---
_id: '14179'
abstract:
- lang: eng
text: Self-supervised representation learning has shown remarkable success in a
number of domains. A common practice is to perform data augmentation via hand-crafted
transformations intended to leave the semantics of the data invariant. We seek
to understand the empirical success of this approach from a theoretical perspective.
We formulate the augmentation process as a latent variable model by postulating
a partition of the latent representation into a content component, which is assumed
invariant to augmentation, and a style component, which is allowed to change.
Unlike prior work on disentanglement and independent component analysis, we allow
for both nontrivial statistical and causal dependencies in the latent space. We
study the identifiability of the latent representation based on pairs of views
of the observations and prove sufficient conditions that allow us to identify
the invariant content partition up to an invertible mapping in both generative
and discriminative settings. We find numerical simulations with dependent latent
variables are consistent with our theory. Lastly, we introduce Causal3DIdent,
a dataset of high-dimensional, visually complex images with rich causal dependencies,
which we use to study the effect of data augmentations performed in practice.
article_processing_charge: No
arxiv: 1
author:
- first_name: Julius von
full_name: Kügelgen, Julius von
last_name: Kügelgen
- first_name: Yash
full_name: Sharma, Yash
last_name: Sharma
- first_name: Luigi
full_name: Gresele, Luigi
last_name: Gresele
- first_name: Wieland
full_name: Brendel, Wieland
last_name: Brendel
- first_name: Bernhard
full_name: Schölkopf, Bernhard
last_name: Schölkopf
- first_name: Michel
full_name: Besserve, Michel
last_name: Besserve
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
citation:
ama: 'Kügelgen J von, Sharma Y, Gresele L, et al. Self-supervised learning with
data augmentations provably isolates content from style. In: Advances in Neural
Information Processing Systems. Vol 34. ; 2021:16451-16467.'
apa: Kügelgen, J. von, Sharma, Y., Gresele, L., Brendel, W., Schölkopf, B., Besserve,
M., & Locatello, F. (2021). Self-supervised learning with data augmentations
provably isolates content from style. In Advances in Neural Information Processing
Systems (Vol. 34, pp. 16451–16467). Virtual.
chicago: Kügelgen, Julius von, Yash Sharma, Luigi Gresele, Wieland Brendel, Bernhard
Schölkopf, Michel Besserve, and Francesco Locatello. “Self-Supervised Learning
with Data Augmentations Provably Isolates Content from Style.” In Advances
in Neural Information Processing Systems, 34:16451–67, 2021.
ieee: J. von Kügelgen et al., “Self-supervised learning with data augmentations
provably isolates content from style,” in Advances in Neural Information Processing
Systems, Virtual, 2021, vol. 34, pp. 16451–16467.
ista: 'Kügelgen J von, Sharma Y, Gresele L, Brendel W, Schölkopf B, Besserve M,
Locatello F. 2021. Self-supervised learning with data augmentations provably isolates
content from style. Advances in Neural Information Processing Systems. NeurIPS:
Neural Information Processing Systems vol. 34, 16451–16467.'
mla: Kügelgen, Julius von, et al. “Self-Supervised Learning with Data Augmentations
Provably Isolates Content from Style.” Advances in Neural Information Processing
Systems, vol. 34, 2021, pp. 16451–67.
short: J. von Kügelgen, Y. Sharma, L. Gresele, W. Brendel, B. Schölkopf, M. Besserve,
F. Locatello, in:, Advances in Neural Information Processing Systems, 2021, pp.
16451–16467.
conference:
end_date: 2021-12-10
location: Virtual
name: 'NeurIPS: Neural Information Processing Systems'
start_date: 2021-12-07
date_created: 2023-08-22T14:04:36Z
date_published: 2021-06-08T00:00:00Z
date_updated: 2023-09-11T10:33:19Z
day: '08'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '2106.04619'
intvolume: ' 34'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2106.04619
month: '06'
oa: 1
oa_version: Preprint
page: 16451-16467
publication: Advances in Neural Information Processing Systems
publication_identifier:
isbn:
- '9781713845393'
publication_status: published
quality_controlled: '1'
status: public
title: Self-supervised learning with data augmentations provably isolates content
from style
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2021'
...
---
_id: '14180'
abstract:
- lang: eng
text: 'Modern neural network architectures can leverage large amounts of data to
generalize well within the training distribution. However, they are less capable
of systematic generalization to data drawn from unseen but related distributions,
a feat that is hypothesized to require compositional reasoning and reuse of knowledge.
In this work, we present Neural Interpreters, an architecture that factorizes
inference in a self-attention network as a system of modules, which we call \emph{functions}.
Inputs to the model are routed through a sequence of functions in a way that is
end-to-end learned. The proposed architecture can flexibly compose computation
along width and depth, and lends itself well to capacity extension after training.
To demonstrate the versatility of Neural Interpreters, we evaluate it in two distinct
settings: image classification and visual abstract reasoning on Raven Progressive
Matrices. In the former, we show that Neural Interpreters perform on par with
the vision transformer using fewer parameters, while being transferrable to a
new task in a sample efficient manner. In the latter, we find that Neural Interpreters
are competitive with respect to the state-of-the-art in terms of systematic generalization. '
article_processing_charge: No
arxiv: 1
author:
- first_name: Nasim
full_name: Rahaman, Nasim
last_name: Rahaman
- first_name: Muhammad Waleed
full_name: Gondal, Muhammad Waleed
last_name: Gondal
- first_name: Shruti
full_name: Joshi, Shruti
last_name: Joshi
- first_name: Peter
full_name: Gehler, Peter
last_name: Gehler
- first_name: Yoshua
full_name: Bengio, Yoshua
last_name: Bengio
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Bernhard
full_name: Schölkopf, Bernhard
last_name: Schölkopf
citation:
ama: 'Rahaman N, Gondal MW, Joshi S, et al. Dynamic inference with neural interpreters.
In: Advances in Neural Information Processing Systems. Vol 34. ; 2021:10985-10998.'
apa: Rahaman, N., Gondal, M. W., Joshi, S., Gehler, P., Bengio, Y., Locatello, F.,
& Schölkopf, B. (2021). Dynamic inference with neural interpreters. In Advances
in Neural Information Processing Systems (Vol. 34, pp. 10985–10998). Virtual.
chicago: Rahaman, Nasim, Muhammad Waleed Gondal, Shruti Joshi, Peter Gehler, Yoshua
Bengio, Francesco Locatello, and Bernhard Schölkopf. “Dynamic Inference with Neural
Interpreters.” In Advances in Neural Information Processing Systems, 34:10985–98,
2021.
ieee: N. Rahaman et al., “Dynamic inference with neural interpreters,” in
Advances in Neural Information Processing Systems, Virtual, 2021, vol.
34, pp. 10985–10998.
ista: 'Rahaman N, Gondal MW, Joshi S, Gehler P, Bengio Y, Locatello F, Schölkopf
B. 2021. Dynamic inference with neural interpreters. Advances in Neural Information
Processing Systems. NeurIPS: Neural Information Processing Systems vol. 34, 10985–10998.'
mla: Rahaman, Nasim, et al. “Dynamic Inference with Neural Interpreters.” Advances
in Neural Information Processing Systems, vol. 34, 2021, pp. 10985–98.
short: N. Rahaman, M.W. Gondal, S. Joshi, P. Gehler, Y. Bengio, F. Locatello, B.
Schölkopf, in:, Advances in Neural Information Processing Systems, 2021, pp. 10985–10998.
conference:
end_date: 2021-12-10
location: Virtual
name: 'NeurIPS: Neural Information Processing Systems'
start_date: 2021-12-07
date_created: 2023-08-22T14:04:55Z
date_published: 2021-10-12T00:00:00Z
date_updated: 2023-09-11T11:33:46Z
day: '12'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '2110.06399'
intvolume: ' 34'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2110.06399
month: '10'
oa: 1
oa_version: Preprint
page: 10985-10998
publication: Advances in Neural Information Processing Systems
publication_identifier:
isbn:
- '9781713845393'
publication_status: published
quality_controlled: '1'
status: public
title: Dynamic inference with neural interpreters
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2021'
...
---
_id: '14181'
abstract:
- lang: eng
text: Variational Inference makes a trade-off between the capacity of the variational
family and the tractability of finding an approximate posterior distribution.
Instead, Boosting Variational Inference allows practitioners to obtain increasingly
good posterior approximations by spending more compute. The main obstacle to widespread
adoption of Boosting Variational Inference is the amount of resources necessary
to improve over a strong Variational Inference baseline. In our work, we trace
this limitation back to the global curvature of the KL-divergence. We characterize
how the global curvature impacts time and memory consumption, address the problem
with the notion of local curvature, and provide a novel approximate backtracking
algorithm for estimating local curvature. We give new theoretical convergence
rates for our algorithms and provide experimental validation on synthetic and
real-world datasets.
article_processing_charge: No
arxiv: 1
author:
- first_name: Gideon
full_name: Dresdner, Gideon
last_name: Dresdner
- first_name: Saurav
full_name: Shekhar, Saurav
last_name: Shekhar
- first_name: Fabian
full_name: Pedregosa, Fabian
last_name: Pedregosa
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Gunnar
full_name: Rätsch, Gunnar
last_name: Rätsch
citation:
ama: 'Dresdner G, Shekhar S, Pedregosa F, Locatello F, Rätsch G. Boosting variational
inference with locally adaptive step-sizes. In: Proceedings of the Thirtieth
International Joint Conference on Artificial Intelligence. International Joint
Conferences on Artificial Intelligence; 2021:2337-2343. doi:10.24963/ijcai.2021/322'
apa: 'Dresdner, G., Shekhar, S., Pedregosa, F., Locatello, F., & Rätsch, G.
(2021). Boosting variational inference with locally adaptive step-sizes. In Proceedings
of the Thirtieth International Joint Conference on Artificial Intelligence
(pp. 2337–2343). Montreal, Canada: International Joint Conferences on Artificial
Intelligence. https://doi.org/10.24963/ijcai.2021/322'
chicago: Dresdner, Gideon, Saurav Shekhar, Fabian Pedregosa, Francesco Locatello,
and Gunnar Rätsch. “Boosting Variational Inference with Locally Adaptive Step-Sizes.”
