---
_id: '6558'
abstract:
- lang: eng
text: This paper studies the problem of distributed stochastic optimization in an
adversarial setting where, out of m machines which allegedly compute stochastic
gradients every iteration, an α-fraction are Byzantine, and may behave adversarially.
Our main result is a variant of stochastic gradient descent (SGD) which finds
ε-approximate minimizers of convex functions in T=O~(1/ε²m+α²/ε²) iterations.
In contrast, traditional mini-batch SGD needs T=O(1/ε²m) iterations, but cannot
tolerate Byzantine failures. Further, we provide a lower bound showing that, up
to logarithmic factors, our algorithm is information-theoretically optimal both
in terms of sample complexity and time complexity.
article_processing_charge: No
arxiv: 1
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: Zeyuan
full_name: Allen-Zhu, Zeyuan
last_name: Allen-Zhu
- first_name: Jerry
full_name: Li, Jerry
last_name: Li
citation:
ama: 'Alistarh D-A, Allen-Zhu Z, Li J. Byzantine stochastic gradient descent. In:
Advances in Neural Information Processing Systems. Vol 2018. Neural Information
Processing Systems Foundation; 2018:4613-4623.'
apa: 'Alistarh, D.-A., Allen-Zhu, Z., & Li, J. (2018). Byzantine stochastic
gradient descent. In Advances in Neural Information Processing Systems
(Vol. 2018, pp. 4613–4623). Montreal, Canada: Neural Information Processing Systems
Foundation.'
chicago: Alistarh, Dan-Adrian, Zeyuan Allen-Zhu, and Jerry Li. “Byzantine Stochastic
Gradient Descent.” In Advances in Neural Information Processing Systems,
2018:4613–23. Neural Information Processing Systems Foundation, 2018.
ieee: D.-A. Alistarh, Z. Allen-Zhu, and J. Li, “Byzantine stochastic gradient descent,”
in Advances in Neural Information Processing Systems, Montreal, Canada,
2018, vol. 2018, pp. 4613–4623.
ista: 'Alistarh D-A, Allen-Zhu Z, Li J. 2018. Byzantine stochastic gradient descent.
Advances in Neural Information Processing Systems. NeurIPS: Conference on Neural
Information Processing Systems vol. 2018, 4613–4623.'
mla: Alistarh, Dan-Adrian, et al. “Byzantine Stochastic Gradient Descent.” Advances
in Neural Information Processing Systems, vol. 2018, Neural Information Processing
Systems Foundation, 2018, pp. 4613–23.
short: D.-A. Alistarh, Z. Allen-Zhu, J. Li, in:, Advances in Neural Information
Processing Systems, Neural Information Processing Systems Foundation, 2018, pp.
4613–4623.
conference:
end_date: 2018-12-08
location: Montreal, Canada
name: 'NeurIPS: Conference on Neural Information Processing Systems'
start_date: 2018-12-02
date_created: 2019-06-13T08:22:37Z
date_published: 2018-12-01T00:00:00Z
date_updated: 2023-09-19T15:12:45Z
day: '01'
department:
- _id: DaAl
external_id:
arxiv:
- '1803.08917'
isi:
- '000461823304061'
intvolume: ' 2018'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1803.08917
month: '12'
oa: 1
oa_version: Published Version
page: 4613-4623
publication: Advances in Neural Information Processing Systems
publication_status: published
publisher: Neural Information Processing Systems Foundation
quality_controlled: '1'
scopus_import: '1'
status: public
title: Byzantine stochastic gradient descent
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2018
year: '2018'
...
---
_id: '6589'
abstract:
- lang: eng
text: Distributed training of massive machine learning models, in particular deep
neural networks, via Stochastic Gradient Descent (SGD) is becoming commonplace.
Several families of communication-reduction methods, such as quantization, large-batch
methods, and gradient sparsification, have been proposed. To date, gradient sparsification
methods--where each node sorts gradients by magnitude, and only communicates a
subset of the components, accumulating the rest locally--are known to yield some
of the largest practical gains. Such methods can reduce the amount of communication
per step by up to \emph{three orders of magnitude}, while preserving model accuracy.
Yet, this family of methods currently has no theoretical justification. This is
the question we address in this paper. We prove that, under analytic assumptions,
sparsifying gradients by magnitude with local error correction provides convergence
guarantees, for both convex and non-convex smooth objectives, for data-parallel
SGD. The main insight is that sparsification methods implicitly maintain bounds
on the maximum impact of stale updates, thanks to selection by magnitude. Our
analysis and empirical validation also reveal that these methods do require analytical
conditions to converge well, justifying existing heuristics.
article_processing_charge: No
arxiv: 1
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: Torsten
full_name: Hoefler, Torsten
last_name: Hoefler
- first_name: Mikael
full_name: Johansson, Mikael
last_name: Johansson
- first_name: Nikola H
full_name: Konstantinov, Nikola H
id: 4B9D76E4-F248-11E8-B48F-1D18A9856A87
last_name: Konstantinov
- first_name: Sarit
full_name: Khirirat, Sarit
last_name: Khirirat
- first_name: Cedric
full_name: Renggli, Cedric
last_name: Renggli
citation:
ama: 'Alistarh D-A, Hoefler T, Johansson M, Konstantinov NH, Khirirat S, Renggli
C. The convergence of sparsified gradient methods. In: Advances in Neural Information
Processing Systems 31. Vol Volume 2018. Neural Information Processing Systems
Foundation; 2018:5973-5983.'
apa: 'Alistarh, D.-A., Hoefler, T., Johansson, M., Konstantinov, N. H., Khirirat,
S., & Renggli, C. (2018). The convergence of sparsified gradient methods.
In Advances in Neural Information Processing Systems 31 (Vol. Volume 2018,
pp. 5973–5983). Montreal, Canada: Neural Information Processing Systems Foundation.'
chicago: Alistarh, Dan-Adrian, Torsten Hoefler, Mikael Johansson, Nikola H Konstantinov,
Sarit Khirirat, and Cedric Renggli. “The Convergence of Sparsified Gradient Methods.”
In Advances in Neural Information Processing Systems 31, Volume 2018:5973–83.
Neural Information Processing Systems Foundation, 2018.
ieee: D.-A. Alistarh, T. Hoefler, M. Johansson, N. H. Konstantinov, S. Khirirat,
and C. Renggli, “The convergence of sparsified gradient methods,” in Advances
in Neural Information Processing Systems 31, Montreal, Canada, 2018, vol.
Volume 2018, pp. 5973–5983.
ista: 'Alistarh D-A, Hoefler T, Johansson M, Konstantinov NH, Khirirat S, Renggli
C. 2018. The convergence of sparsified gradient methods. Advances in Neural Information
Processing Systems 31. NeurIPS: Conference on Neural Information Processing Systems
vol. Volume 2018, 5973–5983.'
mla: Alistarh, Dan-Adrian, et al. “The Convergence of Sparsified Gradient Methods.”
Advances in Neural Information Processing Systems 31, vol. Volume 2018,
Neural Information Processing Systems Foundation, 2018, pp. 5973–83.
short: D.-A. Alistarh, T. Hoefler, M. Johansson, N.H. Konstantinov, S. Khirirat,
C. Renggli, in:, Advances in Neural Information Processing Systems 31, Neural
Information Processing Systems Foundation, 2018, pp. 5973–5983.
conference:
end_date: 2018-12-08
location: Montreal, Canada
name: 'NeurIPS: Conference on Neural Information Processing Systems'
start_date: 2018-12-02
corr_author: '1'
date_created: 2019-06-27T09:32:55Z
date_published: 2018-12-01T00:00:00Z
date_updated: 2025-06-26T12:23:06Z
day: '01'
department:
- _id: DaAl
- _id: ChLa
ec_funded: 1
external_id:
arxiv:
- '1809.10505'
isi:
- '000461852000047'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1809.10505
month: '12'
oa: 1
oa_version: Preprint
page: 5973-5983
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Advances in Neural Information Processing Systems 31
publication_status: published
publisher: Neural Information Processing Systems Foundation
quality_controlled: '1'
scopus_import: '1'
status: public
title: The convergence of sparsified gradient methods
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: Volume 2018
year: '2018'
...
---
_id: '690'
abstract:
- lang: eng
text: We consider spectral properties and the edge universality of sparse random
matrices, the class of random matrices that includes the adjacency matrices of
the Erdős–Rényi graph model G(N, p). We prove a local law for the eigenvalue density
up to the spectral edges. Under a suitable condition on the sparsity, we also
prove that the rescaled extremal eigenvalues exhibit GOE Tracy–Widom fluctuations
if a deterministic shift of the spectral edge due to the sparsity is included.
For the adjacency matrix of the Erdős–Rényi graph this establishes the Tracy–Widom
fluctuations of the second largest eigenvalue when p is much larger than N−2/3
with a deterministic shift of order (Np)−1.
article_number: 543-616
article_processing_charge: No
arxiv: 1
author:
- first_name: Jii
full_name: Lee, Jii
last_name: Lee
- first_name: Kevin
full_name: Schnelli, Kevin
id: 434AD0AE-F248-11E8-B48F-1D18A9856A87
last_name: Schnelli
orcid: 0000-0003-0954-3231
citation:
ama: Lee J, Schnelli K. Local law and Tracy–Widom limit for sparse random matrices.
Probability Theory and Related Fields. 2018;171(1-2). doi:10.1007/s00440-017-0787-8
apa: Lee, J., & Schnelli, K. (2018). Local law and Tracy–Widom limit for sparse
random matrices. Probability Theory and Related Fields. Springer. https://doi.org/10.1007/s00440-017-0787-8
chicago: Lee, Jii, and Kevin Schnelli. “Local Law and Tracy–Widom Limit for Sparse
Random Matrices.” Probability Theory and Related Fields. Springer, 2018.
https://doi.org/10.1007/s00440-017-0787-8.
ieee: J. Lee and K. Schnelli, “Local law and Tracy–Widom limit for sparse random
matrices,” Probability Theory and Related Fields, vol. 171, no. 1–2. Springer,
2018.
ista: Lee J, Schnelli K. 2018. Local law and Tracy–Widom limit for sparse random
matrices. Probability Theory and Related Fields. 171(1–2), 543–616.
mla: Lee, Jii, and Kevin Schnelli. “Local Law and Tracy–Widom Limit for Sparse Random
Matrices.” Probability Theory and Related Fields, vol. 171, no. 1–2, 543–616,
Springer, 2018, doi:10.1007/s00440-017-0787-8.
short: J. Lee, K. Schnelli, Probability Theory and Related Fields 171 (2018).
date_created: 2018-12-11T11:47:56Z
date_published: 2018-06-14T00:00:00Z
date_updated: 2025-09-10T14:00:58Z
day: '14'
department:
- _id: LaEr
doi: 10.1007/s00440-017-0787-8
ec_funded: 1
external_id:
arxiv:
- '1605.08767'
isi:
- '000432129600012'
intvolume: ' 171'
isi: 1
issue: 1-2
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1605.08767
month: '06'
oa: 1
oa_version: Preprint
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Probability Theory and Related Fields
publication_status: published
publisher: Springer
publist_id: '7017'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Local law and Tracy–Widom limit for sparse random matrices
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 171
year: '2018'
...
