---
_id: '8657'
abstract:
- lang: eng
text: "Synthesis of proteins – translation – is a fundamental process of life. Quantitative
studies anchor translation into the context of bacterial physiology and reveal
several mathematical relationships, called “growth laws,” which capture physiological
feedbacks between protein synthesis and cell growth. Growth laws describe the
dependency of the ribosome abundance as a function of growth rate, which can change
depending on the growth conditions. Perturbations of translation reveal that bacteria
employ a compensatory strategy in which the reduced translation capability results
in increased expression of the translation machinery.\r\nPerturbations of translation
are achieved in various ways; clinically interesting is the application of translation-targeting
antibiotics – translation inhibitors. The antibiotic effects on bacterial physiology
are often poorly understood. Bacterial responses to two or more simultaneously
applied antibiotics are even more puzzling. The combined antibiotic effect determines
the type of drug interaction, which ranges from synergy (the effect is stronger
than expected) to antagonism (the effect is weaker) and suppression (one of the
drugs loses its potency).\r\nIn the first part of this work, we systematically
measure the pairwise interaction network for translation inhibitors that interfere
with different steps in translation. We find that the interactions are surprisingly
diverse and tend to be more antagonistic. To explore the underlying mechanisms,
we begin with a minimal biophysical model of combined antibiotic action. We base
this model on the kinetics of antibiotic uptake and binding together with the
physiological response described by the growth laws. The biophysical model explains
some drug interactions, but not all; it specifically fails to predict suppression.\r\nIn
the second part of this work, we hypothesize that elusive suppressive drug interactions
result from the interplay between ribosomes halted in different stages of translation.
To elucidate this putative mechanism of drug interactions between translation
inhibitors, we generate translation bottlenecks genetically using in- ducible
control of translation factors that regulate well-defined translation cycle steps.
These perturbations accurately mimic antibiotic action and drug interactions,
supporting that the interplay of different translation bottlenecks partially causes
these interactions.\r\nWe extend this approach by varying two translation bottlenecks
simultaneously. This approach reveals the suppression of translocation inhibition
by inhibited translation. We rationalize this effect by modeling dense traffic
of ribosomes that move on transcripts in a translation factor-mediated manner.
This model predicts a dissolution of traffic jams caused by inhibited translocation
when the density of ribosome traffic is reduced by lowered initiation. We base
this model on the growth laws and quantitative relationships between different
translation and growth parameters.\r\nIn the final part of this work, we describe
a set of tools aimed at quantification of physiological and translation parameters.
We further develop a simple model that directly connects the abundance of a translation
factor with the growth rate, which allows us to extract physiological parameters
describing initiation. We demonstrate the development of tools for measuring translation
rate.\r\nThis thesis showcases how a combination of high-throughput growth rate
mea- surements, genetics, and modeling can reveal mechanisms of drug interactions.
Furthermore, by a gradual transition from combinations of antibiotics to precise
genetic interventions, we demonstrated the equivalency between genetic and chemi-
cal perturbations of translation. These findings tile the path for quantitative
studies of antibiotic combinations and illustrate future approaches towards the
quantitative description of translation."
acknowledged_ssus:
- _id: LifeSc
- _id: M-Shop
acknowledgement: I thank Life Science Facilities for their continuous support with
providing top-notch laboratory materials, keeping the devices humming, and coordinating
the repairs and building of custom-designed laboratory equipment with the MIBA Machine
shop.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Bor
full_name: Kavcic, Bor
id: 350F91D2-F248-11E8-B48F-1D18A9856A87
last_name: Kavcic
orcid: 0000-0001-6041-254X
citation:
ama: 'Kavcic B. Perturbations of protein synthesis: from antibiotics to genetics
and physiology. 2020. doi:10.15479/AT:ISTA:8657'
apa: 'Kavcic, B. (2020). Perturbations of protein synthesis: from antibiotics
to genetics and physiology. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8657'
chicago: 'Kavcic, Bor. “Perturbations of Protein Synthesis: From Antibiotics to
Genetics and Physiology.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8657.'
ieee: 'B. Kavcic, “Perturbations of protein synthesis: from antibiotics to genetics
and physiology,” Institute of Science and Technology Austria, 2020.'
ista: 'Kavcic B. 2020. Perturbations of protein synthesis: from antibiotics to genetics
and physiology. Institute of Science and Technology Austria.'
mla: 'Kavcic, Bor. Perturbations of Protein Synthesis: From Antibiotics to Genetics
and Physiology. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8657.'
short: 'B. Kavcic, Perturbations of Protein Synthesis: From Antibiotics to Genetics
and Physiology, Institute of Science and Technology Austria, 2020.'
date_created: 2020-10-13T16:46:14Z
date_published: 2020-10-14T00:00:00Z
date_updated: 2023-09-07T13:20:48Z
day: '14'
ddc:
- '571'
- '530'
- '570'
degree_awarded: PhD
department:
- _id: GaTk
doi: 10.15479/AT:ISTA:8657
file:
- access_level: open_access
checksum: d708ecd62b6fcc3bc1feb483b8dbe9eb
content_type: application/pdf
creator: bkavcic
date_created: 2020-10-15T06:41:20Z
date_updated: 2021-10-07T22:30:03Z
embargo: 2021-10-06
file_id: '8663'
file_name: kavcicB_thesis202009.pdf
file_size: 52636162
relation: main_file
- access_level: closed
checksum: bb35f2352a04db19164da609f00501f3
content_type: application/zip
creator: bkavcic
date_created: 2020-10-15T06:41:53Z
date_updated: 2021-10-07T22:30:03Z
embargo_to: open_access
file_id: '8664'
file_name: 2020b.zip
file_size: 321681247
relation: source_file
file_date_updated: 2021-10-07T22:30:03Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '271'
publication_identifier:
isbn:
- 978-3-99078-011-4
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7673'
relation: part_of_dissertation
status: public
- id: '8250'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
title: 'Perturbations of protein synthesis: from antibiotics to genetics and physiology'
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '8669'
abstract:
- lang: eng
text: Pancreatic islets play an essential role in regulating blood glucose level.
Although the molecular pathways underlying islet cell differentiation are beginning
to be resolved, the cellular basis of islet morphogenesis and fate allocation
remain unclear. By combining unbiased and targeted lineage tracing, we address
the events leading to islet formation in the mouse. From the statistical analysis
of clones induced at multiple embryonic timepoints, here we show that, during
the secondary transition, islet formation involves the aggregation of multiple
equipotent endocrine progenitors that transition from a phase of stochastic amplification
by cell division into a phase of sublineage restriction and limited islet fission.
Together, these results explain quantitatively the heterogeneous size distribution
and degree of polyclonality of maturing islets, as well as dispersion of progenitors
within and between islets. Further, our results show that, during the secondary
transition, α- and β-cells are generated in a contemporary manner. Together, these
findings provide insight into the cellular basis of islet development.
article_number: '5037'
article_processing_charge: No
article_type: original
author:
- first_name: Magdalena K.
full_name: Sznurkowska, Magdalena K.
last_name: Sznurkowska
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Roberta
full_name: Azzarelli, Roberta
last_name: Azzarelli
- first_name: Lemonia
full_name: Chatzeli, Lemonia
last_name: Chatzeli
- first_name: Tatsuro
full_name: Ikeda, Tatsuro
last_name: Ikeda
- first_name: Shosei
full_name: Yoshida, Shosei
last_name: Yoshida
- first_name: Anna
full_name: Philpott, Anna
last_name: Philpott
- first_name: Benjamin D
full_name: Simons, Benjamin D
last_name: Simons
citation:
ama: Sznurkowska MK, Hannezo EB, Azzarelli R, et al. Tracing the cellular basis
of islet specification in mouse pancreas. Nature Communications. 2020;11.
doi:10.1038/s41467-020-18837-3
apa: Sznurkowska, M. K., Hannezo, E. B., Azzarelli, R., Chatzeli, L., Ikeda, T.,
Yoshida, S., … Simons, B. D. (2020). Tracing the cellular basis of islet specification
in mouse pancreas. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-18837-3
chicago: Sznurkowska, Magdalena K., Edouard B Hannezo, Roberta Azzarelli, Lemonia
Chatzeli, Tatsuro Ikeda, Shosei Yoshida, Anna Philpott, and Benjamin D Simons.
“Tracing the Cellular Basis of Islet Specification in Mouse Pancreas.” Nature
Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-18837-3.
ieee: M. K. Sznurkowska et al., “Tracing the cellular basis of islet specification
in mouse pancreas,” Nature Communications, vol. 11. Springer Nature, 2020.
ista: Sznurkowska MK, Hannezo EB, Azzarelli R, Chatzeli L, Ikeda T, Yoshida S, Philpott
A, Simons BD. 2020. Tracing the cellular basis of islet specification in mouse
pancreas. Nature Communications. 11, 5037.
mla: Sznurkowska, Magdalena K., et al. “Tracing the Cellular Basis of Islet Specification
in Mouse Pancreas.” Nature Communications, vol. 11, 5037, Springer Nature,
2020, doi:10.1038/s41467-020-18837-3.
short: M.K. Sznurkowska, E.B. Hannezo, R. Azzarelli, L. Chatzeli, T. Ikeda, S. Yoshida,
A. Philpott, B.D. Simons, Nature Communications 11 (2020).
date_created: 2020-10-18T22:01:35Z
date_published: 2020-10-07T00:00:00Z
date_updated: 2023-08-22T10:18:17Z
day: '07'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1038/s41467-020-18837-3
external_id:
isi:
- '000577244600003'
pmid:
- '33028844'
file:
- access_level: open_access
checksum: 0ecc0eab72d2d50694852579611a6624
content_type: application/pdf
creator: dernst
date_created: 2020-10-19T11:27:46Z
date_updated: 2020-10-19T11:27:46Z
file_id: '8677'
file_name: 2020_NatureComm_Sznurkowska.pdf
file_size: 5540540
relation: main_file
success: 1
file_date_updated: 2020-10-19T11:27:46Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- '20411723'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tracing the cellular basis of islet specification in mouse pancreas
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2020'
...
---
_id: '8670'
abstract:
- lang: eng
text: The α–z Rényi relative entropies are a two-parameter family of Rényi relative
entropies that are quantum generalizations of the classical α-Rényi relative entropies.
In the work [Adv. Math. 365, 107053 (2020)], we decided the full range of (α,
z) for which the data processing inequality (DPI) is valid. In this paper, we
give algebraic conditions for the equality in DPI. For the full range of parameters
(α, z), we give necessary conditions and sufficient conditions. For most parameters,
we give equivalent conditions. This generalizes and strengthens the results of
Leditzky et al. [Lett. Math. Phys. 107, 61–80 (2017)].
acknowledgement: This research was supported by the European Union’s Horizon 2020
research and innovation program under the Marie Skłodowska-Curie Grant Agreement
No. 754411. The author would like to thank Anna Vershynina and Sarah Chehade for
their helpful comments.
article_number: '102201'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Haonan
full_name: Zhang, Haonan
id: D8F41E38-9E66-11E9-A9E2-65C2E5697425
last_name: Zhang
citation:
ama: Zhang H. Equality conditions of data processing inequality for α-z Rényi relative
entropies. Journal of Mathematical Physics. 2020;61(10). doi:10.1063/5.0022787
apa: Zhang, H. (2020). Equality conditions of data processing inequality for α-z
Rényi relative entropies. Journal of Mathematical Physics. AIP Publishing.
https://doi.org/10.1063/5.0022787
chicago: Zhang, Haonan. “Equality Conditions of Data Processing Inequality for α-z
Rényi Relative Entropies.” Journal of Mathematical Physics. AIP Publishing,
2020. https://doi.org/10.1063/5.0022787.
ieee: H. Zhang, “Equality conditions of data processing inequality for α-z Rényi
relative entropies,” Journal of Mathematical Physics, vol. 61, no. 10.
AIP Publishing, 2020.
ista: Zhang H. 2020. Equality conditions of data processing inequality for α-z Rényi
relative entropies. Journal of Mathematical Physics. 61(10), 102201.
mla: Zhang, Haonan. “Equality Conditions of Data Processing Inequality for α-z Rényi
Relative Entropies.” Journal of Mathematical Physics, vol. 61, no. 10,
102201, AIP Publishing, 2020, doi:10.1063/5.0022787.
short: H. Zhang, Journal of Mathematical Physics 61 (2020).
date_created: 2020-10-18T22:01:36Z
date_published: 2020-10-01T00:00:00Z
date_updated: 2023-08-22T10:32:29Z
day: '01'
department:
- _id: JaMa
doi: 10.1063/5.0022787
ec_funded: 1
external_id:
arxiv:
- '2007.06644'
isi:
- '000578529200001'
intvolume: ' 61'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2007.06644
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Journal of Mathematical Physics
publication_identifier:
issn:
- '00222488'
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Equality conditions of data processing inequality for α-z Rényi relative entropies
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 61
year: '2020'
...
