---
OA_place: repository
OA_type: green
_id: '22832'
abstract:
- lang: eng
text: "In many scientific experiments, the data annotating cost constraints the
pace\r\nfor testing novel hypotheses. Yet, modern machine learning pipelines offer
a\r\npromising solution—provided their predictions yield correct conclusions.
We\r\nfocus on Prediction-Powered Causal Inferences (PPCI), i.e., estimating the\r\ntreatment
effect in an unlabeled target experiment, relying on training data with\r\nthe
same outcome annotated but potentially different treatment or effect modifiers.\r\nWe
first show that conditional calibration guarantees valid PPCI at population\r\nlevel.
Then, we introduce a sufficient representation constraint transferring validity\r\nacross
experiments, which we propose to enforce in practice in Deconfounded\r\nEmpirical
Risk Minimization, our new model-agnostic training objective. We\r\nvalidate our
method on synthetic and real-world scientific data, solving impossible\r\nproblem
instances for Empirical Risk Minimization even with standard invariance\r\nconstraints.
In particular, for the first time, we achieve valid causal inference\r\non a scientific
experiment with complex recording and no human annotations,\r\nfine-tuning a foundational
model on our similar annotated experiment."
acknowledgement: "We thank the Causal Learning and Artificial Intelligence group at
ISTA for the continuous feedback\r\non the project and valuable discussions. We
thank the Social Immunity group at ISTA, particularly\r\nJinook Oh, for the annotation
program and Michaela Hoenigsberger for supporting our ecological\r\nexperiment.
Riccardo Cadei is supported by a Google Research Scholar Award and a Google Initiated\r\nGift
to Francesco Locatello. This research was funded in part by the Austrian Science
Fund (FWF)\r\n10.55776/COE12). It was further partially supported by the ISTA Interdisciplinary
Project Committee\r\nfor the collaborative project “ALED” between Francesco Locatello
and Sylvia Cremer. For open\r\naccess purposes, the author has applied a CC BY public
copyright license to any author accepted\r\nmanuscript version arising from this
submission.\r\n"
alternative_title:
- Advances in Neural Information Processing Systems
article_processing_charge: No
arxiv: 1
author:
- first_name: Riccardo
full_name: Cadei, Riccardo
id: 0fa8b76f-72f0-11ef-b75a-a5da96e5ad6b
last_name: Cadei
- first_name: Ilker
full_name: Demirel, Ilker
last_name: Demirel
- first_name: Piersilvio
full_name: De Bartolomeis, Piersilvio
last_name: De Bartolomeis
- first_name: Lukas
full_name: Lindorfer, Lukas
id: 85f0e6d3-06b3-11ec-8982-8c5049fa4455
last_name: Lindorfer
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Cordelia
full_name: Schmid, Cordelia
last_name: Schmid
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
citation:
ama: 'Cadei R, Demirel I, De Bartolomeis P, et al. Prediction-Powered Causal Inferences.
In: 39th Conference on Neural Information Processing Systems. Vol 38. Neural
Information Processing Systems Foundation; 2025:82200-82229. doi:10.52202/085713-2479'
apa: 'Cadei, R., Demirel, I., De Bartolomeis, P., Lindorfer, L., Cremer, S., Schmid,
C., & Locatello, F. (2025). Prediction-Powered Causal Inferences. In 39th
Conference on Neural Information Processing Systems (Vol. 38, pp. 82200–82229).
San Diego, CA, United States: Neural Information Processing Systems Foundation.
https://doi.org/10.52202/085713-2479'
chicago: Cadei, Riccardo, Ilker Demirel, Piersilvio De Bartolomeis, Lukas Lindorfer,
Sylvia Cremer, Cordelia Schmid, and Francesco Locatello. “Prediction-Powered Causal
Inferences.” In 39th Conference on Neural Information Processing Systems,
38:82200–229. Neural Information Processing Systems Foundation, 2025. https://doi.org/10.52202/085713-2479.
ieee: R. Cadei et al., “Prediction-Powered Causal Inferences,” in 39th
Conference on Neural Information Processing Systems, San Diego, CA, United
States, 2025, vol. 38, pp. 82200–82229.
ista: 'Cadei R, Demirel I, De Bartolomeis P, Lindorfer L, Cremer S, Schmid C, Locatello
F. 2025. Prediction-Powered Causal Inferences. 39th Conference on Neural Information
Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in
Neural Information Processing Systems, vol. 38, 82200–82229.'
mla: Cadei, Riccardo, et al. “Prediction-Powered Causal Inferences.” 39th Conference
on Neural Information Processing Systems, vol. 38, Neural Information Processing
Systems Foundation, 2025, pp. 82200–29, doi:10.52202/085713-2479.
short: R. Cadei, I. Demirel, P. De Bartolomeis, L. Lindorfer, S. Cremer, C. Schmid,
F. Locatello, in:, 39th Conference on Neural Information Processing Systems, Neural
Information Processing Systems Foundation, 2025, pp. 82200–82229.
conference:
end_date: 2025-12-07
location: San Diego, CA, United States
name: 'NeurIPS: Neural Information Processing Systems'
start_date: 2025-12-02
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: "We share all the code implementation in the supplementary
material.\r\nOur new experimental ecology dataset preview is anonymously shared
on Figshare at\r\nhttps://figshare.com/s/9a490b6f6eeebd73350b. We further rely on
ISTAnt dataset publicly\r\navailable at https://doi.org/10.6084/m9.figshare.26484934.v2.
The synthetic experiments\r\non CausalMNIST relies on MNIST dataset LeCun [1998],
publicly available. Additional\r\nexperimental details are reported in Section 5
and Appendices B-C."
date_created: 2026-09-06T22:02:01Z
date_published: 2025-12-01T00:00:00Z
date_updated: 2026-09-17T06:56:40Z
day: '01'
department:
- _id: FrLo
- _id: GradSch
- _id: SyCr
doi: 10.52202/085713-2479
external_id:
arxiv:
- '2502.06343'
fulldoi: https://doi.org/10.52202/085713-2479
intvolume: ' 38'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2502.06343
month: '12'
oa: 1
oa_version: Preprint
page: 82200-82229
project:
- _id: a392d8f0-b034-11f1-b88e-d3025c6734f6
grant_number: COE12
name: Bilateral Artificial Intelligence (Locatello)
publication: 39th Conference on Neural Information Processing Systems
publication_identifier:
isbn:
- '9798331338275'
issn:
- 1049-5258
publication_status: published
publisher: Neural Information Processing Systems Foundation
quality_controlled: '1'
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Prediction-Powered Causal Inferences
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 38
year: '2025'
...
---
_id: '22831'
abstract:
- lang: eng
text: "Neural models learn representations of high-dimensional data on low-dimensional\r\nmanifolds.
Multiple factors, including stochasticities in the training process, model\r\narchitectures,
and additional inductive biases, may induce different representations,\r\neven
when learning the same task on the same data. However, it has recently been\r\nshown
that when a latent structure is shared between distinct latent spaces, relative\r\ndistances
between representations can be preserved, up to distortions. Building\r\non this
idea, we demonstrate that exploiting the differential-geometric structure of\r\nlatent
spaces of neural models, it is possible to capture precisely the transformations\r\nbetween
representational spaces trained on similar data distributions. Specifically,\r\nwe
assume that distinct neural models parametrize approximately the same underlying
manifold, and introduce a representation based on the pullback metric\r\nthat
captures the intrinsic structure of the latent space, while scaling efficiently\r\nto
large models. We validate experimentally our method on model stitching and\r\nretrieval
tasks, covering autoencoders and vision foundation discriminative models,\r\nacross
diverse architectures, datasets, pretraining schemes and modalities. Code is\r\navailable
at https://github.com/marc0git/RelativeGeodesics."
acknowledgement: "We thank Gregor Krzmanc, German Magai, Vital Fernandez for insightful
discussions in the early\r\nstages of the project. HY was supported by the Research
Council of Finland Flagship programme:\r\nFinnish Center for Artificial Intelligence
FCAI. HY wishes to acknowledge CSC - IT Center for\r\nScience, Finland, for computational
resources. GA was supported by the DFF Sapere Aude Starting\r\nGrant “GADL”. SH
was supported by a research grant (42062) from VILLUM FONDEN and partly\r\nfunded
by the Novo Nordisk Foundation through the Center for Basic Research in Life Science\r\n(NNF20OC0062606).
SH received funding from the European Research Council (ERC) under the\r\nEuropean
Union’s Horizon Programme (grant agreement 101125003). MF is supported by the MSCA\r\nIST-Bridge
fellowship which has received funding from the European Union’s Horizon 2020 research\r\nand
innovation program under the Marie Skłodowska-Curie grant agreement No 101034413."
alternative_title:
- Advances in Neural Information Processing Systems
article_processing_charge: No
arxiv: 1
author:
- first_name: Hanlin
full_name: Yu, Hanlin
last_name: Yu
- first_name: Berfin
full_name: Inal, Berfin
last_name: Inal
- first_name: Georgios
full_name: Arvanitidis, Georgios
last_name: Arvanitidis
- first_name: Søren
full_name: Hauberg, Søren
last_name: Hauberg
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Marco
full_name: Fumero, Marco
id: 1c1593eb-393f-11ef-bb8e-ab4f1e979650
last_name: Fumero
citation:
ama: 'Yu H, Inal B, Arvanitidis G, Hauberg S, Locatello F, Fumero M. Connecting
neural models latent geometries with relative geodesic representations. In: 39th
Conference on Neural Information Processing Systems. Vol 38. Neural Information
Processing Systems Foundation; 2025:125316-125360. doi:10.52202/085713-3769'
apa: 'Yu, H., Inal, B., Arvanitidis, G., Hauberg, S., Locatello, F., & Fumero,
M. (2025). Connecting neural models latent geometries with relative geodesic representations.
In 39th Conference on Neural Information Processing Systems (Vol. 38, pp.
125316–125360). San Diego, CA, United States: Neural Information Processing Systems
Foundation. https://doi.org/10.52202/085713-3769'
chicago: Yu, Hanlin, Berfin Inal, Georgios Arvanitidis, Søren Hauberg, Francesco
Locatello, and Marco Fumero. “Connecting Neural Models Latent Geometries with
Relative Geodesic Representations.” In 39th Conference on Neural Information
Processing Systems, 38:125316–60. Neural Information Processing Systems Foundation,
2025. https://doi.org/10.52202/085713-3769.
ieee: H. Yu, B. Inal, G. Arvanitidis, S. Hauberg, F. Locatello, and M. Fumero, “Connecting
neural models latent geometries with relative geodesic representations,” in 39th
Conference on Neural Information Processing Systems, San Diego, CA, United
States, 2025, vol. 38, pp. 125316–125360.
ista: 'Yu H, Inal B, Arvanitidis G, Hauberg S, Locatello F, Fumero M. 2025. Connecting
neural models latent geometries with relative geodesic representations. 39th Conference
on Neural Information Processing Systems. NeurIPS: Neural Information Processing
Systems, Advances in Neural Information Processing Systems, vol. 38, 125316–125360.'
mla: Yu, Hanlin, et al. “Connecting Neural Models Latent Geometries with Relative
Geodesic Representations.” 39th Conference on Neural Information Processing
Systems, vol. 38, Neural Information Processing Systems Foundation, 2025,
pp. 125316–60, doi:10.52202/085713-3769.
short: H. Yu, B. Inal, G. Arvanitidis, S. Hauberg, F. Locatello, M. Fumero, in:,
39th Conference on Neural Information Processing Systems, Neural Information Processing
Systems Foundation, 2025, pp. 125316–125360.
conference:
end_date: 2025-12-07
location: San Diego, CA, United States
name: 'NeurIPS: Neural Information Processing Systems'
start_date: 2025-12-02
corr_author: '1'
das_tickbox: '0'
date_created: 2026-09-06T22:02:01Z
date_published: 2025-12-01T00:00:00Z
date_updated: 2026-09-17T07:09:28Z
day: '01'
department:
- _id: FrLo
doi: 10.52202/085713-3769
ec_funded: 1
external_id:
arxiv:
- '2506.01599'
fulldoi: https://doi.org/10.52202/085713-3769
intvolume: ' 38'
language:
- iso: eng
month: '12'
oa_version: None
page: 125316-125360
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: 39th Conference on Neural Information Processing Systems
publication_identifier:
eissn:
- 1049-5258
isbn:
- '9798331338275'
publication_status: published
publisher: Neural Information Processing Systems Foundation
quality_controlled: '1'
related_material:
link:
- relation: software
url: ' https://github.com/marc0git/RelativeGeodesics'
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Connecting neural models latent geometries with relative geodesic representations
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 38
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '22929'
abstract:
- lang: eng
text: The circle method has been successfully used over the last century to study
rational points on hypersurfaces. More recently, a version of the method over
function fields, combined with spreading out techniques, has led to a range of
results about moduli spaces of rational curves on hypersurfaces. In this paper
a version of the circle method is implemented in the setting of the Grothendieck
ring of varieties. This allows us to approximate the classes of these moduli spaces
directly, without relying on point counting, and leads to a deeper understanding
of their geometry.
