
- lang: eng
text: We study parameter estimation in linear Gaussian covariance models, which
are p-dimensional Gaussian models with linear constraints on the covariance matrix.
Maximum likelihood estimation for this class of models leads to a non-convex optimization
problem which typically has many local maxima. Using recent results on the asymptotic
distribution of extreme eigenvalues of the Wishart distribution, we provide sufficient
conditions for any hill climbing method to converge to the global maximum. Although
we are primarily interested in the case in which n≫p, the proofs of our results
utilize large sample asymptotic theory under the scheme n/p→γ>1. Remarkably,
our numerical simulations indicate that our results remain valid for p as small
as 2. An important consequence of this analysis is that, for sample sizes n≃14p,
maximum likelihood estimation for linear Gaussian covariance models behaves as
if it were a convex optimization problem. © 2016 The Royal Statistical Society
and Blackwell Publishing Ltd.
article_processing_charge: No
arxiv: 1
author:
- first_name: Piotr
full_name: Zwiernik, Piotr
last_name: Zwiernik
- first_name: Caroline
full_name: Uhler, Caroline
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
- first_name: Donald
full_name: Richards, Donald
last_name: Richards
citation:
ama: 'Zwiernik P, Uhler C, Richards D. Maximum likelihood estimation for linear
Gaussian covariance models. Journal of the Royal Statistical Society Series
B: Statistical Methodology. 2017;79(4):1269-1292. doi:10.1111/rssb.12217'
apa: 'Zwiernik, P., Uhler, C., & Richards, D. (2017). Maximum likelihood estimation
for linear Gaussian covariance models. Journal of the Royal Statistical Society.
Series B: Statistical Methodology. Wiley-Blackwell. https://doi.org/10.1111/rssb.12217'
chicago: 'Zwiernik, Piotr, Caroline Uhler, and Donald Richards. “Maximum Likelihood
Estimation for Linear Gaussian Covariance Models.” Journal of the Royal Statistical
Society. Series B: Statistical Methodology. Wiley-Blackwell, 2017. https://doi.org/10.1111/rssb.12217.'
ieee: 'P. Zwiernik, C. Uhler, and D. Richards, “Maximum likelihood estimation for
linear Gaussian covariance models,” Journal of the Royal Statistical Society.
Series B: Statistical Methodology, vol. 79, no. 4. Wiley-Blackwell, pp. 1269–1292,
2017.'
ista: 'Zwiernik P, Uhler C, Richards D. 2017. Maximum likelihood estimation for
linear Gaussian covariance models. Journal of the Royal Statistical Society. Series
B: Statistical Methodology. 79(4), 1269–1292.'
mla: 'Zwiernik, Piotr, et al. “Maximum Likelihood Estimation for Linear Gaussian
Covariance Models.” Journal of the Royal Statistical Society. Series B: Statistical
Methodology, vol. 79, no. 4, Wiley-Blackwell, 2017, pp. 1269–92, doi:10.1111/rssb.12217.'
short: 'P. Zwiernik, C. Uhler, D. Richards, Journal of the Royal Statistical Society.
Series B: Statistical Methodology 79 (2017) 1269–1292.'
corr_author: '1'
date_created: 2018-12-11T11:50:43Z
date_published: 2017-09-01T00:00:00Z
date_updated: 2025-06-04T09:41:22Z
day: '01'
department:
- _id: CaUh
doi: 10.1111/rssb.12217
external_id:
arxiv:
- '1408.5604'
isi:
- '000411712300012'
intvolume: ' 79'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1408.5604
month: '09'
oa: 1
oa_version: Submitted Version
page: 1269 - 1292
project:
- _id: 2530CA10-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Y 903-N35
name: 'Gaussian Graphical Models: Theory and Applications'
publication: 'Journal of the Royal Statistical Society. Series B: Statistical Methodology'
publication_identifier:
issn:
- 1369-7412
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6142'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Maximum likelihood estimation for linear Gaussian covariance models
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 79
year: '2017'
...
---
_id: '1211'
abstract:
- lang: eng
text: Systems such as fluid flows in channels and pipes or the complex Ginzburg–Landau
system, defined over periodic domains, exhibit both continuous symmetries, translational
and rotational, as well as discrete symmetries under spatial reflections or complex
conjugation. The simplest, and very common symmetry of this type is the equivariance
of the defining equations under the orthogonal group O(2). We formulate a novel
symmetry reduction scheme for such systems by combining the method of slices with
invariant polynomial methods, and show how it works by applying it to the Kuramoto–Sivashinsky
system in one spatial dimension. As an example, we track a relative periodic orbit
through a sequence of bifurcations to the onset of chaos. Within the symmetry-reduced
state space we are able to compute and visualize the unstable manifolds of relative
periodic orbits, their torus bifurcations, a transition to chaos via torus breakdown,
and heteroclinic connections between various relative periodic orbits. It would
be very hard to carry through such analysis in the full state space, without a
symmetry reduction such as the one we present here.
acknowledgement: 'This work was supported by the family of late G. Robinson, Jr. and
NSF Grant DMS-1211827. '
article_processing_charge: No
author:
- 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: Predrag
full_name: Cvitanović, Predrag
last_name: Cvitanović
citation:
ama: Budanur NB, Cvitanović P. Unstable manifolds of relative periodic orbits in
the symmetry reduced state space of the Kuramoto–Sivashinsky system. Journal
of Statistical Physics. 2017;167(3-4):636-655. doi:10.1007/s10955-016-1672-z
apa: Budanur, N. B., & Cvitanović, P. (2017). Unstable manifolds of relative
periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky
system. Journal of Statistical Physics. Springer. https://doi.org/10.1007/s10955-016-1672-z
chicago: Budanur, Nazmi B, and Predrag Cvitanović. “Unstable Manifolds of Relative
Periodic Orbits in the Symmetry Reduced State Space of the Kuramoto–Sivashinsky
System.” Journal of Statistical Physics. Springer, 2017. https://doi.org/10.1007/s10955-016-1672-z.
ieee: N. B. Budanur and P. Cvitanović, “Unstable manifolds of relative periodic
orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system,”
Journal of Statistical Physics, vol. 167, no. 3–4. Springer, pp. 636–655,
2017.
ista: Budanur NB, Cvitanović P. 2017. Unstable manifolds of relative periodic orbits
in the symmetry reduced state space of the Kuramoto–Sivashinsky system. Journal
of Statistical Physics. 167(3–4), 636–655.
mla: Budanur, Nazmi B., and Predrag Cvitanović. “Unstable Manifolds of Relative
Periodic Orbits in the Symmetry Reduced State Space of the Kuramoto–Sivashinsky
System.” Journal of Statistical Physics, vol. 167, no. 3–4, Springer, 2017,
pp. 636–55, doi:10.1007/s10955-016-1672-z.
short: N.B. Budanur, P. Cvitanović, Journal of Statistical Physics 167 (2017) 636–655.
