---
_id: '14177'
abstract:
- lang: eng
text: "The focus of disentanglement approaches has been on identifying independent
factors of variation in data. However, the causal variables underlying real-world
observations are often not statistically independent. In this work, we bridge
the gap to real-world scenarios by analyzing the behavior of the most prominent
disentanglement approaches on correlated data in a large-scale empirical study
(including 4260 models). We show and quantify that systematically induced correlations
in the dataset are being learned and reflected in the latent representations,
which has implications for downstream applications of disentanglement such as
fairness. We also demonstrate how to resolve these latent correlations, either
using weak supervision during\r\ntraining or by post-hoc correcting a pre-trained
model with a small number of labels."
alternative_title:
- PMLR
article_processing_charge: No
arxiv: 1
author:
- first_name: Frederik
full_name: Träuble, Frederik
last_name: Träuble
- first_name: Elliot
full_name: Creager, Elliot
last_name: Creager
- first_name: Niki
full_name: Kilbertus, Niki
last_name: Kilbertus
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Andrea
full_name: Dittadi, Andrea
last_name: Dittadi
- first_name: Anirudh
full_name: Goyal, Anirudh
last_name: Goyal
- first_name: Bernhard
full_name: Schölkopf, Bernhard
last_name: Schölkopf
- first_name: Stefan
full_name: Bauer, Stefan
last_name: Bauer
citation:
ama: 'Träuble F, Creager E, Kilbertus N, et al. On disentangled representations
learned from correlated data. In: Proceedings of the 38th International Conference
on Machine Learning. Vol 139. ML Research Press; 2021:10401-10412.'
apa: 'Träuble, F., Creager, E., Kilbertus, N., Locatello, F., Dittadi, A., Goyal,
A., … Bauer, S. (2021). On disentangled representations learned from correlated
data. In Proceedings of the 38th International Conference on Machine Learning
(Vol. 139, pp. 10401–10412). Virtual: ML Research Press.'
chicago: Träuble, Frederik, Elliot Creager, Niki Kilbertus, Francesco Locatello,
Andrea Dittadi, Anirudh Goyal, Bernhard Schölkopf, and Stefan Bauer. “On Disentangled
Representations Learned from Correlated Data.” In Proceedings of the 38th International
Conference on Machine Learning, 139:10401–12. ML Research Press, 2021.
ieee: F. Träuble et al., “On disentangled representations learned from correlated
data,” in Proceedings of the 38th International Conference on Machine Learning,
Virtual, 2021, vol. 139, pp. 10401–10412.
ista: 'Träuble F, Creager E, Kilbertus N, Locatello F, Dittadi A, Goyal A, Schölkopf
B, Bauer S. 2021. On disentangled representations learned from correlated data.
Proceedings of the 38th International Conference on Machine Learning. ICML: International
Conference on Machine Learning, PMLR, vol. 139, 10401–10412.'
mla: Träuble, Frederik, et al. “On Disentangled Representations Learned from Correlated
Data.” Proceedings of the 38th International Conference on Machine Learning,
vol. 139, ML Research Press, 2021, pp. 10401–12.
short: F. Träuble, E. Creager, N. Kilbertus, F. Locatello, A. Dittadi, A. Goyal,
B. Schölkopf, S. Bauer, in:, Proceedings of the 38th International Conference
on Machine Learning, ML Research Press, 2021, pp. 10401–10412.
conference:
end_date: 2021-07-24
location: Virtual
name: 'ICML: International Conference on Machine Learning'
start_date: 2021-07-18
date_created: 2023-08-22T14:03:47Z
date_published: 2021-08-01T00:00:00Z
date_updated: 2023-09-11T10:18:48Z
day: '01'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '2006.07886'
intvolume: ' 139'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2006.07886
month: '08'
oa: 1
oa_version: Published Version
page: 10401-10412
publication: Proceedings of the 38th International Conference on Machine Learning
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: On disentangled representations learned from correlated data
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 139
year: '2021'
...
---
_id: '14178'
abstract:
- lang: eng
text: Learning meaningful representations that disentangle the underlying structure
of the data generating process is considered to be of key importance in machine
learning. While disentangled representations were found to be useful for diverse
tasks such as abstract reasoning and fair classification, their scalability and
real-world impact remain questionable. We introduce a new high-resolution dataset
with 1M simulated images and over 1,800 annotated real-world images of the same
setup. In contrast to previous work, this new dataset exhibits correlations, a
complex underlying structure, and allows to evaluate transfer to unseen simulated
and real-world settings where the encoder i) remains in distribution or ii) is
out of distribution. We propose new architectures in order to scale disentangled
representation learning to realistic high-resolution settings and conduct a large-scale
empirical study of disentangled representations on this dataset. We observe that
disentanglement is a good predictor for out-of-distribution (OOD) task performance.