---
_id: '691'
abstract:
- lang: eng
text: "Background: Transport protein particle (TRAPP) is a multisubunit complex
that regulates membrane trafficking through the Golgi apparatus. The clinical
phenotype associated with mutations in various TRAPP subunits has allowed elucidation
of their functions in specific tissues. The role of some subunits in human disease,
however, has not been fully established, and their functions remain uncertain.\r\n\r\nObjective:
We aimed to expand the range of neurodevelopmental disorders associated with mutations
in TRAPP subunits by exome sequencing of consanguineous families.\r\n\r\nMethods:
Linkage and homozygosity mapping and candidate gene analysis were used to identify
homozygous mutations in families. Patient fibroblasts were used to study splicing
defect and zebrafish to model the disease.\r\n\r\nResults: We identified six individuals
from three unrelated families with a founder homozygous splice mutation in TRAPPC6B,
encoding a core subunit of the complex TRAPP I. Patients manifested a neurodevelopmental
disorder characterised by microcephaly, epilepsy and autistic features, and showed
splicing defect. Zebrafish trappc6b morphants replicated the human phenotype,
displaying decreased head size and neuronal hyperexcitability, leading to a lower
seizure threshold.\r\n\r\nConclusion: This study provides clinical and functional
evidence of the role of TRAPPC6B in brain development and function."
article_processing_charge: No
article_type: original
author:
- first_name: Isaac
full_name: Marin Valencia, Isaac
last_name: Marin Valencia
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Anide
full_name: Johansen, Anide
last_name: Johansen
- first_name: Başak
full_name: Rosti, Başak
last_name: Rosti
- first_name: Mahmoud
full_name: Issa, Mahmoud
last_name: Issa
- first_name: Damir
full_name: Musaev, Damir
last_name: Musaev
- first_name: Gifty
full_name: Bhat, Gifty
last_name: Bhat
- first_name: Eric
full_name: Scott, Eric
last_name: Scott
- first_name: Jennifer
full_name: Silhavy, Jennifer
last_name: Silhavy
- first_name: Valentina
full_name: Stanley, Valentina
last_name: Stanley
- first_name: Rasim
full_name: Rosti, Rasim
last_name: Rosti
- first_name: Jeremy
full_name: Gleeson, Jeremy
last_name: Gleeson
- first_name: Farhad
full_name: Imam, Farhad
last_name: Imam
- first_name: Maha
full_name: Zaki, Maha
last_name: Zaki
- first_name: Joseph
full_name: Gleeson, Joseph
last_name: Gleeson
citation:
ama: Marin Valencia I, Novarino G, Johansen A, et al. A homozygous founder mutation
in TRAPPC6B associates with a neurodevelopmental disorder characterised by microcephaly
epilepsy and autistic features. Journal of Medical Genetics. 2018;55(1):48-54.
doi:10.1136/jmedgenet-2017-104627
apa: Marin Valencia, I., Novarino, G., Johansen, A., Rosti, B., Issa, M., Musaev,
D., … Gleeson, J. (2018). A homozygous founder mutation in TRAPPC6B associates
with a neurodevelopmental disorder characterised by microcephaly epilepsy and
autistic features. Journal of Medical Genetics. BMJ Publishing Group. https://doi.org/10.1136/jmedgenet-2017-104627
chicago: Marin Valencia, Isaac, Gaia Novarino, Anide Johansen, Başak Rosti, Mahmoud
Issa, Damir Musaev, Gifty Bhat, et al. “A Homozygous Founder Mutation in TRAPPC6B
Associates with a Neurodevelopmental Disorder Characterised by Microcephaly Epilepsy
and Autistic Features.” Journal of Medical Genetics. BMJ Publishing Group,
2018. https://doi.org/10.1136/jmedgenet-2017-104627.
ieee: I. Marin Valencia et al., “A homozygous founder mutation in TRAPPC6B
associates with a neurodevelopmental disorder characterised by microcephaly epilepsy
and autistic features,” Journal of Medical Genetics, vol. 55, no. 1. BMJ
Publishing Group, pp. 48–54, 2018.
ista: Marin Valencia I, Novarino G, Johansen A, Rosti B, Issa M, Musaev D, Bhat
G, Scott E, Silhavy J, Stanley V, Rosti R, Gleeson J, Imam F, Zaki M, Gleeson
J. 2018. A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental
disorder characterised by microcephaly epilepsy and autistic features. Journal
of Medical Genetics. 55(1), 48–54.
mla: Marin Valencia, Isaac, et al. “A Homozygous Founder Mutation in TRAPPC6B Associates
with a Neurodevelopmental Disorder Characterised by Microcephaly Epilepsy and
Autistic Features.” Journal of Medical Genetics, vol. 55, no. 1, BMJ Publishing
Group, 2018, pp. 48–54, doi:10.1136/jmedgenet-2017-104627.
short: I. Marin Valencia, G. Novarino, A. Johansen, B. Rosti, M. Issa, D. Musaev,
G. Bhat, E. Scott, J. Silhavy, V. Stanley, R. Rosti, J. Gleeson, F. Imam, M. Zaki,
J. Gleeson, Journal of Medical Genetics 55 (2018) 48–54.
date_created: 2018-12-11T11:47:57Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2025-04-15T07:50:28Z
day: '01'
department:
- _id: GaNo
doi: 10.1136/jmedgenet-2017-104627
external_id:
isi:
- '000418199800007'
pmid:
- '28626029'
intvolume: ' 55'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6056005/
month: '01'
oa: 1
oa_version: Submitted Version
page: 48 - 54
pmid: 1
project:
- _id: 254BA948-B435-11E9-9278-68D0E5697425
grant_number: '401299'
name: Probing development and reversibility of autism spectrum disorders
publication: Journal of Medical Genetics
publication_identifier:
issn:
- 0022-2593
publication_status: published
publisher: BMJ Publishing Group
publist_id: '7016'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental
disorder characterised by microcephaly epilepsy and autistic features
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2018'
...
---
_id: '692'
abstract:
- lang: eng
text: We consider families of confocal conics and two pencils of Apollonian circles
having the same foci. We will show that these families of curves generate trivial
3-webs and find the exact formulas describing them.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
citation:
ama: Akopyan A. 3-Webs generated by confocal conics and circles. Geometriae Dedicata.
2018;194(1):55-64. doi:10.1007/s10711-017-0265-6
apa: Akopyan, A. (2018). 3-Webs generated by confocal conics and circles. Geometriae
Dedicata. Springer. https://doi.org/10.1007/s10711-017-0265-6
chicago: Akopyan, Arseniy. “3-Webs Generated by Confocal Conics and Circles.” Geometriae
Dedicata. Springer, 2018. https://doi.org/10.1007/s10711-017-0265-6.
ieee: A. Akopyan, “3-Webs generated by confocal conics and circles,” Geometriae
Dedicata, vol. 194, no. 1. Springer, pp. 55–64, 2018.
ista: Akopyan A. 2018. 3-Webs generated by confocal conics and circles. Geometriae
Dedicata. 194(1), 55–64.
mla: Akopyan, Arseniy. “3-Webs Generated by Confocal Conics and Circles.” Geometriae
Dedicata, vol. 194, no. 1, Springer, 2018, pp. 55–64, doi:10.1007/s10711-017-0265-6.
short: A. Akopyan, Geometriae Dedicata 194 (2018) 55–64.
corr_author: '1'
date_created: 2018-12-11T11:47:57Z
date_published: 2018-06-01T00:00:00Z
date_updated: 2025-04-15T06:50:29Z
day: '01'
ddc:
- '510'
department:
- _id: HeEd
doi: 10.1007/s10711-017-0265-6
ec_funded: 1
external_id:
isi:
- '000431418800004'
file:
- access_level: open_access
checksum: 1febcfc1266486053a069e3425ea3713
content_type: application/pdf
creator: kschuh
date_created: 2020-01-03T11:35:08Z
date_updated: 2020-07-14T12:47:44Z
file_id: '7222'
file_name: 2018_Springer_Akopyan.pdf
file_size: 1140860
relation: main_file
file_date_updated: 2020-07-14T12:47:44Z
has_accepted_license: '1'
intvolume: ' 194'
isi: 1
issue: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '06'
oa: 1
oa_version: Published Version
page: 55 - 64
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Geometriae Dedicata
publication_status: published
publisher: Springer
publist_id: '7014'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 3-Webs generated by confocal conics and circles
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: 194
year: '2018'
...
---
_id: '7'
abstract:
- lang: eng
text: Animal social networks are shaped by multiple selection pressures, including
the need to ensure efficient communication and functioning while simultaneously
limiting disease transmission. Social animals could potentially further reduce
epidemic risk by altering their social networks in the presence of pathogens,
yet there is currently no evidence for such pathogen-triggered responses. We tested
this hypothesis experimentally in the ant Lasius niger using a combination of
automated tracking, controlled pathogen exposure, transmission quantification,
and temporally explicit simulations. Pathogen exposure induced behavioral changes
in both exposed ants and their nestmates, which helped contain the disease by
reinforcing key transmission-inhibitory properties of the colony's contact network.