---
_id: '8671'
abstract:
- lang: eng
text: 'We study relations between evidence theory and S-approximation spaces. Both
theories have their roots in the analysis of Dempsterchr(''39'')s multivalued
mappings and lower and upper probabilities, and have close relations to rough
sets. We show that an S-approximation space, satisfying a monotonicity condition,
can induce a natural belief structure which is a fundamental block in evidence
theory. We also demonstrate that one can induce a natural belief structure on
one set, given a belief structure on another set, if the two sets are related
by a partial monotone S-approximation space. '
acknowledgement: We are very grateful to the anonymous reviewer for detailed comments
and suggestions that significantly improved the presentation of this paper. The
research was partially supported by a DOC fellowship of the Austrian Academy of
Sciences.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: A.
full_name: Shakiba, A.
last_name: Shakiba
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- first_name: M.R.
full_name: Hooshmandasl, M.R.
last_name: Hooshmandasl
- first_name: M.
full_name: Alambardar Meybodi, M.
last_name: Alambardar Meybodi
citation:
ama: Shakiba A, Goharshady AK, Hooshmandasl MR, Alambardar Meybodi M. A note on
belief structures and s-approximation spaces. Iranian Journal of Mathematical
Sciences and Informatics. 2020;15(2):117-128. doi:10.29252/ijmsi.15.2.117
apa: Shakiba, A., Goharshady, A. K., Hooshmandasl, M. R., & Alambardar Meybodi,
M. (2020). A note on belief structures and s-approximation spaces. Iranian
Journal of Mathematical Sciences and Informatics. Iranian Academic Center
for Education, Culture and Research. https://doi.org/10.29252/ijmsi.15.2.117
chicago: Shakiba, A., Amir Kafshdar Goharshady, M.R. Hooshmandasl, and M. Alambardar
Meybodi. “A Note on Belief Structures and S-Approximation Spaces.” Iranian
Journal of Mathematical Sciences and Informatics. Iranian Academic Center
for Education, Culture and Research, 2020. https://doi.org/10.29252/ijmsi.15.2.117.
ieee: A. Shakiba, A. K. Goharshady, M. R. Hooshmandasl, and M. Alambardar Meybodi,
“A note on belief structures and s-approximation spaces,” Iranian Journal of
Mathematical Sciences and Informatics, vol. 15, no. 2. Iranian Academic Center
for Education, Culture and Research, pp. 117–128, 2020.
ista: Shakiba A, Goharshady AK, Hooshmandasl MR, Alambardar Meybodi M. 2020. A note
on belief structures and s-approximation spaces. Iranian Journal of Mathematical
Sciences and Informatics. 15(2), 117–128.
mla: Shakiba, A., et al. “A Note on Belief Structures and S-Approximation Spaces.”
Iranian Journal of Mathematical Sciences and Informatics, vol. 15, no.
2, Iranian Academic Center for Education, Culture and Research, 2020, pp. 117–28,
doi:10.29252/ijmsi.15.2.117.
short: A. Shakiba, A.K. Goharshady, M.R. Hooshmandasl, M. Alambardar Meybodi, Iranian
Journal of Mathematical Sciences and Informatics 15 (2020) 117–128.
date_created: 2020-10-18T22:01:36Z
date_published: 2020-10-01T00:00:00Z
date_updated: 2023-10-16T09:25:00Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.29252/ijmsi.15.2.117
external_id:
arxiv:
- '1805.10672'
file:
- access_level: open_access
checksum: f299661a6d51cda6d255a76be696f48d
content_type: application/pdf
creator: dernst
date_created: 2020-10-19T11:14:20Z
date_updated: 2020-10-19T11:14:20Z
file_id: '8676'
file_name: 2020_ijmsi_Shakiba_accepted.pdf
file_size: 261688
relation: main_file
success: 1
file_date_updated: 2020-10-19T11:14:20Z
has_accepted_license: '1'
intvolume: ' 15'
issue: '2'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 117-128
project:
- _id: 267066CE-B435-11E9-9278-68D0E5697425
name: Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies
publication: Iranian Journal of Mathematical Sciences and Informatics
publication_identifier:
eissn:
- 2008-9473
issn:
- 1735-4463
publication_status: published
publisher: Iranian Academic Center for Education, Culture and Research
quality_controlled: '1'
scopus_import: '1'
status: public
title: A note on belief structures and s-approximation spaces
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2020'
...
---
_id: '8672'
abstract:
- lang: eng
text: Cell fate transitions are key to development and homeostasis. It is thus essential
to understand the cellular mechanisms controlling fate transitions. Cell division
has been implicated in fate decisions in many stem cell types, including neuronal
and epithelial progenitors. In other stem cells, such as embryonic stem (ES) cells,
the role of division remains unclear. Here, we show that exit from naive pluripotency
in mouse ES cells generally occurs after a division. We further show that exit
timing is strongly correlated between sister cells, which remain connected by
cytoplasmic bridges long after division, and that bridge abscission progressively
accelerates as cells exit naive pluripotency. Finally, interfering with abscission
impairs naive pluripotency exit, and artificially inducing abscission accelerates
it. Altogether, our data indicate that a switch in the division machinery leading
to faster abscission regulates pluripotency exit. Our study identifies abscission
as a key cellular process coupling cell division to fate transitions.
acknowledgement: This work was supported by the Medical Research Council UK (MRC Program
award MC_UU_12018/5 ), the European Research Council (starting grant 311637 -MorphoCorDiv
and consolidator grant 820188 -NanoMechShape to E.K.P.), and the Leverhulme Trust
(Leverhulme Prize in Biological Sciences to E.K.P.). K.J.C. acknowledges support
from the Royal Society (Royal Society Research Fellowship). A.C. acknowledges support
from EMBO ( ALTF 2015-563 ), the Wellcome Trust ( 201334/Z/16/Z ), and the Fondation
Bettencourt-Schueller (Prix Jeune Chercheur, 2015).
article_processing_charge: No
article_type: original
author:
- first_name: Agathe
full_name: Chaigne, Agathe
last_name: Chaigne
- first_name: Céline
full_name: Labouesse, Céline
last_name: Labouesse
- first_name: Ian J.
full_name: White, Ian J.
last_name: White
- first_name: Meghan
full_name: Agnew, Meghan
last_name: Agnew
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Kevin J.
full_name: Chalut, Kevin J.
last_name: Chalut
- first_name: Ewa K.
full_name: Paluch, Ewa K.
last_name: Paluch
citation:
ama: Chaigne A, Labouesse C, White IJ, et al. Abscission couples cell division to
embryonic stem cell fate. Developmental Cell. 2020;55(2):195-208. doi:10.1016/j.devcel.2020.09.001
apa: Chaigne, A., Labouesse, C., White, I. J., Agnew, M., Hannezo, E. B., Chalut,
K. J., & Paluch, E. K. (2020). Abscission couples cell division to embryonic
stem cell fate. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2020.09.001
chicago: Chaigne, Agathe, Céline Labouesse, Ian J. White, Meghan Agnew, Edouard
B Hannezo, Kevin J. Chalut, and Ewa K. Paluch. “Abscission Couples Cell Division
to Embryonic Stem Cell Fate.” Developmental Cell. Elsevier, 2020. https://doi.org/10.1016/j.devcel.2020.09.001.
ieee: A. Chaigne et al., “Abscission couples cell division to embryonic stem
cell fate,” Developmental Cell, vol. 55, no. 2. Elsevier, pp. 195–208,
2020.
ista: Chaigne A, Labouesse C, White IJ, Agnew M, Hannezo EB, Chalut KJ, Paluch EK.
2020. Abscission couples cell division to embryonic stem cell fate. Developmental
Cell. 55(2), 195–208.
mla: Chaigne, Agathe, et al. “Abscission Couples Cell Division to Embryonic Stem
Cell Fate.” Developmental Cell, vol. 55, no. 2, Elsevier, 2020, pp. 195–208,
doi:10.1016/j.devcel.2020.09.001.
short: A. Chaigne, C. Labouesse, I.J. White, M. Agnew, E.B. Hannezo, K.J. Chalut,
E.K. Paluch, Developmental Cell 55 (2020) 195–208.
date_created: 2020-10-18T22:01:37Z
date_published: 2020-10-26T00:00:00Z
date_updated: 2023-08-22T10:16:58Z
day: '26'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1016/j.devcel.2020.09.001
external_id:
isi:
- '000582501100012'
pmid:
- '32979313'
file:
- access_level: open_access
checksum: 88e1a031a61689165d19a19c2f16d795
content_type: application/pdf
creator: dernst
date_created: 2021-02-04T10:20:02Z
date_updated: 2021-02-04T10:20:02Z
file_id: '9086'
file_name: 2020_DevelopmCell_Chaigne.pdf
file_size: 6929686
relation: main_file
success: 1
file_date_updated: 2021-02-04T10:20:02Z
has_accepted_license: '1'
intvolume: ' 55'
isi: 1
issue: '2'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 195-208
pmid: 1
publication: Developmental Cell
publication_identifier:
eissn:
- '18781551'
issn:
- '15345807'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Abscission couples cell division to embryonic stem cell fate
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 55
year: '2020'
...
---
_id: '8674'
abstract:
- lang: eng
text: 'Extrasynaptic actions of glutamate are limited by high-affinity transporters
expressed by perisynaptic astroglial processes (PAPs): this helps maintain point-to-point
transmission in excitatory circuits. Memory formation in the brain is associated
with synaptic remodeling, but how this affects PAPs and therefore extrasynaptic
glutamate actions is poorly understood. Here, we used advanced imaging methods,
in situ and in vivo, to find that a classical synaptic memory mechanism, long-term
potentiation (LTP), triggers withdrawal of PAPs from potentiated synapses. Optical
glutamate sensors combined with patch-clamp and 3D molecular localization reveal
that LTP induction thus prompts spatial retreat of astroglial glutamate transporters,
boosting glutamate spillover and NMDA-receptor-mediated inter-synaptic cross-talk.
The LTP-triggered PAP withdrawal involves NKCC1 transporters and the actin-controlling
protein cofilin but does not depend on major Ca2+-dependent cascades in astrocytes.
We have therefore uncovered a mechanism by which a memory trace at one synapse
could alter signal handling by multiple neighboring connections.'
acknowledgement: We thank J. Angibaud for organotypic cultures and R. Chereau and
J. Tonnesen for help with the STED microscope; also D. Gonzales and the Neurocentre
Magendie INSERM U1215 Genotyping Platform, for breeding management and genotyping.