article_processing_charge: No
arxiv: 1
author:
- first_name: Andrea
full_name: Dittadi, Andrea
last_name: Dittadi
- first_name: Frederik
full_name: Träuble, Frederik
last_name: Träuble
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Manuel
full_name: Wüthrich, Manuel
last_name: Wüthrich
- first_name: Vaibhav
full_name: Agrawal, Vaibhav
last_name: Agrawal
- first_name: Ole
full_name: Winther, Ole
last_name: Winther
- first_name: Stefan
full_name: Bauer, Stefan
last_name: Bauer
- first_name: Bernhard
full_name: Schölkopf, Bernhard
last_name: Schölkopf
citation:
ama: 'Dittadi A, Träuble F, Locatello F, et al. On the transfer of disentangled
representations in realistic settings. In: The Ninth International Conference
on Learning Representations. ; 2021.'
apa: Dittadi, A., Träuble, F., Locatello, F., Wüthrich, M., Agrawal, V., Winther,
O., … Schölkopf, B. (2021). On the transfer of disentangled representations in
realistic settings. In The Ninth International Conference on Learning Representations.
Virtual.
chicago: Dittadi, Andrea, Frederik Träuble, Francesco Locatello, Manuel Wüthrich,
Vaibhav Agrawal, Ole Winther, Stefan Bauer, and Bernhard Schölkopf. “On the Transfer
of Disentangled Representations in Realistic Settings.” In The Ninth International
Conference on Learning Representations, 2021.
ieee: A. Dittadi et al., “On the transfer of disentangled representations
in realistic settings,” in The Ninth International Conference on Learning Representations,
Virtual, 2021.
ista: 'Dittadi A, Träuble F, Locatello F, Wüthrich M, Agrawal V, Winther O, Bauer
S, Schölkopf B. 2021. On the transfer of disentangled representations in realistic
settings. The Ninth International Conference on Learning Representations. ICLR:
International Conference on Learning Representations.'
mla: Dittadi, Andrea, et al. “On the Transfer of Disentangled Representations in
Realistic Settings.” The Ninth International Conference on Learning Representations,
2021.
short: A. Dittadi, F. Träuble, F. Locatello, M. Wüthrich, V. Agrawal, O. Winther,
S. Bauer, B. Schölkopf, in:, The Ninth International Conference on Learning Representations,
2021.
conference:
end_date: 2021-05-07
location: Virtual
name: 'ICLR: International Conference on Learning Representations'
start_date: 2021-05-03
date_created: 2023-08-22T14:04:16Z
date_published: 2021-05-04T00:00:00Z
date_updated: 2023-09-11T10:55:30Z
day: '04'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '2010.14407'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2010.14407
month: '05'
oa: 1
oa_version: Preprint
publication: The Ninth International Conference on Learning Representations
publication_status: published
quality_controlled: '1'
status: public
title: On the transfer of disentangled representations in realistic settings
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_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: 2024-10-14T12:27:25Z
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'
...
---
OA_place: repository
_id: '14185'
abstract:
- lang: eng
text: A method involves receiving a perceptual representation including a plurality
of feature vectors, and initializing a plurality of slot vectors represented by
a neural network memory unit. Each respective slot vector is configured to represent
a corresponding entity in the perceptual representation. The method also involves
determining an attention matrix based on a product of the plurality of feature
vectors transformed by a key function and the plurality of slot vectors transformed
by a query function. Each respective value of a plurality of values along each
respective dimension of the attention matrix is normalized with respect to the
plurality of values. The method additionally involves determining an update matrix
based on the plurality of feature vectors transformed by a value function and
the attention matrix, and updating the plurality of slot vectors based on the
update matrix by way of the neural network memory unit.
applicant:
- Google LLC
application_date: 2020-07-13
application_number: '16 / 927,018 '
article_processing_charge: No
arxiv: 1
author:
- first_name: Dirk
full_name: Weissenborn, Dirk
last_name: Weissenborn
- first_name: Jakob
full_name: Uszkoreit, Jakob
last_name: Uszkoreit
- first_name: Thomas
full_name: Unterthiner, Thomas
last_name: Unterthiner
- first_name: Aravindh
full_name: Mahendran, Aravindh
last_name: Mahendran
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Thomas
full_name: Kipf, Thomas
last_name: Kipf
- first_name: Georg
full_name: Heigold, Georg
last_name: Heigold
- first_name: Alexey
full_name: Dosovitskiy, Alexey
last_name: Dosovitskiy
citation:
ama: Weissenborn D, Uszkoreit J, Unterthiner T, et al. Object-centric learning with
slot attention. 2021.
apa: Weissenborn, D., Uszkoreit, J., Unterthiner, T., Mahendran, A., Locatello,
F., Kipf, T., … Dosovitskiy, A. (2021). Object-centric learning with slot attention.
chicago: Weissenborn, Dirk, Jakob Uszkoreit, Thomas Unterthiner, Aravindh Mahendran,
Francesco Locatello, Thomas Kipf, Georg Heigold, and Alexey Dosovitskiy. “Object-Centric
Learning with Slot Attention,” 2021.
ieee: D. Weissenborn et al., “Object-centric learning with slot attention.”