date_created: 2018-12-11T11:50:44Z
date_published: 2017-05-01T00:00:00Z
date_updated: 2025-09-22T09:36:50Z
day: '01'
ddc:
- '530'
department:
- _id: BjHo
doi: 10.1007/s10955-016-1672-z
external_id:
isi:
- '000400233600014'
file:
- access_level: open_access
checksum: 3e971d09eb167761aa0888ed415b0056
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:01Z
date_updated: 2020-07-14T12:44:39Z
file_id: '5319'
file_name: IST-2017-782-v1+1_BudCvi15.pdf
file_size: 2820207
relation: main_file
file_date_updated: 2020-07-14T12:44:39Z
has_accepted_license: '1'
intvolume: ' 167'
isi: 1
issue: 3-4
language:
- iso: eng
month: '05'
oa: 1
oa_version: Submitted Version
page: 636-655
publication: Journal of Statistical Physics
publication_status: published
publisher: Springer
publist_id: '6136'
pubrep_id: '782'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Unstable manifolds of relative periodic orbits in the symmetry reduced state
space of the Kuramoto–Sivashinsky system
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 167
year: '2017'
...
---
_id: '1213'
abstract:
- lang: eng
text: Bacterial cytokinesis is commonly initiated by the Z-ring, a dynamic cytoskeletal
structure that assembles at the site of division. Its primary component is FtsZ,
a tubulin-like GTPase, that like its eukaryotic relative forms protein filaments
in the presence of GTP. Since the discovery of the Z-ring 25 years ago, various
models for the role of FtsZ have been suggested. However, important information
about the architecture and dynamics of FtsZ filaments during cytokinesis is still
missing. One reason for this lack of knowledge has been the small size of bacteria,
which has made it difficult to resolve the orientation and dynamics of individual
FtsZ filaments in the Z-ring. While superresolution microscopy experiments have
helped to gain more information about the organization of the Z-ring in the dividing
cell, they were not yet able to elucidate a mechanism of how FtsZ filaments reorganize
during assembly and disassembly of the Z-ring. In this chapter, we explain how
to use an in vitro reconstitution approach to investigate the self-organization
of FtsZ filaments recruited to a biomimetic lipid bilayer by its membrane anchor
FtsA. We show how to perform single-molecule experiments to study the behavior
of individual FtsZ monomers during the constant reorganization of the FtsZ-FtsA
filament network. We describe how to analyze the dynamics of single molecules
and explain why this information can help to shed light onto possible mechanism
of Z-ring constriction. We believe that similar experimental approaches will be
useful to study the mechanism of membrane-based polymerization of other cytoskeletal
systems, not only from prokaryotic but also eukaryotic origin.
acknowledged_ssus:
- _id: Bio
acknowledgement: Natalia Baranova is supported by an EMBO Long-Term Fellowship (EMBO
ALTF 1163-2015) and Martin Loose by an ERC Starting Grant (ERCStG-2015-SelfOrganiCell).
alternative_title:
- Methods in Cell Biology
article_processing_charge: No
author:
- first_name: Natalia
full_name: Baranova, Natalia
id: 38661662-F248-11E8-B48F-1D18A9856A87
last_name: Baranova
orcid: 0000-0002-3086-9124
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
citation:
ama: 'Baranova NS, Loose M. Single-molecule measurements to study polymerization
dynamics of FtsZ-FtsA copolymers. In: Echard A, ed. Cytokinesis. Vol 137.
Academic Press; 2017:355-370. doi:10.1016/bs.mcb.2016.03.036'
apa: Baranova, N. S., & Loose, M. (2017). Single-molecule measurements to study
polymerization dynamics of FtsZ-FtsA copolymers. In A. Echard (Ed.), Cytokinesis
(Vol. 137, pp. 355–370). Academic Press. https://doi.org/10.1016/bs.mcb.2016.03.036
chicago: Baranova, Natalia S., and Martin Loose. “Single-Molecule Measurements to
Study Polymerization Dynamics of FtsZ-FtsA Copolymers.” In Cytokinesis,
edited by Arnaud Echard, 137:355–70. Academic Press, 2017. https://doi.org/10.1016/bs.mcb.2016.03.036.
ieee: N. S. Baranova and M. Loose, “Single-molecule measurements to study polymerization
dynamics of FtsZ-FtsA copolymers,” in Cytokinesis, vol. 137, A. Echard,
Ed. Academic Press, 2017, pp. 355–370.
ista: 'Baranova NS, Loose M. 2017.Single-molecule measurements to study polymerization
dynamics of FtsZ-FtsA copolymers. In: Cytokinesis. Methods in Cell Biology, vol.
137, 355–370.'
mla: Baranova, Natalia S., and Martin Loose. “Single-Molecule Measurements to Study
Polymerization Dynamics of FtsZ-FtsA Copolymers.” Cytokinesis, edited by
Arnaud Echard, vol. 137, Academic Press, 2017, pp. 355–70, doi:10.1016/bs.mcb.2016.03.036.
short: N.S. Baranova, M. Loose, in:, A. Echard (Ed.), Cytokinesis, Academic Press,
2017, pp. 355–370.
date_created: 2018-12-11T11:50:45Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2025-07-10T11:50:24Z
day: '01'
department:
- _id: MaLo
doi: 10.1016/bs.mcb.2016.03.036
ec_funded: 1
editor:
- first_name: 'Arnaud '
full_name: 'Echard, Arnaud '
last_name: Echard
external_id:
isi:
- '000403542900022'
intvolume: ' 137'
isi: 1
language:
- iso: eng
month: '12'
oa_version: None
page: 355 - 370
project:
- _id: 2596EAB6-B435-11E9-9278-68D0E5697425
grant_number: ALTF 2015-1163
name: Synthesis of bacterial cell wall
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Cytokinesis
publication_identifier:
issn:
- 0091-679X
publication_status: published
publisher: Academic Press
publist_id: '6134'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Single-molecule measurements to study polymerization dynamics of FtsZ-FtsA
copolymers
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 137
year: '2017'
...
---
_id: '274'
abstract:
- lang: eng
text: We consider the problem of estimating the partition function Z(β)=∑xexp(−β(H(x))
of a Gibbs distribution with a Hamilton H(⋅), or more precisely the logarithm
of the ratio q=lnZ(0)/Z(β). It has been recently shown how to approximate q with
high probability assuming the existence of an oracle that produces samples from
the Gibbs distribution for a given parameter value in [0,β]. The current best
known approach due to Huber [9] uses O(qlnn⋅[lnq+lnlnn+ε−2]) oracle calls on average
where ε is the desired accuracy of approximation and H(⋅) is assumed to lie in
{0}∪[1,n]. We improve the complexity to O(qlnn⋅ε−2) oracle calls. We also show
that the same complexity can be achieved if exact oracles are replaced with approximate
sampling oracles that are within O(ε2qlnn) variation distance from exact oracles.