- lang: fre
text: "La méthode du cercle a été utilisée avec succès au cours du siècle dernier
pour l’étude\r\ndes points rationnels sur les hypersurfaces. Plus récemment, une
version fonctionnelle de cette méthode,\r\ncombinée à des techniques d’étalement,
a mené à une série de résultats sur les espaces de modules de\r\ncourbes sur les
hypersurfaces. Dans cet article on implémente une version de la méthode du cercle
dans\r\nle cadre de l’anneau de Grothendieck des variétés. Cela permet d’approximer
les classes de ces espaces\r\nde modules directement, sans recours au comptage
de points, ce qui donne accès à une compréhension\r\nplus profonde de leur géométrie."
acknowledgement: "The authors are grateful to Yohan Brunebarbe, Tom Burel, Antoine\r\nChambert-Loir,
Loïs Faisant, Mirko Mauri and Will Sawin for useful comments. Thanks are\r\nalso
due to the anonymous referees for numerous helpful remarks. M.B. received funding\r\nfrom
the European Union’s Horizon 2020 research and innovation programme under the\r\nMarie
Skłodowska-Curie Grant agreement No. 893012. T.B. was supported by a FWF grant\r\n(DOI
10.55776/P36278) and by a grant from the Institute for Advanced Study School of\r\nMathematics."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Margaret
full_name: Bilu, Margaret
id: 98C47862-10D5-11EA-BEDD-0F6F3DDC885E
last_name: Bilu
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
citation:
ama: Bilu M, Browning TD. A motivic circle method. Annales Scientifiques de l’École
Normale Supérieure. 2025;58(5):1179-1242. doi:10.24033/asens.2628
apa: Bilu, M., & Browning, T. D. (2025). A motivic circle method. Annales
Scientifiques de l’École Normale Supérieure. Société Mathématique de France.
https://doi.org/10.24033/asens.2628
chicago: Bilu, Margaret, and Timothy D Browning. “A Motivic Circle Method.” Annales
Scientifiques de l’École Normale Supérieure. Société Mathématique de France,
2025. https://doi.org/10.24033/asens.2628.
ieee: M. Bilu and T. D. Browning, “A motivic circle method,” Annales Scientifiques
de l’École Normale Supérieure, vol. 58, no. 5. Société Mathématique de France,
pp. 1179–1242, 2025.
ista: Bilu M, Browning TD. 2025. A motivic circle method. Annales Scientifiques
de l’École Normale Supérieure. 58(5), 1179–1242.
mla: Bilu, Margaret, and Timothy D. Browning. “A Motivic Circle Method.” Annales
Scientifiques de l’École Normale Supérieure, vol. 58, no. 5, Société Mathématique
de France, 2025, pp. 1179–242, doi:10.24033/asens.2628.
short: M. Bilu, T.D. Browning, Annales Scientifiques de l’École Normale Supérieure
58 (2025) 1179–1242.
corr_author: '1'
das_tickbox: '0'
date_created: 2026-09-13T22:01:57Z
date_published: 2025-05-01T00:00:00Z
date_updated: 2026-09-17T08:22:39Z
day: '01'
department:
- _id: TiBr
doi: 10.24033/asens.2628
ec_funded: 1
external_id:
arxiv:
- '2304.09645'
fulldoi: https://doi.org/10.24033/asens.2628
intvolume: ' 58'
issue: '5'
keyword:
- Circle method
- moduli spaces of curves
- hypersurfaces
- Grothendieck ring of varieties
- motivic integration
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2304.09645
month: '05'
oa: 1
oa_version: Preprint
page: 1179-1242
project:
- _id: 05A4F6F0-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '893012'
name: A motivic circle method
- _id: bd8a4fdc-d553-11ed-ba76-80a0167441a3
grant_number: P36278
name: Rational curves via function field analytic number theory
publication: Annales Scientifiques de l’École Normale Supérieure
publication_identifier:
eissn:
- 1873-2151
issn:
- 0012-9593
publication_status: published
publisher: Société Mathématique de France
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: yes
title: A motivic circle method
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 58
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '18074'
abstract:
- lang: eng
text: The Aharonov–Casher theorem is a result on the number of the so-called zero
modes of a system described by the magnetic Pauli operator in R2. In this paper
we address the same question for the Dirac operator on a flat two-dimensional
manifold with boundary and Atiyah–Patodi–Singer boundary condition. More concretely
we are interested in the plane and a disc with a finite number of circular holes
cut out. We consider a smooth compactly supported magnetic field on the manifold
and an arbitrary magnetic field inside the holes.
acknowledgement: "First and foremost I am grateful to Jan Philip Solovej for fruitful
meetings during (and after) my PhD programme, when this work was done. Further I
would like to thank Joshua Hunt, Anna Sisak, Jakub Löwit, Błażej Ruba, Volodymir
Riabov, Lukas Schimmer and Georgios Koutentakis for valuable discussions. Many thanks
belong to Rafael Benguria for hosting my visit, during which some of the work has
been done. I am also grateful to Marina Prokhorova who first initiated the discussion
of this project topic and to Annemarie Luger for her valuable comments during my
PhD defence and in particular pointing out the qualitative difference in our two
main results. I would like to acknowledge support for research on this paper from
VILLUM FONDEN through the QMATH Centre of Excellence grant. nr. 10059. This project
also received funding from the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie grant agreement No 101034413. I am grateful
to the two reviewers for reading carefully my manuscript and pointing out several
issues contributing thus significantly to the readability and clarity of this paper.\r\nOpen
access funding provided by Institute of Science and Technology (IST Austria)."
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Marie
full_name: Fialova, Marie
id: e9c9844d-9e21-11ec-b482-f96fc09f7c4d
last_name: Fialova
citation:
ama: Fialova M. Aharonov–Casher theorems for Dirac operators on manifolds with boundary
and APS boundary condition. Annales Henri Poincare. 2025;26:2859-2900.
doi:10.1007/s00023-024-01482-7
apa: Fialova, M. (2025). Aharonov–Casher theorems for Dirac operators on manifolds
with boundary and APS boundary condition. Annales Henri Poincare. Springer
Nature. https://doi.org/10.1007/s00023-024-01482-7
chicago: Fialova, Marie. “Aharonov–Casher Theorems for Dirac Operators on Manifolds
with Boundary and APS Boundary Condition.” Annales Henri Poincare. Springer
Nature, 2025. https://doi.org/10.1007/s00023-024-01482-7.
ieee: M. Fialova, “Aharonov–Casher theorems for Dirac operators on manifolds with
boundary and APS boundary condition,” Annales Henri Poincare, vol. 26.
Springer Nature, pp. 2859–2900, 2025.
ista: Fialova M. 2025. Aharonov–Casher theorems for Dirac operators on manifolds
with boundary and APS boundary condition. Annales Henri Poincare. 26, 2859–2900.
mla: Fialova, Marie. “Aharonov–Casher Theorems for Dirac Operators on Manifolds
with Boundary and APS Boundary Condition.” Annales Henri Poincare, vol.
26, Springer Nature, 2025, pp. 2859–900, doi:10.1007/s00023-024-01482-7.
short: M. Fialova, Annales Henri Poincare 26 (2025) 2859–2900.
corr_author: '1'
das_tickbox: '0'
date_created: 2024-09-15T22:01:42Z
date_published: 2025-08-01T00:00:00Z
date_updated: 2026-09-17T11:06:35Z
day: '01'
ddc:
- '510'
department:
- _id: RoSe
doi: 10.1007/s00023-024-01482-7
ec_funded: 1
external_id:
arxiv:
- '2304.13373'
isi:
- '001304370000001'
file:
- access_level: open_access
checksum: d8d2d6dbce293c9ee6eaa9262e597147
content_type: application/pdf
creator: dernst
date_created: 2025-08-05T11:24:25Z
date_updated: 2025-08-05T11:24:25Z
file_id: '20124'
file_name: 2025_AnnalesHenriPoincare_Fialova.pdf
file_size: 728124
relation: main_file
success: 1
file_date_updated: 2025-08-05T11:24:25Z
fulldoi: https://doi.org/10.1007/s00023-024-01482-7
has_accepted_license: '1'
intvolume: ' 26'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 2859-2900
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Annales Henri Poincare
publication_identifier:
issn:
- 1424-0637
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Aharonov–Casher theorems for Dirac operators on manifolds with boundary and
APS boundary condition
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: 26
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '17293'
abstract:
- lang: eng
text: Voltage-gated CaV2.1 (P/Q-type) Ca2+ channels play a crucial role in regulating
neurotransmitter release, thus contributing to synaptic plasticity and to processes
such as learning and memory. Despite their recognized importance in neural function,
there is limited information on their potential involvement in neurodegenerative
conditions such as Alzheimer's disease (AD). Here, we aimed to explore the impact
of AD pathology on the density and nanoscale compartmentalization of CaV2.1 channels
in the hippocampus in association with GABAB receptors. Histoblotting experiments
showed that the density of CaV2.1 channel was significantly reduced in the hippocampus
of APP/PS1 mice in a laminar-dependent manner. CaV2.1 channel was enriched in
the active zone of the axon terminals and was present at a very low density over
the surface of dendritic tree of the CA1 pyramidal cells, as shown by quantitative
SDS-digested freeze-fracture replica labelling (SDS-FRL). In APP/PS1 mice, the
density of CaV2.1 channel in the active zone was significantly reduced in the
strata radiatum and lacunosum-moleculare, while it remained unaltered in the stratum
oriens. The decline in Cav2.1 channel density was found to be associated with
a corresponding impairment in the GABAergic synaptic function, as evidenced by
electrophysiological experiments carried out in the hippocampus of APP/PS1 mice.
Remarkably, double SDS-FRL showed a co-clustering of CaV2.1 channel and GABAB1
receptor in nanodomains (~40–50 nm) in wild type mice, while in APP/PS1 mice this
nanoarchitecture was absent. Together, these findings suggest that the AD pathology-induced
reduction in CaV2.1 channel density and CaV2.1-GABAB1 de-clustering may play a
role in the synaptic transmission alterations shown in the AD hippocampus. Therefore,
uncovering these layer-dependent changes in P/Q calcium currents associated with
AD pathology can benefit the development of future strategies for AD management.
acknowledgement: "Funding sources were Spanish Ministerio de Economía y Competitividad,
Junta de Comunidades de Castilla-La Mancha (Spain), Life Science Innovation Center
at University of Fukui and German Research Foundation.\r\nGrants RTI2018-095812-B-I00
and PID2021-125875OB-I00 funded by MCIN/AEI/10.13039/501100011033 and by “ERDF A
way of making Europe” to Rafael Luján. This study was also supported by a grant
from Junta de Comunidades de Castilla-La Mancha (SBPLY/17/180501/000229 and SBPLY/21/180501/000064)
and Universidad de Castilla-La Mancha (2023-GRIN-34187) to Rafael Luján, and Life
Science Innovation Center (Research and Education Program for Life Science) at University
of Fukui and JSPS KAKENHI Grant Numbers 16H04662, 17K19446, 18H05120 to Yugo Fukazawa
and Margarita Salas fellowship from Ministerio de Universidades and Universidad
de Castilla-La Mancha to Alejandro Martín-Belmonte. German Research Foundation (DFG
FOR 2143) and BIOSS-2 to Akos Kulik."
article_number: e13279
article_processing_charge: Yes
article_type: original
author:
- first_name: Alejandro
full_name: Martín‐Belmonte, Alejandro
last_name: Martín‐Belmonte
- first_name: Carolina
full_name: Aguado, Carolina
last_name: Aguado
- first_name: Rocío
full_name: Alfaro‐Ruiz, Rocío
last_name: Alfaro‐Ruiz
- first_name: Akos
full_name: Kulik, Akos
last_name: Kulik
- first_name: Luis
full_name: de la Ossa, Luis
last_name: de la Ossa
- first_name: Ana Esther
full_name: Moreno‐Martínez, Ana Esther
last_name: Moreno‐Martínez
- first_name: Samuel
full_name: Alberquilla, Samuel
last_name: Alberquilla
- first_name: Lucía
full_name: García‐Carracedo, Lucía
last_name: García‐Carracedo
- first_name: Miriam
full_name: Fernández, Miriam
last_name: Fernández
- first_name: Ana
full_name: Fajardo‐Serrano, Ana
last_name: Fajardo‐Serrano
- first_name: Ester
full_name: Aso, Ester
last_name: Aso
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Eduardo D.
full_name: Martín, Eduardo D.
last_name: Martín
- first_name: Yugo
full_name: Fukazawa, Yugo
last_name: Fukazawa
- first_name: Francisco
full_name: Ciruela, Francisco
last_name: Ciruela
- first_name: Rafael
full_name: Luján, Rafael
last_name: Luján
citation:
ama: 'Martín‐Belmonte A, Aguado C, Alfaro‐Ruiz R, et al. Nanoarchitecture of CaV>2.1
channels and GABAB receptors in the mouse hippocampus: Impact of APP/PS1 pathology.
Brain Pathology. 2025;35(2). doi:10.1111/bpa.13279'
apa: 'Martín‐Belmonte, A., Aguado, C., Alfaro‐Ruiz, R., Kulik, A., de la Ossa, L.,
Moreno‐Martínez, A. E., … Luján, R. (2025). Nanoarchitecture of CaV>2.1 channels
and GABAB receptors in the mouse hippocampus: Impact of APP/PS1 pathology. Brain
Pathology. Wiley. https://doi.org/10.1111/bpa.13279'
chicago: 'Martín‐Belmonte, Alejandro, Carolina Aguado, Rocío Alfaro‐Ruiz, Akos Kulik,
Luis de la Ossa, Ana Esther Moreno‐Martínez, Samuel Alberquilla, et al. “Nanoarchitecture
of CaV>2.1 Channels and GABAB Receptors in the Mouse Hippocampus: Impact of
APP/PS1 Pathology.” Brain Pathology. Wiley, 2025. https://doi.org/10.1111/bpa.13279.'
ieee: 'A. Martín‐Belmonte et al., “Nanoarchitecture of CaV>2.1 channels
and GABAB receptors in the mouse hippocampus: Impact of APP/PS1 pathology,” Brain
Pathology, vol. 35, no. 2. Wiley, 2025.'
ista: 'Martín‐Belmonte A, Aguado C, Alfaro‐Ruiz R, Kulik A, de la Ossa L, Moreno‐Martínez
AE, Alberquilla S, García‐Carracedo L, Fernández M, Fajardo‐Serrano A, Aso E,
Shigemoto R, Martín ED, Fukazawa Y, Ciruela F, Luján R. 2025. Nanoarchitecture
of CaV>2.1 channels and GABAB receptors in the mouse hippocampus: Impact of
APP/PS1 pathology. Brain Pathology. 35(2), e13279.'
mla: 'Martín‐Belmonte, Alejandro, et al. “Nanoarchitecture of CaV>2.1 Channels
and GABAB Receptors in the Mouse Hippocampus: Impact of APP/PS1 Pathology.” Brain
Pathology, vol. 35, no. 2, e13279, Wiley, 2025, doi:10.1111/bpa.13279.'
short: A. Martín‐Belmonte, C. Aguado, R. Alfaro‐Ruiz, A. Kulik, L. de la Ossa, A.E.