In Proceedings of the Thirtieth International Joint Conference on Artificial
Intelligence, 2337–43. International Joint Conferences on Artificial Intelligence,
2021. https://doi.org/10.24963/ijcai.2021/322.
ieee: G. Dresdner, S. Shekhar, F. Pedregosa, F. Locatello, and G. Rätsch, “Boosting
variational inference with locally adaptive step-sizes,” in Proceedings of
the Thirtieth International Joint Conference on Artificial Intelligence, Montreal,
Canada, 2021, pp. 2337–2343.
ista: 'Dresdner G, Shekhar S, Pedregosa F, Locatello F, Rätsch G. 2021. Boosting
variational inference with locally adaptive step-sizes. Proceedings of the Thirtieth
International Joint Conference on Artificial Intelligence. IJCAI: International
Joint Conference on Artificial Intelligence, 2337–2343.'
mla: Dresdner, Gideon, et al. “Boosting Variational Inference with Locally Adaptive
Step-Sizes.” Proceedings of the Thirtieth International Joint Conference on
Artificial Intelligence, International Joint Conferences on Artificial Intelligence,
2021, pp. 2337–43, doi:10.24963/ijcai.2021/322.
short: G. Dresdner, S. Shekhar, F. Pedregosa, F. Locatello, G. Rätsch, in:, Proceedings
of the Thirtieth International Joint Conference on Artificial Intelligence, International
Joint Conferences on Artificial Intelligence, 2021, pp. 2337–2343.
conference:
end_date: 2021-08-27
location: Montreal, Canada
name: 'IJCAI: International Joint Conference on Artificial Intelligence'
start_date: 2021-08-19
date_created: 2023-08-22T14:05:14Z
date_published: 2021-05-19T00:00:00Z
date_updated: 2023-09-11T11:14:30Z
day: '19'
department:
- _id: FrLo
doi: 10.24963/ijcai.2021/322
extern: '1'
external_id:
arxiv:
- '2105.09240'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2105.09240
month: '05'
oa: 1
oa_version: Published Version
page: 2337-2343
publication: Proceedings of the Thirtieth International Joint Conference on Artificial
Intelligence
publication_identifier:
eisbn:
- '9780999241196'
publication_status: published
publisher: International Joint Conferences on Artificial Intelligence
quality_controlled: '1'
status: public
title: Boosting variational inference with locally adaptive step-sizes
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '14182'
abstract:
- lang: eng
text: "When machine learning systems meet real world applications, accuracy is only\r\none
of several requirements. In this paper, we assay a complementary\r\nperspective
originating from the increasing availability of pre-trained and\r\nregularly improving
state-of-the-art models. While new improved models develop\r\nat a fast pace,
downstream tasks vary more slowly or stay constant. Assume that\r\nwe have a large
unlabelled data set for which we want to maintain accurate\r\npredictions. Whenever
a new and presumably better ML models becomes available,\r\nwe encounter two problems:
(i) given a limited budget, which data points should\r\nbe re-evaluated using
the new model?; and (ii) if the new predictions differ\r\nfrom the current ones,
should we update? Problem (i) is about compute cost,\r\nwhich matters for very
large data sets and models. Problem (ii) is about\r\nmaintaining consistency of
the predictions, which can be highly relevant for\r\ndownstream applications;
our demand is to avoid negative flips, i.e., changing\r\ncorrect to incorrect
predictions. In this paper, we formalize the Prediction\r\nUpdate Problem and
present an efficient probabilistic approach as answer to the\r\nabove questions.
In extensive experiments on standard classification benchmark\r\ndata sets, we
show that our method outperforms alternative strategies along key\r\nmetrics for
backward-compatible prediction updates."
article_processing_charge: No
arxiv: 1
author:
- first_name: Frederik
full_name: Träuble, Frederik
last_name: Träuble
- first_name: Julius von
full_name: Kügelgen, Julius von
last_name: Kügelgen
- first_name: Matthäus
full_name: Kleindessner, Matthäus
last_name: Kleindessner
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Bernhard
full_name: Schölkopf, Bernhard
last_name: Schölkopf
- first_name: Peter
full_name: Gehler, Peter
last_name: Gehler
citation:
ama: 'Träuble F, Kügelgen J von, Kleindessner M, Locatello F, Schölkopf B, Gehler
P. Backward-compatible prediction updates: A probabilistic approach. In: 35th
Conference on Neural Information Processing Systems. Vol 34. ; 2021:116-128.'
apa: 'Träuble, F., Kügelgen, J. von, Kleindessner, M., Locatello, F., Schölkopf,
B., & Gehler, P. (2021). Backward-compatible prediction updates: A probabilistic
approach. In 35th Conference on Neural Information Processing Systems (Vol.
34, pp. 116–128). Virtual.'
chicago: 'Träuble, Frederik, Julius von Kügelgen, Matthäus Kleindessner, Francesco
Locatello, Bernhard Schölkopf, and Peter Gehler. “Backward-Compatible Prediction
Updates: A Probabilistic Approach.” In 35th Conference on Neural Information
Processing Systems, 34:116–28, 2021.'
ieee: 'F. Träuble, J. von Kügelgen, M. Kleindessner, F. Locatello, B. Schölkopf,
and P. Gehler, “Backward-compatible prediction updates: A probabilistic approach,”
in 35th Conference on Neural Information Processing Systems, Virtual, 2021,
vol. 34, pp. 116–128.'
ista: 'Träuble F, Kügelgen J von, Kleindessner M, Locatello F, Schölkopf B, Gehler
P. 2021. Backward-compatible prediction updates: A probabilistic approach. 35th
Conference on Neural Information Processing Systems. NeurIPS: Neural Information
Processing Systems vol. 34, 116–128.'
mla: 'Träuble, Frederik, et al. “Backward-Compatible Prediction Updates: A Probabilistic
Approach.” 35th Conference on Neural Information Processing Systems, vol.
34, 2021, pp. 116–28.'
short: F. Träuble, J. von Kügelgen, M. Kleindessner, F. Locatello, B. Schölkopf,
P. Gehler, in:, 35th Conference on Neural Information Processing Systems, 2021,
pp. 116–128.
conference:
end_date: 2021-12-10
location: Virtual
name: 'NeurIPS: Neural Information Processing Systems'
start_date: 2021-12-07
date_created: 2023-08-22T14:05:41Z
date_published: 2021-07-02T00:00:00Z
date_updated: 2023-09-11T11:31:59Z
day: '02'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '2107.01057'
intvolume: ' 34'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2107.01057
month: '07'
oa: 1
oa_version: Preprint
page: 116-128
publication: 35th Conference on Neural Information Processing Systems
publication_identifier:
isbn:
- '9781713845393'
publication_status: published
quality_controlled: '1'
status: public
title: 'Backward-compatible prediction updates: A probabilistic approach'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2021'
...
---
_id: '14221'
abstract:
- lang: eng
text: 'The world is structured in countless ways. It may be prudent to enforce corresponding
structural properties to a learning algorithm''s solution, such as incorporating
prior beliefs, natural constraints, or causal structures. Doing so may translate
to faster, more accurate, and more flexible models, which may directly relate
to real-world impact. In this dissertation, we consider two different research
areas that concern structuring a learning algorithm''s solution: when the structure
is known and when it has to be discovered.'
article_number: '2111.13693'
article_processing_charge: No
arxiv: 1
author:
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
citation:
ama: Locatello F. Enforcing and discovering structure in machine learning. arXiv.
doi:10.48550/arXiv.2111.13693
apa: Locatello, F. (n.d.). Enforcing and discovering structure in machine learning.
arXiv. https://doi.org/10.48550/arXiv.2111.13693
chicago: Locatello, Francesco. “Enforcing and Discovering Structure in Machine Learning.”
ArXiv, n.d. https://doi.org/10.48550/arXiv.2111.13693.
ieee: F. Locatello, “Enforcing and discovering structure in machine learning,” arXiv.
.
ista: Locatello F. Enforcing and discovering structure in machine learning. arXiv,
2111.13693.
mla: Locatello, Francesco. “Enforcing and Discovering Structure in Machine Learning.”
ArXiv, 2111.13693, doi:10.48550/arXiv.2111.13693.
short: F. Locatello, ArXiv (n.d.).
date_created: 2023-08-22T14:23:35Z
date_published: 2021-11-26T00:00:00Z
date_updated: 2023-09-12T07:04:44Z
day: '26'
department:
- _id: FrLo
doi: 10.48550/arXiv.2111.13693
extern: '1'
external_id:
arxiv:
- '2111.13693'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2111.13693
month: '11'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
status: public
title: Enforcing and discovering structure in machine learning
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '9002'
abstract:
- lang: eng
text: ' We prove that, for the binary erasure channel (BEC), the polar-coding paradigm
gives rise to codes that not only approach the Shannon limit but do so under the
best possible scaling of their block length as a function of the gap to capacity.
This result exhibits the first known family of binary codes that attain both optimal
scaling and quasi-linear complexity of encoding and decoding. Our proof is based
on the construction and analysis of binary polar codes with large kernels. When
communicating reliably at rates within ε>0 of capacity, the code length n often
scales as O(1/εμ), where the constant μ is called the scaling exponent. It is
known that the optimal scaling exponent is μ=2, and it is achieved by random linear
codes. The scaling exponent of conventional polar codes (based on the 2×2 kernel)
on the BEC is μ=3.63. This falls far short of the optimal scaling guaranteed by
random codes. Our main contribution is a rigorous proof of the following result:
for the BEC, there exist ℓ×ℓ binary kernels, such that polar codes constructed
from these kernels achieve scaling exponent μ(ℓ) that tends to the optimal value
of 2 as ℓ grows. We furthermore characterize precisely how large ℓ needs to be
as a function of the gap between μ(ℓ) and 2. The resulting binary codes maintain
the recursive structure of conventional polar codes, and thereby achieve construction
complexity O(n) and encoding/decoding complexity O(nlogn).'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Arman
full_name: Fazeli, Arman
last_name: Fazeli
- first_name: Hamed
full_name: Hassani, Hamed
last_name: Hassani
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: Alexander
full_name: Vardy, Alexander
last_name: Vardy
citation:
ama: 'Fazeli A, Hassani H, Mondelli M, Vardy A. Binary linear codes with optimal
scaling: Polar codes with large kernels. IEEE Transactions on Information Theory.