Finally, we prove a lower bound of Ω(q⋅ε−2) oracle calls under a natural model
of computation.
article_processing_charge: No
arxiv: 1
author:
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Kolmogorov V. A faster approximation algorithm for the Gibbs partition function.
In: Proceedings of the 31st Conference On Learning Theory. Vol 75. ML Research
Press; 2017:228-249.'
apa: Kolmogorov, V. (2017). A faster approximation algorithm for the Gibbs partition
function. In Proceedings of the 31st Conference On Learning Theory (Vol.
75, pp. 228–249). ML Research Press.
chicago: Kolmogorov, Vladimir. “A Faster Approximation Algorithm for the Gibbs Partition
Function.” In Proceedings of the 31st Conference On Learning Theory, 75:228–49.
ML Research Press, 2017.
ieee: V. Kolmogorov, “A faster approximation algorithm for the Gibbs partition function,”
in Proceedings of the 31st Conference On Learning Theory, 2017, vol. 75,
pp. 228–249.
ista: 'Kolmogorov V. 2017. A faster approximation algorithm for the Gibbs partition
function. Proceedings of the 31st Conference On Learning Theory. COLT: Annual
Conference on Learning Theory vol. 75, 228–249.'
mla: Kolmogorov, Vladimir. “A Faster Approximation Algorithm for the Gibbs Partition
Function.” Proceedings of the 31st Conference On Learning Theory, vol.
75, ML Research Press, 2017, pp. 228–49.
short: V. Kolmogorov, in:, Proceedings of the 31st Conference On Learning Theory,
ML Research Press, 2017, pp. 228–249.
conference:
end_date: 2018-07-09
name: 'COLT: Annual Conference on Learning Theory '
start_date: 2018-07-06
date_created: 2018-12-11T11:45:33Z
date_published: 2017-12-27T00:00:00Z
date_updated: 2024-11-04T13:52:32Z
day: '27'
ddc:
- '510'
department:
- _id: VlKo
ec_funded: 1
external_id:
arxiv:
- '1608.04223'
file:
- access_level: open_access
checksum: 89db06a0e8083524449cb59b56bf4e5b
content_type: application/pdf
creator: dernst
date_created: 2020-05-12T09:23:27Z
date_updated: 2020-07-14T12:45:45Z
file_id: '7820'
file_name: 2018_PMLR_Kolmogorov.pdf
file_size: 408974
relation: main_file
file_date_updated: 2020-07-14T12:45:45Z
has_accepted_license: '1'
intvolume: ' 75'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 228-249
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication: Proceedings of the 31st Conference On Learning Theory
publication_status: published
publisher: ML Research Press
publist_id: '7628'
quality_controlled: '1'
status: public
title: A faster approximation algorithm for the Gibbs partition function
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: 75
year: '2017'
...
---
OA_place: repository
OA_type: green
_id: '12193'
abstract:
- lang: eng
text: DNA methylation regulates eukaryotic gene expression and is extensively reprogrammed
during animal development. However, whether developmental methylation reprogramming
during the sporophytic life cycle of flowering plants regulates genes is presently
unknown. Here we report a distinctive gene-targeted RNA-directed DNA methylation
(RdDM) activity in the Arabidopsis thaliana male sexual lineage that regulates
gene expression in meiocytes. Loss of sexual-lineage-specific RdDM causes mis-splicing
of the MPS1 gene (also known as PRD2), thereby disrupting meiosis. Our results
establish a regulatory paradigm in which de novo methylation creates a cell-lineage-specific
epigenetic signature that controls gene expression and contributes to cellular
function in flowering plants.
acknowledgement: We thank Daniel Zilberman for intellectual contributions to this
work and assistance with manuscript preparation. We also thank Caroline Dean, Kirsten
Bomblies, Vinod Kumar, Siobhan Brady and Sophien Kamoun for comments on the manuscript,
Hugh Dickinson and Josephine Hellberg for developing the meiocyte isolation method,
Giles Oldroyd for the pGWB13-Bar vector, Elisa Fiume for the pMDC107-NTF vector,
Matthew Hartley, Matthew Couchman and Tjelvar Sten Gunnar Olsson for bioinformatics
support, and the John Innes Centre Bioimaging Facility (Elaine Barclay and Grant
Calder) for their assistance with microscopy. This work was funded by a Biotechnology
and Biological Sciences Research Council (BBSRC) David Phillips Fellowship (BBL0250431)
to X.F., a BBSRC grant (BBM01973X1) to J.H., and a Sainsbury PhD Studentship to
J.W.
article_processing_charge: No
article_type: original
author:
- first_name: James
full_name: Walker, James
last_name: Walker
- first_name: Hongbo
full_name: Gao, Hongbo
last_name: Gao
- first_name: Jingyi
full_name: Zhang, Jingyi
last_name: Zhang
- first_name: Billy
full_name: Aldridge, Billy
last_name: Aldridge
- first_name: Martin
full_name: Vickers, Martin
last_name: Vickers
- first_name: James D.
full_name: Higgins, James D.
last_name: Higgins
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
citation:
ama: Walker J, Gao H, Zhang J, et al. Sexual-lineage-specific DNA methylation regulates
meiosis in Arabidopsis. Nature Genetics. 2017;50(1):130-137. doi:10.1038/s41588-017-0008-5
apa: Walker, J., Gao, H., Zhang, J., Aldridge, B., Vickers, M., Higgins, J. D.,
& Feng, X. (2017). Sexual-lineage-specific DNA methylation regulates meiosis
in Arabidopsis. Nature Genetics. Nature Research. https://doi.org/10.1038/s41588-017-0008-5
chicago: Walker, James, Hongbo Gao, Jingyi Zhang, Billy Aldridge, Martin Vickers,
James D. Higgins, and Xiaoqi Feng. “Sexual-Lineage-Specific DNA Methylation Regulates
Meiosis in Arabidopsis.” Nature Genetics. Nature Research, 2017. https://doi.org/10.1038/s41588-017-0008-5.
ieee: J. Walker et al., “Sexual-lineage-specific DNA methylation regulates
meiosis in Arabidopsis,” Nature Genetics, vol. 50, no. 1. Nature Research,
pp. 130–137, 2017.
ista: Walker J, Gao H, Zhang J, Aldridge B, Vickers M, Higgins JD, Feng X. 2017.
Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. Nature
Genetics. 50(1), 130–137.
mla: Walker, James, et al. “Sexual-Lineage-Specific DNA Methylation Regulates Meiosis
in Arabidopsis.” Nature Genetics, vol. 50, no. 1, Nature Research, 2017,
pp. 130–37, doi:10.1038/s41588-017-0008-5.
short: J. Walker, H. Gao, J. Zhang, B. Aldridge, M. Vickers, J.D. Higgins, X. Feng,
Nature Genetics 50 (2017) 130–137.
date_created: 2023-01-16T09:18:05Z
date_published: 2017-12-18T00:00:00Z
date_updated: 2026-03-19T10:51:18Z
day: '18'
department:
- _id: XiFe
doi: 10.1038/s41588-017-0008-5
extern: '1'
external_id:
pmid:
- '29255257'
intvolume: ' 50'
issue: '1'
keyword:
- Genetics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7611288/
month: '12'
oa: 1
oa_version: Submitted Version
page: 130-137
pmid: 1
publication: Nature Genetics
publication_identifier:
eissn:
- 1546-1718
issn:
- 1061-4036
publication_status: published
publisher: Nature Research
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 50
year: '2017'
...