This work was supported by the Wellcome Trust Principal Fellowships 101896 and 212251,
ERC Advanced Grant 323113, ERC Proof-of-Concept Grant 767372, EC FP7 ITN 606950,
and EU CSA 811011 (D.A.R.); NRW-Rückkehrerpogramm, UCL Excellence Fellowship, German
Research Foundation (DFG) SPP1757 and SFB1089 (C.H.); Human Frontiers Science Program
(C.H., C.J.J., and H.J.); EMBO Long-Term Fellowship (L.B.); Marie Curie FP7 PIRG08-GA-2010-276995
(A.P.), ASTROMODULATION (S.R.); Equipe FRM DEQ 201 303 26519, Conseil Régional d’Aquitaine
R12056GG, INSERM (S.H.R.O.); ANR SUPERTri, ANR Castro (ANR-17-CE16-0002), R-13-BSV4-0007-01,
Université de Bordeaux, labex BRAIN (S.H.R.O. and U.V.N.); CNRS (A.P., S.H.R.O.,
and U.V.N.); HFSP, ANR CEXC, and France-BioImaging ANR-10-INSB-04 (U.V.N.); and
FP7 MemStick Project No. 201600 (M.G.S.).
article_processing_charge: No
article_type: original
author:
- first_name: Christian
full_name: Henneberger, Christian
last_name: Henneberger
- first_name: Lucie
full_name: Bard, Lucie
last_name: Bard
- first_name: Aude
full_name: Panatier, Aude
last_name: Panatier
- first_name: James P.
full_name: Reynolds, James P.
last_name: Reynolds
- first_name: Olga
full_name: Kopach, Olga
last_name: Kopach
- first_name: Nikolay I.
full_name: Medvedev, Nikolay I.
last_name: Medvedev
- first_name: Daniel
full_name: Minge, Daniel
last_name: Minge
- first_name: Michel K.
full_name: Herde, Michel K.
last_name: Herde
- first_name: Stefanie
full_name: Anders, Stefanie
last_name: Anders
- first_name: Igor
full_name: Kraev, Igor
last_name: Kraev
- first_name: Janosch P.
full_name: Heller, Janosch P.
last_name: Heller
- first_name: Sylvain
full_name: Rama, Sylvain
last_name: Rama
- first_name: Kaiyu
full_name: Zheng, Kaiyu
last_name: Zheng
- first_name: Thomas P.
full_name: Jensen, Thomas P.
last_name: Jensen
- first_name: Inmaculada
full_name: Sanchez-Romero, Inmaculada
id: 3D9C5D30-F248-11E8-B48F-1D18A9856A87
last_name: Sanchez-Romero
- first_name: Colin J.
full_name: Jackson, Colin J.
last_name: Jackson
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Ole Petter
full_name: Ottersen, Ole Petter
last_name: Ottersen
- first_name: Erlend Arnulf
full_name: Nagelhus, Erlend Arnulf
last_name: Nagelhus
- first_name: Stephane H.R.
full_name: Oliet, Stephane H.R.
last_name: Oliet
- first_name: Michael G.
full_name: Stewart, Michael G.
last_name: Stewart
- first_name: U. VAlentin
full_name: Nägerl, U. VAlentin
last_name: Nägerl
- first_name: 'Dmitri A. '
full_name: 'Rusakov, Dmitri A. '
last_name: Rusakov
citation:
ama: Henneberger C, Bard L, Panatier A, et al. LTP induction boosts glutamate spillover
by driving withdrawal of perisynaptic astroglia. Neuron. 2020;108(5):P919-936.E11.
doi:10.1016/j.neuron.2020.08.030
apa: Henneberger, C., Bard, L., Panatier, A., Reynolds, J. P., Kopach, O., Medvedev,
N. I., … Rusakov, D. A. (2020). LTP induction boosts glutamate spillover by driving
withdrawal of perisynaptic astroglia. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.08.030
chicago: Henneberger, Christian, Lucie Bard, Aude Panatier, James P. Reynolds, Olga
Kopach, Nikolay I. Medvedev, Daniel Minge, et al. “LTP Induction Boosts Glutamate
Spillover by Driving Withdrawal of Perisynaptic Astroglia.” Neuron. Elsevier,
2020. https://doi.org/10.1016/j.neuron.2020.08.030.
ieee: C. Henneberger et al., “LTP induction boosts glutamate spillover by
driving withdrawal of perisynaptic astroglia,” Neuron, vol. 108, no. 5.
Elsevier, p. P919–936.E11, 2020.
ista: Henneberger C, Bard L, Panatier A, Reynolds JP, Kopach O, Medvedev NI, Minge
D, Herde MK, Anders S, Kraev I, Heller JP, Rama S, Zheng K, Jensen TP, Sanchez-Romero
I, Jackson CJ, Janovjak HL, Ottersen OP, Nagelhus EA, Oliet SHR, Stewart MG, Nägerl
UVa, Rusakov DA. 2020. LTP induction boosts glutamate spillover by driving withdrawal
of perisynaptic astroglia. Neuron. 108(5), P919–936.E11.
mla: Henneberger, Christian, et al. “LTP Induction Boosts Glutamate Spillover by
Driving Withdrawal of Perisynaptic Astroglia.” Neuron, vol. 108, no. 5,
Elsevier, 2020, p. P919–936.E11, doi:10.1016/j.neuron.2020.08.030.
short: C. Henneberger, L. Bard, A. Panatier, J.P. Reynolds, O. Kopach, N.I. Medvedev,
D. Minge, M.K. Herde, S. Anders, I. Kraev, J.P. Heller, S. Rama, K. Zheng, T.P.
Jensen, I. Sanchez-Romero, C.J. Jackson, H.L. Janovjak, O.P. Ottersen, E.A. Nagelhus,
S.H.R. Oliet, M.G. Stewart, U.Va. Nägerl, D.A. Rusakov, Neuron 108 (2020) P919–936.E11.
date_created: 2020-10-18T22:01:38Z
date_published: 2020-12-09T00:00:00Z
date_updated: 2023-08-22T09:59:29Z
day: '09'
ddc:
- '570'
department:
- _id: HaJa
doi: 10.1016/j.neuron.2020.08.030
external_id:
isi:
- '000603428000010'
pmid:
- '32976770'
file:
- access_level: open_access
checksum: 054562bb50165ef9a1f46631c1c5e36b
content_type: application/pdf
creator: dernst
date_created: 2020-12-10T14:42:09Z
date_updated: 2020-12-10T14:42:09Z
file_id: '8939'
file_name: 2020_Neuron_Henneberger.pdf
file_size: 7518960
relation: main_file
success: 1
file_date_updated: 2020-12-10T14:42:09Z
has_accepted_license: '1'
intvolume: ' 108'
isi: 1
issue: '5'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: P919-936.E11
pmid: 1
publication: Neuron
publication_identifier:
eissn:
- '10974199'
issn:
- '08966273'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic
astroglia
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 108
year: '2020'
...
---
_id: '8679'
abstract:
- lang: eng
text: A central goal of artificial intelligence in high-stakes decision-making applications
is to design a single algorithm that simultaneously expresses generalizability
by learning coherent representations of their world and interpretable explanations
of its dynamics. Here, we combine brain-inspired neural computation principles
and scalable deep learning architectures to design compact neural controllers
for task-specific compartments of a full-stack autonomous vehicle control system.
We discover that a single algorithm with 19 control neurons, connecting 32 encapsulated
input features to outputs by 253 synapses, learns to map high-dimensional inputs
into steering commands. This system shows superior generalizability, interpretability
and robustness compared with orders-of-magnitude larger black-box learning systems.
The obtained neural agents enable high-fidelity autonomy for task-specific parts
of a complex autonomous system.
article_processing_charge: No
article_type: original
author:
- first_name: Mathias
full_name: Lechner, Mathias
id: 3DC22916-F248-11E8-B48F-1D18A9856A87
last_name: Lechner
- first_name: Ramin
full_name: Hasani, Ramin
last_name: Hasani
- first_name: Alexander
full_name: Amini, Alexander
last_name: Amini
- 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: Daniela
full_name: Rus, Daniela
last_name: Rus
- first_name: Radu
full_name: Grosu, Radu
last_name: Grosu
citation:
ama: Lechner M, Hasani R, Amini A, Henzinger TA, Rus D, Grosu R. Neural circuit
policies enabling auditable autonomy. Nature Machine Intelligence. 2020;2:642-652.
doi:10.1038/s42256-020-00237-3
apa: Lechner, M., Hasani, R., Amini, A., Henzinger, T. A., Rus, D., & Grosu,
R. (2020). Neural circuit policies enabling auditable autonomy. Nature Machine
Intelligence. Springer Nature. https://doi.org/10.1038/s42256-020-00237-3
chicago: Lechner, Mathias, Ramin Hasani, Alexander Amini, Thomas A Henzinger, Daniela
Rus, and Radu Grosu. “Neural Circuit Policies Enabling Auditable Autonomy.” Nature
Machine Intelligence. Springer Nature, 2020. https://doi.org/10.1038/s42256-020-00237-3.
ieee: M. Lechner, R. Hasani, A. Amini, T. A. Henzinger, D. Rus, and R. Grosu, “Neural
circuit policies enabling auditable autonomy,” Nature Machine Intelligence,
vol. 2. Springer Nature, pp. 642–652, 2020.
ista: Lechner M, Hasani R, Amini A, Henzinger TA, Rus D, Grosu R. 2020. Neural circuit
policies enabling auditable autonomy. Nature Machine Intelligence. 2, 642–652.
mla: Lechner, Mathias, et al. “Neural Circuit Policies Enabling Auditable Autonomy.”
Nature Machine Intelligence, vol. 2, Springer Nature, 2020, pp. 642–52,
doi:10.1038/s42256-020-00237-3.
short: M. Lechner, R. Hasani, A. Amini, T.A. Henzinger, D. Rus, R. Grosu, Nature
Machine Intelligence 2 (2020) 642–652.
date_created: 2020-10-19T13:46:06Z
date_published: 2020-10-01T00:00:00Z
date_updated: 2023-08-22T10:36:06Z
day: '01'
department:
- _id: ToHe
doi: 10.1038/s42256-020-00237-3
external_id:
isi:
- '000583337200011'
intvolume: ' 2'
isi: 1
language:
- iso: eng
month: '10'
oa_version: None
page: 642-652
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: Nature Machine Intelligence
publication_identifier:
eissn:
- 2522-5839
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/new-deep-learning-models/
scopus_import: '1'
status: public
title: Neural circuit policies enabling auditable autonomy
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 2
year: '2020'
...
---
_id: '8680'
abstract:
- lang: eng
text: Animal development entails the organization of specific cell types in space
and time, and spatial patterns must form in a robust manner. In the zebrafish
spinal cord, neural progenitors form stereotypic patterns despite noisy morphogen
signaling and large-scale cellular rearrangements during morphogenesis and growth.
By directly measuring adhesion forces and preferences for three types of endogenous
neural progenitors, we provide evidence for the differential adhesion model in
which differences in intercellular adhesion mediate cell sorting. Cell type–specific
combinatorial expression of different classes of cadherins (N-cadherin, cadherin
11, and protocadherin 19) results in homotypic preference ex vivo and patterning
robustness in vivo. Furthermore, the differential adhesion code is regulated by
the sonic hedgehog morphogen gradient. We propose that robust patterning during
tissue morphogenesis results from interplay between adhesion-based self-organization
and morphogen-directed patterning.
acknowledgement: "We thank the members of the Megason and Heisenberg labs for critical
discussions of and technical assistance during the work and B. Appel, S. Holley,
J. Jontes, and D. Gilmour for transgenic fish. This work is supported by the Damon
Runyon Cancer Foundation, a NICHD K99 fellowship (1K99HD092623), a Travelling Fellowship
of the Company of Biologists, a Collaborative Research grant from the Burroughs
Wellcome Foundation (T.Y.-C.T.), NIH grant 01GM107733 (T.Y.-C.T. and S.G.M.), NIH
grant R01NS102322 (T.C.-C. and H.K.), and an ERC advanced grant\r\n(MECSPEC) (C.-P.H.)."
article_processing_charge: No
article_type: original
author:
- first_name: Tony Y.-C.
full_name: Tsai, Tony Y.-C.
last_name: Tsai
- first_name: Mateusz K
full_name: Sikora, Mateusz K
id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87
last_name: Sikora
- first_name: Peng
full_name: Xia, Peng
id: 4AB6C7D0-F248-11E8-B48F-1D18A9856A87
last_name: Xia
orcid: 0000-0002-5419-7756
- first_name: Tugba
full_name: Colak-Champollion, Tugba
last_name: Colak-Champollion
- first_name: Holger
full_name: Knaut, Holger
last_name: Knaut
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: Sean G.
full_name: Megason, Sean G.
last_name: Megason
citation:
ama: Tsai TY-C, Sikora MK, Xia P, et al. An adhesion code ensures robust pattern
formation during tissue morphogenesis. Science. 2020;370(6512):113-116.
doi:10.1126/science.aba6637
apa: Tsai, T. Y.-C., Sikora, M. K., Xia, P., Colak-Champollion, T., Knaut, H., Heisenberg,
C.-P. J., & Megason, S. G. (2020). An adhesion code ensures robust pattern
formation during tissue morphogenesis. Science. American Association for
the Advancement of Science. https://doi.org/10.1126/science.aba6637
chicago: Tsai, Tony Y.-C., Mateusz K Sikora, Peng Xia, Tugba Colak-Champollion,
Holger Knaut, Carl-Philipp J Heisenberg, and Sean G. Megason. “An Adhesion Code
Ensures Robust Pattern Formation during Tissue Morphogenesis.” Science.