2021.
ista: Weissenborn D, Uszkoreit J, Unterthiner T, Mahendran A, Locatello F, Kipf
T, Heigold G, Dosovitskiy A. 2021. Object-centric learning with slot attention.
mla: Weissenborn, Dirk, et al. Object-Centric Learning with Slot Attention.
2021.
short: D. Weissenborn, J. Uszkoreit, T. Unterthiner, A. Mahendran, F. Locatello,
T. Kipf, G. Heigold, A. Dosovitskiy, (2021).
date_created: 2023-08-22T14:07:06Z
date_published: 2021-12-09T00:00:00Z
date_updated: 2025-01-31T11:35:46Z
day: '09'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '2006.15055'
ipc: G06N 3/063 ; G06N 3/08 ; G06F 17/16
ipn: US20210383199A1
main_file_link:
- open_access: '1'
url: https://patents.google.com/patent/US20210383199A1/en
month: '12'
oa: 1
oa_version: Published Version
publication_date: 2021-12-09
status: public
title: Object-centric learning with slot attention
type: patent
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
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: 2024-10-14T12:27:49Z
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: '14800'
abstract:
- lang: eng
text: 'Research on two-dimensional (2D) materials has been explosively increasing
in last seventeen years in varying subjects including condensed matter physics,
electronic engineering, materials science, and chemistry since the mechanical
exfoliation of graphene in 2004. Starting from graphene, 2D materials now have
become a big family with numerous members and diverse categories. The unique structural
features and physicochemical properties of 2D materials make them one class of
the most appealing candidates for a wide range of potential applications. In particular,
we have seen some major breakthroughs made in the field of 2D materials in last
five years not only in developing novel synthetic methods and exploring new structures/properties
but also in identifying innovative applications and pushing forward commercialisation.
In this review, we provide a critical summary on the recent progress made in the
field of 2D materials with a particular focus on last five years. After a brief
background introduction, we first discuss the major synthetic methods for 2D materials,
including the mechanical exfoliation, liquid exfoliation, vapor phase deposition,
and wet-chemical synthesis as well as phase engineering of 2D materials belonging
to the field of phase engineering of nanomaterials (PEN). We then introduce the
superconducting/optical/magnetic properties and chirality of 2D materials along
with newly emerging magic angle 2D superlattices. Following that, the promising
applications of 2D materials in electronics, optoelectronics, catalysis, energy
storage, solar cells, biomedicine, sensors, environments, etc. are described sequentially.
Thereafter, we present the theoretic calculations and simulations of 2D materials.
Finally, after concluding the current progress, we provide some personal discussions
on the existing challenges and future outlooks in this rapidly developing field. '
article_number: '2108017'
article_processing_charge: No
article_type: review
author:
- first_name: Cheng
full_name: Chang, Cheng
id: 9E331C2E-9F27-11E9-AE48-5033E6697425
last_name: Chang
orcid: 0000-0002-9515-4277
- first_name: Wei
full_name: Chen, Wei
last_name: Chen
- first_name: Ye
full_name: Chen, Ye
last_name: Chen
- first_name: Yonghua
full_name: Chen, Yonghua
last_name: Chen
- first_name: Yu
full_name: Chen, Yu
last_name: Chen
- first_name: Feng
full_name: Ding, Feng
last_name: Ding
- first_name: Chunhai
full_name: Fan, Chunhai
last_name: Fan
- first_name: Hong Jin
full_name: Fan, Hong Jin
last_name: Fan
- first_name: Zhanxi
full_name: Fan, Zhanxi
last_name: Fan
- first_name: Cheng
full_name: Gong, Cheng
last_name: Gong
- first_name: Yongji
full_name: Gong, Yongji
last_name: Gong
- first_name: Qiyuan
full_name: He, Qiyuan
last_name: He
- first_name: Xun
full_name: Hong, Xun
last_name: Hong
- first_name: Sheng
full_name: Hu, Sheng
last_name: Hu
- first_name: Weida
full_name: Hu, Weida
last_name: Hu
- first_name: Wei
full_name: Huang, Wei
last_name: Huang
- first_name: Yuan
full_name: Huang, Yuan
last_name: Huang
- first_name: Wei
full_name: Ji, Wei
last_name: Ji
- first_name: Dehui
full_name: Li, Dehui
last_name: Li
- first_name: Lain Jong
full_name: Li, Lain Jong
last_name: Li
- first_name: Qiang
full_name: Li, Qiang
last_name: Li
- first_name: Li
full_name: Lin, Li
last_name: Lin
- first_name: Chongyi
full_name: Ling, Chongyi
last_name: Ling
- first_name: Minghua
full_name: Liu, Minghua
last_name: Liu
- first_name: 'Nan'
full_name: Liu, Nan
last_name: Liu
- first_name: Zhuang
full_name: Liu, Zhuang
last_name: Liu
- first_name: Kian Ping
full_name: Loh, Kian Ping
last_name: Loh
- first_name: Jianmin
full_name: Ma, Jianmin
last_name: Ma
- first_name: Feng
full_name: Miao, Feng
last_name: Miao
- first_name: Hailin
full_name: Peng, Hailin
last_name: Peng
- first_name: Mingfei
full_name: Shao, Mingfei
last_name: Shao
- first_name: Li
full_name: Song, Li
last_name: Song
- first_name: Shao
full_name: Su, Shao
last_name: Su
- first_name: Shuo
full_name: Sun, Shuo
last_name: Sun
- first_name: Chaoliang
full_name: Tan, Chaoliang
last_name: Tan
- first_name: Zhiyong
full_name: Tang, Zhiyong
last_name: Tang
- first_name: Dingsheng
full_name: Wang, Dingsheng
last_name: Wang
- first_name: Huan
full_name: Wang, Huan
last_name: Wang
- first_name: Jinlan
full_name: Wang, Jinlan
last_name: Wang
- first_name: Xin
full_name: Wang, Xin
last_name: Wang
- first_name: Xinran
full_name: Wang, Xinran
last_name: Wang
- first_name: Andrew T.S.
