---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '21041'
abstract:
- lang: eng
text: "It is common for programmers to assemble their programs from a combination
of trusted and untrusted components. In this context, a trusted program component
is said to be robustly safe if it behaves safely when linked against arbitrary
untrusted code. Prior work has shown how various encapsulation mechanisms (in
both high- and low-level languages) can be used to protect code so that it is
robustly safe, but none of the existing work has explored how robust safety can
be achieved in a patently unsafe language like C.\r\nIn this paper, we show how
to bring robust safety to a simple yet representative C-like language we call
Rec. Although Rec (like C) is inherently ”dangerous” and thus not robustly safe,
we can ”save” Rec programs via compilation to Cap, a CHERI-like capability machine.
To formalize the benefits of such a hardening compiler, we develop Reckon, a separation
logic for verifying robust safety of Rec programs. Reckon is not sound under Rec’s
unsafe, C-like semantics, but it is sound when Rec programs are hardened via compilation
and linked against untrusted code running on Cap. As a crucial step in proving
soundness of Reckon, we introduce a novel technique of semantic back-translation,
which we formalize by building on the DimSum framework for multi-language semantics.
All our results are mechanized in the Rocq prover."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Niklas
full_name: Mück, Niklas
last_name: Mück
- first_name: Aïna Linn
full_name: Georges, Aïna Linn
last_name: Georges
- first_name: Derek
full_name: Dreyer, Derek
last_name: Dreyer
- first_name: Deepak
full_name: Garg, Deepak
last_name: Garg
- first_name: Michael Joachim
full_name: Sammler, Michael Joachim
id: 510d3901-2a03-11ee-914d-d9ae9011f0a7
last_name: Sammler
citation:
ama: 'Mück N, Georges AL, Dreyer D, Garg D, Sammler MJ. Endangered by the language
but saved by the compiler: Robust safety via semantic back-translation. Proceedings
of the ACM on Programming Languages. 2026;10:1153-1182. doi:10.1145/3776682'
apa: 'Mück, N., Georges, A. L., Dreyer, D., Garg, D., & Sammler, M. J. (2026).
Endangered by the language but saved by the compiler: Robust safety via semantic
back-translation. Proceedings of the ACM on Programming Languages. Association
for Computing Machinery. https://doi.org/10.1145/3776682'
chicago: 'Mück, Niklas, Aïna Linn Georges, Derek Dreyer, Deepak Garg, and Michael
Joachim Sammler. “Endangered by the Language but Saved by the Compiler: Robust
Safety via Semantic Back-Translation.” Proceedings of the ACM on Programming
Languages. Association for Computing Machinery, 2026. https://doi.org/10.1145/3776682.'
ieee: 'N. Mück, A. L. Georges, D. Dreyer, D. Garg, and M. J. Sammler, “Endangered
by the language but saved by the compiler: Robust safety via semantic back-translation,”
Proceedings of the ACM on Programming Languages, vol. 10. Association for
Computing Machinery, pp. 1153–1182, 2026.'
ista: 'Mück N, Georges AL, Dreyer D, Garg D, Sammler MJ. 2026. Endangered by the
language but saved by the compiler: Robust safety via semantic back-translation.
Proceedings of the ACM on Programming Languages. 10, 1153–1182.'
mla: 'Mück, Niklas, et al. “Endangered by the Language but Saved by the Compiler:
Robust Safety via Semantic Back-Translation.” Proceedings of the ACM on Programming
Languages, vol. 10, Association for Computing Machinery, 2026, pp. 1153–82,
doi:10.1145/3776682.'
short: N. Mück, A.L. Georges, D. Dreyer, D. Garg, M.J. Sammler, Proceedings of the
ACM on Programming Languages 10 (2026) 1153–1182.
date_created: 2026-01-25T23:01:40Z
date_published: 2026-01-08T00:00:00Z
date_updated: 2026-02-12T13:53:04Z
day: '08'
ddc:
- '000'
department:
- _id: MiSa
doi: 10.1145/3776682
file:
- access_level: open_access
checksum: 79be391061efbf9542638996959ce11a
content_type: application/pdf
creator: dernst
date_created: 2026-02-12T13:51:03Z
date_updated: 2026-02-12T13:51:03Z
file_id: '21221'
file_name: 2026_ProcACMProgrammingLanguages_Mueck.pdf
file_size: 1058876
relation: main_file
success: 1
file_date_updated: 2026-02-12T13:51:03Z
has_accepted_license: '1'
intvolume: ' 10'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 1153-1182
publication: Proceedings of the ACM on Programming Languages
publication_identifier:
eissn:
- 2475-1421
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Endangered by the language but saved by the compiler: Robust safety via semantic
back-translation'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2026'
...
---
OA_place: repository
OA_type: green
_id: '21042'
abstract:
- lang: eng
text: "Many blockchains such as Ethereum execute all incoming transactions sequentially
significantly limiting the potential throughput. A common approach to scale execution
is parallel execution engines that fully utilize modern multi-core architectures.
Parallel execution is then either done optimistically, by executing transactions
in parallel and detecting conflicts on the fly, or guided, by requiring exhaustive
client transaction hints and scheduling transactions accordingly.\r\n\r\nHowever,
recent studies have shown that the performance of parallel execution engines depends
on the nature of the underlying workload. In fact, in some cases, only a 60% speed-up
compared to sequential execution could be obtained. This is the case, as transactions
that access the same resources must be executed sequentially. For example, if
10% of the transactions in a block access the same resource, the execution cannot
meaningfully scale beyond 10 cores. Therefore, a single popular application can
bottleneck the execution and limit the potential throughput.\r\n\r\nIn this paper,
we introduce Anthemius, a block construction algorithm that optimizes parallel
transaction execution throughput. We evaluate Anthemius exhaustively under a range
of workloads, and show that Anthemius enables the underlying parallel execution
engine to process over twice as many transactions."
acknowledgement: This work was supported by the Austrian Science Fund (FWF) SFB project
SpyCoDe F8502 and the Vienna Science and Technology Fund (WWTF) project SCALE2 CT22-045.
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Ray
full_name: Neiheiser, Ray
id: f09651b9-fec0-11ec-b5d8-934aff0e52a4
last_name: Neiheiser
orcid: 0000-0001-7227-8309
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
orcid: 0000-0002-8827-3382
citation:
ama: 'Neiheiser R, Kokoris Kogias E. Anthemius: Efficient and modular block assembly
for concurrent execution. In: 29th International Conference on Financial Cryptography
and Data Security. Vol 15751. Springer Nature; 2026:307-323. doi:10.1007/978-3-032-07024-1_18'
apa: 'Neiheiser, R., & Kokoris Kogias, E. (2026). Anthemius: Efficient and modular
block assembly for concurrent execution. In 29th International Conference on
Financial Cryptography and Data Security (Vol. 15751, pp. 307–323). Miyakojima,
Japan: Springer Nature. https://doi.org/10.1007/978-3-032-07024-1_18'
chicago: 'Neiheiser, Ray, and Eleftherios Kokoris Kogias. “Anthemius: Efficient
and Modular Block Assembly for Concurrent Execution.” In 29th International
Conference on Financial Cryptography and Data Security, 15751:307–23. Springer
Nature, 2026. https://doi.org/10.1007/978-3-032-07024-1_18.'
ieee: 'R. Neiheiser and E. Kokoris Kogias, “Anthemius: Efficient and modular block
assembly for concurrent execution,” in 29th International Conference on Financial
Cryptography and Data Security, Miyakojima, Japan, 2026, vol. 15751, pp. 307–323.'
ista: 'Neiheiser R, Kokoris Kogias E. 2026. Anthemius: Efficient and modular block
assembly for concurrent execution. 29th International Conference on Financial
Cryptography and Data Security. FC: Financial Cryptography and Data Security,
LNCS, vol. 15751, 307–323.'
mla: 'Neiheiser, Ray, and Eleftherios Kokoris Kogias. “Anthemius: Efficient and Modular
Block Assembly for Concurrent Execution.” 29th International Conference on
Financial Cryptography and Data Security, vol. 15751, Springer Nature, 2026,
pp. 307–23, doi:10.1007/978-3-032-07024-1_18.'
short: R. Neiheiser, E. Kokoris Kogias, in:, 29th International Conference on Financial
Cryptography and Data Security, Springer Nature, 2026, pp. 307–323.
conference:
end_date: 2025-04-18
location: Miyakojima, Japan
name: 'FC: Financial Cryptography and Data Security'
start_date: 2025-04-14
corr_author: '1'
date_created: 2026-01-25T23:01:40Z
date_published: 2026-01-01T00:00:00Z
date_updated: 2026-02-12T13:39:07Z
day: '01'
department:
- _id: KrPi
doi: 10.1007/978-3-032-07024-1_18
external_id:
arxiv:
- '2502.10074'
intvolume: ' 15751'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2502.10074
month: '01'
oa: 1
oa_version: Preprint
page: 307-323
project:
- _id: 34a1b658-11ca-11ed-8bc3-c75229f0241e
grant_number: F8502
name: Interface Theory for Security and Privacy
- _id: 7bdd2f70-9f16-11ee-852c-b7950bc6d277
grant_number: ICT22-045
name: SeCure, privAte, and interoperabLe layEr 2
publication: 29th International Conference on Financial Cryptography and Data Security
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783032070234'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Anthemius: Efficient and modular block assembly for concurrent execution'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15751
year: '2026'
...
---
OA_place: repository
_id: '21051'
abstract:
- lang: eng
text: 'In this work, we introduce and study what we believe is an intriguing and,
to the best of our knowledge, previously unknown connection between two areas
in computational topology, topological data analysis (TDA) and knot theory. Given
a function from a topological space to $\mathbb{R}$, TDA provides tools to simplify
and study the importance of topological features: in particular, the $l^{th}$-dimensional
persistence diagram encodes the $l$-homology in the sublevel set as the function
value increases as a set of points in the plane. Given a continuous one-parameter
family of such functions, we can combine the persistence diagrams into an object
known as a vineyard, which track the evolution of points in the persistence diagram.
If we further restrict that family of functions to be periodic, we identify the
two ends of the vineyard, yielding a closed vineyard. This allows the study of
monodromy, which in this context means that following the family of functions
for a period permutes the set of points in a non-trivial way. In this work, given
a link and value $l$, we construct a topological space and periodic family of
functions such that the closed $l$-vineyard contains this link. This shows that
vineyards are topologically as rich as one could possibly hope. Importantly, it
has at least two immediate consequences: First, monodromy of any periodicity can
occur in a $l$-vineyard, answering a variant of a question by [Arya et al 2024].
To exhibit this, we also reformulate monodromy in a more geometric way, which
may be of interest in itself. Second, distinguishing vineyards is likely to be
difficult given the known difficulty of knot and link recognition, which have
strong connections to many NP-hard problems.'
article_processing_charge: No
arxiv: 1
author:
- first_name: Erin
full_name: ' Chambers, Erin'
last_name: ' Chambers'
- first_name: Christopher D
full_name: Fillmore, Christopher D
id: 35638A5C-AAC7-11E9-B0BF-5503E6697425
last_name: Fillmore
- first_name: Elizabeth R
full_name: Stephenson, Elizabeth R
id: 2D04F932-F248-11E8-B48F-1D18A9856A87
last_name: Stephenson
orcid: 0000-0002-6862-208X
- first_name: Mathijs
full_name: Wintraecken, Mathijs
id: 307CFBC8-F248-11E8-B48F-1D18A9856A87
last_name: Wintraecken
orcid: 0000-0002-7472-2220
citation:
ama: Chambers E, Fillmore CD, Stephenson ER, Wintraecken M. Braiding vineyards.
arXiv. doi:10.48550/ARXIV.2504.11203
apa: Chambers, E., Fillmore, C. D., Stephenson, E. R., & Wintraecken, M. (n.d.).
