---
_id: '21145'
abstract:
- lang: eng
text: 'Protein conformational energy landscapes are shaped not only by intramolecular
interactions but also by their environment. In protein crystals and protein-protein
complexes, intermolecular contacts alter this energy landscape, but the exact
nature of this alteration is difficult to decipher. Understanding how the crystal
lattice affects protein dynamics is crucial for crystallography-based studies
of motion, yet its influence on collective motions remains unclear. Aromatic ring
flips in the hydrophobic core represent sensitive probes of such dynamics. Here,
we compare the kinetics of aromatic ring flips in the protein GB1 in crystals,
in complex with its binding partner IgG, and in solution, combining advanced isotope
labeling with quantitative NMR methods. We show that rings in the core flip nearly
a thousand times less frequently in crystals than in solution. Enhanced-sampling
molecular dynamics simulations, based on a new crystal structure, reproduce these
elevated barriers and reveal how the crystal restrains motions. '
acknowledged_ssus:
- _id: NMR
- _id: LifeSc
acknowledgement: "We thank Nikolai R. Skrynnikov and Olga O. Lebedenko (St. Petersburg)
for insightful discussions and for performing exploratory MD simulations. We are
grateful to Tobias Schubeis (Lyon) for advice with GB1 crystallization, and Rebecca
Schmid for initial crystallization trials.\r\nWe thank Sebastian Falkner for assistance
with constructing the structural model of the IgG:GB1 complex.\r\nThis research
was supported by the Scientific Service Units (SSU) of Institute of Science and
Technology Austria (ISTA) through resources provided by the Nuclear Magnetic Resonance
and the Lab Support Facilities. We thank Petra Rovó and Margarita Valhondo Falcón
for excellent support of the NMR facility.\r\nLea M. Becker is recipient of a DOC
fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology
Austria (grant no. PR10660EAW01). Christophe Chipot acknowledges the European Research
Council (grant project 101097272 ``MilliInMicro'') and the Métropole du Grand Nancy
(grant project ``ARC''). BM07-FIP2 is supported by the French ANR PIA3 (France 2030)
EquipEx+ project MAGNIFIX under grant agreement ANR-21-ESRE-0011."
article_processing_charge: No
author:
- first_name: Lea Marie
full_name: Becker, Lea Marie
id: 36336939-eb97-11eb-a6c2-c83f1214ca79
last_name: Becker
orcid: 0000-0002-6401-5151
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Christophe
full_name: Chipot, Christophe
last_name: Chipot
citation:
ama: Becker LM, Schanda P, Chipot C. Additional Data for “Aromatic Ring Flips Reveal
Reshaping of Protein Dynamics in Crystals and Complexes.” 2026. doi:10.15479/AT-ISTA-21145
apa: Becker, L. M., Schanda, P., & Chipot, C. (2026). Additional Data for “Aromatic
Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.” Institute
of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21145
chicago: Becker, Lea Marie, Paul Schanda, and Christophe Chipot. “Additional Data
for ‘Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and
Complexes.’” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21145.
ieee: L. M. Becker, P. Schanda, and C. Chipot, “Additional Data for ‘Aromatic Ring
Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.’” Institute
of Science and Technology Austria, 2026.
ista: Becker LM, Schanda P, Chipot C. 2026. Additional Data for ‘Aromatic Ring Flips
Reveal Reshaping of Protein Dynamics in Crystals and Complexes’, Institute of
Science and Technology Austria, 10.15479/AT-ISTA-21145.
mla: Becker, Lea Marie, et al. Additional Data for “Aromatic Ring Flips Reveal
Reshaping of Protein Dynamics in Crystals and Complexes.” Institute of Science
and Technology Austria, 2026, doi:10.15479/AT-ISTA-21145.
short: L.M. Becker, P. Schanda, C. Chipot, (2026).
contributor:
- contributor_type: researcher
first_name: Haohao
last_name: Fu
- contributor_type: researcher
first_name: Benjamin
id: 71cda2f3-e604-11ee-a1df-da10587eda3f
last_name: Tatman
- contributor_type: researcher
first_name: Matthias
last_name: Dreydoppel
- contributor_type: researcher
first_name: Anna
id: 9fb2a840-89e1-11ee-a8b7-cc5c7ba62471
last_name: Kapitonova
- contributor_type: researcher
first_name: Daniel
id: 302BADF6-85FC-11EA-9E3B-B9493DDC885E
last_name: Balazs
orcid: 0000-0001-7597-043X
- contributor_type: researcher
first_name: Ulrich
last_name: Weininger
- contributor_type: researcher
first_name: Sylvain
last_name: Engilberge
corr_author: '1'
date_created: 2026-02-05T13:54:39Z
date_published: 2026-02-09T00:00:00Z
date_updated: 2026-06-24T08:47:57Z
day: '09'
ddc:
- '572'
department:
- _id: GradSch
- _id: PaSc
doi: 10.15479/AT-ISTA-21145
file:
- access_level: open_access
checksum: 02a419cce8cea450bc952f35488d2df5
content_type: text/plain
creator: lbecker
date_created: 2026-02-05T13:52:37Z
date_updated: 2026-02-05T13:52:37Z
file_id: '21146'
file_name: README.txt
file_size: 4263
relation: table_of_contents
- access_level: open_access
checksum: b0b82b1aa73985b0b308a3fa52d21aea
content_type: application/zip
creator: lbecker
date_created: 2026-02-05T13:52:41Z
date_updated: 2026-02-05T13:52:41Z
file_id: '21147'
file_name: Research_Data.zip
file_size: 50647107
relation: main_file
success: 1
file_date_updated: 2026-02-05T13:52:41Z
has_accepted_license: '1'
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 7be609c4-9f16-11ee-852c-85015ce2b9b0
grant_number: '26777'
name: Exploring protein dynamics by solid-state MAS NMR through specific labeling
approaches
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '20641'
relation: earlier_version
status: public
- id: '22105'
relation: used_in_publication
status: public
status: public
title: Additional Data for "Aromatic Ring Flips Reveal Reshaping of Protein Dynamics
in Crystals and Complexes"
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2026'
...
---
OA_place: publisher
OA_type: gold
_id: '22146'
abstract:
- lang: eng
text: We study differentially private model training with stochastic gradient descent
under learning rate scheduling and correlated noise. Although correlated noise,
in particular via matrix factorizations, has been shown to improve accuracy, prior
theoretical work focused primarily on the prefix-sum workload. That workload assumes
a constant learning rate, whereas in practice learning rate schedules are widely
used to accelerate training and improve convergence. We close this gap by deriving
general upper and lower bounds for a broad class of learning rate schedules in
both single- and multi-epoch settings. Building on these results, we propose a
learning-rate-aware factorization that achieves improvements over prefix-sum factorizations
under both MaxSE and MeanSE error metrics. Our theoretical analysis yields memory-efficient
constructions suitable for practical deployment, and experiments on CIFAR-10 and
IMDB datasets confirm that schedule-aware factorizations improve accuracy in private
training.
acknowledgement: "We thank Rasmus Pagh, Christoph Lampert and Jalaj Upadhyay for valuable\r\ncomments
on an early draft. We thank Ryan Mckenna for a fruitful discussion on the experiment\r\ndesign.
We thank Antti Honkela for sharing insights on learning rate scheduling and DP.\r\nNikita
P. Kalinin: Funded in part by the Austrian Science Fund (FWF) [10.55776/COE12].\r\nJoel
Daniel Andersson: Funded by the European Union. Views and opinions expressed are
however\r\nthose of the author(s) only and do not necessarily reflect those of the
European Union or the European\r\nResearch Council Executive Agency. Neither the
European Union nor the granting authority can be\r\nheld responsible for them. This
project has received funding from the European Research Council\r\n(ERC) under the
European Union’s Horizon 2020 research and innovation programme (MoDynStruct,\r\nNo.
101019564). Additional funding by Providentia, a Data Science Distinguished Investigator
grant\r\nfrom Novo Nordisk Fonden, with additional support from VILLUM Investigator
grant 54451.\r\n"
alternative_title:
- LIPIcs
article_number: 2:1-2:21
article_processing_charge: No
arxiv: 1
author:
- first_name: Nikita
full_name: Kalinin, Nikita
id: 4b14526e-14d2-11ed-ba64-c14c9553d137
last_name: Kalinin
- first_name: Joel D
full_name: Andersson, Joel D
id: 4a893819-d954-11f0-89b1-e360bad9ccc5
last_name: Andersson
citation:
ama: 'Kalinin N, Andersson JD. Learning rate scheduling with matrix factorization
for private training. In: 7th Symposium on Foundations of Responsible Computing.
Vol 368. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2026. doi:10.4230/LIPIcs.FORC.2026.2'
apa: 'Kalinin, N., & Andersson, J. D. (2026). Learning rate scheduling with
matrix factorization for private training. In 7th Symposium on Foundations
of Responsible Computing (Vol. 368). Cambridge, MA; United States: Schloss
Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.FORC.2026.2'
chicago: Kalinin, Nikita, and Joel D Andersson. “Learning Rate Scheduling with Matrix
Factorization for Private Training.” In 7th Symposium on Foundations of Responsible
Computing, Vol. 368. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2026.
https://doi.org/10.4230/LIPIcs.FORC.2026.2.
ieee: N. Kalinin and J. D. Andersson, “Learning rate scheduling with matrix factorization
for private training,” in 7th Symposium on Foundations of Responsible Computing,
Cambridge, MA; United States, 2026, vol. 368.
ista: 'Kalinin N, Andersson JD. 2026. Learning rate scheduling with matrix factorization
for private training. 7th Symposium on Foundations of Responsible Computing. FORC:
Symposium on Foundations of Responsible Computing, LIPIcs, vol. 368, 2:1-2:21.'
mla: Kalinin, Nikita, and Joel D. Andersson. “Learning Rate Scheduling with Matrix
Factorization for Private Training.” 7th Symposium on Foundations of Responsible
Computing, vol. 368, 2:1-2:21, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2026, doi:10.4230/LIPIcs.FORC.2026.2.
short: N. Kalinin, J.D. Andersson, in:, 7th Symposium on Foundations of Responsible
Computing, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2026.
conference:
end_date: 2026-06-05
location: Cambridge, MA; United States
name: 'FORC: Symposium on Foundations of Responsible Computing'
start_date: 2026-06-03
corr_author: '1'
das_tickbox: '0'
date_created: 2026-06-28T22:01:34Z
date_published: 2026-06-01T00:00:00Z
date_updated: 2026-06-29T06:56:34Z
day: '01'
ddc:
- '000'
department:
- _id: ChLa
- _id: GradSch
- _id: MoHe
doi: 10.4230/LIPIcs.FORC.2026.2
ec_funded: 1
external_id:
arxiv:
- '2511.17994'
file:
- access_level: open_access
checksum: c661f016d3861a1c1b590b87a744d087
content_type: application/pdf
creator: dernst
date_created: 2026-06-29T06:55:23Z
date_updated: 2026-06-29T06:55:23Z
file_id: '22149'
file_name: 2026_LIPIcsFORC_Kalinin.pdf
file_size: 1231914
relation: main_file
success: 1
file_date_updated: 2026-06-29T06:55:23Z
has_accepted_license: '1'
intvolume: ' 368'
keyword:
- differential privacy
- machine learning
- matrix factorization
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: bd9ca328-d553-11ed-ba76-dc4f890cfe62
call_identifier: H2020
grant_number: '101019564'
name: The design and evaluation of modern fully dynamic data structures
publication: 7th Symposium on Foundations of Responsible Computing
publication_identifier:
eissn:
- 1868-8969
isbn:
- '9783959774192'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: Learning rate scheduling with matrix factorization for private training
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: 368
year: '2026'
...