full_name: Wee, Andrew T.S.
last_name: Wee
- first_name: Zhongming
full_name: Wei, Zhongming
last_name: Wei
- first_name: Yuen
full_name: Wu, Yuen
last_name: Wu
- first_name: Zhong Shuai
full_name: Wu, Zhong Shuai
last_name: Wu
- first_name: Jie
full_name: Xiong, Jie
last_name: Xiong
- first_name: Qihua
full_name: Xiong, Qihua
last_name: Xiong
- first_name: Weigao
full_name: Xu, Weigao
last_name: Xu
- first_name: Peng
full_name: Yin, Peng
last_name: Yin
- first_name: Haibo
full_name: Zeng, Haibo
last_name: Zeng
- first_name: Zhiyuan
full_name: Zeng, Zhiyuan
last_name: Zeng
- first_name: Tianyou
full_name: Zhai, Tianyou
last_name: Zhai
- first_name: Han
full_name: Zhang, Han
last_name: Zhang
- first_name: Hui
full_name: Zhang, Hui
last_name: Zhang
- first_name: Qichun
full_name: Zhang, Qichun
last_name: Zhang
- first_name: Tierui
full_name: Zhang, Tierui
last_name: Zhang
- first_name: Xiang
full_name: Zhang, Xiang
last_name: Zhang
- first_name: Li Dong
full_name: Zhao, Li Dong
last_name: Zhao
- first_name: Meiting
full_name: Zhao, Meiting
last_name: Zhao
- first_name: Weijie
full_name: Zhao, Weijie
last_name: Zhao
- first_name: Yunxuan
full_name: Zhao, Yunxuan
last_name: Zhao
- first_name: Kai Ge
full_name: Zhou, Kai Ge
last_name: Zhou
- first_name: Xing
full_name: Zhou, Xing
last_name: Zhou
- first_name: Yu
full_name: Zhou, Yu
last_name: Zhou
- first_name: Hongwei
full_name: Zhu, Hongwei
last_name: Zhu
- first_name: Hua
full_name: Zhang, Hua
last_name: Zhang
- first_name: Zhongfan
full_name: Liu, Zhongfan
last_name: Liu
citation:
ama: Chang C, Chen W, Chen Y, et al. Recent progress on two-dimensional materials.
Acta Physico-Chimica Sinica. 2021;37(12). doi:10.3866/PKU.WHXB202108017
apa: Chang, C., Chen, W., Chen, Y., Chen, Y., Chen, Y., Ding, F., … Liu, Z. (2021).
Recent progress on two-dimensional materials. Acta Physico-Chimica Sinica.
Peking University. https://doi.org/10.3866/PKU.WHXB202108017
chicago: Chang, Cheng, Wei Chen, Ye Chen, Yonghua Chen, Yu Chen, Feng Ding, Chunhai
Fan, et al. “Recent Progress on Two-Dimensional Materials.” Acta Physico-Chimica
Sinica. Peking University, 2021. https://doi.org/10.3866/PKU.WHXB202108017.
ieee: C. Chang et al., “Recent progress on two-dimensional materials,” Acta
Physico-Chimica Sinica, vol. 37, no. 12. Peking University, 2021.
ista: Chang C, Chen W, Chen Y, Chen Y, Chen Y, Ding F, Fan C, Fan HJ, Fan Z, Gong
C, Gong Y, He Q, Hong X, Hu S, Hu W, Huang W, Huang Y, Ji W, Li D, Li LJ, Li Q,
Lin L, Ling C, Liu M, Liu N, Liu Z, Loh KP, Ma J, Miao F, Peng H, Shao M, Song
L, Su S, Sun S, Tan C, Tang Z, Wang D, Wang H, Wang J, Wang X, Wang X, Wee ATS,
Wei Z, Wu Y, Wu ZS, Xiong J, Xiong Q, Xu W, Yin P, Zeng H, Zeng Z, Zhai T, Zhang
H, Zhang H, Zhang Q, Zhang T, Zhang X, Zhao LD, Zhao M, Zhao W, Zhao Y, Zhou KG,
Zhou X, Zhou Y, Zhu H, Zhang H, Liu Z. 2021. Recent progress on two-dimensional
materials. Acta Physico-Chimica Sinica. 37(12), 2108017.