Moreno‐Martínez, S. Alberquilla, L. García‐Carracedo, M. Fernández, A. Fajardo‐Serrano,
E. Aso, R. Shigemoto, E.D. Martín, Y. Fukazawa, F. Ciruela, R. Luján, Brain Pathology
35 (2025).
das_tickbox: '1'
dataavailabilitystatement: All data used and/or analyzed during the current study
are available from the corresponding author on reasonable request.
date_created: 2024-07-22T07:48:20Z
date_published: 2025-03-01T00:00:00Z
date_updated: 2026-09-17T11:10:34Z
day: '01'
ddc:
- '570'
department:
- _id: RySh
doi: 10.1111/bpa.13279
external_id:
isi:
- '001250034200001'
pmid:
- '38887180'
file:
- access_level: open_access
checksum: 75a172800ab2e949abb66fba97cf70f0
content_type: application/pdf
creator: dernst
date_created: 2025-04-16T09:56:08Z
date_updated: 2025-04-16T09:56:08Z
file_id: '19582'
file_name: 2025_BrainPathology_MartinBelmonte.pdf
file_size: 8767863
relation: main_file
success: 1
file_date_updated: 2025-04-16T09:56:08Z
fulldoi: https://doi.org/10.1111/bpa.13279
has_accepted_license: '1'
intvolume: ' 35'
isi: 1
issue: '2'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: Brain Pathology
publication_identifier:
eissn:
- 1750-3639
issn:
- 1015-6305
publication_status: published
publisher: Wiley
quality_controlled: '1'
researchdata_availability: upon request
scopus_import: '1'
status: public
supplementarymaterial: yes
title: 'Nanoarchitecture of CaV>2.1 channels and GABAB receptors in the mouse hippocampus:
Impact of APP/PS1 pathology'
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: 35
year: '2025'
...
---
OA_place: publisher
_id: '20292'
abstract:
- lang: eng
text: In automated decision-making, it is desirable that outputs of decision-makers
be robust to slight perturbations in their inputs, a property that may be called
input-output robustness. Input-output robustness appears in various different
forms in the literature, such as robustness of AI models to adversarial or semantic
perturbations and individual fairness of AI models that make decisions about humans.
We propose runtime monitoring of input-output robustness of deployed, black-box
AI models, where the goal is to design monitors that would observe one long execution
sequence of the model, and would raise an alarm whenever it is detected that two
similar inputs from the past led to dissimilar outputs. This way, monitoring will
complement existing offline ''robustification'' approaches to increase the trustworthiness
of AI decision-makers. We show that the monitoring problem can be cast as the
fixed-radius nearest neighbor (FRNN) search problem, which, despite being well-studied,
lacks suitable online solutions. We present our tool Clemont, which offers a number
of lightweight monitors, some of which use upgraded online variants of existing
FRNN algorithms, and one uses a novel algorithm based on binary decision diagrams--a
data-structure commonly used in software and hardware verification. We have also
developed an efficient parallelization technique that can substantially cut down
the computation time of monitors for which the distance between input-output pairs
is measured using the L∞norm. Using standard benchmarks from the literature of
adversarial and semantic robustness and individual fairness, we perform a comparative
study of different monitors in Clemont, and demonstrate their effectiveness in
correctly detecting robustness violations at runtime.
acknowledgement: This work was supported in part by the ERC project ERC-2020-AdG 101020093
and the SBI Foundation Hub for Data Science &Analytics, IIT Bombay.
article_processing_charge: No
arxiv: 1
author:
- first_name: Ashutosh
full_name: Gupta, Ashutosh
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Konstantin
full_name: Kueffner, Konstantin
id: 8121a2d0-dc85-11ea-9058-af578f3b4515
last_name: Kueffner
orcid: 0000-0001-8974-2542
- first_name: Kaushik
full_name: Mallik, Kaushik
id: 0834ff3c-6d72-11ec-94e0-b5b0a4fb8598
last_name: Mallik
orcid: 0000-0001-9864-7475
- first_name: David
full_name: Pape, David
last_name: Pape
citation:
ama: 'Gupta A, Henzinger TA, Kueffner K, Mallik K, Pape D. Monitoring robustness
and individual fairness. In: Proceedings of the 31st ACM SIGKDD Conference
on Knowledge Discovery and Data Mining. Vol 2. Association for Computing Machinery;
2025:790-801. doi:10.1145/3711896.3737054'
apa: 'Gupta, A., Henzinger, T. A., Kueffner, K., Mallik, K., & Pape, D. (2025).
Monitoring robustness and individual fairness. In Proceedings of the 31st ACM
SIGKDD Conference on Knowledge Discovery and Data Mining (Vol. 2, pp. 790–801).
Toronto, Canada: Association for Computing Machinery. https://doi.org/10.1145/3711896.3737054'
chicago: Gupta, Ashutosh, Thomas A Henzinger, Konstantin Kueffner, Kaushik Mallik,
and David Pape. “Monitoring Robustness and Individual Fairness.” In Proceedings
of the 31st ACM SIGKDD Conference on Knowledge Discovery and Data Mining,
2:790–801. Association for Computing Machinery, 2025. https://doi.org/10.1145/3711896.3737054.
ieee: A. Gupta, T. A. Henzinger, K. Kueffner, K. Mallik, and D. Pape, “Monitoring
robustness and individual fairness,” in Proceedings of the 31st ACM SIGKDD
Conference on Knowledge Discovery and Data Mining, Toronto, Canada, 2025,
vol. 2, pp. 790–801.
ista: 'Gupta A, Henzinger TA, Kueffner K, Mallik K, Pape D. 2025. Monitoring robustness
and individual fairness. Proceedings of the 31st ACM SIGKDD Conference on Knowledge
Discovery and Data Mining. KDD: Conference on Knowledge Discovery and Data Mining
vol. 2, 790–801.'
mla: Gupta, Ashutosh, et al. “Monitoring Robustness and Individual Fairness.” Proceedings
of the 31st ACM SIGKDD Conference on Knowledge Discovery and Data Mining,
vol. 2, Association for Computing Machinery, 2025, pp. 790–801, doi:10.1145/3711896.3737054.
short: A. Gupta, T.A. Henzinger, K. Kueffner, K. Mallik, D. Pape, in:, Proceedings
of the 31st ACM SIGKDD Conference on Knowledge Discovery and Data Mining, Association
for Computing Machinery, 2025, pp. 790–801.
conference:
end_date: 2025-08-07
location: Toronto, Canada
name: 'KDD: Conference on Knowledge Discovery and Data Mining'
start_date: 2025-08-03
corr_author: '1'
date_created: 2025-09-07T22:01:33Z
date_published: 2025-08-03T00:00:00Z
date_updated: 2026-09-18T07:41:29Z
day: '03'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1145/3711896.3737054
ec_funded: 1
external_id:
arxiv:
- '2506.00496'
file:
- access_level: open_access
checksum: 81e18cdf9ca5f6dfa79425b326ea9725
content_type: application/pdf
creator: dernst
date_created: 2025-09-08T08:46:31Z
date_updated: 2025-09-08T08:46:31Z
file_id: '20310'
file_name: 2025_KDD_Gupta.pdf
file_size: 7745940
relation: main_file
success: 1
file_date_updated: 2025-09-08T08:46:31Z
fulldoi: https://doi.org/10.1145/3711896.3737054
has_accepted_license: '1'
intvolume: ' 2'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 790-801
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: Proceedings of the 31st ACM SIGKDD Conference on Knowledge Discovery
and Data Mining
publication_identifier:
isbn:
- '9798400714542'
issn:
- 2154-817X
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/ariez-xyz/clemont
record:
- id: '22808'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Monitoring robustness and individual fairness
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: 2
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '21090'
abstract:
- lang: eng
text: Fairness in AI is traditionally studied as a static property evaluated once,
over a fixed dataset. However, real-world AI systems operate sequentially, with
outcomes and environments evolving over time. This paper proposes a framework
for analysing fairness as a runtime property. Using a minimal yet expressive model
based on sequences of coin tosses with possibly evolving biases, we study the
problems of monitoring and enforcing fairness expressed in either toss outcomes
or coin biases. Since there is no one-size-fits-all solution for either problem,
we provide a summary of monitoring and enforcement strategies, parametrised by
environment dynamics, prediction horizon, and confidence thresholds. For both
problems, we present general results under simple or minimal assumptions. We survey
existing solutions for the monitoring problem for Markovian and additive dynamics,
and existing solutions for the enforcement problem in static settings with known
dynamics.
acknowledgement: 'This work is supported by the European Research Council under Grant
No.: ERC-2020-AdG 101020093.'
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Filip
full_name: Cano Cordoba, Filip
id: 708cad98-e86a-11ef-8098-bdae2d7c6af1
last_name: Cano Cordoba
orcid: 0000-0002-0783-904X
- 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: Konstantin
full_name: Kueffner, Konstantin
id: 8121a2d0-dc85-11ea-9058-af578f3b4515
last_name: Kueffner
orcid: 0000-0001-8974-2542
citation:
ama: 'Cano Cordoba F, Henzinger TA, Kueffner K. Algorithmic fairness: A runtime
perspective. In: 25th International Conference on Runtime Verification.
Vol 16087. Springer Nature; 2025:1-21. doi:10.1007/978-3-032-05435-7_1'
apa: 'Cano Cordoba, F., Henzinger, T. A., & Kueffner, K. (2025). Algorithmic
fairness: A runtime perspective. In 25th International Conference on Runtime
Verification (Vol. 16087, pp. 1–21). Graz, Austria: Springer Nature. https://doi.org/10.1007/978-3-032-05435-7_1'
chicago: 'Cano Cordoba, Filip, Thomas A Henzinger, and Konstantin Kueffner. “Algorithmic
Fairness: A Runtime Perspective.” In 25th International Conference on Runtime
Verification, 16087:1–21. Springer Nature, 2025. https://doi.org/10.1007/978-3-032-05435-7_1.'
ieee: 'F. Cano Cordoba, T. A. Henzinger, and K. Kueffner, “Algorithmic fairness:
A runtime perspective,” in 25th International Conference on Runtime Verification,
Graz, Austria, 2025, vol. 16087, pp. 1–21.'
ista: 'Cano Cordoba F, Henzinger TA, Kueffner K. 2025. Algorithmic fairness: A runtime
perspective. 25th International Conference on Runtime Verification. RV: Runtime
Verification, LNCS, vol. 16087, 1–21.'
mla: 'Cano Cordoba, Filip, et al. “Algorithmic Fairness: A Runtime Perspective.”
25th International Conference on Runtime Verification, vol. 16087, Springer
Nature, 2025, pp. 1–21, doi:10.1007/978-3-032-05435-7_1.'
short: F. Cano Cordoba, T.A. Henzinger, K. Kueffner, in:, 25th International Conference
on Runtime Verification, Springer Nature, 2025, pp. 1–21.
conference:
end_date: 2025-09-19
location: Graz, Austria
name: 'RV: Runtime Verification'
start_date: 2025-09-15
corr_author: '1'
date_created: 2026-01-29T16:01:41Z
date_published: 2025-09-13T00:00:00Z
date_updated: 2026-09-18T07:41:29Z
day: '13'
department:
- _id: ToHe
doi: 10.1007/978-3-032-05435-7_1
ec_funded: 1
external_id:
arxiv:
- '2507.20711'
fulldoi: https://doi.org/10.1007/978-3-032-05435-7_1
intvolume: ' 16087'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2507.20711
month: '09'
oa: 1
oa_version: Preprint
page: 1-21
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: 25th International Conference on Runtime Verification
publication_identifier:
eisbn:
- '9783032054357'
eissn:
- 1611-3349
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '22808'
relation: dissertation_contains
status: public
status: public
title: 'Algorithmic fairness: A runtime perspective'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16087
year: '2025'
...
---
APC_amount: 2754,32 EUR
OA_place: publisher
OA_type: hybrid
_id: '19627'
abstract:
- lang: eng
text: Differentially private gradient descent (DP-GD) is a popular algorithm to
train deep learning models with provable guarantees on the privacy of the training
data. In the last decade, the problem of understanding its performance cost with
respect to standard GD has received remarkable attention from the research community,
which formally derived upper bounds on the excess population risk RP in different
learning settings. However, existing bounds typically degrade with over-parameterization,
i.e., as the number of parameters p gets larger than the number of training
samples n -- a regime which is ubiquitous in current deep-learning practice.
As a result, the lack of theoretical insights leaves practitioners without clear
guidance, leading some to reduce the effective number of trainable parameters
to improve performance, while others use larger models to achieve better results
through scale. In this work, we show that in the popular random features model
with quadratic loss, for any sufficiently large p , privacy can be obtained for
free, i.e., |RP|=o(1) , not only when the privacy parameter ε has constant
order, but also in the strongly private setting ε=o(1) . This challenges the
common wisdom that over-parameterization inherently hinders performance in private
learning.
acknowledgement: This research was funded in whole, or in part, by the Austrian Science
Fund (FWF) Grant number COE 12. For the purpose of open access, the author has applied
a CC BY public copyright license to any Author Accepted Manuscript version arising
from this submission. The authors were also supported by the 2019 Lopez-Loreta prize,
and Simone Bombari was supported by a Google PhD fellowship. We thank Diyuan Wu,
Edwige Cyffers, Francesco Pedrotti, Inbar Seroussi, Nikita P. Kalinin, Pietro Pelliconi,
Roodabeh Safavi, Yizhe Zhu, and Zhichao Wang for helpful discussions.
article_number: e2423072122
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Simone
full_name: Bombari, Simone
id: ca726dda-de17-11ea-bc14-f9da834f63aa
last_name: Bombari
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
citation:
ama: Bombari S, Mondelli M. Privacy for free in the overparameterized regime. Proceedings
of the National Academy of Sciences. 2025;122(15). doi:10.1073/pnas.2423072122
apa: Bombari, S., & Mondelli, M. (2025). Privacy for free in the overparameterized
regime. Proceedings of the National Academy of Sciences. National Academy
of Sciences. https://doi.org/10.1073/pnas.2423072122
chicago: Bombari, Simone, and Marco Mondelli. “Privacy for Free in the Overparameterized
Regime.” Proceedings of the National Academy of Sciences. National Academy
of Sciences, 2025. https://doi.org/10.1073/pnas.2423072122.
ieee: S. Bombari and M. Mondelli, “Privacy for free in the overparameterized regime,”
Proceedings of the National Academy of Sciences, vol. 122, no. 15. National
Academy of Sciences, 2025.
ista: Bombari S, Mondelli M. 2025. Privacy for free in the overparameterized regime.