---
_id: '1228'
abstract:
- lang: eng
text: Since 2006, reprogrammed cells have increasingly been used as a biomedical
research technique in addition to neuro-psychiatric methods. These rapidly evolving
techniques allow for the generation of neuronal sub-populations, and have sparked
interest not only in monogenetic neuro-psychiatric diseases, but also in poly-genetic
and poly-aetiological disorders such as schizophrenia (SCZ) and bipolar disorder
(BPD). This review provides a summary of 19 publications on reprogrammed adult
somatic cells derived from patients with SCZ, and five publications using this
technique in patients with BPD. As both disorders are complex and heterogeneous,
there is a plurality of hypotheses to be tested in vitro. In SCZ, data on alterations
of dopaminergic transmission in vitro are sparse, despite the great explanatory
power of the so-called DA hypothesis of SCZ. Some findings correspond to perturbations
of cell energy metabolism, and observations in reprogrammed cells suggest neuro-developmental
alterations. Some studies also report on the efficacy of medicinal compounds to
revert alterations observed in cellular models. However, due to the paucity of
replication studies, no comprehensive conclusions can be drawn from studies using
reprogrammed cells at the present time. In the future, findings from cell culture
methods need to be integrated with clinical, epidemiological, pharmacological
and imaging data in order to generate a more comprehensive picture of SCZ and
BPD.
acknowledgement: This work was supported by grants of the Austrian Science Fund (FWF)
P23585B09 to M.W. and F3506 to H.H.S. and the “Wiener Wissenschafts-, Forschungs-
und Technologiefonds” (Vienna Science and Technology Fund; WWTF) CS15-033 to M.W.
article_processing_charge: No
article_type: review
author:
- first_name: Ulrich
full_name: Sauerzopf, Ulrich
last_name: Sauerzopf
- first_name: Roberto
full_name: Sacco, Roberto
id: 42C9F57E-F248-11E8-B48F-1D18A9856A87
last_name: Sacco
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Marco
full_name: Niello, Marco
last_name: Niello
- first_name: Ana
full_name: Weidenauer, Ana
last_name: Weidenauer
- first_name: Nicole
full_name: Praschak Rieder, Nicole
last_name: Praschak Rieder
- first_name: Harald
full_name: Sitte, Harald
last_name: Sitte
- first_name: Matthaeus
full_name: Willeit, Matthaeus
last_name: Willeit
citation:
ama: Sauerzopf U, Sacco R, Novarino G, et al. Are reprogrammed cells a useful tool
for studying dopamine dysfunction in psychotic disorders? A review of the current
evidence. European Journal of Neuroscience. 2017;45(1):45-57. doi:10.1111/ejn.13418
apa: Sauerzopf, U., Sacco, R., Novarino, G., Niello, M., Weidenauer, A., Praschak
Rieder, N., … Willeit, M. (2017). Are reprogrammed cells a useful tool for studying
dopamine dysfunction in psychotic disorders? A review of the current evidence.
European Journal of Neuroscience. Wiley-Blackwell. https://doi.org/10.1111/ejn.13418
chicago: Sauerzopf, Ulrich, Roberto Sacco, Gaia Novarino, Marco Niello, Ana Weidenauer,
Nicole Praschak Rieder, Harald Sitte, and Matthaeus Willeit. “Are Reprogrammed
Cells a Useful Tool for Studying Dopamine Dysfunction in Psychotic Disorders?
A Review of the Current Evidence.” European Journal of Neuroscience. Wiley-Blackwell,
2017. https://doi.org/10.1111/ejn.13418.
ieee: U. Sauerzopf et al., “Are reprogrammed cells a useful tool for studying
dopamine dysfunction in psychotic disorders? A review of the current evidence,”
European Journal of Neuroscience, vol. 45, no. 1. Wiley-Blackwell, pp.
45–57, 2017.
ista: Sauerzopf U, Sacco R, Novarino G, Niello M, Weidenauer A, Praschak Rieder
N, Sitte H, Willeit M. 2017. Are reprogrammed cells a useful tool for studying
dopamine dysfunction in psychotic disorders? A review of the current evidence.
European Journal of Neuroscience. 45(1), 45–57.
mla: Sauerzopf, Ulrich, et al. “Are Reprogrammed Cells a Useful Tool for Studying
Dopamine Dysfunction in Psychotic Disorders? A Review of the Current Evidence.”
European Journal of Neuroscience, vol. 45, no. 1, Wiley-Blackwell, 2017,
pp. 45–57, doi:10.1111/ejn.13418.
short: U. Sauerzopf, R. Sacco, G. Novarino, M. Niello, A. Weidenauer, N. Praschak
Rieder, H. Sitte, M. Willeit, European Journal of Neuroscience 45 (2017) 45–57.
date_created: 2018-12-11T11:50:50Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-09-20T11:16:01Z
day: '01'
ddc:
- '616'
department:
- _id: GaNo
doi: 10.1111/ejn.13418
external_id:
isi:
- '000392487100005'
pmid:
- '27690184'
file:
- access_level: open_access
checksum: c572cf02be8fbb7020cfcfb892182e4c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:48Z
date_updated: 2020-07-14T12:44:39Z
file_id: '4838'
file_name: IST-2017-738-v1+1_Sauerzopf_et_al-2017-European_Journal_of_Neuroscience.pdf
file_size: 169145
relation: main_file
file_date_updated: 2020-07-14T12:44:39Z
has_accepted_license: '1'
intvolume: ' 45'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 45 - 57
pmid: 1
publication: European Journal of Neuroscience
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6106'
pubrep_id: '738'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic
disorders? A review of the current evidence
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: 45
year: '2017'
...
---
_id: '1294'
abstract:
- lang: eng
text: We study controller synthesis problems for finite-state Markov decision processes,
where the objective is to optimize the expected mean-payoff performance and stability
(also known as variability in the literature). We argue that the basic notion
of expressing the stability using the statistical variance of the mean payoff
is sometimes insufficient, and propose an alternative definition. We show that
a strategy ensuring both the expected mean payoff and the variance below given
bounds requires randomization and memory, under both the above definitions. We
then show that the problem of finding such a strategy can be expressed as a set
of constraints.
article_processing_charge: No
author:
- first_name: Tomáš
full_name: Brázdil, Tomáš
last_name: Brázdil
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Vojtěch
full_name: Forejt, Vojtěch
last_name: Forejt
- first_name: Antonín
full_name: Kučera, Antonín
last_name: Kučera
citation:
ama: Brázdil T, Chatterjee K, Forejt V, Kučera A. Trading performance for stability
in Markov decision processes. Journal of Computer and System Sciences.
