---
OA_place: publisher
OA_type: gold
_id: '18073'
abstract:
- lang: eng
text: Conserved signaling cascades monitor protein-folding homeostasis to ensure
proper cellular function. One of the evolutionary conserved key players is IRE1,
which maintains endoplasmic reticulum (ER) homeostasis through the unfolded protein
response (UPR). Upon accumulation of misfolded proteins in the ER, IRE1 forms
clusters on the ER membrane to initiate UPR signaling. What regulates IRE1 cluster
formation is not fully understood. Here, we show that the ER lumenal domain (LD)
of human IRE1α forms biomolecular condensates in vitro. IRE1α LD condensates were
stabilized both by binding to unfolded polypeptides as well as by tethering to
model membranes, suggesting their role in assembling IRE1α into signaling-competent
stable clusters. Molecular dynamics simulations indicated that weak multivalent
interactions drive IRE1α LD clustering. Mutagenesis experiments identified disordered
regions in IRE1α LD to control its clustering in vitro and in cells. Importantly,
dysregulated clustering of IRE1α mutants led to defects in IRE1α signaling. Our
results revealed that disordered regions in IRE1α LD control its clustering and
suggest their role as a common strategy in regulating protein assembly on membranes.
acknowledgement: We thank late Thomas Peterbauer at the Max Perutz Labs Biooptics
Light Microscopy Facility for his help and support. We are grateful to Kitti Csalyi
and Thomas Sauer at Max Perutz Labs Biooptics FACS facility for their help. We thank
Grzegorz Scibisz and Sertan Atilla for their support with the expression and purification
of mCherry-IRE1α LD-10His. We are grateful to Aleksandra S Anisimova with her help
in the generation of stable cell lines and the statistical analyses of the data.
We thank Venja Vieweger for her help with the characterization of the WLLI and D123P
IRE1 mutants in cells. We are thankful to Monika Kubickova for the help with the
AUC experiments. We acknowledge CF BIC of CIISB, Instruct-CZ Centre, supported by
MEYS CR (LM2023042)) and European Regional Development Fund-Project, UP CIISB“ (No.
CZ.02.1.01/0.0/0.0/18_046/0015974). We thank the members of the Karagöz lab for
the critical reading and editing of the manuscript. We are thankful to our colleagues
Diego Acosta-Alvear, Vladislav Belyy, Jirka Peschek, Yasin Dagdas, Javier Martinez,
Sascha Martens and Alwin Köhler for their invaluable input on the manuscript. We
are grateful to Life Science Editors, especially Katrina Woolcock for her useful
edits and comments on the manuscript. We acknowledge funding from Austrian Science
Fund (FWF-SFB F79 and FWF-W 1261) to GEK. PK acknowledges the support of the Max
Perutz PhD fellowship. GAV is funded by Stand-Alone grants (P30231-B, P30415-B,
P36572), Special Research Grant (SFB grant F79), and Doctoral School grant (DK grant
W1261) from the Austrian Science Fund (FWF). ES and RC acknowledge support and funding
by the Frankfurt Institute of Advanced Studies, the LOEWE Center for Multiscale
Modelling in Life Sciences of the state of Hesse, the Collaborative Research Center
1507 “Membrane-associated Protein Assemblies, Machineries, and Supercomplexes” (Project
ID 450648163), and the International Max Planck Research School on Cellular Biophysics
(to RC), the Center for Scientific Computing of the Goethe University and the Jülich
Supercomputing Centre for computational resources and support.
article_processing_charge: Yes
article_type: original
author:
- first_name: Paulina
full_name: Kettel, Paulina
last_name: Kettel
- first_name: Laura
full_name: Marosits, Laura
last_name: Marosits
- first_name: Elena
full_name: Spinetti, Elena
last_name: Spinetti
- first_name: Michael
full_name: Rechberger, Michael
last_name: Rechberger
- first_name: Caterina
full_name: Giannini, Caterina
id: e3fdddd5-f6e0-11ea-865d-ca99ee6367f4
last_name: Giannini
- first_name: Philipp
full_name: Radler, Philipp
id: 40136C2A-F248-11E8-B48F-1D18A9856A87
last_name: Radler
orcid: '0000-0001-9198-2182 '
- first_name: Isabell
full_name: Niedermoser, Isabell
last_name: Niedermoser
- first_name: Irmgard
full_name: Fischer, Irmgard
last_name: Fischer
- first_name: Gijs A.
full_name: Versteeg, Gijs A.
last_name: Versteeg
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Roberto
full_name: Covino, Roberto
last_name: Covino
- first_name: G. Elif
full_name: Karagöz, G. Elif
last_name: Karagöz
citation:
ama: Kettel P, Marosits L, Spinetti E, et al. Disordered regions in the IRE1α ER
lumenal domain mediate its stress-induced clustering. EMBO Journal. 2024;43(20):4668-4698.
doi:10.1038/s44318-024-00207-0
apa: Kettel, P., Marosits, L., Spinetti, E., Rechberger, M., Giannini, C., Radler,
P., … Karagöz, G. E. (2024). Disordered regions in the IRE1α ER lumenal domain
mediate its stress-induced clustering. EMBO Journal. Embo Press. https://doi.org/10.1038/s44318-024-00207-0
chicago: Kettel, Paulina, Laura Marosits, Elena Spinetti, Michael Rechberger, Caterina
Giannini, Philipp Radler, Isabell Niedermoser, et al. “Disordered Regions in the
IRE1α ER Lumenal Domain Mediate Its Stress-Induced Clustering.” EMBO Journal.
Embo Press, 2024. https://doi.org/10.1038/s44318-024-00207-0.
ieee: P. Kettel et al., “Disordered regions in the IRE1α ER lumenal domain
mediate its stress-induced clustering,” EMBO Journal, vol. 43, no. 20.
Embo Press, pp. 4668–4698, 2024.
ista: Kettel P, Marosits L, Spinetti E, Rechberger M, Giannini C, Radler P, Niedermoser
I, Fischer I, Versteeg GA, Loose M, Covino R, Karagöz GE. 2024. Disordered regions
in the IRE1α ER lumenal domain mediate its stress-induced clustering. EMBO Journal.
43(20), 4668–4698.
mla: Kettel, Paulina, et al. “Disordered Regions in the IRE1α ER Lumenal Domain
Mediate Its Stress-Induced Clustering.” EMBO Journal, vol. 43, no. 20,
Embo Press, 2024, pp. 4668–98, doi:10.1038/s44318-024-00207-0.
short: P. Kettel, L. Marosits, E. Spinetti, M. Rechberger, C. Giannini, P. Radler,
I. Niedermoser, I. Fischer, G.A. Versteeg, M. Loose, R. Covino, G.E. Karagöz,
EMBO Journal 43 (2024) 4668–4698.
das_tickbox: '1'
dataavailabilitystatement: 'All the raw data in this work has been deposited to Biostudies
with the accession number: S-BIAD1023. One can access the data through the link
below: https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD1023?key=426953ee-3da4-4cf4-a496-e607ce240aff. The
source data of this paper are collected in the following database record: biostudies:S-SCDT-10_1038-S44318-024-00207-0.'
date_created: 2024-09-15T22:01:42Z
date_published: 2024-10-15T00:00:00Z
date_updated: 2026-10-16T10:37:47Z
day: '15'
ddc:
- '570'
department:
- _id: MaLo
- _id: JiFr
doi: 10.1038/s44318-024-00207-0
external_id:
isi:
- '001306286100002'
pmid:
- '39232130'
file:
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checksum: 04f4df1a561083f2846676442fc4eb3c
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date_created: 2025-01-13T08:43:20Z
date_updated: 2025-01-13T08:43:20Z
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file_size: 10080854
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file_date_updated: 2025-01-13T08:43:20Z
fulldoi: https://doi.org/10.1038/s44318-024-00207-0
has_accepted_license: '1'
intvolume: ' 43'
isi: 1
issue: '20'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 4668-4698
pmid: 1
publication: EMBO Journal
publication_identifier:
eissn:
- 1460-2075
issn:
- 0261-4189
publication_status: published
publisher: Embo Press
quality_controlled: '1'
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Disordered regions in the IRE1α ER lumenal domain mediate its stress-induced
clustering
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 43
year: '2024'
...
---
_id: '14834'
abstract:
- lang: eng
text: Bacteria divide by binary fission. The protein machine responsible for this
process is the divisome, a transient assembly of more than 30 proteins in and
on the surface of the cytoplasmic membrane. Together, they constrict the cell
envelope and remodel the peptidoglycan layer to eventually split the cell into
two. For Escherichia coli, most molecular players involved in this process have
probably been identified, but obtaining the quantitative information needed for
a mechanistic understanding can often not be achieved from experiments in vivo
alone. Since the discovery of the Z-ring more than 30 years ago, in vitro reconstitution
experiments have been crucial to shed light on molecular processes normally hidden
in the complex environment of the living cell. In this review, we summarize how
rebuilding the divisome from purified components – or at least parts of it - have
been instrumental to obtain the detailed mechanistic understanding of the bacterial
cell division machinery that we have today.
acknowledgement: We acknowledge members of the Loose laboratory at ISTA for helpful
discussions—in particular M. Kojic for his insightful comments. This work was supported
by the Austrian Science Fund (FWF P34607) to M.L.
article_number: '151380'
article_processing_charge: Yes
article_type: review
author:
- first_name: Philipp
full_name: Radler, Philipp
id: 40136C2A-F248-11E8-B48F-1D18A9856A87
last_name: Radler
orcid: '0000-0001-9198-2182 '
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
citation:
ama: 'Radler P, Loose M. A dynamic duo: Understanding the roles of FtsZ and FtsA
for Escherichia coli cell division through in vitro approaches. European Journal
of Cell Biology. 2024;103(1). doi:10.1016/j.ejcb.2023.151380'
apa: 'Radler, P., & Loose, M. (2024). A dynamic duo: Understanding the roles
of FtsZ and FtsA for Escherichia coli cell division through in vitro approaches.
European Journal of Cell Biology. Elsevier. https://doi.org/10.1016/j.ejcb.2023.151380'
chicago: 'Radler, Philipp, and Martin Loose. “A Dynamic Duo: Understanding the Roles
of FtsZ and FtsA for Escherichia Coli Cell Division through in Vitro Approaches.”
European Journal of Cell Biology. Elsevier, 2024. https://doi.org/10.1016/j.ejcb.2023.151380.'
ieee: 'P. Radler and M. Loose, “A dynamic duo: Understanding the roles of FtsZ and
FtsA for Escherichia coli cell division through in vitro approaches,” European
Journal of Cell Biology, vol. 103, no. 1. Elsevier, 2024.'
ista: 'Radler P, Loose M. 2024. A dynamic duo: Understanding the roles of FtsZ and
FtsA for Escherichia coli cell division through in vitro approaches. European
Journal of Cell Biology. 103(1), 151380.'
mla: 'Radler, Philipp, and Martin Loose. “A Dynamic Duo: Understanding the Roles
of FtsZ and FtsA for Escherichia Coli Cell Division through in Vitro Approaches.”