This suggests that social network plasticity in response to pathogens is an effective
strategy for mitigating the effects of disease in social groups.
acknowledgement: This project was funded by two European Research Council Advanced
Grants (Social Life, 249375, and resiliANT, 741491) and two Swiss National Science
Foundation grants (CR32I3_141063 and 310030_156732) to L.K. and a European Research
Council Starting Grant (SocialVaccines, 243071) to S.C.
article_processing_charge: No
article_type: original
author:
- first_name: Nathalie
full_name: Stroeymeyt, Nathalie
last_name: Stroeymeyt
- first_name: Anna V
full_name: Grasse, Anna V
id: 406F989C-F248-11E8-B48F-1D18A9856A87
last_name: Grasse
- first_name: Alessandro
full_name: Crespi, Alessandro
last_name: Crespi
- first_name: Danielle
full_name: Mersch, Danielle
last_name: Mersch
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Laurent
full_name: Keller, Laurent
last_name: Keller
citation:
ama: Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. Social network
plasticity decreases disease transmission in a eusocial insect. Science.
2018;362(6417):941-945. doi:10.1126/science.aat4793
apa: Stroeymeyt, N., Grasse, A. V., Crespi, A., Mersch, D., Cremer, S., & Keller,
L. (2018). Social network plasticity decreases disease transmission in a eusocial
insect. Science. AAAS. https://doi.org/10.1126/science.aat4793
chicago: Stroeymeyt, Nathalie, Anna V Grasse, Alessandro Crespi, Danielle Mersch,
Sylvia Cremer, and Laurent Keller. “Social Network Plasticity Decreases Disease
Transmission in a Eusocial Insect.” Science. AAAS, 2018. https://doi.org/10.1126/science.aat4793.
ieee: N. Stroeymeyt, A. V. Grasse, A. Crespi, D. Mersch, S. Cremer, and L. Keller,
“Social network plasticity decreases disease transmission in a eusocial insect,”
Science, vol. 362, no. 6417. AAAS, pp. 941–945, 2018.
ista: Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. 2018. Social
network plasticity decreases disease transmission in a eusocial insect. Science.
362(6417), 941–945.
mla: Stroeymeyt, Nathalie, et al. “Social Network Plasticity Decreases Disease Transmission
in a Eusocial Insect.” Science, vol. 362, no. 6417, AAAS, 2018, pp. 941–45,
doi:10.1126/science.aat4793.
short: N. Stroeymeyt, A.V. Grasse, A. Crespi, D. Mersch, S. Cremer, L. Keller, Science
362 (2018) 941–945.
date_created: 2018-12-11T11:44:07Z
date_published: 2018-11-23T00:00:00Z
date_updated: 2025-04-15T08:20:52Z
day: '23'
department:
- _id: SyCr
doi: 10.1126/science.aat4793
ec_funded: 1
external_id:
isi:
- '000451124500041'
intvolume: ' 362'
isi: 1
issue: '6417'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://serval.unil.ch/resource/serval:BIB_E9228C205467.P001/REF.pdf
month: '11'
oa: 1
oa_version: Published Version
page: 941 - 945
project:
- _id: 25DC711C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '243071'
name: 'Social Vaccination in Ant Colonies: from Individual Mechanisms to Society
Effects'
publication: Science
publication_identifier:
issn:
- 1095-9203
publication_status: published
publisher: AAAS
publist_id: '8049'
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/for-ants-unity-is-strength-and-health/
record:
- id: '13055'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Social network plasticity decreases disease transmission in a eusocial insect
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 362
year: '2018'
...
---
_id: '70'
abstract:
- lang: eng
text: We consider the totally asymmetric simple exclusion process in a critical
scaling parametrized by a≥0, which creates a shock in the particle density of
order aT−1/3, T the observation time. When starting from step initial data, we
provide bounds on the limiting law which in particular imply that in the double
limit lima→∞limT→∞ one recovers the product limit law and the degeneration of
the correlation length observed at shocks of order 1. This result is shown to
apply to a general last-passage percolation model. We also obtain bounds on the
two-point functions of several airy processes.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Peter
full_name: Nejjar, Peter
id: 4BF426E2-F248-11E8-B48F-1D18A9856A87
last_name: Nejjar
citation:
ama: Nejjar P. Transition to shocks in TASEP and decoupling of last passage times.
Latin American Journal of Probability and Mathematical Statistics. 2018;15(2):1311-1334.
doi:10.30757/ALEA.v15-49
apa: Nejjar, P. (2018). Transition to shocks in TASEP and decoupling of last passage
times. Latin American Journal of Probability and Mathematical Statistics.
Instituto Nacional de Matematica Pura e Aplicada. https://doi.org/10.30757/ALEA.v15-49
chicago: Nejjar, Peter. “Transition to Shocks in TASEP and Decoupling of Last Passage
Times.” Latin American Journal of Probability and Mathematical Statistics.
Instituto Nacional de Matematica Pura e Aplicada, 2018. https://doi.org/10.30757/ALEA.v15-49.
ieee: P. Nejjar, “Transition to shocks in TASEP and decoupling of last passage times,”
Latin American Journal of Probability and Mathematical Statistics, vol.
15, no. 2. Instituto Nacional de Matematica Pura e Aplicada, pp. 1311–1334, 2018.
ista: Nejjar P. 2018. Transition to shocks in TASEP and decoupling of last passage
times. Latin American Journal of Probability and Mathematical Statistics. 15(2),
1311–1334.
mla: Nejjar, Peter. “Transition to Shocks in TASEP and Decoupling of Last Passage
Times.” Latin American Journal of Probability and Mathematical Statistics,
vol. 15, no. 2, Instituto Nacional de Matematica Pura e Aplicada, 2018, pp. 1311–34,
doi:10.30757/ALEA.v15-49.
short: P. Nejjar, Latin American Journal of Probability and Mathematical Statistics
15 (2018) 1311–1334.
date_created: 2018-12-11T11:44:28Z
date_published: 2018-10-01T00:00:00Z
date_updated: 2025-04-14T07:27:49Z
day: '01'
ddc:
- '510'
department:
- _id: LaEr
- _id: JaMa
doi: 10.30757/ALEA.v15-49
ec_funded: 1
external_id:
arxiv:
- '1705.08836'
isi:
- '000460475800022'
file:
- access_level: open_access
checksum: 2ded46aa284a836a8cbb34133a64f1cb
content_type: application/pdf
creator: kschuh
date_created: 2019-02-14T09:44:10Z
date_updated: 2020-07-14T12:47:46Z
file_id: '5981'
file_name: 2018_ALEA_Nejjar.pdf
file_size: 394851
relation: main_file
file_date_updated: 2020-07-14T12:47:46Z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
issue: '2'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 1311-1334
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
publication: Latin American Journal of Probability and Mathematical Statistics
publication_identifier:
issn:
- 1980-0436
publication_status: published
publisher: Instituto Nacional de Matematica Pura e Aplicada
quality_controlled: '1'
scopus_import: '1'
status: public
title: Transition to shocks in TASEP and decoupling of last passage times
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2018'
...
---
_id: '705'
abstract:
- lang: eng
text: Although dopamine receptors D1 and D2 play key roles in hippocampal function,
their synaptic localization within the hippocampus has not been fully elucidated.
In order to understand precise functions of pre- or postsynaptic dopamine receptors
(DRs), the development of protocols to differentiate pre- and postsynaptic DRs
is essential. So far, most studies on determination and quantification of DRs
did not discriminate between subsynaptic localization. Therefore, the aim of the
study was to generate a robust workflow for the localization of DRs. This work
provides the basis for future work on hippocampal DRs, in light that DRs may have
different functions at pre- or postsynaptic sites. Synaptosomes from rat hippocampi
isolated by a sucrose gradient protocol were prepared for super-resolution direct
stochastic optical reconstruction microscopy (dSTORM) using Bassoon as a presynaptic
zone and Homer1 as postsynaptic density marker. Direct labeling of primary validated
antibodies against dopamine receptors D1 (D1R) and D2 (D2R) with Alexa Fluor 594
enabled unequivocal assignment of D1R and D2R to both, pre- and postsynaptic sites.
D1R immunoreactivity clusters were observed within the presynaptic active zone
as well as at perisynaptic sites at the edge of the presynaptic active zone. The
results may be useful for the interpretation of previous studies and the design
of future work on DRs in the hippocampus. Moreover, the reduction of the complexity
of brain tissue by the use of synaptosomal preparations and dSTORM technology
may represent a useful tool for synaptic localization of brain proteins.
article_processing_charge: No
author:
- first_name: Andras
full_name: Miklosi, Andras
last_name: Miklosi
- first_name: Giorgia
full_name: Del Favero, Giorgia
last_name: Del Favero
- first_name: Tanja
full_name: Bulat, Tanja
last_name: Bulat
- first_name: Harald
full_name: Höger, Harald
last_name: Höger
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Doris
full_name: Marko, Doris
last_name: Marko
- first_name: Gert
full_name: Lubec, Gert
last_name: Lubec
citation:
ama: Miklosi A, Del Favero G, Bulat T, et al. Super resolution microscopical localization
of dopamine receptors 1 and 2 in rat hippocampal synaptosomes. Molecular Neurobiology.
2018;55(6):4857 – 4869. doi:10.1007/s12035-017-0688-y
apa: Miklosi, A., Del Favero, G., Bulat, T., Höger, H., Shigemoto, R., Marko, D.,
& Lubec, G. (2018). Super resolution microscopical localization of dopamine
receptors 1 and 2 in rat hippocampal synaptosomes. Molecular Neurobiology.
Springer. https://doi.org/10.1007/s12035-017-0688-y
chicago: Miklosi, Andras, Giorgia Del Favero, Tanja Bulat, Harald Höger, Ryuichi
Shigemoto, Doris Marko, and Gert Lubec. “Super Resolution Microscopical Localization
of Dopamine Receptors 1 and 2 in Rat Hippocampal Synaptosomes.” Molecular Neurobiology.
Springer, 2018. https://doi.org/10.1007/s12035-017-0688-y.
ieee: A. Miklosi et al., “Super resolution microscopical localization of
dopamine receptors 1 and 2 in rat hippocampal synaptosomes,” Molecular Neurobiology,
vol. 55, no. 6. Springer, pp. 4857 – 4869, 2018.
ista: Miklosi A, Del Favero G, Bulat T, Höger H, Shigemoto R, Marko D, Lubec G.