Braiding vineyards. arXiv. https://doi.org/10.48550/ARXIV.2504.11203
chicago: Chambers, Erin, Christopher D Fillmore, Elizabeth R Stephenson, and Mathijs
Wintraecken. “Braiding Vineyards.” ArXiv, n.d. https://doi.org/10.48550/ARXIV.2504.11203.
ieee: E. Chambers, C. D. Fillmore, E. R. Stephenson, and M. Wintraecken, “Braiding
vineyards,” arXiv. .
ista: Chambers E, Fillmore CD, Stephenson ER, Wintraecken M. Braiding vineyards.
arXiv, 10.48550/ARXIV.2504.11203.
mla: Chambers, Erin, et al. “Braiding Vineyards.” ArXiv, doi:10.48550/ARXIV.2504.11203.
short: E. Chambers, C.D. Fillmore, E.R. Stephenson, M. Wintraecken, ArXiv (n.d.).
corr_author: '1'
date_created: 2026-01-27T14:41:44Z
date_published: 2026-01-02T00:00:00Z
date_updated: 2026-04-07T11:42:48Z
day: '02'
department:
- _id: HeEd
doi: 10.48550/ARXIV.2504.11203
external_id:
arxiv:
- '2504.11203'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2504.11203
month: '01'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: draft
related_material:
record:
- id: '21056'
relation: later_version
status: public
- id: '21021'
relation: dissertation_contains
status: public
status: public
title: Braiding vineyards
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: '2026'
...
---
OA_place: repository
OA_type: green
_id: '21056'
abstract:
- lang: eng
text: "In this work, we introduce and study what we believe is an intriguing, and,
to the best of our knowledge, previously unknown connection between two fundamental
areas in computational topology, namely topological data analysis (TDA) and knot
theory. Given a function from a topological space to ℝ, TDA provides tools to
simplify and study the importance of topological features: in particular, the
\U0001D459^\U0001D461ℎ-dimensional persistence diagram encodes the topological
changes (or \U0001D459-homology) in the sublevel set as the function value increases
into a set of points in the plane. Given a continuous one parameter family of
such functions, we can combine the persistence diagrams into an object known as
a vineyard, which tracks the evolution of points in the persistence diagram as
the function changes. If we further restrict that family of functions to be periodic,
we identify the two ends of the vineyard, yielding a closed vineyard. This allows
the study of monodromy, which in this context means that following the family
of functions for a period permutes the set of points in a non-trivial way. Recent
work has studied monodromy in the directional persistent homology transform, demonstrating
some interesting connections between an input shape and monodromy in the persistent
homology transform for 0-dimensional homology embedded in ℝ^2.\r\nIn this work,
given a link and a value \U0001D459, we construct a topological space (based on
the given link) and periodic family of functions on this space (based on the Euclidean
distance function), such that the closed \U0001D459-vineyard contains this link.
This shows that vineyards are topologically as rich as one could possibly hope,
suggesting many future directions of work. Importantly, it has at least two immediate
consequences we explicitly point out:\r\n1.\tMonodromy of any periodicity can
occur in a \U0001D459-vineyard for any \U0001D459. This answers a variant of a
question by Arya and collaborators. To exhibit this as a consequence of our first
main result we also reformulate monodromy in a more geometric way, which may be
of interest in itself.\r\n2.\tTopologically distinguishing closed vineyards is
likely to be difficult (from a complexity theory as well as from a practical perspective)
because of the difficulty of knot and link recognition, which have strong connections
to many NP-hard problems."
acknowledgement: We thank the reviewers for both SODA and ATMCS for their comments,
whichimproved the exposition. We thank Kate Turner for discussion and Clément Maria
for pointing out thatAlexander’s theorem was already (well) known. Mathijs Wintraecken
would like to express his gratitude tothe administrative support he received from
University of Notre Dame during his visit and from Sophie Honnoratand Stephanie
Verdonck at Inria in general.This work has been supported by the ANR grant StratMesh,
ANR-24-CE48-1899, by NSF award 2444309, andthe welcome package from IDEX of the
Université Côte d’Azur, ANR-15-IDEX-01.
article_processing_charge: No
arxiv: 1
author:
- first_name: Erin W.
full_name: Chambers, Erin W.
last_name: Chambers
- first_name: Christopher D
full_name: Fillmore, Christopher D
id: 35638A5C-AAC7-11E9-B0BF-5503E6697425
last_name: Fillmore
- first_name: Elizabeth R
full_name: Stephenson, Elizabeth R
id: 2D04F932-F248-11E8-B48F-1D18A9856A87
last_name: Stephenson
orcid: 0000-0002-6862-208X
- first_name: Mathijs
full_name: Wintraecken, Mathijs
id: 307CFBC8-F248-11E8-B48F-1D18A9856A87
last_name: Wintraecken
orcid: 0000-0002-7472-2220
citation:
ama: 'Chambers EW, Fillmore CD, Stephenson ER, Wintraecken M. Braiding Vineyards.
In: Green Larsen K, Saha B, eds. Proceedings of the 2026 Annual ACM-SIAM Symposium
on Discrete Algorithms. Philadelphia, PA, United States: Society for Industrial
and Applied Mathematics; 2026:6240-6263. doi:10.1137/1.9781611978971.225'
apa: 'Chambers, E. W., Fillmore, C. D., Stephenson, E. R., & Wintraecken, M.
(2026). Braiding Vineyards. In K. Green Larsen & B. Saha (Eds.), Proceedings
of the 2026 Annual ACM-SIAM Symposium on Discrete Algorithms (pp. 6240–6263).
Philadelphia, PA, United States: Society for Industrial and Applied Mathematics.
https://doi.org/10.1137/1.9781611978971.225'
chicago: 'Chambers, Erin W., Christopher D Fillmore, Elizabeth R Stephenson, and
Mathijs Wintraecken. “Braiding Vineyards.” In Proceedings of the 2026 Annual
ACM-SIAM Symposium on Discrete Algorithms, edited by Kasper Green Larsen and
Barna Saha, 6240–63. Philadelphia, PA, United States: Society for Industrial and
Applied Mathematics, 2026. https://doi.org/10.1137/1.9781611978971.225.'
ieee: 'E. W. Chambers, C. D. Fillmore, E. R. Stephenson, and M. Wintraecken, “Braiding
Vineyards,” in Proceedings of the 2026 Annual ACM-SIAM Symposium on Discrete
Algorithms, K. Green Larsen and B. Saha, Eds. Philadelphia, PA, United States:
Society for Industrial and Applied Mathematics, 2026, pp. 6240–6263.'
ista: 'Chambers EW, Fillmore CD, Stephenson ER, Wintraecken M. 2026.Braiding Vineyards.
In: Proceedings of the 2026 Annual ACM-SIAM Symposium on Discrete Algorithms.
, 6240–6263.'
mla: Chambers, Erin W., et al. “Braiding Vineyards.” Proceedings of the 2026
Annual ACM-SIAM Symposium on Discrete Algorithms, edited by Kasper Green Larsen
and Barna Saha, Society for Industrial and Applied Mathematics, 2026, pp. 6240–63,
doi:10.1137/1.9781611978971.225.
short: E.W. Chambers, C.D. Fillmore, E.R. Stephenson, M. Wintraecken, in:, K. Green
Larsen, B. Saha (Eds.), Proceedings of the 2026 Annual ACM-SIAM Symposium on Discrete
Algorithms, Society for Industrial and Applied Mathematics, Philadelphia, PA,
United States, 2026, pp. 6240–6263.
date_created: 2026-01-28T12:58:16Z
date_published: 2026-01-07T00:00:00Z
date_updated: 2026-02-16T08:06:23Z
day: '07'
department:
- _id: HeEd
doi: 10.1137/1.9781611978971.225
editor:
- first_name: Kasper
full_name: Green Larsen, Kasper
last_name: Green Larsen
- first_name: Barna
full_name: Saha, Barna
last_name: Saha
external_id:
arxiv:
- '2504.11203'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2504.11203
month: '01'
oa: 1
oa_version: Preprint
page: 6240-6263
place: Philadelphia, PA, United States
publication: Proceedings of the 2026 Annual ACM-SIAM Symposium on Discrete Algorithms
publication_identifier:
eisbn:
- '9781611978971'
publication_status: published
publisher: Society for Industrial and Applied Mathematics
quality_controlled: '1'
related_material:
record:
- id: '21051'
relation: earlier_version
status: public
status: public
title: Braiding Vineyards
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2026'
...
---
OA_place: publisher
OA_type: gold
_id: '21113'
abstract:
- lang: eng
text: 'Causal discovery from i.i.d. observational data is known to be generally
ill-posed. We demonstrate that if we have access to the distribution induced by
a structural causal model, and additional data from (in the best case) only two
environments that sufficiently differ in the noise statistics, the unique causal
graph is identifiable. Notably, this is the first result in the literature that
guarantees the entire causal graph recovery with a constant number of environments
and arbitrary nonlinear mechanisms. Our only constraint is the Gaussianity of
the noise terms; however, we propose potential ways to relax this requirement.
Of interest on its own, we expand on the well-known duality between independent
component analysis (ICA) and causal discovery; recent advancements have shown
that nonlinear ICA can be solved from multiple environments, at least as many
as the number of sources: we show that the same can be achieved for causal discovery
while having access to much less auxiliary information.'
article_processing_charge: No
arxiv: 1
author:
- first_name: Francesco
full_name: Montagna, Francesco
id: 353afc8e-19f4-11f0-9db9-811f1723c83f
last_name: Montagna
citation:
ama: 'Montagna F. On the identifiability of causal graphs with multiple environments.
In: The 14th International Conference on Learning Representations. OpenReview.'
apa: 'Montagna, F. (n.d.). On the identifiability of causal graphs with multiple
environments. In The 14th International Conference on Learning Representations.
Rio de Janeiro, Brazil: OpenReview.'
chicago: Montagna, Francesco. “On the Identifiability of Causal Graphs with Multiple
Environments.” In The 14th International Conference on Learning Representations.
OpenReview, n.d.
ieee: F. Montagna, “On the identifiability of causal graphs with multiple environments,”
in The 14th International Conference on Learning Representations, Rio de
Janeiro, Brazil.
ista: 'Montagna F. On the identifiability of causal graphs with multiple environments.
The 14th International Conference on Learning Representations. ICLR: International
Conference on Learning Representations.'
mla: Montagna, Francesco. “On the Identifiability of Causal Graphs with Multiple
Environments.” The 14th International Conference on Learning Representations,
OpenReview.
short: F. Montagna, in:, The 14th International Conference on Learning Representations,
OpenReview, n.d.
conference:
end_date: 2026-04-27
location: Rio de Janeiro, Brazil
name: 'ICLR: International Conference on Learning Representations'
start_date: 2026-04-23
corr_author: '1'
date_created: 2026-01-30T08:16:25Z
date_published: 2026-02-11T00:00:00Z
date_updated: 2026-02-16T08:15:11Z
day: '11'
ddc:
- '000'
department:
- _id: FrLo
external_id:
arxiv:
- '2510.13583'
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2510.13583
month: '02'
oa: 1
oa_version: Published Version
publication: The 14th International Conference on Learning Representations
publication_status: accepted
publisher: OpenReview
status: public
title: On the identifiability of causal graphs with multiple environments
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: '2026'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '21115'
abstract:
- lang: eng
text: Quantifying cell morphology is central to understanding cellular regulation,
fate, and heterogeneity, yet conventional image-based analyses often struggle
with diverse or irregular shapes. We present a computational framework that uses
topological data analysis to characterise and compare single-cell morphologies
from fluorescence microscopy. Each cell is represented by its contour together
with the position of its nucleus, from which we construct a filtration based on
a radial distance function and derive a persistence diagram encoding the shape’s
topological evolution. The similarity between two cells is quantified using the
2-Wasserstein distance between their diagrams, yielding a shape distance we call
the PH distance. We apply this method to two representative experimental systems—primary
human mesenchymal stem cells (hMSCs) and HeLa cells—and show that PH distances
enable the detection of outliers in those systems, the identification of sub-populations,
and the quantification of shape heterogeneity. We benchmark PH against three established
contour-based distances (aspect ratio, Fourier descriptors, and elastic shape
analysis) and show that PH offers better separation between cell types and greater
robustness when clustering heterogeneous populations. Together, these results
demonstrate that persistent-homology-based signatures provide a principled and
sensitive approach for analysing cell morphology in settings where traditional
geometric or image-based descriptors are insufficient.
acknowledgement: We thank Stephan Huckemann, Katharine Turner, Benjamin Eltzner, Stephan
Tillmann, Fariza Rashid, Vanessa Robins, and Lamiae Azizi for many useful discussions
at various stages of this project. FR and PY gratefully acknowledge Matthias Weiss
(Experimental Physics I, University of Bayreuth, Germany) for granting access to
cell culture and laboratories, as well as funding consumables and the fruitful discussion
that contributed to this work. For open access purposes, the author has applied
a CC BY public copyright license to any author-accepted manuscript version arising
from this submission.
article_number: e1013890
article_processing_charge: Yes
article_type: original
author:
- first_name: Yossi
full_name: Bleile, Yossi
id: 920a7385-7995-11ef-9bfd-8c434cd8f3c2
last_name: Bleile
orcid: 0000-0002-4861-9174
- first_name: Pooja
full_name: Yadav, Pooja
last_name: Yadav
- first_name: Patrice
full_name: Koehl, Patrice
last_name: Koehl
- first_name: Florian
full_name: Rehfeldt, Florian
last_name: Rehfeldt
citation:
ama: 'Bokor Bleile Y, Yadav P, Koehl P, Rehfeldt F. Persistence diagrams as morphological
signatures of cells: A method to measure and compare cells within a population.