mla: Chang, Cheng, et al. “Recent Progress on Two-Dimensional Materials.” Acta
Physico-Chimica Sinica, vol. 37, no. 12, 2108017, Peking University, 2021,
doi:10.3866/PKU.WHXB202108017.
short: C. Chang, W. Chen, Y. Chen, Y. Chen, Y. Chen, F. Ding, C. Fan, H.J. Fan,
Z. Fan, C. Gong, Y. Gong, Q. He, X. Hong, S. Hu, W. Hu, W. Huang, Y. Huang, W.
Ji, D. Li, L.J. Li, Q. Li, L. Lin, C. Ling, M. Liu, N. Liu, Z. Liu, K.P. Loh,
J. Ma, F. Miao, H. Peng, M. Shao, L. Song, S. Su, S. Sun, C. Tan, Z. Tang, D.
Wang, H. Wang, J. Wang, X. Wang, X. Wang, A.T.S. Wee, Z. Wei, Y. Wu, Z.S. Wu,
J. Xiong, Q. Xiong, W. Xu, P. Yin, H. Zeng, Z. Zeng, T. Zhai, H. Zhang, H. Zhang,
Q. Zhang, T. Zhang, X. Zhang, L.D. Zhao, M. Zhao, W. Zhao, Y. Zhao, K.G. Zhou,
X. Zhou, Y. Zhou, H. Zhu, H. Zhang, Z. Liu, Acta Physico-Chimica Sinica 37 (2021).
date_created: 2024-01-14T23:00:58Z
date_published: 2021-10-13T00:00:00Z
date_updated: 2025-09-10T10:12:25Z
day: '13'
department:
- _id: MaIb
doi: 10.3866/PKU.WHXB202108017
external_id:
isi:
- '000731879300002'
intvolume: ' 37'
isi: 1
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.3866/PKU.WHXB202108017
month: '10'
oa: 1
oa_version: Submitted Version
publication: Acta Physico-Chimica Sinica
publication_identifier:
issn:
- 1001-4861
publication_status: published
publisher: Peking University
quality_controlled: '1'
scopus_import: '1'
status: public
title: Recent progress on two-dimensional materials
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 37
year: '2021'
...
---
_id: '14889'
abstract:
- lang: eng
text: We consider the Fröhlich Hamiltonian with large coupling constant α. For initial
data of Pekar product form with coherent phonon field and with the electron minimizing
the corresponding energy, we provide a norm approximation of the evolution, valid
up to times of order α2. The approximation is given in terms of a Pekar product
state, evolved through the Landau-Pekar equations, corrected by a Bogoliubov dynamics
taking quantum fluctuations into account. This allows us to show that the Landau-Pekar
equations approximately describe the evolution of the electron- and one-phonon
reduced density matrices under the Fröhlich dynamics up to times of order α2.
acknowledgement: "Financial support by the European Union’s Horizon 2020 research
and innovation programme\r\nunder the Marie Skłodowska-Curie grant agreement No.
754411 (S.R.) and the European\r\nResearch Council under grant agreement No. 694227
(N.L. and R.S.), as well as by the SNSF\r\nEccellenza project PCEFP2 181153 (N.L.),
the NCCR SwissMAP (N.L. and B.S.) and by the\r\nDeutsche Forschungsgemeinschaft
(DFG) through the Research Training Group 1838: Spectral\r\nTheory and Dynamics
of Quantum Systems (D.M.) is gratefully acknowledged. B.S. gratefully\r\nacknowledges
financial support from the Swiss National Science Foundation through the Grant\r\n“Dynamical
and energetic properties of Bose-Einstein condensates” and from the European\r\nResearch
Council through the ERC-AdG CLaQS (grant agreement No 834782). D.M. thanks\r\nMarcel
Griesemer for helpful discussions."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Nikolai K
full_name: Leopold, Nikolai K
id: 4BC40BEC-F248-11E8-B48F-1D18A9856A87
last_name: Leopold
orcid: 0000-0002-0495-6822
- first_name: David Johannes
full_name: Mitrouskas, David Johannes
id: cbddacee-2b11-11eb-a02e-a2e14d04e52d
last_name: Mitrouskas
- first_name: Simone Anna Elvira
full_name: Rademacher, Simone Anna Elvira
id: 856966FE-A408-11E9-977E-802DE6697425
last_name: Rademacher
orcid: 0000-0001-5059-4466
- first_name: Benjamin
full_name: Schlein, Benjamin
last_name: Schlein
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Leopold NK, Mitrouskas DJ, Rademacher SAE, Schlein B, Seiringer R. Landau–Pekar
equations and quantum fluctuations for the dynamics of a strongly coupled polaron.
