---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '15169'
abstract:
- lang: eng
text: Interpretation of extracellular recordings can be challenging due to the long
range of electric field. This challenge can be mitigated by estimating the current
source density (CSD). Here we introduce kCSD-python, an open Python package implementing
Kernel Current Source Density (kCSD) method and related tools to facilitate CSD
analysis of experimental data and the interpretation of results. We show how to
counter the limitations imposed by noise and assumptions in the method itself.
kCSD-python allows CSD estimation for an arbitrary distribution of electrodes
in 1D, 2D, and 3D, assuming distributions of sources in tissue, a slice, or in
a single cell, and includes a range of diagnostic aids. We demonstrate its features
in a Jupyter Notebook tutorial which illustrates a typical analytical workflow
and main functionalities useful in validating analysis results.
acknowledgement: 'The Python implementation of kCSD was started by Grzegorz Parka
during Google Summer of Code project through the International Neuroinformatics
Coordinating Facility. Jan Mąka implemented the first Python version of skCSD class.
This work was supported by the Polish National Science Centre (2013/08/W/NZ4/00691
to DKW; 2015/17/B/ST7/04123 to DKW). '
article_number: e1011941
article_processing_charge: Yes
article_type: original
author:
- first_name: Chaitanya
full_name: Chintaluri, Chaitanya
id: BA06AFEE-A4BA-11EA-AE5C-14673DDC885E
last_name: Chintaluri
orcid: 0000-0003-4252-1608
- first_name: Marta
full_name: Bejtka, Marta
last_name: Bejtka
- first_name: Wladyslaw
full_name: Sredniawa, Wladyslaw
last_name: Sredniawa
- first_name: Michal
full_name: Czerwinski, Michal
last_name: Czerwinski
- first_name: Jakub M.
full_name: Dzik, Jakub M.
last_name: Dzik
- first_name: Joanna
full_name: Jedrzejewska-Szmek, Joanna
last_name: Jedrzejewska-Szmek
- first_name: Daniel K.
full_name: Wojciki, Daniel K.
last_name: Wojciki
citation:
ama: Chintaluri C, Bejtka M, Sredniawa W, et al. kCSD-python, reliable current source
density estimation with quality control. PLoS Computational Biology. 2024;20(3).
doi:10.1371/journal.pcbi.1011941
apa: Chintaluri, C., Bejtka, M., Sredniawa, W., Czerwinski, M., Dzik, J. M., Jedrzejewska-Szmek,
J., & Wojciki, D. K. (2024). kCSD-python, reliable current source density
estimation with quality control. PLoS Computational Biology. Public Library
of Science. https://doi.org/10.1371/journal.pcbi.1011941
chicago: Chintaluri, Chaitanya, Marta Bejtka, Wladyslaw Sredniawa, Michal Czerwinski,
Jakub M. Dzik, Joanna Jedrzejewska-Szmek, and Daniel K. Wojciki. “KCSD-Python,
Reliable Current Source Density Estimation with Quality Control.” PLoS Computational
Biology. Public Library of Science, 2024. https://doi.org/10.1371/journal.pcbi.1011941.
ieee: C. Chintaluri et al., “kCSD-python, reliable current source density
estimation with quality control,” PLoS Computational Biology, vol. 20,
no. 3. Public Library of Science, 2024.
ista: Chintaluri C, Bejtka M, Sredniawa W, Czerwinski M, Dzik JM, Jedrzejewska-Szmek
J, Wojciki DK. 2024. kCSD-python, reliable current source density estimation with
quality control. PLoS Computational Biology. 20(3), e1011941.
mla: Chintaluri, Chaitanya, et al. “KCSD-Python, Reliable Current Source Density
Estimation with Quality Control.” PLoS Computational Biology, vol. 20,
no. 3, e1011941, Public Library of Science, 2024, doi:10.1371/journal.pcbi.1011941.
short: C. Chintaluri, M. Bejtka, W. Sredniawa, M. Czerwinski, J.M. Dzik, J. Jedrzejewska-Szmek,
D.K. Wojciki, PLoS Computational Biology 20 (2024).
corr_author: '1'
das_tickbox: '1'
date_created: 2024-03-24T23:00:59Z
date_published: 2024-03-14T00:00:00Z
date_updated: 2026-07-13T12:30:33Z
day: '14'
ddc:
- '000'
- '570'
department:
- _id: TiVo
doi: 10.1371/journal.pcbi.1011941
external_id:
isi:
- '001190689800001'
pmid:
- '38484020'
file:
- access_level: open_access
checksum: c09718d0d09614642d877d0716ce32e8
content_type: application/pdf
creator: dernst
date_created: 2025-06-25T05:47:36Z
date_updated: 2025-06-25T05:47:36Z
file_id: '19897'
file_name: 2024_PLoSCompBio_Chintaluri.pdf
file_size: 2540277
relation: main_file
success: 1
file_date_updated: 2025-06-25T05:47:36Z
has_accepted_license: '1'
intvolume: ' 20'
isi: 1
issue: '3'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS Computational Biology
publication_identifier:
eissn:
- 1553-7358
issn:
- 1553-734X
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/Neuroinflab/kCSD-python
scopus_import: '1'
status: public
title: kCSD-python, reliable current source density estimation with quality control
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 20
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'
date_created: 2024-06-16T22:01:07Z
date_published: 2024-04-19T00:00:00Z
date_updated: 2026-07-13T14:57:55Z
day: '19'
department:
- _id: MaMo
- _id: MaRo
doi: 10.1109/ICASSP48485.2024.10447198
external_id:
isi:
- '001396233806078'
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'
scopus_import: '1'
status: public
title: Inference of genetic effects via approximate message passing
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
_id: '15182'
abstract:
- lang: eng
text: Thermoelectric materials convert heat into electricity, with a broad range
of applications near room temperature (RT). However, the library of RT high-performance
materials is limited. Traditional high-temperature synthetic methods constrain
the range of materials achievable, hindering the ability to surpass crystal structure
limitations and engineer defects. Here, a solution-based synthetic approach is
introduced, enabling RT synthesis of powders and exploration of densification
at lower temperatures to influence the material's microstructure. The approach
is exemplified by Ag2Se, an n-type alternative to bismuth telluride. It is demonstrated
that the concentration of Ag interstitials, grain boundaries, and dislocations
are directly correlated to the sintering temperature, and achieve a figure of
merit of 1.1 from RT to 100 °C after optimization. Moreover, insights into and
resolve Ag2Se's challenges are provided, including stoichiometry issues leading
to irreproducible performances. This work highlights the potential of RT solution
synthesis in expanding the repertoire of high-performance thermoelectric materials
for practical applications.
acknowledged_ssus:
- _id: EM-Fac
- _id: LifeSc
- _id: NanoFab
acknowledgement: This work was supported by the Scientific Service Units (SSU) of
ISTA through resources provided by the Electron Microscopy Facility (EMF), the Lab
Support Facility (LSF), and the Nanofabrication Facility (NNF). This work was financially
supported by ISTA and the Werner Siemens Foundation. The USTEM Service Unit of the
Technical University of Vienna is acknowledged for EBSD sample preparation and analysis.
R.L.B. acknowledges the National Science Foundation for funding the mass spectrometry
analysis under award DMR 1904719. J.L. is a Serra Húnter Fellow and is grateful
to the ICREA Academia program and projects MICINN/FEDER PID2021-124572OB-C31 and
GC 2021 SGR 01061.
article_number: '2400408'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Tobias
full_name: Kleinhanns, Tobias
id: 8BD9DE16-AB3C-11E9-9C8C-2A03E6697425
last_name: Kleinhanns
orcid: 0000-0003-1537-7436
- first_name: Francesco
full_name: Milillo, Francesco
id: 38b830db-ea88-11ee-bf9b-929beaf79054
last_name: Milillo
- first_name: Mariano
full_name: Calcabrini, Mariano
id: 45D7531A-F248-11E8-B48F-1D18A9856A87
last_name: Calcabrini
orcid: 0000-0003-4566-5877
- first_name: Christine
full_name: Fiedler, Christine
id: bd3fceba-dc74-11ea-a0a7-c17f71817366
last_name: Fiedler
- first_name: Sharona
full_name: Horta, Sharona
id: 03a7e858-01b1-11ec-8b71-99ae6c4a05bc
last_name: Horta
- first_name: Daniel
full_name: Balazs, Daniel
id: 302BADF6-85FC-11EA-9E3B-B9493DDC885E
last_name: Balazs
orcid: 0000-0001-7597-043X
- first_name: Marissa J.
full_name: Strumolo, Marissa J.
last_name: Strumolo
- first_name: Roger
full_name: Hasler, Roger
last_name: Hasler
- first_name: Jordi
full_name: Llorca, Jordi
last_name: Llorca
- first_name: Michael
full_name: Tkadletz, Michael
last_name: Tkadletz
- first_name: Richard L.
full_name: Brutchey, Richard L.
last_name: Brutchey
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
citation:
ama: 'Kleinhanns T, Milillo F, Calcabrini M, et al. A route to high thermoelectric
performance: Solution‐based control of microstructure and composition in Ag2Se.
Advanced Energy Materials. 2024;14(22). doi:10.1002/aenm.202400408'
apa: 'Kleinhanns, T., Milillo, F., Calcabrini, M., Fiedler, C., Horta, S., Balazs,
D., … Ibáñez, M. (2024). A route to high thermoelectric performance: Solution‐based
control of microstructure and composition in Ag2Se. Advanced Energy Materials.
Wiley. https://doi.org/10.1002/aenm.202400408'
chicago: 'Kleinhanns, Tobias, Francesco Milillo, Mariano Calcabrini, Christine Fiedler,
Sharona Horta, Daniel Balazs, Marissa J. Strumolo, et al. “A Route to High Thermoelectric
Performance: Solution‐based Control of Microstructure and Composition in Ag2Se.”
Advanced Energy Materials. Wiley, 2024. https://doi.org/10.1002/aenm.202400408.'
ieee: 'T. Kleinhanns et al., “A route to high thermoelectric performance:
Solution‐based control of microstructure and composition in Ag2Se,” Advanced
Energy Materials, vol. 14, no. 22. Wiley, 2024.'
ista: 'Kleinhanns T, Milillo F, Calcabrini M, Fiedler C, Horta S, Balazs D, Strumolo
MJ, Hasler R, Llorca J, Tkadletz M, Brutchey RL, Ibáñez M. 2024. A route to high
thermoelectric performance: Solution‐based control of microstructure and composition
in Ag2Se. Advanced Energy Materials. 14(22), 2400408.'
mla: 'Kleinhanns, Tobias, et al. “A Route to High Thermoelectric Performance: Solution‐based
Control of Microstructure and Composition in Ag2Se.” Advanced Energy Materials,
vol. 14, no. 22, 2400408, Wiley, 2024, doi:10.1002/aenm.202400408.'
short: T. Kleinhanns, F. Milillo, M. Calcabrini, C. Fiedler, S. Horta, D. Balazs,
M.J. Strumolo, R. Hasler, J. Llorca, M. Tkadletz, R.L. Brutchey, M. Ibáñez, Advanced
Energy Materials 14 (2024).
corr_author: '1'
date_created: 2024-03-25T08:57:40Z
date_published: 2024-06-12T00:00:00Z
date_updated: 2026-07-17T07:09:41Z
day: '12'
ddc:
- '530'
department:
- _id: MaIb
- _id: LifeSc
doi: 10.1002/aenm.202400408
external_id:
isi:
- '001184300200001'
file:
- access_level: open_access
checksum: 86b26430e00d5f43ea19e9b610692ab7
content_type: application/pdf
creator: dernst
date_created: 2024-07-22T12:07:56Z
date_updated: 2024-07-22T12:07:56Z
file_id: '17314'
file_name: 2024_AdvancedEnergyMaterials_Kleinhanns.pdf
file_size: 8824301
relation: main_file
success: 1
file_date_updated: 2024-07-22T12:07:56Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
issue: '22'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 9B8F7476-BA93-11EA-9121-9846C619BF3A
name: 'HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of
Semiconductors for Waste Heat Recovery'
publication: Advanced Energy Materials
publication_identifier:
eissn:
- 1614-6840
issn:
- 1614-6832
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '22017'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'A route to high thermoelectric performance: Solution‐based control of microstructure
and composition in Ag2Se'
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 14
year: '2024'
...