Proceedings of the National Academy of Sciences. 122(15), e2423072122.
mla: Bombari, Simone, and Marco Mondelli. “Privacy for Free in the Overparameterized
Regime.” Proceedings of the National Academy of Sciences, vol. 122, no.
15, e2423072122, National Academy of Sciences, 2025, doi:10.1073/pnas.2423072122.
short: S. Bombari, M. Mondelli, Proceedings of the National Academy of Sciences
122 (2025).
corr_author: '1'
date_created: 2025-04-27T22:02:13Z
date_published: 2025-04-15T00:00:00Z
date_updated: 2026-09-21T13:07:01Z
day: '15'
ddc:
- '000'
department:
- _id: MaMo
doi: 10.1073/pnas.2423072122
external_id:
arxiv:
- '2410.14787'
isi:
- '001471214000001'
pmid:
- '40215275'
file:
- access_level: open_access
checksum: 1ac6f78e368d35a0cafb4d2d9bd63443
content_type: application/pdf
creator: dernst
date_created: 2025-05-05T07:27:54Z
date_updated: 2025-05-05T07:27:54Z
file_id: '19648'
file_name: 2025_PNAS_Bombari.pdf
file_size: 2328320
relation: main_file
success: 1
file_date_updated: 2025-05-05T07:27:54Z
fulldoi: https://doi.org/10.1073/pnas.2423072122
has_accepted_license: '1'
intvolume: ' 122'
isi: 1
issue: '15'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 059876FA-7A3F-11EA-A408-12923DDC885E
name: Prix Lopez-Loretta 2019 - Marco Mondelli
- _id: 92099302-16d5-11f0-9cad-f9a785f54fbd
name: 'Trustworthy Deep Learning Theory: Private Over-Parameterized Models and Robust
LLMs'
- _id: 74caaef7-b034-11f1-8f2d-e0e993bb422e
grant_number: COE12
name: Bilateral Artificial Intelligence (Mondelli)
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
record:
- id: '22857'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Privacy for free in the overparameterized regime
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: 122
year: '2025'
...
---
OA_place: publisher
OA_type: gold
_id: '21324'
abstract:
- lang: eng
text: Learning models have been shown to rely on spurious correlations between non-predictive
features and the associated labels in the training data, with negative implications
on robustness, bias and fairness. In this work, we provide a statistical characterization
of this phenomenon for high-dimensional regression, when the data contains a predictive
core feature x and a spurious feature y. Specifically, we quantify the amount
of spurious correlations C learned via linear regression, in terms of the data
covariance and the strength λ of the ridge regularization. As a consequence, we
first capture the simplicity of y through the spectrum of its covariance, and
its correlation with x through the Schur complement of the full data covariance.
Next, we prove a trade-off between C and the in-distribution test loss L, by showing
that the value of λ that minimizes L lies in an interval where C is increasing.
Finally, we investigate the effects of over-parameterization via the random features
model, by showing its equivalence to regularized linear regression. Our theoretical
results are supported by numerical experiments on Gaussian, Color-MNIST, and CIFAR-10
datasets.
acknowledgement: Marco Mondelli is funded by the European Union (ERC, INF2, project
number 101161364). Views and opinions expressed are however those of the author(s)
only and do not necessarily reflect those of the European Union or the European
Research Council Executive Agency. Neither the European Union nor the granting authority
can be held responsible for them. Simone Bombari is supported by a Google PhD fellowship.
The authors would like to thank GuanWen Qiu for helpful discussions.
alternative_title:
- PMLR
article_processing_charge: No
arxiv: 1
author:
- first_name: Simone
full_name: Bombari, Simone
id: ca726dda-de17-11ea-bc14-f9da834f63aa
last_name: Bombari
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
citation:
ama: 'Bombari S, Mondelli M. Spurious correlations in high dimensional regression:
The roles of regularization, simplicity bias and over-parameterization. In: Proceedings
of the 42nd International Conference on Machine Learning. Vol 267. ML Research
Press; 2025:4839-4873.'
apa: 'Bombari, S., & Mondelli, M. (2025). Spurious correlations in high dimensional
regression: The roles of regularization, simplicity bias and over-parameterization.
In Proceedings of the 42nd International Conference on Machine Learning
(Vol. 267, pp. 4839–4873). Vancouver, Canada: ML Research Press.'
chicago: 'Bombari, Simone, and Marco Mondelli. “Spurious Correlations in High Dimensional
Regression: The Roles of Regularization, Simplicity Bias and over-Parameterization.”
In Proceedings of the 42nd International Conference on Machine Learning,
267:4839–73. ML Research Press, 2025.'
ieee: 'S. Bombari and M. Mondelli, “Spurious correlations in high dimensional regression:
The roles of regularization, simplicity bias and over-parameterization,” in Proceedings
of the 42nd International Conference on Machine Learning, Vancouver, Canada,
2025, vol. 267, pp. 4839–4873.'
ista: 'Bombari S, Mondelli M. 2025. Spurious correlations in high dimensional regression:
The roles of regularization, simplicity bias and over-parameterization. Proceedings
of the 42nd International Conference on Machine Learning. ICML: International
Conference on Machine Learning, PMLR, vol. 267, 4839–4873.'
mla: 'Bombari, Simone, and Marco Mondelli. “Spurious Correlations in High Dimensional
Regression: The Roles of Regularization, Simplicity Bias and over-Parameterization.”
Proceedings of the 42nd International Conference on Machine Learning, vol.
267, ML Research Press, 2025, pp. 4839–73.'
short: S. Bombari, M. Mondelli, in:, Proceedings of the 42nd International Conference
on Machine Learning, ML Research Press, 2025, pp. 4839–4873.
conference:
end_date: 2025-07-19
location: Vancouver, Canada
name: 'ICML: International Conference on Machine Learning'
start_date: 2025-07-13
corr_author: '1'
date_created: 2026-02-18T11:58:00Z
date_published: 2025-07-30T00:00:00Z
date_updated: 2026-09-21T13:07:01Z
day: '30'
ddc:
- '000'
department:
- _id: MaMo
external_id:
arxiv:
- '2502.01347'
file:
- access_level: open_access
checksum: d4ba4f7717b362ca38878f45e57bd643
content_type: application/pdf
creator: dernst
date_created: 2026-02-19T08:04:38Z
date_updated: 2026-02-19T08:04:38Z
file_id: '21335'
file_name: 2025_ICML_Bombari.pdf
file_size: 887526
relation: main_file
success: 1
file_date_updated: 2026-02-19T08:04:38Z
has_accepted_license: '1'
intvolume: ' 267'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 4839-4873
project:
- _id: 911e6d1f-16d5-11f0-9cad-c5c68c6a1cdf
grant_number: '101161364'
name: 'Inference in High Dimensions: Light-speed Algorithms and Information Limits'
- _id: 92099302-16d5-11f0-9cad-f9a785f54fbd
name: 'Trustworthy Deep Learning Theory: Private Over-Parameterized Models and Robust
LLMs'
publication: Proceedings of the 42nd International Conference on Machine Learning
publication_identifier:
eissn:
- 2640-3498
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
related_material:
record:
- id: '22857'
relation: dissertation_contains
status: public
status: public
title: 'Spurious correlations in high dimensional regression: The roles of regularization,
simplicity bias and over-parameterization'
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: 267
year: '2025'
...
---
APC_amount: 1395,61 EUR
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '20370'
abstract:
- lang: eng
text: The Huntingtin protein (HTT), named for its role in Huntington’s disease,
has been best understood as a scaffolding protein that promotes vesicle transport
by molecular motors along microtubules. Here, we show that HTT also interacts
with the actin cytoskeleton, and its loss of function disturbs the morphology
and function of the axonal growth cone. We demonstrate that HTT organizes F-actin
into bundles. Cryo–electron tomography (cryo-ET) and subtomogram averaging (STA)
structural analyses reveal that HTT’s N-terminal HEAT and Bridge domains wrap
around F-actin, while the C-terminal HEAT domain is displaced; furthermore, HTT
dimerizes via the N-HEAT domain to bridge parallel actin filaments separated by
~20 nanometers. Our study provides the structural basis for understanding how
HTT interacts with and organizes the actin cytoskeleton.
acknowledgement: 'We thank C. Cuveillier, J. Delaroche, T. Ferraro, and A. Zanchi
for help with TIRF experiments, electron microscopy preparation, data analysis,
and cell cultures, respectively; A. Antkowiak, C. Bosc, C. Fassier, A. Fourest-Lieuvin,
and V. Brandt for helpful discussions. We acknowledge the contribution of the Photonic
Imaging Center of Grenoble Institute Neuroscience which is part of the ISdV core
facility and certified by the IBiSA label and ICM.Quant (RRID:SCR_026393) core facility
of the Paris Brain Institute (ICM); the AniRA lentivector production facility from
the CELPHEDIA Infrastructure and SFR Biosciences (UAR3444/CNRS, US8/Inserm, ENS
de Lyon, UCBL); the Scientific Service Units (SSUs) of ISTA through resources provided
by Scientific Computing (SciComp, A. Schloegl and S. Elefante); and the Electron
Microscopy Facility (EMF, V.V. Hodirnau). The software programs used for the processing
were supported by SBGrid (www.sbgrid.org). This work was supported by the Agence
Nationale pour la Recherche (AXYON: ANR-18-CE16-0009-01, S.H.), Austrian Science
Fund (FWF) grants (P33367, F.K.M.S.; E435, J.M.H.), ChanZuckerberg Initiative (CZI)
grant (DAF2021-234754, F.K.M.S.), Hereditary Disease Foundation Research Grant (HDF
990846, M.C.), European Union (ERC: ActinID 101076260, F.K.M.S.), Fondation pour
la Recherche Médicale (FRM: équipe labellisée DEQ202203014675, S.H.; PhD fellowship,
FDT202001010865, R.C.), Korea Health Industry Development Institute (KHIDI) (Korea-Switzerland
global research support grant: RS-2023-00266300, J.-J.S.), National Research Foundation
(NRF) of Korea (Korea-Austria collaborative grant NRF-2019K1A3A1A181160, J.-J.S.
and F.K.M.S.; NRF-2020R1A2B5B03001517 and RS-2024-00333346 and RS-2024-00436173,
J.-J.S.; 2021R1C1C1006700, D.K.).'
article_number: eadw4124
article_processing_charge: Yes
article_type: original
author:
- first_name: Rémi
full_name: Carpentier, Rémi
last_name: Carpentier
- first_name: Jaesung
full_name: Kim, Jaesung
last_name: Kim
- first_name: Mariacristina
full_name: Capizzi, Mariacristina
last_name: Capizzi
- first_name: Hyeongju
full_name: Kim, Hyeongju
last_name: Kim
- first_name: Florian
full_name: Fäßler, Florian
id: 404F5528-F248-11E8-B48F-1D18A9856A87
last_name: Fäßler
orcid: 0000-0001-7149-769X
- first_name: Jesse
full_name: Hansen, Jesse
id: 1063c618-6f9b-11ec-9123-f912fccded63
last_name: Hansen
orcid: 0000-0001-7967-2085
- first_name: Min Jeong
full_name: Kim, Min Jeong
last_name: Kim
- first_name: Eric
full_name: Denarier, Eric
last_name: Denarier
- first_name: Béatrice
full_name: Blot, Béatrice
last_name: Blot
- first_name: Marine
full_name: Degennaro, Marine
last_name: Degennaro
- first_name: Sophia
full_name: Labou, Sophia
last_name: Labou
- first_name: Isabelle
full_name: Arnal, Isabelle
last_name: Arnal
- first_name: Maria J.
full_name: Marcaida, Maria J.
last_name: Marcaida
- first_name: Matteo Dal
full_name: Peraro, Matteo Dal
last_name: Peraro
- first_name: Doory
full_name: Kim, Doory
last_name: Kim
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Ji-Joon
full_name: Song, Ji-Joon
last_name: Song
- first_name: Sandrine
full_name: Humbert, Sandrine
last_name: Humbert
citation:
ama: Carpentier R, Kim J, Capizzi M, et al. Structure of the Huntingtin F-actin
complex reveals its role in cytoskeleton organization. Science Advances.
2025;11(38). doi:10.1126/sciadv.adw4124
apa: Carpentier, R., Kim, J., Capizzi, M., Kim, H., Fäßler, F., Hansen, J., … Humbert,
S. (2025). Structure of the Huntingtin F-actin complex reveals its role in cytoskeleton
organization. Science Advances. AAAS. https://doi.org/10.1126/sciadv.adw4124
chicago: Carpentier, Rémi, Jaesung Kim, Mariacristina Capizzi, Hyeongju Kim, Florian
Fäßler, Jesse Hansen, Min Jeong Kim, et al. “Structure of the Huntingtin F-Actin
Complex Reveals Its Role in Cytoskeleton Organization.” Science Advances.