2018. Super resolution microscopical localization of dopamine receptors 1 and
2 in rat hippocampal synaptosomes. Molecular Neurobiology. 55(6), 4857 – 4869.
mla: Miklosi, Andras, et al. “Super Resolution Microscopical Localization of Dopamine
Receptors 1 and 2 in Rat Hippocampal Synaptosomes.” Molecular Neurobiology,
vol. 55, no. 6, Springer, 2018, pp. 4857 – 4869, doi:10.1007/s12035-017-0688-y.
short: A. Miklosi, G. Del Favero, T. Bulat, H. Höger, R. Shigemoto, D. Marko, G.
Lubec, Molecular Neurobiology 55 (2018) 4857 – 4869.
date_created: 2018-12-11T11:48:02Z
date_published: 2018-06-01T00:00:00Z
date_updated: 2023-09-19T09:58:11Z
day: '01'
department:
- _id: RySh
doi: 10.1007/s12035-017-0688-y
external_id:
isi:
- '000431991500025'
intvolume: ' 55'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa_version: None
page: 4857 – 4869
publication: Molecular Neurobiology
publication_status: published
publisher: Springer
publist_id: '6991'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Super resolution microscopical localization of dopamine receptors 1 and 2 in
rat hippocampal synaptosomes
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 55
year: '2018'
...
---
_id: '7116'
abstract:
- lang: eng
text: 'Training deep learning models has received tremendous research interest recently.
In particular, there has been intensive research on reducing the communication
cost of training when using multiple computational devices, through reducing the
precision of the underlying data representation. Naturally, such methods induce
system trade-offs—lowering communication precision could de-crease communication
overheads and improve scalability; but, on the other hand, it can also reduce
the accuracy of training. In this paper, we study this trade-off space, and ask:Can
low-precision communication consistently improve the end-to-end performance of
training modern neural networks, with no accuracy loss?From the performance point
of view, the answer to this question may appear deceptively easy: compressing
communication through low precision should help when the ratio between communication
and computation is high. However, this answer is less straightforward when we
try to generalize this principle across various neural network architectures (e.g.,
AlexNet vs. ResNet),number of GPUs (e.g., 2 vs. 8 GPUs), machine configurations(e.g.,
EC2 instances vs. NVIDIA DGX-1), communication primitives (e.g., MPI vs. NCCL),
and even different GPU architectures(e.g., Kepler vs. Pascal). Currently, it is
not clear how a realistic realization of all these factors maps to the speed up
provided by low-precision communication. In this paper, we conduct an empirical
study to answer this question and report the insights.'
article_processing_charge: No
author:
- first_name: Demjan
full_name: Grubic, Demjan
last_name: Grubic
- first_name: Leo
full_name: Tam, Leo
last_name: Tam
- 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: Ce
full_name: Zhang, Ce
last_name: Zhang
citation:
ama: 'Grubic D, Tam L, Alistarh D-A, Zhang C. Synchronous multi-GPU training for
deep learning with low-precision communications: An empirical study. In: Proceedings
of the 21st International Conference on Extending Database Technology. OpenProceedings;
2018:145-156. doi:10.5441/002/EDBT.2018.14'
apa: 'Grubic, D., Tam, L., Alistarh, D.-A., & Zhang, C. (2018). Synchronous
multi-GPU training for deep learning with low-precision communications: An empirical
study. In Proceedings of the 21st International Conference on Extending Database
Technology (pp. 145–156). Vienna, Austria: OpenProceedings. https://doi.org/10.5441/002/EDBT.2018.14'
chicago: 'Grubic, Demjan, Leo Tam, Dan-Adrian Alistarh, and Ce Zhang. “Synchronous
Multi-GPU Training for Deep Learning with Low-Precision Communications: An Empirical
Study.” In Proceedings of the 21st International Conference on Extending Database
Technology, 145–56. OpenProceedings, 2018. https://doi.org/10.5441/002/EDBT.2018.14.'
ieee: 'D. Grubic, L. Tam, D.-A. Alistarh, and C. Zhang, “Synchronous multi-GPU training
for deep learning with low-precision communications: An empirical study,” in Proceedings
of the 21st International Conference on Extending Database Technology, Vienna,
Austria, 2018, pp. 145–156.'
ista: 'Grubic D, Tam L, Alistarh D-A, Zhang C. 2018. Synchronous multi-GPU training
for deep learning with low-precision communications: An empirical study. Proceedings
of the 21st International Conference on Extending Database Technology. EDBT: Conference
on Extending Database Technology, 145–156.'
mla: 'Grubic, Demjan, et al. “Synchronous Multi-GPU Training for Deep Learning with
Low-Precision Communications: An Empirical Study.” Proceedings of the 21st
International Conference on Extending Database Technology, OpenProceedings,
2018, pp. 145–56, doi:10.5441/002/EDBT.2018.14.'
short: D. Grubic, L. Tam, D.-A. Alistarh, C. Zhang, in:, Proceedings of the 21st
International Conference on Extending Database Technology, OpenProceedings, 2018,
pp. 145–156.
conference:
end_date: 2018-03-29
location: Vienna, Austria
name: 'EDBT: Conference on Extending Database Technology'
start_date: 2018-03-26
corr_author: '1'
date_created: 2019-11-26T14:19:11Z
date_published: 2018-03-26T00:00:00Z
date_updated: 2024-10-09T20:59:05Z
day: '26'
ddc:
- '000'
department:
- _id: DaAl
doi: 10.5441/002/EDBT.2018.14
file:
- access_level: open_access
checksum: ec979b56abc71016d6e6adfdadbb4afe
content_type: application/pdf
creator: dernst
date_created: 2019-11-26T14:23:04Z
date_updated: 2020-07-14T12:47:49Z
file_id: '7118'
file_name: 2018_OpenProceedings_Grubic.pdf
file_size: 1603204
relation: main_file
file_date_updated: 2020-07-14T12:47:49Z
has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '03'
oa: 1
oa_version: Published Version
page: 145-156
publication: Proceedings of the 21st International Conference on Extending Database
Technology
publication_identifier:
isbn:
- '9783893180783'
issn:
- 2367-2005
publication_status: published
publisher: OpenProceedings
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Synchronous multi-GPU training for deep learning with low-precision communications:
An empirical study'
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '7123'
abstract:
- lang: eng
text: "Population protocols are a popular model of distributed computing, in which
n agents with limited local state interact randomly, and cooperate to collectively
compute global predicates. Inspired by recent developments in DNA programming,
an extensive series of papers, across different communities, has examined the
computability and complexity characteristics of this model. Majority, or consensus,
is a central task in this model, in which agents need to collectively reach a
decision as to which one of two states A or B had a higher initial count. Two
metrics are important: the time that a protocol requires to stabilize to an output
decision, and the state space size that each agent requires to do so. It is known
that majority requires Ω(log log n) states per agent to allow for fast (poly-logarithmic
time) stabilization, and that O(log2 n) states are sufficient. Thus, there is
an exponential gap between the space upper and lower bounds for this problem.
This paper addresses this question.\r\n\r\nOn the negative side, we provide a
new lower bound of Ω(log n) states for any protocol which stabilizes in O(n1–c)
expected time, for any constant c > 0. This result is conditional on monotonicity
and output assumptions, satisfied by all known protocols. Technically, it represents
a departure from previous lower bounds, in that it does not rely on the existence
of dense configurations. Instead, we introduce a new generalized surgery technique
to prove the existence of incorrect executions for any algorithm which would contradict
the lower bound. Subsequently, our lower bound also applies to general initial
configurations, including ones with a leader. On the positive side, we give a
new algorithm for majority which uses O(log n) states, and stabilizes in O(log2
n) expected time. Central to the algorithm is a new leaderless phase clock technique,
which allows agents to synchronize in phases of Θ(n log n) consecutive interactions
using O(log n) states per agent, exploiting a new connection between population
protocols and power-of-two-choices load balancing mechanisms. We also employ our
phase clock to build a leader election algorithm with a state space of size O(log
n), which stabilizes in O(log2 n) expected time."
article_processing_charge: No
arxiv: 1
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: James
full_name: Aspnes, James
last_name: Aspnes
- first_name: Rati
full_name: Gelashvili, Rati
last_name: Gelashvili
citation:
ama: 'Alistarh D-A, Aspnes J, Gelashvili R. Space-optimal majority in population
protocols. In: Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete
Algorithms. ACM; 2018:2221-2239. doi:10.1137/1.9781611975031.144'
apa: 'Alistarh, D.-A., Aspnes, J., & Gelashvili, R. (2018). Space-optimal majority
in population protocols. In Proceedings of the 29th Annual ACM-SIAM Symposium
on Discrete Algorithms (pp. 2221–2239). New Orleans, LA, United States: ACM.
https://doi.org/10.1137/1.9781611975031.144'
chicago: Alistarh, Dan-Adrian, James Aspnes, and Rati Gelashvili. “Space-Optimal
Majority in Population Protocols.” In Proceedings of the 29th Annual ACM-SIAM
Symposium on Discrete Algorithms, 2221–39. ACM, 2018. https://doi.org/10.1137/1.9781611975031.144.
ieee: D.-A. Alistarh, J. Aspnes, and R. Gelashvili, “Space-optimal majority in population
protocols,” in Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete
Algorithms, New Orleans, LA, United States, 2018, pp. 2221–2239.
ista: 'Alistarh D-A, Aspnes J, Gelashvili R. 2018. Space-optimal majority in population
protocols. Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete Algorithms.
SODA: Symposium on Discrete Algorithms, 2221–2239.'
mla: Alistarh, Dan-Adrian, et al. “Space-Optimal Majority in Population Protocols.”
Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete Algorithms,
ACM, 2018, pp. 2221–39, doi:10.1137/1.9781611975031.144.
short: D.-A. Alistarh, J. Aspnes, R. Gelashvili, in:, Proceedings of the 29th Annual
ACM-SIAM Symposium on Discrete Algorithms, ACM, 2018, pp. 2221–2239.
conference:
end_date: 2018-01-10
location: New Orleans, LA, United States
name: 'SODA: Symposium on Discrete Algorithms'
start_date: 2018-01-07
date_created: 2019-11-26T15:10:55Z
date_published: 2018-01-30T00:00:00Z
date_updated: 2024-10-21T06:02:41Z
day: '30'
department:
- _id: DaAl
doi: 10.1137/1.9781611975031.144
external_id:
arxiv:
- '1704.04947'
isi:
- '000483921200145'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1704.04947
month: '01'
oa: 1
oa_version: Preprint
page: 2221-2239
publication: Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete Algorithms
publication_identifier:
isbn:
- '9781611975031'
publication_status: published
publisher: ACM
quality_controlled: '1'
scopus_import: '1'
status: public
title: Space-optimal majority in population protocols
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '723'
abstract:
- lang: eng
text: Escaping local optima is one of the major obstacles to function optimisation.