---
OA_place: publisher
OA_type: gold
_id: '22119'
article_number: EGU26-19367
article_processing_charge: No
author:
- first_name: José M
full_name: Muñoz Hermosilla, José M
id: e1037a6d-646e-11ef-b402-e0ed9ab0901e
last_name: Muñoz Hermosilla
orcid: 0000-0002-1990-8508
- first_name: Evan
full_name: Miles, Evan
last_name: Miles
- first_name: Michael
full_name: McCarthy, Michael
id: 22a2674a-61ce-11ee-94b5-d18813baf16f
last_name: McCarthy
- first_name: Juan Vicente
full_name: Melo Velasco, Juan Vicente
id: 2611dec0-b9c6-11ed-9bea-a81c2b17a549
last_name: Melo Velasco
- first_name: Florian
full_name: Hardmeier, Florian
last_name: Hardmeier
- first_name: PRATEEK
full_name: GANTAYAT, PRATEEK
id: 02734268-3e8d-11ef-80a1-cec4a088d004
last_name: GANTAYAT
- first_name: Adrià
full_name: Fontrodona-Bach, Adrià
id: f06891fd-9f42-11ee-8632-a20971c43046
last_name: Fontrodona-Bach
- first_name: Guillaume
full_name: Jouvet, Guillaume
last_name: Jouvet
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
orcid: 0000-0002-5554-8087
citation:
ama: 'Muñoz Hermosilla JM, Miles E, McCarthy M, et al. Constraining debris input
to Oberaletsch Glacier using ensemble-based Lagrangian modelling. In: EGU General
Assembly 2026. European Geosciences Union; 2026. doi:10.5194/egusphere-egu26-19367'
apa: 'Muñoz Hermosilla, J. M., Miles, E., McCarthy, M., Melo Velasco, J. V., Hardmeier,
F., GANTAYAT, P., … Pellicciotti, F. (2026). Constraining debris input to Oberaletsch
Glacier using ensemble-based Lagrangian modelling. In EGU General Assembly
2026. Vienna, Austria & Virtual: European Geosciences Union. https://doi.org/10.5194/egusphere-egu26-19367'
chicago: Muñoz Hermosilla, José M, Evan Miles, Michael McCarthy, Juan Vicente Melo
Velasco, Florian Hardmeier, PRATEEK GANTAYAT, Adrià Fontrodona-Bach, Guillaume
Jouvet, and Francesca Pellicciotti. “Constraining Debris Input to Oberaletsch
Glacier Using Ensemble-Based Lagrangian Modelling.” In EGU General Assembly
2026. European Geosciences Union, 2026. https://doi.org/10.5194/egusphere-egu26-19367.
ieee: J. M. Muñoz Hermosilla et al., “Constraining debris input to Oberaletsch
Glacier using ensemble-based Lagrangian modelling,” in EGU General Assembly
2026, Vienna, Austria & Virtual, 2026.
ista: Muñoz Hermosilla JM, Miles E, McCarthy M, Melo Velasco JV, Hardmeier F, GANTAYAT
P, Fontrodona-Bach A, Jouvet G, Pellicciotti F. 2026. Constraining debris input
to Oberaletsch Glacier using ensemble-based Lagrangian modelling. EGU General
Assembly 2026. EGU General Assembly, EGU26-19367.
mla: Muñoz Hermosilla, José M., et al. “Constraining Debris Input to Oberaletsch
Glacier Using Ensemble-Based Lagrangian Modelling.” EGU General Assembly 2026,
EGU26-19367, European Geosciences Union, 2026, doi:10.5194/egusphere-egu26-19367.
short: J.M. Muñoz Hermosilla, E. Miles, M. McCarthy, J.V. Melo Velasco, F. Hardmeier,
P. GANTAYAT, A. Fontrodona-Bach, G. Jouvet, F. Pellicciotti, in:, EGU General
Assembly 2026, European Geosciences Union, 2026.
conference:
end_date: 2026-05-08
location: Vienna, Austria & Virtual
name: EGU General Assembly
start_date: 2026-05-03
corr_author: '1'
date_created: 2026-06-22T12:16:50Z
date_published: 2026-07-02T00:00:00Z
date_updated: 2026-07-02T06:42:37Z
day: '02'
ddc:
- '550'
department:
- _id: FrPe
- _id: GradSch
doi: 10.5194/egusphere-egu26-19367
file:
- access_level: open_access
checksum: 2ea3e691cfa53176d0e801b9172842d6
content_type: application/pdf
creator: dernst
date_created: 2026-07-02T06:22:50Z
date_updated: 2026-07-02T06:22:50Z
file_id: '22233'
file_name: 2026_EGU26_MunozHermosilla.pdf
file_size: 284023
relation: main_file
success: 1
file_date_updated: 2026-07-02T06:22:50Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: EGU General Assembly 2026
publication_status: published
publisher: European Geosciences Union
status: public
title: Constraining debris input to Oberaletsch Glacier using ensemble-based Lagrangian
modelling
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_abstract
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2026'
...
---
_id: '20842'
abstract:
- lang: eng
text: Probing the possibility of entanglement generation through gravity offers
a path to tackle the question of whether gravitational fields possess a quantum
mechanical nature. A potential realization necessitates systems with low-frequency
dynamics at an optimal mass scale, for which the microgram-to-milligram range
is a strong contender. Here, after refining a figure-of-merit for the problem,
we present a 1-milligram torsional pendulum operating at 18 Hz. We demonstrate
laser cooling its motion from room temperature to 240~microkelvins, surpassing
by over 20-fold the coldest motions attained for oscillators ranging from micrograms
to kilograms. We quantify and contrast the utility of the current approach with
other platforms. The achieved performance and large improvement potential highlight
milligram-scale torsional pendulums as a powerful platform for precision measurements
relevant to future studies at the quantum-gravity interface.
article_processing_charge: No
author:
- first_name: Sofya
full_name: Agafonova, Sofya
id: 09501ff6-dca7-11ea-a8ae-b3e0b9166e80
last_name: Agafonova
orcid: 0000-0003-0582-2946
citation:
ama: 'Agafonova S. Research Data for: “One-milligram torsional pendulum toward experiments
at the quantum-gravity interface.” 2025. doi:10.15479/AT-ISTA-20842'
apa: 'Agafonova, S. (2025). Research Data for: “One-milligram torsional pendulum
toward experiments at the quantum-gravity interface.” Institute of Science and
Technology Austria. https://doi.org/10.15479/AT-ISTA-20842'
chicago: 'Agafonova, Sofia. “Research Data for: ‘One-Milligram Torsional Pendulum
toward Experiments at the Quantum-Gravity Interface.’” Institute of Science and
Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20842.'
ieee: 'S. Agafonova, “Research Data for: ‘One-milligram torsional pendulum toward
experiments at the quantum-gravity interface.’” Institute of Science and Technology
Austria, 2025.'
ista: 'Agafonova S. 2025. Research Data for: ‘One-milligram torsional pendulum toward
experiments at the quantum-gravity interface’, Institute of Science and Technology
Austria, 10.15479/AT-ISTA-20842.'
mla: 'Agafonova, Sofia. Research Data for: “One-Milligram Torsional Pendulum
toward Experiments at the Quantum-Gravity Interface.” Institute of Science
and Technology Austria, 2025, doi:10.15479/AT-ISTA-20842.'
short: S. Agafonova, (2025).
contributor:
- first_name: Pere
last_name: Rosello
- first_name: Manuel
last_name: Mekonnen
- contributor_type: supervisor
first_name: Onur
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
corr_author: '1'
date_created: 2025-12-21T14:23:50Z
date_published: 2025-12-22T00:00:00Z
date_updated: 2026-06-10T08:36:07Z
day: '22'
department:
- _id: GradSch
- _id: OnHo
doi: 10.15479/AT-ISTA-20842
file:
- access_level: open_access
checksum: 7af34e4226a00cdcb7f154272050e217
content_type: application/x-zip-compressed
creator: sagafono
date_created: 2025-12-22T13:45:30Z
date_updated: 2025-12-22T13:45:30Z
file_id: '20854'
file_name: AllData.zip
file_size: 146656591
relation: main_file
success: 1
- access_level: open_access
checksum: 71806a2ef9fb26ad7b78e04c6754ee4e
content_type: application/x-zip-compressed
creator: sagafono
date_created: 2025-12-22T13:45:33Z
date_updated: 2025-12-22T13:45:33Z
file_id: '20855'
file_name: SourceData.zip
file_size: 93470129
relation: main_file
success: 1
- access_level: open_access
checksum: 08facd1b4a102f83e4d99d48a85b258d
content_type: text/plain
creator: sagafono
date_created: 2025-12-22T13:51:09Z
date_updated: 2025-12-22T13:51:09Z
file_id: '20856'
file_name: readme.txt
file_size: 461
relation: main_file
success: 1
file_date_updated: 2025-12-22T13:51:09Z
has_accepted_license: '1'
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: bdb2a702-d553-11ed-ba76-f12e3e5a3bc6
grant_number: '101087907'
name: 'A quantum hybrid of atoms and milligram-scale pendulums: towards gravitational
quantum mechanics'
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '20840'
relation: used_in_publication
status: public
status: public
title: 'Research Data for: ''One-milligram torsional pendulum toward experiments at
the quantum-gravity interface'''
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: research_data
user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d
year: '2025'
...
---
OA_place: repository
OA_type: hybrid
_id: '20883'
abstract:
- lang: eng
text: 'Evading imminent predator threat is critical for survival. Effective defensive
strategies can vary, even between closely related species. However, the neural
basis of such species-specific behaviours is still poorly understood. Here we
find that two sister species of deer mice (genus Peromyscus) show different responses
to the same looming stimulus: P. maniculatus, which occupies densely vegetated
habitats, predominantly escapes, while the open field specialist, P. polionotus,
briefly freezes. This difference arises from species-specific escape thresholds,
is largely context-independent, and can be triggered by both visual and auditory
threat stimuli. Using immunohistochemistry and electrophysiological recordings,
we find that although visual threat activates the superior colliculus in both
species, the role of the dorsal periaqueductal gray (dPAG) in driving behaviour
differs. While dPAG activity scales with running speed in P. maniculatus, neural
activity in the dPAG of P. polionotus correlates poorly with movement, including
during visually triggered escape. Moreover, optogenetic activation of dPAG neurons
elicits acceleration in P. maniculatus but not P. polionotus, while their chemogenetic
inhibition during a looming stimulus delays escape onset in P. maniculatus to
match that of P. polionotus. Together, we trace species-specific escape thresholds
to a central circuit node, downstream of peripheral sensory neurons, localizing
an ecologically relevant behavioural difference to a specific region of the mammalian
brain.'
article_processing_charge: No
author:
- first_name: Baier
full_name: Felix, Baier
last_name: Felix
- first_name: Katja
full_name: Reinhard, Katja
last_name: Reinhard
- first_name: Bram
full_name: Nuttin, Bram
last_name: Nuttin
- first_name: Arnau
full_name: Sans Dublanc, Arnau
last_name: Sans Dublanc
- first_name: Chen
full_name: Liu, Chen
last_name: Liu
- first_name: Victoria
full_name: Tong, Victoria
last_name: Tong
- first_name: Julie Stefanie
full_name: Murmann, Julie Stefanie
id: 1d390868-f128-11eb-9611-a0ca5f7833b5
last_name: Murmann
- first_name: Keimpe
full_name: Wierda, Keimpe
last_name: Wierda
- first_name: Karl
full_name: Farrow, Karl
last_name: Farrow
- first_name: Hopi
full_name: Hoekstra, Hopi
last_name: Hoekstra
citation:
ama: Felix B, Reinhard K, Nuttin B, et al. The neural basis of species-specific
defensive behaviour in Peromyscus mice. 2025. doi:10.5061/DRYAD.Q2BVQ83XC
apa: Felix, B., Reinhard, K., Nuttin, B., Sans Dublanc, A., Liu, C., Tong, V., …
Hoekstra, H. (2025). The neural basis of species-specific defensive behaviour
in Peromyscus mice. Dryad. https://doi.org/10.5061/DRYAD.Q2BVQ83XC
chicago: Felix, Baier, Katja Reinhard, Bram Nuttin, Arnau Sans Dublanc, Chen Liu,
Victoria Tong, Julie Stefanie Murmann, Keimpe Wierda, Karl Farrow, and Hopi Hoekstra.
“The Neural Basis of Species-Specific Defensive Behaviour in Peromyscus Mice.”
Dryad, 2025. https://doi.org/10.5061/DRYAD.Q2BVQ83XC.
ieee: B. Felix et al., “The neural basis of species-specific defensive behaviour
in Peromyscus mice.” Dryad, 2025.
ista: Felix B, Reinhard K, Nuttin B, Sans Dublanc A, Liu C, Tong V, Murmann JS,
Wierda K, Farrow K, Hoekstra H. 2025. The neural basis of species-specific defensive
behaviour in Peromyscus mice, Dryad, 10.5061/DRYAD.Q2BVQ83XC.
mla: Felix, Baier, et al. The Neural Basis of Species-Specific Defensive Behaviour
in Peromyscus Mice. Dryad, 2025, doi:10.5061/DRYAD.Q2BVQ83XC.
short: B. Felix, K. Reinhard, B. Nuttin, A. Sans Dublanc, C. Liu, V. Tong, J.S.