AAAS, 2025. https://doi.org/10.1126/sciadv.adw4124.
ieee: R. Carpentier et al., “Structure of the Huntingtin F-actin complex
reveals its role in cytoskeleton organization,” Science Advances, vol.
11, no. 38. AAAS, 2025.
ista: Carpentier R, Kim J, Capizzi M, Kim H, Fäßler F, Hansen J, Kim MJ, Denarier
E, Blot B, Degennaro M, Labou S, Arnal I, Marcaida MJ, Peraro MD, Kim D, Schur
FK, Song J-J, Humbert S. 2025. Structure of the Huntingtin F-actin complex reveals
its role in cytoskeleton organization. Science Advances. 11(38), eadw4124.
mla: Carpentier, Rémi, et al. “Structure of the Huntingtin F-Actin Complex Reveals
Its Role in Cytoskeleton Organization.” Science Advances, vol. 11, no.
38, eadw4124, AAAS, 2025, doi:10.1126/sciadv.adw4124.
short: R. Carpentier, J. Kim, M. Capizzi, H. Kim, F. Fäßler, J. Hansen, M.J. Kim,
E. Denarier, B. Blot, M. Degennaro, S. Labou, I. Arnal, M.J. Marcaida, M.D. Peraro,
D. Kim, F.K. Schur, J.-J. Song, S. Humbert, Science Advances 11 (2025).
corr_author: '1'
date_created: 2025-09-22T08:00:52Z
date_published: 2025-09-19T00:00:00Z
date_updated: 2026-09-24T08:17:37Z
day: '19'
ddc:
- '570'
department:
- _id: FlSc
doi: 10.1126/sciadv.adw4124
external_id:
isi:
- '001575751700013'
pmid:
- '40971423'
file:
- access_level: open_access
checksum: 4e2407bdabf8d53f399eb8a20d86218e
content_type: application/pdf
creator: dernst
date_created: 2025-09-23T07:57:51Z
date_updated: 2025-09-23T07:57:51Z
file_id: '20372'
file_name: 2025_ScienceAdvance_Carpentier.pdf
file_size: 3599137
relation: main_file
success: 1
file_date_updated: 2025-09-23T07:57:51Z
fulldoi: https://doi.org/10.1126/sciadv.adw4124
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
issue: '38'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 9B954C5C-BA93-11EA-9121-9846C619BF3A
grant_number: P33367
name: Structure and isoform diversity of the Arp2/3 complex
- _id: 7bd318a1-9f16-11ee-852c-cc9217763180
grant_number: E435
name: In Situ Actin Structures via Hybrid Cryo-electron Microscopy
- _id: 62909c6f-2b32-11ec-9570-e1476aab5308
grant_number: CZI01
name: CryoMinflux-guided in-situ molecular census and structure determination
- _id: bd980d18-d553-11ed-ba76-ceaa645c97eb
grant_number: '101076260'
name: A molecular atlas of Actin filament IDentities in the cell motility machinery
- _id: 3AC91DDA-15DF-11EA-824D-93A3E7B544D1
call_identifier: FWF
name: FWF Open Access Fund
publication: Science Advances
publication_identifier:
eissn:
- 2375-2548
publication_status: published
publisher: AAAS
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structure of the Huntingtin F-actin complex reveals its role in cytoskeleton
organization
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20324'
abstract:
- lang: eng
text: We report relaxation oscillations in a one-dimensional array of Josephson
junctions, wherein the array dynamically switches between low-current and high-current
states. The oscillations are current-voltage dual to those ordinarily observed
in single junctions. The current-voltage dual circuit quantitatively accounts
for temporal dynamics of the array, including the dependence on biasing conditions.
Injection locking of the oscillations results in well-developed current plateaux.
A thermal model explains the self-consistent reduction of the superconducting
gap due to overheating of the array in the high-current state. Our work suggests
that overheating determines the switching from the high-current state to the low-current
state.
acknowledged_ssus:
- _id: M-Shop
- _id: NanoFab
acknowledgement: We gratefully acknowledge support from the Miba Machine Shop and
the Nanofabrictation Facility at IST Austria. This work was supported by the Austrian
FWF under Grant No. P33692-N (S.M., J.S., and A.P.H.), the European Union’s Horizon
2020 research and innovation program under Marie Skłodowska-Curie Grant Agreement
No. 754411 (J.S.), and a NOMIS Foundation research grant (A.P.H.).
article_number: '014035'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Soham
full_name: Mukhopadhyay, Soham
id: FDE60288-A89D-11E9-947F-1AF6E5697425
last_name: Mukhopadhyay
orcid: 0000-0001-5263-5559
- first_name: Diego A
full_name: Lancheros Naranjo, Diego A
id: 6c55e976-15b2-11ec-abd3-d790e8937fde
last_name: Lancheros Naranjo
- first_name: Jorden L
full_name: Senior, Jorden L
id: 5479D234-2D30-11EA-89CC-40953DDC885E
last_name: Senior
orcid: 0000-0002-0672-9295
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
citation:
ama: Mukhopadhyay S, Lancheros Naranjo DA, Senior JL, Higginbotham AP. Dual relaxation
oscillations in a Josephson-junction array. Physical Review Applied. 2025;24.
doi:10.1103/qvls-7s3q
apa: Mukhopadhyay, S., Lancheros Naranjo, D. A., Senior, J. L., & Higginbotham,
A. P. (2025). Dual relaxation oscillations in a Josephson-junction array. Physical
Review Applied. American Physical Society. https://doi.org/10.1103/qvls-7s3q
chicago: Mukhopadhyay, Soham, Diego A Lancheros Naranjo, Jorden L Senior, and Andrew
P Higginbotham. “Dual Relaxation Oscillations in a Josephson-Junction Array.”
Physical Review Applied. American Physical Society, 2025. https://doi.org/10.1103/qvls-7s3q.
ieee: S. Mukhopadhyay, D. A. Lancheros Naranjo, J. L. Senior, and A. P. Higginbotham,
“Dual relaxation oscillations in a Josephson-junction array,” Physical Review
Applied, vol. 24. American Physical Society, 2025.
ista: Mukhopadhyay S, Lancheros Naranjo DA, Senior JL, Higginbotham AP. 2025. Dual
relaxation oscillations in a Josephson-junction array. Physical Review Applied.
24, 014035.
mla: Mukhopadhyay, Soham, et al. “Dual Relaxation Oscillations in a Josephson-Junction
Array.” Physical Review Applied, vol. 24, 014035, American Physical Society,
2025, doi:10.1103/qvls-7s3q.
short: S. Mukhopadhyay, D.A. Lancheros Naranjo, J.L. Senior, A.P. Higginbotham,
Physical Review Applied 24 (2025).
corr_author: '1'
date_created: 2025-09-10T05:41:30Z
date_published: 2025-07-17T00:00:00Z
date_updated: 2026-09-24T10:13:38Z
day: '17'
ddc:
- '530'
department:
- _id: GradSch
- _id: AnHi
doi: 10.1103/qvls-7s3q
ec_funded: 1
external_id:
arxiv:
- '2408.07829 '
isi:
- '001537333100001'
file:
- access_level: open_access
checksum: 6cc3c9beeb7c0a88ee0a072c9a32b78b
content_type: application/pdf
creator: dernst
date_created: 2025-09-10T07:29:06Z
date_updated: 2025-09-10T07:29:06Z
file_id: '20335'
file_name: 2025_PhysReviewAppl_Mukhopadhyay.pdf
file_size: 1370466
relation: main_file
success: 1
file_date_updated: 2025-09-10T07:29:06Z
fulldoi: https://doi.org/10.1103/qvls-7s3q
has_accepted_license: '1'
intvolume: ' 24'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 0aa3608a-070f-11eb-9043-e9cd8a2bd931
grant_number: P33692
name: Cavity electromechanics across a quantum phase transition
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: eb9b30ac-77a9-11ec-83b8-871f581d53d2
name: Protected states of quantum matter
publication: Physical Review Applied
publication_identifier:
issn:
- 2331-7019
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
record:
- id: '18057'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Dual relaxation oscillations in a Josephson-junction array
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: 24
year: '2025'
...
---
OA_place: publisher
OA_type: gold
_id: '19370'
abstract:
- lang: eng
text: Sex-linked and autosomal loci experience different selective pressures and
evolutionary dynamics. X (or Z) chromosomes are often hemizygous in males (or
females), as Y (or W) chromosomes often degenerate. Such hemizygous regions can
be under greater efficacy of selection, as recessive mutations are immediately
exposed to selection in the heterogametic sex leading to faster adaptation and
faster divergence on the X chromosome (the so-called Faster-X or Faster-Z effect).
However, in young nonrecombining regions, Y/W chromosomes often have many functional
genes, and many X/Z-linked loci are therefore diploid. The sheltering of recessive
mutations on the X/Z by the Y/W homolog is expected to drive slower adaptation
for diploid X/Z loci, i.e. a reduction in the efficacy of selection. While the
Faster-X effect has been studied extensively, much less is known empirically about
the evolutionary dynamics of diploid X or Z chromosomes. Here, we took advantage
of published population genomic data in the female-heterogametic human parasite
Schistosoma japonicum to characterize the gene content and diversity levels of
the diploid and hemizygous regions of the Z chromosome. We used different metrics
of selective pressures acting on genes to test for differences in the efficacy
of selection in hemizygous and diploid Z regions, relative to autosomes. We found
consistent patterns suggesting reduced Ne, and reduced efficacy of purifying selection,
on both hemizygous and diploid Z regions. Moreover, relaxed selection was particularly
pronounced for female-biased genes on the diploid Z, as predicted by recent theoretical
work.
acknowledgement: The authors would like to thank three anonymous reviewers for comments
and suggestions. We are also grateful to Christelle Fraïsse, Marwan Elkrewi, and
Filip Ruzicka for the help in this project.
article_number: evaf021
article_processing_charge: Yes
article_type: original
author:
- first_name: Andrea
full_name: Mrnjavac, Andrea
id: 353FAC84-AE61-11E9-8BFC-00D3E5697425
last_name: Mrnjavac
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Mrnjavac A, Vicoso B. Reduced efficacy of selection on a young Z chromosome
region of schistosoma japonicum. Genome Biology and Evolution. 2025;17(2).
doi:10.1093/gbe/evaf021
apa: Mrnjavac, A., & Vicoso, B. (2025). Reduced efficacy of selection on a young
Z chromosome region of schistosoma japonicum. Genome Biology and Evolution.
Oxford University Press. https://doi.org/10.1093/gbe/evaf021
chicago: Mrnjavac, Andrea, and Beatriz Vicoso. “Reduced Efficacy of Selection on
a Young Z Chromosome Region of Schistosoma Japonicum.” Genome Biology and Evolution.
Oxford University Press, 2025. https://doi.org/10.1093/gbe/evaf021.
ieee: A. Mrnjavac and B. Vicoso, “Reduced efficacy of selection on a young Z chromosome
region of schistosoma japonicum,” Genome Biology and Evolution, vol. 17,
no. 2. Oxford University Press, 2025.
ista: Mrnjavac A, Vicoso B. 2025. Reduced efficacy of selection on a young Z chromosome
region of schistosoma japonicum. Genome Biology and Evolution. 17(2), evaf021.
mla: Mrnjavac, Andrea, and Beatriz Vicoso. “Reduced Efficacy of Selection on a Young
Z Chromosome Region of Schistosoma Japonicum.” Genome Biology and Evolution,
vol. 17, no. 2, evaf021, Oxford University Press, 2025, doi:10.1093/gbe/evaf021.
short: A. Mrnjavac, B. Vicoso, Genome Biology and Evolution 17 (2025).
corr_author: '1'
date_created: 2025-03-09T23:01:27Z
date_published: 2025-02-01T00:00:00Z
date_updated: 2026-09-24T11:18:17Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1093/gbe/evaf021
external_id:
isi:
- '001423671400001'
pmid:
- '39913672'
file:
- access_level: open_access
checksum: e3aa993e3d6dad10cb806c243fa57408
content_type: application/pdf
creator: dernst
date_created: 2025-03-10T08:25:59Z
date_updated: 2025-03-10T08:25:59Z
file_id: '19378'
file_name: 2025_GBE_Mrnjavac.pdf
file_size: 768371
relation: main_file
success: 1
file_date_updated: 2025-03-10T08:25:59Z
fulldoi: https://doi.org/10.1093/gbe/evaf021
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
issue: '2'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genome Biology and Evolution
publication_identifier:
eissn:
- 1759-6653
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://git.ista.ac.at/amrnjava/schistosomes_slower_z
record:
- id: '18549'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Reduced efficacy of selection on a young Z chromosome region of schistosoma
japonicum
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: 17
year: '2025'
...
---
OA_place: publisher
OA_type: diamond
_id: '18866'
abstract:
- lang: eng
text: Using JWST Near Infrared Camera (NIRCam) images of the globular cluster 47,Tucanæ,
(or NGC,104), taken at two epochs just 7 months apart, we derived proper-motion
membership down to F322W2 ∼ 27. We identified an intriguing feature at the very
low-mass end of the main sequence, around ∼ 0.08,M_⋅, at magnitudes F322W2 ∼ 24
and m_ F150W2 ∼ 25. This feature, dubbed 'kink', is characterized by a prominent
discontinuity in the slope of the main sequence. A similar discontinuity is seen
in theoretical isochrones with oxygen-poor chemistries, related to the rapid onset
of absorption. We therefore hypothesize that the cluster hosts disproportionately
more oxygen-poor stars near the bottom of the main sequence compared to the upper
main sequence and the red giant branch. Our results show no strong or conclusive
evidence of a rise in the brown dwarf luminosity function at faint magnitudes,
in contrast to previous findings likely affected by faint red background galaxies.