American Association for the Advancement of Science, 2020. https://doi.org/10.1126/science.aba6637.
ieee: T. Y.-C. Tsai et al., “An adhesion code ensures robust pattern formation
during tissue morphogenesis,” Science, vol. 370, no. 6512. American Association
for the Advancement of Science, pp. 113–116, 2020.
ista: Tsai TY-C, Sikora MK, Xia P, Colak-Champollion T, Knaut H, Heisenberg C-PJ,
Megason SG. 2020. An adhesion code ensures robust pattern formation during tissue
morphogenesis. Science. 370(6512), 113–116.
mla: Tsai, Tony Y. C., et al. “An Adhesion Code Ensures Robust Pattern Formation
during Tissue Morphogenesis.” Science, vol. 370, no. 6512, American Association
for the Advancement of Science, 2020, pp. 113–16, doi:10.1126/science.aba6637.
short: T.Y.-C. Tsai, M.K. Sikora, P. Xia, T. Colak-Champollion, H. Knaut, C.-P.J.
Heisenberg, S.G. Megason, Science 370 (2020) 113–116.
date_created: 2020-10-19T14:09:38Z
date_published: 2020-10-02T00:00:00Z
date_updated: 2023-08-22T10:36:35Z
day: '02'
department:
- _id: CaHe
doi: 10.1126/science.aba6637
ec_funded: 1
external_id:
isi:
- '000579169000053'
intvolume: ' 370'
isi: 1
issue: '6512'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/803635v1
month: '10'
oa: 1
oa_version: Preprint
page: 113-116
project:
- _id: 260F1432-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742573'
name: Interaction and feedback between cell mechanics and fate specification in
vertebrate gastrulation
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/sticking-together/
scopus_import: '1'
status: public
title: An adhesion code ensures robust pattern formation during tissue morphogenesis
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 370
year: '2020'
...
---
_id: '8697'
abstract:
- lang: eng
text: In the computation of the material properties of random alloys, the method
of 'special quasirandom structures' attempts to approximate the properties of
the alloy on a finite volume with higher accuracy by replicating certain statistics
of the random atomic lattice in the finite volume as accurately as possible. In
the present work, we provide a rigorous justification for a variant of this method
in the framework of the Thomas–Fermi–von Weizsäcker (TFW) model. Our approach
is based on a recent analysis of a related variance reduction method in stochastic
homogenization of linear elliptic PDEs and the locality properties of the TFW
model. Concerning the latter, we extend an exponential locality result by Nazar
and Ortner to include point charges, a result that may be of independent interest.
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Julian L
full_name: Fischer, Julian L
id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87
last_name: Fischer
orcid: 0000-0002-0479-558X
- first_name: Michael
full_name: Kniely, Michael
id: 2CA2C08C-F248-11E8-B48F-1D18A9856A87
last_name: Kniely
orcid: 0000-0001-5645-4333
citation:
ama: Fischer JL, Kniely M. Variance reduction for effective energies of random lattices
in the Thomas-Fermi-von Weizsäcker model. Nonlinearity. 2020;33(11):5733-5772.
doi:10.1088/1361-6544/ab9728
apa: Fischer, J. L., & Kniely, M. (2020). Variance reduction for effective energies
of random lattices in the Thomas-Fermi-von Weizsäcker model. Nonlinearity.
IOP Publishing. https://doi.org/10.1088/1361-6544/ab9728
chicago: Fischer, Julian L, and Michael Kniely. “Variance Reduction for Effective
Energies of Random Lattices in the Thomas-Fermi-von Weizsäcker Model.” Nonlinearity.
IOP Publishing, 2020. https://doi.org/10.1088/1361-6544/ab9728.
ieee: J. L. Fischer and M. Kniely, “Variance reduction for effective energies of
random lattices in the Thomas-Fermi-von Weizsäcker model,” Nonlinearity,
vol. 33, no. 11. IOP Publishing, pp. 5733–5772, 2020.
ista: Fischer JL, Kniely M. 2020. Variance reduction for effective energies of random
lattices in the Thomas-Fermi-von Weizsäcker model. Nonlinearity. 33(11), 5733–5772.
mla: Fischer, Julian L., and Michael Kniely. “Variance Reduction for Effective Energies
of Random Lattices in the Thomas-Fermi-von Weizsäcker Model.” Nonlinearity,
vol. 33, no. 11, IOP Publishing, 2020, pp. 5733–72, doi:10.1088/1361-6544/ab9728.
short: J.L. Fischer, M. Kniely, Nonlinearity 33 (2020) 5733–5772.
date_created: 2020-10-25T23:01:16Z
date_published: 2020-11-01T00:00:00Z
date_updated: 2023-08-22T10:38:38Z
day: '01'
ddc:
- '510'
department:
- _id: JuFi
doi: 10.1088/1361-6544/ab9728
external_id:
arxiv:
- '1906.12245'
isi:
- '000576492700001'
file:
- access_level: open_access
checksum: ed90bc6eb5f32ee6157fef7f3aabc057
content_type: application/pdf
creator: cziletti
date_created: 2020-10-27T12:09:57Z
date_updated: 2020-10-27T12:09:57Z
file_id: '8710'
file_name: 2020_Nonlinearity_Fischer.pdf
file_size: 1223899
relation: main_file
success: 1
file_date_updated: 2020-10-27T12:09:57Z
has_accepted_license: '1'
intvolume: ' 33'
isi: 1
issue: '11'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/3.0/
month: '11'
oa: 1
oa_version: Published Version
page: 5733-5772
publication: Nonlinearity
publication_identifier:
eissn:
- '13616544'
issn:
- '09517715'
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Variance reduction for effective energies of random lattices in the Thomas-Fermi-von
Weizsäcker model
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 33
year: '2020'
...
---
_id: '8698'
abstract:
- lang: eng
text: The brain represents and reasons probabilistically about complex stimuli and
motor actions using a noisy, spike-based neural code. A key building block for
such neural computations, as well as the basis for supervised and unsupervised
learning, is the ability to estimate the surprise or likelihood of incoming high-dimensional
neural activity patterns. Despite progress in statistical modeling of neural responses
and deep learning, current approaches either do not scale to large neural populations
or cannot be implemented using biologically realistic mechanisms. Inspired by
the sparse and random connectivity of real neuronal circuits, we present a model
for neural codes that accurately estimates the likelihood of individual spiking
patterns and has a straightforward, scalable, efficient, learnable, and realistic
neural implementation. This model’s performance on simultaneously recorded spiking
activity of >100 neurons in the monkey visual and prefrontal cortices is comparable
with or better than that of state-of-the-art models. Importantly, the model can
be learned using a small number of samples and using a local learning rule that
utilizes noise intrinsic to neural circuits. Slower, structural changes in random
connectivity, consistent with rewiring and pruning processes, further improve
the efficiency and sparseness of the resulting neural representations. Our results
merge insights from neuroanatomy, machine learning, and theoretical neuroscience
to suggest random sparse connectivity as a key design principle for neuronal computation.
acknowledgement: We thank Udi Karpas, Roy Harpaz, Tal Tamir, Adam Haber, and Amir
Bar for discussions and suggestions; and especially Oren Forkosh and Walter Senn
for invaluable discussions of the learning rule. This work was supported by European
Research Council Grant 311238 (to E.S.) and Israel Science Foundation Grant 1629/12
(to E.S.); as well as research support from Martin Kushner Schnur and Mr. and Mrs.
Lawrence Feis (E.S.); National Institute of Mental Health Grant R01MH109180 (to
R.K.); a Pew Scholarship in Biomedical Sciences (to R.K.); Simons Collaboration
on the Global Brain Grant 542997 (to R.K. and E.S.); and a CRCNS (Collaborative
Research in Computational Neuroscience) grant (to R.K. and E.S.).
article_processing_charge: No
article_type: original
author:
- first_name: Ori
full_name: Maoz, Ori
last_name: Maoz
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Mohamad Saleh
full_name: Esteki, Mohamad Saleh
last_name: Esteki
- first_name: Roozbeh
full_name: Kiani, Roozbeh
last_name: Kiani
- first_name: Elad
full_name: Schneidman, Elad
last_name: Schneidman
citation:
ama: Maoz O, Tkačik G, Esteki MS, Kiani R, Schneidman E. Learning probabilistic
neural representations with randomly connected circuits. Proceedings of the
National Academy of Sciences of the United States of America. 2020;117(40):25066-25073.
doi:10.1073/pnas.1912804117
apa: Maoz, O., Tkačik, G., Esteki, M. S., Kiani, R., & Schneidman, E. (2020).
Learning probabilistic neural representations with randomly connected circuits.
Proceedings of the National Academy of Sciences of the United States of America.
National Academy of Sciences. https://doi.org/10.1073/pnas.1912804117
chicago: Maoz, Ori, Gašper Tkačik, Mohamad Saleh Esteki, Roozbeh Kiani, and Elad
Schneidman. “Learning Probabilistic Neural Representations with Randomly Connected
Circuits.” Proceedings of the National Academy of Sciences of the United States
of America. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1912804117.
ieee: O. Maoz, G. Tkačik, M. S. Esteki, R. Kiani, and E. Schneidman, “Learning probabilistic
neural representations with randomly connected circuits,” Proceedings of the
National Academy of Sciences of the United States of America, vol. 117, no.
40. National Academy of Sciences, pp. 25066–25073, 2020.
ista: Maoz O, Tkačik G, Esteki MS, Kiani R, Schneidman E. 2020. Learning probabilistic
neural representations with randomly connected circuits. Proceedings of the National
Academy of Sciences of the United States of America. 117(40), 25066–25073.
mla: Maoz, Ori, et al. “Learning Probabilistic Neural Representations with Randomly
Connected Circuits.” Proceedings of the National Academy of Sciences of the
United States of America, vol. 117, no. 40, National Academy of Sciences,
2020, pp. 25066–73, doi:10.1073/pnas.1912804117.
short: O. Maoz, G. Tkačik, M.S. Esteki, R. Kiani, E. Schneidman, Proceedings of
the National Academy of Sciences of the United States of America 117 (2020) 25066–25073.
date_created: 2020-10-25T23:01:16Z
date_published: 2020-10-06T00:00:00Z
date_updated: 2023-08-22T12:11:23Z
day: '06'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1073/pnas.1912804117
external_id:
isi:
- '000579045200012'
pmid:
- '32948691'
file:
- access_level: open_access
checksum: c6a24fdecf3f28faf447078e7a274a88
content_type: application/pdf
creator: cziletti
date_created: 2020-10-27T14:57:50Z
date_updated: 2020-10-27T14:57:50Z
file_id: '8713'
file_name: 2020_PNAS_Maoz.pdf
file_size: 1755359
relation: main_file
success: 1
file_date_updated: 2020-10-27T14:57:50Z
has_accepted_license: '1'
intvolume: ' 117'
isi: 1
issue: '40'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 25066-25073
pmid: 1
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- '10916490'
issn:
- '00278424'
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Learning probabilistic neural representations with randomly connected circuits
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: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 117
year: '2020'
...
---
_id: '8699'
abstract:
- lang: eng
text: In the high spin–orbit-coupled Sr2IrO4, the high sensitivity of the ground
state to the details of the local lattice structure shows a large potential for
the manipulation of the functional properties by inducing local lattice distortions.
We use epitaxial strain to modify the Ir–O bond geometry in Sr2IrO4 and perform
momentum-dependent resonant inelastic X-ray scattering (RIXS) at the metal and
at the ligand sites to unveil the response of the low-energy elementary excitations.
We observe that the pseudospin-wave dispersion for tensile-strained Sr2IrO4 films
displays large softening along the [h,0] direction, while along the [h,h] direction
it shows hardening. This evolution reveals a renormalization of the magnetic interactions
caused by a strain-driven cross-over from anisotropic to isotropic interactions
between the magnetic moments. Moreover, we detect dispersive electron–hole pair
excitations which shift to lower (higher) energies upon compressive (tensile)
strain, manifesting a reduction (increase) in the size of the charge gap. This
behavior shows an intimate coupling between charge excitations and lattice distortions
in Sr2IrO4, originating from the modified hopping elements between the t2g orbitals.
Our work highlights the central role played by the lattice degrees of freedom
in determining both the pseudospin and charge excitations of Sr2IrO4 and provides
valuable information toward the control of the ground state of complex oxides
in the presence of high spin–orbit coupling.
acknowledgement: 'We gratefully acknowledge C. Sahle for experimental support at the
ID20 beamline of the ESRF. The soft X-ray experiments were carried out at the ADRESS
beamline of the Swiss Light Source, Paul Scherrer Institut (PSI). E. Paris and T.S.
thank X. Lu and C. Monney for valuable discussions. The work at PSI is supported
by the Swiss National Science Foundation (SNSF) through Project 200021_178867, the
NCCR (National Centre of Competence in Research) MARVEL (Materials’ Revolution:
Computational Design and Discovery of Novel Materials) and the Sinergia network
Mott Physics Beyond the Heisenberg Model (MPBH) (SNSF Research Grants CRSII2_160765/1
and CRSII2_141962). K.W. acknowledges support by the Narodowe Centrum Nauki Projects
2016/22/E/ST3/00560 and 2016/23/B/ST3/00839. E.M.P. and M.N. acknowledge funding
from the European Union’s Horizon 2020 research and innovation programme under the
Marie Sklodowska-Curie Grant Agreements 754411 and 701647, respectively. M.R. was
supported by the Swiss National Science Foundation under Project 200021 – 182695.