Murmann, K. Wierda, K. Farrow, H. Hoekstra, (2025).
date_created: 2025-12-30T07:36:29Z
date_published: 2025-06-23T00:00:00Z
date_updated: 2026-01-05T11:38:41Z
day: '23'
department:
- _id: GradSch
doi: 10.5061/DRYAD.Q2BVQ83XC
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.q2bvq83xc
month: '06'
oa: 1
oa_version: Submitted Version
publisher: Dryad
related_material:
record:
- id: '20101'
relation: used_in_publication
status: public
status: public
title: The neural basis of species-specific defensive behaviour in Peromyscus mice
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
OA_place: publisher
_id: '20920'
abstract:
- lang: eng
text: "Verifiable Delay Functions (VDFs) introduced by Boneh et al. (CRYPTO'18)
are functions that require a prescribed number of sequential steps T to evaluate,
yet their output can be verified in time much faster than T. Since their introduction,
VDFs have gained a lot of attention due to their applications in blockchain protocols,
randomness beacons, timestamping and deniability. This thesis explores the theory
and applications of VDFs, focusing on enhancing their soundness, efficiency and
practicality.\r\n\r\nThe only practical VDFs known to date are based on repeated
squaring in hidden order groups. Consider the function VDF(x,T)=x^(2^T).\r\nThe
iterated squaring assumption states that, for a random group element x, the result
of VDF cannot be computed significantly faster than performing T sequential squarings
if the group order is unknown. To make the result verifiable a prover can compute
a proof of exponentiation (PoE) \\pi. Given \\pi, the output of VDF can be verified
in time much less than T.\r\n\r\nWe first present new constructions of statistically
sound proofs of exponentiation, which are an important building block in the construction
of SNARKs (Succinct Non-Interactive Argument of Knowledge). Statistical soundness
means that the proofs remain secure against computationally unbounded adversaries,
in particular, it remains secure even when the group order is known. We thereby
address limitations in previous PoE protocols which either required (non-standard)
hardness assumptions or a lot of parallel repetitions. Our construction significantly
reduces the proof size of statistically sound PoEs that allow for a structured
exponent, which leads to better efficiency of SNARKs and other applications.\r\n\r\nSecondly,
we introduce improved batching techniques for PoEs, which allow multiple proofs
to be aggregated and verified with minimal overhead. These protocols optimize
communication and computation complexity in large-scale blockchain environments
and enable scalable remote benchmarking of parallel computation resources.\r\n\r\nWe
then construct VDFs with enhanced properties such as zero-knowledge and watermarkability.
It was shown by Arun, Bonneau and Clark (ASIACRYPT'22) that these features enable
new cryptographic primitives called short-lived proofs and signatures. The validity
of such proofs and signatures expires after a predefined amount of time T, i.e.,
they are deniable after time T. Our constructions improve upon the constructions
by Arun, Bonneau and Clark in several dimensions (faster forging times, arguably
weaker assumptions).\r\n\r\nFinally, we apply PoEs in the realm of primality testing,
providing cryptographically sound proofs of non-primality for large Proth numbers.
This work gives a surprising application of VDFs in the area of computational
number theory.\r\n\r\nTogether, our contributions advance both the theoretical
foundations and the real-world usability of VDFs in general and in particular
of PoEs, making them more adaptable and secure for current and emerging cryptographic
applications."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Charlotte
full_name: Hoffmann, Charlotte
id: 0f78d746-dc7d-11ea-9b2f-83f92091afe7
last_name: Hoffmann
orcid: 0000-0003-2027-5549
citation:
ama: Hoffmann C. Theory and applications of verifiable delay functions. 2025. doi:10.15479/AT-ISTA-20920
apa: Hoffmann, C. (2025). Theory and applications of verifiable delay functions.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20920
chicago: Hoffmann, Charlotte. “Theory and Applications of Verifiable Delay Functions.”
Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20920.
ieee: C. Hoffmann, “Theory and applications of verifiable delay functions,” Institute
of Science and Technology Austria, 2025.
ista: Hoffmann C. 2025. Theory and applications of verifiable delay functions. Institute
of Science and Technology Austria.
mla: Hoffmann, Charlotte. Theory and Applications of Verifiable Delay Functions.
Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20920.
short: C. Hoffmann, Theory and Applications of Verifiable Delay Functions, Institute
of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2026-01-02T10:46:47Z
date_published: 2025-12-31T00:00:00Z
date_updated: 2026-04-16T09:11:08Z
day: '31'
ddc:
- '004'
degree_awarded: PhD
department:
- _id: GradSch
- _id: KrPi
doi: 10.15479/AT-ISTA-20920
file:
- access_level: closed
checksum: 8a099fbf54963bd0be38f7ce73658682
content_type: application/x-zip-compressed
creator: choffman
date_created: 2026-01-02T10:39:16Z
date_updated: 2026-01-02T10:39:16Z
file_id: '20921'
file_name: 2025_Hoffmann_Charlotte_Source.zip
file_size: 8355494
relation: source_file
- access_level: open_access
checksum: 9521c07bfb2bb5b14a49c09fcfc96474
content_type: application/pdf
creator: choffman
date_created: 2026-01-02T10:39:26Z
date_updated: 2026-01-02T10:39:26Z
file_id: '20922'
file_name: 2025_Hoffmann_Charlotte_Thesis.pdf
file_size: 2258804
relation: main_file
success: 1
file_date_updated: 2026-01-02T10:39:26Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '116'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '13143'
relation: part_of_dissertation
status: public
- id: '20701'
relation: part_of_dissertation
status: public
- id: '12176'
relation: part_of_dissertation
status: public
- id: '20556'
relation: earlier_version
status: public
- id: '19778'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
title: Theory and applications of verifiable delay functions
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '20926'
abstract:
- lang: eng
text: Most current machine learning interatomic potentials (MLIPs) rely on short-range
approximations, without explicit treatment of long-range electrostatics. To address
this, we recently developed the Latent Ewald Summation (LES) method, which infers
electrostatic interactions, polarization, and Born effective charges (BECs), just
by learning from energy and force training data. Here, we present LES as a standalone
library, compatible with any short-range MLIP, and demonstrate its integration
with methods such as MACE, NequIP, Allegro, CACE, CHGNet, and UMA. We benchmark
LES-enhanced models on distinct systems, including bulk water, polar dipeptides,
and gold dimer adsorption on defective substrates, and show that LES not only
captures correct electrostatics but also improves accuracy. Additionally, we scale
LES to large and chemically diverse data by training MACELES-OFF on the SPICE
set containing molecules and clusters, making a universal MLIP with electrostatics
for organic systems, including biomolecules. MACELES-OFF is more accurate than
its short-range counterpart (MACE-OFF) trained on the same data set, predicts
dipoles and BECs reliably, and has better descriptions of bulk liquids. By enabling
efficient long-range electrostatics without directly training on electrical properties,
LES paves the way for electrostatic foundation MLIPs.
acknowledgement: Research reported in this publication was supported by the National
Institute Of General Medical Sciences of the National Institutes of Health under
Award Number R35GM159986. The content is solely the responsibility of the authors
and does not necessarily represent the official views of the National Institutes
of Health. D.K. and B.C. acknowledge funding from Toyota Research Institute Synthesis
Advanced Research Challenge. T.J.I., D.S.K. and P.Z. acknowledge funding from BIDMaP
Postdoctoral Fellowship. T.J.I. used resources of the National Energy Research Scientific
Computing Center (NERSC), a Department of Energy Office of Science User Facility
using NERSC award DOEERCAP0031751 ′GenAI@NERSC’. The authors thank Bowen Deng for
valuable discussions on MatGL implementation, and thank Gabor Csanyi for stimulating
discussions.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Dongjin
full_name: Kim, Dongjin
last_name: Kim
- first_name: Xiaoyu
full_name: Wang, Xiaoyu
id: 8dff9c62-32b0-11ee-9fa8-fc73025e10f3
last_name: Wang
- first_name: Santiago
full_name: Vargas, Santiago
last_name: Vargas
- first_name: Peichen
full_name: Zhong, Peichen
last_name: Zhong
- first_name: Daniel S.
full_name: King, Daniel S.
last_name: King
- first_name: Theo Jaffrelot
full_name: Inizan, Theo Jaffrelot
last_name: Inizan
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
citation:
ama: Kim D, Wang X, Vargas S, et al. A universal augmentation framework for long-range
electrostatics in machine learning interatomic potentials. Journal of Chemical
Theory and Computation. 2025;21(24):12709-12724. doi:10.1021/acs.jctc.5c01400
apa: Kim, D., Wang, X., Vargas, S., Zhong, P., King, D. S., Inizan, T. J., &
Cheng, B. (2025). A universal augmentation framework for long-range electrostatics
in machine learning interatomic potentials. Journal of Chemical Theory and
Computation. American Chemical Society. https://doi.org/10.1021/acs.jctc.5c01400
chicago: Kim, Dongjin, Xiaoyu Wang, Santiago Vargas, Peichen Zhong, Daniel S. King,
Theo Jaffrelot Inizan, and Bingqing Cheng. “A Universal Augmentation Framework
for Long-Range Electrostatics in Machine Learning Interatomic Potentials.” Journal
of Chemical Theory and Computation. American Chemical Society, 2025. https://doi.org/10.1021/acs.jctc.5c01400.
ieee: D. Kim et al., “A universal augmentation framework for long-range electrostatics
in machine learning interatomic potentials,” Journal of Chemical Theory and
Computation, vol. 21, no. 24. American Chemical Society, pp. 12709–12724,
2025.
ista: Kim D, Wang X, Vargas S, Zhong P, King DS, Inizan TJ, Cheng B. 2025. A universal
augmentation framework for long-range electrostatics in machine learning interatomic
potentials. Journal of Chemical Theory and Computation. 21(24), 12709–12724.
mla: Kim, Dongjin, et al. “A Universal Augmentation Framework for Long-Range Electrostatics
in Machine Learning Interatomic Potentials.” Journal of Chemical Theory and
Computation, vol. 21, no. 24, American Chemical Society, 2025, pp. 12709–24,
doi:10.1021/acs.jctc.5c01400.
short: D. Kim, X. Wang, S. Vargas, P. Zhong, D.S. King, T.J. Inizan, B. Cheng, Journal
of Chemical Theory and Computation 21 (2025) 12709–12724.
corr_author: '1'
date_created: 2026-01-04T23:01:33Z
date_published: 2025-12-10T00:00:00Z
date_updated: 2026-01-05T11:34:21Z
day: '10'
department:
- _id: GradSch
- _id: BiCh
doi: 10.1021/acs.jctc.5c01400
external_id:
arxiv:
- '2507.14302'
pmid:
- '41368735 '
intvolume: ' 21'
issue: '24'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2507.14302
month: '12'
oa: 1
oa_version: Preprint
page: 12709-12724
pmid: 1
publication: Journal of Chemical Theory and Computation
publication_identifier:
eissn:
- 1549-9626
issn:
- 1549-9618
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: A universal augmentation framework for long-range electrostatics in machine
learning interatomic potentials
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 21
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '21020'
abstract:
- lang: eng
text: "Runtime verification offers scalable solutions to improve the safety and
reliability of systems. However, systems that require verification or monitoring
by a third party to ensure compliance with a specification might contain sensitive
information, causing privacy concerns when usual runtime verification approaches
are used. Privacy is compromised if protected information about the system, or
sensitive data that is processed by the system, is revealed. In addition, revealing
the specification being monitored may undermine the essence of third-party verification.\r\nIn
this work, we propose two novel protocols for the privacy-preserving runtime verification
of systems against formal sequential specifications. In our first protocol, the
monitor verifies whether the system satisfies the specification without learning
anything else, though both parties are aware of the specification. Our second
protocol ensures that the system remains oblivious to the monitored specification,
while the monitor learns only whether the system satisfies the specification and
nothing more. Our protocols adapt and improve existing techniques used in cryptography,
and more specifically, multi-party computation.\r\nThe sequential specification
defines the observation step of the monitor, whose granularity depends on the
situation (e.g., banks may be monitored on a daily basis). Our protocols exchange
a single message per observation step, after an initialisation phase. This design
minimises communication overhead, enabling relatively lightweight privacy-preserving
monitoring. We implement our approach for monitoring specifications described
by register automata and evaluate it experimentally."
acknowledgement: This work is a part of projects VAMOS that has received fund-ing
from the European Research Council (ERC), grant agreementNo 101020093 and the Austrian
Science Fund (FWF) SFB projectSpyCoDe F8502.We thank anonymous reviewers for pointing
us to related work [ 3] and for their valuable suggestions that improved this paper.
article_processing_charge: Yes (via OA deal)
arxiv: 1
author:
- 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: Mahyar
full_name: Karimi, Mahyar
id: 6e5417ba-5355-11ee-ae5a-94c2e510b26b
last_name: Karimi
orcid: 0009-0005-0820-1696
- first_name: K. S.
full_name: Thejaswini, K. S.
id: 3807fb92-fdc1-11ee-bb4a-b4d8a431c753
last_name: Thejaswini
citation:
ama: 'Henzinger TA, Karimi M, Thejaswini KS. Privacy-preserving runtime verification.