PLoS Computational Biology. 2026;22. doi:10.1371/journal.pcbi.1013890'
apa: 'Bokor Bleile, Y., Yadav, P., Koehl, P., & Rehfeldt, F. (2026). Persistence
diagrams as morphological signatures of cells: A method to measure and compare
cells within a population. PLoS Computational Biology. Public Library of
Science. https://doi.org/10.1371/journal.pcbi.1013890'
chicago: 'Bokor Bleile, Yossi, Pooja Yadav, Patrice Koehl, and Florian Rehfeldt.
“Persistence Diagrams as Morphological Signatures of Cells: A Method to Measure
and Compare Cells within a Population.” PLoS Computational Biology. Public
Library of Science, 2026. https://doi.org/10.1371/journal.pcbi.1013890.'
ieee: 'Y. Bokor Bleile, P. Yadav, P. Koehl, and F. Rehfeldt, “Persistence diagrams
as morphological signatures of cells: A method to measure and compare cells within
a population,” PLoS Computational Biology, vol. 22. Public Library of Science,
2026.'
ista: 'Bokor Bleile Y, Yadav P, Koehl P, Rehfeldt F. 2026. Persistence diagrams
as morphological signatures of cells: A method to measure and compare cells within
a population. PLoS Computational Biology. 22, e1013890.'
mla: 'Bokor Bleile, Yossi, et al. “Persistence Diagrams as Morphological Signatures
of Cells: A Method to Measure and Compare Cells within a Population.” PLoS
Computational Biology, vol. 22, e1013890, Public Library of Science, 2026,
doi:10.1371/journal.pcbi.1013890.'
short: Y. Bokor Bleile, P. Yadav, P. Koehl, F. Rehfeldt, PLoS Computational Biology
22 (2026).
corr_author: '1'
date_created: 2026-01-30T10:36:32Z
date_published: 2026-01-28T00:00:00Z
date_updated: 2026-06-11T11:51:13Z
day: '28'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.1371/journal.pcbi.1013890
external_id:
pmid:
- '41604421'
file:
- access_level: open_access
checksum: 3899d929ee9be0453c95524e49992d72
content_type: application/pdf
creator: dernst
date_created: 2026-02-10T07:13:06Z
date_updated: 2026-02-10T07:13:06Z
file_id: '21204'
file_name: 2026_PloSCompBio_Bleile.pdf
file_size: 8908746
relation: main_file
success: 1
file_date_updated: 2026-02-10T07:13:06Z
has_accepted_license: '1'
intvolume: ' 22'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS Computational Biology
publication_identifier:
issn:
- 1553-7358
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/yossibokorbleile/correa
scopus_import: '1'
status: public
title: 'Persistence diagrams as morphological signatures of cells: A method to measure
and compare cells within a population'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 22
year: '2026'
...
---
_id: '21116'
abstract:
- lang: eng
text: Sex-chromosome systems are highly variable across animals, but how they transition
from one to another is not well understood. Diptera have undergone multiple sex-chromosome
turnovers and expansions while maintaining their general chromosomal content,
which makes them an ideal clade to study such transitions. We analyzed more than
100 dipteran whole-genome assemblies and identified 4 new lineages that underwent
sex-chromosome turnover (in addition to the 5 previously reported). We find that
the majority of turnovers happened in the group Schizophora, which tend to have
fewer genes on Muller element F (the chromosome homologous to the ancestral insect
X chromosome) than lower dipterans, a factor previously hypothesized to facilitate
turnover. Most derived X chromosomes have higher GC content than autosomes, consistent
with a high prevalence of male achiasmy in Diptera. In addition, an excess of
gene movement out of the X is detected for most of these new X chromosomes, and
many of these moved genes have high testis expression in Drosophila, suggesting
that out-of-X gene movement contributes to the long-term demasculinization of
X chromosomes.
article_processing_charge: No
author:
- first_name: Lorena Alexandra
full_name: Layana Franco, Lorena Alexandra
id: 02814589-eb8f-11eb-b029-a70074f3f18f
last_name: Layana Franco
orcid: 0000-0002-1253-6297
- first_name: Melissa A
full_name: Toups, Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
orcid: 0000-0002-9752-7380
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Layana Franco LA, Toups MA, Vicoso B. Research Data for “Causes and consequences
of sex-chromosome turnovers in Diptera.” 2026. doi:10.15479/AT-ISTA-21116
apa: Layana Franco, L. A., Toups, M. A., & Vicoso, B. (2026). Research Data
for “Causes and consequences of sex-chromosome turnovers in Diptera.” Institute
of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21116
chicago: Layana Franco, Lorena Alexandra, Melissa A Toups, and Beatriz Vicoso. “Research
Data for ‘Causes and Consequences of Sex-Chromosome Turnovers in Diptera.’” Institute
of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21116.
ieee: L. A. Layana Franco, M. A. Toups, and B. Vicoso, “Research Data for ‘Causes
and consequences of sex-chromosome turnovers in Diptera.’” Institute of Science
and Technology Austria, 2026.
ista: Layana Franco LA, Toups MA, Vicoso B. 2026. Research Data for ‘Causes and
consequences of sex-chromosome turnovers in Diptera’, Institute of Science and
Technology Austria, 10.15479/AT-ISTA-21116.
mla: Layana Franco, Lorena Alexandra, et al. Research Data for “Causes and Consequences
of Sex-Chromosome Turnovers in Diptera.” Institute of Science and Technology
Austria, 2026, doi:10.15479/AT-ISTA-21116.
short: L.A. Layana Franco, M.A. Toups, B. Vicoso, (2026).
corr_author: '1'
date_created: 2026-01-30T11:04:14Z
date_published: 2026-01-02T00:00:00Z
date_updated: 2026-02-12T12:58:00Z
day: '2'
department:
- _id: BeVi
doi: 10.15479/AT-ISTA-21116
file:
- access_level: open_access
checksum: 0b79be6229f2ad9ac117ef00fc4f5c0e
content_type: text/plain
creator: llayanaf
date_created: 2026-01-30T11:00:24Z
date_updated: 2026-01-30T11:00:24Z
file_id: '21117'
file_name: README.txt
file_size: 1201
relation: main_file
success: 1
- access_level: open_access
checksum: a3cda72e4177fa1e5d3f0f6a88f8a79b
content_type: application/zip
creator: llayanaf
date_created: 2026-01-30T11:00:36Z
date_updated: 2026-01-30T11:00:36Z
file_id: '21118'
file_name: Supplementary_Tables.zip
file_size: 572403
relation: main_file
success: 1
- access_level: open_access
checksum: efb5b64698d6ca9e7b675204f6fc1c29
content_type: application/zip
creator: llayanaf
date_created: 2026-01-30T11:00:48Z
date_updated: 2026-01-30T11:00:48Z
file_id: '21119'
file_name: Supplementary_Datasets.zip
file_size: 19054553
relation: main_file
success: 1
- access_level: open_access
checksum: 254e050f648e9783ba8fe11adb3b49db
content_type: application/zip
creator: llayanaf
date_created: 2026-01-30T11:00:56Z
date_updated: 2026-01-30T11:00:56Z
file_id: '21120'
file_name: Perl_scripts.zip
file_size: 4575
relation: main_file
success: 1
file_date_updated: 2026-01-30T11:00:56Z
has_accepted_license: '1'
keyword:
- Schizophora
- sex chromosomes
- sex-chromosome turnover
- Diptera
- genomic features
- out-of-X movement.
month: '01'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
status: public
title: Research Data for "Causes and consequences of sex-chromosome turnovers in Diptera"
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: '2026'
...
---
OA_place: publisher
OA_type: gold
_id: '21133'
abstract:
- lang: eng
text: "Data structures based on trees and tree traversals are ubiquitous in computer
systems. Many low-level programs, including some implementations of critical systems
like page tables and the web browser DOM, rely on generic tree-traversal functions
that traverse tree nodes in a pre-determined order, applying a client-provided
operation to each visited node. Developing a general approach to specifying and
verifying such traversals is tricky since the client-provided per-node operation
can be stateful and may potentially depend on or modify the structure of the tree
being traversed.\r\nIn this paper, we present a recipe for (semi-)automated verification
of such generic, stateful tree traversals. Our recipe is (a) general: it applies
to a range of tree traversals, in particular, pre-, post- and in-order depth-first
traversals; (b) modular: parts of a traversal’s proof can be reused in verifying
other similar traversals; (c) expressive: using the specification of a tree traversal,
we can verify clients that use the traversal in a variety of different ways; and
(d) automatable: many proof obligations can be discharged automatically.\r\nAt
the heart of our recipe is a novel use of tree zippers to represent a logical
abstraction of the tree traversal state, and zipper transitions as an abstraction
of traversal steps. We realize our recipe in the RefinedC framework in Rocq, which
allows us to verify a number of different tree traversals and their clients written
in C."
acknowledgement: We thank the anonymous reviewers for their insightful suggestions.
This research is supported in part by generous awards from Android Security’s ASPIRE
program and from Google Research. The third author is supported, in part, by ERC
grant COCONUT (grant no. 101171349), funded by the European Union. Views and opinions
expressed are however those of the author(s) only and do not necessarily reflect
those of the European Union or the European Research Council Executive Agency. Neither
the European Union nor the granting authority can be held responsible for them.
article_processing_charge: No
author:
- first_name: Laila
full_name: Elbeheiry, Laila
last_name: Elbeheiry
- first_name: Michael Joachim
full_name: Sammler, Michael Joachim
id: 510d3901-2a03-11ee-914d-d9ae9011f0a7
last_name: Sammler
- first_name: Robbert
full_name: Krebbers, Robbert
last_name: Krebbers
- first_name: Derek
full_name: Dreyer, Derek
last_name: Dreyer
- first_name: Deepak
full_name: Garg, Deepak
last_name: Garg
citation:
ama: 'Elbeheiry L, Sammler MJ, Krebbers R, Dreyer D, Garg D. A recipe for modular
verification of generic tree traversals. In: Proceedings of the 15th ACM SIGPLAN
International Conference on Certified Programs and Proofs. Association for
Computing Machinery; 2026:339-352. doi:10.1145/3779031.3779110'
apa: 'Elbeheiry, L., Sammler, M. J., Krebbers, R., Dreyer, D., & Garg, D. (2026).
A recipe for modular verification of generic tree traversals. In Proceedings
of the 15th ACM SIGPLAN International Conference on Certified Programs and Proofs
(pp. 339–352). Rennes, France: Association for Computing Machinery. https://doi.org/10.1145/3779031.3779110'
chicago: Elbeheiry, Laila, Michael Joachim Sammler, Robbert Krebbers, Derek Dreyer,
and Deepak Garg. “A Recipe for Modular Verification of Generic Tree Traversals.”