---
DOAJ_listed: '1'
OA_place: repository
OA_type: gold
_id: '18951'
abstract:
- lang: eng
text: "We consider local dynamics of the dimer model (perfect matchings) on hypercubic
boxes [n] \r\nd . These consist of successively switching the dimers along alternating
cycles of prescribed (small) lengths. We study the connectivity properties of
the dimer configuration space equipped with these transitions. Answering a question
of Freire, Klivans, Milet, and Saldanha, we show that in three dimensions any
configuration admits an alternating cycle of length at most 6. We further establish
that any configuration on [n] d features order n d−2 alternating cycles of length
at most 4d−2. We also prove that the dynamics of dimer configurations on the unit
hypercube of dimension d is ergodic when switching alternating cycles of length
at most 4d−4. Finally, in the planar but non-bipartite case, we show that parallelogram-shaped
boxes in the triangular lattice are ergodic for switching alternating cycles of
lengths 4 and 6 only, thus improving a result of Kenyon and Rémila, which also
uses 8-cycles. None of our proofs make reference to height functions."
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Ivailo
full_name: Hartarsky, Ivailo
last_name: Hartarsky
- first_name: Lyuben
full_name: Lichev, Lyuben
id: 9aa8388e-d003-11ee-8458-c4c1d7447977
last_name: Lichev
- first_name: Fabio Lucio
full_name: Toninelli, Fabio Lucio
last_name: Toninelli
citation:
ama: Hartarsky I, Lichev L, Toninelli FL. Local dimer dynamics in higher dimensions.
Annales de l’Institut Henri Poincaré D, Combinatorics, Physics and their Interactions.
2024. doi:10.4171/aihpd/200
apa: Hartarsky, I., Lichev, L., & Toninelli, F. L. (2024). Local dimer dynamics
in higher dimensions. Annales de l’Institut Henri Poincaré D, Combinatorics,
Physics and Their Interactions. EMS Press. https://doi.org/10.4171/aihpd/200
chicago: Hartarsky, Ivailo, Lyuben Lichev, and Fabio Lucio Toninelli. “Local Dimer
Dynamics in Higher Dimensions.” Annales de l’Institut Henri Poincaré D, Combinatorics,
Physics and Their Interactions. EMS Press, 2024. https://doi.org/10.4171/aihpd/200.
ieee: I. Hartarsky, L. Lichev, and F. L. Toninelli, “Local dimer dynamics in higher
dimensions,” Annales de l’Institut Henri Poincaré D, Combinatorics, Physics
and their Interactions. EMS Press, 2024.
ista: Hartarsky I, Lichev L, Toninelli FL. 2024. Local dimer dynamics in higher
dimensions. Annales de l’Institut Henri Poincaré D, Combinatorics, Physics and
their Interactions.
mla: Hartarsky, Ivailo, et al. “Local Dimer Dynamics in Higher Dimensions.” Annales
de l’Institut Henri Poincaré D, Combinatorics, Physics and Their Interactions,
EMS Press, 2024, doi:10.4171/aihpd/200.
short: I. Hartarsky, L. Lichev, F.L. Toninelli, Annales de l’Institut Henri Poincaré
D, Combinatorics, Physics and Their Interactions (2024).
das_tickbox: '1'
date_created: 2025-01-29T10:57:09Z
date_published: 2024-08-26T00:00:00Z
date_updated: 2026-07-23T05:41:50Z
day: '26'
department:
- _id: MaKw
doi: 10.4171/aihpd/200
external_id:
arxiv:
- '2304.10930'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2304.10930
mathsc:
- 05B50
- 05C70
- 82C20
month: '08'
oa: 1
oa_version: Preprint
publication: Annales de l’Institut Henri Poincaré D, Combinatorics, Physics and their
Interactions
publication_identifier:
eissn:
- 2308-5835
issn:
- 2308-5827
publication_status: epub_ahead
publisher: EMS Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Local dimer dynamics in higher dimensions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
OA_place: publisher
OA_type: gold
_id: '18917'
abstract:
- lang: eng
text: "An eight-partition of a finite set of points (respectively, of a continuous
mass distribution) in ℝ³ consists of three planes that divide the space into 8
octants, such that each open octant contains at most 1/8 of the points (respectively,
of the mass). In 1966, Hadwiger showed that any mass distribution in ℝ³ admits
an eight-partition; moreover, one can prescribe the normal direction of one of
the three planes. The analogous result for finite point sets follows by a standard
limit argument.\r\nWe prove the following variant of this result: Any mass distribution
(or point set) in ℝ³ admits an eight-partition for which the intersection of two
of the planes is a line with a prescribed direction.\r\nMoreover, we present an
efficient algorithm for calculating an eight-partition of a set of n points in
ℝ³ (with prescribed normal direction of one of the planes) in time O^*(n^{5/2})."
acknowledgement: "Aronov, Boris: Work has been supported by NSF grants CCF 15-40656
and CCF 20-08551, and by grant 2014/170 from the US-Israel Binational Science Foundation.
Part of this research was conducted while BA was visiting ISTA in the summers of
2022 and 2023. The visit of BA to ISTA in the summer of 2022 was supported by an
ISTA Visiting Professorship.\r\nBasit, Abdul: Work has been supported by Australian
Research Council grant DP220102212.\r\nRamesh, Indu: Work supported by a Tandon
School of Engineering Fellowship and by NSF Grant CCF-20-08551.\r\nBA and AB would
like to thank William Steiger for insightful initial discussions of the problems
addressed in this work."
article_processing_charge: Yes
arxiv: 1
author:
- first_name: Boris
full_name: Aronov, Boris
last_name: Aronov
- first_name: Abdul
full_name: Basit, Abdul
last_name: Basit
- first_name: Indu
full_name: Ramesh, Indu
last_name: Ramesh
- first_name: Gianluca
full_name: Tasinato, Gianluca
id: 0433290C-AF8F-11E9-A4C7-F729E6697425
last_name: Tasinato
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: 'Aronov B, Basit A, Ramesh I, Tasinato G, Wagner U. Eight-partitioning points
in 3D, and efficiently too. In: 40th International Symposium on Computational
Geometry. Vol 293. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024:8:1-8:15.
doi:10.4230/LIPIcs.SoCG.2024.8'
apa: 'Aronov, B., Basit, A., Ramesh, I., Tasinato, G., & Wagner, U. (2024).
Eight-partitioning points in 3D, and efficiently too. In 40th International
Symposium on Computational Geometry (Vol. 293, p. 8:1-8:15). Athens, Greece:
Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2024.8'
chicago: Aronov, Boris, Abdul Basit, Indu Ramesh, Gianluca Tasinato, and Uli Wagner.
“Eight-Partitioning Points in 3D, and Efficiently Too.” In 40th International
Symposium on Computational Geometry, 293:8:1-8:15. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2024. https://doi.org/10.4230/LIPIcs.SoCG.2024.8.
ieee: B. Aronov, A. Basit, I. Ramesh, G. Tasinato, and U. Wagner, “Eight-partitioning
points in 3D, and efficiently too,” in 40th International Symposium on Computational
Geometry, Athens, Greece, 2024, vol. 293, p. 8:1-8:15.
ista: 'Aronov B, Basit A, Ramesh I, Tasinato G, Wagner U. 2024. Eight-partitioning
points in 3D, and efficiently too. 40th International Symposium on Computational
Geometry. SoCG: Symposium on Computational Geometry vol. 293, 8:1-8:15.'
mla: Aronov, Boris, et al. “Eight-Partitioning Points in 3D, and Efficiently Too.”
40th International Symposium on Computational Geometry, vol. 293, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2024, p. 8:1-8:15, doi:10.4230/LIPIcs.SoCG.2024.8.
short: B. Aronov, A. Basit, I. Ramesh, G. Tasinato, U. Wagner, in:, 40th International
Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2024, p. 8:1-8:15.
conference:
end_date: 2024-06-14
location: Athens, Greece
name: 'SoCG: Symposium on Computational Geometry'
start_date: 2024-06-11
corr_author: '1'
date_created: 2025-01-27T14:19:17Z
date_published: 2024-06-06T00:00:00Z
date_updated: 2026-07-23T11:14:45Z
day: '06'
ddc:
- '510'
department:
- _id: UlWa
- _id: GradSch
doi: 10.4230/LIPIcs.SoCG.2024.8
external_id:
arxiv:
- '2403.02627'
file:
- access_level: open_access
checksum: 443aa29ea5d948e917cfccd681dcf176
content_type: application/pdf
creator: dernst
date_created: 2025-01-27T14:17:37Z
date_updated: 2025-01-27T14:17:37Z
file_id: '18918'
file_name: 2024_LIPICs_Aronov.pdf
file_size: 880725
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file_date_updated: 2025-01-27T14:17:37Z
has_accepted_license: '1'
intvolume: ' 293'
language:
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month: '06'
oa: 1
oa_version: Published Version
page: 8:1-8:15
publication: 40th International Symposium on Computational Geometry
publication_identifier:
isbn:
- '9783959773164'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
related_material:
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relation: later_version
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scopus_import: '1'
status: public
title: Eight-partitioning points in 3D, and efficiently too
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 293
year: '2024'
...
---
OA_place: publisher
OA_type: gold
_id: '18557'
abstract:
- lang: eng
text: Broadcast and Consensus are most fundamental tasks in distributed computing.
These tasks are particularly challenging in dynamic networks where communication
across the network links may be unreliable, e.g., due to mobility or failures.
Over the last years, researchers have derived several impossibility results and
high time complexity lower bounds for these tasks. Specifically for the setting
where in each round of communication the adversary is allowed to choose one rooted
tree along which the information is disseminated, there is a lower as well as
an upper bound that is linear in the number n of nodes for Broadcast and for n
≥ 3 the adversary can guarantee that Consensus never happens. This setting is
called the oblivious message adversary for rooted trees. Also note that if the
adversary is allowed to choose a graph that does not contain a rooted tree, then
it can guarantee that Broadcast and Consensus will never happen. However, such
deterministic adversarial models may be overly pessimistic, as many processes
in real-world settings are stochastic in nature rather than worst-case. This paper
studies Broadcast on stochastic dynamic networks and shows that the situation
is very different to the deterministic case. In particular, we show that if information
dissemination occurs along random rooted trees and directed Erdős–Rényi graphs,
Broadcast completes in O(log n) rounds of communication with high probability.
The fundamental insight in our analysis is that key variables are mutually independent.
We then study two adversarial models, (a) one with Byzantine nodes and (b) one
where an adversary controls the edges. (a) Our techniques without Byzantine nodes
are general enough so that they can be extended to Byzantine nodes. (b) In the
spirit of smoothed analysis, we introduce the notion of randomized oblivious message
adversary, where in each round, an adversary picks k ≤ 2n/3 edges to appear in
the communication network, and then a graph (e.g. rooted tree or directed Erdős–Rényi
graph) is chosen uniformly at random among the set of all such graphs that include
these edges. We show that Broadcast completes in a finite number of rounds, which
is, e.g., O(k+log n) rounds in rooted trees. We then extend these results to All-to-All
Broadcast, and Consensus, and give lower bounds that show that most of our upper
bounds are tight.
acknowledgement: "Antoine El-Hayek: This project has received funding from the Austrian
Science Fund\r\n(FWF) grant DOI 10.55776/P33775 with additional funding from the
netidee SCIENCE Stiftung,\r\n2020–2024.\r\nMonika Henzinger: This project has received
funding from the European Research Council (ERC)\r\nunder the European Union’s Horizon
2020 research and innovation programme (MoDynStruct,\r\nNo. 101019564) and the Austrian
Science Fund (FWF) grant DOI 10.55776/Z422, grant DOI\r\n10.55776/I5982, and grant
DOI 10.55776/P33775 with additional funding from the netidee SCIENCE\r\nStiftung,
2020–2024.\r\nStefan Schmid: This project has received funding from the German Research
Foundation (DFG),\r\nSPP 2378 (project ReNO), 2023-2027."
alternative_title:
- LIPIcs
article_number: '21'
article_processing_charge: Yes
arxiv: 1
author:
- first_name: Antoine
full_name: El-Hayek, Antoine
id: 888a098e-fcac-11ee-aff7-d347be57b725
last_name: El-Hayek
orcid: 0000-0003-4268-7368
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Stefan
full_name: Schmid, Stefan
last_name: Schmid
citation:
ama: 'El-Hayek A, Henzinger M, Schmid S. Broadcast and Consensus in stochastic dynamic
networks with Byzantine nodes and adversarial edges. In: 38th International
Symposium on Distributed Computing. Vol 319. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik; 2024. doi:10.4230/LIPIcs.DISC.2024.21'
apa: 'El-Hayek, A., Henzinger, M., & Schmid, S. (2024). Broadcast and Consensus
in stochastic dynamic networks with Byzantine nodes and adversarial edges. In
38th International Symposium on Distributed Computing (Vol. 319). Madrid,
Spain: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.DISC.2024.21'
chicago: El-Hayek, Antoine, Monika Henzinger, and Stefan Schmid. “Broadcast and
Consensus in Stochastic Dynamic Networks with Byzantine Nodes and Adversarial
Edges.” In 38th International Symposium on Distributed Computing, Vol.
319. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. https://doi.org/10.4230/LIPIcs.DISC.2024.21.
ieee: A. El-Hayek, M. Henzinger, and S. Schmid, “Broadcast and Consensus in stochastic
dynamic networks with Byzantine nodes and adversarial edges,” in 38th International
Symposium on Distributed Computing, Madrid, Spain, 2024, vol. 319.
ista: 'El-Hayek A, Henzinger M, Schmid S. 2024. Broadcast and Consensus in stochastic
dynamic networks with Byzantine nodes and adversarial edges. 38th International
Symposium on Distributed Computing. DISC: Symposium on Distributed Computing,
LIPIcs, vol. 319, 21.'
mla: El-Hayek, Antoine, et al. “Broadcast and Consensus in Stochastic Dynamic Networks
with Byzantine Nodes and Adversarial Edges.” 38th International Symposium on
Distributed Computing, vol. 319, 21, Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, 2024, doi:10.4230/LIPIcs.DISC.2024.21.
short: A. El-Hayek, M. Henzinger, S. Schmid, in:, 38th International Symposium on
Distributed Computing, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.
conference:
end_date: 2024-11-01
location: Madrid, Spain
name: 'DISC: Symposium on Distributed Computing'
start_date: 2024-10-28
corr_author: '1'
date_created: 2024-11-17T23:01:47Z
date_published: 2024-10-24T00:00:00Z
date_updated: 2026-07-24T12:48:28Z
day: '24'
ddc:
- '000'
department:
- _id: MoHe
doi: 10.4230/LIPIcs.DISC.2024.21
ec_funded: 1
external_id:
arxiv:
- '2302.11988'
isi:
- '001542467600021'
file:
- access_level: open_access
checksum: d6c8277331cafa188c33ba1717206cf4
content_type: application/pdf
creator: dernst
date_created: 2024-11-18T08:02:45Z
date_updated: 2024-11-18T08:02:45Z
file_id: '18561'
file_name: 2024_LIPIcs_ElHayek.pdf
file_size: 809666
relation: main_file
success: 1
file_date_updated: 2024-11-18T08:02:45Z
has_accepted_license: '1'
intvolume: ' 319'
isi: 1
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: bd9e3a2e-d553-11ed-ba76-8aa684ce17fe
grant_number: P33775
name: Fast Algorithms for a Reactive Network Layer
- _id: bd9ca328-d553-11ed-ba76-dc4f890cfe62
call_identifier: H2020
grant_number: '101019564'
name: The design and evaluation of modern fully dynamic data structures
- _id: 34def286-11ca-11ed-8bc3-da5948e1613c
grant_number: Z00422
name: Efficient algorithms
- _id: bda196b2-d553-11ed-ba76-8e8ee6c21103
grant_number: I05982
name: Static and Dynamic Hierarchical Graph Decompositions
publication: 38th International Symposium on Distributed Computing
publication_identifier:
isbn:
- '9783959773522'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
related_material:
record:
- id: '22281'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Broadcast and Consensus in stochastic dynamic networks with Byzantine nodes
and adversarial edges
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 319
year: '2024'
...
---
_id: '17146'
abstract:
- lang: eng
text: The Upper Bound Theorem for convex polytopes implies that the p-th Betti number
of the Čech complex of any set of N points in ℝ^d and any radius satisfies β_p
= O(N^m), with m = min{p+1, ⌈d/2⌉}. We construct sets in even and odd dimensions,
which prove that this upper bound is asymptotically tight. For example, we describe
a set of N = 2(n+1) points in ℝ³ and two radii such that the first Betti number
of the Čech complex at one radius is (n+1)² - 1, and the second Betti number of
the Čech complex at the other radius is n². In particular, there is an arrangement
of n contruent balls in ℝ³ that enclose a quadratic number of voids, which answers
a long-standing open question in computational geometry.
acknowledgement: "The first author is supported by the European Research Council (ERC),
grant no. 788183, and by the DFG Collaborative Research Center TRR 109, Austrian
Science Fund (FWF), grant no. {I 02979-N35.} The second author is supported by the
European Research Council (ERC), grant \"GeoScape\" and by the Hungarian Science
Foundation (NKFIH), grant K-131529. Both authors are supported by the Wittgenstein
Prize, Austrian Science Fund (FWF), grant no. Z 342-N31.\r\nThe authors thank Matt
Kahle for communicating the question about extremal Čech complexes, Ben Schweinhart
for early discussions on the linked circles construction in three dimensions, and
Gábor Tardos for helpful remarks and suggestions."
alternative_title:
- LIPIcs
article_number: '53'
article_processing_charge: No
arxiv: 1
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: János
full_name: Pach, János
id: E62E3130-B088-11EA-B919-BF823C25FEA4
last_name: Pach
citation:
ama: 'Edelsbrunner H, Pach J. Maximum Betti numbers of Čech complexes. In: 40th
International Symposium on Computational Geometry. Vol 293. Schloss Dagstuhl
- Leibniz-Zentrum für Informatik; 2024. doi:10.4230/LIPIcs.SoCG.2024.53'
apa: 'Edelsbrunner, H., & Pach, J. (2024). Maximum Betti numbers of Čech complexes.
In 40th International Symposium on Computational Geometry (Vol. 293). Athens,
Greece: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2024.53'
chicago: Edelsbrunner, Herbert, and János Pach. “Maximum Betti Numbers of Čech Complexes.”
In 40th International Symposium on Computational Geometry, Vol. 293. Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2024. https://doi.org/10.4230/LIPIcs.SoCG.2024.53.
ieee: H. Edelsbrunner and J. Pach, “Maximum Betti numbers of Čech complexes,” in
40th International Symposium on Computational Geometry, Athens, Greece,
2024, vol. 293.
ista: 'Edelsbrunner H, Pach J. 2024. Maximum Betti numbers of Čech complexes. 40th
International Symposium on Computational Geometry. SoCG: Symposium on Computational
Geometry, LIPIcs, vol. 293, 53.'
mla: Edelsbrunner, Herbert, and János Pach. “Maximum Betti Numbers of Čech Complexes.”
40th International Symposium on Computational Geometry, vol. 293, 53, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:10.4230/LIPIcs.SoCG.2024.53.
short: H. Edelsbrunner, J. Pach, in:, 40th International Symposium on Computational
Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.
conference:
end_date: 2024-06-14
location: Athens, Greece
name: 'SoCG: Symposium on Computational Geometry'
start_date: 2024-06-11
date_created: 2024-06-16T22:01:06Z
date_published: 2024-06-01T00:00:00Z
date_updated: 2026-07-27T08:15:58Z
day: '01'
ddc:
- '510'
department:
- _id: HeEd
doi: 10.4230/LIPIcs.SoCG.2024.53
ec_funded: 1
external_id:
arxiv:
- '2310.14801'
file:
- access_level: open_access
checksum: 5442d44fb89d77477a87668d6e61aac9
content_type: application/pdf
creator: dernst
date_created: 2024-06-17T08:46:33Z
date_updated: 2024-06-17T08:46:33Z
file_id: '17152'
file_name: 2024_LIPICS_Edelsbrunner.pdf
file_size: 766562
relation: main_file
success: 1
file_date_updated: 2024-06-17T08:46:33Z
has_accepted_license: '1'
intvolume: ' 293'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 266A2E9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '788183'
name: Alpha Shape Theory Extended
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I02979-N35
name: Persistence and stability of geometric complexes
- _id: 268116B8-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00342
name: Mathematics, Computer Science
publication: 40th International Symposium on Computational Geometry
publication_identifier:
isbn:
- '9783959773164'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
related_material:
record:
- id: '20657'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Maximum Betti numbers of Čech complexes
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 293
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '17426'
abstract:
- lang: eng
text: "The robustness of neural networks against input perturbations with bounded\r\nmagnitude
represents a serious concern in the deployment of deep learning\r\nmodels in safety-critical
systems. Recently, the scientific community has\r\nfocused on enhancing certifiable
robustness guarantees by crafting 1-Lipschitz\r\nneural networks that leverage
Lipschitz bounded dense and convolutional layers.\r\nAlthough different methods
have been proposed in the literature to achieve this\r\ngoal, understanding the
performance of such methods is not straightforward,\r\nsince different metrics
can be relevant (e.g., training time, memory usage,\r\naccuracy, certifiable robustness)
for different applications. For this reason,\r\nthis work provides a thorough
theoretical and empirical comparison between\r\nmethods by evaluating them in
terms of memory usage, speed, and certifiable\r\nrobust accuracy. The paper also
provides some guidelines and recommendations to\r\nsupport the user in selecting
the methods that work best depending on the\r\navailable resources. We provide
code at\r\nhttps://github.com/berndprach/1LipschitzLayersCompared."
acknowledgement: "This work was partially supported by project SERICS (PE00000014)
under the MUR National Recovery and Resilience Plan funded by the European Union
- NextGenerationEU.\r\n"
article_processing_charge: No
arxiv: 1
author:
- first_name: Bernd
full_name: Prach, Bernd
id: 2D561D42-C427-11E9-89B4-9C1AE6697425
last_name: Prach
- first_name: Fabio
full_name: Brau, Fabio
last_name: Brau
- first_name: Giorgio
full_name: Buttazzo, Giorgio
last_name: Buttazzo
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Prach B, Brau F, Buttazzo G, Lampert C. 1-Lipschitz layers compared: Memory,
speed, and certifiable robustness. In: Proceedings of the IEEE/CVF Conference
on Computer Vision and Pattern Recognition. Computer Vision Foundation; 2024:24574-24583.
doi:10.1109/CVPR52733.2024.02320'
apa: 'Prach, B., Brau, F., Buttazzo, G., & Lampert, C. (2024). 1-Lipschitz layers
compared: Memory, speed, and certifiable robustness. In Proceedings of the
IEEE/CVF Conference on Computer Vision and Pattern Recognition (pp. 24574–24583).
Seattle, WA, United States: Computer Vision Foundation. https://doi.org/10.1109/CVPR52733.2024.02320'
chicago: 'Prach, Bernd, Fabio Brau, Giorgio Buttazzo, and Christoph Lampert. “1-Lipschitz
Layers Compared: Memory, Speed, and Certifiable Robustness.” In Proceedings
of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, 24574–83.
Computer Vision Foundation, 2024. https://doi.org/10.1109/CVPR52733.2024.02320.'
ieee: 'B. Prach, F. Brau, G. Buttazzo, and C. Lampert, “1-Lipschitz layers compared:
Memory, speed, and certifiable robustness,” in Proceedings of the IEEE/CVF
Conference on Computer Vision and Pattern Recognition, Seattle, WA, United
States, 2024, pp. 24574–24583.'
ista: 'Prach B, Brau F, Buttazzo G, Lampert C. 2024. 1-Lipschitz layers compared:
Memory, speed, and certifiable robustness. Proceedings of the IEEE/CVF Conference
on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision
and Pattern Recognition, 24574–24583.'
mla: 'Prach, Bernd, et al. “1-Lipschitz Layers Compared: Memory, Speed, and Certifiable
Robustness.” Proceedings of the IEEE/CVF Conference on Computer Vision and
Pattern Recognition, Computer Vision Foundation, 2024, pp. 24574–83, doi:10.1109/CVPR52733.2024.02320.'
short: B. Prach, F. Brau, G. Buttazzo, C. Lampert, in:, Proceedings of the IEEE/CVF
Conference on Computer Vision and Pattern Recognition, Computer Vision Foundation,
2024, pp. 24574–24583.
conference:
end_date: 2024-06-22
location: Seattle, WA, United States
name: 'CVPR: Conference on Computer Vision and Pattern Recognition'
start_date: 2024-06-16
corr_author: '1'
date_created: 2024-08-14T08:42:32Z
date_published: 2024-06-01T00:00:00Z
date_updated: 2026-07-27T12:47:43Z
day: '01'
department:
- _id: GradSch
- _id: ChLa
doi: 10.1109/CVPR52733.2024.02320
external_id:
arxiv:
- '2311.16833'
isi:
- '001344387500055'
has_accepted_license: '1'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2311.16833
month: '06'
oa: 1
oa_version: Preprint
page: 24574-24583
publication: Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern
Recognition
publication_status: published
publisher: Computer Vision Foundation
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/berndprach/1LipschitzLayersCompared
record:
- id: '19759'
relation: dissertation_contains
status: public
status: public
title: '1-Lipschitz layers compared: Memory, speed, and certifiable robustness'
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
OA_place: repository
_id: '18874'
abstract:
- lang: eng
text: "Despite extensive research since the community learned about adversarial\r\nexamples
10 years ago, we still do not know how to train high-accuracy\r\nclassifiers that
are guaranteed to be robust to small perturbations of their\r\ninputs. Previous
works often argued that this might be because no classifier\r\nexists that is
robust and accurate at the same time. However, in computer\r\nvision this assumption
does not match reality where humans are usually accurate\r\nand robust on most
tasks of interest. We offer an alternative explanation and\r\nshow that in certain
settings robust generalization is only possible with\r\nunrealistically large
amounts of data. More precisely we find a setting where a\r\nrobust classifier
exists, it is easy to learn an accurate classifier, yet it\r\nrequires an exponential
amount of data to learn a robust classifier. Based on\r\nthis theoretical result,
we explore how well robust classifiers generalize on\r\ndatasets such as CIFAR-10.