Using the metaphor of a fitness landscape, local optima correspond to hills separated
by fitness valleys that have to be overcome. We define a class of fitness valleys
of tunable difficulty by considering their length, representing the Hamming path
between the two optima and their depth, the drop in fitness. For this function
class we present a runtime comparison between stochastic search algorithms using
different search strategies. The (1+1) EA is a simple and well-studied evolutionary
algorithm that has to jump across the valley to a point of higher fitness because
it does not accept worsening moves (elitism). In contrast, the Metropolis algorithm
and the Strong Selection Weak Mutation (SSWM) algorithm, a famous process in population
genetics, are both able to cross the fitness valley by accepting worsening moves.
We show that the runtime of the (1+1) EA depends critically on the length of the
valley while the runtimes of the non-elitist algorithms depend crucially on the
depth of the valley. Moreover, we show that both SSWM and Metropolis can also
efficiently optimise a rugged function consisting of consecutive valleys.
article_processing_charge: No
author:
- first_name: Pietro
full_name: Oliveto, Pietro
last_name: Oliveto
- 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: Oliveto P, Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. How to escape
local optima in black box optimisation when non elitism outperforms elitism. Algorithmica.
2018;80(5):1604-1633. doi:10.1007/s00453-017-0369-2
apa: Oliveto, P., Paixao, T., Pérez Heredia, J., Sudholt, D., & Trubenova, B.
(2018). How to escape local optima in black box optimisation when non elitism
outperforms elitism. Algorithmica. Springer. https://doi.org/10.1007/s00453-017-0369-2
chicago: Oliveto, Pietro, Tiago Paixao, Jorge Pérez Heredia, Dirk Sudholt, and Barbora
Trubenova. “How to Escape Local Optima in Black Box Optimisation When Non Elitism
Outperforms Elitism.” Algorithmica. Springer, 2018. https://doi.org/10.1007/s00453-017-0369-2.
ieee: P. Oliveto, T. Paixao, J. Pérez Heredia, D. Sudholt, and B. Trubenova, “How
to escape local optima in black box optimisation when non elitism outperforms
elitism,” Algorithmica, vol. 80, no. 5. Springer, pp. 1604–1633, 2018.
ista: Oliveto P, Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. 2018. How to
escape local optima in black box optimisation when non elitism outperforms elitism.
Algorithmica. 80(5), 1604–1633.
mla: Oliveto, Pietro, et al. “How to Escape Local Optima in Black Box Optimisation
When Non Elitism Outperforms Elitism.” Algorithmica, vol. 80, no. 5, Springer,
2018, pp. 1604–33, doi:10.1007/s00453-017-0369-2.
short: P. Oliveto, T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica
80 (2018) 1604–1633.
date_created: 2018-12-11T11:48:09Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2025-04-15T08:22:22Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
- _id: CaGu
doi: 10.1007/s00453-017-0369-2
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oa_version: Published Version
page: 1604 - 1633
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_status: published
publisher: Springer
publist_id: '6957'
pubrep_id: '1014'
quality_controlled: '1'
scopus_import: '1'
status: public
title: How to escape local optima in black box optimisation when non elitism outperforms
elitism
tmp:
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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: 80
year: '2018'
...
---
_id: '738'
abstract:
- lang: eng
text: 'This paper is devoted to automatic competitive analysis of real-time scheduling
algorithms for firm-deadline tasksets, where only completed tasks con- tribute
some utility to the system. Given such a taskset T , the competitive ratio of
an on-line scheduling algorithm A for T is the worst-case utility ratio of A over
the utility achieved by a clairvoyant algorithm. We leverage the theory of quantitative
graph games to address the competitive analysis and competitive synthesis problems.
For the competitive analysis case, given any taskset T and any finite-memory on-
line scheduling algorithm A , we show that the competitive ratio of A in T can
be computed in polynomial time in the size of the state space of A . Our approach
is flexible as it also provides ways to model meaningful constraints on the released
task sequences that determine the competitive ratio. We provide an experimental
study of many well-known on-line scheduling algorithms, which demonstrates the
feasibility of our competitive analysis approach that effectively replaces human
ingenuity (required Preliminary versions of this paper have appeared in Chatterjee
et al. ( 2013 , 2014 ). B Andreas Pavlogiannis pavlogiannis@ist.ac.at Krishnendu
Chatterjee krish.chat@ist.ac.at Alexander Kößler koe@ecs.tuwien.ac.at Ulrich Schmid
s@ecs.tuwien.ac.at 1 IST Austria (Institute of Science and Technology Austria),
Am Campus 1, 3400 Klosterneuburg, Austria 2 Embedded Computing Systems Group,
Vienna University of Technology, Treitlstrasse 3, 1040 Vienna, Austria 123 Real-Time
Syst for finding worst-case scenarios) by computing power. For the competitive
synthesis case, we are just given a taskset T , and the goal is to automatically
synthesize an opti- mal on-line scheduling algorithm A , i.e., one that guarantees
the largest competitive ratio possible for T . We show how the competitive synthesis
problem can be reduced to a two-player graph game with partial information, and
establish that the compu- tational complexity of solving this game is Np -complete.
The competitive synthesis problem is hence in Np in the size of the state space
of the non-deterministic labeled transition system encoding the taskset. Overall,
the proposed framework assists in the selection of suitable scheduling algorithms
for a given taskset, which is in fact the most common situation in real-time systems
design. '
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Alexander
full_name: Kößler, Alexander
last_name: Kößler
- first_name: Ulrich
full_name: Schmid, Ulrich
last_name: Schmid
citation:
ama: Chatterjee K, Pavlogiannis A, Kößler A, Schmid U. Automated competitive analysis
of real time scheduling with graph games. Real-Time Systems. 2018;54(1):166-207.
doi:10.1007/s11241-017-9293-4
apa: Chatterjee, K., Pavlogiannis, A., Kößler, A., & Schmid, U. (2018). Automated
competitive analysis of real time scheduling with graph games. Real-Time Systems.
Springer. https://doi.org/10.1007/s11241-017-9293-4
chicago: Chatterjee, Krishnendu, Andreas Pavlogiannis, Alexander Kößler, and Ulrich
Schmid. “Automated Competitive Analysis of Real Time Scheduling with Graph Games.”
Real-Time Systems. Springer, 2018. https://doi.org/10.1007/s11241-017-9293-4.
ieee: K. Chatterjee, A. Pavlogiannis, A. Kößler, and U. Schmid, “Automated competitive
analysis of real time scheduling with graph games,” Real-Time Systems,
vol. 54, no. 1. Springer, pp. 166–207, 2018.
ista: Chatterjee K, Pavlogiannis A, Kößler A, Schmid U. 2018. Automated competitive
analysis of real time scheduling with graph games. Real-Time Systems. 54(1), 166–207.
mla: Chatterjee, Krishnendu, et al. “Automated Competitive Analysis of Real Time
Scheduling with Graph Games.” Real-Time Systems, vol. 54, no. 1, Springer,
2018, pp. 166–207, doi:10.1007/s11241-017-9293-4.
short: K. Chatterjee, A. Pavlogiannis, A. Kößler, U. Schmid, Real-Time Systems 54
(2018) 166–207.
corr_author: '1'
date_created: 2018-12-11T11:48:14Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2025-04-15T08:12:27Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1007/s11241-017-9293-4
ec_funded: 1
external_id:
isi:
- '000419955500006'
file:
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checksum: c2590ef160709d8054cf29ee173f1454
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:14Z
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file_id: '5267'
file_name: IST-2018-960-v1+1_2017_Chatterjee_Automated_competetive.pdf
file_size: 1163507
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month: '01'
oa: 1
oa_version: Published Version
page: 166 - 207
project:
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call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _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: Real-Time Systems
publication_status: published
publisher: Springer
publist_id: '6929'
pubrep_id: '960'
quality_controlled: '1'
related_material:
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title: Automated competitive analysis of real time scheduling with graph games
tmp:
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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: 54
year: '2018'
...
---
_id: '7407'
abstract:
- lang: eng
text: 'Proofs of space (PoS) [Dziembowski et al., CRYPTO''15] are proof systems
where a prover can convince a verifier that he "wastes" disk space. PoS were introduced
as a more ecological and economical replacement for proofs of work which are currently
used to secure blockchains like Bitcoin. In this work we investigate extensions
of PoS which allow the prover to embed useful data into the dedicated space, which
later can be recovered. Our first contribution is a security proof for the original
PoS from CRYPTO''15 in the random oracle model (the original proof only applied
to a restricted class of adversaries which can store a subset of the data an honest
prover would store). When this PoS is instantiated with recent constructions of
maximally depth robust graphs, our proof implies basically optimal security. As
a second contribution we show three different extensions of this PoS where useful
data can be embedded into the space required by the prover. Our security proof
for the PoS extends (non-trivially) to these constructions. We discuss how some
of these variants can be used as proofs of catalytic space (PoCS), a notion we
put forward in this work, and which basically is a PoS where most of the space
required by the prover can be used to backup useful data. Finally we discuss how
one of the extensions is a candidate construction for a proof of replication (PoR),
a proof system recently suggested in the Filecoin whitepaper. '
alternative_title:
- LIPIcs
article_processing_charge: No
author:
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Pietrzak KZ. Proofs of catalytic space. In: 10th Innovations in Theoretical
Computer Science Conference. Vol 124. Schloss Dagstuhl - Leibniz-Zentrum für
Informatik; 2018:59:1-59:25. doi:10.4230/LIPICS.ITCS.2019.59'
apa: 'Pietrzak, K. Z. (2018). Proofs of catalytic space. In 10th Innovations
in Theoretical Computer Science Conference (Vol. 124, p. 59:1-59:25). San
Diego, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ITCS.2019.59'
chicago: Pietrzak, Krzysztof Z. “Proofs of Catalytic Space.” In 10th Innovations
in Theoretical Computer Science Conference, 124:59:1-59:25. Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPICS.ITCS.2019.59.