In Proceedings of the 15th ACM SIGPLAN International Conference on Certified
Programs and Proofs, 339–52. Association for Computing Machinery, 2026. https://doi.org/10.1145/3779031.3779110.
ieee: L. Elbeheiry, M. J. Sammler, R. Krebbers, D. Dreyer, and D. Garg, “A recipe
for modular verification of generic tree traversals,” in Proceedings of the
15th ACM SIGPLAN International Conference on Certified Programs and Proofs,
Rennes, France, 2026, pp. 339–352.
ista: 'Elbeheiry L, Sammler MJ, Krebbers R, Dreyer D, Garg D. 2026. A recipe for
modular verification of generic tree traversals. Proceedings of the 15th ACM SIGPLAN
International Conference on Certified Programs and Proofs. CPP: Conference on
Certified Programs and Proofs, 339–352.'
mla: Elbeheiry, Laila, et al. “A Recipe for Modular Verification of Generic Tree
Traversals.” Proceedings of the 15th ACM SIGPLAN International Conference on
Certified Programs and Proofs, Association for Computing Machinery, 2026,
pp. 339–52, doi:10.1145/3779031.3779110.
short: L. Elbeheiry, M.J. Sammler, R. Krebbers, D. Dreyer, D. Garg, in:, Proceedings
of the 15th ACM SIGPLAN International Conference on Certified Programs and Proofs,
Association for Computing Machinery, 2026, pp. 339–352.
conference:
end_date: 2026-01-13
location: Rennes, France
name: 'CPP: Conference on Certified Programs and Proofs'
start_date: 2026-01-12
date_created: 2026-02-01T23:01:43Z
date_published: 2026-01-08T00:00:00Z
date_updated: 2026-02-16T08:43:24Z
day: '08'
ddc:
- '000'
department:
- _id: MiSa
doi: 10.1145/3779031.3779110
file:
- access_level: open_access
checksum: 7df99991493e907d83a197151f378e3e
content_type: application/pdf
creator: dernst
date_created: 2026-02-16T08:40:29Z
date_updated: 2026-02-16T08:40:29Z
file_id: '21225'
file_name: 2026_CPP_Elbeheiry.pdf
file_size: 811872
relation: main_file
success: 1
file_date_updated: 2026-02-16T08:40:29Z
has_accepted_license: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 339-352
publication: Proceedings of the 15th ACM SIGPLAN International Conference on Certified
Programs and Proofs
publication_identifier:
isbn:
- '9798400723414'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: A recipe for modular verification of generic tree traversals
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: '2026'
...
---
OA_place: repository
OA_type: green
_id: '21134'
abstract:
- lang: eng
text: "The Nakamoto consensus protocol underlying the Bitcoin blockchain uses proof
of work as a voting mechanism. Honest miners who contribute hashing power towards
securing the chain try to extend the longest chain they are aware of. Despite
its simplicity, Nakamoto consensus achieves meaningful security guarantees assuming
that at any point in time, a majority of the hashing power is controlled by honest
parties. This also holds under “resource variability”, i.e., if the total hashing
power varies greatly over time.\r\nProofs of space (PoSpace) have been suggested
as a more sustainable replacement for proofs of work. Unfortunately, no construction
of a “longest-chain” blockchain based on PoSpace, that is secure under dynamic
availability, is known. In this work, we prove that without additional assumptions
no such protocol exists. We exactly quantify this impossibility result by proving
a bound on the length of the fork required for double spending as a function of
the adversarial capabilities. This bound holds for any chain selection rule, and
we also show a chain selection rule (albeit a very strange one) that almost matches
this bound.\r\nThe Nakamoto consensus protocol underlying the Bitcoin blockchain
uses proof of work as a voting mechanism. Honest miners who contribute hashing
power towards securing the chain try to extend the longest chain they are aware
of. Despite its simplicity, Nakamoto consensus achieves meaningful security guarantees
assuming that at any point in time, a majority of the hashing power is controlled
by honest parties. This also holds under “resource variability”, i.e., if the
total hashing power varies greatly over time.\r\n\r\nProofs of space (PoSpace)
have been suggested as a more sustainable replacement for proofs of work. Unfortunately,
no construction of a “longest-chain” blockchain based on PoSpace, that is secure
under dynamic availability, is known. In this work, we prove that without additional
assumptions no such protocol exists. We exactly quantify this impossibility result
by proving a bound on the length of the fork required for double spending as a
function of the adversarial capabilities. This bound holds for any chain selection
rule, and we also show a chain selection rule (albeit a very strange one) that
almost matches this bound.\r\n\r\nConcretely, we consider a security game in which
the honest parties at any point control 0 > 1\r\n times more space than the adversary.
The adversary can change the honest space by a factor 1+- E with every block (dynamic
availability), and “replotting” the space (which allows answering two challenges
using the same space) takes as much time as p blocks.\r\nWe prove that no matter
what chain selection rule is used, in this game the adversary can create a fork
of length o^2 . p/E that will be picked as the winner by the chain selection rule.\r\nWe
also provide an upper bound that matches the lower bound up to a factor o. There
exists a chain selection rule (albeit a very strange one) which in the above game
requires forks of length at least o . p/E\r\nOur results show the necessity of
additional assumptions to create a secure PoSpace based longest-chain blockchain.
The Chia network in addition to PoSpace uses a verifiable delay function. Our
bounds show that an additional primitive like that is necessary."
acknowledgement: This research was funded in whole or in part by the Austrian Science
Fund (FWF) 10.55776/F85.
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Mirza Ahad
full_name: Baig, Mirza Ahad
id: 3EDE6DE4-AA5A-11E9-986D-341CE6697425
last_name: Baig
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Baig MA, Pietrzak KZ. On the (in)security of Proofs-of-space based longest-chain
blockchains. In: 29th International Conference on Financial Cryptography and
Data Security. Vol 15752. Springer Nature; 2026:127-142. doi:10.1007/978-3-032-07035-7_8'
apa: 'Baig, M. A., & Pietrzak, K. Z. (2026). On the (in)security of Proofs-of-space
based longest-chain blockchains. In 29th International Conference on Financial
Cryptography and Data Security (Vol. 15752, pp. 127–142). Miyakojima, Japan:
Springer Nature. https://doi.org/10.1007/978-3-032-07035-7_8'
chicago: Baig, Mirza Ahad, and Krzysztof Z Pietrzak. “On the (in)Security of Proofs-of-Space
Based Longest-Chain Blockchains.” In 29th International Conference on Financial
Cryptography and Data Security, 15752:127–42. Springer Nature, 2026. https://doi.org/10.1007/978-3-032-07035-7_8.
ieee: M. A. Baig and K. Z. Pietrzak, “On the (in)security of Proofs-of-space based
longest-chain blockchains,” in 29th International Conference on Financial Cryptography
and Data Security, Miyakojima, Japan, 2026, vol. 15752, pp. 127–142.
ista: 'Baig MA, Pietrzak KZ. 2026. On the (in)security of Proofs-of-space based
longest-chain blockchains. 29th International Conference on Financial Cryptography
and Data Security. FC: Financial Cryptography and Data Security, LNCS, vol. 15752,
127–142.'
mla: Baig, Mirza Ahad, and Krzysztof Z. Pietrzak. “On the (in)Security of Proofs-of-Space
Based Longest-Chain Blockchains.” 29th International Conference on Financial
Cryptography and Data Security, vol. 15752, Springer Nature, 2026, pp. 127–42,
doi:10.1007/978-3-032-07035-7_8.
short: M.A. Baig, K.Z. Pietrzak, in:, 29th International Conference on Financial
Cryptography and Data Security, Springer Nature, 2026, pp. 127–142.
conference:
end_date: 2025-04-18
location: Miyakojima, Japan
name: 'FC: Financial Cryptography and Data Security'
start_date: 2025-04-14
corr_author: '1'
date_created: 2026-02-01T23:01:43Z
date_published: 2026-01-01T00:00:00Z
date_updated: 2026-04-15T08:45:18Z
day: '01'
department:
- _id: KrPi
doi: 10.1007/978-3-032-07035-7_8
external_id:
arxiv:
- '2505.14891'
intvolume: ' 15752'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2505.14891
month: '01'
oa: 1
oa_version: Preprint
page: 127-142
project:
- _id: 34a34d57-11ca-11ed-8bc3-a2688a8724e1
grant_number: F8509
name: Security and Privacy by Design for Complex Systems
publication: 29th International Conference on Financial Cryptography and Data Security
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783032070340'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '21651'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: On the (in)security of Proofs-of-space based longest-chain blockchains
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15752
year: '2026'
...
---
OA_place: repository
OA_type: green
_id: '21135'
abstract:
- lang: eng
text: Three-dimensional (3D) microscopy data is often anisotropic with significantly
lower resolution (up to 8x) along the z axis than along the xy axes. Computationally
generating plausible isotropic resolution from anisotropic imaging data would
benefit the visual analysis of large-scale volumes. This paper proposes niiv,
a self-supervised method for isotropic reconstruction of 3D microscopy data that
can quickly produce images at arbitrary output resolutions. The representation
embeds a learned latent code within a neural field that describes the implicit
higher-resolution isotropic image region. We use an attention-guided latent interpolation
approach, which allows flexible information exchange over a local latent neighborhood.
Under isotropic volume assumptions, we self-supervise this representation on low-/high-resolution
lateral image pairs to reconstruct an isotropic volume from low-resolution axial
images. We evaluate our method on simulated and real anisotropic electron (EM)
and light microscopy (LM) data. Compared to diffusion-based baselines, niiv shows
improved reconstruction quality (+1 dB PSNR) and is over three orders of magnitude
faster (1,000x) to infer. Specifically, niiv reconstructs a 128^3 voxel volume
in 2/10th of a second, renderable at varying (continuous) high resolutions for
display. Our code is available at https://github.com/jakobtroidl/niiv-miccai.
acknowledgement: This work was supported by NIH grants 1U01NS132158 and R01HD104969.
We thank the reviewers for their constructive feedback.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Jakob
full_name: Troidl, Jakob
last_name: Troidl
- first_name: Yiqing
full_name: Liang, Yiqing
last_name: Liang
- first_name: Johanna
full_name: Beyer, Johanna
last_name: Beyer
- first_name: Mojtaba
full_name: Tavakoli, Mojtaba
id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87
last_name: Tavakoli
orcid: 0000-0002-7667-6854
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Markus
full_name: Hadwiger, Markus
last_name: Hadwiger
- first_name: Hanspeter
full_name: Pfister, Hanspeter
last_name: Pfister
- first_name: James
full_name: Tompkin, James
last_name: Tompkin
citation:
ama: 'Troidl J, Liang Y, Beyer J, et al. niiv: Interactive Self-supervised Neural
Implicit Isotropic Volume Reconstruction. In: 1st International Workshop on
Efficient Medical Artificial Intelligence. Vol 16318. Springer Nature; 2026:257-267.
doi:10.1007/978-3-032-13961-0_26'
apa: 'Troidl, J., Liang, Y., Beyer, J., Tavakoli, M., Danzl, J. G., Hadwiger, M.,
… Tompkin, J. (2026). niiv: Interactive Self-supervised Neural Implicit Isotropic
Volume Reconstruction. In 1st International Workshop on Efficient Medical Artificial
Intelligence (Vol. 16318, pp. 257–267). Daejeon, South Korea: Springer Nature.
https://doi.org/10.1007/978-3-032-13961-0_26'
chicago: 'Troidl, Jakob, Yiqing Liang, Johanna Beyer, Mojtaba Tavakoli, Johann G
Danzl, Markus Hadwiger, Hanspeter Pfister, and James Tompkin. “Niiv: Interactive
Self-Supervised Neural Implicit Isotropic Volume Reconstruction.” In 1st International
Workshop on Efficient Medical Artificial Intelligence, 16318:257–67. Springer
Nature, 2026. https://doi.org/10.1007/978-3-032-13961-0_26.'
ieee: 'J. Troidl et al., “niiv: Interactive Self-supervised Neural Implicit
Isotropic Volume Reconstruction,” in 1st International Workshop on Efficient
Medical Artificial Intelligence, Daejeon, South Korea, 2026, vol. 16318, pp.
257–267.'
ista: 'Troidl J, Liang Y, Beyer J, Tavakoli M, Danzl JG, Hadwiger M, Pfister H,
Tompkin J. 2026. niiv: Interactive Self-supervised Neural Implicit Isotropic Volume
Reconstruction. 1st International Workshop on Efficient Medical Artificial Intelligence.
EMA4MICCAI: Efficient Medical Artificial Intelligence, LNCS, vol. 16318, 257–267.'
mla: 'Troidl, Jakob, et al. “Niiv: Interactive Self-Supervised Neural Implicit Isotropic
Volume Reconstruction.” 1st International Workshop on Efficient Medical Artificial
Intelligence, vol. 16318, Springer Nature, 2026, pp. 257–67, doi:10.1007/978-3-032-13961-0_26.'
short: J. Troidl, Y. Liang, J. Beyer, M. Tavakoli, J.G. Danzl, M. Hadwiger, H. Pfister,
J. Tompkin, in:, 1st International Workshop on Efficient Medical Artificial Intelligence,
Springer Nature, 2026, pp. 257–267.
conference:
end_date: 2025-09-23
location: Daejeon, South Korea
name: 'EMA4MICCAI: Efficient Medical Artificial Intelligence'
start_date: 2025-09-23
date_created: 2026-02-01T23:01:44Z
date_published: 2026-01-03T00:00:00Z
date_updated: 2026-02-16T08:50:50Z
day: '03'
department:
- _id: JoDa
doi: 10.1007/978-3-032-13961-0_26
intvolume: ' 16318'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2024.09.07.611785
month: '01'
oa: 1
oa_version: Preprint
page: 257-267
publication: 1st International Workshop on Efficient Medical Artificial Intelligence
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783032139603'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/jakobtroidl/niiv-miccai
scopus_import: '1'
status: public
title: 'niiv: Interactive Self-supervised Neural Implicit Isotropic Volume Reconstruction'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16318
year: '2026'
...