We come to the conclusion that on this datasets, the\r\nlimitation of current
robust models also lies in the generalization, and that\r\nthey require a lot
of data to do well on the test set. We also show that the\r\nproblem is not in
the expressiveness or generalization capabilities of current\r\narchitectures,
and that there are low magnitude features in the data which are\r\nuseful for
non-robust generalization but are not available for robust\r\nclassifiers."
article_number: '2412.04245'
article_processing_charge: No
arxiv: 1
author:
- first_name: Bernd
full_name: Prach, Bernd
id: 2D561D42-C427-11E9-89B4-9C1AE6697425
last_name: Prach
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: Prach B, Lampert C. Intriguing properties of robust classification. arXiv.
doi:10.48550/arXiv.2412.04245
apa: Prach, B., & Lampert, C. (n.d.). Intriguing properties of robust classification.
arXiv. https://doi.org/10.48550/arXiv.2412.04245
chicago: Prach, Bernd, and Christoph Lampert. “Intriguing Properties of Robust Classification.”
ArXiv, n.d. https://doi.org/10.48550/arXiv.2412.04245.
ieee: B. Prach and C. Lampert, “Intriguing properties of robust classification,”
arXiv. .
ista: Prach B, Lampert C. Intriguing properties of robust classification. arXiv,
2412.04245.
mla: Prach, Bernd, and Christoph Lampert. “Intriguing Properties of Robust Classification.”
ArXiv, 2412.04245, doi:10.48550/arXiv.2412.04245.
short: B. Prach, C. Lampert, ArXiv (n.d.).
corr_author: '1'
date_created: 2025-01-24T16:57:29Z
date_published: 2024-12-05T00:00:00Z
date_updated: 2026-07-27T12:47:43Z
day: '05'
department:
- _id: GradSch
- _id: ChLa
doi: 10.48550/arXiv.2412.04245
external_id:
arxiv:
- '2412.04245'
language:
- iso: eng
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month: '12'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: draft
related_material:
record:
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status: public
title: Intriguing properties of robust classification
type: preprint
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2024'
...
---
APC_amount: 2748 EUR
OA_place: publisher
OA_type: hybrid
_id: '17634'
abstract:
- lang: eng
text: System behaviors are traditionally evaluated through binary classifications
of correctness, which do not suffice for properties involving quantitative aspects
of systems and executions. Quantitative automata offer a more nuanced approach,
mapping each execution to a real number by incorporating weighted transitions
and value functions generalizing acceptance conditions. In this paper, we introduce
QuAK, the first tool designed to automate the analysis of quantitative automata.
QuAK currently supports a variety of quantitative automaton types, including Inf,
Sup, LimInf, LimSup, LimInfAvg, and LimSupAvg automata, and implements decision
procedures for problems such as emptiness, universality, inclusion, equivalence,
as well as for checking whether an automaton is safe, live, or constant. Additionally,
QuAK is able to compute extremal values when possible, construct safety-liveness
decompositions, and monitor system behaviors. We demonstrate the effectiveness
of QuAK through experiments focusing on the inclusion, constant-function check,
and monitoring problems.
acknowledgement: This work was supported in part by the ERC-2020-AdG 101020093. N.
Mazzocchi was affiliated with ISTA when his collaboration started.
alternative_title:
- LNCS
article_processing_charge: Yes (in subscription journal)
arxiv: 1
author:
- first_name: Marek
full_name: Chalupa, Marek
id: 87e34708-d6c6-11ec-9f5b-9391e7be2463
last_name: Chalupa
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Nicolas Adrien
full_name: Mazzocchi, Nicolas Adrien
id: b26baa86-3308-11ec-87b0-8990f34baa85
last_name: Mazzocchi
- first_name: Naci E
full_name: Sarac, Naci E
id: 8C6B42F8-C8E6-11E9-A03A-F2DCE5697425
last_name: Sarac
citation:
ama: 'Chalupa M, Henzinger TA, Mazzocchi NA, Sarac NE. QuAK: Quantitative Automata
Kit. In: 12th International Symposium on Leveraging Applications of Formal
Methods, Verification and Validation. Vol 15222. Springer Nature; 2024:3-20.
doi:10.1007/978-3-031-75387-9_1'
apa: 'Chalupa, M., Henzinger, T. A., Mazzocchi, N. A., & Sarac, N. E. (2024).
QuAK: Quantitative Automata Kit. In 12th International Symposium on Leveraging
Applications of Formal Methods, Verification and Validation (Vol. 15222, pp.
3–20). Crete, Greece: Springer Nature. https://doi.org/10.1007/978-3-031-75387-9_1'
chicago: 'Chalupa, Marek, Thomas A Henzinger, Nicolas Adrien Mazzocchi, and Naci
E Sarac. “QuAK: Quantitative Automata Kit.” In 12th International Symposium
on Leveraging Applications of Formal Methods, Verification and Validation,
15222:3–20. Springer Nature, 2024. https://doi.org/10.1007/978-3-031-75387-9_1.'
ieee: 'M. Chalupa, T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “QuAK: Quantitative
Automata Kit,” in 12th International Symposium on Leveraging Applications of
Formal Methods, Verification and Validation, Crete, Greece, 2024, vol. 15222,
pp. 3–20.'
ista: 'Chalupa M, Henzinger TA, Mazzocchi NA, Sarac NE. 2024. QuAK: Quantitative
Automata Kit. 12th International Symposium on Leveraging Applications of Formal
Methods, Verification and Validation. ISoLA: International Symposium on Leveraging
Applications, LNCS, vol. 15222, 3–20.'
mla: 'Chalupa, Marek, et al. “QuAK: Quantitative Automata Kit.” 12th International
Symposium on Leveraging Applications of Formal Methods, Verification and Validation,
vol. 15222, Springer Nature, 2024, pp. 3–20, doi:10.1007/978-3-031-75387-9_1.'
short: M. Chalupa, T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, in:, 12th International
Symposium on Leveraging Applications of Formal Methods, Verification and Validation,
Springer Nature, 2024, pp. 3–20.
conference:
end_date: 2024-10-31
location: Crete, Greece
name: 'ISoLA: International Symposium on Leveraging Applications'
start_date: 2024-10-27
corr_author: '1'
date_created: 2024-09-05T14:27:08Z
date_published: 2024-10-26T00:00:00Z
date_updated: 2026-07-27T12:48:18Z
day: '26'
ddc:
- '000'
department:
- _id: GradSch
- _id: ToHe
doi: 10.1007/978-3-031-75387-9_1
ec_funded: 1
external_id:
arxiv:
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isi:
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oa_version: Published Version
page: 3-20
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call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: 12th International Symposium on Leveraging Applications of Formal Methods,
Verification and Validation
publication_identifier:
eissn:
- 1611-3349
isbn:
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issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
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relation: dissertation_contains
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scopus_import: '1'
status: public
title: 'QuAK: Quantitative Automata Kit'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 15222
year: '2024'
...
---
_id: '18121'
abstract:
- lang: eng
text: It is known that sparsity can improve interpretability for deep neural networks.
However, existing methods in the area either require networks that are pre-trained
with sparsity constraints, or impose sparsity after the fact, altering the network’s
general behavior. In this paper, we demonstrate, for the first time, that sparsity
can instead be incorporated into the interpretation process itself, as a sample-specific
preprocessing step. Unlike previous work, this approach, which we call SPADE,
does not place constraints on the trained model and does not affect its behavior
during inference on the sample. Given a trained model and a target sample, SPADE
uses sample-targeted pruning to provide a "trace" of the network’s execution on
the sample, reducing the network to the most important connections prior to computing
an interpretation. We demonstrate that preprocessing with SPADE significantly
increases the accuracy of image saliency maps across several interpretability
methods. Additionally, SPADE improves the usefulness of neuron visualizations,
aiding humans in reasoning about network behavior. Our code is available at https://github.com/IST-DASLab/SPADE.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: The authors would like to thank Stephen Casper and Tony Wang for
their feedback on this work, and Eldar Kurtic for his advice on aspects of the project.
This research was supported by the Scientific Service Units (SSU) of IST Austria
through resources provided by Scientific Computing (SciComp). EI was supported in
part by the FWF DK VGSCO, grant agreement number W1260-N35.
alternative_title:
- PMLR
article_processing_charge: No
arxiv: 1
author:
- first_name: Arshia Soltani
full_name: Moakhar, Arshia Soltani
last_name: Moakhar
- first_name: Eugenia B
full_name: Iofinova, Eugenia B
id: f9a17499-f6e0-11ea-865d-fdf9a3f77117
last_name: Iofinova
orcid: 0000-0002-7778-3221
- first_name: Elias
full_name: Frantar, Elias
id: 09a8f98d-ec99-11ea-ae11-c063a7b7fe5f
last_name: Frantar
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
citation:
ama: 'Moakhar AS, Iofinova EB, Frantar E, Alistarh D-A. SPADE: Sparsity-guided debugging
for deep neural networks. In: Proceedings of the 41st International Conference
on Machine Learning. Vol 235. ML Research Press; 2024:45955-45987.'
apa: 'Moakhar, A. S., Iofinova, E. B., Frantar, E., & Alistarh, D.-A. (2024).
SPADE: Sparsity-guided debugging for deep neural networks. In Proceedings of
the 41st International Conference on Machine Learning (Vol. 235, pp. 45955–45987).
Vienna, Austria: ML Research Press.'
chicago: 'Moakhar, Arshia Soltani, Eugenia B Iofinova, Elias Frantar, and Dan-Adrian
Alistarh. “SPADE: Sparsity-Guided Debugging for Deep Neural Networks.” In Proceedings
of the 41st International Conference on Machine Learning, 235:45955–87. ML
Research Press, 2024.'
ieee: 'A. S. Moakhar, E. B. Iofinova, E. Frantar, and D.-A. Alistarh, “SPADE: Sparsity-guided
debugging for deep neural networks,” in Proceedings of the 41st International
Conference on Machine Learning, Vienna, Austria, 2024, vol. 235, pp. 45955–45987.'
ista: 'Moakhar AS, Iofinova EB, Frantar E, Alistarh D-A. 2024. SPADE: Sparsity-guided
debugging for deep neural networks. Proceedings of the 41st International Conference
on Machine Learning. ICML: International Conference on Machine Learning, PMLR,
vol. 235, 45955–45987.'
mla: 'Moakhar, Arshia Soltani, et al. “SPADE: Sparsity-Guided Debugging for Deep
Neural Networks.” Proceedings of the 41st International Conference on Machine
Learning, vol. 235, ML Research Press, 2024, pp. 45955–87.'
short: A.S. Moakhar, E.B. Iofinova, E. Frantar, D.-A. Alistarh, in:, Proceedings
of the 41st International Conference on Machine Learning, ML Research Press, 2024,
pp. 45955–45987.
conference:
end_date: 2024-07-27
location: Vienna, Austria
name: 'ICML: International Conference on Machine Learning'
start_date: 2024-07-21
corr_author: '1'
date_created: 2024-09-22T22:01:46Z
date_published: 2024-09-01T00:00:00Z
date_updated: 2026-07-27T12:50:03Z
day: '01'
department:
- _id: DaAl
external_id:
arxiv:
- '2310.04519'
intvolume: ' 235'
language:
- iso: eng
main_file_link:
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url: https://doi.org/10.48550/arXiv.2310.04519
month: '09'
oa: 1
oa_version: Preprint
page: 45955-45987
project:
- _id: 9B9290DE-BA93-11EA-9121-9846C619BF3A
grant_number: W1260-N35
name: Vienna Graduate School on Computational Optimization
publication: Proceedings of the 41st International Conference on Machine Learning
publication_identifier:
eissn:
- 2640-3498
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/IST-DASLab/SPADE
record:
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relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'SPADE: Sparsity-guided debugging for deep neural networks'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 235
year: '2024'
...