European Journal of Cell Biology, vol. 103, no. 1, 151380, Elsevier, 2024,
doi:10.1016/j.ejcb.2023.151380.'
short: P. Radler, M. Loose, European Journal of Cell Biology 103 (2024).
corr_author: '1'
das_tickbox: '0'
date_created: 2024-01-18T08:16:43Z
date_published: 2024-03-01T00:00:00Z
date_updated: 2026-10-16T10:15:15Z
day: '01'
ddc:
- '570'
department:
- _id: MaLo
doi: 10.1016/j.ejcb.2023.151380
external_id:
isi:
- '001166216800001'
pmid:
- '38218128'
file:
- access_level: open_access
checksum: 5d170abbc87585205c010657e4552360
content_type: application/pdf
creator: dernst
date_created: 2024-07-16T12:07:20Z
date_updated: 2024-07-16T12:07:20Z
file_id: '17265'
file_name: 2024_EJCB_Radler.pdf
file_size: 9995304
relation: main_file
success: 1
file_date_updated: 2024-07-16T12:07:20Z
fulldoi: https://doi.org/10.1016/j.ejcb.2023.151380
has_accepted_license: '1'
intvolume: ' 103'
isi: 1
issue: '1'
keyword:
- Cell Biology
- General Medicine
- Histology
- Pathology and Forensic Medicine
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: fc38323b-9c52-11eb-aca3-ff8afb4a011d
grant_number: P34607
name: In vitro reconstitution of bacterial cell division
publication: European Journal of Cell Biology
publication_identifier:
issn:
- 0171-9335
publication_status: published
publisher: Elsevier
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: 'A dynamic duo: Understanding the roles of FtsZ and FtsA for Escherichia coli
cell division through in vitro approaches'
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 103
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '18702'
abstract:
- lang: eng
text: 'In this work we prove lower bounds on the (communication) cost of maintaining
a shared key among a dynamic group of users. Being “dynamic” means one can add
and remove users from the group. This captures important protocols like multicast
encryption (ME) and continuous group-key agreement (CGKA), which is the primitive
underlying many group messaging applications. We prove our bounds in a combinatorial
setting where the state of the protocol progresses in rounds. The state of the
protocol in each round is captured by a set system, with each of its elements
specifying a set of users who share a secret key. We show this combinatorial model
implies bounds in symbolic models for ME and CGKA that capture, as building blocks,
PRGs, PRFs, dual PRFs, secret sharing, and symmetric encryption in the setting
of ME, and PRGs, PRFs, dual PRFs, secret sharing, public-key encryption, and key-updatable
public-key encryption in the setting of CGKA. The models are related to the ones
used by Micciancio and Panjwani (Eurocrypt’04) and Bienstock et al. (TCC’20) to
analyze ME and CGKA, respectively. We prove – using the Bollobás’ Set Pairs Inequality
– that the cost (number of uploaded ciphertexts) for replacing a set of d users
in a group of size n is Ω(dln(n/d)). Our lower bound is asymptotically tight and
both improves on a bound of Ω(d) by Bienstock et al. (TCC’20), and generalizes
a result by Micciancio and Panjwani (Eurocrypt’04), who proved a lower bound of
Ω(log(n)) for d=1. '
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Michael
full_name: Anastos, Michael
id: 0b2a4358-bb35-11ec-b7b9-e3279b593dbb
last_name: Anastos
- first_name: Benedikt
full_name: Auerbach, Benedikt
id: D33D2B18-E445-11E9-ABB7-15F4E5697425
last_name: Auerbach
orcid: 0000-0002-7553-6606
- first_name: Mirza Ahad
full_name: Baig, Mirza Ahad
id: 3EDE6DE4-AA5A-11E9-986D-341CE6697425
last_name: Baig
- first_name: Miguel
full_name: Cueto Noval, Miguel
id: ffc563a3-f6e0-11ea-865d-e3cce03d17cc
last_name: Cueto Noval
orcid: 0000-0002-2505-4246
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
- first_name: Guillermo
full_name: Pascual Perez, Guillermo
id: 2D7ABD02-F248-11E8-B48F-1D18A9856A87
last_name: Pascual Perez
orcid: 0000-0001-8630-415X
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Anastos M, Auerbach B, Baig MA, et al. The cost of maintaining keys in dynamic
groups with applications to multicast encryption and group messaging. In: 22nd
International Conference on Theory of Cryptography. Vol 15364. Springer Nature;
2024:413-443. doi:10.1007/978-3-031-78011-0_14'
apa: 'Anastos, M., Auerbach, B., Baig, M. A., Cueto Noval, M., Kwan, M. A., Pascual
Perez, G., & Pietrzak, K. Z. (2024). The cost of maintaining keys in dynamic
groups with applications to multicast encryption and group messaging. In 22nd
International Conference on Theory of Cryptography (Vol. 15364, pp. 413–443).
Milan, Italy: Springer Nature. https://doi.org/10.1007/978-3-031-78011-0_14'
chicago: Anastos, Michael, Benedikt Auerbach, Mirza Ahad Baig, Miguel Cueto Noval,
Matthew Alan Kwan, Guillermo Pascual Perez, and Krzysztof Z Pietrzak. “The Cost
of Maintaining Keys in Dynamic Groups with Applications to Multicast Encryption
and Group Messaging.” In 22nd International Conference on Theory of Cryptography,
15364:413–43. Springer Nature, 2024. https://doi.org/10.1007/978-3-031-78011-0_14.
ieee: M. Anastos et al., “The cost of maintaining keys in dynamic groups
with applications to multicast encryption and group messaging,” in 22nd International
Conference on Theory of Cryptography, Milan, Italy, 2024, vol. 15364, pp.
413–443.
ista: 'Anastos M, Auerbach B, Baig MA, Cueto Noval M, Kwan MA, Pascual Perez G,
Pietrzak KZ. 2024. The cost of maintaining keys in dynamic groups with applications
to multicast encryption and group messaging. 22nd International Conference on
Theory of Cryptography. TCC: Theory of Cryptography, LNCS, vol. 15364, 413–443.'
mla: Anastos, Michael, et al. “The Cost of Maintaining Keys in Dynamic Groups with Applications
to Multicast Encryption and Group Messaging.” 22nd International Conference
on Theory of Cryptography, vol. 15364, Springer Nature, 2024, pp. 413–43,
doi:10.1007/978-3-031-78011-0_14.
short: M. Anastos, B. Auerbach, M.A. Baig, M. Cueto Noval, M.A. Kwan, G. Pascual
Perez, K.Z. Pietrzak, in:, 22nd International Conference on Theory of Cryptography,
Springer Nature, 2024, pp. 413–443.
conference:
end_date: 2024-12-06
location: Milan, Italy
name: 'TCC: Theory of Cryptography'
start_date: 2024-12-02
corr_author: '1'
das_tickbox: '0'
date_created: 2024-12-22T23:01:47Z
date_published: 2024-12-02T00:00:00Z
date_updated: 2026-10-16T10:14:41Z
day: '02'
department:
- _id: MaKw
- _id: KrPi
doi: 10.1007/978-3-031-78011-0_14
external_id:
isi:
- '001545628900014'
fulldoi: https://doi.org/10.1007/978-3-031-78011-0_14
intvolume: ' 15364'
isi: 1
language:
- iso: eng
main_file_link:
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url: https://eprint.iacr.org/2024/1097
month: '12'
oa: 1
oa_version: Preprint
page: 413-443
publication: 22nd International Conference on Theory of Cryptography
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031780103'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '22664'
relation: dissertation_contains
status: public
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: The cost of maintaining keys in dynamic groups with applications to multicast
encryption and group messaging
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 15364
year: '2024'
...
---
_id: '17475'
abstract:
- lang: eng
text: "As a discrete analogue of Kac’s celebrated question on ‘hearing the shape
of a drum’ and towards a practical\r\ngraph isomorphism test, it is of interest
to understand which graphs are determined up to isomorphism by\r\ntheir spectrum
(of their adjacency matrix). A striking conjecture in this area, due to van Dam
and Haemers,\r\nis that ‘almost all graphs are determined by their spectrum’,
meaning that the fraction of unlabelled n-vertex\r\ngraphs which are determined
by their spectrum converges to 1 as n → ∞.\r\nIn this paper, we make a step towards
this conjecture, showing that there are exponentially many n-vertex\r\ngraphs
which are determined by their spectrum. This improves on previous bounds (of shape
e\r\nc\r\n√\r\nn\r\n). We also\r\npropose a number of further directions of research.\r\n"
acknowledgement: Matthew Kwan was supported by ERC Starting Grant ‘RANDSTRUCT’ No.
101076777.
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Illya
full_name: Koval, Illya
id: 2eed1f3b-896a-11ed-bdf8-93c7c4bf159e
last_name: Koval
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
citation:
ama: Koval I, Kwan MA. Exponentially many graphs are determined by their spectrum.
Quarterly Journal of Mathematics. 2024;75(3):869-899. doi:10.1093/qmath/haae030
apa: Koval, I., & Kwan, M. A. (2024). Exponentially many graphs are determined
by their spectrum. Quarterly Journal of Mathematics. Oxford University
Press. https://doi.org/10.1093/qmath/haae030
chicago: Koval, Illya, and Matthew Alan Kwan. “Exponentially Many Graphs Are Determined
by Their Spectrum.” Quarterly Journal of Mathematics. Oxford University
Press, 2024. https://doi.org/10.1093/qmath/haae030.
ieee: I. Koval and M. A. Kwan, “Exponentially many graphs are determined by their
spectrum,” Quarterly Journal of Mathematics, vol. 75, no. 3. Oxford University
Press, pp. 869–899, 2024.
ista: Koval I, Kwan MA. 2024. Exponentially many graphs are determined by their
spectrum. Quarterly Journal of Mathematics. 75(3), 869–899.
mla: Koval, Illya, and Matthew Alan Kwan. “Exponentially Many Graphs Are Determined
by Their Spectrum.” Quarterly Journal of Mathematics, vol. 75, no. 3, Oxford
University Press, 2024, pp. 869–99, doi:10.1093/qmath/haae030.
short: I. Koval, M.A. Kwan, Quarterly Journal of Mathematics 75 (2024) 869–899.
corr_author: '1'
das_tickbox: '0'
date_created: 2024-09-01T22:01:07Z
date_published: 2024-06-19T00:00:00Z
date_updated: 2026-10-16T10:14:59Z
day: '19'
ddc:
- '500'
department:
- _id: MaKw
- _id: VaKa
doi: 10.1093/qmath/haae030
external_id:
arxiv:
- '2309.09788'
isi:
- '001249741500001'
file:
- access_level: open_access
checksum: abf200d37ad69e6f2c0750a30296ad97
content_type: application/pdf
creator: cchlebak
date_created: 2024-09-06T12:23:57Z
date_updated: 2024-09-06T12:23:57Z
file_id: '17851'
file_name: 2024_QuJofMath_Koval.pdf
file_size: 946411
relation: main_file
success: 1
file_date_updated: 2024-09-06T12:23:57Z
fulldoi: https://doi.org/10.1093/qmath/haae030
has_accepted_license: '1'
intvolume: ' 75'
isi: 1
issue: '3'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 869-899
project:
- _id: bd95085b-d553-11ed-ba76-e55d3349be45
grant_number: '101076777'
name: Randomness and structure in combinatorics
publication: Quarterly Journal of Mathematics
publication_identifier:
eissn:
- 1464-3847
issn:
- 0033-5606
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: Exponentially many graphs are determined by their spectrum
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 75
year: '2024'
...
---
_id: '15118'
abstract:
- lang: eng
text: Cell division in all domains of life requires the orchestration of many proteins,
but in Archaea most of the machinery remains poorly characterized. Here we investigate
the FtsZ-based cell division mechanism in Haloferax volcanii and find proteins
containing photosynthetic reaction centre (PRC) barrel domains that play an essential
role in archaeal cell division. We rename these proteins cell division protein
B 1 (CdpB1) and CdpB2. Depletions and deletions in their respective genes cause
severe cell division defects, generating drastically enlarged cells. Fluorescence
microscopy of tagged FtsZ1, FtsZ2 and SepF in CdpB1 and CdpB2 mutant strains revealed
an unusually disordered divisome that is not organized into a distinct ring-like
structure. Biochemical analysis shows that SepF forms a tripartite complex with
CdpB1/2 and crystal structures suggest that these two proteins might form filaments,
possibly aligning SepF and the FtsZ2 ring during cell division. Overall our results
indicate that PRC-domain proteins play essential roles in FtsZ-based cell division
in Archaea.
acknowledged_ssus:
- _id: LifeSc
acknowledgement: We thank X. Ye (ISTA) for providing the His–SUMO expression plasmid
pSVA13429. pCDB302 was a gift from C. Bahl (Addgene plasmid number 113673; http://n2t.net/addgene:113673;
RRID Addgene_113673). We thank B. Ahsan, G. Sharov, G. Cannone and S. Chen from
the Medical Research Council (MRC) LMB Electron Microscopy Facility for help and
support. We thank Scientific Computing at the MRC LMB for their support. We thank
L. Trübestein and N. Krasnici of the protein service unit of the ISTA Lab Support
Facility for help with the SEC coupled with multi-angle light scattering experiments.