---
OA_place: repository
_id: '21137'
acknowledged_ssus:
- _id: Bio
- _id: EM-Fac
- _id: ScienComp
- _id: LifeSc
acknowledgement: We thank all members of the Heisenberg, Henkes, and Hannezo groups
for their support. We are also grateful to the Imaging and Optics, Scientific Computing,
Life Science Support, and Cryo-Electron Microscopy facilities at ISTA for their
technical assistance and support. Numerical simulations were performed using the
computational resources from Lorentz Institute and the Academic Leiden Interdisciplinary
Cluster Environment (ALICE) provided by Leiden University, and from PMMH provided
by Sorbonne Université. S.N has received funding from European Union’s Horizon 2020
research and innovation programme (grant agreement No. 665385). This work was supported
by the Austrian Science Fund (FWF) under projects PAT5044023 and W1250 awarded to
C.-P.H.
article_processing_charge: No
author:
- first_name: Suyash
full_name: Naik, Suyash
id: 2C0B105C-F248-11E8-B48F-1D18A9856A87
last_name: Naik
orcid: 0000-0001-8421-5508
citation:
ama: Naik S. Data associated with Keratins coordinate tissue spreading . 2026. doi:10.15479/AT-ISTA-21137
apa: Naik, S. (2026). Data associated with Keratins coordinate tissue spreading
. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21137
chicago: Naik, Suyash. “Data Associated with Keratins Coordinate Tissue Spreading
.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21137.
ieee: S. Naik, “Data associated with Keratins coordinate tissue spreading .” Institute
of Science and Technology Austria, 2026.
ista: Naik S. 2026. Data associated with Keratins coordinate tissue spreading ,
Institute of Science and Technology Austria, 10.15479/AT-ISTA-21137.
mla: Naik, Suyash. Data Associated with Keratins Coordinate Tissue Spreading
. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21137.
short: S. Naik, (2026).
contributor:
- contributor_type: researcher
first_name: Yann-Edwin
last_name: Keta
- contributor_type: supervisor
first_name: 'Silke '
last_name: Henkes
- contributor_type: supervisor
first_name: Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- contributor_type: supervisor
first_name: Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
corr_author: '1'
date_created: 2026-02-04T16:38:02Z
date_published: 2026-03-24T00:00:00Z
date_updated: 2026-06-10T09:44:10Z
day: '24'
department:
- _id: GradSch
- _id: CaHe
- _id: EdHa
doi: 10.15479/AT-ISTA-21137
ec_funded: 1
file:
- access_level: open_access
checksum: 5d1fda7e410f24c311fcf6bcf725698f
content_type: application/zip
creator: snaik
date_created: 2026-03-16T11:51:10Z
date_updated: 2026-03-16T11:51:10Z
description: 'Python3 library written in C++20 to integrate vertex models. Please
read the readme at https://github.com/yketa/cells/blob/main/README.md for detailed
instructions for installation and usage of the code in this repository. '
file_id: '21461'
file_name: cells-main.zip
file_size: 725916
relation: main_file
title: Cell git repository
- access_level: open_access
checksum: ee350c8eaed99f3ca348c47c8b190d3c
content_type: application/x-zip-compressed
creator: snaik
date_created: 2026-03-18T14:52:02Z
date_updated: 2026-03-18T14:52:02Z
file_id: '21464'
file_name: DevBranchDataRepo.zip
file_size: 282168895
relation: main_file
success: 1
- access_level: open_access
checksum: 1ecaf2c1a2ce8ff9c75a128cc02d0b8f
content_type: text/markdown
creator: snaik
date_created: 2026-03-18T15:01:32Z
date_updated: 2026-03-18T15:01:32Z
file_id: '21466'
file_name: ReadMe.md
file_size: 2231
relation: main_file
success: 1
- access_level: open_access
checksum: da9a4687e5144b61a64ca341f922046a
content_type: image/svg+xml
creator: snaik
date_created: 2026-03-18T15:12:57Z
date_updated: 2026-03-18T15:12:57Z
file_id: '21467'
file_name: PaperSchematics.svg
file_size: 1951210
relation: main_file
success: 1
- access_level: open_access
checksum: 9ac1054b16c212c6f34d402dce2c80e0
content_type: application/octet-stream
creator: snaik
date_created: 2026-03-21T03:37:43Z
date_updated: 2026-03-21T03:37:43Z
file_id: '21468'
file_name: maxwell_sketch.tex
file_size: 1897
relation: main_file
success: 1
- access_level: open_access
checksum: 7c9ecf78e2593b3830d96fa94baa08df
content_type: application/x-zip-compressed
creator: snaik
date_created: 2026-03-24T07:21:43Z
date_updated: 2026-03-24T07:21:43Z
file_id: '21495'
file_name: DataRepo.zip
file_size: 749368723
relation: main_file
success: 1
file_date_updated: 2026-03-24T07:21:43Z
has_accepted_license: '1'
license: https://creativecommons.org/licenses/by-sa/4.0/
month: '3'
oa: 1
oa_version: Published Version
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 8f060199-16d5-11f0-9cad-f3253b266c46
grant_number: PAT 5044023
name: Keratins in epithelial tissue spreading
- _id: 252C3B08-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1250-B20
name: Nano-Analytics of Cellular Systems
publisher: Institute of Science and Technology Austria
status: public
title: 'Data associated with Keratins coordinate tissue spreading '
tmp:
image: /images/cc_by_sa.png
legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode
name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC
BY-SA 4.0)
short: CC BY-SA (4.0)
type: research_data
user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d
year: '2026'
...
---
OA_place: repository
OA_type: green
_id: '21140'
abstract:
- lang: eng
text: 'We consider several problems related to packing forests in graphs. The first
one is to find k edge-disjoint forests in a directed graph G of maximal size such
that the indegree of each vertex in these forests is at most k. We describe a
min-max characterization for this problem and show that it can be solved in almost
linear time for fixed k, extending the algorithm of [Gabow, 1995]. Specifically,
the complexity is O(kδm log n), where n, m are the number of vertices and edges
in G respectively, and δ = max{1, k − kG}, where kG is the edge connectivity of
the graph. Using our solution to this problem, we improve complexities for two
existing applications:(1) k-forest problem: find k forests in an undirected graph
G maximizing the number of edges in their union. We show how to solve this problem
in O(k3 min{kn, m} log2 n + k · MAXFLOW(m, m) log n) time, breaking the Ok(n3/2)
complexity barrier of previously known approaches.(2) Directed edge-connectivity
augmentation problem: find a smallest set of directed edges whose addition to
the given directed graph makes it strongly k-connected. We improve the deterministic
complexity for this problem from O(kδ(m + δn) log n) [Gabow, STOC 1994] to O(kδm
log n). A similar approach with the same complexity also works for the undirected
version of the problem.'
article_processing_charge: No
arxiv: 1
author:
- first_name: Pavel
full_name: Arkhipov, Pavel
id: b25f2ab2-1fed-11ee-8599-fe02d211784f
last_name: Arkhipov
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Arkhipov P, Kolmogorov V. Faster algorithms for packing forests in graphs
and related problems. In: Proceedings of the 2026 Annual ACM-SIAM Symposium
on Discrete Algorithms. Society for Industrial and Applied Mathematics; 2026:4023-4042.
doi:10.1137/1.9781611978971.148'
apa: 'Arkhipov, P., & Kolmogorov, V. (2026). Faster algorithms for packing forests
in graphs and related problems. In Proceedings of the 2026 Annual ACM-SIAM
Symposium on Discrete Algorithms (pp. 4023–4042). Vancouver, Canada: Society
for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611978971.148'
chicago: Arkhipov, Pavel, and Vladimir Kolmogorov. “Faster Algorithms for Packing
Forests in Graphs and Related Problems.” In Proceedings of the 2026 Annual
ACM-SIAM Symposium on Discrete Algorithms, 4023–42. Society for Industrial
and Applied Mathematics, 2026. https://doi.org/10.1137/1.9781611978971.148.
ieee: P. Arkhipov and V. Kolmogorov, “Faster algorithms for packing forests in graphs
and related problems,” in Proceedings of the 2026 Annual ACM-SIAM Symposium
on Discrete Algorithms, Vancouver, Canada, 2026, pp. 4023–4042.
ista: 'Arkhipov P, Kolmogorov V. 2026. Faster algorithms for packing forests in
graphs and related problems. Proceedings of the 2026 Annual ACM-SIAM Symposium
on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 4023–4042.'
mla: Arkhipov, Pavel, and Vladimir Kolmogorov. “Faster Algorithms for Packing Forests
in Graphs and Related Problems.” Proceedings of the 2026 Annual ACM-SIAM Symposium
on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2026,
pp. 4023–42, doi:10.1137/1.9781611978971.148.
short: P. Arkhipov, V. Kolmogorov, in:, Proceedings of the 2026 Annual ACM-SIAM
Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics,
2026, pp. 4023–4042.
conference:
end_date: 2026-01-14
location: Vancouver, Canada
name: 'SODA: Symposium on Discrete Algorithms'
start_date: 2026-01-11
corr_author: '1'
date_created: 2026-02-05T10:51:34Z
date_published: 2026-01-07T00:00:00Z
date_updated: 2026-02-16T09:18:33Z
day: '07'
department:
- _id: VlKo
doi: 10.1137/1.9781611978971.148
external_id:
arxiv:
- '2409.20314'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2409.20314
month: '01'
oa: 1
oa_version: Preprint
page: 4023-4042
publication: Proceedings of the 2026 Annual ACM-SIAM Symposium on Discrete Algorithms
publication_identifier:
eisbn:
- '9781611978971'
publication_status: published
publisher: Society for Industrial and Applied Mathematics
quality_controlled: '1'
status: public
title: Faster algorithms for packing forests in graphs and related problems
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '21149'
abstract:
- lang: eng
text: We present a general theoretical framework for helical dichroism (HD), establishing
an explicit link between chiral resolution and orbital angular momentum (OAM)
exchange in light–matter interaction. Tracing microscopic mechanisms of the OAM
transfer, we derive rotational selection rules, which establish that HD emerges
only from the spin–orbit coupling of light, even for beams without the far-field
OAM. Our findings refine the conditions for observing HD, provide a tool to re-examine
the outcome of prior experiments, and guide future designs for chiral sensing
with structured light.
acknowledgement: This research was funded in whole or in part by the Austrian Science
Fund (FWF) [10.55776/F1004].
article_number: '053204'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Mateja
full_name: Hrast, Mateja
id: 48dbb294-2a9c-11ef-905d-f56be71f0e5d
last_name: Hrast
- first_name: Georgios
full_name: Koutentakis, Georgios
id: d7b23d3a-9e21-11ec-b482-f76739596b95
last_name: Koutentakis
- first_name: Mikhail
full_name: Maslov, Mikhail
id: 2E65BB0E-F248-11E8-B48F-1D18A9856A87
last_name: Maslov
orcid: 0000-0003-4074-2570
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Hrast M, Koutentakis G, Maslov M, Lemeshko M. Bottom-up analysis of rovibrational
helical dichroism. Physical Review Letters. 2026;136(5). doi:10.1103/fkf1-1jml
apa: Hrast, M., Koutentakis, G., Maslov, M., & Lemeshko, M. (2026). Bottom-up
analysis of rovibrational helical dichroism. Physical Review Letters. American
Physical Society. https://doi.org/10.1103/fkf1-1jml
chicago: Hrast, Mateja, Georgios Koutentakis, Mikhail Maslov, and Mikhail Lemeshko.
“Bottom-up Analysis of Rovibrational Helical Dichroism.” Physical Review Letters.