2021;67(9):5693-5710. doi:10.1109/TIT.2020.3038806'
apa: 'Fazeli, A., Hassani, H., Mondelli, M., & Vardy, A. (2021). Binary linear
codes with optimal scaling: Polar codes with large kernels. IEEE Transactions
on Information Theory. IEEE. https://doi.org/10.1109/TIT.2020.3038806'
chicago: 'Fazeli, Arman, Hamed Hassani, Marco Mondelli, and Alexander Vardy. “Binary
Linear Codes with Optimal Scaling: Polar Codes with Large Kernels.” IEEE Transactions
on Information Theory. IEEE, 2021. https://doi.org/10.1109/TIT.2020.3038806.'
ieee: 'A. Fazeli, H. Hassani, M. Mondelli, and A. Vardy, “Binary linear codes with
optimal scaling: Polar codes with large kernels,” IEEE Transactions on Information
Theory, vol. 67, no. 9. IEEE, pp. 5693–5710, 2021.'
ista: 'Fazeli A, Hassani H, Mondelli M, Vardy A. 2021. Binary linear codes with
optimal scaling: Polar codes with large kernels. IEEE Transactions on Information
Theory. 67(9), 5693–5710.'
mla: 'Fazeli, Arman, et al. “Binary Linear Codes with Optimal Scaling: Polar Codes
with Large Kernels.” IEEE Transactions on Information Theory, vol. 67,
no. 9, IEEE, 2021, pp. 5693–710, doi:10.1109/TIT.2020.3038806.'
short: A. Fazeli, H. Hassani, M. Mondelli, A. Vardy, IEEE Transactions on Information
Theory 67 (2021) 5693–5710.
date_created: 2021-01-10T23:01:18Z
date_published: 2021-09-01T00:00:00Z
date_updated: 2024-03-07T12:18:50Z
day: '01'
department:
- _id: MaMo
doi: 10.1109/TIT.2020.3038806
external_id:
arxiv:
- '1711.01339'
intvolume: ' 67'
issue: '9'
language:
- iso: eng
month: '09'
oa_version: Preprint
page: 5693-5710
publication: IEEE Transactions on Information Theory
publication_identifier:
eissn:
- 1557-9654
issn:
- 0018-9448
publication_status: published
publisher: IEEE
quality_controlled: '1'
related_material:
record:
- id: '6665'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: 'Binary linear codes with optimal scaling: Polar codes with large kernels'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 67
year: '2021'
...
---
_id: '9005'
abstract:
- lang: eng
text: Studies on the experimental realization of two-dimensional anyons in terms
of quasiparticles have been restricted, so far, to only anyons on the plane. It
is known, however, that the geometry and topology of space can have significant
effects on quantum statistics for particles moving on it. Here, we have undertaken
the first step toward realizing the emerging fractional statistics for particles
restricted to move on the sphere instead of on the plane. We show that such a
model arises naturally in the context of quantum impurity problems. In particular,
we demonstrate a setup in which the lowest-energy spectrum of two linear bosonic
or fermionic molecules immersed in a quantum many-particle environment can coincide
with the anyonic spectrum on the sphere. This paves the way toward the experimental
realization of anyons on the sphere using molecular impurities. Furthermore, since
a change in the alignment of the molecules corresponds to the exchange of the
particles on the sphere, such a realization reveals a novel type of exclusion
principle for molecular impurities, which could also be of use as a powerful technique
to measure the statistics parameter. Finally, our approach opens up a simple numerical
route to investigate the spectra of many anyons on the sphere. Accordingly, we
present the spectrum of two anyons on the sphere in the presence of a Dirac monopole
field.
acknowledgement: "We are grateful to A. Ghazaryan for valuable discussions and also
thank the anonymous referees for comments. D.L. acknowledges financial support from
the G¨oran Gustafsson Foundation (grant no. 1804) and LMU Munich. M.L. gratefully
acknowledges financial support\r\nby the European Research Council (ERC) under the
European Union’s Horizon 2020 research and innovation programme (grant agreements
No 801770)."
article_number: '015301'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Morris
full_name: Brooks, Morris
id: B7ECF9FC-AA38-11E9-AC9A-0930E6697425
last_name: Brooks
orcid: 0000-0002-6249-0928
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: D.
full_name: Lundholm, D.
last_name: Lundholm
- first_name: Enderalp
full_name: Yakaboylu, Enderalp
id: 38CB71F6-F248-11E8-B48F-1D18A9856A87
last_name: Yakaboylu
orcid: 0000-0001-5973-0874
citation:
ama: Brooks M, Lemeshko M, Lundholm D, Yakaboylu E. Molecular impurities as a realization
of anyons on the two-sphere. Physical Review Letters. 2021;126(1). doi:10.1103/PhysRevLett.126.015301
apa: Brooks, M., Lemeshko, M., Lundholm, D., & Yakaboylu, E. (2021). Molecular
impurities as a realization of anyons on the two-sphere. Physical Review Letters.
American Physical Society. https://doi.org/10.1103/PhysRevLett.126.015301
chicago: Brooks, Morris, Mikhail Lemeshko, D. Lundholm, and Enderalp Yakaboylu.
“Molecular Impurities as a Realization of Anyons on the Two-Sphere.” Physical
Review Letters. American Physical Society, 2021. https://doi.org/10.1103/PhysRevLett.126.015301.
ieee: M. Brooks, M. Lemeshko, D. Lundholm, and E. Yakaboylu, “Molecular impurities
as a realization of anyons on the two-sphere,” Physical Review Letters,
vol. 126, no. 1. American Physical Society, 2021.
ista: Brooks M, Lemeshko M, Lundholm D, Yakaboylu E. 2021. Molecular impurities
as a realization of anyons on the two-sphere. Physical Review Letters. 126(1),
015301.
mla: Brooks, Morris, et al. “Molecular Impurities as a Realization of Anyons on
the Two-Sphere.” Physical Review Letters, vol. 126, no. 1, 015301, American
Physical Society, 2021, doi:10.1103/PhysRevLett.126.015301.
short: M. Brooks, M. Lemeshko, D. Lundholm, E. Yakaboylu, Physical Review Letters
126 (2021).
date_created: 2021-01-17T23:01:10Z
date_published: 2021-01-08T00:00:00Z
date_updated: 2023-08-07T13:32:10Z
day: '08'
department:
- _id: MiLe
- _id: RoSe
doi: 10.1103/PhysRevLett.126.015301
ec_funded: 1
external_id:
arxiv:
- '2009.05948'
isi:
- '000606325000003'
intvolume: ' 126'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2009.05948
month: '01'
oa: 1
oa_version: Preprint
project:
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication: Physical Review Letters
publication_identifier:
eissn:
- '10797114'
issn:
- '00319007'
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/dancing-molecules-and-two-dimensional-particles/
record:
- id: '12390'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Molecular impurities as a realization of anyons on the two-sphere
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 126
year: '2021'
...
---
_id: '9006'
abstract:
- lang: eng
text: Cytoplasm is a gel-like crowded environment composed of various macromolecules,
organelles, cytoskeletal networks, and cytosol. The structure of the cytoplasm
is highly organized and heterogeneous due to the crowding of its constituents
and their effective compartmentalization. In such an environment, the diffusive
dynamics of the molecules are restricted, an effect that is further amplified
by clustering and anchoring of molecules. Despite the crowded nature of the cytoplasm
at the microscopic scale, large-scale reorganization of the cytoplasm is essential
for important cellular functions, such as cell division and polarization. How
such mesoscale reorganization of the cytoplasm is achieved, especially for large
cells such as oocytes or syncytial tissues that can span hundreds of micrometers
in size, is only beginning to be understood. In this review, we will discuss recent
advances in elucidating the molecular, cellular, and biophysical mechanisms by
which the cytoskeleton drives cytoplasmic reorganization across different scales,
structures, and species.
acknowledgement: We would like to thank Justine Renno for illustrations and Edouard
Hannezo and members of the Heisenberg group for their comments on previous versions
of the manuscript.
article_processing_charge: No
article_type: original
author:
- first_name: Shayan
full_name: Shamipour, Shayan
id: 40B34FE2-F248-11E8-B48F-1D18A9856A87
last_name: Shamipour
- first_name: Silvia
full_name: Caballero Mancebo, Silvia
id: 2F1E1758-F248-11E8-B48F-1D18A9856A87
last_name: Caballero Mancebo
orcid: 0000-0002-5223-3346
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Shamipour S, Caballero Mancebo S, Heisenberg C-PJ. Cytoplasm’s got moves. Developmental
Cell. 2021;56(2):P213-226. doi:10.1016/j.devcel.2020.12.002
apa: Shamipour, S., Caballero Mancebo, S., & Heisenberg, C.-P. J. (2021). Cytoplasm’s
got moves. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2020.12.002
chicago: Shamipour, Shayan, Silvia Caballero Mancebo, and Carl-Philipp J Heisenberg.
“Cytoplasm’s Got Moves.” Developmental Cell. Elsevier, 2021. https://doi.org/10.1016/j.devcel.2020.12.002.
ieee: S. Shamipour, S. Caballero Mancebo, and C.-P. J. Heisenberg, “Cytoplasm’s
got moves,” Developmental Cell, vol. 56, no. 2. Elsevier, pp. P213-226,
2021.
ista: Shamipour S, Caballero Mancebo S, Heisenberg C-PJ. 2021. Cytoplasm’s got moves.
Developmental Cell. 56(2), P213-226.
mla: Shamipour, Shayan, et al. “Cytoplasm’s Got Moves.” Developmental Cell,
vol. 56, no. 2, Elsevier, 2021, pp. P213-226, doi:10.1016/j.devcel.2020.12.002.
short: S. Shamipour, S. Caballero Mancebo, C.-P.J. Heisenberg, Developmental Cell
56 (2021) P213-226.
date_created: 2021-01-17T23:01:10Z
date_published: 2021-01-25T00:00:00Z
date_updated: 2024-03-25T23:30:10Z
day: '25'
department:
- _id: CaHe
doi: 10.1016/j.devcel.2020.12.002
external_id:
isi:
- '000613273900009'
pmid:
- '33321104'
intvolume: ' 56'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.devcel.2020.12.002
month: '01'
oa: 1
oa_version: Published Version
page: P213-226
pmid: 1
publication: Developmental Cell
publication_identifier:
eissn:
- '18781551'
issn:
- '15345807'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '9623'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Cytoplasm's got moves
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 56
year: '2021'
...
---
_id: '9009'
abstract:
- lang: eng
text: Recent advancements in live cell imaging technologies have identified the
phenomenon of intracellular propagation of late apoptotic events, such as cytochrome
c release and caspase activation. The mechanism, prevalence, and speed of apoptosis
propagation remain unclear. Additionally, no studies have demonstrated propagation
of the pro-apoptotic protein, BAX. To evaluate the role of BAX in intracellular
apoptotic propagation, we used high speed live-cell imaging to visualize fluorescently
tagged-BAX recruitment to mitochondria in four immortalized cell lines. We show
that propagation of mitochondrial BAX recruitment occurs in parallel to cytochrome
c and SMAC/Diablo release and is affected by cellular morphology, such that cells
with processes are more likely to exhibit propagation. The initiation of propagation
events is most prevalent in the distal tips of processes, while the rate of propagation
is influenced by the 2-dimensional width of the process. Propagation was rarely
observed in the cell soma, which exhibited near synchronous recruitment of BAX.