In: Proceedings of the 2025 ACM SIGSAC Conference on Computer and Communications
Security. Association for Computing Machinery; 2025:2774-2787. doi:10.1145/3719027.3765137'
apa: 'Henzinger, T. A., Karimi, M., & Thejaswini, K. S. (2025). Privacy-preserving
runtime verification. In Proceedings of the 2025 ACM SIGSAC Conference on Computer
and Communications Security (pp. 2774–2787). Taipei, Taiwan: Association for
Computing Machinery. https://doi.org/10.1145/3719027.3765137'
chicago: Henzinger, Thomas A, Mahyar Karimi, and K. S. Thejaswini. “Privacy-Preserving
Runtime Verification.” In Proceedings of the 2025 ACM SIGSAC Conference on
Computer and Communications Security, 2774–87. Association for Computing Machinery,
2025. https://doi.org/10.1145/3719027.3765137.
ieee: T. A. Henzinger, M. Karimi, and K. S. Thejaswini, “Privacy-preserving runtime
verification,” in Proceedings of the 2025 ACM SIGSAC Conference on Computer
and Communications Security, Taipei, Taiwan, 2025, pp. 2774–2787.
ista: 'Henzinger TA, Karimi M, Thejaswini KS. 2025. Privacy-preserving runtime verification.
Proceedings of the 2025 ACM SIGSAC Conference on Computer and Communications Security.
CCS: Conference on Computer and Communications Security, 2774–2787.'
mla: Henzinger, Thomas A., et al. “Privacy-Preserving Runtime Verification.” Proceedings
of the 2025 ACM SIGSAC Conference on Computer and Communications Security,
Association for Computing Machinery, 2025, pp. 2774–87, doi:10.1145/3719027.3765137.
short: T.A. Henzinger, M. Karimi, K.S. Thejaswini, in:, Proceedings of the 2025
ACM SIGSAC Conference on Computer and Communications Security, Association for
Computing Machinery, 2025, pp. 2774–2787.
conference:
end_date: 2025-10-17
location: Taipei, Taiwan
name: 'CCS: Conference on Computer and Communications Security'
start_date: 2025-10-13
corr_author: '1'
date_created: 2026-01-20T10:17:10Z
date_published: 2025-11-22T00:00:00Z
date_updated: 2026-03-13T13:37:19Z
day: '22'
ddc:
- '000'
department:
- _id: ToHe
- _id: GradSch
doi: 10.1145/3719027.3765137
ec_funded: 1
external_id:
arxiv:
- '2505.09276'
file:
- access_level: open_access
checksum: 615ffddab6c7285158c2953acec6fa6f
content_type: application/pdf
creator: dernst
date_created: 2026-01-21T07:34:58Z
date_updated: 2026-01-21T07:34:58Z
file_id: '21024'
file_name: 2025_CCS_HenzingerT.pdf
file_size: 1241912
relation: main_file
success: 1
file_date_updated: 2026-01-21T07:34:58Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 2774-2787
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
- _id: 34a1b658-11ca-11ed-8bc3-c75229f0241e
grant_number: F8502
name: Interface Theory for Security and Privacy
publication: Proceedings of the 2025 ACM SIGSAC Conference on Computer and Communications
Security
publication_identifier:
isbn:
- '9798400715259'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
record:
- id: '21401'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Privacy-preserving runtime verification
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
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '21136'
abstract:
- lang: eng
text: The plant hormone auxin regulates growth and development through at least
two distinct signaling pathways. The nuclear pathway, involving TIR1/AFB receptors,
mediates transcription; whereas the cell surface ABP1-TMK1 auxin perception triggers
global ultrafast phosphorylation response. Here, we revisit the rich history of
the disputed ABP1 auxin receptor, highlighting recent findings of the involvement
of TMKs and other molecular components and focusing on their role in auxin canalization-mediated
development.
acknowledgement: We gratefully acknowledge the funding by the Austrian Science Fund
(FWF; I 6123-B and P 37051-B) and the European Research Council (ERC; 101142681
CYNIPS).We would like to thank Lukas Fiedler for his significant input and thoughtful
revision of this manuscript.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Aline
full_name: Monzer, Aline
id: 2DB5D88C-D7B3-11E9-B8FD-7907E6697425
last_name: Monzer
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Monzer A, Friml J. Historical and mechanistic perspective on ABP1-TMK1-mediated
cell surface auxin signaling. npj Science of Plants. 2025;1(1):2. doi:10.1038/s44383-025-00002-8
apa: Monzer, A., & Friml, J. (2025). Historical and mechanistic perspective
on ABP1-TMK1-mediated cell surface auxin signaling. Npj Science of Plants.
Springer Nature. https://doi.org/10.1038/s44383-025-00002-8
chicago: Monzer, Aline, and Jiří Friml. “Historical and Mechanistic Perspective
on ABP1-TMK1-Mediated Cell Surface Auxin Signaling.” Npj Science of Plants.
Springer Nature, 2025. https://doi.org/10.1038/s44383-025-00002-8.
ieee: A. Monzer and J. Friml, “Historical and mechanistic perspective on ABP1-TMK1-mediated
cell surface auxin signaling.,” npj Science of Plants, vol. 1, no. 1. Springer
Nature, p. 2, 2025.
ista: Monzer A, Friml J. 2025. Historical and mechanistic perspective on ABP1-TMK1-mediated
cell surface auxin signaling. npj Science of Plants. 1(1), 2.
mla: Monzer, Aline, and Jiří Friml. “Historical and Mechanistic Perspective on ABP1-TMK1-Mediated
Cell Surface Auxin Signaling.” Npj Science of Plants, vol. 1, no. 1, Springer
Nature, 2025, p. 2, doi:10.1038/s44383-025-00002-8.
short: A. Monzer, J. Friml, Npj Science of Plants 1 (2025) 2.
corr_author: '1'
date_created: 2026-02-03T13:03:53Z
date_published: 2025-07-01T00:00:00Z
date_updated: 2026-02-10T09:39:20Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
- _id: GradSch
doi: 10.1038/s44383-025-00002-8
external_id:
pmid:
- '40630787'
file:
- access_level: open_access
checksum: 6c190faacf0e3bef98311dc8a12132d4
content_type: application/pdf
creator: dernst
date_created: 2026-02-10T09:35:43Z
date_updated: 2026-02-10T09:35:43Z
file_id: '21208'
file_name: 2025_NPJSciencePlants_Monzer.pdf
file_size: 974106
relation: main_file
success: 1
file_date_updated: 2026-02-10T09:35:43Z
has_accepted_license: '1'
intvolume: ' 1'
issue: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '07'
oa: 1
oa_version: Published Version
page: '2'
pmid: 1
project:
- _id: bd76d395-d553-11ed-ba76-f678c14f9033
grant_number: I06123
name: Peptide receptors for auxin canalization in Arabidopsis
- _id: 7bcece63-9f16-11ee-852c-ae94e099eeb6
grant_number: P37051
name: Guanylate cyclase activity of TIR1/AFBs auxin receptors
- _id: 8f347782-16d5-11f0-9cad-8c19706ee739
grant_number: '101142681'
name: Cyclic nucleotides as second messengers in plants
publication: npj Science of Plants
publication_identifier:
eissn:
- 3005-1401
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Historical and mechanistic perspective on ABP1-TMK1-mediated cell surface auxin
signaling.
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '21144'
abstract:
- lang: eng
text: 'This paper deals with the algorithmic aspects of solving feasibility problems
of semidefinite programming (SDP), aka linear matrix inequalities (LMIs). Since
in some SDP instances all feasible solutions have irrational entries, numerical
solvers that work with rational numbers can only find an approximate solution.
We study the following question: Is it possible to certify feasibility of a given
SDP using an approximate solution that is sufficiently close to some exact solution?
Existing approaches make the assumption that there exist rational feasible solutions
(and use techniques such as rounding and lattice reduction algorithms). We propose
an alternative approach that does not need this assumption. More specifically,
we show how to construct a system of polynomial equations whose set of real solutions
is guaranteed to have an isolated correct solution (assuming that the target exact
solution is maximum-rank). This allows, in particular, for us to use algorithms
from real algebraic geometry for solving systems of polynomial equations, yielding
a hybrid (or symbolic-numerical) method for SDPs. We experimentally compare it
with a pure symbolic method in [D. Henrion, S. Naldi, and M. Safey El Din, SIAM
J. Optim., 26 (2016), pp. 2512–2539]; the hybrid method was able to certify feasibility
of many SDP instances on which the aforementioned paper failed. Our approach may
have further applications, such as refining an approximate solution using methods
of numerical algebraic geometry for systems of polynomial equations.'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Simone
full_name: Naldi, Simone
last_name: Naldi
- first_name: Jeferson
full_name: Zapata, Jeferson
id: 00223538-AF8F-11E9-A4C7-F729E6697425
last_name: Zapata
citation:
ama: Kolmogorov V, Naldi S, Zapata J. Certifying solutions of degenerate semidefinite
programs. SIAM Journal on Optimization. 2025;35(3):1630-1654. doi:10.1137/24m1664691
apa: Kolmogorov, V., Naldi, S., & Zapata, J. (2025). Certifying solutions of
degenerate semidefinite programs. SIAM Journal on Optimization. Society
for Industrial and Applied Mathematics. https://doi.org/10.1137/24m1664691
chicago: Kolmogorov, Vladimir, Simone Naldi, and Jeferson Zapata. “Certifying Solutions
of Degenerate Semidefinite Programs.” SIAM Journal on Optimization. Society
for Industrial and Applied Mathematics, 2025. https://doi.org/10.1137/24m1664691.
ieee: V. Kolmogorov, S. Naldi, and J. Zapata, “Certifying solutions of degenerate
semidefinite programs,” SIAM Journal on Optimization, vol. 35, no. 3. Society
for Industrial and Applied Mathematics, pp. 1630–1654, 2025.
ista: Kolmogorov V, Naldi S, Zapata J. 2025. Certifying solutions of degenerate
semidefinite programs. SIAM Journal on Optimization. 35(3), 1630–1654.
mla: Kolmogorov, Vladimir, et al. “Certifying Solutions of Degenerate Semidefinite
Programs.” SIAM Journal on Optimization, vol. 35, no. 3, Society for Industrial
and Applied Mathematics, 2025, pp. 1630–54, doi:10.1137/24m1664691.
short: V. Kolmogorov, S. Naldi, J. Zapata, SIAM Journal on Optimization 35 (2025)
1630–1654.
date_created: 2026-02-05T13:33:05Z
date_published: 2025-09-01T00:00:00Z
date_updated: 2026-06-12T10:36:59Z
day: '01'
department:
- _id: VlKo
- _id: GradSch
doi: 10.1137/24m1664691
external_id:
arxiv:
- '2405.13625'
intvolume: ' 35'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2405.13625
month: '09'
oa: 1
oa_version: Preprint
page: 1630-1654
publication: SIAM Journal on Optimization
publication_identifier:
eissn:
- 1095-7189
issn:
- 1052-6234
publication_status: published
publisher: Society for Industrial and Applied Mathematics
quality_controlled: '1'
related_material:
record:
- id: '21957'
relation: dissertation_contains
status: public
status: public
title: Certifying solutions of degenerate semidefinite programs
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '21248'
abstract:
- lang: eng
text: Camera-type eyes in vertebrates and cephalopods are striking examples of parallel
evolution of a complex structure. While comparisons have focused on these two
groups, camera-type eyes with likely high functionality are also found in other
invertebrate phyla with simpler brains. Employing single-cell RNA sequencing,
we identify neurogenic cells in the adult eyes and brain of the marine annelid
worm Platynereis dumerilii. Distinct neural stem cells in the camera-type adult
eyes, located at the edge of the cup-shaped retina, and adjacent to the glass
body/lens, produce radial lines of cells, reminiscent of stem cells in ciliary
marginal zones of vertebrate eyes exhibiting life-long growth. Normal proliferation
in the eye depends on ambient light, a phenomenon that depends on the integrity
of the photoreceptor gene c-opsin1, which is present in emerging rhabdomeric photoreceptors,
and impacts on their differentiation. During reproductive maturation, proliferation
in the eye as well as the entire brain sharply declines, while cells upregulate
molecular characteristics of mammalian adult neural stem cell quiescence. Our
data provide insights into the development and modulation of annelid head and
brain cells, revealing similarities and differences to vertebrate eye development,
neurogenesis and brain plasticity.
acknowledgement: 'We are grateful to Andrij Belokurov, Margaryta Borysova and Netsanet
Getachew for routine worm cultures and genotyping support, Lena Stumbauer for practical
help, as well as all members of the Tessmar-Raible and Raible labs for constructive
discussions. This work was supported by, Helmholtz Society, distinguished professorship
by the Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research (K.T.-R.),
H2020 European Research Council, ERC Grant Agreement #819952 (K.T.-R.), Austrian
Science Funds (FWF), SFB F78 (F.R., K.T-R; https://doi.org/10.55776/F78), the Human
Frontier Science Program (HFSP), #RGP021/2024, https://doi.org/10.52044/HFSP.RGP0212024.pc.gr.194174
(KT-R), University of Vienna Research Platform SinCeReSt (F.R.), For open access
purposes, K.T.-R. has applied a CC BY public copyright license to any author accepted
manuscript version arising from this submission. We acknowledge support by the Open
Access publication fund of Alfred-Wegener-Institut Helmholtz-Zentrum für Polar-
und Meeresforschung. None of the funding bodies was involved in the design of the
study, the collection, analysis, and interpretation of data or in writing the manuscript.