Pure and Applied Analysis. 2021;3(4):653-676. doi:10.2140/paa.2021.3.653
apa: Leopold, N. K., Mitrouskas, D. J., Rademacher, S. A. E., Schlein, B., &
Seiringer, R. (2021). Landau–Pekar equations and quantum fluctuations for the
dynamics of a strongly coupled polaron. Pure and Applied Analysis. Mathematical
Sciences Publishers. https://doi.org/10.2140/paa.2021.3.653
chicago: Leopold, Nikolai K, David Johannes Mitrouskas, Simone Anna Elvira Rademacher,
Benjamin Schlein, and Robert Seiringer. “Landau–Pekar Equations and Quantum Fluctuations
for the Dynamics of a Strongly Coupled Polaron.” Pure and Applied Analysis.
Mathematical Sciences Publishers, 2021. https://doi.org/10.2140/paa.2021.3.653.
ieee: N. K. Leopold, D. J. Mitrouskas, S. A. E. Rademacher, B. Schlein, and R. Seiringer,
“Landau–Pekar equations and quantum fluctuations for the dynamics of a strongly
coupled polaron,” Pure and Applied Analysis, vol. 3, no. 4. Mathematical
Sciences Publishers, pp. 653–676, 2021.
ista: Leopold NK, Mitrouskas DJ, Rademacher SAE, Schlein B, Seiringer R. 2021. Landau–Pekar
equations and quantum fluctuations for the dynamics of a strongly coupled polaron.
Pure and Applied Analysis. 3(4), 653–676.
mla: Leopold, Nikolai K., et al. “Landau–Pekar Equations and Quantum Fluctuations
for the Dynamics of a Strongly Coupled Polaron.” Pure and Applied Analysis,
vol. 3, no. 4, Mathematical Sciences Publishers, 2021, pp. 653–76, doi:10.2140/paa.2021.3.653.
short: N.K. Leopold, D.J. Mitrouskas, S.A.E. Rademacher, B. Schlein, R. Seiringer,
Pure and Applied Analysis 3 (2021) 653–676.
corr_author: '1'
date_created: 2024-01-28T23:01:43Z
date_published: 2021-10-01T00:00:00Z
date_updated: 2025-04-14T07:27:00Z
day: '01'
department:
- _id: RoSe
doi: 10.2140/paa.2021.3.653
ec_funded: 1
external_id:
arxiv:
- '2005.02098'
intvolume: ' 3'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2005.02098
month: '10'
oa: 1
oa_version: Preprint
page: 653-676
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication: Pure and Applied Analysis
publication_identifier:
eissn:
- 2578-5885
issn:
- 2578-5893
publication_status: published
publisher: Mathematical Sciences Publishers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Landau–Pekar equations and quantum fluctuations for the dynamics of a strongly
coupled polaron
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2021'
...
---
_id: '14890'
abstract:
- lang: eng
text: We consider a system of N interacting bosons in the mean-field scaling regime
and construct corrections to the Bogoliubov dynamics that approximate the true
N-body dynamics in norm to arbitrary precision. The N-independent corrections
are given in terms of the solutions of the Bogoliubov and Hartree equations and
satisfy a generalized form of Wick's theorem. We determine the n-point correlation
functions of the excitations around the condensate, as well as the reduced densities
of the N-body system, to arbitrary accuracy, given only the knowledge of the two-point
functions of a quasi-free state and the solution of the Hartree equation. In this
way, the complex problem of computing all n-point correlation functions for an
interacting N-body system is essentially reduced to the problem of solving the
Hartree equation and the PDEs for the Bogoliubov two-point functions.
acknowledgement: "We are grateful for the hospitality of Central China Normal University
(CCNU),\r\nwhere parts of this work were done, and thank Phan Th`anh Nam, Simone\r\nRademacher,
Robert Seiringer and Stefan Teufel for helpful discussions. L.B. gratefully acknowledges
the support by the German Research Foundation (DFG) within the Research\r\nTraining
Group 1838 “Spectral Theory and Dynamics of Quantum Systems”, and the funding\r\nfrom
the European Union’s Horizon 2020 research and innovation programme under the Marie\r\nSk
lodowska-Curie Grant Agreement No. 754411."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Lea
full_name: Bossmann, Lea
id: A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425
last_name: Bossmann
orcid: 0000-0002-6854-1343
- first_name: Sören P
full_name: Petrat, Sören P
id: 40AC02DC-F248-11E8-B48F-1D18A9856A87
last_name: Petrat
orcid: 0000-0002-9166-5889
- first_name: Peter
full_name: Pickl, Peter
last_name: Pickl
- first_name: Avy
full_name: Soffer, Avy
last_name: Soffer
citation:
ama: Bossmann L, Petrat SP, Pickl P, Soffer A. Beyond Bogoliubov dynamics. Pure
and Applied Analysis. 2021;3(4):677-726. doi:10.2140/paa.2021.3.677
apa: Bossmann, L., Petrat, S. P., Pickl, P., & Soffer, A. (2021). Beyond Bogoliubov
dynamics. Pure and Applied Analysis. Mathematical Sciences Publishers.
https://doi.org/10.2140/paa.2021.3.677
chicago: Bossmann, Lea, Sören P Petrat, Peter Pickl, and Avy Soffer. “Beyond Bogoliubov
Dynamics.” Pure and Applied Analysis. Mathematical Sciences Publishers,
2021. https://doi.org/10.2140/paa.2021.3.677.
ieee: L. Bossmann, S. P. Petrat, P. Pickl, and A. Soffer, “Beyond Bogoliubov dynamics,”
Pure and Applied Analysis, vol. 3, no. 4. Mathematical Sciences Publishers,
pp. 677–726, 2021.
ista: Bossmann L, Petrat SP, Pickl P, Soffer A. 2021. Beyond Bogoliubov dynamics.