American Physical Society, 2026. https://doi.org/10.1103/fkf1-1jml.
ieee: M. Hrast, G. Koutentakis, M. Maslov, and M. Lemeshko, “Bottom-up analysis
of rovibrational helical dichroism,” Physical Review Letters, vol. 136,
no. 5. American Physical Society, 2026.
ista: Hrast M, Koutentakis G, Maslov M, Lemeshko M. 2026. Bottom-up analysis of
rovibrational helical dichroism. Physical Review Letters. 136(5), 053204.
mla: Hrast, Mateja, et al. “Bottom-up Analysis of Rovibrational Helical Dichroism.”
Physical Review Letters, vol. 136, no. 5, 053204, American Physical Society,
2026, doi:10.1103/fkf1-1jml.
short: M. Hrast, G. Koutentakis, M. Maslov, M. Lemeshko, Physical Review Letters
136 (2026).
corr_author: '1'
date_created: 2026-02-06T10:53:17Z
date_published: 2026-02-05T00:00:00Z
date_updated: 2026-02-10T11:30:37Z
day: '05'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1103/fkf1-1jml
external_id:
arxiv:
- '2505.16393'
file:
- access_level: open_access
checksum: 805c929fff9fd4d0e733293eaace67b8
content_type: application/pdf
creator: dernst
date_created: 2026-02-10T11:25:46Z
date_updated: 2026-02-10T11:25:46Z
file_id: '21210'
file_name: 2026_PhysicalReviewLetters_Hrast.pdf
file_size: 511312
relation: main_file
success: 1
file_date_updated: 2026-02-10T11:25:46Z
has_accepted_license: '1'
intvolume: ' 136'
issue: '5'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 7c040762-9f16-11ee-852c-dd79eeee4ab3
grant_number: F100403
name: Coherent Optical Metrology Beyond Electric-Dipole-Allowed Transitions
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Bottom-up analysis of rovibrational helical dichroism
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 136
year: '2026'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '21158'
abstract:
- lang: eng
text: Vernalization-regulated flowering is vital for wheat yield and geographical
distribution, and the diversity of flowering time genes is essential for the breeding
of climate-resilient varieties. Sugars have long been recognized in regulating
flowering; however, the intrinsic connection between carbohydrate metabolism and
vernalization response remains largely unexplored. Here, we identify a fructose
1,6-bisphosphate aldolase (FBA) encoding gene, HtL1/FBA10, as a modulator of heading
time variation based on a genome-wide association study utilizing wheat core germplasm
collections. Evolutionary analysis shows a decrease in the proportion of haplotype-2
of HtL1, which is linked to delayed flowering, in Chinese and American wheat varieties
compared to landraces. Vernalization reduces HtL1/FBA10 phosphorylation levels
and increases its O-GlcNAcylation, which in turn enhances its enzymatic activity
and facilitates VERNALIZATION 1 (VRN1) transcription by regulating histone acetylation
at the VRN1 locus. Our findings provide mechanistic insights into the interplay
between glucose metabolism and the epigenetic regulation of vernalization in winter
wheat.
acknowledgement: This work was supported by the Basic Science Center Project of National
Natural Science Foundation of China (32388201) to K.C and the National Natural Science
Foundation of China (31970331) to L.X. We thank Dr. Zhuang Lu, Dr. Bin Han and Ms.
Jingquan Li (Plant Science Facility of the Institute of Botany, Chinese Academy
of Sciences) for their technical assistance in LC-MS/MS assay, small molecule compound
analysis and the subcellular localization assay, respectively. We thank Dr. Wei
Luo and Dr. Dongfeng Liu for helpful discussions.
article_number: '999'
article_processing_charge: Yes
article_type: original
author:
- first_name: Pengfang
full_name: Yang, Pengfang
last_name: Yang
- first_name: Yangyang
full_name: Liu, Yangyang
last_name: Liu
- first_name: Qi
full_name: Dong, Qi
last_name: Dong
- first_name: Yuting
full_name: Miao, Yuting
last_name: Miao
- first_name: Jianlong
full_name: Zhang, Jianlong
last_name: Zhang
- first_name: Shujuan
full_name: Xu, Shujuan
id: 9724dd9d-f591-11ee-bd51-e97ed0652286
last_name: Xu
- first_name: Hong
full_name: Zhao, Hong
last_name: Zhao
- first_name: Yuda
full_name: Niu, Yuda
last_name: Niu
- first_name: Xueyong
full_name: Zhang, Xueyong
last_name: Zhang
- first_name: Yunyuan
full_name: Xu, Yunyuan
last_name: Xu
- first_name: Zifeng
full_name: Guo, Zifeng
last_name: Guo
- first_name: Lijing
full_name: Xing, Lijing
last_name: Xing
- first_name: Kang
full_name: Chong, Kang
last_name: Chong
citation:
ama: Yang P, Liu Y, Dong Q, et al. O-GlcNAc and phosphorylation modifications on
HtL1/FBA10 regulate wheat vernalization for flowering. Nature Communications.
2026;17. doi:10.1038/s41467-025-67734-0
apa: Yang, P., Liu, Y., Dong, Q., Miao, Y., Zhang, J., Xu, S., … Chong, K. (2026).
O-GlcNAc and phosphorylation modifications on HtL1/FBA10 regulate wheat vernalization
for flowering. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-025-67734-0
chicago: Yang, Pengfang, Yangyang Liu, Qi Dong, Yuting Miao, Jianlong Zhang, Shujuan
Xu, Hong Zhao, et al. “O-GlcNAc and Phosphorylation Modifications on HtL1/FBA10
Regulate Wheat Vernalization for Flowering.” Nature Communications. Springer
Nature, 2026. https://doi.org/10.1038/s41467-025-67734-0.
ieee: P. Yang et al., “O-GlcNAc and phosphorylation modifications on HtL1/FBA10
regulate wheat vernalization for flowering,” Nature Communications, vol.
17. Springer Nature, 2026.
ista: Yang P, Liu Y, Dong Q, Miao Y, Zhang J, Xu S, Zhao H, Niu Y, Zhang X, Xu Y,
Guo Z, Xing L, Chong K. 2026. O-GlcNAc and phosphorylation modifications on HtL1/FBA10
regulate wheat vernalization for flowering. Nature Communications. 17, 999.
mla: Yang, Pengfang, et al. “O-GlcNAc and Phosphorylation Modifications on HtL1/FBA10
Regulate Wheat Vernalization for Flowering.” Nature Communications, vol.
17, 999, Springer Nature, 2026, doi:10.1038/s41467-025-67734-0.
short: P. Yang, Y. Liu, Q. Dong, Y. Miao, J. Zhang, S. Xu, H. Zhao, Y. Niu, X. Zhang,
Y. Xu, Z. Guo, L. Xing, K. Chong, Nature Communications 17 (2026).
date_created: 2026-02-08T23:02:48Z
date_published: 2026-01-27T00:00:00Z
date_updated: 2026-02-12T14:34:24Z
day: '27'
ddc:
- '580'
department:
- _id: XiFe
doi: 10.1038/s41467-025-67734-0
external_id:
pmid:
- '41455723'
file:
- access_level: open_access
checksum: 9ae170ec70ba1ab56b6f1ffe67d1de7f
content_type: application/pdf
creator: dernst
date_created: 2026-02-12T14:33:14Z
date_updated: 2026-02-12T14:33:14Z
file_id: '21223'
file_name: 2026_NatureComm_Yang.pdf
file_size: 4685882
relation: main_file
success: 1
file_date_updated: 2026-02-12T14:33:14Z
has_accepted_license: '1'
intvolume: ' 17'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: O-GlcNAc and phosphorylation modifications on HtL1/FBA10 regulate wheat vernalization
for flowering
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '21159'
abstract:
- lang: eng
text: "One of the foundational theorems of extremal graph theory is Dirac’s theorem,
which\r\nsays that if an n-vertex graph G has minimum degree at least n/2, then
G has a\r\nHamilton cycle, and therefore a perfect matching (if n is even). Later
work by Sárközy,\r\nSelkow and Szemerédi showed that in fact Dirac graphs have
many Hamilton cycles\r\nand perfect matchings, culminating in a result of Cuckler
and Kahn that gives a precise\r\ndescription of the numbers of Hamilton cycles
and perfect matchings in a Dirac graph\r\nG (in terms of an entropy-like parameter
of G). In this paper we extend Cuckler\r\nand Kahn’s result to perfect matchings
in hypergraphs. For positive integers d < k,\r\nand for n divisible by k, let
md (k, n) be the minimum d-degree that ensures the\r\nexistence of a perfect matching
in an n-vertex k-uniform hypergraph. In general, it is\r\nan open question to
determine (even asymptotically) the values of md (k, n), but we are\r\nnonetheless
able to prove an analogue of the Cuckler–Kahn theorem, showing that if\r\nan n-vertex
k-uniform hypergraph G has minimum d-degree at least (1+γ )md (k, n)\r\n(for any
constantγ > 0), then the number of perfect matchings in G is controlled by\r\nan
entropy-like parameter of G. This strengthens cruder estimates arising from work\r\nof
Kang–Kelly–Kühn–Osthus–Pfenninger and Pham–Sah–Sawhney–Simkin."
acknowledgement: We would like to thank the referees for a number of helpful comments
and suggestions, which have substantially improved the paper. Open access funding
provided by Institute of Science and Technology (IST Austria).
article_number: '5'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
- first_name: Roodabeh
full_name: Safavi Hemami, Roodabeh
id: 72ed2640-8972-11ed-ae7b-f9c81ec75154
last_name: Safavi Hemami
- first_name: Yiting
full_name: Wang, Yiting
id: 1917d194-076e-11ed-97cd-837255f88785
last_name: Wang
orcid: 0000-0002-2856-767X
citation:
ama: Kwan MA, Safavi Hemami R, Wang Y. Counting perfect matchings in Dirac hypergraphs.
Combinatorica. 2026;46. doi:10.1007/s00493-025-00194-8
apa: Kwan, M. A., Safavi Hemami, R., & Wang, Y. (2026). Counting perfect matchings
in Dirac hypergraphs. Combinatorica. Springer Nature. https://doi.org/10.1007/s00493-025-00194-8
chicago: Kwan, Matthew Alan, Roodabeh Safavi Hemami, and Yiting Wang. “Counting
Perfect Matchings in Dirac Hypergraphs.” Combinatorica. Springer Nature,
2026. https://doi.org/10.1007/s00493-025-00194-8.
ieee: M. A. Kwan, R. Safavi Hemami, and Y. Wang, “Counting perfect matchings in
Dirac hypergraphs,” Combinatorica, vol. 46. Springer Nature, 2026.
ista: Kwan MA, Safavi Hemami R, Wang Y. 2026. Counting perfect matchings in Dirac
hypergraphs. Combinatorica. 46, 5.
mla: Kwan, Matthew Alan, et al. “Counting Perfect Matchings in Dirac Hypergraphs.”
Combinatorica, vol. 46, 5, Springer Nature, 2026, doi:10.1007/s00493-025-00194-8.
short: M.A. Kwan, R. Safavi Hemami, Y. Wang, Combinatorica 46 (2026).
corr_author: '1'
date_created: 2026-02-08T23:02:49Z
date_published: 2026-02-01T00:00:00Z
date_updated: 2026-02-16T09:55:17Z
day: '01'
ddc:
- '510'
department:
- _id: MaKw
- _id: MoHe
doi: 10.1007/s00493-025-00194-8
external_id:
arxiv:
- '2408.09589'
file:
- access_level: open_access
checksum: 47b0031d90b0e6b9a843f422a1486089
content_type: application/pdf
creator: dernst
date_created: 2026-02-16T09:52:38Z
date_updated: 2026-02-16T09:52:38Z
file_id: '21228'
file_name: 2026_Combinatorica_Kwan.pdf
file_size: 539646
relation: main_file
success: 1
file_date_updated: 2026-02-16T09:52:38Z
has_accepted_license: '1'
intvolume: ' 46'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
publication: Combinatorica
publication_identifier:
eissn:
- 1439-6912
issn:
- 0209-9683
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Counting perfect matchings in Dirac hypergraphs
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 46
year: '2026'
...
---
OA_place: repository
OA_type: free access
_id: '21174'
abstract:
- lang: eng
text: UTe2 exhibits the remarkable phenomenon of re-entrant superconductivity, whereby
the zero-resistance state reappears above 40 tesla after being suppressed with
a field of around 10 tesla. One potential pairing mechanism, invoked in the related
re-entrant superconductors UCoGe and URhGe, involves transverse fluctuations of
a ferromagnetic order parameter. However, the requisite ferromagnetic order -
present in both UCoGe and URhGe - is absent in UTe2, and magnetization measurements
show no sign of strong fluctuations. Here, we measure the magnetotropic susceptibility
of UTe2 across two field-angle planes. This quantity is sensitive to the magnetic
susceptibility in a direction transverse to the applied magnetic field - a quantity
that is not accessed in conventional magnetization measurements. We observe a
very large decrease in the magnetotropic susceptibility over a broad range of
field orientations, indicating a large increase in the transverse magnetic susceptibility.