Open Access funding enabled and organized by Projekt DEAL.'
article_number: '9861'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Nadja
full_name: Milivojev, Nadja
last_name: Milivojev
- first_name: Federico
full_name: Scaramuzza, Federico
last_name: Scaramuzza
- first_name: Pedro Ozório
full_name: Brum, Pedro Ozório
last_name: Brum
- first_name: Camila L
full_name: Velastegui Gamboa, Camila L
id: 625aea67-91c1-11f0-aad8-f71452b4174d
last_name: Velastegui Gamboa
- first_name: Gabriele
full_name: Andreatta, Gabriele
last_name: Andreatta
- first_name: Florian
full_name: Raible, Florian
last_name: Raible
- first_name: Kristin
full_name: Tessmar-Raible, Kristin
last_name: Tessmar-Raible
citation:
ama: Milivojev N, Scaramuzza F, Brum PO, et al. Light-modulated stem cells in the
camera-type eye of an annelid model for adult brain plasticity. Nature Communications.
2025;16. doi:10.1038/s41467-025-65631-0
apa: Milivojev, N., Scaramuzza, F., Brum, P. O., Velastegui Gamboa, C. L., Andreatta,
G., Raible, F., & Tessmar-Raible, K. (2025). Light-modulated stem cells in
the camera-type eye of an annelid model for adult brain plasticity. Nature
Communications. Springer Nature. https://doi.org/10.1038/s41467-025-65631-0
chicago: Milivojev, Nadja, Federico Scaramuzza, Pedro Ozório Brum, Camila L Velastegui
Gamboa, Gabriele Andreatta, Florian Raible, and Kristin Tessmar-Raible. “Light-Modulated
Stem Cells in the Camera-Type Eye of an Annelid Model for Adult Brain Plasticity.”
Nature Communications. Springer Nature, 2025. https://doi.org/10.1038/s41467-025-65631-0.
ieee: N. Milivojev et al., “Light-modulated stem cells in the camera-type
eye of an annelid model for adult brain plasticity,” Nature Communications,
vol. 16. Springer Nature, 2025.
ista: Milivojev N, Scaramuzza F, Brum PO, Velastegui Gamboa CL, Andreatta G, Raible
F, Tessmar-Raible K. 2025. Light-modulated stem cells in the camera-type eye of
an annelid model for adult brain plasticity. Nature Communications. 16, 9861.
mla: Milivojev, Nadja, et al. “Light-Modulated Stem Cells in the Camera-Type Eye
of an Annelid Model for Adult Brain Plasticity.” Nature Communications,
vol. 16, 9861, Springer Nature, 2025, doi:10.1038/s41467-025-65631-0.
short: N. Milivojev, F. Scaramuzza, P.O. Brum, C.L. Velastegui Gamboa, G. Andreatta,
F. Raible, K. Tessmar-Raible, Nature Communications 16 (2025).
date_created: 2026-02-16T15:38:11Z
date_published: 2025-12-01T00:00:00Z
date_updated: 2026-06-18T18:30:32Z
day: '01'
ddc:
- '570'
department:
- _id: GradSch
doi: 10.1038/s41467-025-65631-0
intvolume: ' 16'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41467-025-65631-0
month: '12'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Light-modulated stem cells in the camera-type eye of an annelid model for adult
brain plasticity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2025'
...
---
OA_place: publisher
OA_type: gold
_id: '21250'
abstract:
- lang: eng
text: We investigate the step complexity of the Leader Election problem (and implementing
the corresponding test-and-set object) in asynchronous shared memory, where processes
communicate through registers supporting atomic read and write and must coordinate
so that a single process becomes the leader. Determining tight step complexity
bounds for solving this problem is one of the key open problems in the theory
of shared memory distributed computing. The best known algorithm is a randomized
tournament-tree, which has worst-case expected step complexity O(log N) for N
processes. There are provably no deterministic wait-free algorithms, and only
restricted lower bounds are known for obstruction-free and randomized wait-free
algorithms. We introduce a new lower bound that establishes an Ω((log N)/(log
log N + log Q)) step complexity for any obstruction-free Leader Election algorithm,
where N is the number of processes, and 2 ≤ Q ≤ N is a bound on the value contention,
which we define as the maximum number of different values that processes can be
simultaneously poised to write to the same register in any execution of the algorithm.
Our result is strictly stronger than previous bounds based on write contention.
In particular, it implies new lower bounds on step complexity that depend on register
size.
acknowledgement: The work of Dan Alistarh is supported by grants from ERC, Austrian
FWF, and the Google and NVIDIA corporations. Faith Ellen was supported in part by
the Natural Science and Engineering Research Council of Canada (NSERC) grant RGPIN-2020-04178.
alternative_title:
- LIPIcs
article_processing_charge: Yes
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Faith
full_name: Ellen, Faith
last_name: Ellen
- first_name: Alexander
full_name: Fedorov, Alexander
id: 2e711909-896a-11ed-bdf8-eb0f5a2984c6
last_name: Fedorov
citation:
ama: 'Alistarh D-A, Ellen F, Fedorov A. An almost-logarithmic lower bound for leader
election with bounded value contention. In: 39th International Symposium on
Distributed Computing. Vol 356. Schloss Dagstuhl - Leibniz-Zentrum für Informatik;
2025:3:1-3:16. doi:10.4230/LIPIcs.DISC.2025.3'
apa: 'Alistarh, D.-A., Ellen, F., & Fedorov, A. (2025). An almost-logarithmic
lower bound for leader election with bounded value contention. In 39th International
Symposium on Distributed Computing (Vol. 356, p. 3:1-3:16). Berlin, Germany:
Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.DISC.2025.3'
chicago: Alistarh, Dan-Adrian, Faith Ellen, and Alexander Fedorov. “An Almost-Logarithmic
Lower Bound for Leader Election with Bounded Value Contention.” In 39th International
Symposium on Distributed Computing, 356:3:1-3:16. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2025. https://doi.org/10.4230/LIPIcs.DISC.2025.3.
ieee: D.-A. Alistarh, F. Ellen, and A. Fedorov, “An almost-logarithmic lower bound
for leader election with bounded value contention,” in 39th International Symposium
on Distributed Computing, Berlin, Germany, 2025, vol. 356, p. 3:1-3:16.
ista: 'Alistarh D-A, Ellen F, Fedorov A. 2025. An almost-logarithmic lower bound
for leader election with bounded value contention. 39th International Symposium
on Distributed Computing. DISC: Symposium on Distributed Computing, LIPIcs, vol.
356, 3:1-3:16.'
mla: Alistarh, Dan-Adrian, et al. “An Almost-Logarithmic Lower Bound for Leader
Election with Bounded Value Contention.” 39th International Symposium on Distributed
Computing, vol. 356, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2025,
p. 3:1-3:16, doi:10.4230/LIPIcs.DISC.2025.3.
short: D.-A. Alistarh, F. Ellen, A. Fedorov, in:, 39th International Symposium on
Distributed Computing, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2025,
p. 3:1-3:16.
conference:
end_date: 2025-10-31
location: Berlin, Germany
name: 'DISC: Symposium on Distributed Computing'
start_date: 2025-10-27
corr_author: '1'
date_created: 2026-02-16T15:41:15Z
date_published: 2025-10-22T00:00:00Z
date_updated: 2026-02-18T06:49:38Z
day: '22'
ddc:
- '000'
department:
- _id: DaAl
- _id: GradSch
doi: 10.4230/LIPIcs.DISC.2025.3
file:
- access_level: open_access
checksum: 3825a0e6e6a05503e842a59f95528bd9
content_type: application/pdf
creator: dernst
date_created: 2026-02-18T06:46:02Z
date_updated: 2026-02-18T06:46:02Z
file_id: '21310'
file_name: 2025_LIPIcs_Alistarh.pdf
file_size: 1492189
relation: main_file
success: 1
file_date_updated: 2026-02-18T06:46:02Z
has_accepted_license: '1'
intvolume: ' 356'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 3:1-3:16
publication: 39th International Symposium on Distributed Computing
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
status: public
title: An almost-logarithmic lower bound for leader election with bounded value contention
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: 356
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '21257'
abstract:
- lang: eng
text: 'We investigate the problem of accurate sparse fine-tuning of large language
models (LLMs), that is, fine-tuning pre-trained LLMs on specialized tasks, while
inducing sparsity in their weights. Our work is motivated by experiments showing
that standard loss-based fine-tuning methods are not able to achieve high accuracy
in this setting, especially at high sparsity targets. To address this issue, we
perform a detailed study of knowledge distillation losses for fine-tuning of sparse
models. We determine an L2-based distillation approach that we term ‘SquareHead’,
which enables accurate recovery even at higher sparsities. Investigating the question
of efficient inference, we show that sparse LLMs can be executed faster by taking
advantage of sparsity. Specifically, we exhibit end-to-end results showing speedups
enabled by sparsity, while recovering accuracy, on the following models and tasks,
respectively: T5 for language translation, Whisper for speech translation, and
open GPT-type models such as the Mosaic Pre-Trained Transformer (MPT) and Llama-2
models for text generation. In particular, for popular generative tasks, we show
for the first time that sparse fine-tuning can reach 75% sparsity without drops
in accuracy, and provide notable end-to-end speedups for inference on CPUs. Moreover,
we also highlight that sparsity is compatible with other compression approaches,
such as quantization.'
acknowledgement: We would like to thank Eugenia Iofinova for useful comments on an
earlier version of this draft, and Artur Niederfahrenhorst for useful suggestions
regarding fine-tuning on the GSM8k dataset.
alternative_title:
- 'Machine Translation: Technologies and Applications'
article_processing_charge: No
arxiv: 1
author:
- first_name: Eldar
full_name: Kurtic, Eldar
id: 47beb3a5-07b5-11eb-9b87-b108ec578218
last_name: Kurtic
- first_name: Denis
full_name: Kuznedelev, Denis
last_name: Kuznedelev
- first_name: Elias
full_name: Frantar, Elias
id: 09a8f98d-ec99-11ea-ae11-c063a7b7fe5f
last_name: Frantar
- first_name: Michael
full_name: Goinv, Michael
last_name: Goinv
- first_name: Shubhra
full_name: Pandit, Shubhra
last_name: Pandit
- first_name: Abhinav
full_name: Agarwalla, Abhinav
last_name: Agarwalla
- first_name: Tuan
full_name: Nguyen, Tuan
last_name: Nguyen
- first_name: Alexandre
full_name: Marques, Alexandre
last_name: Marques
- first_name: Mark
full_name: Kurtz, Mark
last_name: Kurtz
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
citation:
ama: 'Kurtic E, Kuznedelev D, Frantar E, et al. Sparse Fine-Tuning for Inference
Acceleration of Large Language Models. In: Passban P, Way A, Rezagholizadeh M,
eds. Enhancing LLM Performance. Efficacy, Fine-Tuning, and Inference Techniques.
Springer Nature; 2025:83-97. doi:10.1007/978-3-031-85747-8_6'
apa: Kurtic, E., Kuznedelev, D., Frantar, E., Goinv, M., Pandit, S., Agarwalla,
A., … Alistarh, D.-A. (2025). Sparse Fine-Tuning for Inference Acceleration of
Large Language Models. In P. Passban, A. Way, & M. Rezagholizadeh (Eds.),
Enhancing LLM Performance. Efficacy, Fine-Tuning, and Inference Techniques
(pp. 83–97). Springer Nature. https://doi.org/10.1007/978-3-031-85747-8_6
chicago: Kurtic, Eldar, Denis Kuznedelev, Elias Frantar, Michael Goinv, Shubhra
Pandit, Abhinav Agarwalla, Tuan Nguyen, Alexandre Marques, Mark Kurtz, and Dan-Adrian
Alistarh. “Sparse Fine-Tuning for Inference Acceleration of Large Language Models.”