Propagation velocity is not affected by mitochondrial volume in segments of processes,
but is negatively affected by mitochondrial density. There was no evidence of
a propagating wave of increased levels of intracellular calcium ions. Alternatively,
we did observe a uniform increase in superoxide build-up in cellular mitochondria,
which was released as a propagating wave simultaneously with the propagating recruitment
of BAX to the mitochondrial outer membrane.
acknowledgement: This work was supported by National Institute of Health grants R01
EY030123, P30 EY016665, and T32 GM081061, an unrestricted research grant from Research
to Prevent Blindness, Inc., and the Frederick A. Davis Endowment from the Department
of Ophthalmology and Visual Sciences at the University of Wisconsin-Madison.
article_processing_charge: No
article_type: original
author:
- first_name: Joshua A.
full_name: Grosser, Joshua A.
last_name: Grosser
- first_name: Margaret E
full_name: Maes, Margaret E
id: 3838F452-F248-11E8-B48F-1D18A9856A87
last_name: Maes
orcid: 0000-0001-9642-1085
- first_name: Robert W.
full_name: Nickells, Robert W.
last_name: Nickells
citation:
ama: Grosser JA, Maes ME, Nickells RW. Characteristics of intracellular propagation
of mitochondrial BAX recruitment during apoptosis. Apoptosis. 2021;26(2):132-145.
doi:10.1007/s10495-020-01654-w
apa: Grosser, J. A., Maes, M. E., & Nickells, R. W. (2021). Characteristics
of intracellular propagation of mitochondrial BAX recruitment during apoptosis.
Apoptosis. Springer Nature. https://doi.org/10.1007/s10495-020-01654-w
chicago: Grosser, Joshua A., Margaret E Maes, and Robert W. Nickells. “Characteristics
of Intracellular Propagation of Mitochondrial BAX Recruitment during Apoptosis.”
Apoptosis. Springer Nature, 2021. https://doi.org/10.1007/s10495-020-01654-w.
ieee: J. A. Grosser, M. E. Maes, and R. W. Nickells, “Characteristics of intracellular
propagation of mitochondrial BAX recruitment during apoptosis,” Apoptosis,
vol. 26, no. 2. Springer Nature, pp. 132–145, 2021.
ista: Grosser JA, Maes ME, Nickells RW. 2021. Characteristics of intracellular propagation
of mitochondrial BAX recruitment during apoptosis. Apoptosis. 26(2), 132–145.
mla: Grosser, Joshua A., et al. “Characteristics of Intracellular Propagation of
Mitochondrial BAX Recruitment during Apoptosis.” Apoptosis, vol. 26, no.
2, Springer Nature, 2021, pp. 132–45, doi:10.1007/s10495-020-01654-w.
short: J.A. Grosser, M.E. Maes, R.W. Nickells, Apoptosis 26 (2021) 132–145.
date_created: 2021-01-17T23:01:11Z
date_published: 2021-02-01T00:00:00Z
date_updated: 2023-08-07T13:32:40Z
day: '01'
department:
- _id: SaSi
doi: 10.1007/s10495-020-01654-w
external_id:
isi:
- '000606722600001'
pmid:
- '33426618'
intvolume: ' 26'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8082518/
month: '02'
oa: 1
oa_version: Submitted Version
page: 132-145
pmid: 1
publication: Apoptosis
publication_identifier:
eissn:
- 1573-675X
issn:
- 1360-8185
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Characteristics of intracellular propagation of mitochondrial BAX recruitment
during apoptosis
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 26
year: '2021'
...
---
_id: '9010'
abstract:
- lang: eng
text: Availability of the essential macronutrient nitrogen in soil plays a critical
role in plant growth, development, and impacts agricultural productivity. Plants
have evolved different strategies for sensing and responding to heterogeneous
nitrogen distribution. Modulation of root system architecture, including primary
root growth and branching, is among the most essential plant adaptions to ensure
adequate nitrogen acquisition. However, the immediate molecular pathways coordinating
the adjustment of root growth in response to distinct nitrogen sources, such as
nitrate or ammonium, are poorly understood. Here, we show that growth as manifested
by cell division and elongation is synchronized by coordinated auxin flux between
two adjacent outer tissue layers of the root. This coordination is achieved by
nitrate‐dependent dephosphorylation of the PIN2 auxin efflux carrier at a previously
uncharacterized phosphorylation site, leading to subsequent PIN2 lateralization
and thereby regulating auxin flow between adjacent tissues. A dynamic computer
model based on our experimental data successfully recapitulates experimental observations.
Our study provides mechanistic insights broadening our understanding of root growth
mechanisms in dynamic environments.
acknowledged_ssus:
- _id: Bio
acknowledgement: 'We acknowledge Gergely Molnar for critical reading of the manuscript,
Alexander Johnson for language editing and Yulija Salanenka for technical assistance.
Work in the Benkova laboratory was supported by the Austrian Science Fund (FWF01_I1774S)
to KO, RA and EB. Work in the Benkova laboratory was supported by the Austrian Science
Fund (FWF01_I1774S) to KO, RA and EB and by the DOC Fellowship Programme of the
AustrianAcademy of Sciences (25008) to C.A. Work in the Wabnik laboratory was supported
by the Programa de Atraccion de Talento 2017 (Comunidad deMadrid, 2017-T1/BIO-5654
to K.W.), Severo Ochoa Programme for Centres of Excellence in R&D from the Agencia
Estatal de Investigacion of Spain (grantSEV-2016-0672 (2017-2021) to K.W. via the
CBGP) and Programa Estatal de Generacion del Conocimiento y Fortalecimiento Científico
y Tecnologico del Sistema de I+D+I 2019 (PGC2018-093387-A-I00) from MICIU (to K.W.).
M.M.was supported by a postdoctoral contract associated to SEV-2016-0672.We acknowledge
the Bioimaging Facility in IST-Austria and the Advanced Microscopy Facility of the
Vienna Bio Center Core Facilities, member of the Vienna Bio Center Austria, for
use of the OMX v43D SIM microscope. AJ was supported by the Austrian Science Fund
(FWF): I03630 to J.F'
article_number: e106862
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Krisztina
full_name: Ötvös, Krisztina
id: 29B901B0-F248-11E8-B48F-1D18A9856A87
last_name: Ötvös
orcid: 0000-0002-5503-4983
- first_name: Marco
full_name: Marconi, Marco
last_name: Marconi
- first_name: Andrea
full_name: Vega, Andrea
last_name: Vega
- first_name: Jose
full_name: O’Brien, Jose
last_name: O’Brien
- first_name: Alexander J
full_name: Johnson, Alexander J
id: 46A62C3A-F248-11E8-B48F-1D18A9856A87
last_name: Johnson
orcid: 0000-0002-2739-8843
- first_name: Rashed
full_name: Abualia, Rashed
id: 4827E134-F248-11E8-B48F-1D18A9856A87
last_name: Abualia
orcid: 0000-0002-9357-9415
- first_name: Livio
full_name: Antonielli, Livio
last_name: Antonielli
- first_name: Juan C
full_name: Montesinos López, Juan C
id: 310A8E3E-F248-11E8-B48F-1D18A9856A87
last_name: Montesinos López
orcid: 0000-0001-9179-6099
- first_name: Yuzhou
full_name: Zhang, Yuzhou
id: 3B6137F2-F248-11E8-B48F-1D18A9856A87
last_name: Zhang
orcid: 0000-0003-2627-6956
- first_name: Shutang
full_name: Tan, Shutang
id: 2DE75584-F248-11E8-B48F-1D18A9856A87
last_name: Tan
orcid: 0000-0002-0471-8285
- first_name: Candela
full_name: Cuesta, Candela
id: 33A3C818-F248-11E8-B48F-1D18A9856A87
last_name: Cuesta
orcid: 0000-0003-1923-2410
- first_name: Christina
full_name: Artner, Christina
id: 45DF286A-F248-11E8-B48F-1D18A9856A87
last_name: Artner
- first_name: Eleonore
full_name: Bouguyon, Eleonore
last_name: Bouguyon
- first_name: Alain
full_name: Gojon, Alain
last_name: Gojon
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Rodrigo A.
full_name: Gutiérrez, Rodrigo A.
last_name: Gutiérrez
- first_name: Krzysztof T
full_name: Wabnik, Krzysztof T
id: 4DE369A4-F248-11E8-B48F-1D18A9856A87
last_name: Wabnik
orcid: 0000-0001-7263-0560
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Ötvös K, Marconi M, Vega A, et al. Modulation of plant root growth by nitrogen
source-defined regulation of polar auxin transport. EMBO Journal. 2021;40(3).
doi:10.15252/embj.2020106862
apa: Ötvös, K., Marconi, M., Vega, A., O’Brien, J., Johnson, A. J., Abualia, R.,
… Benková, E. (2021). Modulation of plant root growth by nitrogen source-defined
regulation of polar auxin transport. EMBO Journal. Embo Press. https://doi.org/10.15252/embj.2020106862
chicago: Ötvös, Krisztina, Marco Marconi, Andrea Vega, Jose O’Brien, Alexander J
Johnson, Rashed Abualia, Livio Antonielli, et al. “Modulation of Plant Root Growth
by Nitrogen Source-Defined Regulation of Polar Auxin Transport.” EMBO Journal.
Embo Press, 2021. https://doi.org/10.15252/embj.2020106862.
ieee: K. Ötvös et al., “Modulation of plant root growth by nitrogen source-defined
regulation of polar auxin transport,” EMBO Journal, vol. 40, no. 3. Embo
Press, 2021.
ista: Ötvös K, Marconi M, Vega A, O’Brien J, Johnson AJ, Abualia R, Antonielli L,
Montesinos López JC, Zhang Y, Tan S, Cuesta C, Artner C, Bouguyon E, Gojon A,
Friml J, Gutiérrez RA, Wabnik KT, Benková E. 2021. Modulation of plant root growth
by nitrogen source-defined regulation of polar auxin transport. EMBO Journal.
40(3), e106862.
mla: Ötvös, Krisztina, et al. “Modulation of Plant Root Growth by Nitrogen Source-Defined
Regulation of Polar Auxin Transport.” EMBO Journal, vol. 40, no. 3, e106862,
Embo Press, 2021, doi:10.15252/embj.2020106862.
short: K. Ötvös, M. Marconi, A. Vega, J. O’Brien, A.J. Johnson, R. Abualia, L. Antonielli,
J.C. Montesinos López, Y. Zhang, S. Tan, C. Cuesta, C. Artner, E. Bouguyon, A.