We thank D. Grohmann and R. Reichelt from the Archaea Centre at the University of
Regensburg for providing the P. furiosus cell material. P.N. and S.-V.A. were supported
by a Momentum grant from the Volkswagen (VW) Foundation (grant number 94933). D.K.-C.
and D.B. were supported by the VW Stiftung ‘Life?’ programme (to J.L.; grant number
Az 96727) and by the MRC, as part of UK Research and Innovation (UKRI), MRC file
reference number U105184326 (to J.L.). N.T. and S.G. acknowledge support from the
French Government’s Investissement d’Avenir program, Laboratoire d’Excellence ‘Integrative
Biology of Emerging Infectious Diseases’ (grant number ANR-10-LABX-62-IBEID), and
the computational and storage services (Maestro cluster) provided by the IT department
at Institut Pasteur. M.K. and M.L. were supported by the Austrian Science Fund (FWF)
Stand-Alone P34607. For the purpose of open access, the MRC Laboratory of Molecular
Biology has applied a CC BY public copyright licence to any author accepted manuscript
version arising.
article_processing_charge: No
article_type: original
author:
- first_name: Phillip
full_name: Nußbaum, Phillip
last_name: Nußbaum
- first_name: Danguole
full_name: Kureisaite-Ciziene, Danguole
last_name: Kureisaite-Ciziene
- first_name: Dom
full_name: Bellini, Dom
last_name: Bellini
- first_name: Chris
full_name: Van Der Does, Chris
last_name: Van Der Does
- first_name: Marko
full_name: Kojic, Marko
id: 73e7ecd4-dc85-11ea-9058-88a16394b160
last_name: Kojic
orcid: 0000-0001-7244-8128
- first_name: Najwa
full_name: Taib, Najwa
last_name: Taib
- first_name: Anna
full_name: Yeates, Anna
last_name: Yeates
- first_name: Maxime
full_name: Tourte, Maxime
last_name: Tourte
- first_name: Simonetta
full_name: Gribaldo, Simonetta
last_name: Gribaldo
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Jan
full_name: Löwe, Jan
last_name: Löwe
- first_name: Sonja Verena
full_name: Albers, Sonja Verena
last_name: Albers
citation:
ama: Nußbaum P, Kureisaite-Ciziene D, Bellini D, et al. Proteins containing photosynthetic
reaction centre domains modulate FtsZ-based archaeal cell division. Nature
Microbiology. 2024;9(3):698-711. doi:10.1038/s41564-024-01600-5
apa: Nußbaum, P., Kureisaite-Ciziene, D., Bellini, D., Van Der Does, C., Kojic,
M., Taib, N., … Albers, S. V. (2024). Proteins containing photosynthetic reaction
centre domains modulate FtsZ-based archaeal cell division. Nature Microbiology.
Springer Nature. https://doi.org/10.1038/s41564-024-01600-5
chicago: Nußbaum, Phillip, Danguole Kureisaite-Ciziene, Dom Bellini, Chris Van Der
Does, Marko Kojic, Najwa Taib, Anna Yeates, et al. “Proteins Containing Photosynthetic
Reaction Centre Domains Modulate FtsZ-Based Archaeal Cell Division.” Nature
Microbiology. Springer Nature, 2024. https://doi.org/10.1038/s41564-024-01600-5.
ieee: P. Nußbaum et al., “Proteins containing photosynthetic reaction centre
domains modulate FtsZ-based archaeal cell division,” Nature Microbiology,
vol. 9, no. 3. Springer Nature, pp. 698–711, 2024.
ista: Nußbaum P, Kureisaite-Ciziene D, Bellini D, Van Der Does C, Kojic M, Taib
N, Yeates A, Tourte M, Gribaldo S, Loose M, Löwe J, Albers SV. 2024. Proteins
containing photosynthetic reaction centre domains modulate FtsZ-based archaeal
cell division. Nature Microbiology. 9(3), 698–711.
mla: Nußbaum, Phillip, et al. “Proteins Containing Photosynthetic Reaction Centre
Domains Modulate FtsZ-Based Archaeal Cell Division.” Nature Microbiology,
vol. 9, no. 3, Springer Nature, 2024, pp. 698–711, doi:10.1038/s41564-024-01600-5.
short: P. Nußbaum, D. Kureisaite-Ciziene, D. Bellini, C. Van Der Does, M. Kojic,
N. Taib, A. Yeates, M. Tourte, S. Gribaldo, M. Loose, J. Löwe, S.V. Albers, Nature
Microbiology 9 (2024) 698–711.
das_tickbox: '1'
dataavailabilitystatement: The data that support the findings of this study are available
in the Source Data. Source data are provided with this paper. Coordinates have been
submitted to the Protein Data Bank (PDB) with accession code 8QZO.
date_created: 2024-03-17T23:00:58Z
date_published: 2024-03-04T00:00:00Z
date_updated: 2026-10-16T10:35:48Z
day: '04'
department:
- _id: MaLo
doi: 10.1038/s41564-024-01600-5
external_id:
isi:
- '001183270800021'
pmid:
- '38443575'
fulldoi: https://doi.org/10.1038/s41564-024-01600-5
intvolume: ' 9'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa_version: None
page: 698-711
pmid: 1
project:
- _id: fc38323b-9c52-11eb-aca3-ff8afb4a011d
grant_number: P34607
name: In vitro reconstitution of bacterial cell division
publication: Nature Microbiology
publication_identifier:
eissn:
- 2058-5276
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '20741'
relation: dissertation_contains
status: public
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Proteins containing photosynthetic reaction centre domains modulate FtsZ-based
archaeal cell division
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 9
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '15330'
abstract:
- lang: eng
text: Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth
and development by controlling plasma membrane protein composition and cargo uptake.
CME relies on the precise recruitment of regulators for vesicle maturation and
release. Homologues of components of mammalian vesicle scission are strong candidates
to be part of the scission machinery in plants, but the precise roles of these
proteins in this process are not fully understood. Here, we characterised the
roles of Plant Dynamin-Related Proteins 2 (DRP2s) and SH3-domain containing protein
2 (SH3P2), the plant homologue to Dynamins’ recruiters, like Endophilin and Amphiphysin,
in the CME by combining high-resolution imaging of endocytic events in vivo and
characterisation of the purified proteins in vitro. Although DRP2s and SH3P2 arrive
similarly late during CME and physically interact, genetic analysis of the sh3p123
triple-mutant and complementation assays with non-SH3P2-interacting DRP2 variants
suggests that SH3P2 does not directly recruit DRP2s to the site of endocytosis.
These observations imply that despite the presence of many well-conserved endocytic
components, plants have acquired a distinct mechanism for CME.
acknowledged_ssus:
- _id: EM-Fac
- _id: LifeSc
- _id: Bio
acknowledgement: "Nataliia Gnyliukh was partially funded by the European Union’s Horizon
2020 research and\r\ninnovation program (2018-2020) under the Marie Sklodowska-Curie
Grant (agreement no.\r\n665385). Taif University Researchers Supporting Project:
TURSP-HC2022/02. and Austrian\r\nScience Fund (FWF): I 6123-B.We thank Prof. Eileen
Lafer and Liping Wang for their suggestions regarding the optimisation of protein
expression and purification. We thank Prof. Sebastian Y. Bednarek for the useful
comments and constructive criticism of the project. We thank Maciek Adamowski for
providing genetic material. This research was supported by the Scientific Service
Units (SSU) of IST-Austria through resources provided by the Electron microscopy
(EMF), Lab Support Facility (LSF) (particularly Dorota Jaworska) and the Bioimaging
Facility (BIF)."
article_number: jcs.261720
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Nataliia
full_name: Gnyliukh, Nataliia
id: 390C1120-F248-11E8-B48F-1D18A9856A87
last_name: Gnyliukh
orcid: 0000-0002-2198-0509
- first_name: Alexander J
full_name: Johnson, Alexander J
id: 46A62C3A-F248-11E8-B48F-1D18A9856A87
last_name: Johnson
orcid: 0000-0002-2739-8843
- first_name: MK
full_name: Nagel, MK
last_name: Nagel
- first_name: Aline
full_name: Monzer, Aline
id: 2DB5D88C-D7B3-11E9-B8FD-7907E6697425
last_name: Monzer
- first_name: David
full_name: Babic, David
id: db566d23-f6e0-11ea-865d-e6f270e968e7
last_name: Babic
- first_name: Annamaria
full_name: Hlavata, Annamaria
id: 36062FEC-F248-11E8-B48F-1D18A9856A87
last_name: Hlavata
- first_name: SS
full_name: Alotaibi, SS
last_name: Alotaibi
- first_name: E
full_name: Isono, E
last_name: Isono
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Gnyliukh N, Johnson AJ, Nagel M, et al. Role of dynamin-related proteins 2
and SH3P2 in clathrin-mediated endocytosis in Arabidopsis thaliana. Journal
of Cell Science. 2024;137(8). doi:10.1242/jcs.261720
apa: Gnyliukh, N., Johnson, A. J., Nagel, M., Monzer, A., Babic, D., Hlavata, A.,
… Friml, J. (2024). Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated
endocytosis in Arabidopsis thaliana. Journal of Cell Science. The Company
of Biologists. https://doi.org/10.1242/jcs.261720
chicago: Gnyliukh, Nataliia, Alexander J Johnson, MK Nagel, Aline Monzer, David
Babic, Annamaria Hlavata, SS Alotaibi, E Isono, Martin Loose, and Jiří Friml.
“Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis
in Arabidopsis Thaliana.” Journal of Cell Science. The Company of Biologists,
2024. https://doi.org/10.1242/jcs.261720.
ieee: N. Gnyliukh et al., “Role of dynamin-related proteins 2 and SH3P2 in
clathrin-mediated endocytosis in Arabidopsis thaliana,” Journal of Cell Science,
vol. 137, no. 8. The Company of Biologists, 2024.
ista: Gnyliukh N, Johnson AJ, Nagel M, Monzer A, Babic D, Hlavata A, Alotaibi S,
Isono E, Loose M, Friml J. 2024. Role of dynamin-related proteins 2 and SH3P2
in clathrin-mediated endocytosis in Arabidopsis thaliana. Journal of Cell Science.
137(8), jcs. 261720.
mla: Gnyliukh, Nataliia, et al. “Role of Dynamin-Related Proteins 2 and SH3P2 in
Clathrin-Mediated Endocytosis in Arabidopsis Thaliana.” Journal of Cell Science,
vol. 137, no. 8, jcs. 261720, The Company of Biologists, 2024, doi:10.1242/jcs.261720.
short: N. Gnyliukh, A.J. Johnson, M. Nagel, A. Monzer, D. Babic, A. Hlavata, S.
Alotaibi, E. Isono, M. Loose, J. Friml, Journal of Cell Science 137 (2024).
corr_author: '1'
das_tickbox: '0'
date_created: 2024-04-19T09:54:59Z
date_published: 2024-04-01T00:00:00Z
date_updated: 2026-10-16T10:38:13Z
day: '01'
ddc:
- '570'
department:
- _id: MaLo
- _id: JiFr
- _id: CaBe
doi: 10.1242/jcs.261720
ec_funded: 1
external_id:
isi:
- '001266917100005'
pmid:
- '38506228'
file:
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checksum: 6dc023f0cc7052ad3cf0a42589d2e30f
content_type: application/pdf
creator: dernst
date_created: 2025-01-09T08:41:16Z
date_updated: 2025-01-09T08:41:16Z
file_id: '18792'
file_name: 2024_JourCellScience_Gnyliukh.pdf
file_size: 25845948
relation: main_file
success: 1
file_date_updated: 2025-01-09T08:41:16Z
fulldoi: https://doi.org/10.1242/jcs.261720
has_accepted_license: '1'
intvolume: ' 137'
isi: 1
issue: '8'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: bd76d395-d553-11ed-ba76-f678c14f9033
grant_number: I06123
name: Peptide receptors for auxin canalization in Arabidopsis
publication: Journal of Cell Science
publication_identifier:
eissn:
- 1477-9137
issn:
- 0021-9533
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
related_material:
record:
- id: '14591'
relation: earlier_version
status: public
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis
in Arabidopsis thaliana
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 137
year: '2024'
...
---
_id: '15172'
abstract:
- lang: eng
text: 'We propose a novel approach to concentration for non-independent random variables.
The main idea is to “pretend” that the random variables are independent and pay
a multiplicative price measuring how far they are from actually being independent.