In Enhancing LLM Performance. Efficacy, Fine-Tuning, and Inference Techniques,
edited by Peyman Passban, Andy Way, and Mehdi Rezagholizadeh, 83–97. Springer
Nature, 2025. https://doi.org/10.1007/978-3-031-85747-8_6.
ieee: E. Kurtic et al., “Sparse Fine-Tuning for Inference Acceleration of
Large Language Models,” in Enhancing LLM Performance. Efficacy, Fine-Tuning,
and Inference Techniques, P. Passban, A. Way, and M. Rezagholizadeh, Eds.
Springer Nature, 2025, pp. 83–97.
ista: 'Kurtic E, Kuznedelev D, Frantar E, Goinv M, Pandit S, Agarwalla A, Nguyen
T, Marques A, Kurtz M, Alistarh D-A. 2025.Sparse Fine-Tuning for Inference Acceleration
of Large Language Models. In: Enhancing LLM Performance. Efficacy, Fine-Tuning,
and Inference Techniques. Machine Translation: Technologies and Applications,
, 83–97.'
mla: Kurtic, Eldar, et al. “Sparse Fine-Tuning for Inference Acceleration of Large
Language Models.” Enhancing LLM Performance. Efficacy, Fine-Tuning, and Inference
Techniques, edited by Peyman Passban et al., Springer Nature, 2025, pp. 83–97,
doi:10.1007/978-3-031-85747-8_6.
short: E. Kurtic, D. Kuznedelev, E. Frantar, M. Goinv, S. Pandit, A. Agarwalla,
T. Nguyen, A. Marques, M. Kurtz, D.-A. Alistarh, in:, P. Passban, A. Way, M. Rezagholizadeh
(Eds.), Enhancing LLM Performance. Efficacy, Fine-Tuning, and Inference Techniques,
Springer Nature, 2025, pp. 83–97.
corr_author: '1'
date_created: 2026-02-16T15:57:53Z
date_published: 2025-07-05T00:00:00Z
date_updated: 2026-02-19T09:26:54Z
day: '05'
department:
- _id: DaAl
- _id: GradSch
doi: 10.1007/978-3-031-85747-8_6
editor:
- first_name: Peyman
full_name: Passban, Peyman
last_name: Passban
- first_name: Andy
full_name: Way, Andy
last_name: Way
- first_name: Mehdi
full_name: Rezagholizadeh, Mehdi
last_name: Rezagholizadeh
external_id:
arxiv:
- '2310.06927'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2310.06927
month: '07'
oa: 1
oa_version: Preprint
page: 83-97
publication: Enhancing LLM Performance. Efficacy, Fine-Tuning, and Inference Techniques
publication_identifier:
eisbn:
- '9783031857478'
eissn:
- 2522-803X
isbn:
- '9783031857461'
issn:
- 2522-8021
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Sparse Fine-Tuning for Inference Acceleration of Large Language Models
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
OA_place: publisher
OA_type: gold
_id: '21281'
abstract:
- lang: eng
text: "A strategy profile in a multi-player game is a Nash equilibrium if no player
can unilaterally deviate to achieve a strictly better payoff. A profile is an
ε-Nash equilibrium if no player can gain more than ε by unilaterally deviating
from their strategy. In this work, we use ε-Nash equilibria to approximate the
computation of Nash equilibria. Specifically, we focus on turn-based, multiplayer
stochastic games played on graphs, where players are restricted to stationary
strategies - strategies that use randomness but not memory.\r\nThe problem of
deciding the constrained existence of stationary Nash equilibria - where each
player’s payoff must lie within a given interval - is known to be ∃ℝ-complete
in such a setting (Hansen and Sølvsten, 2020). We extend this line of work to
stationary ε-Nash equilibria and present an algorithm that solves the following
promise problem: given a game with a Nash equilibrium satisfying the constraints,
compute an ε-Nash equilibrium that ε-satisfies those same constraints - satisfies
the constraints up to an ε additive error. Our algorithm runs in FNP^NP time.\r\nTo
achieve this, we first show that if a constrained Nash equilibrium exists, then
one exists where the non-zero probabilities are at least an inverse of a double-exponential
in the input. We further prove that such a strategy can be encoded using floating-point
representations, as in the work of Frederiksen and Miltersen (2013), which finally
gives us our FNP^NP algorithm. \r\nWe further show that the decision version of
the promise problem is NP-hard. Finally, we show a partial tightness result by
proving a lower bound for such techniques: if a constrained Nash equilibrium exists,
then there must be one where the probabilities in the strategies are double-exponentially
small."
acknowledgement: "This work is a part of project VAMOS that has received funding from
the European\r\nResearch Council (ERC), grant agreement No 101020093.\r\n"
alternative_title:
- LIPIcs
article_processing_charge: Yes
arxiv: 1
author:
- first_name: Ali
full_name: Asadi, Ali
id: 02d96aae-000e-11ec-b801-cadd0a5eefbb
last_name: Asadi
- first_name: Leonard
full_name: Brice, Leonard
last_name: Brice
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: K. S.
full_name: Thejaswini, K. S.
id: 3807fb92-fdc1-11ee-bb4a-b4d8a431c753
last_name: Thejaswini
citation:
ama: 'Asadi A, Brice L, Chatterjee K, Thejaswini KS. ε-stationary Nash equilibria
in multi-player stochastic graph games. In: 45th Annual Conference on Foundations
of Software Technology and Theoretical Computer Science. Vol 360. Schloss
Dagstuhl - Leibniz-Zentrum für Informatik; 2025:9:1-9:17. doi:10.4230/lipics.fsttcs.2025.9'
apa: 'Asadi, A., Brice, L., Chatterjee, K., & Thejaswini, K. S. (2025). ε-stationary
Nash equilibria in multi-player stochastic graph games. In 45th Annual Conference
on Foundations of Software Technology and Theoretical Computer Science (Vol.
360, p. 9:1-9:17). Pilani, India: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
https://doi.org/10.4230/lipics.fsttcs.2025.9'
chicago: Asadi, Ali, Leonard Brice, Krishnendu Chatterjee, and K. S. Thejaswini.
“ε-Stationary Nash Equilibria in Multi-Player Stochastic Graph Games.” In 45th
Annual Conference on Foundations of Software Technology and Theoretical Computer
Science, 360:9:1-9:17. Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2025. https://doi.org/10.4230/lipics.fsttcs.2025.9.
ieee: A. Asadi, L. Brice, K. Chatterjee, and K. S. Thejaswini, “ε-stationary Nash
equilibria in multi-player stochastic graph games,” in 45th Annual Conference
on Foundations of Software Technology and Theoretical Computer Science, Pilani,
India, 2025, vol. 360, p. 9:1-9:17.
ista: 'Asadi A, Brice L, Chatterjee K, Thejaswini KS. 2025. ε-stationary Nash equilibria
in multi-player stochastic graph games. 45th Annual Conference on Foundations
of Software Technology and Theoretical Computer Science. FSTTCS: Conference on
Foundations of Software Technology and Theoretical Computer Science, LIPIcs, vol.
360, 9:1-9:17.'
mla: Asadi, Ali, et al. “ε-Stationary Nash Equilibria in Multi-Player Stochastic
Graph Games.” 45th Annual Conference on Foundations of Software Technology
and Theoretical Computer Science, vol. 360, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2025, p. 9:1-9:17, doi:10.4230/lipics.fsttcs.2025.9.
short: A. Asadi, L. Brice, K. Chatterjee, K.S. Thejaswini, in:, 45th Annual Conference
on Foundations of Software Technology and Theoretical Computer Science, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2025, p. 9:1-9:17.
conference:
end_date: 2025-12-19
location: Pilani, India
name: 'FSTTCS: Conference on Foundations of Software Technology and Theoretical
Computer Science'
start_date: 2025-12-17
corr_author: '1'
date_created: 2026-02-17T08:27:14Z
date_published: 2025-12-09T00:00:00Z
date_updated: 2026-02-19T09:39:15Z
day: '09'
ddc:
- '000'
department:
- _id: KrCh
- _id: GradSch
doi: 10.4230/lipics.fsttcs.2025.9
ec_funded: 1
external_id:
arxiv:
- '2508.15356'
file:
- access_level: open_access
checksum: a66343e3ccc4a9cc5bc699c03d5764ff
content_type: application/pdf
creator: dernst
date_created: 2026-02-18T09:13:25Z
date_updated: 2026-02-18T09:13:25Z
file_id: '21316'
file_name: 2025_FSTTCS_Asadi.pdf
file_size: 1054007
relation: main_file
success: 1
file_date_updated: 2026-02-18T09:13:25Z
has_accepted_license: '1'
intvolume: ' 360'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 9:1-9:17
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: 45th Annual Conference on Foundations of Software Technology and Theoretical
Computer Science
publication_identifier:
isbn:
- '9783959774062'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
status: public
title: ε-stationary Nash equilibria in multi-player stochastic graph games
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: 360
year: '2025'
...
---
OA_place: publisher
OA_type: gold
_id: '21327'
abstract:
- lang: eng
text: Proteins exist as a dynamic ensemble of multiple conformations, and these
motions are often crucial for their functions. However, current structure prediction
methods predominantly yield a single conformation, overlooking the conformational
heterogeneity revealed by diverse experimental modalities. Here, we present a
framework for building experiment-grounded protein structure generative models
that infer conformational ensembles consistent with measured experimental data.
The key idea is to treat stateof-the-art protein structure predictors (e.g., AlphaFold3)
as sequence-conditioned structural priors, and cast ensemble modeling as posterior
inference of protein structures given experimental measurements. Through extensive
real-data experiments, we demonstrate the generality of our method to incorporate
a variety of experimental measurements. In particular, our framework uncovers
previously unmodeled conformational heterogeneity from crystallographic densities,
and generates high-accuracy NMR ensembles orders of magnitude faster than the
status quo. Notably, we demonstrate that our ensembles outperform AlphaFold3 (Abramson
et al., 2024) and sometimes better fit experimental data than publicly deposited
structures to the Protein Data Bank (PDB, Burley et al. (2017)). We believe that
this approach will unlock building predictive models that fully embrace experimentally
observed conformational diversity.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: 'This work was supported by the Israeli Science Foundation (ISF)
grant number 1834/24. We acknowledge support from the Austrian Science Fund (FWF,
grant numbers I5812-B and I6223) and the financial support of the Helmsley Fellowships
Program for Sustainability and Health. This research uses resources of the Institute
of Science and Technology Austria’s scientific computing cluster. '
alternative_title:
- PMLR
article_processing_charge: No
arxiv: 1
author:
- first_name: Sai A
full_name: Maddipatla, Sai A
id: e957f5e5-91c9-11f0-a95f-e090f66ecb4d
last_name: Maddipatla
- first_name: Nadav E
full_name: Sellam, Nadav E
id: ef280fe0-91c9-11f0-a95f-8dea3f5bc513
last_name: Sellam
- first_name: Meital I
full_name: Bojan, Meital I
id: 11d88cf5-91ca-11f0-a95f-edf9f08f47b7
last_name: Bojan
- first_name: Sanketh
full_name: Vedula, Sanketh
id: 94f2fe44-70fa-11f0-b76b-92922c09452b
last_name: Vedula
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Ailie
full_name: Marx, Ailie
last_name: Marx
- first_name: Alexander
full_name: Bronstein, Alexander
id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6
last_name: Bronstein
orcid: 0000-0001-9699-8730
citation:
ama: 'Maddipatla SA, Sellam NE, Bojan MI, et al. Inverse problems with experiment-guided
AlphaFold. In: Proceedings of the 42nd International Conference on Machine
Learning. Vol 267. ML Research Press; 2025:42366-42393.'
apa: 'Maddipatla, S. A., Sellam, N. E., Bojan, M. I., Vedula, S., Schanda, P., Marx,
A., & Bronstein, A. M. (2025). Inverse problems with experiment-guided AlphaFold.
In Proceedings of the 42nd International Conference on Machine Learning
(Vol. 267, pp. 42366–42393). Vancouver, Canada: ML Research Press.'
chicago: Maddipatla, Sai A, Nadav E Sellam, Meital I Bojan, Sanketh Vedula, Paul
Schanda, Ailie Marx, and Alex M. Bronstein. “Inverse Problems with Experiment-Guided
AlphaFold.” In Proceedings of the 42nd International Conference on Machine
Learning, 267:42366–93. ML Research Press, 2025.
ieee: S. A. Maddipatla et al., “Inverse problems with experiment-guided AlphaFold,”
in Proceedings of the 42nd International Conference on Machine Learning,
Vancouver, Canada, 2025, vol. 267, pp. 42366–42393.
ista: 'Maddipatla SA, Sellam NE, Bojan MI, Vedula S, Schanda P, Marx A, Bronstein
AM. 2025. Inverse problems with experiment-guided AlphaFold. Proceedings of the
42nd International Conference on Machine Learning. ICML: International Conference
on Machine Learning, PMLR, vol. 267, 42366–42393.'
mla: Maddipatla, Sai A., et al. “Inverse Problems with Experiment-Guided AlphaFold.”