Gojon, J. Friml, R.A. Gutiérrez, K.T. Wabnik, E. Benková, EMBO Journal 40 (2021).
date_created: 2021-01-17T23:01:12Z
date_published: 2021-02-01T00:00:00Z
date_updated: 2024-03-25T23:30:22Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
- _id: EvBe
doi: 10.15252/embj.2020106862
external_id:
isi:
- '000604645600001'
pmid:
- ' 33399250'
file:
- access_level: open_access
checksum: dc55c900f3b061d6c2790b8813d759a3
content_type: application/pdf
creator: dernst
date_created: 2021-02-11T12:28:29Z
date_updated: 2021-02-11T12:28:29Z
file_id: '9110'
file_name: 2021_Embo_Otvos.pdf
file_size: 2358617
relation: main_file
success: 1
file_date_updated: 2021-02-11T12:28:29Z
has_accepted_license: '1'
intvolume: ' 40'
isi: 1
issue: '3'
language:
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month: '02'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2542D156-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I 1774-B16
name: Hormone cross-talk drives nutrient dependent plant development
- _id: 2685A872-B435-11E9-9278-68D0E5697425
name: Hormonal regulation of plant adaptive responses to environmental signals
- _id: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
publication: EMBO Journal
publication_identifier:
eissn:
- '14602075'
issn:
- '02614189'
publication_status: published
publisher: Embo Press
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/a-plants-way-to-its-favorite-food/
record:
- id: '10303'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Modulation of plant root growth by nitrogen source-defined regulation of polar
auxin transport
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 40
year: '2021'
...
---
_id: '9020'
abstract:
- lang: eng
text: 'We study dynamics and thermodynamics of ion transport in narrow, water-filled
channels, considered as effective 1D Coulomb systems. The long range nature of
the inter-ion interactions comes about due to the dielectric constants mismatch
between the water and the surrounding medium, confining the electric filed to
stay mostly within the water-filled channel. Statistical mechanics of such Coulomb
systems is dominated by entropic effects which may be accurately accounted for
by mapping onto an effective quantum mechanics. In presence of multivalent ions
the corresponding quantum mechanics appears to be non-Hermitian. In this review
we discuss a framework for semiclassical calculations for the effective non-Hermitian
Hamiltonians. Non-Hermiticity elevates WKB action integrals from the real line
to closed cycles on a complex Riemann surfaces where direct calculations are not
attainable. We circumvent this issue by applying tools from algebraic topology,
such as the Picard-Fuchs equation. We discuss how its solutions relate to the
thermodynamics and correlation functions of multivalent solutions within narrow,
water-filled channels. '
acknowledgement: "A.K. was supported by NSF grants DMR-2037654. T.G. acknowledges
funding from the Institute of Science and Technology (IST) Austria, and from the
European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie
Grant Agreement No. 754411.\r\nWe are indebted to Boris Shklovskii for introducing
us to the problem, and Alexander Gorsky and Peter Koroteev for introducing us to
the Picard-Fuchs methods. A very special thanks goes to Michael Janas for several
years of excellent collaboration on these topics. TG thanks Michael Kreshchuk for
introduction to the exact WKB method and great collaboration on related projects.
Figure 3 and Figure 4 are reproduced from Reference [25] with friendly permission
by the Russian Academy of Sciences. Figure 2, Figure 4, Figure 5, Figure 6, and
Figure 8 are reproduced from Reference [26] with friendly permission by IOP Publishing."
article_number: e23010125
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Tobias
full_name: Gulden, Tobias
id: 1083E038-9F73-11E9-A4B5-532AE6697425
last_name: Gulden
orcid: 0000-0001-6814-7541
- first_name: Alex
full_name: Kamenev, Alex
last_name: Kamenev
citation:
ama: Gulden T, Kamenev A. Dynamics of ion channels via non-hermitian quantum mechanics.
Entropy. 2021;23(1). doi:10.3390/e23010125
apa: Gulden, T., & Kamenev, A. (2021). Dynamics of ion channels via non-hermitian
quantum mechanics. Entropy. MDPI. https://doi.org/10.3390/e23010125
chicago: Gulden, Tobias, and Alex Kamenev. “Dynamics of Ion Channels via Non-Hermitian
Quantum Mechanics.” Entropy. MDPI, 2021. https://doi.org/10.3390/e23010125.
ieee: T. Gulden and A. Kamenev, “Dynamics of ion channels via non-hermitian quantum
mechanics,” Entropy, vol. 23, no. 1. MDPI, 2021.
ista: Gulden T, Kamenev A. 2021. Dynamics of ion channels via non-hermitian quantum
mechanics. Entropy. 23(1), e23010125.
mla: Gulden, Tobias, and Alex Kamenev. “Dynamics of Ion Channels via Non-Hermitian
Quantum Mechanics.” Entropy, vol. 23, no. 1, e23010125, MDPI, 2021, doi:10.3390/e23010125.
short: T. Gulden, A. Kamenev, Entropy 23 (2021).
date_created: 2021-01-19T11:12:06Z
date_published: 2021-01-19T00:00:00Z
date_updated: 2023-08-07T13:34:18Z
day: '19'
ddc:
- '530'
department:
- _id: MaSe
doi: 10.3390/e23010125
ec_funded: 1
external_id:
arxiv:
- '2012.01390'
isi:
- '000610122000001'
file:
- access_level: open_access
checksum: 6cd0e706156827c45c740534bd32c179
content_type: application/pdf
creator: tgulden
date_created: 2021-01-19T11:11:14Z
date_updated: 2021-01-19T11:11:14Z
file_id: '9021'
file_name: Final published paper.pdf
file_size: 981285
relation: main_file
file_date_updated: 2021-01-19T11:11:14Z
has_accepted_license: '1'
intvolume: ' 23'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Entropy
publication_identifier:
eissn:
- 1099-4300
publication_status: published
publisher: MDPI
quality_controlled: '1'
status: public
title: Dynamics of ion channels via non-hermitian quantum mechanics
tmp:
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user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 23
year: '2021'
...
---
_id: '9022'
abstract:
- lang: eng
text: "In the first part of the thesis we consider Hermitian random matrices. Firstly,
we consider sample covariance matrices XX∗ with X having independent identically
distributed (i.i.d.) centred entries. We prove a Central Limit Theorem for differences
of linear statistics of XX∗ and its minor after removing the first column of X.
Secondly, we consider Wigner-type matrices and prove that the eigenvalue statistics
near cusp singularities of the limiting density of states are universal and that
they form a Pearcey process. Since the limiting eigenvalue distribution admits
only square root (edge) and cubic root (cusp) singularities, this concludes the
third and last remaining case of the Wigner-Dyson-Mehta universality conjecture.
The main technical ingredients are an optimal local law at the cusp, and the proof
of the fast relaxation to equilibrium of the Dyson Brownian motion in the cusp
regime.\r\nIn the second part we consider non-Hermitian matrices X with centred
i.i.d. entries. We normalise the entries of X to have variance N −1. It is well
known that the empirical eigenvalue density converges to the uniform distribution
on the unit disk (circular law). In the first project, we prove universality of
the local eigenvalue statistics close to the edge of the spectrum. This is the
non-Hermitian analogue of the TracyWidom universality at the Hermitian edge. Technically
we analyse the evolution of the spectral distribution of X along the Ornstein-Uhlenbeck
flow for very long time\r\n(up to t = +∞). In the second project, we consider
linear statistics of eigenvalues for macroscopic test functions f in the Sobolev
space H2+ϵ and prove their convergence to the projection of the Gaussian Free
Field on the unit disk. We prove this result for non-Hermitian matrices with real
or complex entries. The main technical ingredients are: (i) local law for products
of two resolvents at different spectral parameters, (ii) analysis of correlated
Dyson Brownian motions.\r\nIn the third and final part we discuss the mathematically
rigorous application of supersymmetric techniques (SUSY ) to give a lower tail
estimate of the lowest singular value of X − z, with z ∈ C. More precisely, we
use superbosonisation formula to give an integral representation of the resolvent
of (X − z)(X − z)∗ which reduces to two and three contour integrals in the complex
and real case, respectively. The rigorous analysis of these integrals is quite
challenging since simple saddle point analysis cannot be applied (the main contribution
comes from a non-trivial manifold). Our result\r\nimproves classical smoothing
inequalities in the regime |z| ≈ 1; this result is essential to prove edge universality
for i.i.d. non-Hermitian matrices."
acknowledgement: I gratefully acknowledge the financial support from the European
Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie
Grant Agreement No. 665385 and my advisor’s ERC Advanced Grant No. 338804.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Giorgio
full_name: Cipolloni, Giorgio
id: 42198EFA-F248-11E8-B48F-1D18A9856A87
last_name: Cipolloni
orcid: 0000-0002-4901-7992
citation:
ama: Cipolloni G. Fluctuations in the spectrum of random matrices. 2021. doi:10.15479/AT:ISTA:9022
apa: Cipolloni, G. (2021). Fluctuations in the spectrum of random matrices.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9022
chicago: Cipolloni, Giorgio. “Fluctuations in the Spectrum of Random Matrices.”
Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9022.
ieee: G. Cipolloni, “Fluctuations in the spectrum of random matrices,” Institute
of Science and Technology Austria, 2021.
ista: Cipolloni G. 2021. Fluctuations in the spectrum of random matrices. Institute
of Science and Technology Austria.
mla: Cipolloni, Giorgio. Fluctuations in the Spectrum of Random Matrices.
Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9022.
short: G. Cipolloni, Fluctuations in the Spectrum of Random Matrices, Institute
of Science and Technology Austria, 2021.
date_created: 2021-01-21T18:16:54Z
date_published: 2021-01-25T00:00:00Z
date_updated: 2023-09-07T13:29:32Z
day: '25'
ddc:
- '510'
degree_awarded: PhD
department:
- _id: GradSch
- _id: LaEr
doi: 10.15479/AT:ISTA:9022
ec_funded: 1
file:
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creator: gcipollo
date_created: 2021-01-25T14:19:03Z
date_updated: 2021-01-25T14:19:03Z
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file_name: thesis.pdf
file_size: 4127796
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content_type: application/zip
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date_created: 2021-01-25T14:19:10Z
date_updated: 2021-01-25T14:19:10Z
file_id: '9044'
file_name: Thesis_files.zip
file_size: 12775206
relation: source_file
file_date_updated: 2021-01-25T14:19:10Z
has_accepted_license: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: '380'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
title: Fluctuations in the spectrum of random matrices
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '9036'
abstract:
- lang: eng
text: In this short note, we prove that the square root of the quantum Jensen-Shannon
divergence is a true metric on the cone of positive matrices, and hence in particular
on the quantum state space.
acknowledgement: D. Virosztek was supported by the European Union's Horizon 2020 research
and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 846294,
and partially supported by the Hungarian National Research, Development and Innovation
Office (NKFIH) via grants no. K124152, and no. KH129601.
article_number: '107595'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Daniel
full_name: Virosztek, Daniel
id: 48DB45DA-F248-11E8-B48F-1D18A9856A87
last_name: Virosztek
orcid: 0000-0003-1109-5511
citation:
ama: Virosztek D. The metric property of the quantum Jensen-Shannon divergence.