Pure and Applied Analysis. 3(4), 677–726.
mla: Bossmann, Lea, et al. “Beyond Bogoliubov Dynamics.” Pure and Applied Analysis,
vol. 3, no. 4, Mathematical Sciences Publishers, 2021, pp. 677–726, doi:10.2140/paa.2021.3.677.
short: L. Bossmann, S.P. Petrat, P. Pickl, A. Soffer, Pure and Applied Analysis
3 (2021) 677–726.
corr_author: '1'
date_created: 2024-01-28T23:01:43Z
date_published: 2021-10-01T00:00:00Z
date_updated: 2025-04-14T07:44:02Z
day: '01'
department:
- _id: RoSe
doi: 10.2140/paa.2021.3.677
ec_funded: 1
external_id:
arxiv:
- '1912.11004'
intvolume: ' 3'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1912.11004
month: '10'
oa: 1
oa_version: Preprint
page: 677-726
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Pure and Applied Analysis
publication_identifier:
eissn:
- 2578-5885
issn:
- 2578-5893
publication_status: published
publisher: Mathematical Sciences Publishers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Beyond Bogoliubov dynamics
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2021'
...
---
_id: '14988'
abstract:
- lang: eng
text: Raw data generated from the publication - The TPLATE complex mediates membrane
bending during plant clathrin-mediated endocytosis by Johnson et al., 2021 In
PNAS
article_processing_charge: No
author:
- first_name: Alexander J
full_name: Johnson, Alexander J
id: 46A62C3A-F248-11E8-B48F-1D18A9856A87
last_name: Johnson
orcid: 0000-0002-2739-8843
citation:
ama: Johnson AJ. Raw data from Johnson et al, PNAS, 2021. 2021. doi:10.5281/ZENODO.5747100
apa: Johnson, A. J. (2021). Raw data from Johnson et al, PNAS, 2021. Zenodo. https://doi.org/10.5281/ZENODO.5747100
chicago: Johnson, Alexander J. “Raw Data from Johnson et Al, PNAS, 2021.” Zenodo,
2021. https://doi.org/10.5281/ZENODO.5747100.
ieee: A. J. Johnson, “Raw data from Johnson et al, PNAS, 2021.” Zenodo, 2021.
ista: Johnson AJ. 2021. Raw data from Johnson et al, PNAS, 2021, Zenodo, 10.5281/ZENODO.5747100.
mla: Johnson, Alexander J. Raw Data from Johnson et Al, PNAS, 2021. Zenodo,
2021, doi:10.5281/ZENODO.5747100.
short: A.J. Johnson, (2021).
corr_author: '1'
date_created: 2024-02-14T14:13:48Z
date_published: 2021-12-01T00:00:00Z
date_updated: 2025-05-14T09:25:33Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.5281/ZENODO.5747100
has_accepted_license: '1'
license: https://creativecommons.org/licenses/by/4.0/
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.5747100
month: '12'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '9887'
relation: used_in_publication
status: public
status: public
title: Raw data from Johnson et al, PNAS, 2021
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_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '15013'
abstract:
- lang: eng
text: We consider random n×n matrices X with independent and centered entries and
a general variance profile. We show that the spectral radius of X converges with
very high probability to the square root of the spectral radius of the variance
matrix of X when n tends to infinity. We also establish the optimal rate of convergence,
that is a new result even for general i.i.d. matrices beyond the explicitly solvable
Gaussian cases. The main ingredient is the proof of the local inhomogeneous circular
law [arXiv:1612.07776] at the spectral edge.
acknowledgement: Partially supported by ERC Starting Grant RandMat No. 715539 and
the SwissMap grant of Swiss National Science Foundation. Partially supported by
ERC Advanced Grant RanMat No. 338804. Partially supported by the Hausdorff Center
for Mathematics in Bonn.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Johannes
full_name: Alt, Johannes
id: 36D3D8B6-F248-11E8-B48F-1D18A9856A87
last_name: Alt
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Torben H
full_name: Krüger, Torben H
id: 3020C786-F248-11E8-B48F-1D18A9856A87
last_name: Krüger
orcid: 0000-0002-4821-3297
citation:
ama: Alt J, Erdös L, Krüger TH. Spectral radius of random matrices with independent
entries. Probability and Mathematical Physics. 2021;2(2):221-280. doi:10.2140/pmp.2021.2.221
apa: Alt, J., Erdös, L., & Krüger, T. H. (2021). Spectral radius of random matrices
with independent entries. Probability and Mathematical Physics. Mathematical
Sciences Publishers. https://doi.org/10.2140/pmp.2021.2.221
chicago: Alt, Johannes, László Erdös, and Torben H Krüger. “Spectral Radius of Random
Matrices with Independent Entries.” Probability and Mathematical Physics.