This price is encapsulated in the Hellinger integral between the joint and the
product of the marginals, which is then upper bounded leveraging tensorisation
properties. Our bounds represent a natural generalisation of concentration inequalities
in the presence of dependence: we recover exactly the classical bounds (McDiarmid’s
inequality) when the random variables are independent. Furthermore, in a “large
deviations” regime, we obtain the same decay in the probability as for the independent
case, even when the random variables display non-trivial dependencies. To show
this, we consider a number of applications of interest. First, we provide a bound
for Markov chains with finite state space. Then, we consider the Simple Symmetric
Random Walk, which is a non-contracting Markov chain, and a non-Markovian setting
in which the stochastic process depends on its entire past. To conclude, we propose
an application to Markov Chain Monte Carlo methods, where our approach leads to
an improved lower bound on the minimum burn-in period required to reach a certain
accuracy. In all of these settings, we provide a regime of parameters in which
our bound fares better than what the state of the art can provide.'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Amedeo Roberto
full_name: Esposito, Amedeo Roberto
id: 9583e921-e1ad-11ec-9862-cef099626dc9
last_name: Esposito
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
citation:
ama: Esposito AR, Mondelli M. Concentration without independence via information
measures. IEEE Transactions on Information Theory. 2024;70(6):3823-3839.
doi:10.1109/TIT.2024.3367767
apa: Esposito, A. R., & Mondelli, M. (2024). Concentration without independence
via information measures. IEEE Transactions on Information Theory. IEEE.
https://doi.org/10.1109/TIT.2024.3367767
chicago: Esposito, Amedeo Roberto, and Marco Mondelli. “Concentration without Independence
via Information Measures.” IEEE Transactions on Information Theory. IEEE,
2024. https://doi.org/10.1109/TIT.2024.3367767.
ieee: A. R. Esposito and M. Mondelli, “Concentration without independence via information
measures,” IEEE Transactions on Information Theory, vol. 70, no. 6. IEEE,
pp. 3823–3839, 2024.
ista: Esposito AR, Mondelli M. 2024. Concentration without independence via information
measures. IEEE Transactions on Information Theory. 70(6), 3823–3839.
mla: Esposito, Amedeo Roberto, and Marco Mondelli. “Concentration without Independence
via Information Measures.” IEEE Transactions on Information Theory, vol.
70, no. 6, IEEE, 2024, pp. 3823–39, doi:10.1109/TIT.2024.3367767.
short: A.R. Esposito, M. Mondelli, IEEE Transactions on Information Theory 70 (2024)
3823–3839.
corr_author: '1'
das_tickbox: '0'
date_created: 2024-03-24T23:01:00Z
date_published: 2024-06-01T00:00:00Z
date_updated: 2026-10-16T10:39:43Z
day: '01'
department:
- _id: MaMo
doi: 10.1109/TIT.2024.3367767
external_id:
arxiv:
- '2303.07245'
isi:
- '001230181100001'
fulldoi: https://doi.org/10.1109/TIT.2024.3367767
intvolume: ' 70'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2303.07245
month: '06'
oa: 1
oa_version: Preprint
page: 3823-3839
project:
- _id: 059876FA-7A3F-11EA-A408-12923DDC885E
name: Prix Lopez-Loretta 2019 - Marco Mondelli
publication: IEEE Transactions on Information Theory
publication_identifier:
eissn:
- 1557-9654
issn:
- 0018-9448
publication_status: published
publisher: IEEE
quality_controlled: '1'
related_material:
record:
- id: '14922'
relation: earlier_version
status: public
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Concentration without independence via information measures
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 70
year: '2024'
...
---
_id: '17893'
abstract:
- lang: eng
text: Strong data processing inequalities (SDPI) are an important object of study
in Information Theory and have been well studied for f -divergences. Universal
upper and lower bounds have been provided along with several applications, connecting
them to impossibility (converse) results, concentration of measure, hypercontractivity,
and so on. In this paper, we study Renyi divergence and the corresponding SDPI
constant whose behavior seems to deviate from that of ordinary <1>-divergences.
In particular, one can find examples showing that the universal upper bound relating
its SDPI constant to the one of Total Variation does not hold in general. In this
work, we prove, however, that the universal lower bound involving the SDPI constant
of the Chi-square divergence does indeed hold. Furthermore, we also provide a
characterization of the distribution that achieves the supremum when is equal
to 2 and consequently compute the SDPI constant for Renyi divergence of the general
binary channel.
acknowledgement: "The work in this paper was supported in part by the Swiss National
Science Foundation under Grant 200364.\r\n"
article_processing_charge: No
arxiv: 1
author:
- first_name: Lifu
full_name: Jin, Lifu
last_name: Jin
- first_name: Amedeo Roberto
full_name: Esposito, Amedeo Roberto
id: 9583e921-e1ad-11ec-9862-cef099626dc9
last_name: Esposito
- first_name: Michael
full_name: Gastpar, Michael
last_name: Gastpar
citation:
ama: 'Jin L, Esposito AR, Gastpar M. Properties of the strong data processing constant
for Rényi divergence. In: Proceedings of the 2024 IEEE International Symposium
on Information Theory. IEEE; 2024:3178-3183. doi:10.1109/ISIT57864.2024.10619367'
apa: 'Jin, L., Esposito, A. R., & Gastpar, M. (2024). Properties of the strong
data processing constant for Rényi divergence. In Proceedings of the 2024 IEEE
International Symposium on Information Theory (pp. 3178–3183). Athens, Greece:
IEEE. https://doi.org/10.1109/ISIT57864.2024.10619367'
chicago: Jin, Lifu, Amedeo Roberto Esposito, and Michael Gastpar. “Properties of
the Strong Data Processing Constant for Rényi Divergence.” In Proceedings of
the 2024 IEEE International Symposium on Information Theory, 3178–83. IEEE,
2024. https://doi.org/10.1109/ISIT57864.2024.10619367.
ieee: L. Jin, A. R. Esposito, and M. Gastpar, “Properties of the strong data processing
constant for Rényi divergence,” in Proceedings of the 2024 IEEE International
Symposium on Information Theory, Athens, Greece, 2024, pp. 3178–3183.
ista: 'Jin L, Esposito AR, Gastpar M. 2024. Properties of the strong data processing
constant for Rényi divergence. Proceedings of the 2024 IEEE International Symposium
on Information Theory. ISIT: International Symposium on Information Theory, 3178–3183.'
mla: Jin, Lifu, et al. “Properties of the Strong Data Processing Constant for Rényi
Divergence.” Proceedings of the 2024 IEEE International Symposium on Information
Theory, IEEE, 2024, pp. 3178–83, doi:10.1109/ISIT57864.2024.10619367.
short: L. Jin, A.R. Esposito, M. Gastpar, in:, Proceedings of the 2024 IEEE International
Symposium on Information Theory, IEEE, 2024, pp. 3178–3183.
conference:
end_date: 2024-07-12
location: Athens, Greece
name: 'ISIT: International Symposium on Information Theory'
start_date: 2024-07-07
corr_author: '1'
das_tickbox: '0'
date_created: 2024-09-08T22:01:12Z
date_published: 2024-08-19T00:00:00Z
date_updated: 2026-10-16T10:38:29Z
day: '19'
department:
- _id: MaMo
doi: 10.1109/ISIT57864.2024.10619367
external_id:
arxiv:
- '2403.10656'
isi:
- '001304426903055'
fulldoi: https://doi.org/10.1109/ISIT57864.2024.10619367
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: 'https://doi.org/10.48550/arXiv.2403.10656 '
month: '08'
oa: 1
oa_version: Preprint
page: 3178-3183
publication: Proceedings of the 2024 IEEE International Symposium on Information Theory
publication_identifier:
isbn:
- '9798350382846'
issn:
- 2157-8095
publication_status: published
publisher: IEEE
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: Properties of the strong data processing constant for Rényi divergence
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
_id: '14665'
abstract:
- lang: eng
text: We derive lower bounds on the maximal rates for multiple packings in high-dimensional
Euclidean spaces. For any N > 0 and L ∈ Z ≥2 , a multiple packing is a set C of
points in R n such that any point in R n lies in the intersection of at most L
- 1 balls of radius √ nN around points in C . This is a natural generalization
of the sphere packing problem. We study the multiple packing problem for both
bounded point sets whose points have norm at most √ nP for some constant P > 0,
and unbounded point sets whose points are allowed to be anywhere in R n . Given
a well-known connection with coding theory, multiple packings can be viewed as
the Euclidean analog of list-decodable codes, which are well-studied over finite
fields. We derive the best known lower bounds on the optimal multiple packing
density. This is accomplished by establishing an inequality which relates the
list-decoding error exponent for additive white Gaussian noise channels, a quantity
of average-case nature, to the list-decoding radius, a quantity of worst-case
nature. We also derive novel bounds on the list-decoding error exponent for infinite
constellations and closed-form expressions for the list-decoding error exponents
for the power-constrained AWGN channel, which may be of independent interest beyond
multiple packing.
acknowledgement: "The work of Yihan Zhang was supported by the European Union’s Horizon
2020 Research and Innovation Programme under Grant 682203-ERC-[Inf-Speed-Tradeoff].
The work of Shashank Vatedka was supported in part by the Core Research Grant from
the Science and\r\nEngineering Research Board, India, under Grant CRG/2022/004464;
and in\r\npart by the Department of Science and Technology (DST), India, under Grant\r\nDST/INT/RUS/RSF/P-41/2020
(TPN No. 65025)."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Yihan
full_name: Zhang, Yihan
id: 2ce5da42-b2ea-11eb-bba5-9f264e9d002c
last_name: Zhang
orcid: 0000-0002-6465-6258
- first_name: Shashank
full_name: Vatedka, Shashank
last_name: Vatedka
citation:
ama: 'Zhang Y, Vatedka S. Multiple packing: Lower bounds via error exponents. IEEE
Transactions on Information Theory. 2024;70(2):1008-1039. doi:10.1109/TIT.2023.3334032'
apa: 'Zhang, Y., & Vatedka, S. (2024). Multiple packing: Lower bounds via error
exponents. IEEE Transactions on Information Theory. IEEE. https://doi.org/10.1109/TIT.2023.3334032'
chicago: 'Zhang, Yihan, and Shashank Vatedka. “Multiple Packing: Lower Bounds via
Error Exponents.” IEEE Transactions on Information Theory. IEEE, 2024.
https://doi.org/10.1109/TIT.2023.3334032.'
ieee: 'Y. Zhang and S. Vatedka, “Multiple packing: Lower bounds via error exponents,”
IEEE Transactions on Information Theory, vol. 70, no. 2. IEEE, pp. 1008–1039,
2024.'
ista: 'Zhang Y, Vatedka S. 2024. Multiple packing: Lower bounds via error exponents.
IEEE Transactions on Information Theory. 70(2), 1008–1039.'
mla: 'Zhang, Yihan, and Shashank Vatedka. “Multiple Packing: Lower Bounds via Error
Exponents.” IEEE Transactions on Information Theory, vol. 70, no. 2, IEEE,
2024, pp. 1008–39, doi:10.1109/TIT.2023.3334032.'
short: Y. Zhang, S. Vatedka, IEEE Transactions on Information Theory 70 (2024) 1008–1039.
corr_author: '1'
das_tickbox: '0'
date_created: 2023-12-10T23:01:00Z
date_published: 2024-02-01T00:00:00Z
date_updated: 2026-10-16T10:39:20Z
day: '01'
department:
- _id: MaMo
doi: 10.1109/TIT.2023.3334032
external_id:
arxiv:
- '2211.04408'
isi:
- '001166812100008'
fulldoi: https://doi.org/10.1109/TIT.2023.3334032
intvolume: ' 70'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2211.04408
month: '02'
oa: 1
oa_version: Preprint
page: 1008-1039
publication: IEEE Transactions on Information Theory
publication_identifier:
eissn:
- 1557-9654
issn:
- 0018-9448
publication_status: published
publisher: IEEE
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: yes
title: 'Multiple packing: Lower bounds via error exponents'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 70
year: '2024'
...
---
_id: '17895'
abstract:
- lang: eng
text: We propose a concatenated code construction for a class of discrete-alphabet
oblivious arbitrarily varying channels (AVCs) with cost constraints. The code
has time and space complexity polynomial in the blocklength n . It uses a Reed-Solomon
outer code, logarithmic blocklength random inner codes, and stochastic encoding
by permuting the codeword before transmission. When the channel satisfies a condition
called strong DS-nonsymmetrizability (a modified version of nonsymmetrizability
originally due to Dobrushin and Stambler), we show that the code achieves a rate
that for a variety of oblivious AVCs (such as classically studied error/erasure
channels) match the known capacities.
acknowledgement: "The work of M. Langberg and A. D. Sarwate was supported in part
by the US NSF under awards CCF-1909451 and CCF1909468. B. K. Dey was supported in
part by the Bharti Centre\r\nfor Communication in IIT Bombay. "
article_processing_charge: No
author:
- first_name: B. K.
full_name: Dey, B. K.
last_name: Dey
- first_name: S.
full_name: Jaggi, S.
last_name: Jaggi
- first_name: M.
full_name: Langberg, M.
last_name: Langberg
- first_name: A. D.
full_name: Sarwate, A. D.
last_name: Sarwate
- first_name: Yihan
full_name: Zhang, Yihan
id: 2ce5da42-b2ea-11eb-bba5-9f264e9d002c
last_name: Zhang
orcid: 0000-0002-6465-6258
citation:
ama: 'Dey BK, Jaggi S, Langberg M, Sarwate AD, Zhang Y. Computationally efficient
codes for strongly Dobrushin-Stambler nonsymmetrizable oblivious AVCs. In: Proceedings
of the 2024 IEEE International Symposium on Information Theory . IEEE; 2024:1586-1591.
doi:10.1109/ISIT57864.2024.10619362'
apa: 'Dey, B. K., Jaggi, S., Langberg, M., Sarwate, A. D., & Zhang, Y. (2024).