Advances in Mathematics. 2021;380(3). doi:10.1016/j.aim.2021.107595
apa: Virosztek, D. (2021). The metric property of the quantum Jensen-Shannon divergence.
Advances in Mathematics. Elsevier. https://doi.org/10.1016/j.aim.2021.107595
chicago: Virosztek, Daniel. “The Metric Property of the Quantum Jensen-Shannon Divergence.”
Advances in Mathematics. Elsevier, 2021. https://doi.org/10.1016/j.aim.2021.107595.
ieee: D. Virosztek, “The metric property of the quantum Jensen-Shannon divergence,”
Advances in Mathematics, vol. 380, no. 3. Elsevier, 2021.
ista: Virosztek D. 2021. The metric property of the quantum Jensen-Shannon divergence.
Advances in Mathematics. 380(3), 107595.
mla: Virosztek, Daniel. “The Metric Property of the Quantum Jensen-Shannon Divergence.”
Advances in Mathematics, vol. 380, no. 3, 107595, Elsevier, 2021, doi:10.1016/j.aim.2021.107595.
short: D. Virosztek, Advances in Mathematics 380 (2021).
date_created: 2021-01-22T17:55:17Z
date_published: 2021-03-26T00:00:00Z
date_updated: 2023-08-07T13:34:48Z
day: '26'
department:
- _id: LaEr
doi: 10.1016/j.aim.2021.107595
ec_funded: 1
external_id:
arxiv:
- '1910.10447'
isi:
- '000619676100035'
intvolume: ' 380'
isi: 1
issue: '3'
keyword:
- General Mathematics
language:
- iso: eng
main_file_link:
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url: https://arxiv.org/abs/1910.10447
month: '03'
oa: 1
oa_version: Preprint
project:
- _id: 26A455A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '846294'
name: Geometric study of Wasserstein spaces and free probability
publication: Advances in Mathematics
publication_identifier:
issn:
- 0001-8708
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: The metric property of the quantum Jensen-Shannon divergence
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 380
year: '2021'
...
---
_id: '9037'
abstract:
- lang: eng
text: "We continue our study of ‘no‐dimension’ analogues of basic theorems in combinatorial
and convex geometry in Banach spaces. We generalize some results of the paper
(Adiprasito, Bárány and Mustafa, ‘Theorems of Carathéodory, Helly, and Tverberg
without dimension’, Proceedings of the Thirtieth Annual ACM‐SIAM Symposium on
Discrete Algorithms (Society for Industrial and Applied Mathematics, San Diego,
California, 2019) 2350–2360) and prove no‐dimension versions of the colored Tverberg
theorem, the selection lemma and the weak \U0001D700 ‐net theorem in Banach spaces
of type \U0001D45D>1 . To prove these results, we use the original ideas of Adiprasito,
Bárány and Mustafa for the Euclidean case, our no‐dimension version of the Radon
theorem and slightly modified version of the celebrated Maurey lemma."
acknowledgement: "I wish to thank Imre Bárány for bringing the problem to my attention.
I am grateful to Marton Naszódi and Igor Tsiutsiurupa for useful remarks and help
with the text.\r\nThe author acknowledges the financial support from the Ministry
of Educational and Science of the Russian Federation in the framework of MegaGrant
no 075‐15‐2019‐1926."
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Grigory
full_name: Ivanov, Grigory
id: 87744F66-5C6F-11EA-AFE0-D16B3DDC885E
last_name: Ivanov
citation:
ama: Ivanov G. No-dimension Tverberg’s theorem and its corollaries in Banach spaces
of type p. Bulletin of the London Mathematical Society. 2021;53(2):631-641.
doi:10.1112/blms.12449
apa: Ivanov, G. (2021). No-dimension Tverberg’s theorem and its corollaries in Banach
spaces of type p. Bulletin of the London Mathematical Society. London Mathematical
Society. https://doi.org/10.1112/blms.12449
chicago: Ivanov, Grigory. “No-Dimension Tverberg’s Theorem and Its Corollaries in
Banach Spaces of Type P.” Bulletin of the London Mathematical Society.
London Mathematical Society, 2021. https://doi.org/10.1112/blms.12449.
ieee: G. Ivanov, “No-dimension Tverberg’s theorem and its corollaries in Banach
spaces of type p,” Bulletin of the London Mathematical Society, vol. 53,
no. 2. London Mathematical Society, pp. 631–641, 2021.
ista: Ivanov G. 2021. No-dimension Tverberg’s theorem and its corollaries in Banach
spaces of type p. Bulletin of the London Mathematical Society. 53(2), 631–641.
mla: Ivanov, Grigory. “No-Dimension Tverberg’s Theorem and Its Corollaries in Banach
Spaces of Type P.” Bulletin of the London Mathematical Society, vol. 53,
no. 2, London Mathematical Society, 2021, pp. 631–41, doi:10.1112/blms.12449.
short: G. Ivanov, Bulletin of the London Mathematical Society 53 (2021) 631–641.
date_created: 2021-01-24T23:01:08Z
date_published: 2021-04-01T00:00:00Z
date_updated: 2023-08-07T13:35:20Z
day: '01'
ddc:
- '510'
department:
- _id: UlWa
doi: 10.1112/blms.12449
external_id:
arxiv:
- '1912.08561'
isi:
- '000607265100001'
file:
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checksum: e6ceaa6470d835eb4c211cbdd38fdfd1
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date_updated: 2021-08-06T09:59:45Z
file_id: '9796'
file_name: 2021_BLMS_Ivanov.pdf
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language:
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license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '04'
oa: 1
oa_version: Published Version
page: 631-641
publication: Bulletin of the London Mathematical Society
publication_identifier:
eissn:
- '14692120'
issn:
- '00246093'
publication_status: published
publisher: London Mathematical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: No-dimension Tverberg's theorem and its corollaries in Banach spaces of type
p
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volume: 53
year: '2021'
...
---
_id: '9046'
acknowledgement: Our work was supported by the Swedish Research Council (grant 2017-01527)
to DIA
article_number: e1009172
article_processing_charge: No
article_type: original
author:
- first_name: Roderich
full_name: Römhild, Roderich
id: 68E56E44-62B0-11EA-B963-444F3DDC885E
last_name: Römhild
orcid: 0000-0001-9480-5261
- first_name: Dan I.
full_name: Andersson, Dan I.
last_name: Andersson
citation:
ama: Römhild R, Andersson DI. Mechanisms and therapeutic potential of collateral
sensitivity to antibiotics. PLoS Pathogens. 2021;17(1). doi:10.1371/journal.ppat.1009172
apa: Römhild, R., & Andersson, D. I. (2021). Mechanisms and therapeutic potential
of collateral sensitivity to antibiotics. PLoS Pathogens. Public Library
of Science. https://doi.org/10.1371/journal.ppat.1009172
chicago: Römhild, Roderich, and Dan I. Andersson. “Mechanisms and Therapeutic Potential
of Collateral Sensitivity to Antibiotics.” PLoS Pathogens. Public Library
of Science, 2021. https://doi.org/10.1371/journal.ppat.1009172.
ieee: R. Römhild and D. I. Andersson, “Mechanisms and therapeutic potential of collateral
sensitivity to antibiotics,” PLoS Pathogens, vol. 17, no. 1. Public Library
of Science, 2021.
ista: Römhild R, Andersson DI. 2021. Mechanisms and therapeutic potential of collateral
sensitivity to antibiotics. PLoS Pathogens. 17(1), e1009172.
mla: Römhild, Roderich, and Dan I. Andersson. “Mechanisms and Therapeutic Potential
of Collateral Sensitivity to Antibiotics.” PLoS Pathogens, vol. 17, no.
1, e1009172, Public Library of Science, 2021, doi:10.1371/journal.ppat.1009172.
short: R. Römhild, D.I. Andersson, PLoS Pathogens 17 (2021).
date_created: 2021-01-31T23:01:21Z
date_published: 2021-01-14T00:00:00Z
date_updated: 2023-08-07T13:36:55Z
day: '14'
ddc:
- '570'
department:
- _id: CaGu
doi: 10.1371/journal.ppat.1009172
external_id:
isi:
- '000610190400007'
pmid:
- '33444399'
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- access_level: open_access
checksum: d745d7f8fcbb9b95fea16a36f94dee31
content_type: application/pdf
creator: dernst
date_created: 2021-02-03T12:13:03Z
date_updated: 2021-02-03T12:13:03Z
file_id: '9070'
file_name: 2021_PlosPathogens_Roemhild.pdf
file_size: 570066
relation: main_file
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file_date_updated: 2021-02-03T12:13:03Z
has_accepted_license: '1'
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isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS Pathogens
publication_identifier:
eissn:
- '15537374'
issn:
- '15537366'
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanisms and therapeutic potential of collateral sensitivity to antibiotics
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 17
year: '2021'
...
---
_id: '9047'
abstract:
- lang: eng
text: This work analyzes the latency of the simplified successive cancellation (SSC)
decoding scheme for polar codes proposed by Alamdar-Yazdi and Kschischang. It
is shown that, unlike conventional successive cancellation decoding, where latency
is linear in the block length, the latency of SSC decoding is sublinear. More
specifically, the latency of SSC decoding is O(N1−1/μ) , where N is the block
length and μ is the scaling exponent of the channel, which captures the speed
of convergence of the rate to capacity. Numerical results demonstrate the tightness
of the bound and show that most of the latency reduction arises from the parallel
decoding of subcodes of rate 0 or 1.
acknowledgement: M. Mondelli was partially supported by grants NSF DMS-1613091, CCF-1714305,
IIS-1741162, and ONR N00014-18-1-2729. S. A. Hashemi is supported by a Postdoctoral
Fellowship from the Natural Sciences and Engineering Research Council of Canada
(NSERC) and by Huawei. The authors would like to thank the anonymous reviewers for
their comments that helped improving the quality of the manuscript.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: Seyyed Ali
full_name: Hashemi, Seyyed Ali
last_name: Hashemi
- first_name: John M.
full_name: Cioffi, John M.
last_name: Cioffi
- first_name: Andrea
full_name: Goldsmith, Andrea
last_name: Goldsmith
citation:
ama: Mondelli M, Hashemi SA, Cioffi JM, Goldsmith A. Sublinear latency for simplified
successive cancellation decoding of polar codes. IEEE Transactions on Wireless
Communications. 2021;20(1):18-27. doi:10.1109/TWC.2020.3022922
apa: Mondelli, M., Hashemi, S. A., Cioffi, J. M., & Goldsmith, A. (2021). Sublinear
latency for simplified successive cancellation decoding of polar codes. IEEE
Transactions on Wireless Communications. IEEE. https://doi.org/10.1109/TWC.2020.3022922
chicago: Mondelli, Marco, Seyyed Ali Hashemi, John M. Cioffi, and Andrea Goldsmith.