2017;84:144-170. doi:10.1016/j.jcss.2016.09.009
apa: Brázdil, T., Chatterjee, K., Forejt, V., & Kučera, A. (2017). Trading performance
for stability in Markov decision processes. Journal of Computer and System
Sciences. Elsevier. https://doi.org/10.1016/j.jcss.2016.09.009
chicago: Brázdil, Tomáš, Krishnendu Chatterjee, Vojtěch Forejt, and Antonín Kučera.
“Trading Performance for Stability in Markov Decision Processes.” Journal of
Computer and System Sciences. Elsevier, 2017. https://doi.org/10.1016/j.jcss.2016.09.009.
ieee: T. Brázdil, K. Chatterjee, V. Forejt, and A. Kučera, “Trading performance
for stability in Markov decision processes,” Journal of Computer and System
Sciences, vol. 84. Elsevier, pp. 144–170, 2017.
ista: Brázdil T, Chatterjee K, Forejt V, Kučera A. 2017. Trading performance for
stability in Markov decision processes. Journal of Computer and System Sciences.
84, 144–170.
mla: Brázdil, Tomáš, et al. “Trading Performance for Stability in Markov Decision
Processes.” Journal of Computer and System Sciences, vol. 84, Elsevier,
2017, pp. 144–70, doi:10.1016/j.jcss.2016.09.009.
short: T. Brázdil, K. Chatterjee, V. Forejt, A. Kučera, Journal of Computer and
System Sciences 84 (2017) 144–170.
date_created: 2018-12-11T11:51:12Z
date_published: 2017-03-01T00:00:00Z
date_updated: 2025-09-29T14:16:56Z
day: '01'
ddc:
- '004'
- '006'
department:
- _id: KrCh
doi: 10.1016/j.jcss.2016.09.009
ec_funded: 1
external_id:
isi:
- '000388430000011'
file:
- access_level: open_access
checksum: 91271b23cf884d7c06d33bef0cd623b1
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:30Z
date_updated: 2020-07-14T12:44:42Z
file_id: '4885'
file_name: IST-2016-717-v1+1_1-s2.0-S0022000016300897-main.pdf
file_size: 708657
relation: main_file
file_date_updated: 2020-07-14T12:44:42Z
has_accepted_license: '1'
intvolume: ' 84'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 144 - 170
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Journal of Computer and System Sciences
publication_status: published
publisher: Elsevier
publist_id: '6009'
pubrep_id: '717'
quality_controlled: '1'
related_material:
record:
- id: '2305'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Trading performance for stability in Markov decision processes
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: 84
year: '2017'
...
---
_id: '13160'
abstract:
- lang: eng
text: "Transforming deterministic ω\r\n-automata into deterministic parity automata
is traditionally done using variants of appearance records. We present a more
efficient variant of this approach, tailored to Rabin automata, and several optimizations
applicable to all appearance records. We compare the methods experimentally and
find out that our method produces smaller automata than previous approaches. Moreover,
the experiments demonstrate the potential of our method for LTL synthesis, using
LTL-to-Rabin translators. It leads to significantly smaller parity automata when
compared to state-of-the-art approaches on complex formulae."
acknowledgement: This work is partially funded by the DFG project “Verified Model
Checkers” and by the Czech Science Foundation, grant No. P202/12/G061.
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
- first_name: Tobias
full_name: Meggendorfer, Tobias
id: b21b0c15-30a2-11eb-80dc-f13ca25802e1
last_name: Meggendorfer
orcid: 0000-0002-1712-2165
- first_name: Clara
full_name: Waldmann, Clara
last_name: Waldmann
- first_name: Maximilian
full_name: Weininger, Maximilian
last_name: Weininger
citation:
ama: 'Kretinsky J, Meggendorfer T, Waldmann C, Weininger M. Index appearance record
for transforming Rabin automata into parity automata. In: Tools and Algorithms
for the Construction and Analysis of Systems. Vol 10205. Springer; 2017:443-460.
doi:10.1007/978-3-662-54577-5_26'
apa: 'Kretinsky, J., Meggendorfer, T., Waldmann, C., & Weininger, M. (2017).
Index appearance record for transforming Rabin automata into parity automata.
In Tools and Algorithms for the Construction and Analysis of Systems (Vol.
10205, pp. 443–460). Uppsala, Sweden: Springer. https://doi.org/10.1007/978-3-662-54577-5_26'
chicago: Kretinsky, Jan, Tobias Meggendorfer, Clara Waldmann, and Maximilian Weininger.
“Index Appearance Record for Transforming Rabin Automata into Parity Automata.”
In Tools and Algorithms for the Construction and Analysis of Systems, 10205:443–60.
Springer, 2017. https://doi.org/10.1007/978-3-662-54577-5_26.
ieee: J. Kretinsky, T. Meggendorfer, C. Waldmann, and M. Weininger, “Index appearance
record for transforming Rabin automata into parity automata,” in Tools and
Algorithms for the Construction and Analysis of Systems, Uppsala, Sweden,
2017, vol. 10205, pp. 443–460.
ista: 'Kretinsky J, Meggendorfer T, Waldmann C, Weininger M. 2017. Index appearance
record for transforming Rabin automata into parity automata. Tools and Algorithms
for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for
the Construction and Analysis of Systems, LNCS, vol. 10205, 443–460.'
mla: Kretinsky, Jan, et al. “Index Appearance Record for Transforming Rabin Automata
into Parity Automata.” Tools and Algorithms for the Construction and Analysis
of Systems, vol. 10205, Springer, 2017, pp. 443–60, doi:10.1007/978-3-662-54577-5_26.
short: J. Kretinsky, T. Meggendorfer, C. Waldmann, M. Weininger, in:, Tools and
Algorithms for the Construction and Analysis of Systems, Springer, 2017, pp. 443–460.
conference:
end_date: 2017-04-29
location: Uppsala, Sweden
name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems'
start_date: 2017-04-22
corr_author: '1'
date_created: 2023-06-21T13:21:14Z
date_published: 2017-03-31T00:00:00Z
date_updated: 2025-09-18T10:42:48Z
day: '31'
department:
- _id: KrCh
doi: 10.1007/978-3-662-54577-5_26
external_id:
arxiv:
- '1701.05738'
isi:
- '000440734900026'
intvolume: ' 10205'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1701.05738
month: '03'
oa: 1
oa_version: Preprint
page: 443-460
publication: Tools and Algorithms for the Construction and Analysis of Systems
publication_identifier:
eisbn:
- '9783662545775'
eissn:
- 1611-3349
isbn:
- '9783662545768'
issn:
- 0302-9743
publication_status: published
publisher: Springer
quality_controlled: '1'
status: public
title: Index appearance record for transforming Rabin automata into parity automata
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 10205
year: '2017'
...