In our analysis, we accounted for this contamination by using proper motion membership.
acknowledgement: We dedicate this paper to the memory of our colleague Prof. Harvey
Richer (⋆ April 1944 —† 13 November 2023), a highly accomplished astronomer and
expert in stellar populations and in particular within globular clusters, who passed
away during this project. Harvey grew up in Montreal and was at least the second
star man to graduate from his high school, having been preceded by William Shatner
by more than a decade. He worked at the University of British Columbia for most
of his career, and his focus was the late stages of stellar evolution, in particular
carbon stars and white dwarfs. We thank the referee for his valuable suggestions
and comments, which helped improve the paper, as well as for his prompt revision.
article_number: A68
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: M.
full_name: Scalco, M.
last_name: Scalco
- first_name: R.
full_name: Gerasimov, R.
last_name: Gerasimov
- first_name: L. R.
full_name: Bedin, L. R.
last_name: Bedin
- first_name: E.
full_name: Vesperini, E.
last_name: Vesperini
- first_name: M.
full_name: Correnti, M.
last_name: Correnti
- first_name: D.
full_name: Nardiello, D.
last_name: Nardiello
- first_name: A.
full_name: Burgasser, A.
last_name: Burgasser
- first_name: H.
full_name: Richer, H.
last_name: Richer
- first_name: Ilaria
full_name: Caiazzo, Ilaria
id: 8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d
last_name: Caiazzo
orcid: 0000-0002-4770-5388
- first_name: J.
full_name: Heyl, J.
last_name: Heyl
- first_name: M.
full_name: Libralato, M.
last_name: Libralato
- first_name: J.
full_name: Anderson, J.
last_name: Anderson
- first_name: M.
full_name: Griggio, M.
last_name: Griggio
citation:
ama: Scalco M, Gerasimov R, Bedin LR, et al. JWST photometry and astrometry of 47
Tucanæ. Discontinuity in the stellar sequence at the star--brown dwarf transition.
Astronomy & Astrophysics. 2025;694. doi:10.1051/0004-6361/202452907
apa: Scalco, M., Gerasimov, R., Bedin, L. R., Vesperini, E., Correnti, M., Nardiello,
D., … Griggio, M. (2025). JWST photometry and astrometry of 47 Tucanæ. Discontinuity
in the stellar sequence at the star--brown dwarf transition. Astronomy &
Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/202452907
chicago: Scalco, M., R. Gerasimov, L. R. Bedin, E. Vesperini, M. Correnti, D. Nardiello,
A. Burgasser, et al. “JWST Photometry and Astrometry of 47 Tucanæ. Discontinuity
in the Stellar Sequence at the Star--Brown Dwarf Transition.” Astronomy &
Astrophysics. EDP Sciences, 2025. https://doi.org/10.1051/0004-6361/202452907.
ieee: M. Scalco et al., “JWST photometry and astrometry of 47 Tucanæ. Discontinuity
in the stellar sequence at the star--brown dwarf transition,” Astronomy &
Astrophysics, vol. 694. EDP Sciences, 2025.
ista: Scalco M, Gerasimov R, Bedin LR, Vesperini E, Correnti M, Nardiello D, Burgasser
A, Richer H, Caiazzo I, Heyl J, Libralato M, Anderson J, Griggio M. 2025. JWST
photometry and astrometry of 47 Tucanæ. Discontinuity in the stellar sequence
at the star--brown dwarf transition. Astronomy & Astrophysics. 694, A68.
mla: Scalco, M., et al. “JWST Photometry and Astrometry of 47 Tucanæ. Discontinuity
in the Stellar Sequence at the Star--Brown Dwarf Transition.” Astronomy &
Astrophysics, vol. 694, A68, EDP Sciences, 2025, doi:10.1051/0004-6361/202452907.
short: M. Scalco, R. Gerasimov, L.R. Bedin, E. Vesperini, M. Correnti, D. Nardiello,
A. Burgasser, H. Richer, I. Caiazzo, J. Heyl, M. Libralato, J. Anderson, M. Griggio,
Astronomy & Astrophysics 694 (2025).
date_created: 2025-01-21T15:29:36Z
date_published: 2025-02-04T00:00:00Z
date_updated: 2026-09-24T13:45:58Z
day: '04'
ddc:
- '520'
department:
- _id: IlCa
doi: 10.1051/0004-6361/202452907
external_id:
arxiv:
- '2501.04446'
isi:
- '001414753300007'
file:
- access_level: open_access
checksum: db765ce222df60a1e7c19da1968906a8
content_type: application/pdf
creator: dernst
date_created: 2025-04-16T07:13:31Z
date_updated: 2025-04-16T07:13:31Z
file_id: '19569'
file_name: 2025_AstronomyAstrophysics_Scalco.pdf
file_size: 18080704
relation: main_file
success: 1
file_date_updated: 2025-04-16T07:13:31Z
fulldoi: https://doi.org/10.1051/0004-6361/202452907
has_accepted_license: '1'
intvolume: ' 694'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
publication: Astronomy & Astrophysics
publication_identifier:
eissn:
- 1432-0746
issn:
- 0004-6361
publication_status: published
publisher: EDP Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: JWST photometry and astrometry of 47 Tucanæ. Discontinuity in the stellar sequence
at the star--brown dwarf transition
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: 694
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18936'
abstract:
- lang: eng
text: A major obstacle to predictive understanding of evolution stems from the complexity
of biological systems, which prevents detailed characterization of key evolutionary
properties. Here, we highlight some of the major sources of complexity that arise
when relating molecular mechanisms to their evolutionary consequences and ask
whether accounting for every mechanistic detail is important to accurately predict
evolutionary outcomes. To do this, we developed a mechanistic model of a bacterial
promoter regulated by 2 proteins, allowing us to connect any promoter genotype
to 6 phenotypes that capture the dynamics of gene expression following an environmental
switch. Accounting for the mechanisms that govern how this system works enabled
us to provide an in-depth picture of how regulated bacterial promoters might evolve.
More importantly, we used the model to explore which factors that contribute to
the complexity of this system are essential for understanding its evolution, and
which can be simplified without information loss. We found that several key evolutionary
properties—the distribution of phenotypic and fitness effects of mutations, the
evolutionary trajectories during selection for regulation—can be accurately captured
without accounting for all, or even most, parameters of the system. Our findings
point to the need for a mechanistic approach to studying evolution, as it enables
tackling biological complexity and in doing so improves the ability to predict
evolutionary outcomes.
acknowledgement: "The authors thank Nick Barton, Stepan Denisov, Claudia Igler, Srdjan
Sarikas, Anna Staron, and the anonymous reviewers for useful comments and discussions
that helped improve our work.\r\nFunding for this work was provided by the Wellcome
Trust–Royal Society Sir Henry Dale Fellowship (216779/Z/19/Z) and the Royal Society
Research Grant (RG\\R2\\232522) to M.L."
article_number: iyae191
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Rok
full_name: Grah, Rok
id: 483E70DE-F248-11E8-B48F-1D18A9856A87
last_name: Grah
orcid: 0000-0003-2539-3560
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Mato
full_name: Lagator, Mato
id: 345D25EC-F248-11E8-B48F-1D18A9856A87
last_name: Lagator
citation:
ama: 'Grah R, Guet CC, Tkačik G, Lagator M. Linking molecular mechanisms to their
evolutionary consequences: a primer. Genetics. 2025;229(2). doi:10.1093/genetics/iyae191'
apa: 'Grah, R., Guet, C. C., Tkačik, G., & Lagator, M. (2025). Linking molecular
mechanisms to their evolutionary consequences: a primer. Genetics. Oxford
University Press. https://doi.org/10.1093/genetics/iyae191'
chicago: 'Grah, Rok, Calin C Guet, Gašper Tkačik, and Mato Lagator. “Linking Molecular
Mechanisms to Their Evolutionary Consequences: A Primer.” Genetics. Oxford
University Press, 2025. https://doi.org/10.1093/genetics/iyae191.'
ieee: 'R. Grah, C. C. Guet, G. Tkačik, and M. Lagator, “Linking molecular mechanisms
to their evolutionary consequences: a primer,” Genetics, vol. 229, no.
2. Oxford University Press, 2025.'
ista: 'Grah R, Guet CC, Tkačik G, Lagator M. 2025. Linking molecular mechanisms
to their evolutionary consequences: a primer. Genetics. 229(2), iyae191.'
mla: 'Grah, Rok, et al. “Linking Molecular Mechanisms to Their Evolutionary Consequences:
A Primer.” Genetics, vol. 229, no. 2, iyae191, Oxford University Press,
2025, doi:10.1093/genetics/iyae191.'
short: R. Grah, C.C. Guet, G. Tkačik, M. Lagator, Genetics 229 (2025).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: Strains and plasmids are available upon request. All experimental
raw data can be found in Supplementary Data 1. All code underpinning this work is
available at https://github.com/Lagator-Group/Linking-Molecular-Mechanisms-to-their-Evolutionary-consequence-a-primer
or upon request. Supplemental material available at GENETICS online
date_created: 2025-01-29T08:21:35Z
date_published: 2025-02-01T00:00:00Z
date_updated: 2026-10-01T08:30:12Z
day: '01'
ddc:
- '570'
department:
- _id: CaGu
- _id: GaTk
doi: 10.1093/genetics/iyae191
external_id:
isi:
- '001379194200001'
pmid:
- '39601269'
file:
- access_level: open_access
checksum: f730e416795969449ef49d97b82ac494
content_type: application/pdf
creator: dernst
date_created: 2025-04-16T09:41:04Z
date_updated: 2025-04-16T09:41:04Z
file_id: '19580'
file_name: 2025_Genetics_Grah.pdf
file_size: 1511688
relation: main_file
success: 1
file_date_updated: 2025-04-16T09:41:04Z
fulldoi: https://doi.org/10.1093/genetics/iyae191
has_accepted_license: '1'
intvolume: ' 229'
isi: 1
issue: '2'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genetics
publication_identifier:
eissn:
- 1943-2631
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
researchdata_availability: upon request
scopus_import: '1'
status: public
supplementarymaterial: yes
title: 'Linking molecular mechanisms to their evolutionary consequences: a primer'
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: 229
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18605'
abstract:
- lang: eng
text: The response of clouds and moist-convective processes to heat loss to space
by long-wave radiative cooling is an important feedback in the Earth's atmosphere.
It is known that moist convection increases roughly in equilibrium with radiative
cooling, an assumption often made in simplified models of the tropical atmosphere.
In this study, we use an idealised two-dimensional model of the atmosphere introduced
by Vallis et. al. and incorporate a bulk-cooling term, which is an idealisation
of radiative cooling in the atmosphere. We comment briefly on the static stability
of the system to dry and moist convection and characteris its moist convective
response to changes in the bulk cooling. We find that, while the clear-sky regions
of the model respond directly to the change in the cooling term, the regions dominated
by moist convective plumes are insensitive to changes in cooling. Similar to previous
findings from cloud-resolving models, we too find in our idealised setting that
the majority of the increase in convection occurs via an increase in the areal
coverage of convection, rather than its intensity. We argue that these small-scale
convective processes are an upper bound on how quickly convective intensity can
change to stay in equilibrium with radiative cooling.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "The authors gratefully acknowledge the help of Julian Renaud and
Alzbeta “Bety” Pechacova. Julian went through the relevant literature on the topic
in the initial stages of the study in a very thorough manner and allowed the authors
to understand the various types of idealised models that have been studied and the
various approaches used. Bety ran simulations and performed analysis of the outputs
of several simulations, which were crucial to bringing the article to its final
form.\r\n\r\nThe authors also acknowledge the input of Prof. Martin Singh (Monash
University, Australia) and discussions with Gregory Dritschel, Prof. Steven Tobias,
and Prof. Douglas Parker (Leeds University, United Kingdom).\r\n\r\nThis project
has received funding from the European Union's Horizon 2020 research and innovation
programme under the Marie Sklodowska-Curie grant agreement No. 101034413. C. Muller
gratefully acknowledges funding from the European Research Council (ERC) under the
European Union's Horizon 2020 research and innovation program (Project CLUSTER,
Grant Agreement No. 805041). This research was supported by the Scientific Service
Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp)."
article_number: e4902
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Lokahith N
full_name: Agasthya, Lokahith N
id: cd100965-0804-11ed-9c55-f4878ff4e877
last_name: Agasthya
- first_name: Caroline J
full_name: Muller, Caroline J
id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
last_name: Muller
orcid: 0000-0001-5836-5350
- first_name: Mathis
full_name: Cheve, Mathis
id: c2cdb722-b15c-11ef-9e63-db902a30b40d
last_name: Cheve
citation:
ama: 'Agasthya LN, Muller CJ, Cheve M. Moist convective scaling: Insights from an
idealised model. Quarterly Journal of the Royal Meteorological Society.
2025;151(766). doi:10.1002/qj.4902'
apa: 'Agasthya, L. N., Muller, C. J., & Cheve, M. (2025). Moist convective scaling:
Insights from an idealised model. Quarterly Journal of the Royal Meteorological
Society. Wiley. https://doi.org/10.1002/qj.4902'
chicago: 'Agasthya, Lokahith N, Caroline J Muller, and Mathis Cheve. “Moist Convective
Scaling: Insights from an Idealised Model.” Quarterly Journal of the Royal
Meteorological Society. Wiley, 2025. https://doi.org/10.1002/qj.4902.'
ieee: 'L. N. Agasthya, C. J. Muller, and M. Cheve, “Moist convective scaling: Insights
from an idealised model,” Quarterly Journal of the Royal Meteorological Society,
vol. 151, no. 766. Wiley, 2025.'
ista: 'Agasthya LN, Muller CJ, Cheve M. 2025. Moist convective scaling: Insights
from an idealised model. Quarterly Journal of the Royal Meteorological Society.