ieee: K. Z. Pietrzak, “Proofs of catalytic space,” in 10th Innovations in Theoretical
Computer Science Conference, San Diego, CA, United States, 2018, vol. 124,
p. 59:1-59:25.
ista: 'Pietrzak KZ. 2018. Proofs of catalytic space. 10th Innovations in Theoretical
Computer Science Conference. ITCS: Innovations in Theoretical Computer Science,
LIPIcs, vol. 124, 59:1-59:25.'
mla: Pietrzak, Krzysztof Z. “Proofs of Catalytic Space.” 10th Innovations in
Theoretical Computer Science Conference, vol. 124, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2018, p. 59:1-59:25, doi:10.4230/LIPICS.ITCS.2019.59.
short: K.Z. Pietrzak, in:, 10th Innovations in Theoretical Computer Science Conference,
Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 59:1-59:25.
conference:
end_date: 2019-01-12
location: San Diego, CA, United States
name: 'ITCS: Innovations in Theoretical Computer Science'
start_date: 2019-01-10
corr_author: '1'
date_created: 2020-01-30T09:16:05Z
date_published: 2018-12-31T00:00:00Z
date_updated: 2025-07-03T11:55:28Z
day: '31'
ddc:
- '000'
department:
- _id: KrPi
doi: 10.4230/LIPICS.ITCS.2019.59
ec_funded: 1
file:
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checksum: 5cebb7f7849a3beda898f697d755dd96
content_type: application/pdf
creator: dernst
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url: https://eprint.iacr.org/2018/194
month: '12'
oa: 1
oa_version: Published Version
page: 59:1-59:25
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication: 10th Innovations in Theoretical Computer Science Conference
publication_identifier:
isbn:
- 978-3-95977-095-8
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Proofs of catalytic space
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: 124
year: '2018'
...
---
_id: '742'
abstract:
- lang: eng
text: 'We give a detailed and easily accessible proof of Gromov’s Topological Overlap
Theorem. Let X be a finite simplicial complex or, more generally, a finite polyhedral
cell complex of dimension d. Informally, the theorem states that if X has sufficiently
strong higher-dimensional expansion properties (which generalize edge expansion
of graphs and are defined in terms of cellular cochains of X) then X has the following
topological overlap property: for every continuous map (Formula presented.) there
exists a point (Formula presented.) that is contained in the images of a positive
fraction (Formula presented.) of the d-cells of X. More generally, the conclusion
holds if (Formula presented.) is replaced by any d-dimensional piecewise-linear
manifold M, with a constant (Formula presented.) that depends only on d and on
the expansion properties of X, but not on M.'
article_processing_charge: Yes (via OA deal)
author:
- first_name: Dominic
full_name: Dotterrer, Dominic
last_name: Dotterrer
- first_name: Tali
full_name: Kaufman, Tali
last_name: Kaufman
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: Dotterrer D, Kaufman T, Wagner U. On expansion and topological overlap. Geometriae
Dedicata. 2018;195(1):307–317. doi:10.1007/s10711-017-0291-4
apa: Dotterrer, D., Kaufman, T., & Wagner, U. (2018). On expansion and topological
overlap. Geometriae Dedicata. Springer. https://doi.org/10.1007/s10711-017-0291-4
chicago: Dotterrer, Dominic, Tali Kaufman, and Uli Wagner. “On Expansion and Topological
Overlap.” Geometriae Dedicata. Springer, 2018. https://doi.org/10.1007/s10711-017-0291-4.
ieee: D. Dotterrer, T. Kaufman, and U. Wagner, “On expansion and topological overlap,”
Geometriae Dedicata, vol. 195, no. 1. Springer, pp. 307–317, 2018.
ista: Dotterrer D, Kaufman T, Wagner U. 2018. On expansion and topological overlap.
Geometriae Dedicata. 195(1), 307–317.
mla: Dotterrer, Dominic, et al. “On Expansion and Topological Overlap.” Geometriae
Dedicata, vol. 195, no. 1, Springer, 2018, pp. 307–317, doi:10.1007/s10711-017-0291-4.
short: D. Dotterrer, T. Kaufman, U. Wagner, Geometriae Dedicata 195 (2018) 307–317.
corr_author: '1'
date_created: 2018-12-11T11:48:16Z
date_published: 2018-08-01T00:00:00Z
date_updated: 2025-06-03T11:41:00Z
day: '01'
ddc:
- '514'
- '516'
department:
- _id: UlWa
doi: 10.1007/s10711-017-0291-4
external_id:
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file_size: 412486
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file_date_updated: 2020-07-14T12:47:58Z
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intvolume: ' 195'
isi: 1
issue: '1'
language:
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month: '08'
oa: 1
oa_version: Published Version
page: 307–317
project:
- _id: 25FA3206-B435-11E9-9278-68D0E5697425
grant_number: PP00P2_138948
name: 'Embeddings in Higher Dimensions: Algorithms and Combinatorics'
publication: Geometriae Dedicata
publication_status: published
publisher: Springer
publist_id: '6925'
pubrep_id: '912'
quality_controlled: '1'
related_material:
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relation: earlier_version
status: public
scopus_import: '1'
status: public
title: On expansion and topological overlap
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: 195
year: '2018'
...
---
_id: '76'
abstract:
- lang: eng
text: 'Consider a fully-connected synchronous distributed system consisting of n
nodes, where up to f nodes may be faulty and every node starts in an arbitrary
initial state. In the synchronous C-counting problem, all nodes need to eventually
agree on a counter that is increased by one modulo C in each round for given C>1.
In the self-stabilising firing squad problem, the task is to eventually guarantee
that all non-faulty nodes have simultaneous responses to external inputs: if a
subset of the correct nodes receive an external “go” signal as input, then all
correct nodes should agree on a round (in the not-too-distant future) in which
to jointly output a “fire” signal. Moreover, no node should generate a “fire”
signal without some correct node having previously received a “go” signal as input.
We present a framework reducing both tasks to binary consensus at very small cost.
For example, we obtain a deterministic algorithm for self-stabilising Byzantine
firing squads with optimal resilience f<n/3, asymptotically optimal stabilisation
and response time O(f), and message size O(log f). As our framework does not restrict
the type of consensus routines used, we also obtain efficient randomised solutions.'
article_processing_charge: Yes (via OA deal)
author:
- first_name: Christoph
full_name: Lenzen, Christoph
last_name: Lenzen
- first_name: Joel
full_name: Rybicki, Joel
id: 334EFD2E-F248-11E8-B48F-1D18A9856A87
last_name: Rybicki
orcid: 0000-0002-6432-6646
citation:
ama: Lenzen C, Rybicki J. Near-optimal self-stabilising counting and firing squads.
Distributed Computing. 2018. doi:10.1007/s00446-018-0342-6
apa: Lenzen, C., & Rybicki, J. (2018). Near-optimal self-stabilising counting
and firing squads. Distributed Computing. Springer. https://doi.org/10.1007/s00446-018-0342-6
chicago: Lenzen, Christoph, and Joel Rybicki. “Near-Optimal Self-Stabilising Counting
and Firing Squads.” Distributed Computing. Springer, 2018. https://doi.org/10.1007/s00446-018-0342-6.
ieee: C. Lenzen and J. Rybicki, “Near-optimal self-stabilising counting and firing
squads,” Distributed Computing. Springer, 2018.
ista: Lenzen C, Rybicki J. 2018. Near-optimal self-stabilising counting and firing
squads. Distributed Computing.
mla: Lenzen, Christoph, and Joel Rybicki. “Near-Optimal Self-Stabilising Counting
and Firing Squads.” Distributed Computing, Springer, 2018, doi:10.1007/s00446-018-0342-6.
short: C. Lenzen, J. Rybicki, Distributed Computing (2018).
corr_author: '1'
date_created: 2018-12-11T11:44:30Z
date_published: 2018-09-12T00:00:00Z
date_updated: 2025-04-15T06:53:15Z
day: '12'
ddc:
- '000'
department:
- _id: DaAl
doi: 10.1007/s00446-018-0342-6
external_id:
isi:
- '000475627800005'
file:
- access_level: open_access
checksum: 872db70bba9b401500abe3c6ae2f1a61
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creator: dernst
date_created: 2018-12-17T14:21:22Z
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language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Distributed Computing
publication_status: published
publisher: Springer
publist_id: '7978'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Near-optimal self-stabilising counting and firing squads
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
year: '2018'
...
---
_id: '9831'
abstract:
- lang: eng
text: 'Implementation of the inference method in Matlab, including three applications
of the method: The first one for the model of ant motion, the second one for bacterial
chemotaxis, and the third one for the motion of fish.'
article_processing_charge: No
author:
- first_name: Katarína
full_name: Bod’Ová, Katarína
last_name: Bod’Ová
- first_name: Gabriel
full_name: Mitchell, Gabriel
id: 315BCD80-F248-11E8-B48F-1D18A9856A87
last_name: Mitchell
- first_name: Roy
full_name: Harpaz, Roy
last_name: Harpaz
- first_name: Elad
full_name: Schneidman, Elad
last_name: Schneidman
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. Implementation of
the inference method in Matlab. 2018. doi:10.1371/journal.pone.0193049.s001
apa: Bod’Ová, K., Mitchell, G., Harpaz, R., Schneidman, E., & Tkačik, G. (2018).
Implementation of the inference method in Matlab. Public Library of Science. https://doi.org/10.1371/journal.pone.0193049.s001
chicago: Bod’Ová, Katarína, Gabriel Mitchell, Roy Harpaz, Elad Schneidman, and Gašper
Tkačik. “Implementation of the Inference Method in Matlab.” Public Library of
Science, 2018. https://doi.org/10.1371/journal.pone.0193049.s001.
ieee: K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, and G. Tkačik, “Implementation
of the inference method in Matlab.” Public Library of Science, 2018.
ista: Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. 2018. Implementation
of the inference method in Matlab, Public Library of Science, 10.1371/journal.pone.0193049.s001.
mla: Bod’Ová, Katarína, et al. Implementation of the Inference Method in Matlab.
Public Library of Science, 2018, doi:10.1371/journal.pone.0193049.s001.
short: K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkačik, (2018).
date_created: 2021-08-09T07:01:24Z
date_published: 2018-03-07T00:00:00Z
date_updated: 2025-04-15T06:44:30Z
day: '07'
department:
- _id: GaTk
doi: 10.1371/journal.pone.0193049.s001
month: '03'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '406'
relation: used_in_publication
status: public
status: public
title: Implementation of the inference method in Matlab
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '9837'
abstract:
- lang: eng
text: Both classical and recent studies suggest that chromosomal inversion polymorphisms
are important in adaptation and speciation. However, biases in discovery and reporting
of inversions make it difficult to assess their prevalence and biological importance.