Computationally efficient codes for strongly Dobrushin-Stambler nonsymmetrizable
oblivious AVCs. In Proceedings of the 2024 IEEE International Symposium on
Information Theory (pp. 1586–1591). Athens, Greece: IEEE. https://doi.org/10.1109/ISIT57864.2024.10619362'
chicago: Dey, B. K., S. Jaggi, M. Langberg, A. D. Sarwate, and Yihan Zhang. “Computationally
Efficient Codes for Strongly Dobrushin-Stambler Nonsymmetrizable Oblivious AVCs.”
In Proceedings of the 2024 IEEE International Symposium on Information Theory
, 1586–91. IEEE, 2024. https://doi.org/10.1109/ISIT57864.2024.10619362.
ieee: B. K. Dey, S. Jaggi, M. Langberg, A. D. Sarwate, and Y. Zhang, “Computationally
efficient codes for strongly Dobrushin-Stambler nonsymmetrizable oblivious AVCs,”
in Proceedings of the 2024 IEEE International Symposium on Information Theory
, Athens, Greece, 2024, pp. 1586–1591.
ista: 'Dey BK, Jaggi S, Langberg M, Sarwate AD, Zhang Y. 2024. Computationally efficient
codes for strongly Dobrushin-Stambler nonsymmetrizable oblivious AVCs. Proceedings
of the 2024 IEEE International Symposium on Information Theory . ISIT: International
Symposium on Information Theory, 1586–1591.'
mla: Dey, B. K., et al. “Computationally Efficient Codes for Strongly Dobrushin-Stambler
Nonsymmetrizable Oblivious AVCs.” Proceedings of the 2024 IEEE International
Symposium on Information Theory , IEEE, 2024, pp. 1586–91, doi:10.1109/ISIT57864.2024.10619362.
short: B.K. Dey, S. Jaggi, M. Langberg, A.D. Sarwate, Y. Zhang, in:, Proceedings
of the 2024 IEEE International Symposium on Information Theory , IEEE, 2024, pp.
1586–1591.
conference:
end_date: 2024-07-12
location: Athens, Greece
name: 'ISIT: International Symposium on Information Theory'
start_date: 2024-07-07
das_tickbox: '0'
date_created: 2024-09-08T22:01:12Z
date_published: 2024-08-19T00:00:00Z
date_updated: 2026-10-16T10:39:03Z
day: '19'
department:
- _id: MaMo
doi: 10.1109/ISIT57864.2024.10619362
external_id:
isi:
- '001304426901091'
fulldoi: https://doi.org/10.1109/ISIT57864.2024.10619362
isi: 1
language:
- iso: eng
month: '08'
oa_version: None
page: 1586-1591
publication: 'Proceedings of the 2024 IEEE International Symposium on Information
Theory '
publication_identifier:
isbn:
- '9798350382846'
issn:
- 2157-8095
publication_status: published
publisher: IEEE
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: Computationally efficient codes for strongly Dobrushin-Stambler nonsymmetrizable
oblivious AVCs
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
_id: '17894'
abstract:
- lang: eng
text: 'Sibson''s α -mutual information has received renewed attention recently in
several contexts: concentration of measure under dependence, statistical learning,
hypothesis testing, and estimation theory. In this work, we introduce several
variational representations of Sibson''s α -mutual information: 1) as a supremum
over joint distributions of (a combination of) KL divergences; and 2) as a supremum
over functions of opportune expected values. Leveraging them, we produce a variety
of novel and known results, including a generalization of transportation-cost
inequalities and Fano''s inequality.'
acknowledgement: The work in this paper was supported in part by the Swiss National
Science Foundation under Grant 200364.
article_processing_charge: No
author:
- first_name: Amedeo Roberto
full_name: Esposito, Amedeo Roberto
id: 9583e921-e1ad-11ec-9862-cef099626dc9
last_name: Esposito
- first_name: Michael
full_name: Gastpar, Michael
last_name: Gastpar
- first_name: Ibrahim
full_name: Issa, Ibrahim
last_name: Issa
citation:
ama: 'Esposito AR, Gastpar M, Issa I. Variational characterizations of Sibson’s
α-mutual information. In: Proceedings of the 2024 IEEE International Symposium
on Information Theory . IEEE; 2024:2110-2115. doi:10.1109/ISIT57864.2024.10619378'
apa: 'Esposito, A. R., Gastpar, M., & Issa, I. (2024). Variational characterizations
of Sibson’s α-mutual information. In Proceedings of the 2024 IEEE International
Symposium on Information Theory (pp. 2110–2115). Athens, Greece: IEEE. https://doi.org/10.1109/ISIT57864.2024.10619378'
chicago: Esposito, Amedeo Roberto, Michael Gastpar, and Ibrahim Issa. “Variational
Characterizations of Sibson’s α-Mutual Information.” In Proceedings of the
2024 IEEE International Symposium on Information Theory , 2110–15. IEEE, 2024.
https://doi.org/10.1109/ISIT57864.2024.10619378.
ieee: A. R. Esposito, M. Gastpar, and I. Issa, “Variational characterizations of
Sibson’s α-mutual information,” in Proceedings of the 2024 IEEE International
Symposium on Information Theory , Athens, Greece, 2024, pp. 2110–2115.
ista: 'Esposito AR, Gastpar M, Issa I. 2024. Variational characterizations of Sibson’s
α-mutual information. Proceedings of the 2024 IEEE International Symposium on
Information Theory . ISIT: International Symposium on Information Theory, 2110–2115.'
mla: Esposito, Amedeo Roberto, et al. “Variational Characterizations of Sibson’s
α-Mutual Information.” Proceedings of the 2024 IEEE International Symposium
on Information Theory , IEEE, 2024, pp. 2110–15, doi:10.1109/ISIT57864.2024.10619378.
short: A.R. Esposito, M. Gastpar, I. Issa, in:, Proceedings of the 2024 IEEE International
Symposium on Information Theory , IEEE, 2024, pp. 2110–2115.
conference:
end_date: 2024-07-12
location: Athens, Greece
name: 'ISIT: International Symposium on Information Theory'
start_date: 2024-07-07
corr_author: '1'
das_tickbox: '0'
date_created: 2024-09-08T22:01:12Z
date_published: 2024-08-19T00:00:00Z
date_updated: 2026-10-16T10:38:46Z
day: '19'
department:
- _id: MaMo
doi: 10.1109/ISIT57864.2024.10619378
external_id:
isi:
- '001304426902023'
fulldoi: https://doi.org/10.1109/ISIT57864.2024.10619378
isi: 1
language:
- iso: eng
month: '08'
oa_version: None
page: 2110-2115
publication: 'Proceedings of the 2024 IEEE International Symposium on Information
Theory '
publication_identifier:
isbn:
- '9798350382846'
issn:
- 2157-8095
publication_status: published
publisher: IEEE
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: Variational characterizations of Sibson's α-mutual information
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
_id: '14932'
abstract:
- lang: eng
text: The huge antlers of the extinct Irish elk have invited evolutionary speculation
since Darwin. In the 1970s, Stephen Jay Gould presented the first extensive data
on antler size in the Irish elk and combined these with comparative data from
other deer to test the hypothesis that the gigantic antlers were the outcome of
a positive allometry that constrained large-bodied deer to have proportionally
even larger antlers. He concluded that the Irish elk had antlers as predicted
for its size and interpreted this within his emerging framework of developmental
constraints as an explanatory factor in evolution. Here we reanalyze antler allometry
based on new morphometric data for 57 taxa of the family Cervidae. We also present
a new phylogeny for the Cervidae, which we use for comparative analyses. In contrast
to Gould, we find that the antlers of Irish elk were larger than predicted from
the allometry within the true deer, Cervini, as analyzed by Gould, but follow
the allometry across Cervidae as a whole. After dissecting the discrepancy, we
reject the allometric-constraint hypothesis because, contrary to Gould, we find
no similarity between static and evolutionary allometries, and because we document
extensive non-allometric evolution of antler size across the Cervidae.
acknowledgement: "Open access funding provided by University of Oslo (incl Oslo University
Hospital).\r\nWe thank Adrian Lister, Louis Tomsett, Roberto Portela Miguez and
Roula Pappa (NHMUK), Brian O'Toole and Eileen Westwig (AMNH), Daniela Kalthoff (NHRM),
Alexander Bibl and Zachos Frank (NHMW), Darrin Lunde and John Ososky (NMNH), Matthew
Parkes and Nigel Monaghan (NMI), Elizabetta Cioppi and Luca Bellucci (IGF), and
Yoshihiro Tanaka and Hiroyuki Taruno (OMNH), who helped us in obtaining the museum
data, and a special thanks to Jørgen Sikkeland (NTNU NHM) for assistance in obtaining
the ontogenetic data for the red deer. We thank Olja Toljagic and Kjetil L. Voje
for discussions, Ayumu Tsuboi for assistance with data collection, and Jean-Michel
Gaillard and the anonymous reviewers for comments on the manuscript. We thank the
Centre of Advanced Study (CAS) at the Norwegian Academy of Sciences and Letters
for hosting us during the academic year of 2019/2020 when much of the analysis and
writing were done. MT was funded by JSPS Research Fellowship for Young Scientists
(201603238)."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Masahito
full_name: Tsuboi, Masahito
last_name: Tsuboi
- first_name: Bjørn Tore
full_name: Kopperud, Bjørn Tore
last_name: Kopperud
- first_name: Michael
full_name: Matschiner, Michael
last_name: Matschiner
- first_name: Mark
full_name: Grabowski, Mark
last_name: Grabowski
- first_name: Chrsitine
full_name: Syrowatka, Chrsitine
id: 205ffb76-7fe7-11eb-aa17-958bd11b99ad
last_name: Syrowatka
- first_name: Christophe
full_name: Pélabon, Christophe
last_name: Pélabon
- first_name: Thomas F.
full_name: Hansen, Thomas F.
last_name: Hansen
citation:
ama: Tsuboi M, Kopperud BT, Matschiner M, et al. Antler allometry, the Irish elk
and Gould revisited. Evolutionary Biology. 2024;51:149-165. doi:10.1007/s11692-023-09624-1
apa: Tsuboi, M., Kopperud, B. T., Matschiner, M., Grabowski, M., Syrowatka, C.,
Pélabon, C., & Hansen, T. F. (2024). Antler allometry, the Irish elk and Gould
revisited. Evolutionary Biology. Springer Nature. https://doi.org/10.1007/s11692-023-09624-1
chicago: Tsuboi, Masahito, Bjørn Tore Kopperud, Michael Matschiner, Mark Grabowski,
Chrsitine Syrowatka, Christophe Pélabon, and Thomas F. Hansen. “Antler Allometry,
the Irish Elk and Gould Revisited.” Evolutionary Biology. Springer Nature,
2024. https://doi.org/10.1007/s11692-023-09624-1.
ieee: M. Tsuboi et al., “Antler allometry, the Irish elk and Gould revisited,”
Evolutionary Biology, vol. 51. Springer Nature, pp. 149–165, 2024.
ista: Tsuboi M, Kopperud BT, Matschiner M, Grabowski M, Syrowatka C, Pélabon C,
Hansen TF. 2024. Antler allometry, the Irish elk and Gould revisited. Evolutionary
Biology. 51, 149–165.
mla: Tsuboi, Masahito, et al. “Antler Allometry, the Irish Elk and Gould Revisited.”