---
_id: '1336'
abstract:
- lang: eng
text: Evolutionary algorithms (EAs) form a popular optimisation paradigm inspired
by natural evolution. In recent years the field of evolutionary computation has
developed a rigorous analytical theory to analyse the runtimes of EAs on many
illustrative problems. Here we apply this theory to a simple model of natural
evolution. In the Strong Selection Weak Mutation (SSWM) evolutionary regime the
time between occurrences of new mutations is much longer than the time it takes
for a mutated genotype to take over the population. In this situation, the population
only contains copies of one genotype and evolution can be modelled as a stochastic
process evolving one genotype by means of mutation and selection between the resident
and the mutated genotype. The probability of accepting the mutated genotype then
depends on the change in fitness. We study this process, SSWM, from an algorithmic
perspective, quantifying its expected optimisation time for various parameters
and investigating differences to a similar evolutionary algorithm, the well-known
(1+1) EA. We show that SSWM can have a moderate advantage over the (1+1) EA at
crossing fitness valleys and study an example where SSWM outperforms the (1+1)
EA by taking advantage of information on the fitness gradient.
article_processing_charge: No
author:
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Jorge
full_name: Pérez Heredia, Jorge
last_name: Pérez Heredia
- first_name: Dirk
full_name: Sudholt, Dirk
last_name: Sudholt
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
citation:
ama: Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. Towards a runtime comparison
of natural and artificial evolution. Algorithmica. 2017;78(2):681-713.
doi:10.1007/s00453-016-0212-1
apa: Paixao, T., Pérez Heredia, J., Sudholt, D., & Trubenova, B. (2017). Towards
a runtime comparison of natural and artificial evolution. Algorithmica.
Springer. https://doi.org/10.1007/s00453-016-0212-1
chicago: Paixao, Tiago, Jorge Pérez Heredia, Dirk Sudholt, and Barbora Trubenova.
“Towards a Runtime Comparison of Natural and Artificial Evolution.” Algorithmica.
Springer, 2017. https://doi.org/10.1007/s00453-016-0212-1.
ieee: T. Paixao, J. Pérez Heredia, D. Sudholt, and B. Trubenova, “Towards a runtime
comparison of natural and artificial evolution,” Algorithmica, vol. 78,
no. 2. Springer, pp. 681–713, 2017.
ista: Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. 2017. Towards a runtime
comparison of natural and artificial evolution. Algorithmica. 78(2), 681–713.
mla: Paixao, Tiago, et al. “Towards a Runtime Comparison of Natural and Artificial
Evolution.” Algorithmica, vol. 78, no. 2, Springer, 2017, pp. 681–713,
doi:10.1007/s00453-016-0212-1.
short: T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica 78 (2017)
681–713.
date_created: 2018-12-11T11:51:27Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2026-04-16T09:55:33Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
- _id: CaGu
doi: 10.1007/s00453-016-0212-1
ec_funded: 1
external_id:
isi:
- '000400379500013'
file:
- access_level: open_access
checksum: 7873f665a0c598ac747c908f34cb14b9
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:19Z
date_updated: 2020-07-14T12:44:44Z
file_id: '4805'
file_name: IST-2016-658-v1+1_s00453-016-0212-1.pdf
file_size: 710206
relation: main_file
file_date_updated: 2020-07-14T12:44:44Z
has_accepted_license: '1'
intvolume: ' 78'
isi: 1
issue: '2'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 681 - 713
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
publication: Algorithmica
publication_identifier:
issn:
- 0178-4617
publication_status: published
publisher: Springer
publist_id: '5931'
pubrep_id: '658'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Towards a runtime comparison of natural and artificial evolution
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 78
year: '2017'
...
---
_id: '1337'
abstract:
- lang: eng
text: We consider the local eigenvalue distribution of large self-adjoint N×N random
matrices H=H∗ with centered independent entries. In contrast to previous works
the matrix of variances sij=\mathbbmE|hij|2 is not assumed to be stochastic. Hence
the density of states is not the Wigner semicircle law. Its possible shapes are
described in the companion paper (Ajanki et al. in Quadratic Vector Equations
on the Complex Upper Half Plane. arXiv:1506.05095). We show that as N grows, the
resolvent, G(z)=(H−z)−1, converges to a diagonal matrix, diag(m(z)), where m(z)=(m1(z),…,mN(z))
solves the vector equation −1/mi(z)=z+∑jsijmj(z) that has been analyzed in Ajanki
et al. (Quadratic Vector Equations on the Complex Upper Half Plane. arXiv:1506.05095).
We prove a local law down to the smallest spectral resolution scale, and bulk
universality for both real symmetric and complex hermitian symmetry classes.
acknowledgement: 'Open access funding provided by Institute of Science and Technology
(IST Austria). '
article_processing_charge: Yes (via OA deal)
author:
- first_name: Oskari H
full_name: Ajanki, Oskari H
id: 36F2FB7E-F248-11E8-B48F-1D18A9856A87
last_name: Ajanki
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Torben H
full_name: Krüger, Torben H
id: 3020C786-F248-11E8-B48F-1D18A9856A87
last_name: Krüger
orcid: 0000-0002-4821-3297
citation:
ama: Ajanki OH, Erdös L, Krüger TH. Universality for general Wigner-type matrices.
Probability Theory and Related Fields. 2017;169(3-4):667-727. doi:10.1007/s00440-016-0740-2
apa: Ajanki, O. H., Erdös, L., & Krüger, T. H. (2017). Universality for general
Wigner-type matrices. Probability Theory and Related Fields. Springer.
https://doi.org/10.1007/s00440-016-0740-2
chicago: Ajanki, Oskari H, László Erdös, and Torben H Krüger. “Universality for
General Wigner-Type Matrices.” Probability Theory and Related Fields. Springer,
2017. https://doi.org/10.1007/s00440-016-0740-2.
ieee: O. H. Ajanki, L. Erdös, and T. H. Krüger, “Universality for general Wigner-type
matrices,” Probability Theory and Related Fields, vol. 169, no. 3–4. Springer,
pp. 667–727, 2017.
ista: Ajanki OH, Erdös L, Krüger TH. 2017. Universality for general Wigner-type
matrices. Probability Theory and Related Fields. 169(3–4), 667–727.
mla: Ajanki, Oskari H., et al. “Universality for General Wigner-Type Matrices.”
Probability Theory and Related Fields, vol. 169, no. 3–4, Springer, 2017,
pp. 667–727, doi:10.1007/s00440-016-0740-2.
short: O.H. Ajanki, L. Erdös, T.H. Krüger, Probability Theory and Related Fields
169 (2017) 667–727.
corr_author: '1'
date_created: 2018-12-11T11:51:27Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2026-04-16T09:55:44Z
day: '01'
ddc:
- '510'
- '530'
department:
- _id: LaEr
doi: 10.1007/s00440-016-0740-2
ec_funded: 1
external_id:
isi:
- '000414358400002'
file:
- access_level: open_access
checksum: 29f5a72c3f91e408aeb9e78344973803
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:25Z
date_updated: 2020-07-14T12:44:44Z
file_id: '4686'
file_name: IST-2017-657-v1+2_s00440-016-0740-2.pdf
file_size: 988843
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has_accepted_license: '1'
intvolume: ' 169'
isi: 1
issue: 3-4
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 667 - 727
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Probability Theory and Related Fields
publication_identifier:
issn:
- 0178-8051
publication_status: published
publisher: Springer
publist_id: '5930'
pubrep_id: '657'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Universality for general Wigner-type matrices
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 169
year: '2017'
...