Here, we use an approach based on linkage disequilibrium among markers genotyped
for samples collected across a transect between contrasting habitats to detect
chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in
a single locality for the coastal marine snail, Littorina saxatilis. Patterns
of diversity in the field and of recombination in controlled crosses provide strong
evidence that at least the majority of these rearrangements are inversions. Most
show clinal changes in frequency between habitats, suggestive of divergent selection,
but only one appears to be fixed for different arrangements in the two habitats.
Consistent with widespread evidence for balancing selection on inversion polymorphisms,
we argue that a combination of heterosis and divergent selection can explain the
observed patterns and should be considered in other systems spanning environmental
gradients.
article_processing_charge: No
author:
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Pragya
full_name: Chaube, Pragya
last_name: Chaube
- first_name: Hernán E.
full_name: Morales, Hernán E.
last_name: Morales
- first_name: Tomas
full_name: Larsson, Tomas
last_name: Larsson
- first_name: Alan R.
full_name: Lemmon, Alan R.
last_name: Lemmon
- first_name: Emily M.
full_name: Lemmon, Emily M.
last_name: Lemmon
- first_name: Marina
full_name: Rafajlović, Marina
last_name: Rafajlović
- first_name: Marina
full_name: Panova, Marina
last_name: Panova
- first_name: Mark
full_name: Ravinet, Mark
last_name: Ravinet
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
citation:
ama: 'Faria R, Chaube P, Morales HE, et al. Data from: Multiple chromosomal rearrangements
in a hybrid zone between Littorina saxatilis ecotypes. 2018. doi:10.5061/dryad.72cg113'
apa: 'Faria, R., Chaube, P., Morales, H. E., Larsson, T., Lemmon, A. R., Lemmon,
E. M., … Butlin, R. K. (2018). Data from: Multiple chromosomal rearrangements
in a hybrid zone between Littorina saxatilis ecotypes. Dryad. https://doi.org/10.5061/dryad.72cg113'
chicago: 'Faria, Rui, Pragya Chaube, Hernán E. Morales, Tomas Larsson, Alan R. Lemmon,
Emily M. Lemmon, Marina Rafajlović, et al. “Data from: Multiple Chromosomal Rearrangements
in a Hybrid Zone between Littorina Saxatilis Ecotypes.” Dryad, 2018. https://doi.org/10.5061/dryad.72cg113.'
ieee: 'R. Faria et al., “Data from: Multiple chromosomal rearrangements in
a hybrid zone between Littorina saxatilis ecotypes.” Dryad, 2018.'
ista: 'Faria R, Chaube P, Morales HE, Larsson T, Lemmon AR, Lemmon EM, Rafajlović
M, Panova M, Ravinet M, Johannesson K, Westram AM, Butlin RK. 2018. Data from:
Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis
ecotypes, Dryad, 10.5061/dryad.72cg113.'
mla: 'Faria, Rui, et al. Data from: Multiple Chromosomal Rearrangements in a
Hybrid Zone between Littorina Saxatilis Ecotypes. Dryad, 2018, doi:10.5061/dryad.72cg113.'
short: R. Faria, P. Chaube, H.E. Morales, T. Larsson, A.R. Lemmon, E.M. Lemmon,
M. Rafajlović, M. Panova, M. Ravinet, K. Johannesson, A.M. Westram, R.K. Butlin,
(2018).
date_created: 2021-08-09T12:46:39Z
date_published: 2018-10-09T00:00:00Z
date_updated: 2023-08-24T14:50:26Z
day: '09'
department:
- _id: NiBa
doi: 10.5061/dryad.72cg113
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.72cg113
month: '10'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '6095'
relation: used_in_publication
status: public
status: public
title: 'Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina
saxatilis ecotypes'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '9838'
abstract:
- lang: eng
text: 'Facial shape is the basis for facial recognition and categorization. Facial
features reflect the underlying geometry of the skeletal structures. Here we reveal
that cartilaginous nasal capsule (corresponding to upper jaw and face) is shaped
by signals generated by neural structures: brain and olfactory epithelium. Brain-derived
Sonic Hedgehog (SHH) enables the induction of nasal septum and posterior nasal
capsule, whereas the formation of a capsule roof is controlled by signals from
the olfactory epithelium. Unexpectedly, the cartilage of the nasal capsule turned
out to be important for shaping membranous facial bones during development. This
suggests that conserved neurosensory structures could benefit from protection
and have evolved signals inducing cranial cartilages encasing them. Experiments
with mutant mice revealed that the genomic regulatory regions controlling production
of SHH in the nervous system contribute to facial cartilage morphogenesis, which
might be a mechanism responsible for the adaptive evolution of animal faces and
snouts.'
article_processing_charge: No
author:
- first_name: Marketa
full_name: Kaucka, Marketa
last_name: Kaucka
- first_name: Julian
full_name: Petersen, Julian
last_name: Petersen
- first_name: Marketa
full_name: Tesarova, Marketa
last_name: Tesarova
- first_name: Bara
full_name: Szarowska, Bara
last_name: Szarowska
- first_name: Maria Eleni
full_name: Kastriti, Maria Eleni
last_name: Kastriti
- first_name: Meng
full_name: Xie, Meng
last_name: Xie
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
- first_name: Karl
full_name: Annusver, Karl
last_name: Annusver
- first_name: Maria
full_name: Kasper, Maria
last_name: Kasper
- first_name: Orsolya
full_name: Symmons, Orsolya
last_name: Symmons
- first_name: Leslie
full_name: Pan, Leslie
last_name: Pan
- first_name: Francois
full_name: Spitz, Francois
last_name: Spitz
- first_name: Jozef
full_name: Kaiser, Jozef
last_name: Kaiser
- first_name: Maria
full_name: Hovorakova, Maria
last_name: Hovorakova
- first_name: Tomas
full_name: Zikmund, Tomas
last_name: Zikmund
- first_name: Kazunori
full_name: Sunadome, Kazunori
last_name: Sunadome
- first_name: Michael P
full_name: Matise, Michael P
last_name: Matise
- first_name: Hui
full_name: Wang, Hui
last_name: Wang
- first_name: Ulrika
full_name: Marklund, Ulrika
last_name: Marklund
- first_name: Hind
full_name: Abdo, Hind
last_name: Abdo
- first_name: Patrik
full_name: Ernfors, Patrik
last_name: Ernfors
- first_name: Pascal
full_name: Maire, Pascal
last_name: Maire
- first_name: Maud
full_name: Wurmser, Maud
last_name: Wurmser
- first_name: Andrei S
full_name: Chagin, Andrei S
last_name: Chagin
- first_name: Kaj
full_name: Fried, Kaj
last_name: Fried
- first_name: Igor
full_name: Adameyko, Igor
last_name: Adameyko
citation:
ama: 'Kaucka M, Petersen J, Tesarova M, et al. Data from: Signals from the brain
and olfactory epithelium control shaping of the mammalian nasal capsule cartilage.
2018. doi:10.5061/dryad.f1s76f2'
apa: 'Kaucka, M., Petersen, J., Tesarova, M., Szarowska, B., Kastriti, M. E., Xie,
M., … Adameyko, I. (2018). Data from: Signals from the brain and olfactory epithelium
control shaping of the mammalian nasal capsule cartilage. Dryad. https://doi.org/10.5061/dryad.f1s76f2'
chicago: 'Kaucka, Marketa, Julian Petersen, Marketa Tesarova, Bara Szarowska, Maria
Eleni Kastriti, Meng Xie, Anna Kicheva, et al. “Data from: Signals from the Brain
and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.”
Dryad, 2018. https://doi.org/10.5061/dryad.f1s76f2.'
ieee: 'M. Kaucka et al., “Data from: Signals from the brain and olfactory
epithelium control shaping of the mammalian nasal capsule cartilage.” Dryad, 2018.'
ista: 'Kaucka M, Petersen J, Tesarova M, Szarowska B, Kastriti ME, Xie M, Kicheva
A, Annusver K, Kasper M, Symmons O, Pan L, Spitz F, Kaiser J, Hovorakova M, Zikmund
T, Sunadome K, Matise MP, Wang H, Marklund U, Abdo H, Ernfors P, Maire P, Wurmser
M, Chagin AS, Fried K, Adameyko I. 2018. Data from: Signals from the brain and
olfactory epithelium control shaping of the mammalian nasal capsule cartilage,
Dryad, 10.5061/dryad.f1s76f2.'
mla: 'Kaucka, Marketa, et al. Data from: Signals from the Brain and Olfactory
Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage. Dryad,
2018, doi:10.5061/dryad.f1s76f2.'
short: M. Kaucka, J. Petersen, M. Tesarova, B. Szarowska, M.E. Kastriti, M. Xie,
A. Kicheva, K. Annusver, M. Kasper, O. Symmons, L. Pan, F. Spitz, J. Kaiser, M.
Hovorakova, T. Zikmund, K. Sunadome, M.P. Matise, H. Wang, U. Marklund, H. Abdo,
P. Ernfors, P. Maire, M. Wurmser, A.S. Chagin, K. Fried, I. Adameyko, (2018).
date_created: 2021-08-09T12:54:35Z
date_published: 2018-06-14T00:00:00Z
date_updated: 2025-04-14T13:02:22Z
day: '14'
department:
- _id: AnKi
doi: 10.5061/dryad.f1s76f2
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.f1s76f2
month: '06'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '162'
relation: used_in_publication
status: public
status: public
title: 'Data from: Signals from the brain and olfactory epithelium control shaping
of the mammalian nasal capsule cartilage'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '9840'
abstract:
- lang: eng
text: Herd immunity, a process in which resistant individuals limit the spread of
a pathogen among susceptible hosts has been extensively studied in eukaryotes.
Even though bacteria have evolved multiple immune systems against their phage
pathogens, herd immunity in bacteria remains unexplored. Here we experimentally
demonstrate that herd immunity arises during phage epidemics in structured and
unstructured Escherichia coli populations consisting of differing frequencies
of susceptible and resistant cells harboring CRISPR immunity. In addition, we
develop a mathematical model that quantifies how herd immunity is affected by
spatial population structure, bacterial growth rate, and phage replication rate.