Evolutionary Biology, vol. 51, Springer Nature, 2024, pp. 149–65, doi:10.1007/s11692-023-09624-1.
short: M. Tsuboi, B.T. Kopperud, M. Matschiner, M. Grabowski, C. Syrowatka, C. Pélabon,
T.F. Hansen, Evolutionary Biology 51 (2024) 149–165.
das_tickbox: '1'
dataavailabilitystatement: All data used in this paper are available from the authors
on request.
date_created: 2024-02-04T23:00:53Z
date_published: 2024-03-01T00:00:00Z
date_updated: 2026-10-16T10:43:26Z
day: '01'
ddc:
- '570'
department:
- _id: MaRo
doi: 10.1007/s11692-023-09624-1
external_id:
isi:
- '001151285200001'
file:
- access_level: open_access
checksum: 416ab4dac751c443b9de51fb58278ff2
content_type: application/pdf
creator: dernst
date_created: 2024-07-22T11:53:43Z
date_updated: 2024-07-22T11:53:43Z
file_id: '17311'
file_name: 2024_EvolutionaryBio_Tsuboi.pdf
file_size: 1705974
relation: main_file
success: 1
file_date_updated: 2024-07-22T11:53:43Z
fulldoi: https://doi.org/10.1007/s11692-023-09624-1
has_accepted_license: '1'
intvolume: ' 51'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 149-165
publication: Evolutionary Biology
publication_identifier:
eissn:
- 1934-2845
issn:
- 0071-3260
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
researchdata_availability: upon request
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Antler allometry, the Irish elk and Gould revisited
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 51
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '17147'
abstract:
- lang: eng
text: Efficient utilization of large-scale biobank data is crucial for inferring
the genetic basis of disease and predicting health outcomes from the DNA. Yet
we lack efficient, accurate methods that scale to data where electronic health
records are linked to whole genome sequence information. To address this issue,
our paper develops a new algorithmic paradigm based on Approximate Message Passing
(AMP), which is specifically tailored for genomic prediction and association testing.
Our method yields comparable out-of-sample prediction accuracy to the state of
the art on UK Biobank traits, whilst dramatically improving computational complexity,
with a 8x-speed up in the run time. In addition, AMP theory provides a joint association
testing framework, which outperforms the currently used REGENIE method, in roughly
a third of the compute time. This first, truly large-scale application of the
AMP framework lays the foundations for a far wider range of statistical analyses
for hundreds of millions of variables measured on millions of people.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "This work was supported by a Lopez-Loreta Prize to MM, an SNSF Eccellenza
Grant to MRR (PCEGP3-181181), and core funding from ISTA. The authors thank Philip
Schniter, Matthew Stephens and Pragya Sur for valuable suggestions on an early version
of the work. The authors acknowledge the participants and investigators of the UK
Biobank study. High-performance\r\ncomputing was supported by the Scientific Service
Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp)."
article_processing_charge: No
author:
- first_name: Al
full_name: Depope, Al
id: 0b77531d-dbcd-11ea-9d1d-a8eee0bf3830
last_name: Depope
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
citation:
ama: 'Depope A, Mondelli M, Robinson MR. Inference of genetic effects via approximate
message passing. In: 2024 IEEE International Conference on Acoustics, Speech,
and Signal Processing. IEEE; 2024:13151-13155. doi:10.1109/ICASSP48485.2024.10447198'
apa: 'Depope, A., Mondelli, M., & Robinson, M. R. (2024). Inference of genetic
effects via approximate message passing. In 2024 IEEE International Conference
on Acoustics, Speech, and Signal Processing (pp. 13151–13155). Seoul, Korea:
IEEE. https://doi.org/10.1109/ICASSP48485.2024.10447198'
chicago: Depope, Al, Marco Mondelli, and Matthew Richard Robinson. “Inference of
Genetic Effects via Approximate Message Passing.” In 2024 IEEE International
Conference on Acoustics, Speech, and Signal Processing, 13151–55. IEEE, 2024.
https://doi.org/10.1109/ICASSP48485.2024.10447198.
ieee: A. Depope, M. Mondelli, and M. R. Robinson, “Inference of genetic effects
via approximate message passing,” in 2024 IEEE International Conference on
Acoustics, Speech, and Signal Processing, Seoul, Korea, 2024, pp. 13151–13155.
ista: 'Depope A, Mondelli M, Robinson MR. 2024. Inference of genetic effects via
approximate message passing. 2024 IEEE International Conference on Acoustics,
Speech, and Signal Processing. ICASSP: International Conference on Acoustics,
Speech and Signal Processing, 13151–13155.'
mla: Depope, Al, et al. “Inference of Genetic Effects via Approximate Message Passing.”
2024 IEEE International Conference on Acoustics, Speech, and Signal Processing,
IEEE, 2024, pp. 13151–55, doi:10.1109/ICASSP48485.2024.10447198.
short: A. Depope, M. Mondelli, M.R. Robinson, in:, 2024 IEEE International Conference
on Acoustics, Speech, and Signal Processing, IEEE, 2024, pp. 13151–13155.
conference:
end_date: 2024-04-19
location: Seoul, Korea
name: 'ICASSP: International Conference on Acoustics, Speech and Signal Processing'
start_date: 2024-04-14
corr_author: '1'
das_tickbox: '0'
date_created: 2024-06-16T22:01:07Z
date_published: 2024-04-19T00:00:00Z
date_updated: 2026-10-16T10:42:55Z
day: '19'
department:
- _id: MaMo
- _id: MaRo
doi: 10.1109/ICASSP48485.2024.10447198
external_id:
isi:
- '001396233806078'
fulldoi: https://doi.org/10.1109/ICASSP48485.2024.10447198
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://openreview.net/forum?id=aQYCDxfZV0
month: '04'
oa: 1
oa_version: Submitted Version
page: 13151-13155
project:
- _id: 059876FA-7A3F-11EA-A408-12923DDC885E
name: Prix Lopez-Loretta 2019 - Marco Mondelli
- _id: 9B8D11D6-BA93-11EA-9121-9846C619BF3A
grant_number: PCEGP3_181181
name: Improving estimation and prediction of common complex disease risk
publication: 2024 IEEE International Conference on Acoustics, Speech, and Signal Processing
publication_identifier:
isbn:
- '9798350344851'
issn:
- 1520-6149
publication_status: published
publisher: IEEE
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: Inference of genetic effects via approximate message passing
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '18973'
abstract:
- lang: eng
text: 'Understanding the reasons behind the exceptional success of transformers
requires a better analysis of why attention layers are suitable for NLP tasks.
In particular, such tasks require predictive models to capture contextual meaning
which often depends on one or few words, even if the sentence is long. Our work
studies this key property, dubbed word sensitivity (WS), in the prototypical setting
of random features. We show that attention layers enjoy high WS, namely, there
exists a vector in the space of embeddings that largely perturbs the random attention
features map. The argument critically exploits the role of the softmax in the
attention layer, highlighting its benefit compared to other activations (e.g.,
ReLU). In contrast, the WS of standard random features is of order 1/n−−√, n being
the number of words in the textual sample, and thus it decays with the length
of the context. We then translate these results on the word sensitivity into generalization
bounds: due to their low WS, random features provably cannot learn to distinguish
between two sentences that differ only in a single word; in contrast, due to their
high WS, random attention features have higher generalization capabilities. We
validate our theoretical results with experimental evidence over the BERT-Base
word embeddings of the imdb review dataset.'
acknowledgement: The authors were partially supported by the 2019 LopezLoreta prize,
and they would like to thank Mohammad Hossein Amani, Lorenzo Beretta, and Clement
Rebuffel for helpful discussions.
alternative_title:
- PMLR
article_processing_charge: No
arxiv: 1
author:
- first_name: Simone
full_name: Bombari, Simone
id: ca726dda-de17-11ea-bc14-f9da834f63aa
last_name: Bombari
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
citation:
ama: 'Bombari S, Mondelli M. Towards understanding the word sensitivity of attention
layers: A study via random features. In: 41st International Conference on Machine
Learning. Vol 235. ML Research Press; 2024:4300-4328.'
apa: 'Bombari, S., & Mondelli, M. (2024). Towards understanding the word sensitivity
of attention layers: A study via random features. In 41st International Conference
on Machine Learning (Vol. 235, pp. 4300–4328). Vienna, Austria: ML Research
Press.'
chicago: 'Bombari, Simone, and Marco Mondelli. “Towards Understanding the Word Sensitivity
of Attention Layers: A Study via Random Features.” In 41st International Conference
on Machine Learning, 235:4300–4328. ML Research Press, 2024.'
ieee: 'S. Bombari and M. Mondelli, “Towards understanding the word sensitivity of
attention layers: A study via random features,” in 41st International Conference
on Machine Learning, Vienna, Austria, 2024, vol. 235, pp. 4300–4328.'
ista: 'Bombari S, Mondelli M. 2024. Towards understanding the word sensitivity of
attention layers: A study via random features. 41st International Conference on
Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol.
235, 4300–4328.'
mla: 'Bombari, Simone, and Marco Mondelli. “Towards Understanding the Word Sensitivity
of Attention Layers: A Study via Random Features.” 41st International Conference
on Machine Learning, vol. 235, ML Research Press, 2024, pp. 4300–28.'
short: S. Bombari, M. Mondelli, in:, 41st International Conference on Machine Learning,
ML Research Press, 2024, pp. 4300–4328.
conference:
end_date: 2024-07-27
location: Vienna, Austria
name: 'ICML: International Conference on Machine Learning'
start_date: 2024-07-21
corr_author: '1'
das_tickbox: '0'
date_created: 2025-01-30T07:35:49Z
date_published: 2024-07-30T00:00:00Z
date_updated: 2026-10-16T10:42:17Z
day: '30'
department:
- _id: MaMo
external_id:
arxiv:
- '2402.02969'
intvolume: ' 235'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2402.02969
month: '07'
oa: 1
oa_version: Preprint
page: 4300-4328
project:
- _id: 059876FA-7A3F-11EA-A408-12923DDC885E
name: Prix Lopez-Loretta 2019 - Marco Mondelli
publication: 41st International Conference on Machine Learning
publication_identifier:
eissn:
- 2640-3498
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
related_material:
record:
- id: '22857'
relation: dissertation_contains
status: public
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: 'Towards understanding the word sensitivity of attention layers: A study via
random features'
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 235
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '18972'
abstract:
- lang: eng
text: 'Deep learning models are known to overfit and memorize spurious features
in the training dataset. While numerous empirical studies have aimed at understanding
this phenomenon, a rigorous theoretical framework to quantify it is still missing.
In this paper, we consider spurious features that are uncorrelated with the learning
task, and we provide a precise characterization of how they are memorized via
two separate terms: (i) the stability of the model with respect to individual
training samples, and (ii) the feature alignment between the spurious pattern
and the full sample. While the first term is well established in learning theory
and it is connected to the generalization error in classical work, the second
one is, to the best of our knowledge, novel. Our key technical result gives a
precise characterization of the feature alignment for the two prototypical settings
of random features (RF) and neural tangent kernel (NTK) regression. We prove that
the memorization of spurious features weakens as the generalization capability
increases and, through the analysis of the feature alignment, we unveil the role
of the model and of its activation function. Numerical experiments show the predictive
power of our theory on standard datasets (MNIST, CIFAR-10).'
acknowledgement: "The authors were partially supported by the 2019 LopezLoreta prize,
and they would like to thank (in alphabetical order) Grigorios Chrysos, Simone Maria
Giancola, Mahyar\r\nJafari Nodeh, Christoph Lampert, Marco Miani, GuanWen Qiu, and
Peter Sukenık for helpful discussions."
alternative_title:
- PMLR
article_processing_charge: No
arxiv: 1
author:
- first_name: Simone
full_name: Bombari, Simone
id: ca726dda-de17-11ea-bc14-f9da834f63aa
last_name: Bombari
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
citation:
ama: 'Bombari S, Mondelli M. How spurious features are memorized: Precise analysis
for random and NTK features. In: 41st International Conference on Machine Learning.