---
_id: '1338'
abstract:
- lang: eng
text: We present a computer-aided programming approach to concurrency. The approach
allows programmers to program assuming a friendly, non-preemptive scheduler, and
our synthesis procedure inserts synchronization to ensure that the final program
works even with a preemptive scheduler. The correctness specification is implicit,
inferred from the non-preemptive behavior. Let us consider sequences of calls
that the program makes to an external interface. The specification requires that
any such sequence produced under a preemptive scheduler should be included in
the set of sequences produced under a non-preemptive scheduler. We guarantee that
our synthesis does not introduce deadlocks and that the synchronization inserted
is optimal w.r.t. a given objective function. The solution is based on a finitary
abstraction, an algorithm for bounded language inclusion modulo an independence
relation, and generation of a set of global constraints over synchronization placements.
Each model of the global constraints set corresponds to a correctness-ensuring
synchronization placement. The placement that is optimal w.r.t. the given objective
function is chosen as the synchronization solution. We apply the approach to device-driver
programming, where the driver threads call the software interface of the device
and the API provided by the operating system. Our experiments demonstrate that
our synthesis method is precise and efficient. The implicit specification helped
us find one concurrency bug previously missed when model-checking using an explicit,
user-provided specification. We implemented objective functions for coarse-grained
and fine-grained locking and observed that different synchronization placements
are produced for our experiments, favoring a minimal number of synchronization
operations or maximum concurrency, respectively.
article_processing_charge: No
author:
- first_name: Pavol
full_name: Cerny, Pavol
id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87
last_name: Cerny
- first_name: Edmund
full_name: Clarke, Edmund
last_name: Clarke
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Arjun
full_name: Radhakrishna, Arjun
id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87
last_name: Radhakrishna
- first_name: Leonid
full_name: Ryzhyk, Leonid
last_name: Ryzhyk
- first_name: Roopsha
full_name: Samanta, Roopsha
id: 3D2AAC08-F248-11E8-B48F-1D18A9856A87
last_name: Samanta
- first_name: Thorsten
full_name: Tarrach, Thorsten
id: 3D6E8F2C-F248-11E8-B48F-1D18A9856A87
last_name: Tarrach
orcid: 0000-0003-4409-8487
citation:
ama: Cerny P, Clarke E, Henzinger TA, et al. From non-preemptive to preemptive scheduling
using synchronization synthesis. Formal Methods in System Design. 2017;50(2-3):97-139.
doi:10.1007/s10703-016-0256-5
apa: Cerny, P., Clarke, E., Henzinger, T. A., Radhakrishna, A., Ryzhyk, L., Samanta,
R., & Tarrach, T. (2017). From non-preemptive to preemptive scheduling using
synchronization synthesis. Formal Methods in System Design. Springer. https://doi.org/10.1007/s10703-016-0256-5
chicago: Cerny, Pavol, Edmund Clarke, Thomas A Henzinger, Arjun Radhakrishna, Leonid
Ryzhyk, Roopsha Samanta, and Thorsten Tarrach. “From Non-Preemptive to Preemptive
Scheduling Using Synchronization Synthesis.” Formal Methods in System Design.
Springer, 2017. https://doi.org/10.1007/s10703-016-0256-5.
ieee: P. Cerny et al., “From non-preemptive to preemptive scheduling using
synchronization synthesis,” Formal Methods in System Design, vol. 50, no.
2–3. Springer, pp. 97–139, 2017.
ista: Cerny P, Clarke E, Henzinger TA, Radhakrishna A, Ryzhyk L, Samanta R, Tarrach
T. 2017. From non-preemptive to preemptive scheduling using synchronization synthesis.
Formal Methods in System Design. 50(2–3), 97–139.
mla: Cerny, Pavol, et al. “From Non-Preemptive to Preemptive Scheduling Using Synchronization
Synthesis.” Formal Methods in System Design, vol. 50, no. 2–3, Springer,
2017, pp. 97–139, doi:10.1007/s10703-016-0256-5.
short: P. Cerny, E. Clarke, T.A. Henzinger, A. Radhakrishna, L. Ryzhyk, R. Samanta,
T. Tarrach, Formal Methods in System Design 50 (2017) 97–139.
corr_author: '1'
date_created: 2018-12-11T11:51:27Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2025-09-23T08:54:01Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/s10703-016-0256-5
ec_funded: 1
external_id:
isi:
- '000399888900001'
pmid:
- '28490835'
file:
- access_level: open_access
checksum: 1163dfd997e8212c789525d4178b1653
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:05Z
date_updated: 2020-07-14T12:44:44Z
file_id: '4985'
file_name: IST-2016-656-v1+1_s10703-016-0256-5.pdf
file_size: 1416170
relation: main_file
file_date_updated: 2020-07-14T12:44:44Z
has_accepted_license: '1'
intvolume: ' 50'
isi: 1
issue: 2-3
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 97 - 139
pmid: 1
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _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: Formal methods for the design and analysis of complex systems
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Formal Methods in System Design
publication_status: published
publisher: Springer
publist_id: '5929'
pubrep_id: '656'
quality_controlled: '1'
related_material:
record:
- id: '1729'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: From non-preemptive to preemptive scheduling using synchronization synthesis
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: 50
year: '2017'
...
---
_id: '1351'
abstract:
- lang: eng
text: The behaviour of gene regulatory networks (GRNs) is typically analysed using
simulation-based statistical testing-like methods. In this paper, we demonstrate
that we can replace this approach by a formal verification-like method that gives
higher assurance and scalability. We focus on Wagner’s weighted GRN model with
varying weights, which is used in evolutionary biology. In the model, weight parameters
represent the gene interaction strength that may change due to genetic mutations.
For a property of interest, we synthesise the constraints over the parameter space
that represent the set of GRNs satisfying the property. We experimentally show
that our parameter synthesis procedure computes the mutational robustness of GRNs—an
important problem of interest in evolutionary biology—more efficiently than the
classical simulation method. We specify the property in linear temporal logic.