This research used resources of the APS, a U.S. Department of Energy (DOE) Office
of Science User Facility operated for the DOE Office of Science by Argonne National
Laboratory under Contract DE-AC02-06CH11357.'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Eugenio
full_name: Paris, Eugenio
last_name: Paris
- first_name: Yi
full_name: Tseng, Yi
last_name: Tseng
- first_name: Ekaterina
full_name: Paerschke, Ekaterina
id: 8275014E-6063-11E9-9B7F-6338E6697425
last_name: Paerschke
orcid: 0000-0003-0853-8182
- first_name: Wenliang
full_name: Zhang, Wenliang
last_name: Zhang
- first_name: Mary H
full_name: Upton, Mary H
last_name: Upton
- first_name: Anna
full_name: Efimenko, Anna
last_name: Efimenko
- first_name: Katharina
full_name: Rolfs, Katharina
last_name: Rolfs
- first_name: Daniel E
full_name: McNally, Daniel E
last_name: McNally
- first_name: Laura
full_name: Maurel, Laura
last_name: Maurel
- first_name: Muntaser
full_name: Naamneh, Muntaser
last_name: Naamneh
- first_name: Marco
full_name: Caputo, Marco
last_name: Caputo
- first_name: Vladimir N
full_name: Strocov, Vladimir N
last_name: Strocov
- first_name: Zhiming
full_name: Wang, Zhiming
last_name: Wang
- first_name: Diego
full_name: Casa, Diego
last_name: Casa
- first_name: Christof W
full_name: Schneider, Christof W
last_name: Schneider
- first_name: Ekaterina
full_name: Pomjakushina, Ekaterina
last_name: Pomjakushina
- first_name: Krzysztof
full_name: Wohlfeld, Krzysztof
last_name: Wohlfeld
- first_name: Milan
full_name: Radovic, Milan
last_name: Radovic
- first_name: Thorsten
full_name: Schmitt, Thorsten
last_name: Schmitt
citation:
ama: Paris E, Tseng Y, Paerschke E, et al. Strain engineering of the charge and
spin-orbital interactions in Sr2IrO4. Proceedings of the National Academy of
Sciences of the United States of America. 2020;117(40):24764-24770. doi:10.1073/pnas.2012043117
apa: Paris, E., Tseng, Y., Paerschke, E., Zhang, W., Upton, M. H., Efimenko, A.,
… Schmitt, T. (2020). Strain engineering of the charge and spin-orbital interactions
in Sr2IrO4. Proceedings of the National Academy of Sciences of the United States
of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2012043117
chicago: Paris, Eugenio, Yi Tseng, Ekaterina Paerschke, Wenliang Zhang, Mary H Upton,
Anna Efimenko, Katharina Rolfs, et al. “Strain Engineering of the Charge and Spin-Orbital
Interactions in Sr2IrO4.” Proceedings of the National Academy of Sciences of
the United States of America. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.2012043117.
ieee: E. Paris et al., “Strain engineering of the charge and spin-orbital
interactions in Sr2IrO4,” Proceedings of the National Academy of Sciences of
the United States of America, vol. 117, no. 40. National Academy of Sciences,
pp. 24764–24770, 2020.
ista: Paris E, Tseng Y, Paerschke E, Zhang W, Upton MH, Efimenko A, Rolfs K, McNally
DE, Maurel L, Naamneh M, Caputo M, Strocov VN, Wang Z, Casa D, Schneider CW, Pomjakushina
E, Wohlfeld K, Radovic M, Schmitt T. 2020. Strain engineering of the charge and
spin-orbital interactions in Sr2IrO4. Proceedings of the National Academy of Sciences
of the United States of America. 117(40), 24764–24770.
mla: Paris, Eugenio, et al. “Strain Engineering of the Charge and Spin-Orbital Interactions
in Sr2IrO4.” Proceedings of the National Academy of Sciences of the United
States of America, vol. 117, no. 40, National Academy of Sciences, 2020, pp.
24764–70, doi:10.1073/pnas.2012043117.
short: E. Paris, Y. Tseng, E. Paerschke, W. Zhang, M.H. Upton, A. Efimenko, K. Rolfs,
D.E. McNally, L. Maurel, M. Naamneh, M. Caputo, V.N. Strocov, Z. Wang, D. Casa,
C.W. Schneider, E. Pomjakushina, K. Wohlfeld, M. Radovic, T. Schmitt, Proceedings
of the National Academy of Sciences of the United States of America 117 (2020)
24764–24770.
date_created: 2020-10-25T23:01:17Z
date_published: 2020-10-06T00:00:00Z
date_updated: 2023-08-22T12:11:52Z
day: '06'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1073/pnas.2012043117
ec_funded: 1
external_id:
arxiv:
- '2009.12262'
isi:
- '000579059100029'
pmid:
- '32958669'
file:
- access_level: open_access
checksum: 1638fa36b442e2868576c6dd7d6dc505
content_type: application/pdf
creator: cziletti
date_created: 2020-10-28T11:53:12Z
date_updated: 2020-10-28T11:53:12Z
file_id: '8715'
file_name: 2020_PNAS_Paris.pdf
file_size: 1176522
relation: main_file
success: 1
file_date_updated: 2020-10-28T11:53:12Z
has_accepted_license: '1'
intvolume: ' 117'
isi: 1
issue: '40'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 24764-24770
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- '10916490'
issn:
- '00278424'
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Strain engineering of the charge and spin-orbital interactions in Sr2IrO4
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: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 117
year: '2020'
...
---
_id: '8700'
abstract:
- lang: eng
text: Translation termination is a finishing step of protein biosynthesis. The significant
role in this process belongs not only to protein factors of translation termination
but also to the nearest nucleotide environment of stop codons. There are numerous
descriptions of stop codons readthrough, which is due to specific nucleotide sequences
behind them. However, represented data are segmental and don’t explain the mechanism
of the nucleotide context influence on translation termination. It is well known
that stop codon UAA usage is preferential for A/T-rich genes, and UAG, UGA—for
G/C-rich genes, which is related to an expression level of these genes. We investigated
the connection between a frequency of nucleotides occurrence in 3' area of stop
codons in the human genome and their influence on translation termination efficiency.
We found that 3' context motif, which is cognate to the sequence of a stop codon,
stimulates translation termination. At the same time, the nucleotide composition
of 3' sequence that differs from stop codon, decreases translation termination
efficiency.
acknowledgement: We would like to thank the staff of CCU Genome for sequencing, Tat’yana
Pestova, Christopher Helen, and Lyudmila Yur’evna Frolova for the plasmids provided,
as well as the laboratory staff for productive discussion of the results. We also
thank former laboratory employees Yuliya Vladimirovna Bocharova and Polina Nikolaevna
Kryuchkova for the exceptional contribution to the present work.
article_processing_charge: No
article_type: original
author:
- first_name: E. E.
full_name: Sokolova, E. E.
last_name: Sokolova
- first_name: Petr
full_name: Vlasov, Petr
id: 38BB9AC4-F248-11E8-B48F-1D18A9856A87
last_name: Vlasov
- first_name: T. V.
full_name: Egorova, T. V.
last_name: Egorova
- first_name: A. V.
full_name: Shuvalov, A. V.
last_name: Shuvalov
- first_name: E. Z.
full_name: Alkalaeva, E. Z.
last_name: Alkalaeva
citation:
ama: Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. The influence
of A/G composition of 3’ stop codon contexts on translation termination efficiency
in eukaryotes. Molecular Biology. 2020;54(5):739-748. doi:10.1134/S0026893320050088
apa: Sokolova, E. E., Vlasov, P., Egorova, T. V., Shuvalov, A. V., & Alkalaeva,
E. Z. (2020). The influence of A/G composition of 3’ stop codon contexts on translation
termination efficiency in eukaryotes. Molecular Biology. Springer Nature.
https://doi.org/10.1134/S0026893320050088
chicago: Sokolova, E. E., Petr Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z.
Alkalaeva. “The Influence of A/G Composition of 3’ Stop Codon Contexts on Translation
Termination Efficiency in Eukaryotes.” Molecular Biology. Springer Nature,
2020. https://doi.org/10.1134/S0026893320050088.
ieee: E. E. Sokolova, P. Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva,
“The influence of A/G composition of 3’ stop codon contexts on translation termination
efficiency in eukaryotes,” Molecular Biology, vol. 54, no. 5. Springer
Nature, pp. 739–748, 2020.
ista: Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. 2020. The influence
of A/G composition of 3’ stop codon contexts on translation termination efficiency
in eukaryotes. Molecular Biology. 54(5), 739–748.
mla: Sokolova, E. E., et al. “The Influence of A/G Composition of 3’ Stop Codon
Contexts on Translation Termination Efficiency in Eukaryotes.” Molecular Biology,
vol. 54, no. 5, Springer Nature, 2020, pp. 739–48, doi:10.1134/S0026893320050088.
short: E.E. Sokolova, P. Vlasov, T.V. Egorova, A.V. Shuvalov, E.Z. Alkalaeva, Molecular
Biology 54 (2020) 739–748.
date_created: 2020-10-25T23:01:17Z
date_published: 2020-09-01T00:00:00Z
date_updated: 2023-08-22T10:39:38Z
day: '01'
department:
- _id: FyKo
doi: 10.1134/S0026893320050088
external_id:
isi:
- '000579441200009'
intvolume: ' 54'
isi: 1
issue: '5'
language:
- iso: eng
month: '09'
oa_version: None
page: 739-748
publication: Molecular Biology
publication_identifier:
eissn:
- '16083245'
issn:
- '00268933'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '8701'
relation: original
status: public
scopus_import: '1'
status: public
title: The influence of A/G composition of 3' stop codon contexts on translation termination
efficiency in eukaryotes
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 54
year: '2020'
...
---
_id: '8701'
abstract:
- lang: eng
text: Translation termination is a finishing step of protein biosynthesis. The significant
role in this process belongs not only to protein factors of translation termination
but also to the nearest nucleotide environment of stop codons. There are numerous
descriptions of stop codons readthrough, which is due to specific nucleotide sequences
behind them. However, represented data are segmental and don’t explain the mechanism
of the nucleotide context influence on translation termination. It is well known
that stop codon UAA usage is preferential for A/T-rich genes, and UAG, UGA—for
G/C-rich genes, which is related to an expression level of these genes. We investigated
the connection between a frequency of nucleotides occurrence in 3' area of stop
codons in the human genome and their influence on translation termination efficiency.
We found that 3' context motif, which is cognate to the sequence of a stop codon,
stimulates translation termination. At the same time, the nucleotide composition
of 3' sequence that differs from stop codon, decreases translation termination
efficiency.
article_processing_charge: No
article_type: original
author:
- first_name: E. E.
full_name: Sokolova, E. E.
last_name: Sokolova
- first_name: Petr
full_name: Vlasov, Petr
id: 38BB9AC4-F248-11E8-B48F-1D18A9856A87
last_name: Vlasov
- first_name: T. V.
full_name: Egorova, T. V.
last_name: Egorova
- first_name: A. V.
full_name: Shuvalov, A. V.
last_name: Shuvalov
- first_name: E. Z.
full_name: Alkalaeva, E. Z.
last_name: Alkalaeva
citation:
ama: Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. The influence
of A/G composition of 3’ stop codon contexts on translation termination efficiency
in eukaryotes. Molekuliarnaia biologiia. 2020;54(5):837-848. doi:10.31857/S0026898420050080
apa: Sokolova, E. E., Vlasov, P., Egorova, T. V., Shuvalov, A. V., & Alkalaeva,
E. Z. (2020). The influence of A/G composition of 3’ stop codon contexts on translation
termination efficiency in eukaryotes. Molekuliarnaia biologiia. Russian
Academy of Sciences. https://doi.org/10.31857/S0026898420050080
chicago: Sokolova, E. E., Petr Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z.