Using our model we infer a general epidemiological rule describing the relative
speed of an epidemic in partially resistant spatially structured populations.
Our experimental and theoretical findings indicate that herd immunity may be important
in bacterial communities, allowing for stable coexistence of bacteria and their
phages and the maintenance of polymorphism in bacterial immunity.
article_processing_charge: No
author:
- first_name: Pavel
full_name: Payne, Pavel
id: 35F78294-F248-11E8-B48F-1D18A9856A87
last_name: Payne
orcid: 0000-0002-2711-9453
- first_name: Lukas
full_name: Geyrhofer, Lukas
last_name: Geyrhofer
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
citation:
ama: 'Payne P, Geyrhofer L, Barton NH, Bollback JP. Data from: CRISPR-based herd
immunity limits phage epidemics in bacterial populations. 2018. doi:10.5061/dryad.42n44'
apa: 'Payne, P., Geyrhofer, L., Barton, N. H., & Bollback, J. P. (2018). Data
from: CRISPR-based herd immunity limits phage epidemics in bacterial populations.
Dryad. https://doi.org/10.5061/dryad.42n44'
chicago: 'Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback.
“Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations.”
Dryad, 2018. https://doi.org/10.5061/dryad.42n44.'
ieee: 'P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “Data from: CRISPR-based
herd immunity limits phage epidemics in bacterial populations.” Dryad, 2018.'
ista: 'Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. Data from: CRISPR-based
herd immunity limits phage epidemics in bacterial populations, Dryad, 10.5061/dryad.42n44.'
mla: 'Payne, Pavel, et al. Data from: CRISPR-Based Herd Immunity Limits Phage
Epidemics in Bacterial Populations. Dryad, 2018, doi:10.5061/dryad.42n44.'
short: P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, (2018).
date_created: 2021-08-09T13:10:02Z
date_published: 2018-03-12T00:00:00Z
date_updated: 2025-04-15T08:17:50Z
day: '12'
department:
- _id: NiBa
- _id: JoBo
doi: 10.5061/dryad.42n44
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.42n44
month: '03'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '423'
relation: used_in_publication
status: public
status: public
title: 'Data from: CRISPR-based herd immunity limits phage epidemics in bacterial
populations'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '9841'
abstract:
- lang: eng
text: Around 150 million years ago, eusocial termites evolved from within the cockroaches,
50 million years before eusocial Hymenoptera, such as bees and ants, appeared.
Here, we report the 2-Gb genome of the German cockroach, Blattella germanica,
and the 1.3-Gb genome of the drywood termite Cryptotermes secundus. We show evolutionary
signatures of termite eusociality by comparing the genomes and transcriptomes
of three termites and the cockroach against the background of 16 other eusocial
and non-eusocial insects. Dramatic adaptive changes in genes underlying the production
and perception of pheromones confirm the importance of chemical communication
in the termites. These are accompanied by major changes in gene regulation and
the molecular evolution of caste determination. Many of these results parallel
molecular mechanisms of eusocial evolution in Hymenoptera. However, the specific
solutions are remarkably different, thus revealing a striking case of convergence
in one of the major evolutionary transitions in biological complexity.
article_processing_charge: No
author:
- first_name: Mark C.
full_name: Harrison, Mark C.
last_name: Harrison
- first_name: Evelien
full_name: Jongepier, Evelien
last_name: Jongepier
- first_name: Hugh M.
full_name: Robertson, Hugh M.
last_name: Robertson
- first_name: Nicolas
full_name: Arning, Nicolas
last_name: Arning
- first_name: Tristan
full_name: Bitard-Feildel, Tristan
last_name: Bitard-Feildel
- first_name: Hsu
full_name: Chao, Hsu
last_name: Chao
- first_name: Christopher P.
full_name: Childers, Christopher P.
last_name: Childers
- first_name: Huyen
full_name: Dinh, Huyen
last_name: Dinh
- first_name: Harshavardhan
full_name: Doddapaneni, Harshavardhan
last_name: Doddapaneni
- first_name: Shannon
full_name: Dugan, Shannon
last_name: Dugan
- first_name: Johannes
full_name: Gowin, Johannes
last_name: Gowin
- first_name: Carolin
full_name: Greiner, Carolin
last_name: Greiner
- first_name: Yi
full_name: Han, Yi
last_name: Han
- first_name: Haofu
full_name: Hu, Haofu
last_name: Hu
- first_name: Daniel S. T.
full_name: Hughes, Daniel S. T.
last_name: Hughes
- first_name: Ann K
full_name: Huylmans, Ann K
id: 4C0A3874-F248-11E8-B48F-1D18A9856A87
last_name: Huylmans
orcid: 0000-0001-8871-4961
- first_name: Carsten
full_name: Kemena, Carsten
last_name: Kemena
- first_name: Lukas P. M.
full_name: Kremer, Lukas P. M.
last_name: Kremer
- first_name: Sandra L.
full_name: Lee, Sandra L.
last_name: Lee
- first_name: Alberto
full_name: Lopez-Ezquerra, Alberto
last_name: Lopez-Ezquerra
- first_name: Ludovic
full_name: Mallet, Ludovic
last_name: Mallet
- first_name: Jose M.
full_name: Monroy-Kuhn, Jose M.
last_name: Monroy-Kuhn
- first_name: Annabell
full_name: Moser, Annabell
last_name: Moser
- first_name: Shwetha C.
full_name: Murali, Shwetha C.
last_name: Murali
- first_name: Donna M.
full_name: Muzny, Donna M.
last_name: Muzny
- first_name: Saria
full_name: Otani, Saria
last_name: Otani
- first_name: Maria-Dolors
full_name: Piulachs, Maria-Dolors
last_name: Piulachs
- first_name: Monica
full_name: Poelchau, Monica
last_name: Poelchau
- first_name: Jiaxin
full_name: Qu, Jiaxin
last_name: Qu
- first_name: Florentine
full_name: Schaub, Florentine
last_name: Schaub
- first_name: Ayako
full_name: Wada-Katsumata, Ayako
last_name: Wada-Katsumata
- first_name: Kim C.
full_name: Worley, Kim C.
last_name: Worley
- first_name: Qiaolin
full_name: Xie, Qiaolin
last_name: Xie
- first_name: Guillem
full_name: Ylla, Guillem
last_name: Ylla
- first_name: Michael
full_name: Poulsen, Michael
last_name: Poulsen
- first_name: Richard A.
full_name: Gibbs, Richard A.
last_name: Gibbs
- first_name: Coby
full_name: Schal, Coby
last_name: Schal
- first_name: Stephen
full_name: Richards, Stephen
last_name: Richards
- first_name: Xavier
full_name: Belles, Xavier
last_name: Belles
- first_name: Judith
full_name: Korb, Judith
last_name: Korb
- first_name: Erich
full_name: Bornberg-Bauer, Erich
last_name: Bornberg-Bauer
citation:
ama: 'Harrison MC, Jongepier E, Robertson HM, et al. Data from: Hemimetabolous genomes
reveal molecular basis of termite eusociality. 2018. doi:10.5061/dryad.51d4r'
apa: 'Harrison, M. C., Jongepier, E., Robertson, H. M., Arning, N., Bitard-Feildel,
T., Chao, H., … Bornberg-Bauer, E. (2018). Data from: Hemimetabolous genomes reveal
molecular basis of termite eusociality. Dryad. https://doi.org/10.5061/dryad.51d4r'
chicago: 'Harrison, Mark C., Evelien Jongepier, Hugh M. Robertson, Nicolas Arning,
Tristan Bitard-Feildel, Hsu Chao, Christopher P. Childers, et al. “Data from:
Hemimetabolous Genomes Reveal Molecular Basis of Termite Eusociality.” Dryad,
2018. https://doi.org/10.5061/dryad.51d4r.'
ieee: 'M. C. Harrison et al., “Data from: Hemimetabolous genomes reveal molecular
basis of termite eusociality.” Dryad, 2018.'
ista: 'Harrison MC, Jongepier E, Robertson HM, Arning N, Bitard-Feildel T, Chao
H, Childers CP, Dinh H, Doddapaneni H, Dugan S, Gowin J, Greiner C, Han Y, Hu
H, Hughes DST, Huylmans AK, Kemena C, Kremer LPM, Lee SL, Lopez-Ezquerra A, Mallet
L, Monroy-Kuhn JM, Moser A, Murali SC, Muzny DM, Otani S, Piulachs M-D, Poelchau
M, Qu J, Schaub F, Wada-Katsumata A, Worley KC, Xie Q, Ylla G, Poulsen M, Gibbs
RA, Schal C, Richards S, Belles X, Korb J, Bornberg-Bauer E. 2018. Data from:
Hemimetabolous genomes reveal molecular basis of termite eusociality, Dryad, 10.5061/dryad.51d4r.'
mla: 'Harrison, Mark C., et al. Data from: Hemimetabolous Genomes Reveal Molecular
Basis of Termite Eusociality. Dryad, 2018, doi:10.5061/dryad.51d4r.'
short: M.C. Harrison, E. Jongepier, H.M. Robertson, N. Arning, T. Bitard-Feildel,
H. Chao, C.P. Childers, H. Dinh, H. Doddapaneni, S. Dugan, J. Gowin, C. Greiner,
Y. Han, H. Hu, D.S.T. Hughes, A.K. Huylmans, C. Kemena, L.P.M. Kremer, S.L. Lee,
A. Lopez-Ezquerra, L. Mallet, J.M. Monroy-Kuhn, A. Moser, S.C. Murali, D.M. Muzny,
S. Otani, M.-D. Piulachs, M. Poelchau, J. Qu, F. Schaub, A. Wada-Katsumata, K.C.
Worley, Q. Xie, G. Ylla, M. Poulsen, R.A. Gibbs, C. Schal, S. Richards, X. Belles,
J. Korb, E. Bornberg-Bauer, (2018).
date_created: 2021-08-09T13:13:48Z
date_published: 2018-12-12T00:00:00Z
date_updated: 2023-09-11T14:10:56Z
day: '12'
department:
- _id: BeVi
doi: 10.5061/dryad.51d4r
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.51d4r
month: '12'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '448'
relation: used_in_publication
status: public
status: public
title: 'Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...