Vol 235. ML Research Press; 2024:4267-4299.'
apa: 'Bombari, S., & Mondelli, M. (2024). How spurious features are memorized:
Precise analysis for random and NTK features. In 41st International Conference
on Machine Learning (Vol. 235, pp. 4267–4299). Vienna, Austria: ML Research
Press.'
chicago: 'Bombari, Simone, and Marco Mondelli. “How Spurious Features Are Memorized:
Precise Analysis for Random and NTK Features.” In 41st International Conference
on Machine Learning, 235:4267–99. ML Research Press, 2024.'
ieee: 'S. Bombari and M. Mondelli, “How spurious features are memorized: Precise
analysis for random and NTK features,” in 41st International Conference on
Machine Learning, Vienna, Austria, 2024, vol. 235, pp. 4267–4299.'
ista: 'Bombari S, Mondelli M. 2024. How spurious features are memorized: Precise
analysis for random and NTK features. 41st International Conference on Machine
Learning. ICML: International Conference on Machine Learning, PMLR, vol. 235,
4267–4299.'
mla: 'Bombari, Simone, and Marco Mondelli. “How Spurious Features Are Memorized:
Precise Analysis for Random and NTK Features.” 41st International Conference
on Machine Learning, vol. 235, ML Research Press, 2024, pp. 4267–99.'
short: S. Bombari, M. Mondelli, in:, 41st International Conference on Machine Learning,
ML Research Press, 2024, pp. 4267–4299.
conference:
end_date: 2024-07-27
location: Vienna, Austria
name: 'ICML: International Conference on Machine Learning'
start_date: 2024-07-21
corr_author: '1'
das_tickbox: '0'
date_created: 2025-01-30T07:29:47Z
date_published: 2024-07-30T00:00:00Z
date_updated: 2026-10-16T10:42:37Z
day: '30'
department:
- _id: MaMo
external_id:
arxiv:
- '2305.12100'
intvolume: ' 235'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2305.12100
month: '07'
oa: 1
oa_version: Preprint
page: 4267-4299
project:
- _id: 059876FA-7A3F-11EA-A408-12923DDC885E
name: Prix Lopez-Loretta 2019 - Marco Mondelli
publication: 41st International Conference on Machine Learning
publication_identifier:
eissn:
- 2640-3498
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
related_material:
record:
- id: '22857'
relation: dissertation_contains
status: public
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: yes
title: 'How spurious features are memorized: Precise analysis for random and NTK features'
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 235
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '17330'
abstract:
- lang: eng
text: In this work we consider the list-decodability and list-recoverability of
arbitrary q -ary codes, for all integer values of q ⩾ 2. A code is called ( p
, L ) q -list-decodable if every radius pn Hamming ball contains less than L codewords;
( p , ℓ, L ) q -recoverability is a generalization where we place radius pn Hamming
balls on every point of a combinatorial rectangle with side length ℓ and again
stipulate that there be less than L codewords. Our main contribution is to precisely
calculate the maximum value of p for which there exist infinite families of positive
rate ( p , ℓ, L ) q -list-recoverable codes, the quantity we call the zero-rate
threshold . Denoting this value by p *, we in fact show that codes correcting
a p * + ε fraction of errors must have size O ε (1), i.e., independent of n .
Such a result is typically referred to as a “Plotkin bound.” To complement this,
a standard random code with expurgation construction shows that there exist positive
rate codes correcting a p * − ε fraction of errors. We also follow a classical
proof template (typically attributed to Elias and Bassalygo) to derive from the
zero-rate threshold other tradeoffs between rate and decoding radius for list-decoding
and list-recovery. Technically, proving the Plotkin bound boils down to demon-strating
the Schur convexity of a certain function defined on the q -simplex as well as
the convexity of a univariate function derived from it. We remark that an earlier
argument claimed similar results for q -ary list-decoding; however, we point out
that this earlier proof is flawed.
acknowledgement: Part of this work was done while Nicolas Resch was affiliated with
the Centrum Wiskunde & Informatica and supported in part by ERC H2020 grant No.74079
(ALGSTRONGCRYPTO). Chen Yuan is supported in part by the National Key Research and
Development Projects under Grant 2022YFA1004900 and Grant 2021YFE0109900, the National
Natural Science Foundation of China under Grant 12101403 and Grant 12031011.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Nicolas
full_name: Resch, Nicolas
last_name: Resch
- first_name: Chen
full_name: Yuan, Chen
last_name: Yuan
- first_name: Yihan
full_name: Zhang, Yihan
id: 2ce5da42-b2ea-11eb-bba5-9f264e9d002c
last_name: Zhang
orcid: 0000-0002-6465-6258
citation:
ama: Resch N, Yuan C, Zhang Y. Zero-rate thresholds and new capacity bounds for
list-decoding and list-recovery. IEEE Transactions on Information Theory.
2024;70(9):6211-6238. doi:10.1109/TIT.2024.3430842
apa: Resch, N., Yuan, C., & Zhang, Y. (2024). Zero-rate thresholds and new capacity
bounds for list-decoding and list-recovery. IEEE Transactions on Information
Theory. IEEE. https://doi.org/10.1109/TIT.2024.3430842
chicago: Resch, Nicolas, Chen Yuan, and Yihan Zhang. “Zero-Rate Thresholds and New
Capacity Bounds for List-Decoding and List-Recovery.” IEEE Transactions on
Information Theory. IEEE, 2024. https://doi.org/10.1109/TIT.2024.3430842.
ieee: N. Resch, C. Yuan, and Y. Zhang, “Zero-rate thresholds and new capacity bounds
for list-decoding and list-recovery,” IEEE Transactions on Information Theory,
vol. 70, no. 9. IEEE, pp. 6211–6238, 2024.
ista: Resch N, Yuan C, Zhang Y. 2024. Zero-rate thresholds and new capacity bounds
for list-decoding and list-recovery. IEEE Transactions on Information Theory.
70(9), 6211–6238.
mla: Resch, Nicolas, et al. “Zero-Rate Thresholds and New Capacity Bounds for List-Decoding
and List-Recovery.” IEEE Transactions on Information Theory, vol. 70, no.
9, IEEE, 2024, pp. 6211–38, doi:10.1109/TIT.2024.3430842.
short: N. Resch, C. Yuan, Y. Zhang, IEEE Transactions on Information Theory 70 (2024)
6211–6238.
corr_author: '1'
das_tickbox: '0'
date_created: 2024-07-28T22:01:10Z
date_published: 2024-09-01T00:00:00Z
date_updated: 2026-10-16T10:41:59Z
day: '01'
department:
- _id: MaMo
doi: 10.1109/TIT.2024.3430842
external_id:
arxiv:
- '2210.07754'
isi:
- '001299623600019'
fulldoi: https://doi.org/10.1109/TIT.2024.3430842
intvolume: ' 70'
isi: 1
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2210.07754
month: '09'
oa: 1
oa_version: Preprint
page: 6211-6238
publication: IEEE Transactions on Information Theory
publication_identifier:
eissn:
- 1557-9654
issn:
- 0018-9448
publication_status: published
publisher: IEEE
quality_controlled: '1'
related_material:
record:
- id: '14083'
relation: earlier_version
status: public
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 70
year: '2024'
...
---
OA_type: closed access
_id: '18652'
abstract:
- lang: eng
text: 'Over the last 70 years, information theory and coding has enabled communication
technologies that have had an astounding impact on our lives. This is possible
due to the match between encoding/decoding strategies and corresponding channel
models. Traditional studies of channels have taken one of two extremes: Shannon-theoretic
models are inherently average-case in which channel noise is governed by a memoryless
stochastic process, whereas coding-theoretic (referred to as “Hamming”) models
take a worst-case, adversarial, view of the noise. However, for several existing
and emerging communication systems the Shannon/average-case view may be too optimistic,
whereas the Hamming/worstcase view may be too pessimistic. This monograph takes
up the challenge of studying adversarial channel models that lie between the Shannon
and Hamming extremes.'
article_processing_charge: No
article_type: original
author:
- first_name: Bikash Kumar
full_name: Dey, Bikash Kumar
last_name: Dey
- first_name: Sidharth
full_name: Jaggi, Sidharth
last_name: Jaggi
- first_name: Michael
full_name: Langberg, Michael
last_name: Langberg
- first_name: Anand D.
full_name: Sarwate, Anand D.
last_name: Sarwate
- first_name: Yihan
full_name: Zhang, Yihan
id: 2ce5da42-b2ea-11eb-bba5-9f264e9d002c
last_name: Zhang
orcid: 0000-0002-6465-6258
citation:
ama: 'Dey BK, Jaggi S, Langberg M, Sarwate AD, Zhang Y. Codes for adversaries: Between
worst-case and average-case jamming. Foundations and Trends in Communications
and Information Theory. 2024;21(3-4):300-588. doi:10.1561/0100000112'
apa: 'Dey, B. K., Jaggi, S., Langberg, M., Sarwate, A. D., & Zhang, Y. (2024).
Codes for adversaries: Between worst-case and average-case jamming. Foundations
and Trends in Communications and Information Theory. Now Publishers. https://doi.org/10.1561/0100000112'
chicago: 'Dey, Bikash Kumar, Sidharth Jaggi, Michael Langberg, Anand D. Sarwate,
and Yihan Zhang. “Codes for Adversaries: Between Worst-Case and Average-Case Jamming.”
Foundations and Trends in Communications and Information Theory. Now Publishers,
2024. https://doi.org/10.1561/0100000112.'
ieee: 'B. K. Dey, S. Jaggi, M. Langberg, A. D. Sarwate, and Y. Zhang, “Codes for
adversaries: Between worst-case and average-case jamming,” Foundations and
Trends in Communications and Information Theory, vol. 21, no. 3–4. Now Publishers,
pp. 300–588, 2024.'
ista: 'Dey BK, Jaggi S, Langberg M, Sarwate AD, Zhang Y. 2024. Codes for adversaries:
Between worst-case and average-case jamming. Foundations and Trends in Communications
and Information Theory. 21(3–4), 300–588.'
mla: 'Dey, Bikash Kumar, et al. “Codes for Adversaries: Between Worst-Case and Average-Case
Jamming.” Foundations and Trends in Communications and Information Theory,
vol. 21, no. 3–4, Now Publishers, 2024, pp. 300–588, doi:10.1561/0100000112.'
short: B.K. Dey, S. Jaggi, M. Langberg, A.D. Sarwate, Y. Zhang, Foundations and
Trends in Communications and Information Theory 21 (2024) 300–588.
corr_author: '1'
date_created: 2024-12-15T23:01:50Z
date_published: 2024-12-03T00:00:00Z
date_updated: 2026-10-16T10:40:55Z
day: '03'
department:
- _id: MaMo
doi: 10.1561/0100000112
fulldoi: https://doi.org/10.1561/0100000112
intvolume: ' 21'
issue: 3-4
language:
- iso: eng
month: '12'
oa_version: None
page: 300-588
publication: Foundations and Trends in Communications and Information Theory
publication_identifier:
eissn:
- 1567-2328
issn:
- 1567-2190
publication_status: published
publisher: Now Publishers
quality_controlled: '1'
researchdata_availability: unclear
scopus_import: '1'
status: public
supplementarymaterial: unclear
title: 'Codes for adversaries: Between worst-case and average-case jamming'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 21
year: '2024'
...
---
APC_amount: 3711,01 EUR
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '18488'
abstract:
- lang: eng
text: The advancement of quantum simulators motivates the development of a theoretical
framework to assist with efficient state preparation in quantum many-body systems.
Generally, preparing a target entangled state via unitary evolution with time-dependent
couplings is a challenging task and very little is known about the existence of
solutions and their properties. In this work we develop a constructive approach
for preparing matrix product states (MPS) via continuous unitary evolution. We
provide an explicit construction of the operator that exactly implements the evolution
of a given MPS along a specified direction in its tangent space. This operator
can be written as a sum of local terms of finite range, yet it is in general non-Hermitian.
Relying on the explicit construction of the non-Hermitian generator of the dynamics,
we demonstrate the existence of a Hermitian sequence of operators that implements
the desired MPS evolution with an error that decreases exponentially with the
operator range. The construction is benchmarked on an explicit periodic trajectory
in a translationally invariant MPS manifold. We demonstrate that the Floquet unitary
generating the dynamics over one period of the trajectory features an approximate
MPS-like eigenstate embedded among a sea of thermalizing eigenstates. These results
show that our construction is not only useful for state preparation and control
of many-body systems, but also provides a generic route towards Floquet scars—periodically
driven models with quasilocal generators of dynamics that have exact MPS eigenstates
in their spectrum.
acknowledgement: We thank L. Piroli, S. Garratt, and A. Molnár for insightful discussions.
This research was funded in part by the European Research Council (ERC) under the
European Union’s Horizon 2020 research and innovation programme (Grant Agreements
No. 850899 and No. 863476), the Austrian Science Fund (FWF) (Grant DOIs 10.55776/COE1,
10.55776/P36305, and 10.55776/F71), and the European Union (NextGenerationEU). This
work was performed in part at the Aspen Center for Physics, which is supported by
National Science Foundation Grant PHY-2210452. This research was supported in part
by NSF Grant PHY-2309135 to the Kavli Institute for Theoretical Physics (KITP).
article_number: '040311'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Marko
full_name: Ljubotina, Marko
id: F75EE9BE-5C90-11EA-905D-16643DDC885E
last_name: Ljubotina
orcid: 0000-0003-0038-7068
- first_name: Elena
full_name: Petrova, Elena
id: 0ac84990-897b-11ed-a09c-f5abb56a4ede
last_name: Petrova
- first_name: Norbert
full_name: Schuch, Norbert
last_name: Schuch
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: Ljubotina M, Petrova E, Schuch N, Serbyn M. Tangent space generators of matrix
product states and exact floquet quantum scars. PRX Quantum. 2024;5(4).
doi:10.1103/prxquantum.5.040311
apa: Ljubotina, M., Petrova, E., Schuch, N., & Serbyn, M. (2024). Tangent space
generators of matrix product states and exact floquet quantum scars. PRX Quantum.