Alkalaeva. “The influence of A/G composition of 3’ stop codon contexts on translation
termination efficiency in eukaryotes.” Molekuliarnaia biologiia. Russian
Academy of Sciences, 2020. https://doi.org/10.31857/S0026898420050080.
ieee: E. E. Sokolova, P. Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva,
“The influence of A/G composition of 3’ stop codon contexts on translation termination
efficiency in eukaryotes,” Molekuliarnaia biologiia, vol. 54, no. 5. Russian
Academy of Sciences, pp. 837–848, 2020.
ista: Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. 2020. The influence
of A/G composition of 3’ stop codon contexts on translation termination efficiency
in eukaryotes. Molekuliarnaia biologiia. 54(5), 837–848.
mla: Sokolova, E. E., et al. “The influence of A/G composition of 3’ stop codon
contexts on translation termination efficiency in eukaryotes.” Molekuliarnaia
biologiia, vol. 54, no. 5, Russian Academy of Sciences, 2020, pp. 837–48,
doi:10.31857/S0026898420050080.
short: E.E. Sokolova, P. Vlasov, T.V. Egorova, A.V. Shuvalov, E.Z. Alkalaeva, Molekuliarnaia
biologiia 54 (2020) 837–848.
date_created: 2020-10-25T23:01:17Z
date_published: 2020-09-01T00:00:00Z
date_updated: 2023-08-22T10:39:37Z
day: '01'
department:
- _id: FyKo
doi: 10.31857/S0026898420050080
external_id:
pmid:
- '33009793'
intvolume: ' 54'
issue: '5'
language:
- iso: rus
month: '09'
oa_version: None
page: 837-848
pmid: 1
publication: Molekuliarnaia biologiia
publication_identifier:
issn:
- '00268984'
publication_status: published
publisher: Russian Academy of Sciences
quality_controlled: '1'
related_material:
record:
- id: '8700'
relation: translation
status: public
scopus_import: '1'
status: public
title: The influence of A/G composition of 3' stop codon contexts on translation termination
efficiency in eukaryotes
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 54
year: '2020'
...
---
_id: '8703'
abstract:
- lang: eng
text: 'Even though Delaunay originally introduced his famous triangulations in the
case of infinite point sets with translational periodicity, a software that computes
such triangulations in the general case is not yet available, to the best of our
knowledge. Combining and generalizing previous work, we present a practical algorithm
for computing such triangulations. The algorithm has been implemented and experiments
show that its performance is as good as the one of the CGAL package, which is
restricted to cubic periodicity. '
alternative_title:
- LIPIcs
article_number: '75'
article_processing_charge: No
author:
- first_name: Georg F
full_name: Osang, Georg F
id: 464B40D6-F248-11E8-B48F-1D18A9856A87
last_name: Osang
orcid: 0000-0002-8882-5116
- first_name: Mael
full_name: Rouxel-Labbé, Mael
last_name: Rouxel-Labbé
- first_name: Monique
full_name: Teillaud, Monique
last_name: Teillaud
citation:
ama: 'Osang GF, Rouxel-Labbé M, Teillaud M. Generalizing CGAL periodic Delaunay
triangulations. In: 28th Annual European Symposium on Algorithms. Vol 173.
Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:10.4230/LIPIcs.ESA.2020.75'
apa: 'Osang, G. F., Rouxel-Labbé, M., & Teillaud, M. (2020). Generalizing CGAL
periodic Delaunay triangulations. In 28th Annual European Symposium on Algorithms
(Vol. 173). Virtual, Online; Pisa, Italy: Schloss Dagstuhl - Leibniz-Zentrum für
Informatik. https://doi.org/10.4230/LIPIcs.ESA.2020.75'
chicago: Osang, Georg F, Mael Rouxel-Labbé, and Monique Teillaud. “Generalizing
CGAL Periodic Delaunay Triangulations.” In 28th Annual European Symposium on
Algorithms, Vol. 173. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.
https://doi.org/10.4230/LIPIcs.ESA.2020.75.
ieee: G. F. Osang, M. Rouxel-Labbé, and M. Teillaud, “Generalizing CGAL periodic
Delaunay triangulations,” in 28th Annual European Symposium on Algorithms,
Virtual, Online; Pisa, Italy, 2020, vol. 173.
ista: 'Osang GF, Rouxel-Labbé M, Teillaud M. 2020. Generalizing CGAL periodic Delaunay
triangulations. 28th Annual European Symposium on Algorithms. ESA: Annual European
Symposium on Algorithms, LIPIcs, vol. 173, 75.'
mla: Osang, Georg F., et al. “Generalizing CGAL Periodic Delaunay Triangulations.”
28th Annual European Symposium on Algorithms, vol. 173, 75, Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 2020, doi:10.4230/LIPIcs.ESA.2020.75.
short: G.F. Osang, M. Rouxel-Labbé, M. Teillaud, in:, 28th Annual European Symposium
on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.
conference:
end_date: 2020-09-09
location: Virtual, Online; Pisa, Italy
name: 'ESA: Annual European Symposium on Algorithms'
start_date: 2020-09-07
date_created: 2020-10-25T23:01:18Z
date_published: 2020-08-26T00:00:00Z
date_updated: 2023-09-07T13:29:00Z
day: '26'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.4230/LIPIcs.ESA.2020.75
ec_funded: 1
file:
- access_level: open_access
checksum: fe0f7c49a99ed870c671b911e10d5496
content_type: application/pdf
creator: cziletti
date_created: 2020-10-27T14:31:52Z
date_updated: 2020-10-27T14:31:52Z
file_id: '8712'
file_name: 2020_LIPIcs_Osang.pdf
file_size: 733291
relation: main_file
success: 1
file_date_updated: 2020-10-27T14:31:52Z
has_accepted_license: '1'
intvolume: ' 173'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 266A2E9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '788183'
name: Alpha Shape Theory Extended
publication: 28th Annual European Symposium on Algorithms
publication_identifier:
isbn:
- '9783959771627'
issn:
- '18688969'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
related_material:
record:
- id: '9056'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Generalizing CGAL periodic Delaunay triangulations
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 173
year: '2020'
...
---
_id: '8704'
abstract:
- lang: eng
text: Traditional robotic control suits require profound task-specific knowledge
for designing, building and testing control software. The rise of Deep Learning
has enabled end-to-end solutions to be learned entirely from data, requiring minimal
knowledge about the application area. We design a learning scheme to train end-to-end
linear dynamical systems (LDS)s by gradient descent in imitation learning robotic
domains. We introduce a new regularization loss component together with a learning
algorithm that improves the stability of the learned autonomous system, by forcing
the eigenvalues of the internal state updates of an LDS to be negative reals.
We evaluate our approach on a series of real-life and simulated robotic experiments,
in comparison to linear and nonlinear Recurrent Neural Network (RNN) architectures.
Our results show that our stabilizing method significantly improves test performance
of LDS, enabling such linear models to match the performance of contemporary nonlinear
RNN architectures. A video of the obstacle avoidance performance of our method
on a mobile robot, in unseen environments, compared to other methods can be viewed
at https://youtu.be/mhEsCoNao5E.
acknowledgement: M.L. is supported in parts by the Austrian Science Fund (FWF) under
grant Z211-N23 (Wittgenstein Award). R.H., and R.G. are partially supported by the
Horizon-2020 ECSELProject grant No. 783163 (iDev40), and the Austrian Research Promotion
Agency (FFG), Project No. 860424. R.H. and D.R. is partially supported by the Boeing
Company.
alternative_title:
- ICRA
article_processing_charge: No
author:
- first_name: Mathias
full_name: Lechner, Mathias
id: 3DC22916-F248-11E8-B48F-1D18A9856A87
last_name: Lechner
- first_name: Ramin
full_name: Hasani, Ramin
last_name: Hasani
- first_name: Daniela
full_name: Rus, Daniela
last_name: Rus
- first_name: Radu
full_name: Grosu, Radu
last_name: Grosu
citation:
ama: 'Lechner M, Hasani R, Rus D, Grosu R. Gershgorin loss stabilizes the recurrent
neural network compartment of an end-to-end robot learning scheme. In: Proceedings
- IEEE International Conference on Robotics and Automation. IEEE; 2020:5446-5452.
doi:10.1109/ICRA40945.2020.9196608'
apa: 'Lechner, M., Hasani, R., Rus, D., & Grosu, R. (2020). Gershgorin loss
stabilizes the recurrent neural network compartment of an end-to-end robot learning
scheme. In Proceedings - IEEE International Conference on Robotics and Automation
(pp. 5446–5452). Paris, France: IEEE. https://doi.org/10.1109/ICRA40945.2020.9196608'
chicago: Lechner, Mathias, Ramin Hasani, Daniela Rus, and Radu Grosu. “Gershgorin
Loss Stabilizes the Recurrent Neural Network Compartment of an End-to-End Robot
Learning Scheme.” In Proceedings - IEEE International Conference on Robotics
and Automation, 5446–52. IEEE, 2020. https://doi.org/10.1109/ICRA40945.2020.9196608.
ieee: M. Lechner, R. Hasani, D. Rus, and R. Grosu, “Gershgorin loss stabilizes the
recurrent neural network compartment of an end-to-end robot learning scheme,”
in Proceedings - IEEE International Conference on Robotics and Automation,
Paris, France, 2020, pp. 5446–5452.
ista: 'Lechner M, Hasani R, Rus D, Grosu R. 2020. Gershgorin loss stabilizes the
recurrent neural network compartment of an end-to-end robot learning scheme. Proceedings
- IEEE International Conference on Robotics and Automation. ICRA: International
Conference on Robotics and Automation, ICRA, , 5446–5452.'
mla: Lechner, Mathias, et al. “Gershgorin Loss Stabilizes the Recurrent Neural Network
Compartment of an End-to-End Robot Learning Scheme.” Proceedings - IEEE International
Conference on Robotics and Automation, IEEE, 2020, pp. 5446–52, doi:10.1109/ICRA40945.2020.9196608.
short: M. Lechner, R. Hasani, D. Rus, R. Grosu, in:, Proceedings - IEEE International
Conference on Robotics and Automation, IEEE, 2020, pp. 5446–5452.
conference:
end_date: 2020-08-31
location: Paris, France
name: 'ICRA: International Conference on Robotics and Automation'
start_date: 2020-05-31
date_created: 2020-10-25T23:01:19Z
date_published: 2020-05-01T00:00:00Z
date_updated: 2023-08-22T10:40:15Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1109/ICRA40945.2020.9196608
external_id:
isi:
- '000712319503110'
file:
- access_level: open_access
checksum: fccf7b986ac78046918a298cc6849a50
content_type: application/pdf
creator: dernst
date_created: 2020-11-06T10:58:49Z
date_updated: 2020-11-06T10:58:49Z
file_id: '8733'
file_name: 2020_ICRA_Lechner.pdf
file_size: 1070010
relation: main_file
success: 1
file_date_updated: 2020-11-06T10:58:49Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Submitted Version
page: 5446-5452
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: Proceedings - IEEE International Conference on Robotics and Automation
publication_identifier:
isbn:
- '9781728173955'
issn:
- '10504729'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end
robot learning scheme
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2020'
...
---
_id: '8705'
abstract:
- lang: eng
text: We consider the quantum mechanical many-body problem of a single impurity
particle immersed in a weakly interacting Bose gas. The impurity interacts with
the bosons via a two-body potential. We study the Hamiltonian of this system in
the mean-field limit and rigorously show that, at low energies, the problem is
well described by the Fröhlich polaron model.
acknowledgement: Financial support through the European Research Council (ERC) under
the European Union’s Horizon 2020 research and innovation programme Grant agreement
No. 694227 (R.S.) and the Maria Skłodowska-Curie Grant agreement No. 665386 (K.M.)
is gratefully acknowledged. Funding Open access funding provided by Institute of
Science and Technology (IST Austria)
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Krzysztof
full_name: Mysliwy, Krzysztof
id: 316457FC-F248-11E8-B48F-1D18A9856A87
last_name: Mysliwy
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Mysliwy K, Seiringer R. Microscopic derivation of the Fröhlich Hamiltonian
for the Bose polaron in the mean-field limit. Annales Henri Poincare. 2020;21(12):4003-4025.
doi:10.1007/s00023-020-00969-3
apa: Mysliwy, K., & Seiringer, R. (2020). Microscopic derivation of the Fröhlich
Hamiltonian for the Bose polaron in the mean-field limit. Annales Henri Poincare.