---
APC_amount: 3149,96 EUR
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '15297'
abstract:
- lang: eng
text: Populations evolve by accumulating advantageous mutations. Every population
has some spatial structure that can be modeled by an underlying network. The network
then influences the probability that new advantageous mutations fixate. Amplifiers
of selection are networks that increase the fixation probability of advantageous
mutants, as compared to the unstructured fully-connected network. Whether or not
a network is an amplifier depends on the choice of the random process that governs
the evolutionary dynamics. Two popular choices are Moran process with Birth-death
updating and Moran process with death-Birth updating. Interestingly, while some
networks are amplifiers under Birth-death updating and other networks are amplifiers
under death-Birth updating, so far no spatial structures have been found that
function as an amplifier under both types of updating simultaneously. In this
work, we identify networks that act as amplifiers of selection under both versions
of the Moran process. The amplifiers are robust, modular, and increase fixation
probability for any mutant fitness advantage in a range r ∈ (1, 1.2). To complement
this positive result, we also prove that for certain quantities closely related
to fixation probability, it is impossible to improve them simultaneously for both
versions of the Moran process. Together, our results highlight how the two versions
of the Moran process differ and what they have in common.
acknowledgement: "We thank Gavin Rees for helpful discussions. J.S., S.J., and K.C
were supported by\r\nEuropean Research Council (ERC) CoG 863818 (ForM-SMArt). J.T
was supported by Center for Foundations of Modern Computer Science (Charles University
project UNCE/SCI/004) and by the project PRIMUS/24/SCI/012 from Charles University. "
article_number: e1012008
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Jakub
full_name: Svoboda, Jakub
id: 130759D2-D7DD-11E9-87D2-DE0DE6697425
last_name: Svoboda
orcid: 0000-0002-1419-3267
- first_name: Soham Shrikant
full_name: Joshi, Soham Shrikant
id: f97aac0e-f57c-11ee-93d0-a5a82d8df168
last_name: Joshi
- first_name: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: Svoboda J, Joshi SS, Tkadlec J, Chatterjee K. Amplifiers of selection for the
Moran process with both Birth-death and death-Birth updating. PLoS Computational
Biology. 2024;20(3). doi:10.1371/journal.pcbi.1012008
apa: Svoboda, J., Joshi, S. S., Tkadlec, J., & Chatterjee, K. (2024). Amplifiers
of selection for the Moran process with both Birth-death and death-Birth updating.
PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1012008
chicago: Svoboda, Jakub, Soham Shrikant Joshi, Josef Tkadlec, and Krishnendu Chatterjee.
“Amplifiers of Selection for the Moran Process with Both Birth-Death and Death-Birth
Updating.” PLoS Computational Biology. Public Library of Science, 2024.
https://doi.org/10.1371/journal.pcbi.1012008.
ieee: J. Svoboda, S. S. Joshi, J. Tkadlec, and K. Chatterjee, “Amplifiers of selection
for the Moran process with both Birth-death and death-Birth updating,” PLoS
Computational Biology, vol. 20, no. 3. Public Library of Science, 2024.
ista: Svoboda J, Joshi SS, Tkadlec J, Chatterjee K. 2024. Amplifiers of selection
for the Moran process with both Birth-death and death-Birth updating. PLoS Computational
Biology. 20(3), e1012008.
mla: Svoboda, Jakub, et al. “Amplifiers of Selection for the Moran Process with
Both Birth-Death and Death-Birth Updating.” PLoS Computational Biology,
vol. 20, no. 3, e1012008, Public Library of Science, 2024, doi:10.1371/journal.pcbi.1012008.
short: J. Svoboda, S.S. Joshi, J. Tkadlec, K. Chatterjee, PLoS Computational Biology
20 (2024).
corr_author: '1'
date_created: 2024-04-07T22:00:55Z
date_published: 2024-03-29T00:00:00Z
date_updated: 2026-07-27T12:52:03Z
day: '29'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1371/journal.pcbi.1012008
ec_funded: 1
external_id:
arxiv:
- '2401.14914'
isi:
- '001194482400002'
file:
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checksum: a511cf369d9172beb123fe73f291b5cc
content_type: application/pdf
creator: dernst
date_created: 2024-08-20T10:52:28Z
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file_name: 2024_PloSComBio_Svoboda.pdf
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has_accepted_license: '1'
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month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: PLoS Computational Biology
publication_identifier:
eissn:
- 1553-7358
issn:
- 1553-734X
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
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relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Amplifiers of selection for the Moran process with both Birth-death and death-Birth
updating
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: 20
year: '2024'
...
---
APC_amount: 3143,76 EUR
OA_place: publisher
OA_type: hybrid
_id: '18703'
abstract:
- lang: eng
text: 'Spatial games provide a simple and elegant mathematical model to study the
evolution of cooperation in networks. In spatial games, individuals reside in
vertices, adopt simple strategies, and interact with neighbors to receive a payoff.
Depending on their own and neighbors’ payoffs, individuals can change their strategy.
The payoff is determined by the Prisoners’ Dilemma, a classical matrix game, where
players cooperate or defect. While cooperation is the desired behavior, defection
provides a higher payoff for a selfish individual. There are many theoretical
and empirical studies related to the role of the network in the evolution of cooperation.
However, the fundamental question of whether there exist networks that for low
initial cooperation rate ensure a high chance of fixation, i.e., cooperation spreads
across the whole population, has remained elusive for spatial games with strong
selection. In this work, we answer this fundamental question in the affirmative
by presenting network structures that ensure high fixation probability for cooperators
in the strong selection regime. Besides, our structures have many desirable properties:
(a) they ensure the spread of cooperation even for a low initial density of cooperation
and high temptation of defection, (b) they have constant degrees, and (c) the
number of steps, until cooperation spreads, is at most quadratic in the size of
the network.'
acknowledgement: J.S. and K.C. were supported by the European Research Council CoG
863818 (ForM-SMArt) and Austrian Science Fund 10.55776/COE12.
article_number: e2405605121
article_processing_charge: Yes
article_type: original
author:
- first_name: Jakub
full_name: Svoboda, Jakub
id: 130759D2-D7DD-11E9-87D2-DE0DE6697425
last_name: Svoboda
orcid: 0000-0002-1419-3267
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: Svoboda J, Chatterjee K. Density amplifiers of cooperation for spatial games.
Proceedings of the National Academy of Sciences of the United States of America.
2024;121(50). doi:10.1073/pnas.2405605121
apa: Svoboda, J., & Chatterjee, K. (2024). Density amplifiers of cooperation
for spatial games. Proceedings of the National Academy of Sciences of the United
States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2405605121
chicago: Svoboda, Jakub, and Krishnendu Chatterjee. “Density Amplifiers of Cooperation
for Spatial Games.” Proceedings of the National Academy of Sciences of the
United States of America. National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2405605121.
ieee: J. Svoboda and K. Chatterjee, “Density amplifiers of cooperation for spatial
games,” Proceedings of the National Academy of Sciences of the United States
of America, vol. 121, no. 50. National Academy of Sciences, 2024.
ista: Svoboda J, Chatterjee K. 2024. Density amplifiers of cooperation for spatial
games. Proceedings of the National Academy of Sciences of the United States of
America. 121(50), e2405605121.
mla: Svoboda, Jakub, and Krishnendu Chatterjee. “Density Amplifiers of Cooperation
for Spatial Games.” Proceedings of the National Academy of Sciences of the
United States of America, vol. 121, no. 50, e2405605121, National Academy
of Sciences, 2024, doi:10.1073/pnas.2405605121.
short: J. Svoboda, K. Chatterjee, Proceedings of the National Academy of Sciences
of the United States of America 121 (2024).
corr_author: '1'
date_created: 2024-12-22T23:01:47Z
date_published: 2024-12-10T00:00:00Z
date_updated: 2026-07-27T12:52:03Z
day: '10'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1073/pnas.2405605121
ec_funded: 1
external_id:
isi:
- '001379596100014'
pmid:
- '39642209'
file:
- access_level: open_access
checksum: 0115e9090b478e0644308c6dab58605b
content_type: application/pdf
creator: dernst
date_created: 2025-01-02T12:14:15Z
date_updated: 2025-01-02T12:14:15Z
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file_name: 2024_PNAS_Svoboda.pdf
file_size: 2491151
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intvolume: ' 121'
isi: 1
issue: '50'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
record:
- id: '20138'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Density amplifiers of cooperation for spatial games
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 121
year: '2024'
...
---
OA_place: repository
_id: '18689'
abstract:
- lang: eng
text: Multiplexed fluorescence microscopy imaging is widely used in biomedical applications.
However, simultaneous imaging of multiple fluorophores can result in spectral
leaks and overlapping, which greatly degrades image quality and subsequent analysis.
Existing popular spectral unmixing methods are mainly based on computational intensive
linear models and the performance is heavily dependent on the reference spectra,
which may greatly preclude its further applications. In this paper, we propose
a deep learning-based blindly spectral unmixing method, termed AutoUnmix, to imitate
the physical spectral mixing process. A tranfer learning framework is further
devised to allow our AutoUnmix adapting to a variety of imaging systems without
retraining the network. Our proposed method has demonstrated real-time unmixing
capabilities, surpassing existing methods by up to 100-fold in terms of unmixing
speed. We further validate the reconstruction performance on both synthetic datasets
and biological samples. The unmixing results of AutoUnmix achieve a highest SSIM
of 0.99 in both three- and four-color imaging, with nearly up to 20% higher than
other popular unmixing methods. Due to the desirable property of data independency
and superior blind unmixing performance, we believe AutoUnmix is a powerful tool
to study the interaction process of different organelles labeled by multiple fluorophores.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: M-Shop
- _id: E-Lib
acknowledgement: "We gratefully acknowledge support by the Scientific Service Units
at ISTA, including the Imaging and Optics and Lab Support facilities and the mechanical
workshop and Library. We thank Philipp Velicky for STED microscope alignment.\r\n\r\nThis
project has received funding from the Austrian Science Fund (FWF): I 3630-B25 (J.G.D)
and the European Research Council (ERC) under the European Union’s Horizon 2020
research and innovation programme (grant agreement No 742985, J.F.). It has also
received funding from the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie Grant Agreement No. 665385. S.T. has
received funding as an ISTplus Fellow from the European Union’s Horizon 2020 Research
and Innovation Programme under Marie Skłodowska-Curie grant agreement no. 754411
and from an EMBO Long-Term Fellowship (grant number ALTF 679-2018). It has further
received funding from the Austrian Science Fund (FWF) grant DK W1232 (M.T, N.A-D.,
J.G.D). W.J. received funding via a Human Frontier Science Program postdoctoral
fellowship LT000557/2018.\r\n\r\nThe funders had no role in study design, data collection
and analysis, decision to publish or preparation of the manuscript."