151(766), e4902.'
mla: 'Agasthya, Lokahith N., et al. “Moist Convective Scaling: Insights from an
Idealised Model.” Quarterly Journal of the Royal Meteorological Society,
vol. 151, no. 766, e4902, Wiley, 2025, doi:10.1002/qj.4902.'
short: L.N. Agasthya, C.J. Muller, M. Cheve, Quarterly Journal of the Royal Meteorological
Society 151 (2025).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: The data that support the findings of this study are available
from the corresponding author, Lokahith Agasthya, upon reasonable request.
date_created: 2024-12-01T23:01:54Z
date_published: 2025-01-01T00:00:00Z
date_updated: 2026-10-01T09:23:20Z
day: '01'
ddc:
- '550'
department:
- _id: CaMu
doi: 10.1002/qj.4902
ec_funded: 1
external_id:
isi:
- '001363135200001'
file:
- access_level: open_access
checksum: 2b4968f1c794da56d1eb7b856a406de7
content_type: application/pdf
creator: dernst
date_created: 2025-07-03T06:46:27Z
date_updated: 2025-07-03T06:46:27Z
file_id: '19958'
file_name: 2025_QuartJRMS_Agasthya.pdf
file_size: 5924105
relation: main_file
success: 1
file_date_updated: 2025-07-03T06:46:27Z
fulldoi: https://doi.org/10.1002/qj.4902
has_accepted_license: '1'
intvolume: ' 151'
isi: 1
issue: '766'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
- _id: 629205d8-2b32-11ec-9570-e1356ff73576
call_identifier: H2020
grant_number: '805041'
name: Organization of CLoUdS, and implications of Tropical cyclones and for the
Energetics of the tropics, in current and waRming climate
publication: Quarterly Journal of the Royal Meteorological Society
publication_identifier:
eissn:
- 1477-870X
issn:
- 0035-9009
publication_status: published
publisher: Wiley
quality_controlled: '1'
researchdata_availability: upon request
scopus_import: '1'
status: public
supplementarymaterial: yes
title: 'Moist convective scaling: Insights from an idealised model'
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: 151
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '12662'
abstract:
- lang: eng
text: 'Modern machine learning tasks often require considering not just one but
multiple objectives. For example, besides the prediction quality, this could be
the efficiency, robustness or fairness of the learned models, or any of their
combinations. Multi-objective learning offers a natural framework for handling
such problems without having to commit to early trade-offs. Surprisingly, statistical
learning theory so far offers almost no insight into the generalization properties
of multi-objective learning. In this work, we make first steps to fill this gap:
We establish foundational generalization bounds for the multi-objective setting
as well as generalization and excess bounds for learning with scalarizations.
We also provide the first theoretical analysis of the relation between the Pareto-optimal
sets of the true objectives and the Pareto-optimal sets of their empirical approximations
from training data. In particular, we show a surprising asymmetry: All Pareto-optimal
solutions can be approximated by empirically Pareto-optimal ones, but not vice
versa.'
acknowledgement: Open access funding provided by Institute of Science and Technology
(IST Austria).
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Peter
full_name: Súkeník, Peter
id: d64d6a8d-eb8e-11eb-b029-96fd216dec3c
last_name: Súkeník
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: Súkeník P, Lampert C. Generalization in multi-objective machine learning. Neural
Computing and Applications. 2025;37:24669–24683. doi:10.1007/s00521-024-10616-1
apa: Súkeník, P., & Lampert, C. (2025). Generalization in multi-objective machine
learning. Neural Computing and Applications. Springer Nature. https://doi.org/10.1007/s00521-024-10616-1
chicago: Súkeník, Peter, and Christoph Lampert. “Generalization in Multi-Objective
Machine Learning.” Neural Computing and Applications. Springer Nature,
2025. https://doi.org/10.1007/s00521-024-10616-1.
ieee: P. Súkeník and C. Lampert, “Generalization in multi-objective machine learning,”
Neural Computing and Applications, vol. 37. Springer Nature, pp. 24669–24683,
2025.
ista: Súkeník P, Lampert C. 2025. Generalization in multi-objective machine learning.
Neural Computing and Applications. 37, 24669–24683.
mla: Súkeník, Peter, and Christoph Lampert. “Generalization in Multi-Objective Machine
Learning.” Neural Computing and Applications, vol. 37, Springer Nature,
2025, pp. 24669–24683, doi:10.1007/s00521-024-10616-1.
short: P. Súkeník, C. Lampert, Neural Computing and Applications 37 (2025) 24669–24683.
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: Our manuscript does not include or refer to any data sources.
date_created: 2023-02-20T08:23:06Z
date_published: 2025-10-01T00:00:00Z
date_updated: 2026-10-01T09:29:43Z
day: '01'
ddc:
- '004'
department:
- _id: ChLa
doi: 10.1007/s00521-024-10616-1
external_id:
arxiv:
- '2208.13499'
file:
- access_level: open_access
checksum: 61ad4591aee16b1e02daf6c164321a42
content_type: application/pdf
creator: dernst
date_created: 2025-12-30T06:39:11Z
date_updated: 2025-12-30T06:39:11Z
file_id: '20877'
file_name: 2025_NeuralCompApplic_Sukenik.pdf
file_size: 500213
relation: main_file
success: 1
file_date_updated: 2025-12-30T06:39:11Z
fulldoi: https://doi.org/10.1007/s00521-024-10616-1
has_accepted_license: '1'
intvolume: ' 37'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 24669–24683
publication: Neural Computing and Applications
publication_identifier:
eissn:
- 1433-3058
issn:
- 0941-0643
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
researchdata_availability: not applicable
scopus_import: '1'
status: public
supplementarymaterial: no
title: Generalization in multi-objective machine learning
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: 37
year: '2025'
...
---
OA_type: closed access
_id: '18960'
abstract:
- lang: eng
text: The importance of physical forces in the morphogenesis, homeostatic function,
and pathological dysfunction of multicellular tissues is being increasingly characterized,
both theoretically and experimentally. Analogies between biological systems and
inert materials such as foams, gels, and liquid crystals have provided striking
insights into the core design principles underlying multicellular organization.
However, these connections can seem surprising given that a key feature of multicellular
systems is their ability to constantly consume energy, providing an active origin
for the forces that they produce. Key emerging questions are, therefore, to understand
whether and how this activity grants tissues novel properties that do not have
counterparts in classical materials, as well as their consequences for biological
function. Here, we review recent discoveries at the intersection of active matter
and tissue biology, with an emphasis on how modeling and experiments can be combined
to understand the dynamics of multicellular systems. These approaches suggest
that a number of key biological tissue-scale phenomena, such as morphogenetic
shape changes, collective migration, or fate decisions, share unifying design
principles that can be described by physical models of tissue active matter.
acknowledgement: We thank Fridtjof Brauns, Anna Kicheva, and Carl-Philipp Heisenberg
for a critical reading of the manuscript and Claudia Flandoli for the artwork in
the figures. D.B.B. was supported by the NOMIS foundation as a NOMIS Fellow and
by an EMBO Postdoctoral Fellowship (ALTF 343-2022). This work received funding from
the European Research Council (ERC) under the European Union\u2019s Horizon 2020
Research and Innovation Programme Grant Agreement no. 851288.
article_number: a041653
article_processing_charge: No
article_type: original
author:
- first_name: David
full_name: Brückner, David
id: e1e86031-6537-11eb-953a-f7ab92be508d
last_name: Brückner
orcid: 0000-0001-7205-2975
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
citation:
ama: 'Brückner D, Hannezo EB. Tissue active matter: Integrating mechanics and signaling
into dynamical models. Cold Spring Harbor Perspectives in Biology. 2025;17(4).
doi:10.1101/cshperspect.a041653'
apa: 'Brückner, D., & Hannezo, E. B. (2025). Tissue active matter: Integrating
mechanics and signaling into dynamical models. Cold Spring Harbor Perspectives
in Biology. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/cshperspect.a041653'
chicago: 'Brückner, David, and Edouard B Hannezo. “Tissue Active Matter: Integrating
Mechanics and Signaling into Dynamical Models.” Cold Spring Harbor Perspectives
in Biology. Cold Spring Harbor Laboratory Press, 2025. https://doi.org/10.1101/cshperspect.a041653.'
ieee: 'D. Brückner and E. B. Hannezo, “Tissue active matter: Integrating mechanics
and signaling into dynamical models,” Cold Spring Harbor Perspectives in Biology,
vol. 17, no. 4. Cold Spring Harbor Laboratory Press, 2025.'
ista: 'Brückner D, Hannezo EB. 2025. Tissue active matter: Integrating mechanics
and signaling into dynamical models. Cold Spring Harbor Perspectives in Biology.
17(4), a041653.'
mla: 'Brückner, David, and Edouard B. Hannezo. “Tissue Active Matter: Integrating
Mechanics and Signaling into Dynamical Models.” Cold Spring Harbor Perspectives
in Biology, vol. 17, no. 4, a041653, Cold Spring Harbor Laboratory Press,
2025, doi:10.1101/cshperspect.a041653.'
short: D. Brückner, E.B. Hannezo, Cold Spring Harbor Perspectives in Biology 17
(2025).
corr_author: '1'
das_tickbox: '0'
date_created: 2025-01-29T13:33:47Z
date_published: 2025-04-01T00:00:00Z
date_updated: 2026-10-01T11:03:02Z
day: '01'
department:
- _id: EdHa
doi: 10.1101/cshperspect.a041653
ec_funded: 1
external_id:
isi:
- '001456660400001'
pmid:
- '38951023'
fulldoi: https://doi.org/10.1101/cshperspect.a041653
intvolume: ' 17'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa_version: None
pmid: 1
project:
- _id: 34e2a5b5-11ca-11ed-8bc3-b2265616ef0b
grant_number: ALTF 343-2022
name: A mechano-chemical theory for stem cell fate decisions in organoid development
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
publication: Cold Spring Harbor Perspectives in Biology
publication_identifier:
issn:
- 1943-0264
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: 'Tissue active matter: Integrating mechanics and signaling into dynamical models'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 17
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '19003'
abstract:
- lang: eng
text: 'Super-resolution methods provide far better spatial resolution than the optical
diffraction limit of about half the wavelength of light (∼200-300 nm). Nevertheless,
they have yet to attain widespread use in plants, largely due to plants’ challenging
optical properties. Expansion microscopy improves effective resolution by isotropically
increasing the physical distances between sample structures while preserving relative
spatial arrangements and clearing the sample. However, its application to plants
has been hindered by the rigid, mechanically cohesive structure of plant tissues.
Here, we report on whole-mount expansion microscopy of thale cress (Arabidopsis
thaliana) root tissues (PlantEx), achieving a four-fold resolution increase over
conventional microscopy. Our results highlight the microtubule cytoskeleton organization
and interaction between molecularly defined cellular constituents. Combining PlantEx
with stimulated emission depletion (STED) microscopy, we increase nanoscale resolution
and visualize the complex organization of subcellular organelles from intact tissues
by example of the densely packed COPI-coated vesicles associated with the Golgi
apparatus and put these into a cellular structural context. Our results show that
expansion microscopy can be applied to increase effective imaging resolution in
Arabidopsis root specimens. '
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: E-Lib
- _id: M-Shop
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\nThis
project has received funding from the European Research Council under the Horizon
2020 Framework Programme (grant agreement No 742985, J.F.). It has also received
funding from the Horizon 2020 Framework Programme under the Marie Skłodowska-Curie
Grant Agreement No. 665385 (M.G.). S.T. has received funding as an ISTplus Fellow
from the Horizon 2020 Framework Programme under Marie Skłodowska-Curie grant agreement
no. 754411 and from EMBO via a Long-Term Fellowship (grant number ALTF 679-2018).
M.R.T. received funding from the Austrian Academy of Sciences with DOC fellowship
no. 26137. The project has further received funding from the Austrian Science Fund,
via grant DK W1232 (M.R.T., N.A.D., and J.G.D). W.J. received a postdoctoral fellowship
from the Human Frontier Science Program (LT000557/2018). The funders had no role
in study design, data collection and analysis, decision to publish or preparation
of the manuscript."
article_number: koaf006
article_processing_charge: Yes (via OA deal)
article_type: original
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. The Plant Cell. 2025;37(4). doi:10.1093/plcell/koaf006
apa: Gallei, M. C., Truckenbrodt, S. M., Kreuzinger, C., Inumella, S., Vistunou,
V., Sommer, C. M., … Danzl, J. G. (2025). Super-resolution expansion microscopy
in plant roots. The Plant Cell. Oxford University Press. https://doi.org/10.1093/plcell/koaf006
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.” The Plant Cell. Oxford University
Press, 2025. https://doi.org/10.1093/plcell/koaf006.
ieee: M. C. Gallei et al., “Super-resolution expansion microscopy in plant
roots,” The Plant Cell, vol. 37, no. 4. Oxford University Press, 2025.
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. 2025. Super-resolution expansion microscopy in plant roots.
The Plant Cell. 37(4), koaf006.
mla: Gallei, Michelle C., et al. “Super-Resolution Expansion Microscopy in Plant
Roots.” The Plant Cell, vol. 37, no. 4, koaf006, Oxford University Press,
2025, doi:10.1093/plcell/koaf006.
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, The Plant Cell 37 (2025).
corr_author: '1'
date_created: 2025-02-05T06:52:06Z
date_published: 2025-04-01T00:00:00Z
date_updated: 2026-10-01T11:19:12Z
day: '01'
ddc:
- '580'
department:
- _id: EvBe
- _id: JoDa
- _id: JiFr
doi: 10.1093/plcell/koaf006
ec_funded: 1
external_id:
isi:
- '001462763100001'
pmid:
- '39792900'
file:
- access_level: open_access
checksum: 9d3f8218ff37a29f29c48a7bbe831bd3
content_type: application/pdf
creator: dernst
date_created: 2025-07-31T07:03:43Z
date_updated: 2025-07-31T07:03:43Z
file_id: '20092'
file_name: 2025_PlantCell_Gallei.pdf
file_size: 53904111
relation: main_file
success: 1
file_date_updated: 2025-07-31T07:03:43Z
fulldoi: https://doi.org/10.1093/plcell/koaf006
has_accepted_license: '1'
intvolume: ' 37'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
- _id: 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: 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
- _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: The Plant Cell
publication_identifier:
eissn:
- 1532-298X
issn:
- 1040-4651
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
record:
- id: '18837'
relation: research_data
status: public
- id: '18689'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Super-resolution expansion microscopy in plant roots
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: 37
year: '2025'
...