“Sublinear Latency for Simplified Successive Cancellation Decoding of Polar Codes.”
IEEE Transactions on Wireless Communications. IEEE, 2021. https://doi.org/10.1109/TWC.2020.3022922.
ieee: M. Mondelli, S. A. Hashemi, J. M. Cioffi, and A. Goldsmith, “Sublinear latency
for simplified successive cancellation decoding of polar codes,” IEEE Transactions
on Wireless Communications, vol. 20, no. 1. IEEE, pp. 18–27, 2021.
ista: Mondelli M, Hashemi SA, Cioffi JM, Goldsmith A. 2021. Sublinear latency for
simplified successive cancellation decoding of polar codes. IEEE Transactions
on Wireless Communications. 20(1), 18–27.
mla: Mondelli, Marco, et al. “Sublinear Latency for Simplified Successive Cancellation
Decoding of Polar Codes.” IEEE Transactions on Wireless Communications,
vol. 20, no. 1, IEEE, 2021, pp. 18–27, doi:10.1109/TWC.2020.3022922.
short: M. Mondelli, S.A. Hashemi, J.M. Cioffi, A. Goldsmith, IEEE Transactions on
Wireless Communications 20 (2021) 18–27.
date_created: 2021-01-31T23:01:21Z
date_published: 2021-01-01T00:00:00Z
date_updated: 2023-08-07T13:36:25Z
day: '01'
department:
- _id: MaMo
doi: 10.1109/TWC.2020.3022922
external_id:
arxiv:
- '1909.04892'
isi:
- '000607808800002'
intvolume: ' 20'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1909.04892
month: '01'
oa: 1
oa_version: Preprint
page: 18-27
publication: IEEE Transactions on Wireless Communications
publication_identifier:
eissn:
- '15582248'
issn:
- '15361276'
publication_status: published
publisher: IEEE
quality_controlled: '1'
related_material:
record:
- id: '8536'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Sublinear latency for simplified successive cancellation decoding of polar
codes
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 20
year: '2021'
...
---
_id: '9048'
abstract:
- lang: eng
text: The analogy between an equilibrium partition function and the return probability
in many-body unitary dynamics has led to the concept of dynamical quantum phase
transition (DQPT). DQPTs are defined by nonanalyticities in the return amplitude
and are present in many models. In some cases, DQPTs can be related to equilibrium
concepts, such as order parameters, yet their universal description is an open
question. In this Letter, we provide first steps toward a classification of DQPTs
by using a matrix product state description of unitary dynamics in the thermodynamic
limit. This allows us to distinguish the two limiting cases of “precession” and
“entanglement” DQPTs, which are illustrated using an analytical description in
the quantum Ising model. While precession DQPTs are characterized by a large entanglement
gap and are semiclassical in their nature, entanglement DQPTs occur near avoided
crossings in the entanglement spectrum and can be distinguished by a complex pattern
of nonlocal correlations. We demonstrate the existence of precession and entanglement
DQPTs beyond Ising models, discuss observables that can distinguish them, and
relate their interplay to complex DQPT phenomenology.
acknowledgement: "S. D. N. acknowledges funding from the Institute of Science and
Technology (IST) Austria and from the European Union’s Horizon 2020 Research and
Innovation Programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.
A. M. and M. S. were supported by the European Research Council (ERC) under the
European Union’s Horizon 2020 Research and\r\nInnovation Programme (Grant Agreement
No. 850899)."
article_number: '040602'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Stefano
full_name: De Nicola, Stefano
id: 42832B76-F248-11E8-B48F-1D18A9856A87
last_name: De Nicola
orcid: 0000-0002-4842-6671
- first_name: Alexios
full_name: Michailidis, Alexios
id: 36EBAD38-F248-11E8-B48F-1D18A9856A87
last_name: Michailidis
orcid: 0000-0002-8443-1064
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: De Nicola S, Michailidis A, Serbyn M. Entanglement view of dynamical quantum
phase transitions. Physical Review Letters. 2021;126(4). doi:10.1103/physrevlett.126.040602
apa: De Nicola, S., Michailidis, A., & Serbyn, M. (2021). Entanglement view
of dynamical quantum phase transitions. Physical Review Letters. American
Physical Society. https://doi.org/10.1103/physrevlett.126.040602
chicago: De Nicola, Stefano, Alexios Michailidis, and Maksym Serbyn. “Entanglement
View of Dynamical Quantum Phase Transitions.” Physical Review Letters.
American Physical Society, 2021. https://doi.org/10.1103/physrevlett.126.040602.
ieee: S. De Nicola, A. Michailidis, and M. Serbyn, “Entanglement view of dynamical
quantum phase transitions,” Physical Review Letters, vol. 126, no. 4. American
Physical Society, 2021.
ista: De Nicola S, Michailidis A, Serbyn M. 2021. Entanglement view of dynamical
quantum phase transitions. Physical Review Letters. 126(4), 040602.
mla: De Nicola, Stefano, et al. “Entanglement View of Dynamical Quantum Phase Transitions.”
Physical Review Letters, vol. 126, no. 4, 040602, American Physical Society,
2021, doi:10.1103/physrevlett.126.040602.
short: S. De Nicola, A. Michailidis, M. Serbyn, Physical Review Letters 126 (2021).
date_created: 2021-02-01T09:20:00Z
date_published: 2021-01-29T00:00:00Z
date_updated: 2023-09-05T12:08:58Z
day: '29'
ddc:
- '530'
department:
- _id: MaSe
doi: 10.1103/physrevlett.126.040602
ec_funded: 1
external_id:
arxiv:
- '2008.04894'
isi:
- '000613148200001'
file:
- access_level: open_access
checksum: d9acbc502390ed7a97e631d23ae19ecd
content_type: application/pdf
creator: dernst
date_created: 2021-02-03T12:47:04Z
date_updated: 2021-02-03T12:47:04Z
file_id: '9074'
file_name: 2021_PhysicalRevLett_DeNicola.pdf
file_size: 398075
relation: main_file
success: 1
file_date_updated: 2021-02-03T12:47:04Z
has_accepted_license: '1'
intvolume: ' 126'
isi: 1
issue: '4'
keyword:
- General Physics and Astronomy
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Entanglement view of dynamical quantum phase transitions
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 126
year: '2021'
...
---
_id: '9056'
abstract:
- lang: eng
text: "In this thesis we study persistence of multi-covers of Euclidean balls and
the geometric structures underlying their computation, in particular Delaunay
mosaics and Voronoi tessellations. The k-fold cover for some discrete input point
set consists of the space where at least k balls of radius r around the input
points overlap. Persistence is a notion that captures, in some sense, the topology
of the shape underlying the input. While persistence is usually computed for the
union of balls, the k-fold cover is of interest as it captures local density,\r\nand
thus might approximate the shape of the input better if the input data is noisy.
To compute persistence of these k-fold covers, we need a discretization that is
provided by higher-order Delaunay mosaics. We present and implement a simple and
efficient algorithm for the computation of higher-order Delaunay mosaics, and
use it to give experimental results for their combinatorial properties. The algorithm
makes use of a new geometric structure, the rhomboid tiling. It contains the higher-order
Delaunay mosaics as slices, and by introducing a filtration\r\nfunction on the
tiling, we also obtain higher-order α-shapes as slices. These allow us to compute
persistence of the multi-covers for varying radius r; the computation for varying
k is less straight-foward and involves the rhomboid tiling directly. We apply
our algorithms to experimental sphere packings to shed light on their structural
properties. Finally, inspired by periodic structures in packings and materials,
we propose and implement an algorithm for periodic Delaunay triangulations to
be integrated into the Computational Geometry Algorithms Library (CGAL), and discuss
the implications on persistence for periodic data sets."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Georg F
full_name: Osang, Georg F
id: 464B40D6-F248-11E8-B48F-1D18A9856A87
last_name: Osang
orcid: 0000-0002-8882-5116
citation:
ama: Osang GF. Multi-cover persistence and Delaunay mosaics. 2021. doi:10.15479/AT:ISTA:9056
apa: Osang, G. F. (2021). Multi-cover persistence and Delaunay mosaics. Institute
of Science and Technology Austria, Klosterneuburg. https://doi.org/10.15479/AT:ISTA:9056
chicago: Osang, Georg F. “Multi-Cover Persistence and Delaunay Mosaics.” Institute
of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9056.
ieee: G. F. Osang, “Multi-cover persistence and Delaunay mosaics,” Institute of
Science and Technology Austria, Klosterneuburg, 2021.
ista: 'Osang GF. 2021. Multi-cover persistence and Delaunay mosaics. Klosterneuburg:
Institute of Science and Technology Austria.'
mla: Osang, Georg F. Multi-Cover Persistence and Delaunay Mosaics. Institute
of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9056.
short: G.F. Osang, Multi-Cover Persistence and Delaunay Mosaics, Institute of Science
and Technology Austria, 2021.
date_created: 2021-02-02T14:11:06Z
date_published: 2021-02-01T00:00:00Z
date_updated: 2023-09-07T13:29:01Z
day: '01'
ddc:
- '006'
- '514'
- '516'
degree_awarded: PhD
department:
- _id: HeEd
- _id: GradSch
doi: 10.15479/AT:ISTA:9056
file:
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checksum: bcf27986147cab0533b6abadd74e7629
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creator: patrickd
date_created: 2021-02-02T14:09:25Z
date_updated: 2021-02-03T10:37:28Z
file_id: '9063'
file_name: thesis_source.zip
file_size: 13446994
relation: source_file
- access_level: open_access
checksum: 9cc8af266579a464385bbe2aff6af606
content_type: application/pdf
creator: patrickd
date_created: 2021-02-02T14:09:18Z
date_updated: 2021-02-02T14:09:18Z
file_id: '9064'
file_name: thesis_pdfA2b.pdf
file_size: 5210329
relation: main_file
success: 1
file_date_updated: 2021-02-03T10:37:28Z
has_accepted_license: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '134'
place: Klosterneuburg
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '187'
relation: part_of_dissertation
status: public
- id: '8703'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
title: Multi-cover persistence and Delaunay mosaics
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: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '9073'
abstract:
- lang: eng
text: The sensory and cognitive abilities of the mammalian neocortex are underpinned
by intricate columnar and laminar circuits formed from an array of diverse neuronal
populations. One approach to determining how interactions between these circuit
components give rise to complex behavior is to investigate the rules by which
cortical circuits are formed and acquire functionality during development. This
review summarizes recent research on the development of the neocortex, from genetic
determination in neural stem cells through to the dynamic role that specific neuronal
populations play in the earliest circuits of neocortex, and how they contribute
to emergent function and cognition. While many of these endeavors take advantage
of model systems, consideration will also be given to advances in our understanding
of activity in nascent human circuits. Such cross-species perspective is imperative
when investigating the mechanisms underlying the dysfunction of early neocortical
circuits in neurodevelopmental disorders, so that one can identify targets amenable
to therapeutic intervention.
acknowledgement: Work in the I.L.H.-O. laboratory was supported by European Research
Council Grant ERC-2015-CoG 681577 and German Research Foundation Ha 4466/10-1, Ha4466/11-1,
Ha4466/12-1, SPP 1665, and SFB 936B5. Work in the S.J.B.B. laboratory was supported
by Biotechnology and Biological Sciences Research Council BB/P003796/1, Medical
Research Council MR/K004387/1 and MR/T033320/1, Wellcome Trust 215199/Z/19/Z and
102386/Z/13/Z, and John Fell Fund. Work in the S.H. laboratory was supported by
European Research Council Grants ERC-2016-CoG 725780 LinPro and FWF SFB F78. This
work was supported by National Institutes of Health Grant NIMH 1R01MH110553 to N.V.D.M.G.