Springer Nature. https://doi.org/10.1007/s00023-020-00969-3
chicago: Mysliwy, Krzysztof, and Robert Seiringer. “Microscopic Derivation of the
Fröhlich Hamiltonian for the Bose Polaron in the Mean-Field Limit.” Annales
Henri Poincare. Springer Nature, 2020. https://doi.org/10.1007/s00023-020-00969-3.
ieee: K. Mysliwy and R. Seiringer, “Microscopic derivation of the Fröhlich Hamiltonian
for the Bose polaron in the mean-field limit,” Annales Henri Poincare,
vol. 21, no. 12. Springer Nature, pp. 4003–4025, 2020.
ista: Mysliwy K, Seiringer R. 2020. Microscopic derivation of the Fröhlich Hamiltonian
for the Bose polaron in the mean-field limit. Annales Henri Poincare. 21(12),
4003–4025.
mla: Mysliwy, Krzysztof, and Robert Seiringer. “Microscopic Derivation of the Fröhlich
Hamiltonian for the Bose Polaron in the Mean-Field Limit.” Annales Henri Poincare,
vol. 21, no. 12, Springer Nature, 2020, pp. 4003–25, doi:10.1007/s00023-020-00969-3.
short: K. Mysliwy, R. Seiringer, Annales Henri Poincare 21 (2020) 4003–4025.
date_created: 2020-10-25T23:01:19Z
date_published: 2020-12-01T00:00:00Z
date_updated: 2023-09-07T13:43:51Z
day: '01'
ddc:
- '530'
department:
- _id: RoSe
doi: 10.1007/s00023-020-00969-3
ec_funded: 1
external_id:
arxiv:
- '2003.12371'
isi:
- '000578111800002'
file:
- access_level: open_access
checksum: c12c9c1e6f08def245e42f3cb1d83827
content_type: application/pdf
creator: cziletti
date_created: 2020-10-27T12:49:04Z
date_updated: 2020-10-27T12:49:04Z
file_id: '8711'
file_name: 2020_Annales_Mysliwy.pdf
file_size: 469831
relation: main_file
success: 1
file_date_updated: 2020-10-27T12:49:04Z
has_accepted_license: '1'
intvolume: ' 21'
isi: 1
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 4003-4025
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Annales Henri Poincare
publication_identifier:
issn:
- 1424-0637
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '11473'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in
the mean-field 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 21
year: '2020'
...
---
_id: '8707'
abstract:
- lang: eng
text: Dynamic changes in the three-dimensional (3D) organization of chromatin are
associated with central biological processes, such as transcription, replication
and development. Therefore, the comprehensive identification and quantification
of these changes is fundamental to understanding of evolutionary and regulatory
mechanisms. Here, we present Comparison of Hi-C Experiments using Structural Similarity
(CHESS), an algorithm for the comparison of chromatin contact maps and automatic
differential feature extraction. We demonstrate the robustness of CHESS to experimental
variability and showcase its biological applications on (1) interspecies comparisons
of syntenic regions in human and mouse models; (2) intraspecies identification
of conformational changes in Zelda-depleted Drosophila embryos; (3) patient-specific
aberrant chromatin conformation in a diffuse large B-cell lymphoma sample; and
(4) the systematic identification of chromatin contact differences in high-resolution
Capture-C data. In summary, CHESS is a computationally efficient method for the
comparison and classification of changes in chromatin contact data.
acknowledgement: 'Work in the Vaquerizas laboratory is funded by the Max Planck Society,
the Deutsche Forschungsgemeinschaft (DFG) Priority Programme SPP 2202 ‘Spatial Genome
Architecture in Development and Disease’ (project no. 422857230 to J.M.V.), the
DFG Clinical Research Unit CRU326 ‘Male Germ Cells: from Genes to Function’ (project
no. 329621271 to J.M.V.), the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie grant agreement no. 643062—ZENCODE-ITN
to J.M.V.) and the Medical Research Council in the UK. This research was partially
funded by the European Union’s H2020 Framework Programme through the European Research
Council (grant no. 609989 to M.A.M.-R.). We thank the support of the Spanish Ministerio
de Ciencia, Innovación y Universidades through grant no. BFU2017-85926-P to M.A.M.-R.
The Centre for Genomic Regulation thanks the support of the Ministerio de Ciencia,
Innovación y Universidades to the European Molecular Biology Laboratory partnership,
the ‘Centro de Excelencia Severo Ochoa 2013–2017’, agreement no. SEV-2012-0208,
the CERCA Programme/Generalitat de Catalunya, Spanish Ministerio de Ciencia, Innovación
y Universidades through the Instituto de Salud Carlos III, the Generalitat de Catalunya
through the Departament de Salut and Departament d’Empresa i Coneixement and cofinancing
by the Spanish Ministerio de Ciencia, Innovación y Universidades with funds from
the European Regional Development Fund corresponding to the 2014–2020 Smart Growth
Operating Program. S.G. thanks the support from the Company of Biologists (grant
no. JCSTF181158) and the European Molecular Biology Organization Short-Term Fellowship
programme.'
article_processing_charge: No
article_type: original
author:
- first_name: Silvia
full_name: ' Galan, Silvia'
last_name: ' Galan'
- first_name: Nick N
full_name: Machnik, Nick N
id: 3591A0AA-F248-11E8-B48F-1D18A9856A87
last_name: Machnik
orcid: 0000-0001-6617-9742
- first_name: Kai
full_name: Kruse, Kai
last_name: Kruse
- first_name: Noelia
full_name: Díaz, Noelia
last_name: Díaz
- first_name: Marc A
full_name: Marti-Renom, Marc A
last_name: Marti-Renom
- first_name: Juan M
full_name: Vaquerizas, Juan M
last_name: Vaquerizas
citation:
ama: Galan S, Machnik NN, Kruse K, Díaz N, Marti-Renom MA, Vaquerizas JM. CHESS
enables quantitative comparison of chromatin contact data and automatic feature
extraction. Nature Genetics. 2020;52:1247-1255. doi:10.1038/s41588-020-00712-y
apa: Galan, S., Machnik, N. N., Kruse, K., Díaz, N., Marti-Renom, M. A., & Vaquerizas,
J. M. (2020). CHESS enables quantitative comparison of chromatin contact data
and automatic feature extraction. Nature Genetics. Springer Nature. https://doi.org/10.1038/s41588-020-00712-y
chicago: Galan, Silvia, Nick N Machnik, Kai Kruse, Noelia Díaz, Marc A Marti-Renom,
and Juan M Vaquerizas. “CHESS Enables Quantitative Comparison of Chromatin Contact
Data and Automatic Feature Extraction.” Nature Genetics. Springer Nature,
2020. https://doi.org/10.1038/s41588-020-00712-y.
ieee: S. Galan, N. N. Machnik, K. Kruse, N. Díaz, M. A. Marti-Renom, and J. M.
Vaquerizas, “CHESS enables quantitative comparison of chromatin contact data and
automatic feature extraction,” Nature Genetics, vol. 52. Springer Nature,
pp. 1247–1255, 2020.
ista: Galan S, Machnik NN, Kruse K, Díaz N, Marti-Renom MA, Vaquerizas JM. 2020.
CHESS enables quantitative comparison of chromatin contact data and automatic
feature extraction. Nature Genetics. 52, 1247–1255.
mla: Galan, Silvia, et al. “CHESS Enables Quantitative Comparison of Chromatin Contact
Data and Automatic Feature Extraction.” Nature Genetics, vol. 52, Springer
Nature, 2020, pp. 1247–55, doi:10.1038/s41588-020-00712-y.
short: S. Galan, N.N. Machnik, K. Kruse, N. Díaz, M.A. Marti-Renom, J.M. Vaquerizas,
Nature Genetics 52 (2020) 1247–1255.
date_created: 2020-10-25T23:01:20Z
date_published: 2020-10-19T00:00:00Z
date_updated: 2023-08-22T10:37:10Z
day: '19'
department:
- _id: FyKo
doi: 10.1038/s41588-020-00712-y
external_id:
isi:
- '000579693500004'
pmid:
- '33077914'
intvolume: ' 52'
isi: 1
language:
- iso: eng
month: '10'
oa_version: None
page: 1247-1255
pmid: 1
publication: Nature Genetics
publication_identifier:
eissn:
- '15461718'
issn:
- '10614036'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: CHESS enables quantitative comparison of chromatin contact data and automatic
feature extraction
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 52
year: '2020'
...
---
_id: '8721'
abstract:
- lang: eng
text: Spontaneously arising channels that transport the phytohormone auxin provide
positional cues for self-organizing aspects of plant development such as flexible
vasculature regeneration or its patterning during leaf venation. The auxin canalization
hypothesis proposes a feedback between auxin signaling and transport as the underlying
mechanism, but molecular players await discovery. We identified part of the machinery
that routes auxin transport. The auxin-regulated receptor CAMEL (Canalization-related
Auxin-regulated Malectin-type RLK) together with CANAR (Canalization-related Receptor-like
kinase) interact with and phosphorylate PIN auxin transporters. camel and canar
mutants are impaired in PIN1 subcellular trafficking and auxin-mediated PIN polarization,
which macroscopically manifests as defects in leaf venation and vasculature regeneration
after wounding. The CAMEL-CANAR receptor complex is part of the auxin feedback
that coordinates polarization of individual cells during auxin canalization.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: 'We acknowledge M. Glanc and Y. Zhang for providing entryclones;
Vienna Biocenter Core Facilities (VBCF) for recombinantprotein production and purification;
Vienna Biocenter Massspectrometry Facility, Bioimaging, and Life Science Facilities
at IST Austria and Proteomics Core Facility CEITEC for a great assistance.Funding:This
project received funding from the European Research Council (ERC) under the European
Union’s Horizon 2020 research and innovation program (grant agreement 742985) and
Austrian Science Fund (FWF): I 3630-B25 to J.F.and by grants from the Austrian Academy
of Science through the Gregor Mendel Institute (Y.B.) and the Austrian Agency for
International Cooperation in Education and Research (D.D.); the Netherlands Organization
for Scientific Research (NWO; VIDI-864.13.001) (W.S.); the Research Foundation–Flanders
(FWO;Odysseus II G0D0515N) and a European Research Council grant (ERC; StG TORPEDO;
714055) to B.D.R., B.Y., and E.M.; and the Hertha Firnberg Programme postdoctoral
fellowship (T-947) from the FWF Austrian Science Fund to E.S.-L.; J.H. is the recipient
of a DOC Fellowship of the Austrian Academy of Sciences at IST Austria.'
article_processing_charge: No
article_type: original
author:
- first_name: Jakub
full_name: Hajny, Jakub
id: 4800CC20-F248-11E8-B48F-1D18A9856A87
last_name: Hajny
orcid: 0000-0003-2140-7195
- first_name: Tomas
full_name: Prat, Tomas
id: 3DA3BFEE-F248-11E8-B48F-1D18A9856A87
last_name: Prat
- first_name: N
full_name: Rydza, N
last_name: Rydza
- first_name: Lesia
full_name: Rodriguez Solovey, Lesia
id: 3922B506-F248-11E8-B48F-1D18A9856A87
last_name: Rodriguez Solovey
orcid: 0000-0002-7244-7237
- first_name: Shutang
full_name: Tan, Shutang
id: 2DE75584-F248-11E8-B48F-1D18A9856A87
last_name: Tan
orcid: 0000-0002-0471-8285
- first_name: Inge
full_name: Verstraeten, Inge
id: 362BF7FE-F248-11E8-B48F-1D18A9856A87
last_name: Verstraeten
orcid: 0000-0001-7241-2328
- first_name: David
full_name: Domjan, David
id: C684CD7A-257E-11EA-9B6F-D8588B4F947F
last_name: Domjan
orcid: 0000-0003-2267-106X
- first_name: E
full_name: Mazur, E
last_name: Mazur
- first_name: E
full_name: Smakowska-Luzan, E
last_name: Smakowska-Luzan
- first_name: W
full_name: Smet, W
last_name: Smet
- first_name: E
full_name: Mor, E
last_name: Mor
- first_name: J
full_name: Nolf, J
last_name: Nolf
- first_name: B
full_name: Yang, B
last_name: Yang
- first_name: W
full_name: Grunewald, W
last_name: Grunewald
- first_name: Gergely
full_name: Molnar, Gergely
id: 34F1AF46-F248-11E8-B48F-1D18A9856A87
last_name: Molnar
- first_name: Y
full_name: Belkhadir, Y
last_name: Belkhadir
- first_name: B
full_name: De Rybel, B
last_name: De Rybel
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Hajny J, Prat T, Rydza N, et al. Receptor kinase module targets PIN-dependent
auxin transport during canalization. Science. 2020;370(6516):550-557. doi:10.1126/science.aba3178
apa: Hajny, J., Prat, T., Rydza, N., Rodriguez Solovey, L., Tan, S., Verstraeten,
I., … Friml, J. (2020). Receptor kinase module targets PIN-dependent auxin transport
during canalization. Science. American Association for the Advancement
of Science. https://doi.org/10.1126/science.aba3178
chicago: Hajny, Jakub, Tomas Prat, N Rydza, Lesia Rodriguez Solovey, Shutang Tan,
Inge Verstraeten, David Domjan, et al. “Receptor Kinase Module Targets PIN-Dependent
Auxin Transport during Canalization.” Science. American Association for
the Advancement of Science, 2020. https://doi.org/10.1126/science.aba3178.