We employ symbolic bounded model checking and SMT solving to compute the space
of GRNs that satisfy the property, which amounts to synthesizing a set of linear
constraints on the weights.
article_processing_charge: No
author:
- first_name: Mirco
full_name: Giacobbe, Mirco
id: 3444EA5E-F248-11E8-B48F-1D18A9856A87
last_name: Giacobbe
orcid: 0000-0001-8180-0904
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Ashutosh
full_name: Gupta, Ashutosh
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
- 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: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Tatjana
full_name: Petrov, Tatjana
id: 3D5811FC-F248-11E8-B48F-1D18A9856A87
last_name: Petrov
orcid: 0000-0002-9041-0905
citation:
ama: Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. Model checking
the evolution of gene regulatory networks. Acta Informatica. 2017;54(8):765-787.
doi:10.1007/s00236-016-0278-x
apa: Giacobbe, M., Guet, C. C., Gupta, A., Henzinger, T. A., Paixao, T., & Petrov,
T. (2017). Model checking the evolution of gene regulatory networks. Acta Informatica.
Springer. https://doi.org/10.1007/s00236-016-0278-x
chicago: Giacobbe, Mirco, Calin C Guet, Ashutosh Gupta, Thomas A Henzinger, Tiago
Paixao, and Tatjana Petrov. “Model Checking the Evolution of Gene Regulatory Networks.”
Acta Informatica. Springer, 2017. https://doi.org/10.1007/s00236-016-0278-x.
ieee: M. Giacobbe, C. C. Guet, A. Gupta, T. A. Henzinger, T. Paixao, and T. Petrov,
“Model checking the evolution of gene regulatory networks,” Acta Informatica,
vol. 54, no. 8. Springer, pp. 765–787, 2017.
ista: Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. 2017. Model
checking the evolution of gene regulatory networks. Acta Informatica. 54(8), 765–787.
mla: Giacobbe, Mirco, et al. “Model Checking the Evolution of Gene Regulatory Networks.”
Acta Informatica, vol. 54, no. 8, Springer, 2017, pp. 765–87, doi:10.1007/s00236-016-0278-x.
short: M. Giacobbe, C.C. Guet, A. Gupta, T.A. Henzinger, T. Paixao, T. Petrov, Acta
Informatica 54 (2017) 765–787.
corr_author: '1'
date_created: 2018-12-11T11:51:32Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2025-07-10T11:50:42Z
day: '01'
ddc:
- '006'
- '576'
department:
- _id: ToHe
- _id: CaGu
- _id: NiBa
doi: 10.1007/s00236-016-0278-x
ec_funded: 1
external_id:
isi:
- '000414343200003'
file:
- access_level: open_access
checksum: 4e661d9135d7f8c342e8e258dee76f3e
content_type: application/pdf
creator: dernst
date_created: 2019-01-17T15:57:29Z
date_updated: 2020-07-14T12:44:46Z
file_id: '5841'
file_name: 2017_ActaInformatica_Giacobbe.pdf
file_size: 755241
relation: main_file
file_date_updated: 2020-07-14T12:44:46Z
has_accepted_license: '1'
intvolume: ' 54'
isi: 1
issue: '8'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 765 - 787
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _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: Formal methods for the design and analysis of complex systems
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Acta Informatica
publication_identifier:
issn:
- 0001-5903
publication_status: published
publisher: Springer
publist_id: '5898'
pubrep_id: '649'
quality_controlled: '1'
related_material:
record:
- id: '1835'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Model checking the evolution of gene regulatory networks
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: 54
year: '2017'
...
---
_id: '1367'
abstract:
- lang: eng
text: One of the major challenges in physically based modelling is making simulations
efficient. Adaptive models provide an essential solution to these efficiency goals.
These models are able to self-adapt in space and time, attempting to provide the
best possible compromise between accuracy and speed. This survey reviews the adaptive
solutions proposed so far in computer graphics. Models are classified according
to the strategy they use for adaptation, from time-stepping and freezing techniques
to geometric adaptivity in the form of structured grids, meshes and particles.
Applications range from fluids, through deformable bodies, to articulated solids.
acknowledgement: This work was partly supported by the starting grants ADAPT and BigSplash,
as well as the advanced grant EXPRESSIVE from the European Research Council (ERC-2012-StG_20111012,
ERC-2014-StG_638176 and ERC-2011-ADG_20110209).
article_processing_charge: No
author:
- first_name: Pierre
full_name: Manteaux, Pierre
last_name: Manteaux
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
- first_name: Rahul
full_name: Narain, Rahul
last_name: Narain
- first_name: Stéphane
full_name: Redon, Stéphane
last_name: Redon
- first_name: François
full_name: Faure, François
last_name: Faure
- first_name: Marie
full_name: Cani, Marie
last_name: Cani
citation:
ama: Manteaux P, Wojtan C, Narain R, Redon S, Faure F, Cani M. Adaptive physically
based models in computer graphics. Computer Graphics Forum. 2017;36(6):312-337.
doi:10.1111/cgf.12941
apa: Manteaux, P., Wojtan, C., Narain, R., Redon, S., Faure, F., & Cani, M.
(2017). Adaptive physically based models in computer graphics. Computer Graphics
Forum. Wiley-Blackwell. https://doi.org/10.1111/cgf.12941
chicago: Manteaux, Pierre, Chris Wojtan, Rahul Narain, Stéphane Redon, François
Faure, and Marie Cani. “Adaptive Physically Based Models in Computer Graphics.”
Computer Graphics Forum. Wiley-Blackwell, 2017. https://doi.org/10.1111/cgf.12941.
ieee: P. Manteaux, C. Wojtan, R. Narain, S. Redon, F. Faure, and M. Cani, “Adaptive
physically based models in computer graphics,” Computer Graphics Forum,
vol. 36, no. 6. Wiley-Blackwell, pp. 312–337, 2017.
ista: Manteaux P, Wojtan C, Narain R, Redon S, Faure F, Cani M. 2017. Adaptive physically
based models in computer graphics. Computer Graphics Forum. 36(6), 312–337.
mla: Manteaux, Pierre, et al. “Adaptive Physically Based Models in Computer Graphics.”
Computer Graphics Forum, vol. 36, no. 6, Wiley-Blackwell, 2017, pp. 312–37,
doi:10.1111/cgf.12941.
short: P. Manteaux, C. Wojtan, R. Narain, S. Redon, F. Faure, M. Cani, Computer
Graphics Forum 36 (2017) 312–337.
date_created: 2018-12-11T11:51:37Z
date_published: 2017-09-01T00:00:00Z
date_updated: 2023-09-20T11:05:36Z
day: '01'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1111/cgf.12941
external_id:
isi:
- '000408634200019'
file:
- access_level: open_access
checksum: 7676e9a9ead6d58c3000988c97deb2ef
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:21Z
date_updated: 2020-07-14T12:44:47Z
file_id: '5208'
file_name: IST-2016-634-v1+1_starAdaptivity-cgf.pdf
file_size: 1434439
relation: main_file
file_date_updated: 2020-07-14T12:44:47Z
has_accepted_license: '1'
intvolume: ' 36'
isi: 1
issue: '6'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 312 - 337
publication: Computer Graphics Forum
publication_identifier:
issn:
- '01677055'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5873'
pubrep_id: '634'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Adaptive physically based models in computer graphics
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 36
year: '2017'
...