The three superconducting phases of UTe2, including the high-field re-entrant
phase, surround this region of enhanced susceptibility in the field-angle phase
diagram. The strongest transverse susceptibility is found near the critical end
point of the high-field metamagnetic transition, suggesting that quantum critical
fluctuations of a field-induced magnetic order parameter may be responsible for
the large transverse susceptibility, and may provide a pairing mechanism for field-induced
superconductivity in UTe2.
acknowledged_ssus:
- _id: NanoFab
acknowledgement: Thanks to Salvatore Bagiante, Evgeniia Volobueva, Lubuna Shafeek,
Ali Bangura and Zoltan Kollo.
article_processing_charge: Yes
author:
- first_name: Kimberly A
full_name: Modic, Kimberly A
id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425
last_name: Modic
orcid: 0000-0001-9760-3147
citation:
ama: Modic KA. Research data for “Giant transverse magnetic fluctuations at the
edge of re-entrant superconductivity in UTe2.” 2026. doi:10.15479/AT-ISTA-21174
apa: Modic, K. A. (2026). Research data for “Giant transverse magnetic fluctuations
at the edge of re-entrant superconductivity in UTe2.” Institute of Science and
Technology Austria. https://doi.org/10.15479/AT-ISTA-21174
chicago: Modic, Kimberly A. “Research Data for ‘Giant Transverse Magnetic Fluctuations
at the Edge of Re-Entrant Superconductivity in UTe2.’” Institute of Science and
Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21174.
ieee: K. A. Modic, “Research data for ‘Giant transverse magnetic fluctuations at
the edge of re-entrant superconductivity in UTe2.’” Institute of Science and Technology
Austria, 2026.
ista: Modic KA. 2026. Research data for ‘Giant transverse magnetic fluctuations
at the edge of re-entrant superconductivity in UTe2’, Institute of Science and
Technology Austria, 10.15479/AT-ISTA-21174.
mla: Modic, Kimberly A. Research Data for “Giant Transverse Magnetic Fluctuations
at the Edge of Re-Entrant Superconductivity in UTe2.” Institute of Science
and Technology Austria, 2026, doi:10.15479/AT-ISTA-21174.
short: K.A. Modic, (2026).
contributor:
- contributor_type: project_member
first_name: Valeska
id: 467ed36b-dc96-11ea-b7c8-b043a380b282
last_name: Zambra
orcid: 0000-0002-8806-5719
corr_author: '1'
date_created: 2026-02-09T12:04:20Z
date_published: 2026-02-19T00:00:00Z
date_updated: 2026-05-11T06:35:59Z
day: '19'
ddc:
- '530'
department:
- _id: KiMo
doi: 10.15479/AT-ISTA-21174
file:
- access_level: open_access
checksum: 53157d908fba663275c2b8dc6ee84fdb
content_type: text/plain
creator: kmodic
date_created: 2026-02-19T07:38:15Z
date_updated: 2026-02-19T07:38:15Z
file_id: '21332'
file_name: README.txt
file_size: 1347
relation: main_file
success: 1
- access_level: open_access
checksum: b2c8ca5620ee9c181a42082068d3d73c
content_type: application/zip
creator: kmodic
date_created: 2026-02-19T07:39:03Z
date_updated: 2026-02-19T07:39:03Z
file_id: '21333'
file_name: processed_data_bc_plane_Fig2d.zip
file_size: 534853
relation: main_file
success: 1
- access_level: open_access
checksum: 976bf113da4b1133313f0b292e71289f
content_type: application/zip
creator: kmodic
date_created: 2026-02-19T07:39:07Z
date_updated: 2026-02-19T07:39:07Z
file_id: '21334'
file_name: processed_data_ac_plane_Fig2c.zip
file_size: 427144
relation: main_file
success: 1
file_date_updated: 2026-02-19T07:39:07Z
has_accepted_license: '1'
keyword:
- transverse magnetic susceptibility
- magnetotropic
- superconductivity
- magnetic fluctuations
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: bd968c70-d553-11ed-ba76-cde40b0aba64
grant_number: '101078696'
name: Gaining leverage with spin liquids and superconductors
publisher: Institute of Science and Technology Austria
related_material:
link:
- relation: preprint
url: https://arxiv.org/pdf/2506.08984
record:
- id: '21845'
relation: used_in_publication
status: public
status: public
title: Research data for "Giant transverse magnetic fluctuations at the edge of re-entrant
superconductivity in UTe2"
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: '2026'
...
---
OA_place: repository
OA_type: green
_id: '21212'
abstract:
- lang: eng
text: "Malignant glioma is incurable. Using a mouse genetic mosaic system to generate
sporadic Trp53,Nf1-null OPCs, we previously identified oligodendrocyte precursor
cell (OPC) as a cell-of-origin of glioma. Here, we report that pre-malignant Trp53,Nf1-null
OPCs outcompete wildtype counterparts during their expansion. Blocking competition
by mutating/strengthening wildtype OPCs impeded both pre-malignant progression
and malignant expansion of glioma.\r\n\r\n“In-tissue” phosphoproteomic profiling
revealed an enrichment of phosphopeptides related to RNA splicing and protein
translation at the peak of cell competition, suggesting that competitiveness may
stem from unique protein species. Among candidates was mTORC1, whose pharmacological
inhibition or genetic disruption resulted in a loss of competitiveness in our
mouse model. Finally, analysis of patient biopsies and interrogating the role
of individual gliomagenic mutations in OPC competition supported its relevance
in human gliomas. Together, these findings identified the driving role of competitive
interactions among OPCs in gliomagenesis, and suggest unconventional therapeutic
strategies to target this process."
acknowledgement: "We thank Dr. Wenjie Liu for providing critical feedback on the manuscript.
We also thank Dr.\r\nPat Pramoonjago at the Biorepository and Tissue Research Facility,
and Hope Davis at the\r\nvivarium for their assistance on the project. These Core
Facilities are supported by UVA Cancer\r\nCenter grant #P30-CA044579. We are grateful
to Dr. Jonathan A. Epstein for providing the\r\nNf1GRD/+ mouse strain (https://pubmed.ncbi.nlm.nih.gov/26460546/).
This work was partly\r\nsupported by the National Institute of Neurological Diseases
and Stroke R21 NS125479-01A1\r\n(H.Z.), American Cancer Society Institutional Research
Grant to the University of Virginia\r\n(Y.J.), the National Natural Science Foundation
of China #82072787 (M.Y.), the National\r\nCancer Institute U54 CA238114 (F.W.),
U01 CA284193 (K.M.N.), and U54 CA274499 (K.A.J.,\r\nM.F-S.), the National institute
of General Medical Sciences R35 GM133404 (M.F-S.), the Dr.\r\nMiriam and Sheldon
G. Adelson Medical Research Foundation (H.I.K., S.A.G.), the National\r\nCenter
for Advancing Translational Sciences KL2TR001882 (K.S.P.), Tower Cancer Career Development
Grant (K.S.P.), McKnight Neurobiology of Brain Disorders Grant (K.S.P.). The\r\ncontent
is solely the responsibility of the authors and does not necessarily represent the
official\r\nviews of the National Institutes of Health. Illustrations in this manuscript
were created with\r\nBioRender (BioRender.com)."
article_processing_charge: No
author:
- first_name: Ying
full_name: Jiang, Ying
last_name: Jiang
- first_name: Ryuhjin
full_name: Ahn, Ryuhjin
last_name: Ahn
- first_name: Arthur
full_name: Huang, Arthur
last_name: Huang
- first_name: Phillippe P.
full_name: Gonzalez, Phillippe P.
last_name: Gonzalez
- first_name: Jungeun
full_name: Kim, Jungeun
last_name: Kim
- first_name: Guoxin
full_name: Zhang, Guoxin
last_name: Zhang
- first_name: Zihao
full_name: Liu, Zihao
last_name: Liu
- first_name: Zhenqiang
full_name: He, Zhenqiang
last_name: He
- first_name: Lindsey
full_name: Dudley, Lindsey
last_name: Dudley
- first_name: Kunal S.
full_name: Patel, Kunal S.
last_name: Patel
- first_name: Godfrey A.
full_name: Dzhivhuho, Godfrey A.
last_name: Dzhivhuho
- first_name: Sam
full_name: Crowl, Sam
last_name: Crowl
- first_name: Piotr
full_name: Przanowski, Piotr
last_name: Przanowski
- first_name: Luisa Quesada
full_name: Camacho, Luisa Quesada
last_name: Camacho
- first_name: Sijie
full_name: Hao, Sijie
last_name: Hao
- first_name: Jianhao
full_name: Zeng, Jianhao
last_name: Zeng
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Mohammad
full_name: Fallahi-Sichani, Mohammad
last_name: Fallahi-Sichani
- first_name: Kevin A.
full_name: Janes, Kevin A.
last_name: Janes
- first_name: Kristen M.
full_name: Naegle, Kristen M.
last_name: Naegle
- first_name: Marie-Louise
full_name: Hammarskjold, Marie-Louise
last_name: Hammarskjold
- first_name: Steven A.
full_name: Goldman, Steven A.
last_name: Goldman
- first_name: Harley I.
full_name: Kornblum, Harley I.
last_name: Kornblum
- first_name: Maojin
full_name: Yao, Maojin
last_name: Yao
- first_name: Forest
full_name: White, Forest
last_name: White
- first_name: Hui
full_name: Zong, Hui
last_name: Zong
citation:
ama: Jiang Y, Ahn R, Huang A, et al. Critical role of cell competition in gliomagenesis.
bioRxiv. 2026. doi:10.64898/2026.01.15.699808
apa: Jiang, Y., Ahn, R., Huang, A., Gonzalez, P. P., Kim, J., Zhang, G., … Zong,
H. (2026). Critical role of cell competition in gliomagenesis. bioRxiv.
https://doi.org/10.64898/2026.01.15.699808
chicago: Jiang, Ying, Ryuhjin Ahn, Arthur Huang, Phillippe P. Gonzalez, Jungeun
Kim, Guoxin Zhang, Zihao Liu, et al. “Critical Role of Cell Competition in Gliomagenesis.”
BioRxiv, 2026. https://doi.org/10.64898/2026.01.15.699808.
ieee: Y. Jiang et al., “Critical role of cell competition in gliomagenesis,”
bioRxiv. 2026.
ista: Jiang Y, Ahn R, Huang A, Gonzalez PP, Kim J, Zhang G, Liu Z, He Z, Dudley
L, Patel KS, Dzhivhuho GA, Crowl S, Przanowski P, Camacho LQ, Hao S, Zeng J, Hippenmeyer
S, Fallahi-Sichani M, Janes KA, Naegle KM, Hammarskjold M-L, Goldman SA, Kornblum
HI, Yao M, White F, Zong H. 2026. Critical role of cell competition in gliomagenesis.
bioRxiv, 10.64898/2026.01.15.699808.
mla: Jiang, Ying, et al. “Critical Role of Cell Competition in Gliomagenesis.” BioRxiv,
2026, doi:10.64898/2026.01.15.699808.
short: Y. Jiang, R. Ahn, A. Huang, P.P. Gonzalez, J. Kim, G. Zhang, Z. Liu, Z. He,
L. Dudley, K.S. Patel, G.A. Dzhivhuho, S. Crowl, P. Przanowski, L.Q. Camacho,
S. Hao, J. Zeng, S. Hippenmeyer, M. Fallahi-Sichani, K.A. Janes, K.M. Naegle,
M.-L. Hammarskjold, S.A. Goldman, H.I. Kornblum, M. Yao, F. White, H. Zong, BioRxiv
(2026).
date_created: 2026-02-10T12:55:55Z
date_published: 2026-01-16T00:00:00Z
date_updated: 2026-02-16T10:12:42Z
day: '16'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.64898/2026.01.15.699808
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.64898/2026.01.15.699808
month: '01'
oa: 1
oa_version: Preprint
publication: bioRxiv
publication_status: published
status: public
title: Critical role of cell competition in gliomagenesis
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2026'
...