Proceedings of the 42nd International Conference on Machine Learning, vol.
267, ML Research Press, 2025, pp. 42366–93.
short: S.A. Maddipatla, N.E. Sellam, M.I. Bojan, S. Vedula, P. Schanda, A. Marx,
A.M. Bronstein, in:, Proceedings of the 42nd International Conference on Machine
Learning, ML Research Press, 2025, pp. 42366–42393.
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: 2026-02-18T12:11:17Z
date_published: 2025-07-30T00:00:00Z
date_updated: 2026-02-19T08:56:43Z
day: '30'
ddc:
- '000'
- '540'
department:
- _id: PaSc
- _id: AlBr
- _id: GradSch
external_id:
arxiv:
- '2502.09372'
file:
- access_level: open_access
checksum: f33230a6d59b7978d4cd72795e4e9059
content_type: application/pdf
creator: dernst
date_created: 2026-02-19T08:56:10Z
date_updated: 2026-02-19T08:56:10Z
file_id: '21338'
file_name: 2025_ICML_Maddipatla.pdf
file_size: 1924177
relation: main_file
success: 1
file_date_updated: 2026-02-19T08:56:10Z
has_accepted_license: '1'
intvolume: ' 267'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 42366 - 42393
project:
- _id: eb9c82eb-77a9-11ec-83b8-aadd536561cf
grant_number: I05812
name: AlloSpace. The emergence and mechanisms of allostery
- _id: bdb9578d-d553-11ed-ba76-ed5d39fce6f0
grant_number: I06223
name: Structure and mechanism of the mitochondrial MIM insertase
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'
status: public
title: Inverse problems with experiment-guided AlphaFold
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'
...
---
OA_place: repository
_id: '21398'
abstract:
- lang: eng
text: Seymour's decomposition theorem is a hallmark result in matroid theory presenting
a structural characterization of the class of regular matroids. Formalization
of matroid theory faces many challenges, most importantly that only a limited
number of notions and results have been implemented so far. In this work, we formalize
the proof of the forward (composition) direction of Seymour's theorem for regular
matroids. To this end, we develop a library in Lean 4 that implements definitions
and results about totally unimodular matrices, vector matroids, their standard
representations, regular matroids, and 1-, 2-, and 3-sums of matrices and binary
matroids given by their standard representations. Using this framework, we formally
state Seymour's decomposition theorem and implement a formally verified proof
of the composition direction in the setting where the matroids have finite rank
and may have infinite ground sets.
acknowledgement: "We would like to dedicate the paper to the memory of Klaus Truemper,
whose monograph Matroid Decomposition [12]\r\nlaid the foundation for our entire
work."
article_processing_charge: No
arxiv: 1
author:
- first_name: Martin
full_name: Dvorak, Martin
id: 40ED02A8-C8B4-11E9-A9C0-453BE6697425
last_name: Dvorak
orcid: 0000-0001-5293-214X
- first_name: Tristan
full_name: Figueroa-Reid, Tristan
last_name: Figueroa-Reid
- first_name: Rida
full_name: Hamadani, Rida
last_name: Hamadani
- first_name: Byung-Hak
full_name: Hwang, Byung-Hak
last_name: Hwang
- first_name: Evgenia
full_name: Karunus, Evgenia
last_name: Karunus
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Alexander
full_name: Meiburg, Alexander
last_name: Meiburg
- first_name: Alexander
full_name: Nelson, Alexander
last_name: Nelson
- first_name: Peter
full_name: Nelson, Peter
last_name: Nelson
- first_name: Mark
full_name: Sandey, Mark
last_name: Sandey
- first_name: Ivan
full_name: Sergeev, Ivan
id: ca3c9187-9a72-11ee-a009-8af825d896b0
last_name: Sergeev
orcid: 0009-0004-9145-8785
citation:
ama: Dvorak M, Figueroa-Reid T, Hamadani R, et al. Composition direction of Seymour’s
theorem for regular matroids — Formally verified. arXiv. doi:10.48550/arXiv.2509.20539
apa: Dvorak, M., Figueroa-Reid, T., Hamadani, R., Hwang, B.-H., Karunus, E., Kolmogorov,
V., … Sergeev, I. (n.d.). Composition direction of Seymour’s theorem for regular
matroids — Formally verified. arXiv. https://doi.org/10.48550/arXiv.2509.20539
chicago: Dvorak, Martin, Tristan Figueroa-Reid, Rida Hamadani, Byung-Hak Hwang,
Evgenia Karunus, Vladimir Kolmogorov, Alexander Meiburg, et al. “Composition Direction
of Seymour’s Theorem for Regular Matroids — Formally Verified.” ArXiv,
n.d. https://doi.org/10.48550/arXiv.2509.20539.
ieee: M. Dvorak et al., “Composition direction of Seymour’s theorem for regular
matroids — Formally verified,” arXiv. .
ista: Dvorak M, Figueroa-Reid T, Hamadani R, Hwang B-H, Karunus E, Kolmogorov V,
Meiburg A, Nelson A, Nelson P, Sandey M, Sergeev I. Composition direction of Seymour’s
theorem for regular matroids — Formally verified. arXiv, 10.48550/arXiv.2509.20539.
mla: Dvorak, Martin, et al. “Composition Direction of Seymour’s Theorem for Regular
Matroids — Formally Verified.” ArXiv, doi:10.48550/arXiv.2509.20539.
short: M. Dvorak, T. Figueroa-Reid, R. Hamadani, B.-H. Hwang, E. Karunus, V. Kolmogorov,
A. Meiburg, A. Nelson, P. Nelson, M. Sandey, I. Sergeev, ArXiv (n.d.).
corr_author: '1'
date_created: 2026-03-04T11:56:29Z
date_published: 2025-09-23T00:00:00Z
date_updated: 2026-03-27T12:36:59Z
day: '23'
department:
- _id: GradSch
- _id: VlKo
doi: 10.48550/arXiv.2509.20539
external_id:
arxiv:
- '2509.20539'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2509.20539
month: '09'
oa: 1
oa_version: Preprint
page: '21'
publication: arXiv
publication_status: draft
related_material:
record:
- id: '21393'
relation: dissertation_contains
status: public
status: public
title: Composition direction of Seymour's theorem for regular matroids — Formally
verified
type: preprint
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2025'
...
---
OA_place: repository
_id: '21399'
abstract:
- lang: eng
text: We report on the Equational Theories Project (ETP), an online collaborative
pilot project to explore new ways to collaborate in mathematics with machine assistance.
The project successfully determined all 22 028 942 edges of the implication graph
between the 4694 simplest equational laws on magmas, by a combination of human-generated
and automated proofs, all validated by the formal proof assistant language Lean.
As a result of this project, several new constructions of magmas satisfying specific
laws were discovered, and several auxiliary questions were also addressed, such
as the effect of restricting attention to finite magmas.
article_processing_charge: No
arxiv: 1
author:
- first_name: Matthew
full_name: Bolan, Matthew
last_name: Bolan
- first_name: Joachim
full_name: Breitner, Joachim
last_name: Breitner
- first_name: Jose
full_name: Brox, Jose
last_name: Brox
- first_name: Nicholas
full_name: Carlini, Nicholas
last_name: Carlini
- first_name: Mario
full_name: Carneiro, Mario
last_name: Carneiro
- first_name: Floris van
full_name: Doorn, Floris van
last_name: Doorn
- first_name: Martin
full_name: Dvorak, Martin
id: 40ED02A8-C8B4-11E9-A9C0-453BE6697425
last_name: Dvorak
orcid: 0000-0001-5293-214X
- first_name: Andrés
full_name: Goens, Andrés
last_name: Goens
- first_name: Aaron
full_name: Hill, Aaron
last_name: Hill
- first_name: Harald
full_name: Husum, Harald
last_name: Husum
- first_name: Hernán Ibarra
full_name: Mejia, Hernán Ibarra
last_name: Mejia
- first_name: Zoltan A.
full_name: Kocsis, Zoltan A.
last_name: Kocsis
- first_name: Bruno Le
full_name: Floch, Bruno Le
last_name: Floch
- first_name: Amir
full_name: Bar-on, Amir
last_name: Bar-on
- first_name: Lorenzo
full_name: Luccioli, Lorenzo
last_name: Luccioli
- first_name: Douglas
full_name: McNeil, Douglas
last_name: McNeil
- first_name: Alex
full_name: Meiburg, Alex
last_name: Meiburg
- first_name: Pietro
full_name: Monticone, Pietro
last_name: Monticone
- first_name: Pace P.
full_name: Nielsen, Pace P.
last_name: Nielsen
- first_name: Emmanuel Osalotioman
full_name: Osazuwa, Emmanuel Osalotioman
last_name: Osazuwa
- first_name: Giovanni
full_name: Paolini, Giovanni
last_name: Paolini
- first_name: Marco
full_name: Petracci, Marco
last_name: Petracci
- first_name: Bernhard
full_name: Reinke, Bernhard
last_name: Reinke
- first_name: David
full_name: Renshaw, David
last_name: Renshaw
- first_name: Marcus
full_name: Rossel, Marcus
last_name: Rossel
- first_name: Cody
full_name: Roux, Cody
last_name: Roux
- first_name: Jérémy
full_name: Scanvic, Jérémy
last_name: Scanvic
- first_name: Shreyas
full_name: Srinivas, Shreyas
last_name: Srinivas
- first_name: Anand Rao
full_name: Tadipatri, Anand Rao
last_name: Tadipatri
- first_name: Terence
full_name: Tao, Terence
last_name: Tao
- first_name: Vlad
full_name: Tsyrklevich, Vlad
last_name: Tsyrklevich
- first_name: Fernando
full_name: Vaquerizo-Villar, Fernando
last_name: Vaquerizo-Villar
- first_name: Daniel
full_name: Weber, Daniel
last_name: Weber
- first_name: Fan
full_name: Zheng, Fan
last_name: Zheng
citation:
ama: 'Bolan M, Breitner J, Brox J, et al. The equational theories project: Advancing
collaborative mathematical research at scale. arXiv. doi:10.48550/arXiv.2512.07087'
apa: 'Bolan, M., Breitner, J., Brox, J., Carlini, N., Carneiro, M., Doorn, F. van,
… Zheng, F. (n.d.). The equational theories project: Advancing collaborative mathematical
research at scale. arXiv. https://doi.org/10.48550/arXiv.2512.07087'
chicago: 'Bolan, Matthew, Joachim Breitner, Jose Brox, Nicholas Carlini, Mario Carneiro,
Floris van Doorn, Martin Dvorak, et al. “The Equational Theories Project: Advancing
Collaborative Mathematical Research at Scale.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2512.07087.'
ieee: 'M. Bolan et al., “The equational theories project: Advancing collaborative
mathematical research at scale,” arXiv. .'
ista: 'Bolan M, Breitner J, Brox J, Carlini N, Carneiro M, Doorn F van, Dvorak M,
Goens A, Hill A, Husum H, Mejia HI, Kocsis ZA, Floch BL, Bar-on A, Luccioli L,
McNeil D, Meiburg A, Monticone P, Nielsen PP, Osazuwa EO, Paolini G, Petracci
M, Reinke B, Renshaw D, Rossel M, Roux C, Scanvic J, Srinivas S, Tadipatri AR,
Tao T, Tsyrklevich V, Vaquerizo-Villar F, Weber D, Zheng F. The equational theories
project: Advancing collaborative mathematical research at scale. arXiv, 10.48550/arXiv.2512.07087.'
mla: 'Bolan, Matthew, et al. “The Equational Theories Project: Advancing Collaborative
Mathematical Research at Scale.” ArXiv, doi:10.48550/arXiv.2512.07087.'
short: M. Bolan, J. Breitner, J. Brox, N. Carlini, M. Carneiro, F. van Doorn, M.