American Physical Society. https://doi.org/10.1103/prxquantum.5.040311
chicago: Ljubotina, Marko, Elena Petrova, Norbert Schuch, and Maksym Serbyn. “Tangent
Space Generators of Matrix Product States and Exact Floquet Quantum Scars.” PRX
Quantum. American Physical Society, 2024. https://doi.org/10.1103/prxquantum.5.040311.
ieee: M. Ljubotina, E. Petrova, N. Schuch, and M. Serbyn, “Tangent space generators
of matrix product states and exact floquet quantum scars,” PRX Quantum,
vol. 5, no. 4. American Physical Society, 2024.
ista: Ljubotina M, Petrova E, Schuch N, Serbyn M. 2024. Tangent space generators
of matrix product states and exact floquet quantum scars. PRX Quantum. 5(4), 040311.
mla: Ljubotina, Marko, et al. “Tangent Space Generators of Matrix Product States
and Exact Floquet Quantum Scars.” PRX Quantum, vol. 5, no. 4, 040311, American
Physical Society, 2024, doi:10.1103/prxquantum.5.040311.
short: M. Ljubotina, E. Petrova, N. Schuch, M. Serbyn, PRX Quantum 5 (2024).
corr_author: '1'
das_tickbox: '0'
date_created: 2024-10-29T16:04:05Z
date_published: 2024-10-23T00:00:00Z
date_updated: 2026-10-16T12:13:31Z
day: '23'
ddc:
- '530'
department:
- _id: MaSe
doi: 10.1103/prxquantum.5.040311
ec_funded: 1
external_id:
arxiv:
- '2403.12325'
isi:
- '001346198800001'
file:
- access_level: open_access
checksum: 2e057ba021744d0a74602517935326b3
content_type: application/pdf
creator: dernst
date_created: 2024-10-30T08:59:09Z
date_updated: 2024-10-30T08:59:09Z
file_id: '18489'
file_name: 2024_PRXQuantum_Ljubotina.pdf
file_size: 1151431
relation: main_file
success: 1
file_date_updated: 2024-10-30T08:59:09Z
fulldoi: https://doi.org/10.1103/prxquantum.5.040311
has_accepted_license: '1'
intvolume: ' 5'
isi: 1
issue: '4'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: PRX Quantum
publication_identifier:
eissn:
- 2691-3399
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Tangent space generators of matrix product states and exact floquet quantum
scars
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 5
year: '2024'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '18176'
abstract:
- lang: eng
text: Introducing a class of SU(2) invariant quantum unitary circuits generating
chiral transport, we examine the role of broken space-reflection and time-reversal
symmetries on spin-transport properties. Upon adjusting parameters of local unitary
gates, the dynamics can be either chaotic or integrable. The latter corresponds
to a generalization of the space-time discretized (Trotterized) higher-spin quantum
Heisenberg chain. We demonstrate that breaking of space-reflection symmetry results
in a drift in the dynamical spin susceptibility. Remarkably, we find a universal
drift velocity given by a simple formula, which, at zero average magnetization,
depends only on the values of SU(2) Casimir invariants associated with local spins.
In the integrable case, the drift velocity formula is confirmed analytically based
on the exact solution of thermodynamic Bethe ansatz equations. Finally, by inspecting
the large fluctuations of the time-integrated current between two halves of the
system in stationary maximum-entropy states, we demonstrate violation of the Gallavotti-Cohen
symmetry, implying that such states cannot be regarded as equilibrium ones. We
show that the scaled cumulant generating function of the time-integrated current
instead obeys a generalized fluctuation relation.
acknowledgement: "The authors thank Denis Bernard, Jérôme Dubail, Hosho Katsura, Kareljan
Schoutens, and Alberto Zorzato for stimulating discussions. This work has been supported
by: Slovenian Research Agency (ARIS) under Grants No. N1-0219 (T.P., L.Z.), No.
N1-0334 (T.P., L.Z.), No. N1-0243 (E.I.), and under Research Program P1-0402 (E.I.,
T.P., L.Z.). European Research Council (ERC) under Consolidator Grant No. 771536—NEMO
(L.Z.), Advanced Grant No.\r\n101096208—QUEST (T.P., L.Z.), and Starting Grant No.
850899—NEQuM (M.L.). Simons Foundation under Simons Junior Fellowship Grant No.
1141511 (Ž.K.). M.L. acknowledges the hospitality of the Aspen Center for Physics,
which is supported by National Science Foundation Grant No. PHY-2210452. Numerical
simulations were performed using the ITensor library [117]. "
article_number: '030356'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Lenart
full_name: Zadnik, Lenart
last_name: Zadnik
- first_name: Marko
full_name: Ljubotina, Marko
id: F75EE9BE-5C90-11EA-905D-16643DDC885E
last_name: Ljubotina
orcid: 0000-0003-0038-7068
- first_name: Žiga
full_name: Krajnik, Žiga
last_name: Krajnik
- first_name: Enej
full_name: Ilievski, Enej
last_name: Ilievski
- first_name: Tomaž
full_name: Prosen, Tomaž
last_name: Prosen
citation:
ama: Zadnik L, Ljubotina M, Krajnik Ž, Ilievski E, Prosen T. Quantum many-body spin
ratchets. PRX Quantum. 2024;5(3). doi:10.1103/PRXQuantum.5.030356
apa: Zadnik, L., Ljubotina, M., Krajnik, Ž., Ilievski, E., & Prosen, T. (2024).
Quantum many-body spin ratchets. PRX Quantum. American Physical Society.
https://doi.org/10.1103/PRXQuantum.5.030356
chicago: Zadnik, Lenart, Marko Ljubotina, Žiga Krajnik, Enej Ilievski, and Tomaž
Prosen. “Quantum Many-Body Spin Ratchets.” PRX Quantum. American Physical
Society, 2024. https://doi.org/10.1103/PRXQuantum.5.030356.
ieee: L. Zadnik, M. Ljubotina, Ž. Krajnik, E. Ilievski, and T. Prosen, “Quantum
many-body spin ratchets,” PRX Quantum, vol. 5, no. 3. American Physical
Society, 2024.
ista: Zadnik L, Ljubotina M, Krajnik Ž, Ilievski E, Prosen T. 2024. Quantum many-body
spin ratchets. PRX Quantum. 5(3), 030356.
mla: Zadnik, Lenart, et al. “Quantum Many-Body Spin Ratchets.” PRX Quantum,
vol. 5, no. 3, 030356, American Physical Society, 2024, doi:10.1103/PRXQuantum.5.030356.
short: L. Zadnik, M. Ljubotina, Ž. Krajnik, E. Ilievski, T. Prosen, PRX Quantum
5 (2024).
das_tickbox: '0'
date_created: 2024-10-06T22:01:12Z
date_published: 2024-09-25T00:00:00Z
date_updated: 2026-10-16T12:13:08Z
day: '25'
ddc:
- '530'
department:
- _id: MaSe
doi: 10.1103/PRXQuantum.5.030356
ec_funded: 1
external_id:
arxiv:
- '2406.01571'
isi:
- '001327172800001'
file:
- access_level: open_access
checksum: bc230631255d3bcf8bcbbc8fdbfefcf2
content_type: application/pdf
creator: dernst
date_created: 2024-10-07T11:04:12Z
date_updated: 2024-10-07T11:04:12Z
file_id: '18183'
file_name: 2024_PRXQuantum_Zadnik.pdf
file_size: 1061648
relation: main_file
success: 1
file_date_updated: 2024-10-07T11:04:12Z
fulldoi: https://doi.org/10.1103/PRXQuantum.5.030356
has_accepted_license: '1'
intvolume: ' 5'
isi: 1
issue: '3'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: PRX Quantum
publication_identifier:
eissn:
- 2691-3399
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Quantum many-body spin ratchets
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 5
year: '2024'
...
---
DOAJ_listed: '1'
_id: '15122'
abstract:
- lang: eng
text: Quantum computers are increasing in size and quality but are still very noisy.
Error mitigation extends the size of the quantum circuits that noisy devices can
meaningfully execute. However, state-of-the-art error mitigation methods are hard
to implement and the limited qubit connectivity in superconducting qubit devices
restricts most applications to the hardware's native topology. Here we show a
quantum approximate optimization algorithm (QAOA) on nonplanar random regular
graphs with up to 40 nodes enabled by a machine learning-based error mitigation.
We use a swap network with careful decision-variable-to-qubit mapping and a feed-forward
neural network to optimize a depth-two QAOA on up to 40 qubits. We observe a meaningful
parameter optimization for the largest graph which requires running quantum circuits
with 958 two-qubit gates. Our paper emphasizes the need to mitigate samples, and
not only expectation values, in quantum approximate optimization. These results
are a step towards executing quantum approximate optimization at a scale that
is not classically simulable. Reaching such system sizes is key to properly understanding
the true potential of heuristic algorithms like QAOA.
acknowledgement: S.H.S. acknowledges support from the IBM Ph.D. fellowship 2022 in
quantum computing. The authors also thank M. Serbyn, R. Kueng, R. A. Medina, and
S. Woerner for fruitful discussions.
article_number: '013223'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Stefan
full_name: Sack, Stefan
id: dd622248-f6e0-11ea-865d-ce382a1c81a5
last_name: Sack
orcid: 0000-0001-5400-8508
- first_name: Daniel J.
full_name: Egger, Daniel J.
last_name: Egger
citation:
ama: Sack S, Egger DJ. Large-scale quantum approximate optimization on nonplanar
graphs with machine learning noise mitigation. Physical Review Research.
2024;6(1). doi:10.1103/PhysRevResearch.6.013223
apa: Sack, S., & Egger, D. J. (2024). Large-scale quantum approximate optimization
on nonplanar graphs with machine learning noise mitigation. Physical Review
Research. American Physical Society. https://doi.org/10.1103/PhysRevResearch.6.013223
chicago: Sack, Stefan, and Daniel J. Egger. “Large-Scale Quantum Approximate Optimization
on Nonplanar Graphs with Machine Learning Noise Mitigation.” Physical Review
Research. American Physical Society, 2024. https://doi.org/10.1103/PhysRevResearch.6.013223.
ieee: S. Sack and D. J. Egger, “Large-scale quantum approximate optimization on
nonplanar graphs with machine learning noise mitigation,” Physical Review Research,
vol. 6, no. 1. American Physical Society, 2024.
ista: Sack S, Egger DJ. 2024. Large-scale quantum approximate optimization on nonplanar
graphs with machine learning noise mitigation. Physical Review Research. 6(1),
013223.
mla: Sack, Stefan, and Daniel J. Egger. “Large-Scale Quantum Approximate Optimization
on Nonplanar Graphs with Machine Learning Noise Mitigation.” Physical Review
Research, vol. 6, no. 1, 013223, American Physical Society, 2024, doi:10.1103/PhysRevResearch.6.013223.
short: S. Sack, D.J. Egger, Physical Review Research 6 (2024).
corr_author: '1'
das_tickbox: '0'
date_created: 2024-03-17T23:00:59Z
date_published: 2024-03-01T00:00:00Z
date_updated: 2026-10-16T12:12:26Z
day: '01'
ddc:
- '530'
department:
- _id: MaSe
doi: 10.1103/PhysRevResearch.6.013223
external_id:
arxiv:
- '2307.14427'
file:
- access_level: open_access
checksum: 274c9f1b15b3547a10a03f39e4ccc582
content_type: application/pdf
creator: dernst
date_created: 2024-03-19T07:16:38Z
date_updated: 2024-03-19T07:16:38Z
file_id: '15123'
file_name: 2024_PhysicalReviewResearch_Sack.pdf
file_size: 2777593
relation: main_file
success: 1
file_date_updated: 2024-03-19T07:16:38Z
fulldoi: https://doi.org/10.1103/PhysRevResearch.6.013223
has_accepted_license: '1'
intvolume: ' 6'
issue: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: bd660c93-d553-11ed-ba76-fb0fb6f49c0d
name: IBM PhD Nomination Fellowship - Stefan Sack
publication: Physical Review Research
publication_identifier:
eissn:
- 2643-1564
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Large-scale quantum approximate optimization on nonplanar graphs with machine
learning noise mitigation
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 6
year: '2024'
...