---
OA_place: repository
OA_type: green
_id: '21230'
abstract:
- lang: eng
text: Asteroseismology is the study of the interior physics and structure of stars
using their pulsations. It is applicable to stars across the Hertzsprung–Russell
(HR) diagram and a powerful technique not only to measure masses, radii, and ages
but also directly constrain interior rotation, chemical mixing, and magnetism.
This is because a star's self-excited pulsation modes are sensitive to its structure.
Asteroseismology generally requires long-duration and high-precision time-series
data. The method of forward asteroseismic modeling, which is the statistical comparison
of observed pulsation mode frequencies to theoretically predicted pulsation frequencies
calculated from a grid of models, provides precise constraints for calibrating
various transport phenomena. In this introduction to asteroseismology, we provide
an overview of its principles, and the typical data sets and methodologies used
to constrain stellar interiors. Finally, we present key highlights of asteroseismic
results from across the HR diagram, and conclude with ongoing challenges and future
prospects for this ever-expanding field within stellar astrophysics.
article_processing_charge: No
arxiv: 1
author:
- first_name: Dominic M.
full_name: Bowman, Dominic M.
last_name: Bowman
- first_name: Lisa Annabelle
full_name: Bugnet, Lisa Annabelle
id: d9edb345-f866-11ec-9b37-d119b5234501
last_name: Bugnet
orcid: 0000-0003-0142-4000
citation:
ama: 'Bowman DM, Bugnet LA. Asteroseismology. In: Mandel I, ed. Encyclopedia
of Astrophysics. Vol 2. Elsevier; 2026:133-153. doi:10.1016/b978-0-443-21439-4.00036-5'
apa: Bowman, D. M., & Bugnet, L. A. (2026). Asteroseismology. In I. Mandel (Ed.),
Encyclopedia of Astrophysics (Vol. 2, pp. 133–153). Elsevier. https://doi.org/10.1016/b978-0-443-21439-4.00036-5
chicago: Bowman, Dominic M., and Lisa Annabelle Bugnet. “Asteroseismology.” In Encyclopedia
of Astrophysics, edited by Ilya Mandel, 2:133–53. Elsevier, 2026. https://doi.org/10.1016/b978-0-443-21439-4.00036-5.
ieee: D. M. Bowman and L. A. Bugnet, “Asteroseismology,” in Encyclopedia of Astrophysics,
vol. 2, I. Mandel, Ed. Elsevier, 2026, pp. 133–153.
ista: 'Bowman DM, Bugnet LA. 2026.Asteroseismology. In: Encyclopedia of Astrophysics.
vol. 2, 133–153.'
mla: Bowman, Dominic M., and Lisa Annabelle Bugnet. “Asteroseismology.” Encyclopedia
of Astrophysics, edited by Ilya Mandel, vol. 2, Elsevier, 2026, pp. 133–53,
doi:10.1016/b978-0-443-21439-4.00036-5.
short: D.M. Bowman, L.A. Bugnet, in:, I. Mandel (Ed.), Encyclopedia of Astrophysics,
Elsevier, 2026, pp. 133–153.
date_created: 2026-02-16T10:43:01Z
date_published: 2026-01-01T00:00:00Z
date_updated: 2026-02-17T11:05:20Z
day: '01'
department:
- _id: LiBu
doi: 10.1016/b978-0-443-21439-4.00036-5
editor:
- first_name: Ilya
full_name: Mandel, Ilya
last_name: Mandel
external_id:
arxiv:
- '2410.01715'
intvolume: ' 2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2410.01715
month: '01'
oa: 1
oa_version: Preprint
page: 133-153
publication: Encyclopedia of Astrophysics
publication_identifier:
isbn:
- '9780443214400'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Asteroseismology
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2026'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '21231'
abstract:
- lang: eng
text: To assess cell migration in complex spatial environments, microfabricated
chips, such as mazes and pillar forests, are routinely used to impose spatial
and mechanical constraints, and cell trajectories are followed within these structures
by advanced imaging techniques. In systems mechanobiology, computational models
serve as essential tools to uncover how physical geometry influences intracellular
dynamics; however, decoding such complex behaviors requires advanced inference
techniques. Here, we integrated experimental observations of dendritic cell migration
in a geometrically constrained microenvironment into a Cellular Potts model. We
demonstrated that these spatial constraints modulate the motility dynamics, including
speed and directional changes. We show that classical summary statistics, such
as mean squared displacement and turning angle distributions, can resolve key
mechanistic features but fail to extract richer spatiotemporal patterns, limiting
accurate parameter inference. To solve this, we applied neural posterior estimation
with in-the-loop learning of summary features. This learned summary representation
of the data enables robust and flexible parameter inference, providing a data-driven
framework for model calibration and advancing quantitative analysis of cell migration
in structured microenvironments.
acknowledgement: 'This work was supported by the German Federal Ministry of Education
and Research (BMBF) (EMUNE/031L0293C), the European Union via the ERC grant INTEGRATE,
grant agreement number 101126146, and under Germany’s Excellence Strategy by the
Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) (EXC 2047—390685813,
EXC 2151—390873048, FOR5775 — 533863915, and 524747443), the University of Bonn
via the Schlegel Professorship of J.H., and the returning experts fellowship of
the Ministry of Innovation, Science, and Research of North-Rhine-Westphalia (AZ:
421-8.03.03.02-137069). J.M. is a member of the Nanofabrication Facility and is
supported by the Institute of Science and Technology Austria. E.K. acknowledges
the TRA Life and Health (University of Bonn) as part of the Excellence Strategy
of the federal and state governments. The authors thank Laeschkir Würthner for his
insightful comments on the implementation of the authors’ model. The views and opinions
expressed are those of the authors only and do not necessarily reflect those of
the funding agencies. Parts of Fig. 1 were created using BioRender. Open Access
funding enabled and organized by Projekt DEAL.'
article_number: '20'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Jonas
full_name: Arruda, Jonas
last_name: Arruda
- first_name: Emad
full_name: Alamoudi, Emad
last_name: Alamoudi
- first_name: Robert
full_name: Mueller, Robert
last_name: Mueller
- first_name: Marc
full_name: Vaisband, Marc
last_name: Vaisband
- first_name: Ronja
full_name: Molkenbur, Ronja
last_name: Molkenbur
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Eva
full_name: Kiermaier, Eva
last_name: Kiermaier
- first_name: Jan
full_name: Hasenauer, Jan
last_name: Hasenauer
citation:
ama: Arruda J, Alamoudi E, Mueller R, et al. Simulation-based inference of cell
migration dynamics in complex spatial environments. npj Systems Biology and
Applications. 2026;12. doi:10.1038/s41540-026-00648-9
apa: Arruda, J., Alamoudi, E., Mueller, R., Vaisband, M., Molkenbur, R., Merrin,
J., … Hasenauer, J. (2026). Simulation-based inference of cell migration dynamics
in complex spatial environments. Npj Systems Biology and Applications.
Springer Nature. https://doi.org/10.1038/s41540-026-00648-9
chicago: Arruda, Jonas, Emad Alamoudi, Robert Mueller, Marc Vaisband, Ronja Molkenbur,
Jack Merrin, Eva Kiermaier, and Jan Hasenauer. “Simulation-Based Inference of
Cell Migration Dynamics in Complex Spatial Environments.” Npj Systems Biology
and Applications. Springer Nature, 2026. https://doi.org/10.1038/s41540-026-00648-9.
ieee: J. Arruda et al., “Simulation-based inference of cell migration dynamics
in complex spatial environments,” npj Systems Biology and Applications,
vol. 12. Springer Nature, 2026.
ista: Arruda J, Alamoudi E, Mueller R, Vaisband M, Molkenbur R, Merrin J, Kiermaier
E, Hasenauer J. 2026. Simulation-based inference of cell migration dynamics in
complex spatial environments. npj Systems Biology and Applications. 12, 20.
mla: Arruda, Jonas, et al. “Simulation-Based Inference of Cell Migration Dynamics
in Complex Spatial Environments.” Npj Systems Biology and Applications,
vol. 12, 20, Springer Nature, 2026, doi:10.1038/s41540-026-00648-9.
short: J. Arruda, E. Alamoudi, R. Mueller, M. Vaisband, R. Molkenbur, J. Merrin,
E. Kiermaier, J. Hasenauer, Npj Systems Biology and Applications 12 (2026).
date_created: 2026-02-16T10:44:31Z
date_published: 2026-02-05T00:00:00Z
date_updated: 2026-02-23T10:10:10Z
day: '05'
ddc:
- '570'
department:
- _id: NanoFab
doi: 10.1038/s41540-026-00648-9
external_id:
pmid:
- '41611727'
file:
- access_level: open_access
checksum: 99b2e6bbaaedf45f22e07751948669f5
content_type: application/pdf
creator: dernst
date_created: 2026-02-23T10:09:03Z
date_updated: 2026-02-23T10:09:03Z
file_id: '21346'
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file_date_updated: 2026-02-23T10:09:03Z
has_accepted_license: '1'
intvolume: ' 12'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: npj Systems Biology and Applications
publication_identifier:
eissn:
- 2056-7189
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Simulation-based inference of cell migration dynamics in complex spatial environments
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '21232'
abstract:
- lang: eng
text: "Abstract\r\n In this paper,
we consider a simple class of stratified spaces – 2-complexes. We present an algorithm
that learns the abstract structure of an embedded 2-complex from a point cloud
sampled from it. We use tools and inspiration from computational geometry, algebraic
topology, and topological data analysis and prove the correctness of the identified
abstract structure under assumptions on the embedding."
acknowledgement: The author would like to thank Kate Turner, Chris Williams, Jonathan
Spreer, Stephan Tillmann, Vanessa Robins, Vigleik Angeltveit, Martin Helmer, and
James Morgan for very helpful discussions; and thanks Sara Kališnik Hintz and Paul
Bendich for comments on an earlier version. Additonally, the author would like to
thank both reviewers for their very insightful and helpful comments, without which
the paper would be infinitely less coherent than it currently is. Open access funding
provided by Institute of Science and Technology (IST Austria). The work in this
paper was supported by an Australian Federal Government Grant, 2019-2022, Stratified
Space Learning.
article_number: '17'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Yossi
full_name: Bleile, Yossi
id: 920a7385-7995-11ef-9bfd-8c434cd8f3c2
last_name: Bleile
orcid: 0000-0002-4861-9174
citation:
ama: 'Bokor Bleile Y. Towards stratified space learning: 2-complexes. La Matematica.
2026;5. doi:10.1007/s44007-025-00183-9'
apa: 'Bokor Bleile, Y. (2026). Towards stratified space learning: 2-complexes. La
Matematica. Springer Nature. https://doi.org/10.1007/s44007-025-00183-9'
chicago: 'Bokor Bleile, Yossi. “Towards Stratified Space Learning: 2-Complexes.”
La Matematica. Springer Nature, 2026. https://doi.org/10.1007/s44007-025-00183-9.'
ieee: 'Y. Bokor Bleile, “Towards stratified space learning: 2-complexes,” La
Matematica, vol. 5. Springer Nature, 2026.'
ista: 'Bokor Bleile Y. 2026. Towards stratified space learning: 2-complexes. La
Matematica. 5, 17.'
mla: 'Bokor Bleile, Yossi. “Towards Stratified Space Learning: 2-Complexes.” La
Matematica, vol. 5, 17, Springer Nature, 2026, doi:10.1007/s44007-025-00183-9.'
short: Y. Bokor Bleile, La Matematica 5 (2026).
corr_author: '1'
date_created: 2026-02-16T10:44:44Z
date_published: 2026-02-08T00:00:00Z
date_updated: 2026-06-11T11:51:14Z
day: '08'
ddc:
- '510'
department:
- _id: HeEd
doi: 10.1007/s44007-025-00183-9
external_id:
arxiv:
- '2305.02724'
file:
- access_level: open_access
checksum: 6cae2efb47b025af22a8539c606a4e09
content_type: application/pdf
creator: dernst
date_created: 2026-02-23T10:18:52Z
date_updated: 2026-02-23T10:18:52Z
file_id: '21347'
file_name: 2026_LaMatematica_Bleile.pdf
file_size: 15051582
relation: main_file
success: 1
file_date_updated: 2026-02-23T10:18:52Z
has_accepted_license: '1'
intvolume: ' 5'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
publication: La Matematica
publication_identifier:
issn:
- 2730-9657
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Towards stratified space learning: 2-complexes'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2026'
...