---
APC_amount: 12348 EUR
OA_place: publisher
OA_type: hybrid
_id: '17884'
abstract:
- lang: eng
text: Human T cell leukemia virus type 1 (HTLV-1) immature particles differ in morphology
from other retroviruses, suggesting a distinct way of assembly. Here we report
the results of cryo-electron tomography studies of HTLV-1 virus-like particles
assembled in vitro, as well as derived from cells. This work shows that HTLV-1
uses a distinct mechanism of Gag–Gag interactions to form the immature viral lattice.
Analysis of high-resolution structural information from immature capsid (CA) tubular
arrays reveals that the primary stabilizing component in HTLV-1 is the N-terminal
domain of CA. Mutagenesis analysis supports this observation. This distinguishes
HTLV-1 from other retroviruses, in which the stabilization is provided primarily
by the C-terminal domain of CA. These results provide structural details of the
quaternary arrangement of Gag for an immature deltaretrovirus and this helps explain
why HTLV-1 particles are morphologically distinct.
acknowledged_ssus:
- _id: ScienComp
- _id: LifeSc
- _id: EM-Fac
acknowledgement: This work was funded by the Institute of Science and Technology Austria
(ISTA) and the Austrian Science Fund (grant P31445 to F.K.M.S.). Access to high-resolution
cryo-ET data acquisition at European Molecular Biology Laboratory (EMBL) Heidelberg
was supported through the EMBL cryo-EM platform. We thank V.-V. Hodirnau at ISTA
and W. Hagen and F. Weis at EMBL Heidelberg for support in cryo-ET data acquisition.
This research was also supported by the scientific service units of ISTA through
resources provided by Scientific Computing, the Life Science Facility, and the EM
Facility. L.M.M. was supported by National Institutes of Health grants R01 GM151775
and R21 DE032878 and by the University of Minnesota Masonic Cancer Center. D.P.
was supported by the DOC doctoral fellowship program of the Austrian Academy of
Sciences. R.A.D was supported by the National Institute of Allergy and Infectious
Diseases (grant R01AI147890). The funders had no role in study design, data collection
and analysis, decision to publish or preparation of the manuscript. Specifically,
we also want to thank A. Schlögl for computational support and J. Hansen and V.
Vogt for critical comments on the manuscript. We also thank the other members of
the Schur lab for helpful discussions and experimental advice.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Martin
full_name: Obr, Martin
id: 4741CA5A-F248-11E8-B48F-1D18A9856A87
last_name: Obr
orcid: 0000-0003-1756-6564
- first_name: Mathias
full_name: Percipalle, Mathias
id: 4986e21c-eb97-11eb-a6c2-a4ef0b629971
last_name: Percipalle
- first_name: Darya
full_name: Chernikova, Darya
id: 7dbaf460-fa9e-11eb-b0ca-bc7c7ff21ad0
last_name: Chernikova
- first_name: Huixin
full_name: Yang, Huixin
last_name: Yang
- first_name: Andreas
full_name: Thader, Andreas
id: 3A18A7B8-F248-11E8-B48F-1D18A9856A87
last_name: Thader
- first_name: Gergely
full_name: Pinke, Gergely
id: 4D5303E6-F248-11E8-B48F-1D18A9856A87
last_name: Pinke
- first_name: Dario J
full_name: Porley, Dario J
id: 2FD6EA6C-F248-11E8-B48F-1D18A9856A87
last_name: Porley
- first_name: Louis M.
full_name: Mansky, Louis M.
last_name: Mansky
- first_name: Robert A.
full_name: Dick, Robert A.
last_name: Dick
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
citation:
ama: Obr M, Percipalle M, Chernikova D, et al. Distinct stabilization of the human
T cell leukemia virus type 1 immature Gag lattice. Nature Structural &
Molecular Biology. 2025;32:268-276. doi:10.1038/s41594-024-01390-8
apa: Obr, M., Percipalle, M., Chernikova, D., Yang, H., Thader, A., Pinke, G., …
Schur, F. K. (2025). Distinct stabilization of the human T cell leukemia virus
type 1 immature Gag lattice. Nature Structural & Molecular Biology.
Springer Nature. https://doi.org/10.1038/s41594-024-01390-8
chicago: Obr, Martin, Mathias Percipalle, Darya Chernikova, Huixin Yang, Andreas
Thader, Gergely Pinke, Darío Porley Esteves, Louis M. Mansky, Robert A. Dick,
and Florian KM Schur. “Distinct Stabilization of the Human T Cell Leukemia Virus
Type 1 Immature Gag Lattice.” Nature Structural & Molecular Biology.
Springer Nature, 2025. https://doi.org/10.1038/s41594-024-01390-8.
ieee: M. Obr et al., “Distinct stabilization of the human T cell leukemia
virus type 1 immature Gag lattice,” Nature Structural & Molecular Biology,
vol. 32. Springer Nature, pp. 268–276, 2025.
ista: Obr M, Percipalle M, Chernikova D, Yang H, Thader A, Pinke G, Porley Esteves
D, Mansky LM, Dick RA, Schur FK. 2025. Distinct stabilization of the human T cell
leukemia virus type 1 immature Gag lattice. Nature Structural & Molecular
Biology. 32, 268–276.
mla: Obr, Martin, et al. “Distinct Stabilization of the Human T Cell Leukemia Virus
Type 1 Immature Gag Lattice.” Nature Structural & Molecular Biology,
vol. 32, Springer Nature, 2025, pp. 268–76, doi:10.1038/s41594-024-01390-8.
short: M. Obr, M. Percipalle, D. Chernikova, H. Yang, A. Thader, G. Pinke, D. Porley
Esteves, L.M. Mansky, R.A. Dick, F.K. Schur, Nature Structural & Molecular
Biology 32 (2025) 268–276.
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: The EM density maps and models for the immature HTLV-1
CA-NTD lattice and representative tomograms were deposited to the EM Data Bank under
accession codes EMD-17929, EMD-17930, EMD-17931, EMD-17932, EMD-17933, EMD-17934,
EMD-17935, EMD-17936, EMD-17937, EMD-17938, EMD-17939, EMD-17940, EMD-17941, EMD-17942
and EMD-17943 and the PDB under accession codes 8PU6, 8PU7, 8PU8, 8PU9, 8PUA, 8PUB,
8PUC, 8PUD, 8PUE, 8PUF, 8PUG and 8PUH. PDB 1QRJ was used as starting model to derive
a refined model of the HTLV-1 CA-NTD. The models used to generate Fig. 3 and Extended
Data Fig. 3 were PDB 5L93 (HIV-1), PDB 5A9E (RSV), PDB 6HWI (M-PMV) and PDB 6HWW
(MLV). The UniProt codes for the protein sequences used for generating Extended
Data Fig. 9 were P03345 (GAG_HTL1A), P03346 (GAG_HTLV2), Q0R5R4 (GAG_HTL32), P25058
(GAG_BLVAU), P04585 (POL_HV1H2), P15832 (GAG_HV2D2), P16087 (GAG_FIVPE), P69732
(GAG_EIAVY), P03322 (GAG_RSVP), P0C776 (GAG_ALVA), P07567 (GAG_MPMV), P31622 (GAG_JSRV),
P10258 (GAG_MMTVB), P03355 (POL_MLVMS), P10262 (GAG_FLV) and Q9TTC2 (GAG_KORV).
Source data are provided with this paper.
date_created: 2024-09-08T10:29:06Z
date_published: 2025-02-01T00:00:00Z
date_updated: 2026-10-01T11:23:34Z
day: '01'
ddc:
- '570'
department:
- _id: FlSc
- _id: LeSa
doi: 10.1038/s41594-024-01390-8
external_id:
isi:
- '001306564000001'
oaworkid:
- W4402316284
pmid:
- '39242978'
file:
- access_level: open_access
checksum: c641ad94afb28917b20425db676fc3ee
content_type: application/pdf
creator: dernst
date_created: 2025-04-23T07:02:33Z
date_updated: 2025-04-23T07:02:33Z
file_id: '19608'
file_name: 2025_NatureStrucBio_Obr.pdf
file_size: 13724041
relation: main_file
success: 1
file_date_updated: 2025-04-23T07:02:33Z
fulldoi: https://doi.org/10.1038/s41594-024-01390-8
has_accepted_license: '1'
intvolume: ' 32'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
oaworkid: 1
page: 268-276
pmid: 1
project:
- _id: 26736D6A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31445
name: Structural conservation and diversity in retroviral capsid
- _id: 9B9C98E0-BA93-11EA-9121-9846C619BF3A
grant_number: '25762'
name: Structural characterization of spumavirus capsid assemblies to understand
conserved Ortervirales assembly mechanisms
publication: Nature Structural & Molecular Biology
publication_identifier:
eissn:
- 1545-9985
issn:
- 1545-9993
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Distinct stabilization of the human T cell leukemia virus type 1 immature Gag
lattice
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: 32
year: '2025'
...
---
OA_place: publisher
OA_type: gold
_id: '19010'
abstract:
- lang: eng
text: Causal representation learning aims at recovering latent causal variables
from high-dimensional observations to solve causal downstream tasks, such as predicting
the effect of new interventions or more robust classification. A plethora of methods
have been developed, each tackling carefully crafted problem settings that lead
to different types of identifiability. The folklore is that these different settings
are important, as they are often linked to different rungs of Pearl's causal hierarchy,
although not all neatly fit. Our main contribution is to show that many existing
causal representation learning approaches methodologically align the representation
to known data symmetries. Identification of the variables is guided by equivalence
classes across different "data pockets" that are not necessarily causal. This
result suggests important implications, allowing us to unify many existing approaches
in a single method that can mix and match different assumptions, including non-causal
ones, based on the invariances relevant to our application. It also significantly
benefits applicability, which we demonstrate by improving treatment effect estimation
on real-world high-dimensional ecological data. Overall, this paper clarifies
the role of causality assumptions in the discovery of causal variables and shifts
the focus to preserving data symmetries.
acknowledgement: "We thank Jiaqi Zhang, Francesco Montagna, David Lopez-Paz, Kartik
Ahuja, Thomas Kipf, Sara\r\nMagliacane, Julius von Kügelgen, Kun Zhang, and Bernhard
Schölkopf for extremely helpful discussion. Riccardo Cadei was supported by a Google
Research Scholar Award to Francesco Locatello. We acknowledge the Third Bellairs
Workshop on Causal Representation Learning held at the Bellairs Research Institute,
February 9/16, 2024, and a debate on the difference between interventions and counterfactuals
in disentanglement and CRL that took place during Dhanya Sridhar’s lecture, which
motivated us to significantly broaden the scope of the paper. We thank Dhanya and
all participants of the workshop."
article_processing_charge: No
arxiv: 1
author:
- first_name: Dingling
full_name: Yao, Dingling
id: d3e02e50-48a8-11ee-8f62-c108061797fa
last_name: Yao
- first_name: Dario
full_name: Rancati, Dario
id: feb58f2e-72ef-11ef-b75a-8f0894539cd0
last_name: Rancati
- first_name: Riccardo
full_name: Cadei, Riccardo
id: 0fa8b76f-72f0-11ef-b75a-a5da96e5ad6b
last_name: Cadei
- first_name: Marco
full_name: Fumero, Marco
id: 1c1593eb-393f-11ef-bb8e-ab4f1e979650
last_name: Fumero
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
citation:
ama: 'Yao D, Rancati D, Cadei R, Fumero M, Locatello F. Unifying causal representation
learning with the invariance principle. In: 13th International Conference on
Learning Representations. ICLR; 2025.'
apa: 'Yao, D., Rancati, D., Cadei, R., Fumero, M., & Locatello, F. (2025). Unifying
causal representation learning with the invariance principle. In 13th International
Conference on Learning Representations. Singapore: ICLR.'
chicago: Yao, Dingling, Dario Rancati, Riccardo Cadei, Marco Fumero, and Francesco
Locatello. “Unifying Causal Representation Learning with the Invariance Principle.”
In 13th International Conference on Learning Representations. ICLR, 2025.
ieee: D. Yao, D. Rancati, R. Cadei, M. Fumero, and F. Locatello, “Unifying causal
representation learning with the invariance principle,” in 13th International
Conference on Learning Representations, Singapore, 2025.
ista: 'Yao D, Rancati D, Cadei R, Fumero M, Locatello F. 2025. Unifying causal representation
learning with the invariance principle. 13th International Conference on Learning
Representations. ICLR: International Conference on Learning Representations.'
mla: Yao, Dingling, et al. “Unifying Causal Representation Learning with the Invariance
Principle.” 13th International Conference on Learning Representations,
ICLR, 2025.
short: D. Yao, D. Rancati, R. Cadei, M. Fumero, F. Locatello, in:, 13th International
Conference on Learning Representations, ICLR, 2025.
conference:
end_date: 2025-04-28
location: Singapore
name: 'ICLR: International Conference on Learning Representations'
start_date: 2025-04-24
corr_author: '1'
das_tickbox: '0'
date_created: 2025-02-05T09:23:25Z
date_published: 2025-01-22T00:00:00Z
date_updated: 2026-10-02T08:49:53Z
day: '22'
ddc:
- '000'
department:
- _id: FrLo
external_id:
arxiv:
- '2409.02772'
file:
- access_level: open_access
checksum: c4b5a4a644228c6d1b0283e1368bce9e
content_type: application/pdf
creator: flocatel
date_created: 2026-01-27T12:43:25Z
date_updated: 2026-01-27T12:43:25Z
file_id: '21048'
file_name: 4356_Unifying_Causal_Represent (1).pdf
file_size: 877014
relation: main_file
success: 1
file_date_updated: 2026-01-27T12:43:25Z
has_accepted_license: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: 13th International Conference on Learning Representations
publication_status: published
publisher: ICLR
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: Unifying causal representation learning with the invariance principle
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
year: '2025'
...