article_processing_charge: No
author:
- first_name: Michelle C
full_name: Gallei, Michelle C
id: 35A03822-F248-11E8-B48F-1D18A9856A87
last_name: Gallei
orcid: 0000-0003-1286-7368
- first_name: Sven M
full_name: Truckenbrodt, Sven M
id: 45812BD4-F248-11E8-B48F-1D18A9856A87
last_name: Truckenbrodt
- first_name: Caroline
full_name: Kreuzinger, Caroline
id: 382077BA-F248-11E8-B48F-1D18A9856A87
last_name: Kreuzinger
- first_name: Syamala
full_name: Inumella, Syamala
id: F8660870-D756-11E9-98C5-34DFE5697425
last_name: Inumella
orcid: 0009-0002-5890-120X
- first_name: Vitali
full_name: Vistunou, Vitali
id: 7e146587-8972-11ed-ae7b-d7a32ea86a81
last_name: Vistunou
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Mojtaba
full_name: Tavakoli, Mojtaba
id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87
last_name: Tavakoli
orcid: 0000-0002-7667-6854
- first_name: Nathalie
full_name: Agudelo Duenas, Nathalie
id: 40E7F008-F248-11E8-B48F-1D18A9856A87
last_name: Agudelo Duenas
- first_name: Jakob
full_name: Vorlaufer, Jakob
id: 937696FA-C996-11E9-8C7C-CF13E6697425
last_name: Vorlaufer
orcid: 0009-0000-7590-3501
- first_name: Wiebke
full_name: Jahr, Wiebke
id: 425C1CE8-F248-11E8-B48F-1D18A9856A87
last_name: Jahr
orcid: 0000-0003-0201-2315
- first_name: Marek
full_name: Randuch, Marek
id: 6ac4636d-15b2-11ec-abd3-fb8df79972ae
last_name: Randuch
- 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: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
citation:
ama: Gallei MC, Truckenbrodt SM, Kreuzinger C, et al. Super-resolution expansion
microscopy in plant roots. bioRxiv. doi:10.1101/2024.02.21.581330
apa: Gallei, M. C., Truckenbrodt, S. M., Kreuzinger, C., Inumella, S., Vistunou,
V., Sommer, C. M., … Danzl, J. G. (n.d.). Super-resolution expansion microscopy
in plant roots. bioRxiv. https://doi.org/10.1101/2024.02.21.581330
chicago: Gallei, Michelle C, Sven M Truckenbrodt, Caroline Kreuzinger, Syamala Inumella,
Vitali Vistunou, Christoph M Sommer, Mojtaba Tavakoli, et al. “Super-Resolution
Expansion Microscopy in Plant Roots.” BioRxiv, n.d. https://doi.org/10.1101/2024.02.21.581330.
ieee: M. C. Gallei et al., “Super-resolution expansion microscopy in plant
roots,” bioRxiv. .
ista: Gallei MC, Truckenbrodt SM, Kreuzinger C, Inumella S, Vistunou V, Sommer CM,
Tavakoli M, Agudelo Duenas N, Vorlaufer J, Jahr W, Randuch M, Johnson AJ, Benková
E, Friml J, Danzl JG. Super-resolution expansion microscopy in plant roots. bioRxiv,
10.1101/2024.02.21.581330.
mla: Gallei, Michelle C., et al. “Super-Resolution Expansion Microscopy in Plant
Roots.” BioRxiv, doi:10.1101/2024.02.21.581330.
short: M.C. Gallei, S.M. Truckenbrodt, C. Kreuzinger, S. Inumella, V. Vistunou,
C.M. Sommer, M. Tavakoli, N. Agudelo Duenas, J. Vorlaufer, W. Jahr, M. Randuch,
A.J. Johnson, E. Benková, J. Friml, J.G. Danzl, BioRxiv (n.d.).
corr_author: '1'
date_created: 2024-12-19T12:28:00Z
date_published: 2024-02-21T00:00:00Z
date_updated: 2026-07-28T08:33:52Z
day: '21'
department:
- _id: EvBe
- _id: JoDa
- _id: JiFr
doi: 10.1101/2024.02.21.581330
ec_funded: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2024.02.21.581330
month: '02'
oa: 1
oa_version: Preprint
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 26AA4EF2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
- _id: 269B5B22-B435-11E9-9278-68D0E5697425
grant_number: ALTF 679-2018
name: UltraX - achieving sub-nanometer resolution in light microscopy using iterative
X10 microscopy in combination with nanobodies and STED
publication: bioRxiv
publication_status: draft
related_material:
record:
- id: '19003'
relation: later_version
status: public
- id: '18681'
relation: dissertation_contains
status: public
status: public
title: Super-resolution expansion microscopy in plant roots
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
OA_place: repository
_id: '18688'
abstract:
- lang: eng
text: The human brain has remarkable computational power. It generates sophisticated
behavioral sequences, stores engrams over an individual’s lifetime, and produces
higher cognitive functions up to the level of consciousness. However, so little
of our neuroscience knowledge covers the human brain, and it remains unknown whether
this organ is truly unique, or is a scaled version of the extensively studied
rodent brain. To address this fundamental question, we determined the cellular,
synaptic, and connectivity rules of the hippocampal CA3 recurrent circuit using
multicellular patch clamp-recording. This circuit is the largest autoassociative
network in the brain, and plays a key role in memory and higher-order computations
such as pattern separation and pattern completion. We demonstrate that human hippocampal
CA3 employs sparse connectivity, in stark contrast to neocortical recurrent networks.
Connectivity sparsifies from rodents to humans, providing a circuit architecture
that maximizes associational power. Unitary synaptic events at human CA3–CA3 synapses
showed both distinct species-specific and circuit-dependent properties, with high
reliability, unique amplitude precision, and long integration times. We also identify
differential scaling rules between hippocampal pathways from rodents to humans,
with a moderate increase in the convergence of CA3 inputs per cell, but a marked
increase in human mossy fiber innervation. Anatomically guided full-scale modeling
suggests that the human brain’s sparse connectivity, expanded neuronal number,
and reliable synaptic signaling combine to enhance the associative memory storage
capacity of CA3. Together, our results reveal unique rules of connectivity and
synaptic signaling in the human hippocampus, demonstrating the absolute necessity
of human brain research and beginning to unravel the remarkable performance of
our autoassociative memory circuits.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: M-Shop
- _id: PreCl
- _id: ScienComp
acknowledgement: We thank Florian Marr for excellent technical assistance, Christina
Altmutter and Julia Flor for technical support, Alois Schlögl for programming, Todor
Asenov for development of the transportation box for human brain tissue, Tim Vogels
for guidance on simulations, Marcus Huber for mathematical advice, and Eleftheria
Kralli-Beller for manuscript editing. This research was supported by the Scientific
Services Units (SSUs) of ISTA, and we are particularly grateful for assistance from
Christoph Sommer and the Imaging and Optics Facility, Preclinical Facility, Life
Science Facility, Miba Machine Shop, and Scientific Computing. We also acknowledge
the excellent support of the Medical University of Vienna Department of Neurosurgery
staff, Romana Hoeftberger and the Division of Neuropathology and Neurochemistry,
and Gregor Kasprian and the Division of Neuroradiology and Musculoskeletal Radiology.
The project received funding from the European Research Council (ERC) under the
European Union’s Horizon 2020 research and innovation programme (Marie Skłodowska-Curie
Actions Individual Fellowship no. 101026635 to J.F.W.), the Austrian Science Fund
(FWF; grant PAT 4178023 to P.J.; grant DK W1232 to M.R.T. and J.G.D.) and the Austrian
Academy of Sciences (DOC fellowship 26137 to M.R.T.).
article_processing_charge: No
author:
- first_name: Jake F.
full_name: Watson, Jake F.
last_name: Watson
- first_name: Victor
full_name: Vargas-Barroso, Victor
last_name: Vargas-Barroso
- first_name: Rebecca J.
full_name: Morse-Mora, Rebecca J.
last_name: Morse-Mora
- first_name: Andrea
full_name: Navas-Olive, Andrea
last_name: Navas-Olive
- first_name: Mojtaba
full_name: Tavakoli, Mojtaba
id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87
last_name: Tavakoli
orcid: 0000-0002-7667-6854
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Matthias
full_name: Tomschik, Matthias
last_name: Tomschik
- first_name: Karl
full_name: Rössler, Karl
last_name: Rössler
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Watson JF, Vargas-Barroso V, Morse-Mora RJ, et al. Human hippocampal CA3 uses
specific functional connectivity rules for efficient associative memory. bioRxiv.
doi:10.1101/2024.05.02.592169
apa: Watson, J. F., Vargas-Barroso, V., Morse-Mora, R. J., Navas-Olive, A., Tavakoli,
M., Danzl, J. G., … Jonas, P. M. (n.d.). Human hippocampal CA3 uses specific functional
connectivity rules for efficient associative memory. bioRxiv. https://doi.org/10.1101/2024.05.02.592169
chicago: Watson, Jake F., Victor Vargas-Barroso, Rebecca J. Morse-Mora, Andrea Navas-Olive,
Mojtaba Tavakoli, Johann G Danzl, Matthias Tomschik, Karl Rössler, and Peter M
Jonas. “Human Hippocampal CA3 Uses Specific Functional Connectivity Rules for
Efficient Associative Memory.” BioRxiv, n.d. https://doi.org/10.1101/2024.05.02.592169.
ieee: J. F. Watson et al., “Human hippocampal CA3 uses specific functional
connectivity rules for efficient associative memory,” bioRxiv. .
ista: Watson JF, Vargas-Barroso V, Morse-Mora RJ, Navas-Olive A, Tavakoli M, Danzl
JG, Tomschik M, Rössler K, Jonas PM. Human hippocampal CA3 uses specific functional
connectivity rules for efficient associative memory. bioRxiv, 10.1101/2024.05.02.592169.
mla: Watson, Jake F., et al. “Human Hippocampal CA3 Uses Specific Functional Connectivity
Rules for Efficient Associative Memory.” BioRxiv, doi:10.1101/2024.05.02.592169.
short: J.F. Watson, V. Vargas-Barroso, R.J. Morse-Mora, A. Navas-Olive, M. Tavakoli,
J.G. Danzl, M. Tomschik, K. Rössler, P.M. Jonas, BioRxiv (n.d.).
corr_author: '1'
date_created: 2024-12-19T11:35:08Z
date_published: 2024-05-02T00:00:00Z
date_updated: 2026-07-28T08:33:51Z
day: '02'
department:
- _id: JoDa
- _id: PeJo
doi: 10.1101/2024.05.02.592169
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2024.05.02.592169
month: '05'
oa: 1
oa_version: Preprint
project:
- _id: fc2be41b-9c52-11eb-aca3-faa90aa144e9
call_identifier: H2020
grant_number: '101026635'
name: Synaptic computations of the hippocampal CA3 circuitry
- _id: 26AA4EF2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
- _id: 6285a163-2b32-11ec-9570-8e204ca2dba5
grant_number: '26137'
name: Studying Organelle Structure and Function at Nanoscale Resolution with Expansion
Microscopy
publication: bioRxiv
publication_status: draft
related_material:
record:
- id: '18879'
relation: later_version
status: public
- id: '18681'
relation: dissertation_contains
status: public
status: public
title: Human hippocampal CA3 uses specific functional connectivity rules for efficient
associative memory
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
OA_embargo: '20'
OA_place: publisher
_id: '18681'
acknowledged_ssus:
- _id: Bio
- _id: PreCl
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Mojtaba
full_name: Tavakoli, Mojtaba
id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87
last_name: Tavakoli
orcid: 0000-0002-7667-6854
citation:
ama: 'Tavakoli M. Developing molecular and structural tools for studying brain architecture
with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics
reconstruction with light microscopy. 2024. doi:10.15479/at:ista:18681'
apa: 'Tavakoli, M. (2024). Developing molecular and structural tools for studying
brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed
connectomics reconstruction with light microscopy. Institute of Science and
Technology Austria. https://doi.org/10.15479/at:ista:18681'
chicago: 'Tavakoli, Mojtaba. “Developing Molecular and Structural Tools for Studying
Brain Architecture with Super Resolution Expansion Microscopy. LICONN: Molecularly-Informed
Connectomics Reconstruction with Light Microscopy.” Institute of Science and Technology
Austria, 2024. https://doi.org/10.15479/at:ista:18681.'
ieee: 'M. Tavakoli, “Developing molecular and structural tools for studying brain
architecture with super resolution expansion microscopy. LICONN: Molecularly-informed
connectomics reconstruction with light microscopy,” Institute of Science and Technology
Austria, 2024.'
ista: 'Tavakoli M. 2024. Developing molecular and structural tools for studying
brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed
connectomics reconstruction with light microscopy. Institute of Science and Technology
Austria.'
mla: 'Tavakoli, Mojtaba. Developing Molecular and Structural Tools for Studying
Brain Architecture with Super Resolution Expansion Microscopy. LICONN: Molecularly-Informed
Connectomics Reconstruction with Light Microscopy. Institute of Science and
Technology Austria, 2024, doi:10.15479/at:ista:18681.'
short: 'M. Tavakoli, Developing Molecular and Structural Tools for Studying Brain
Architecture with Super Resolution Expansion Microscopy. LICONN: Molecularly-Informed
Connectomics Reconstruction with Light Microscopy, Institute of Science and Technology
Austria, 2024.'
corr_author: '1'
das_tickbox: '1'
date_created: 2024-12-19T02:30:39Z
date_published: 2024-12-20T00:00:00Z
date_updated: 2026-07-28T08:33:52Z
day: '20'
ddc:
- '600'
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JoDa
doi: 10.15479/at:ista:18681
doi_confirm: '1'
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checksum: b61651d417cafddd740a8528f46068c5
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
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date_created: 2024-12-20T10:23:17Z
date_updated: 2024-12-20T10:31:37Z
file_id: '18699'
file_name: Thesis_Mojtaba Tavakoli_.docx
file_size: 118593521
relation: source_file
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checksum: c80bcfd1a34c23afc3538052325283e5
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date_created: 2024-12-20T10:25:12Z
date_updated: 2026-07-28T08:33:51Z
embargo: 2027-08-01
embargo_to: open_access
file_id: '18700'
file_name: Thesis_Mojtaba Tavakoli_.pdf
file_size: 63885521
relation: main_file
file_date_updated: 2026-07-28T08:33:51Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa_version: Published Version
page: '230'
project:
- _id: 6285a163-2b32-11ec-9570-8e204ca2dba5
grant_number: '26137'
name: Studying Organelle Structure and Function at Nanoscale Resolution with Expansion
Microscopy
- _id: 26AA4EF2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
publication_identifier:
isbn:
- 978-3-99078-048-0
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '11160'
relation: part_of_dissertation
status: public
- id: '18688'
relation: part_of_dissertation
status: public
- id: '18677'
relation: part_of_dissertation
status: public
- id: '18689'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
title: 'Developing molecular and structural tools for studying brain architecture
with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics
reconstruction with light microscopy'
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2024'
...