Work in the J.A.C. laboratory was supported by the Ludwig Family Foundation, Simons
Foundation SFARI Research Award, and National Institutes of Health/National Institute
of Mental Health R01 MH102365 and R01MH113852. The B.V. laboratory was supported
by Whitehall Foundation 2017-12-73, National Science Foundation 1736028, National
Institutes of Health, National Institute of General Medical Sciences R01GM134363-01,
and Halıcıoğlu Data Science Institute Fellowship. This work was supported by the
University of California San Diego School of Medicine.
article_processing_charge: No
article_type: original
author:
- first_name: Ileana L.
full_name: Hanganu-Opatz, Ileana L.
last_name: Hanganu-Opatz
- first_name: Simon J. B.
full_name: Butt, Simon J. B.
last_name: Butt
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Natalia V.
full_name: De Marco García, Natalia V.
last_name: De Marco García
- first_name: Jessica A.
full_name: Cardin, Jessica A.
last_name: Cardin
- first_name: Bradley
full_name: Voytek, Bradley
last_name: Voytek
- first_name: Alysson R.
full_name: Muotri, Alysson R.
last_name: Muotri
citation:
ama: Hanganu-Opatz IL, Butt SJB, Hippenmeyer S, et al. The logic of developing neocortical
circuits in health and disease. The Journal of Neuroscience. 2021;41(5):813-822.
doi:10.1523/jneurosci.1655-20.2020
apa: Hanganu-Opatz, I. L., Butt, S. J. B., Hippenmeyer, S., De Marco García, N.
V., Cardin, J. A., Voytek, B., & Muotri, A. R. (2021). The logic of developing
neocortical circuits in health and disease. The Journal of Neuroscience.
Society for Neuroscience. https://doi.org/10.1523/jneurosci.1655-20.2020
chicago: Hanganu-Opatz, Ileana L., Simon J. B. Butt, Simon Hippenmeyer, Natalia
V. De Marco García, Jessica A. Cardin, Bradley Voytek, and Alysson R. Muotri.
“The Logic of Developing Neocortical Circuits in Health and Disease.” The Journal
of Neuroscience. Society for Neuroscience, 2021. https://doi.org/10.1523/jneurosci.1655-20.2020.
ieee: I. L. Hanganu-Opatz et al., “The logic of developing neocortical circuits
in health and disease,” The Journal of Neuroscience, vol. 41, no. 5. Society
for Neuroscience, pp. 813–822, 2021.
ista: Hanganu-Opatz IL, Butt SJB, Hippenmeyer S, De Marco García NV, Cardin JA,
Voytek B, Muotri AR. 2021. The logic of developing neocortical circuits in health
and disease. The Journal of Neuroscience. 41(5), 813–822.
mla: Hanganu-Opatz, Ileana L., et al. “The Logic of Developing Neocortical Circuits
in Health and Disease.” The Journal of Neuroscience, vol. 41, no. 5, Society
for Neuroscience, 2021, pp. 813–22, doi:10.1523/jneurosci.1655-20.2020.
short: I.L. Hanganu-Opatz, S.J.B. Butt, S. Hippenmeyer, N.V. De Marco García, J.A.
Cardin, B. Voytek, A.R. Muotri, The Journal of Neuroscience 41 (2021) 813–822.
date_created: 2021-02-03T12:23:51Z
date_published: 2021-02-03T00:00:00Z
date_updated: 2023-09-05T14:03:17Z
day: '03'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1523/jneurosci.1655-20.2020
ec_funded: 1
external_id:
isi:
- '000616763400002'
pmid:
- '33431633'
file:
- access_level: open_access
checksum: 578fd7ed1a0aef74bce61bea2d987b33
content_type: application/pdf
creator: dernst
date_created: 2022-05-27T06:59:55Z
date_updated: 2022-05-27T06:59:55Z
file_id: '11414'
file_name: 2021_JourNeuroscience_Hanganu.pdf
file_size: 1031150
relation: main_file
success: 1
file_date_updated: 2022-05-27T06:59:55Z
has_accepted_license: '1'
intvolume: ' 41'
isi: 1
issue: '5'
keyword:
- General Neuroscience
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 813-822
pmid: 1
project:
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
- _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E
grant_number: F07805
name: Molecular Mechanisms of Neural Stem Cell Lineage Progression
publication: The Journal of Neuroscience
publication_identifier:
eissn:
- 1529-2401
issn:
- 0270-6474
publication_status: published
publisher: Society for Neuroscience
quality_controlled: '1'
scopus_import: '1'
status: public
title: The logic of developing neocortical circuits in health and disease
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 41
year: '2021'
...
---
_id: '9082'
abstract:
- lang: eng
text: Acquired mutations are sufficiently frequent such that the genome of a single
cell offers a record of its history of cell divisions. Among more common somatic
genomic alterations are loss of heterozygosity (LOH). Large LOH events are potentially
detectable in single cell RNA sequencing (scRNA-seq) datasets as tracts of monoallelic
expression for constitutionally heterozygous single nucleotide variants (SNVs)
located among contiguous genes. We identified runs of monoallelic expression,
consistent with LOH, uniquely distributed throughout the genome in single cell
brain cortex transcriptomes of F1 hybrids involving different inbred mouse strains.
We then phylogenetically reconstructed single cell lineages and simultaneously
identified cell types by corresponding gene expression patterns. Our results are
consistent with progenitor cells giving rise to multiple cortical cell types through
stereotyped expansion and distinct waves of neurogenesis. Compared to engineered
recording systems, LOH events accumulate throughout the genome and across the
lifetime of an organism, affording tremendous capacity for encoding lineage information
and increasing resolution for later cell divisions. This approach can conceivably
be computationally incorporated into scRNA-seq analysis and may be useful for
organisms where genetic engineering is prohibitive, such as humans.
acknowledgement: "We thank Bill Bolosky, Microsoft Research, for earlier work showing
proof of concept in TCGA\r\nbulk RNA-seq data. Supported by the Paul G. Allen Frontiers
Group (University of Washington);\r\nNIH R00HG010152 (Dartmouth); and NÖ Forschung
und Bildung n[f+b] life science call grant\r\n(C13-002) to SH, and the European
Research Council (ERC) under the European Union’s\r\nHorizon 2020 research and innovation
program 725780 LinPro to SH."
article_processing_charge: No
author:
- first_name: Donovan J.
full_name: Anderson, Donovan J.
last_name: Anderson
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
- first_name: Aaron
full_name: McKenna, Aaron
last_name: McKenna
- first_name: Jay
full_name: Shendure, Jay
last_name: Shendure
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Marshall S.
full_name: Horwitz, Marshall S.
last_name: Horwitz
citation:
ama: Anderson DJ, Pauler F, McKenna A, Shendure J, Hippenmeyer S, Horwitz MS. Simultaneous
identification of brain cell type and lineage via single cell RNA sequencing.
bioRxiv. doi:10.1101/2020.12.31.425016
apa: Anderson, D. J., Pauler, F., McKenna, A., Shendure, J., Hippenmeyer, S., &
Horwitz, M. S. (n.d.). Simultaneous identification of brain cell type and lineage
via single cell RNA sequencing. bioRxiv. Cold Spring Harbor Laboratory.
https://doi.org/10.1101/2020.12.31.425016
chicago: Anderson, Donovan J., Florian Pauler, Aaron McKenna, Jay Shendure, Simon
Hippenmeyer, and Marshall S. Horwitz. “Simultaneous Identification of Brain Cell
Type and Lineage via Single Cell RNA Sequencing.” BioRxiv. Cold Spring
Harbor Laboratory, n.d. https://doi.org/10.1101/2020.12.31.425016.
ieee: D. J. Anderson, F. Pauler, A. McKenna, J. Shendure, S. Hippenmeyer, and M.
S. Horwitz, “Simultaneous identification of brain cell type and lineage via single
cell RNA sequencing,” bioRxiv. Cold Spring Harbor Laboratory.
ista: Anderson DJ, Pauler F, McKenna A, Shendure J, Hippenmeyer S, Horwitz MS. Simultaneous
identification of brain cell type and lineage via single cell RNA sequencing.
bioRxiv, 10.1101/2020.12.31.425016.
mla: Anderson, Donovan J., et al. “Simultaneous Identification of Brain Cell Type
and Lineage via Single Cell RNA Sequencing.” BioRxiv, Cold Spring Harbor
Laboratory, doi:10.1101/2020.12.31.425016.
short: D.J. Anderson, F. Pauler, A. McKenna, J. Shendure, S. Hippenmeyer, M.S. Horwitz,
BioRxiv (n.d.).
date_created: 2021-02-04T07:23:23Z
date_published: 2021-01-01T00:00:00Z
date_updated: 2021-02-04T07:29:53Z
day: '01'
department:
- _id: SiHi
doi: 10.1101/2020.12.31.425016
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2020.12.31.425016
month: '01'
oa: 1
oa_version: Preprint
project:
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
publication: bioRxiv
publication_status: submitted
publisher: Cold Spring Harbor Laboratory
status: public
title: Simultaneous identification of brain cell type and lineage via single cell
RNA sequencing
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...