ieee: J. Hajny et al., “Receptor kinase module targets PIN-dependent auxin
transport during canalization,” Science, vol. 370, no. 6516. American Association
for the Advancement of Science, pp. 550–557, 2020.
ista: Hajny J, Prat T, Rydza N, Rodriguez Solovey L, Tan S, Verstraeten I, Domjan
D, Mazur E, Smakowska-Luzan E, Smet W, Mor E, Nolf J, Yang B, Grunewald W, Molnar
G, Belkhadir Y, De Rybel B, Friml J. 2020. Receptor kinase module targets PIN-dependent
auxin transport during canalization. Science. 370(6516), 550–557.
mla: Hajny, Jakub, et al. “Receptor Kinase Module Targets PIN-Dependent Auxin Transport
during Canalization.” Science, vol. 370, no. 6516, American Association
for the Advancement of Science, 2020, pp. 550–57, doi:10.1126/science.aba3178.
short: J. Hajny, T. Prat, N. Rydza, L. Rodriguez Solovey, S. Tan, I. Verstraeten,
D. Domjan, E. Mazur, E. Smakowska-Luzan, W. Smet, E. Mor, J. Nolf, B. Yang, W.
Grunewald, G. Molnar, Y. Belkhadir, B. De Rybel, J. Friml, Science 370 (2020)
550–557.
date_created: 2020-11-02T10:04:46Z
date_published: 2020-10-30T00:00:00Z
date_updated: 2023-09-05T12:02:35Z
day: '30'
department:
- _id: JiFr
doi: 10.1126/science.aba3178
ec_funded: 1
external_id:
isi:
- '000583031800041'
pmid:
- '33122378'
intvolume: ' 370'
isi: 1
issue: '6516'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://europepmc.org/article/MED/33122378#free-full-text
month: '10'
oa: 1
oa_version: Published Version
page: 550-557
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
- _id: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
- _id: 2699E3D2-B435-11E9-9278-68D0E5697425
grant_number: '25239'
name: Cell surface receptor complexes for PIN polarity and auxin-mediated development
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/molecular-compass-for-cell-orientation/
scopus_import: '1'
status: public
title: Receptor kinase module targets PIN-dependent auxin transport during canalization
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 370
year: '2020'
...
---
_id: '8722'
abstract:
- lang: eng
text: "Load imbalance pervasively exists in distributed deep learning training systems,
either caused by the inherent imbalance in learned tasks or by the system itself.
Traditional synchronous Stochastic Gradient Descent (SGD)\r\nachieves good accuracy
for a wide variety of tasks, but relies on global synchronization to accumulate
the gradients at every training step. In this paper, we propose eager-SGD, which
relaxes the global synchronization for\r\ndecentralized accumulation. To implement
eager-SGD, we propose to use two partial collectives: solo and majority. With
solo allreduce, the faster processes contribute their gradients eagerly without
waiting for the slower processes, whereas with majority allreduce, at least half
of the participants must contribute gradients before continuing, all without using
a central parameter server. We theoretically prove the convergence of the algorithms
and describe the partial collectives in detail. Experimental results on load-imbalanced
environments (CIFAR-10, ImageNet, and UCF101 datasets) show\r\nthat eager-SGD
achieves 1.27x speedup over the state-of-the-art synchronous SGD, without losing
accuracy."
article_processing_charge: No
arxiv: 1
author:
- first_name: Shigang
full_name: Li, Shigang
last_name: Li
- first_name: Tal Ben-Nun
full_name: Tal Ben-Nun, Tal Ben-Nun
last_name: Tal Ben-Nun
- first_name: Salvatore Di
full_name: Girolamo, Salvatore Di
last_name: Girolamo
- 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
citation:
ama: 'Li S, Tal Ben-Nun TB-N, Girolamo SD, Alistarh D-A, Hoefler T. Taming unbalanced
training workloads in deep learning with partial collective operations. In: Proceedings
of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming.
Association for Computing Machinery; 2020:45-61. doi:10.1145/3332466.3374528'
apa: 'Li, S., Tal Ben-Nun, T. B.-N., Girolamo, S. D., Alistarh, D.-A., & Hoefler,
T. (2020). Taming unbalanced training workloads in deep learning with partial
collective operations. In Proceedings of the 25th ACM SIGPLAN Symposium on
Principles and Practice of Parallel Programming (pp. 45–61). San Diego, CA,
United States: Association for Computing Machinery. https://doi.org/10.1145/3332466.3374528'
chicago: Li, Shigang, Tal Ben-Nun Tal Ben-Nun, Salvatore Di Girolamo, Dan-Adrian
Alistarh, and Torsten Hoefler. “Taming Unbalanced Training Workloads in Deep Learning
with Partial Collective Operations.” In Proceedings of the 25th ACM SIGPLAN
Symposium on Principles and Practice of Parallel Programming, 45–61. Association
for Computing Machinery, 2020. https://doi.org/10.1145/3332466.3374528.
ieee: S. Li, T. B.-N. Tal Ben-Nun, S. D. Girolamo, D.-A. Alistarh, and T. Hoefler,
“Taming unbalanced training workloads in deep learning with partial collective
operations,” in Proceedings of the 25th ACM SIGPLAN Symposium on Principles
and Practice of Parallel Programming, San Diego, CA, United States, 2020,
pp. 45–61.
ista: 'Li S, Tal Ben-Nun TB-N, Girolamo SD, Alistarh D-A, Hoefler T. 2020. Taming
unbalanced training workloads in deep learning with partial collective operations.
Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel
Programming. PPoPP: Sympopsium on Principles and Practice of Parallel Programming,
45–61.'
mla: Li, Shigang, et al. “Taming Unbalanced Training Workloads in Deep Learning
with Partial Collective Operations.” Proceedings of the 25th ACM SIGPLAN Symposium
on Principles and Practice of Parallel Programming, Association for Computing
Machinery, 2020, pp. 45–61, doi:10.1145/3332466.3374528.
short: S. Li, T.B.-N. Tal Ben-Nun, S.D. Girolamo, D.-A. Alistarh, T. Hoefler, in:,
Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel
Programming, Association for Computing Machinery, 2020, pp. 45–61.
conference:
end_date: 2020-02-26
location: San Diego, CA, United States
name: 'PPoPP: Sympopsium on Principles and Practice of Parallel Programming'
start_date: 2020-02-22
date_created: 2020-11-05T15:25:30Z
date_published: 2020-02-01T00:00:00Z
date_updated: 2023-08-22T12:13:48Z
day: '01'
department:
- _id: DaAl
doi: 10.1145/3332466.3374528
ec_funded: 1
external_id:
arxiv:
- '1908.04207'
isi:
- '000564476500004'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1908.04207
month: '02'
oa: 1
oa_version: Preprint
page: 45-61
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication: Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice
of Parallel Programming
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
status: public
title: Taming unbalanced training workloads in deep learning with partial collective
operations
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2020'
...
---
_id: '8724'
abstract:
- lang: eng
text: "We study the problem of learning from multiple untrusted data sources, a
scenario of increasing practical relevance given the recent emergence of crowdsourcing
and collaborative learning paradigms. Specifically, we analyze the situation in
which a learning system obtains datasets from multiple sources, some of which
might be biased or even adversarially perturbed. It is\r\nknown that in the single-source
case, an adversary with the power to corrupt a fixed fraction of the training
data can prevent PAC-learnability, that is, even in the limit of infinitely much
training data, no learning system can approach the optimal test error. In this
work we show that, surprisingly, the same is not true in the multi-source setting,
where the adversary can arbitrarily\r\ncorrupt a fixed fraction of the data sources.
Our main results are a generalization bound that provides finite-sample guarantees
for this learning setting, as well as corresponding lower bounds. Besides establishing
PAC-learnability our results also show that in a cooperative learning setting
sharing data with other parties has provable benefits, even if some\r\nparticipants
are malicious. "
acknowledged_ssus:
- _id: ScienComp
acknowledgement: Dan Alistarh is supported in part by the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme
(grant agreement No 805223 ScaleML). This research was supported by the Scientific
Service Units (SSU) of IST Austria through resources provided by Scientific Computing
(SciComp).
article_processing_charge: No
arxiv: 1
author:
- first_name: Nikola H
full_name: Konstantinov, Nikola H
id: 4B9D76E4-F248-11E8-B48F-1D18A9856A87
last_name: Konstantinov
- first_name: Elias
full_name: Frantar, Elias
id: 09a8f98d-ec99-11ea-ae11-c063a7b7fe5f
last_name: Frantar
- 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: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Konstantinov NH, Frantar E, Alistarh D-A, Lampert C. On the sample complexity
of adversarial multi-source PAC learning. In: Proceedings of the 37th International
Conference on Machine Learning. Vol 119. ML Research Press; 2020:5416-5425.'
apa: 'Konstantinov, N. H., Frantar, E., Alistarh, D.-A., & Lampert, C. (2020).
On the sample complexity of adversarial multi-source PAC learning. In Proceedings
of the 37th International Conference on Machine Learning (Vol. 119, pp. 5416–5425).
Online: ML Research Press.'
chicago: Konstantinov, Nikola H, Elias Frantar, Dan-Adrian Alistarh, and Christoph
Lampert. “On the Sample Complexity of Adversarial Multi-Source PAC Learning.”
In Proceedings of the 37th International Conference on Machine Learning,
119:5416–25. ML Research Press, 2020.
ieee: N. H. Konstantinov, E. Frantar, D.-A. Alistarh, and C. Lampert, “On the sample
complexity of adversarial multi-source PAC learning,” in Proceedings of the
37th International Conference on Machine Learning, Online, 2020, vol. 119,
pp. 5416–5425.
ista: 'Konstantinov NH, Frantar E, Alistarh D-A, Lampert C. 2020. On the sample
complexity of adversarial multi-source PAC learning. Proceedings of the 37th International
Conference on Machine Learning. ICML: International Conference on Machine Learning
vol. 119, 5416–5425.'
mla: Konstantinov, Nikola H., et al. “On the Sample Complexity of Adversarial Multi-Source
PAC Learning.” Proceedings of the 37th International Conference on Machine
Learning, vol. 119, ML Research Press, 2020, pp. 5416–25.
short: N.H. Konstantinov, E. Frantar, D.-A. Alistarh, C. Lampert, in:, Proceedings
of the 37th International Conference on Machine Learning, ML Research Press, 2020,
pp. 5416–5425.
conference:
end_date: 2020-07-18
location: Online
name: 'ICML: International Conference on Machine Learning'
start_date: 2020-07-12
date_created: 2020-11-05T15:25:58Z
date_published: 2020-07-12T00:00:00Z
date_updated: 2023-09-07T13:42:08Z
day: '12'
ddc:
- '000'
department:
- _id: DaAl
- _id: ChLa
ec_funded: 1
external_id:
arxiv:
- '2002.10384'
file:
- access_level: open_access
checksum: cc755d0054bc4b2be778ea7aa7884d2f
content_type: application/pdf
creator: dernst
date_created: 2021-02-15T09:00:01Z
date_updated: 2021-02-15T09:00:01Z
file_id: '9120'
file_name: 2020_PMLR_Konstantinov.pdf
file_size: 281286
relation: main_file
success: 1
file_date_updated: 2021-02-15T09:00:01Z
has_accepted_license: '1'
intvolume: ' 119'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 5416-5425
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication: Proceedings of the 37th International Conference on Machine Learning
publication_identifier:
issn:
- 2640-3498
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
related_material:
link:
- relation: supplementary_material
url: http://proceedings.mlr.press/v119/konstantinov20a/konstantinov20a-supp.pdf
record:
- id: '10799'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: On the sample complexity of adversarial multi-source PAC learning
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 119
year: '2020'
...