---
OA_place: repository
_id: '18677'
abstract:
- lang: eng
text: The information-processing capability of the brain’s cellular network depends
on the physical wiring pattern between neurons and their molecular and functional
characteristics. Mapping neurons and resolving their individual synaptic connections
can be achieved by volumetric imaging at nanoscale resolution with dense cellular
labeling. Light microscopy is uniquely positioned to visualize specific molecules
but dense, synapse-level circuit reconstruction by light microscopy has been out
of reach due to limitations in resolution, contrast, and volumetric imaging capability.
Here we developed light-microscopy based connectomics (LICONN). We integrated
specifically engineered hydrogel embedding and expansion with comprehensive deep-learning
based segmentation and analysis of connectivity, thus directly incorporating molecular
information in synapse-level brain tissue reconstructions. LICONN will allow synapse-level
brain tissue phenotyping in biological experiments in a readily adoptable manner.
acknowledged_ssus:
- _id: E-Lib
- _id: M-Shop
- _id: LifeSc
- _id: Bio
- _id: ScienComp
acknowledgement: "We thank Sven Dorkenwald and Peter Li for critical reading of the\r\nmanuscript.
We acknowledge expert support by ISTA’s scientific service units: Imaging and\r\nOptics,
Lab Support, Scientific Computing, Preclinical Facility, Miba Machine Shop, and
Library.\r\nWe gratefully acknowledge funding by the following sources:\r\nAustrian
Science Fund (FWF) grant DK W1232 (JGD, MRT)\r\nAustrian Academy of Sciences DOC
fellowship 26137 (MRT)\r\nEU Horizon 2020 program, Marie Skłodowska-Curie Actions
Fellowship 665385 (JL)\r\nGesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022
(JGD)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European
Research\r\nCouncil (ERC) grant 101044865 “SecretAutism.”\r\n"
article_processing_charge: No
author:
- first_name: Mojtaba
full_name: Tavakoli, Mojtaba
id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87
last_name: Tavakoli
orcid: 0000-0002-7667-6854
- first_name: Julia
full_name: Lyudchik, Julia
id: 46E28B80-F248-11E8-B48F-1D18A9856A87
last_name: Lyudchik
- first_name: Michał
full_name: Januszewski, Michał
last_name: Januszewski
- first_name: Vitali
full_name: Vistunou, Vitali
id: 7e146587-8972-11ed-ae7b-d7a32ea86a81
last_name: Vistunou
- first_name: Nathalie
full_name: Agudelo Duenas, Nathalie
id: 40E7F008-F248-11E8-B48F-1D18A9856A87
last_name: Agudelo Duenas
- first_name: Jakob
full_name: Vorlaufer, Jakob
id: 937696FA-C996-11E9-8C7C-CF13E6697425
last_name: Vorlaufer
orcid: 0009-0000-7590-3501
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Caroline
full_name: Kreuzinger, Caroline
id: 382077BA-F248-11E8-B48F-1D18A9856A87
last_name: Kreuzinger
- first_name: Bárbara
full_name: Oliveira, Bárbara
id: 3B03AA1A-F248-11E8-B48F-1D18A9856A87
last_name: Oliveira
- first_name: Alban
full_name: Cenameri, Alban
id: 9ac8f577-2357-11eb-997a-e566c5550886
last_name: Cenameri
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Viren
full_name: Jain, Viren
last_name: Jain
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
citation:
ama: Tavakoli M, Lyudchik J, Januszewski M, et al. Light-microscopy based dense
connectomic reconstruction of mammalian brain tissue. bioRxiv. doi:10.1101/2024.03.01.582884
apa: Tavakoli, M., Lyudchik, J., Januszewski, M., Vistunou, V., Agudelo Duenas,
N., Vorlaufer, J., … Danzl, J. G. (n.d.). Light-microscopy based dense connectomic
reconstruction of mammalian brain tissue. bioRxiv. https://doi.org/10.1101/2024.03.01.582884
chicago: Tavakoli, Mojtaba, Julia Lyudchik, Michał Januszewski, Vitali Vistunou,
Nathalie Agudelo Duenas, Jakob Vorlaufer, Christoph M Sommer, et al. “Light-Microscopy
Based Dense Connectomic Reconstruction of Mammalian Brain Tissue.” BioRxiv,
n.d. https://doi.org/10.1101/2024.03.01.582884.
ieee: M. Tavakoli et al., “Light-microscopy based dense connectomic reconstruction
of mammalian brain tissue,” bioRxiv. .
ista: Tavakoli M, Lyudchik J, Januszewski M, Vistunou V, Agudelo Duenas N, Vorlaufer
J, Sommer CM, Kreuzinger C, Oliveira B, Cenameri A, Novarino G, Jain V, Danzl
JG. Light-microscopy based dense connectomic reconstruction of mammalian brain
tissue. bioRxiv, 10.1101/2024.03.01.582884.
mla: Tavakoli, Mojtaba, et al. “Light-Microscopy Based Dense Connectomic Reconstruction
of Mammalian Brain Tissue.” BioRxiv, doi:10.1101/2024.03.01.582884.
short: M. Tavakoli, J. Lyudchik, M. Januszewski, V. Vistunou, N. Agudelo Duenas,
J. Vorlaufer, C.M. Sommer, C. Kreuzinger, B. Oliveira, A. Cenameri, G. Novarino,
V. Jain, J.G. Danzl, BioRxiv (n.d.).
corr_author: '1'
date_created: 2024-12-18T14:48:24Z
date_published: 2024-07-08T00:00:00Z
date_updated: 2026-07-28T08:33:51Z
day: '08'
department:
- _id: GaNo
- _id: JoDa
doi: 10.1101/2024.03.01.582884
ec_funded: 1
language:
- iso: eng
main_file_link:
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url: https://doi.org/10.1101/2024.03.01.582884
month: '07'
oa: 1
oa_version: Preprint
project:
- _id: 6285a163-2b32-11ec-9570-8e204ca2dba5
grant_number: '26137'
name: Studying Organelle Structure and Function at Nanoscale Resolution with Expansion
Microscopy
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 34ba8964-11ca-11ed-8bc3-e15864e7e9a6
grant_number: '101044865'
name: Toward an understanding of the brain interstitial system and the extracellular
proteome in health and autism spectrum disorders
- _id: 26AA4EF2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
publication: bioRxiv
publication_status: draft
related_material:
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relation: dissertation_contains
status: public
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- id: '18681'
relation: dissertation_contains
status: public
status: public
title: Light-microscopy based dense connectomic reconstruction of mammalian brain
tissue
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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...
---
APC_amount: 6468 EUR
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OA_place: publisher
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abstract:
- lang: eng
text: Superconductor/semiconductor hybrid devices have attracted increasing interest
in the past years. Superconducting electronics aims to complement semiconductor
technology, while hybrid architectures are at the forefront of new ideas such
as topological superconductivity and protected qubits. In this work, we engineer
the induced superconductivity in two-dimensional germanium hole gas by varying
the distance between the quantum well and the aluminum. We demonstrate a hard
superconducting gap and realize an electrically and flux tunable superconducting
diode using a superconducting quantum interference device (SQUID). This allows
to tune the current phase relation (CPR), to a regime where single Cooper pair
tunneling is suppressed, creating a sin(2y) CPR. Shapiro experiments complement
this interpretation and the microwave drive allows to create a diode with ≈ 100%
efficiency. The reported results open up the path towards integration of spin
qubit devices, microwave resonators and (protected) superconducting qubits on the
same silicon technology compatible platform.
acknowledged_ssus:
- _id: M-Shop
- _id: NanoFab
acknowledgement: "We acknowledge Alexander Brinkmann, Alessandro Crippa, Francesco
Giazotto, Andrew Higginbotham, Andrea Iorio, Giordano Scappucci, Christian Schonenberger,
and Lukas Splitthoff for helpful discussions. We thank Marcel Verheijen for the
support in the TEM analysis. This research and related results were made possible
with the support of the NOMIS\r\nFoundation. It was supported by the Scientific
Service Units of ISTA through resources provided by the MIBA Machine Shop and the
nanofabrication facility, the European Union’s Horizon 2020 research andinnovation
programme under Grant Agreement No 862046, the HORIZONRIA\r\n101069515 project,
the European Innovation Council Pathfinder grant no. 101115315 (QuKiT), and the
FWF Projects #P-32235, #P-36507 and #F-8606. For the purpose of open access, the
authors have applied a CC BY public copyright licence to any Author Accepted Manuscript
version arising from this submission. R.S.S. acknowledges Spanish CM “Talento Program\"\r\nProject
No. 2022-T1/IND-24070. J.J. acknowledges European Research Council TOCINA 834290."
article_number: '169'
article_processing_charge: Yes
article_type: original
author:
- first_name: Marco
full_name: Valentini, Marco
id: C0BB2FAC-D767-11E9-B658-BC13E6697425
last_name: Valentini
- first_name: Oliver
full_name: Sagi, Oliver
id: 71616374-A8E9-11E9-A7CA-09ECE5697425
last_name: Sagi
- first_name: Levon
full_name: Baghumyan, Levon
id: 7aa1f788-b527-11ee-aa9e-e6111a79e0c7
last_name: Baghumyan
- first_name: Thijs
full_name: de Gijsel, Thijs
id: a0ece13c-b527-11ee-929d-bad130106eee
last_name: de Gijsel
- first_name: Jason
full_name: Jung, Jason
id: 4C9ACE7A-F248-11E8-B48F-1D18A9856A87
last_name: Jung
- first_name: Stefano
full_name: Calcaterra, Stefano
last_name: Calcaterra
- first_name: Andrea
full_name: Ballabio, Andrea
last_name: Ballabio
- first_name: Juan L
full_name: Aguilera Servin, Juan L
id: 2A67C376-F248-11E8-B48F-1D18A9856A87
last_name: Aguilera Servin
orcid: 0000-0002-2862-8372
- first_name: Kushagra
full_name: Aggarwal, Kushagra
id: b22ab905-3539-11eb-84c3-fc159dcd79cb
last_name: Aggarwal
orcid: 0000-0001-9985-9293
- first_name: Marian
full_name: Janik, Marian
id: 396A1950-F248-11E8-B48F-1D18A9856A87
last_name: Janik
orcid: 0009-0003-9037-8831
- first_name: Thomas
full_name: Adletzberger, Thomas
id: 38756BB2-F248-11E8-B48F-1D18A9856A87
last_name: Adletzberger
- first_name: Rubén
full_name: Seoane Souto, Rubén
last_name: Seoane Souto
- first_name: Martin
full_name: Leijnse, Martin
last_name: Leijnse
- first_name: Jeroen
full_name: Danon, Jeroen
last_name: Danon
- first_name: Constantin
full_name: Schrade, Constantin
last_name: Schrade
- first_name: Erik
full_name: Bakkers, Erik
last_name: Bakkers
- first_name: Daniel
full_name: Chrastina, Daniel
last_name: Chrastina
- first_name: Giovanni
full_name: Isella, Giovanni
last_name: Isella
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
citation:
ama: Valentini M, Sagi O, Baghumyan L, et al. Parity-conserving Cooper-pair transport
and ideal superconducting diode in planar germanium. Nature Communications.