Dvorak, A. Goens, A. Hill, H. Husum, H.I. Mejia, Z.A. Kocsis, B.L. Floch, A. Bar-on,
L. Luccioli, D. McNeil, A. Meiburg, P. Monticone, P.P. Nielsen, E.O. Osazuwa,
G. Paolini, M. Petracci, B. Reinke, D. Renshaw, M. Rossel, C. Roux, J. Scanvic,
S. Srinivas, A.R. Tadipatri, T. Tao, V. Tsyrklevich, F. Vaquerizo-Villar, D. Weber,
F. Zheng, ArXiv (n.d.).
date_created: 2026-03-04T12:00:16Z
date_published: 2025-12-16T00:00:00Z
date_updated: 2026-03-12T08:36:21Z
day: '16'
department:
- _id: GradSch
- _id: VlKo
doi: 10.48550/arXiv.2512.07087
external_id:
arxiv:
- '2512.07087'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2512.07087
month: '12'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
status: public
title: 'The equational theories project: Advancing collaborative mathematical research
at scale'
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: preprint
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2025'
...
---
OA_place: repository
_id: '21427'
abstract:
- lang: eng
text: While tumor malignancy has been extensively studied under the prism of genetic
and epigenetic heterogeneity, tumor cell states also critically depend on reciprocal
interactions with the microenvironment. This raises the hitherto untested possibility
that heterogeneity of the untransformed tumor stroma can actively fuel malignant
progression. As biological heterogeneity is inherently difficult to control, we
adopted a reductionist approach and let tumor cells invade micro-engineered environments
harboring obstacles with precision-controlled geometry. We find that not only
the presence of obstacles, but more surprisingly their spatial disorder, causes
a drastic shift from a collective to a single-cell mode of invasion – comparable
in strength to cadherin loss. Combining live-imaging and perturbation experiments
with minimal biophysical modeling, we demonstrate that cell detachments result
both from local geometrical constraints and a global integration of spatial disorder
over time. We show that different types of microenvironments map onto different
universality classes of invasion dynamics - homogeneous substrates follow Kardar–Parisi–Zhang
(KPZ) scaling, while disordered ones exhibit exponents consistent with KPZ with
quenched disorder (KPZq). Our findings highlight generic physical principles for
how the mode of cancer cell invasion depends on environmental heterogeneity, with
potential implications to understand tumor evolution in vivo.
acknowledgement: "European Research Council, https://ror.org/0472cxd90, 101071793\r\nAustrian
Academy of Sciences, 26360"
article_processing_charge: No
author:
- first_name: Zuzana
full_name: Dunajova, Zuzana
id: 4B39F286-F248-11E8-B48F-1D18A9856A87
last_name: Dunajova
- first_name: Saren
full_name: Tasciyan, Saren
id: 4323B49C-F248-11E8-B48F-1D18A9856A87
last_name: Tasciyan
orcid: 0000-0003-1671-393X
- first_name: Juraj
full_name: Majek, Juraj
id: 3e6d9473-f38e-11ec-8ae0-c4e05a8aa9e1
last_name: Majek
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Erik
full_name: Sahai, Erik
last_name: Sahai
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- 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: Dunajova Z, Tasciyan S, Majek J, et al. Substrate heterogeneity promotes cancer
cell dissemination through interface roughening. doi:10.1101/2025.05.20.655037
apa: Dunajova, Z., Tasciyan, S., Majek, J., Merrin, J., Sahai, E., Sixt, M. K.,
& Hannezo, E. B. (n.d.). Substrate heterogeneity promotes cancer cell dissemination
through interface roughening. bioRxiv. https://doi.org/10.1101/2025.05.20.655037
chicago: Dunajova, Zuzana, Saren Tasciyan, Juraj Majek, Jack Merrin, Erik Sahai,
Michael K Sixt, and Edouard B Hannezo. “Substrate Heterogeneity Promotes Cancer
Cell Dissemination through Interface Roughening.” bioRxiv, n.d. https://doi.org/10.1101/2025.05.20.655037.
ieee: Z. Dunajova et al., “Substrate heterogeneity promotes cancer cell dissemination
through interface roughening.” bioRxiv.
ista: Dunajova Z, Tasciyan S, Majek J, Merrin J, Sahai E, Sixt MK, Hannezo EB. Substrate
heterogeneity promotes cancer cell dissemination through interface roughening.
10.1101/2025.05.20.655037.
mla: Dunajova, Zuzana, et al. Substrate Heterogeneity Promotes Cancer Cell Dissemination
through Interface Roughening. bioRxiv, doi:10.1101/2025.05.20.655037.
short: Z. Dunajova, S. Tasciyan, J. Majek, J. Merrin, E. Sahai, M.K. Sixt, E.B.
Hannezo, (n.d.).
corr_author: '1'
date_created: 2026-03-11T08:40:06Z
date_published: 2025-09-25T00:00:00Z
date_updated: 2026-06-10T09:41:11Z
day: '25'
ddc:
- '539'
- '570'
department:
- _id: GradSch
- _id: EdHa
- _id: MiSi
- _id: NanoFab
- _id: AnSa
doi: 10.1101/2025.05.20.655037
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2025.05.20.655037
month: '09'
oa: 1
oa_version: Preprint
project:
- _id: bd91e723-d553-11ed-ba76-fe7eeb2185fd
grant_number: '101071793'
name: 'Pushing from within: Control of cell shape, integrity and motility by cytoskeletal
pushing forces'
- _id: 34d75525-11ca-11ed-8bc3-89b6307fee9d
grant_number: '26360'
name: Motile active matter models of migrating cells and chiral filaments
publication_status: draft
publisher: bioRxiv
related_material:
record:
- id: '21423'
relation: dissertation_contains
status: public
- id: '21439'
relation: research_data
status: public
status: public
title: Substrate heterogeneity promotes cancer cell dissemination through interface
roughening
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: preprint
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '21858'
abstract:
- lang: eng
text: "The recent surge in high-quality open-source Generative AI text models (colloquially:
LLMs), as well as efficient finetuning techniques, have opened the possibility
of creating high-quality personalized models that generate text attuned to a specific
individual’s needs and are capable of credibly imitating their writing style by
refining an open-source model with that person’s own data. The technology to create
such models is accessible to private individuals, and training and running such
models can be done cheaply on consumer-grade hardware. While these advancements
are a huge gain for usability and privacy, this position paper argues that the
practical feasibility of impersonating specific individuals also introduces novel
safety risks. For instance, this technology enables the creation of phishing emails\r\nor
fraudulent social media accounts, based on small amounts of publicly available
text, or by the individuals themselves to escape AI text detection. We further
argue that these risks are complementary to—and distinct from—the much-discussed
risks of other impersonation attacks such as image, voice, or video deepfakes,
and are not adequately addressed by the larger research community, or the current
generation of open- and closed-source models."
acknowledgement: "This research was supported by the Scientific Service Units (SSU)
of IST Austria through resources\r\nprovided by Scientific Computing (SciComp).
EI was supported in part by the FWF DK VGSCO,\r\ngrant agreement number W1260-N35.
AJ was supported in part by ERC Proof-of-Concept Grant\r\nFastML, grant agreement
101158077."
article_processing_charge: No
arxiv: 1
author:
- first_name: Eugenia B
full_name: Iofinova, Eugenia B
id: f9a17499-f6e0-11ea-865d-fdf9a3f77117
last_name: Iofinova
orcid: 0000-0002-7778-3221
- first_name: Andrej
full_name: Jovanovic, Andrej
last_name: Jovanovic
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
citation:
ama: 'Iofinova EB, Jovanovic A, Alistarh D-A. Position: It’s time to act on the
risk of efficient personalized text generation. arXiv. doi:10.48550/arXiv.2502.06560'
apa: 'Iofinova, E. B., Jovanovic, A., & Alistarh, D.-A. (n.d.). Position: It’s
time to act on the risk of efficient personalized text generation. arXiv.
https://doi.org/10.48550/arXiv.2502.06560'
chicago: 'Iofinova, Eugenia B, Andrej Jovanovic, and Dan-Adrian Alistarh. “Position:
It’s Time to Act on the Risk of Efficient Personalized Text Generation.” ArXiv,
n.d. https://doi.org/10.48550/arXiv.2502.06560.'
ieee: 'E. B. Iofinova, A. Jovanovic, and D.-A. Alistarh, “Position: It’s time to
act on the risk of efficient personalized text generation,” arXiv. .'
ista: 'Iofinova EB, Jovanovic A, Alistarh D-A. Position: It’s time to act on the
risk of efficient personalized text generation. arXiv, 10.48550/arXiv.2502.06560.'
mla: 'Iofinova, Eugenia B., et al. “Position: It’s Time to Act on the Risk of Efficient
Personalized Text Generation.” ArXiv, doi:10.48550/arXiv.2502.06560.'
short: E.B. Iofinova, A. Jovanovic, D.-A. Alistarh, ArXiv (n.d.).
corr_author: '1'
date_created: 2026-05-11T08:55:23Z
date_published: 2025-06-02T00:00:00Z
date_updated: 2026-05-19T11:20:27Z
day: '02'
department:
- _id: GradSch
- _id: DaAl
doi: 10.48550/arXiv.2502.06560
external_id:
arxiv:
- '2502.06560'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2502.06560
month: '06'
oa: 1
oa_version: Preprint
project:
- _id: 8e35c14b-16d5-11f0-9cad-a3fc35339161
grant_number: '101158077'
name: 'FastML: Efficient and Cost-Effective Distributed Machine Learning'
- _id: 9B9290DE-BA93-11EA-9121-9846C619BF3A
grant_number: W1260-N35
name: Vienna Graduate School on Computational Optimization
publication: arXiv
publication_status: draft
related_material:
record:
- id: '21854'
relation: dissertation_contains
status: public
status: public
title: 'Position: It''s time to act on the risk of efficient personalized text generation'
type: preprint
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '14278'
abstract:
- lang: eng
text: 'The Birkhoff conjecture says that the boundary of a strictly convex integrable
billiard table is necessarily an ellipse. In this article, we consider a stronger
notion of integrability, namely, integrability close to the boundary, and prove
a local version of this conjecture: a small perturbation of almost every ellipse
that preserves integrability near the boundary, is itself an ellipse. We apply
this result to study local spectral uniqueness of ellipses using the connection
between the wave trace of the Laplacian and the dynamics near the boundary and
establish local uniqueness for almost all of them.'
acknowledgement: 'The author acknowledges the partial support of the European Research
Council Grant #885707. He also thanks Vadim Kaloshin for proposing the idea of the
project and greatly aiding the implementation. The author is also grateful to Hamid
Hezari, Amir Vig, Steve Zelditch, Comlan E. Koudjinan, Corentin Fierobe, Ngo Nhok
Tkhai Shon and Roman Sarapin for useful discussions. The author also acknowledges
partial support of ISTern summer program. The project started in the summer of 2021,
when the author was an intern at ISTA. 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: Illya
full_name: Koval, Illya
id: 2eed1f3b-896a-11ed-bdf8-93c7c4bf159e
last_name: Koval
citation:
ama: Koval I. Local strong Birkhoff conjecture and local spectral rigidity of almost
every ellipse. Inventiones Mathematicae. 2025. doi:10.1007/s00222-025-01397-y
apa: Koval, I. (2025). Local strong Birkhoff conjecture and local spectral rigidity
of almost every ellipse. Inventiones Mathematicae. Springer Nature. https://doi.org/10.1007/s00222-025-01397-y
chicago: Koval, Illya. “Local Strong Birkhoff Conjecture and Local Spectral Rigidity
of Almost Every Ellipse.” Inventiones Mathematicae. Springer Nature, 2025.
https://doi.org/10.1007/s00222-025-01397-y.
ieee: I. Koval, “Local strong Birkhoff conjecture and local spectral rigidity of
almost every ellipse,” Inventiones Mathematicae. Springer Nature, 2025.
ista: Koval I. 2025. Local strong Birkhoff conjecture and local spectral rigidity
of almost every ellipse. Inventiones Mathematicae.
mla: Koval, Illya. “Local Strong Birkhoff Conjecture and Local Spectral Rigidity
of Almost Every Ellipse.” Inventiones Mathematicae, Springer Nature, 2025,
doi:10.1007/s00222-025-01397-y.
short: I. Koval, Inventiones Mathematicae (2025).
corr_author: '1'
date_created: 2023-09-06T08:35:43Z
date_published: 2025-12-11T00:00:00Z
date_updated: 2025-12-29T11:37:48Z
day: '11'
ddc:
- '510'
department:
- _id: GradSch
- _id: VaKa
doi: 10.1007/s00222-025-01397-y
ec_funded: 1
external_id:
arxiv:
- '2111.12171'
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1007/s00222-025-01397-y
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 9B8B92DE-BA93-11EA-9121-9846C619BF3A
call_identifier: H2020
grant_number: '885707'
name: Spectral rigidity and integrability for billiards and geodesic flows
publication: Inventiones Mathematicae
publication_identifier:
eissn:
- 1432-1297
issn:
- 0020-9910
publication_status: epub_ahead
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Local strong Birkhoff conjecture and local spectral rigidity of almost every
ellipse
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
year: '2025'
...