2024;15. doi:10.1038/s41467-023-44114-0
apa: Valentini, M., Sagi, O., Baghumyan, L., de Gijsel, T., Jung, J., Calcaterra,
S., … Katsaros, G. (2024). Parity-conserving Cooper-pair transport and ideal superconducting
diode in planar germanium. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-44114-0
chicago: Valentini, Marco, Oliver Sagi, Levon Baghumyan, Thijs de Gijsel, Jason
Jung, Stefano Calcaterra, Andrea Ballabio, et al. “Parity-Conserving Cooper-Pair
Transport and Ideal Superconducting Diode in Planar Germanium.” Nature Communications.
Springer Nature, 2024. https://doi.org/10.1038/s41467-023-44114-0.
ieee: M. Valentini et al., “Parity-conserving Cooper-pair transport and ideal
superconducting diode in planar germanium,” Nature Communications, vol.
15. Springer Nature, 2024.
ista: Valentini M, Sagi O, Baghumyan L, de Gijsel T, Jung J, Calcaterra S, Ballabio
A, Aguilera Servin JL, Aggarwal K, Janik M, Adletzberger T, Seoane Souto R, Leijnse
M, Danon J, Schrade C, Bakkers E, Chrastina D, Isella G, Katsaros G. 2024. Parity-conserving
Cooper-pair transport and ideal superconducting diode in planar germanium. Nature
Communications. 15, 169.
mla: Valentini, Marco, et al. “Parity-Conserving Cooper-Pair Transport and Ideal
Superconducting Diode in Planar Germanium.” Nature Communications, vol.
15, 169, Springer Nature, 2024, doi:10.1038/s41467-023-44114-0.
short: M. Valentini, O. Sagi, L. Baghumyan, T. de Gijsel, J. Jung, S. Calcaterra,
A. Ballabio, J.L. Aguilera Servin, K. Aggarwal, M. Janik, T. Adletzberger, R.
Seoane Souto, M. Leijnse, J. Danon, C. Schrade, E. Bakkers, D. Chrastina, G. Isella,
G. Katsaros, Nature Communications 15 (2024).
corr_author: '1'
date_created: 2024-01-14T23:00:56Z
date_published: 2024-01-02T00:00:00Z
date_updated: 2026-07-29T07:04:56Z
day: '02'
ddc:
- '530'
department:
- _id: GeKa
doi: 10.1038/s41467-023-44114-0
ec_funded: 1
external_id:
isi:
- '001142794000839'
pmid:
- '38167818'
file:
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file_size: 2336595
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has_accepted_license: '1'
intvolume: ' 15'
isi: 1
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month: '01'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 237E5020-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '862046'
name: TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS
- _id: 34c0acea-11ca-11ed-8bc3-8775e10fd452
grant_number: '101069515'
name: Integrated Germanium Quantum Technology
- _id: bdc2ca30-d553-11ed-ba76-cf164a5bb811
grant_number: '101115315'
name: Quantum bits with Kitaev Transmons
- _id: 237B3DA4-32DE-11EA-91FC-C7463DDC885E
call_identifier: FWF
grant_number: P32235
name: Towards scalable hut wire quantum devices
- _id: bd8bd29e-d553-11ed-ba76-f0070d4b237a
grant_number: P36507
name: Merging spin and superconducting qubits in planar Ge
- _id: 34a66131-11ca-11ed-8bc3-a31681c6b03e
grant_number: F8606
name: 'Center for Correlated Quantum Materials and Solid State Quantum Systems:
Conventional and unconventional topological superconductors'
- _id: 3AC91DDA-15DF-11EA-824D-93A3E7B544D1
call_identifier: FWF
name: FWF Open Access Fund
publication: Nature Communications
publication_identifier:
eissn:
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publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
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relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Parity-conserving Cooper-pair transport and ideal superconducting diode in
planar germanium
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2024'
...
---
_id: '12312'
abstract:
- lang: eng
text: "Let $\\ell$ be a prime number. We classify the subgroups $G$ of $\\operatorname{Sp}_4(\\mathbb{F}_\\ell)$
and $\\operatorname{GSp}_4(\\mathbb{F}_\\ell)$ that act irreducibly on $\\mathbb{F}_\\ell^4$,
but such that every element of $G$ fixes an $\\mathbb{F}_\\ell$-vector subspace
of dimension 1. We use this classification to prove that the local-global principle
for isogenies of degree $\\ell$ between abelian surfaces over number fields holds
in many cases -- in particular, whenever the abelian surface has non-trivial endomorphisms
and $\\ell$ is large enough with respect to the field of definition. Finally,
we prove that there exist arbitrarily large primes $\\ell$ for which some abelian
surface\r\n$A/\\mathbb{Q}$ fails the local-global principle for isogenies of degree
$\\ell$."
acknowledgement: "It is a pleasure to thank Samuele Anni for his interest in this
project and for several discussions on the topic of this paper, which led in particular
to Remark 6.30 and to a better understanding of the difficulties with [6]. We also
thank John Cullinan for correspondence about [6] and Barinder Banwait for his many
insightful comments on the first version of this paper. Finally, we thank the referee
for their thorough reading of the manuscript.\r\nOpen access funding provided by
Università di Pisa within the CRUI-CARE Agreement. The authors have been partially
supported by MIUR (Italy) through PRIN 2017 “Geometric, algebraic and analytic methods
in arithmetic\" and PRIN 2022 “Semiabelian varieties, Galois representations and
related Diophantine problems\", and by the University of Pisa through PRA 2018-19
and 2022 “Spazi di moduli, rappresentazioni e strutture combinatorie\". The first
author is a member of the INdAM group GNSAGA."
article_number: '18'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Davide
full_name: Lombardo, Davide
last_name: Lombardo
- first_name: Matteo
full_name: Verzobio, Matteo
id: 7aa8f170-131e-11ed-88e1-a9efd01027cb
last_name: Verzobio
orcid: 0000-0002-0854-0306
citation:
ama: Lombardo D, Verzobio M. On the local-global principle for isogenies of abelian
surfaces. Selecta Mathematica. 2024;30(2). doi:10.1007/s00029-023-00908-0
apa: Lombardo, D., & Verzobio, M. (2024). On the local-global principle for
isogenies of abelian surfaces. Selecta Mathematica. Springer Nature. https://doi.org/10.1007/s00029-023-00908-0
chicago: Lombardo, Davide, and Matteo Verzobio. “On the Local-Global Principle for
Isogenies of Abelian Surfaces.” Selecta Mathematica. Springer Nature, 2024.
https://doi.org/10.1007/s00029-023-00908-0.
ieee: D. Lombardo and M. Verzobio, “On the local-global principle for isogenies
of abelian surfaces,” Selecta Mathematica, vol. 30, no. 2. Springer Nature,
2024.
ista: Lombardo D, Verzobio M. 2024. On the local-global principle for isogenies
of abelian surfaces. Selecta Mathematica. 30(2), 18.
mla: Lombardo, Davide, and Matteo Verzobio. “On the Local-Global Principle for Isogenies
of Abelian Surfaces.” Selecta Mathematica, vol. 30, no. 2, 18, Springer
Nature, 2024, doi:10.1007/s00029-023-00908-0.
short: D. Lombardo, M. Verzobio, Selecta Mathematica 30 (2024).
corr_author: '1'
das_tickbox: '0'
date_created: 2023-01-16T11:45:53Z
date_published: 2024-01-26T00:00:00Z
date_updated: 2026-07-29T09:53:10Z
day: '26'
ddc:
- '510'
department:
- _id: TiBr
doi: 10.1007/s00029-023-00908-0
external_id:
arxiv:
- '2206.15240'
isi:
- '001148959100001'
file:
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checksum: ae75441420aabd80c5828bce38272ba1
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creator: dernst
date_created: 2024-07-22T09:33:58Z
date_updated: 2024-07-22T09:33:58Z
file_id: '17298'
file_name: 2024_SelectaMath_Lombardo.pdf
file_size: 1301415
relation: main_file
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has_accepted_license: '1'
intvolume: ' 30'
isi: 1
issue: '2'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: Selecta Mathematica
publication_identifier:
eissn:
- 1420-9020
issn:
- 1022-1824
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: On the local-global principle for isogenies of abelian surfaces
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: 30
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '19425'
abstract:
- lang: eng
text: "We demonstrate that periodically driven quantum rotors provide a promising
and broadly applicable platform to implement multi-gap topological phases, where
groups of bands can acquire topological invariants due to non-Abelian braiding
of band degeneracies. By adiabatically varying the periodic kicks to the rotor
we find nodal-line braiding, which causes sign flips of topological charges of
band nodes and can prevent them from annihilating, indicated by non-zero values
of the %non-Abelian patch Euler class. In particular, we report\r\non the emergence
of an anomalous Dirac string phase arising in the strongly driven regime, a truly
out-of-equilibrium phase of the quantum rotor. This phase emanates from braiding
processes involving all (quasienergy) gaps and manifests itself with edge states
at zero angular momentum. Our results reveal direct applications in state-of-the-art
experiments of quantum rotors, such as linear molecules driven by periodic far-off-resonant
laser pulses or artificial\r\nquantum rotors in optical lattices, whose extensive
versatility offers precise modification and observation of novel non-Abelian topological
properties. "
acknowledgement: "We thank G. M. Koutentakis, S. Wimberger, J. G. E. Harris, T. Enss
and A. Ghazaryan for fruitful discussions. M.L. acknowledges support by the European
Research Council (ERC) Starting Grant No. 801770 (ANGULON). R.-J. S. acknowledges
funding from a EPSRC ERC underwrite grant EP/X025829/1, a EPSRC New Investigator
Award grant EP/W00187X/1, as well as Trinity College, Cambridge. F.N.U. acknowledges
support from the Marie ¨Sk lodowska-Curie programme of the European Commission [Grant
No. 893915], Simons Investigator Award\r\n[Grant No. 511029] and Trinity College
Cambridge."
article_number: '2408.16848'
article_processing_charge: No
arxiv: 1
author:
- first_name: Volker
full_name: Karle, Volker
id: D7C012AE-D7ED-11E9-95E8-1EC5E5697425
last_name: Karle
orcid: 0000-0002-6963-0129
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Adrien
full_name: Bouhon, Adrien
last_name: Bouhon
- first_name: Robert-Jan
full_name: Slager, Robert-Jan
last_name: Slager
- first_name: F. Nur
full_name: Ünal, F. Nur
last_name: Ünal
citation:
ama: Karle V, Lemeshko M, Bouhon A, Slager R-J, Ünal FN. Anomalous multi-gap topological
phases in periodically driven quantum rotors. arXiv. doi:10.48550/arXiv.2408.16848
apa: Karle, V., Lemeshko, M., Bouhon, A., Slager, R.-J., & Ünal, F. N. (n.d.).
Anomalous multi-gap topological phases in periodically driven quantum rotors.
arXiv. https://doi.org/10.48550/arXiv.2408.16848
chicago: Karle, Volker, Mikhail Lemeshko, Adrien Bouhon, Robert-Jan Slager, and
F. Nur Ünal. “Anomalous Multi-Gap Topological Phases in Periodically Driven Quantum
Rotors.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2408.16848.
ieee: V. Karle, M. Lemeshko, A. Bouhon, R.-J. Slager, and F. N. Ünal, “Anomalous
multi-gap topological phases in periodically driven quantum rotors,” arXiv.
.
ista: Karle V, Lemeshko M, Bouhon A, Slager R-J, Ünal FN. Anomalous multi-gap topological
phases in periodically driven quantum rotors. arXiv, 2408.16848.
mla: Karle, Volker, et al. “Anomalous Multi-Gap Topological Phases in Periodically
Driven Quantum Rotors.” ArXiv, 2408.16848, doi:10.48550/arXiv.2408.16848.
short: V. Karle, M. Lemeshko, A. Bouhon, R.-J. Slager, F.N. Ünal, ArXiv (n.d.).
date_created: 2025-03-20T07:48:23Z
date_published: 2024-08-29T00:00:00Z
date_updated: 2026-07-29T08:59:31Z
day: '29'
department:
- _id: MiLe
doi: 10.48550/arXiv.2408.16848
ec_funded: 1
external_id:
arxiv:
- '2408.16848'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2408.16848
month: '08'
oa: 1
oa_version: Preprint
project:
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication: arXiv
publication_status: draft
related_material:
record:
- id: '19393'
relation: dissertation_contains
status: public
- id: '21009'
relation: later_version
status: public
status: public
title: Anomalous multi-gap topological phases in periodically driven quantum rotors
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...