Mathematical Sciences Publishers, 2021. https://doi.org/10.2140/pmp.2021.2.221.
ieee: J. Alt, L. Erdös, and T. H. Krüger, “Spectral radius of random matrices with
independent entries,” Probability and Mathematical Physics, vol. 2, no.
2. Mathematical Sciences Publishers, pp. 221–280, 2021.
ista: Alt J, Erdös L, Krüger TH. 2021. Spectral radius of random matrices with independent
entries. Probability and Mathematical Physics. 2(2), 221–280.
mla: Alt, Johannes, et al. “Spectral Radius of Random Matrices with Independent
Entries.” Probability and Mathematical Physics, vol. 2, no. 2, Mathematical
Sciences Publishers, 2021, pp. 221–80, doi:10.2140/pmp.2021.2.221.
short: J. Alt, L. Erdös, T.H. Krüger, Probability and Mathematical Physics 2 (2021)
221–280.
corr_author: '1'
date_created: 2024-02-18T23:01:03Z
date_published: 2021-05-21T00:00:00Z
date_updated: 2025-04-15T08:05:02Z
day: '21'
department:
- _id: LaEr
doi: 10.2140/pmp.2021.2.221
ec_funded: 1
external_id:
arxiv:
- '1907.13631'
intvolume: ' 2'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1907.13631
month: '05'
oa: 1
oa_version: Preprint
page: 221-280
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Probability and Mathematical Physics
publication_identifier:
eissn:
- 2690-1005
issn:
- 2690-0998
publication_status: published
publisher: Mathematical Sciences Publishers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Spectral radius of random matrices with independent entries
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2021'
...
---
_id: '15137'
abstract:
- lang: eng
text: Characteristic properties of type III CRISPR-Cas systems include recognition
of target RNA and the subsequent induction of a multifaceted immune response.
This involves sequence-specific cleavage of the target RNA and production of cyclic
oligoadenylate (cOA) molecules. Here we report that an exposed seed region at
the 3′ end of the crRNA is essential for target RNA binding and cleavage, whereas
cOA production requires base pairing at the 5′ end of the crRNA. Moreover, we
uncover that the variation in the size and composition of type III complexes within
a single host results in variable seed regions. This may prevent escape by invading
genetic elements, while controlling cOA production tightly to prevent unnecessary
damage to the host. Lastly, we use these findings to develop a new diagnostic
tool, SCOPE, for the specific detection of SARS-CoV-2 from human nasal swab samples,
revealing sensitivities in the atto-molar range.
article_number: '5033'
article_processing_charge: Yes
article_type: original
author:
- first_name: Jurre A.
full_name: Steens, Jurre A.
last_name: Steens
- first_name: Yifan
full_name: Zhu, Yifan
last_name: Zhu
- first_name: David W.
full_name: Taylor, David W.
last_name: Taylor
- first_name: Jack Peter Kelly
full_name: Bravo, Jack Peter Kelly
id: 96aecfa5-8931-11ee-af30-aa6a5d6eee0e
last_name: Bravo
orcid: 0000-0003-0456-0753
- first_name: Stijn H. P.
full_name: Prinsen, Stijn H. P.
last_name: Prinsen
- first_name: Cor D.
full_name: Schoen, Cor D.
last_name: Schoen
- first_name: Bart J. F.
full_name: Keijser, Bart J. F.
last_name: Keijser
- first_name: Michel
full_name: Ossendrijver, Michel
last_name: Ossendrijver
- first_name: L. Marije
full_name: Hofstra, L. Marije
last_name: Hofstra
- first_name: Stan J. J.
full_name: Brouns, Stan J. J.
last_name: Brouns
- first_name: Akeo
full_name: Shinkai, Akeo
last_name: Shinkai
- first_name: John
full_name: van der Oost, John
last_name: van der Oost
- first_name: Raymond H. J.
full_name: Staals, Raymond H. J.
last_name: Staals
citation:
ama: Steens JA, Zhu Y, Taylor DW, et al. SCOPE enables type III CRISPR-Cas diagnostics
using flexible targeting and stringent CARF ribonuclease activation. Nature
Communications. 2021;12. doi:10.1038/s41467-021-25337-5
apa: Steens, J. A., Zhu, Y., Taylor, D. W., Bravo, J. P. K., Prinsen, S. H. P.,
Schoen, C. D., … Staals, R. H. J. (2021). SCOPE enables type III CRISPR-Cas diagnostics
using flexible targeting and stringent CARF ribonuclease activation. Nature
Communications. Springer Nature. https://doi.org/10.1038/s41467-021-25337-5
chicago: Steens, Jurre A., Yifan Zhu, David W. Taylor, Jack Peter Kelly Bravo, Stijn
H. P. Prinsen, Cor D. Schoen, Bart J. F. Keijser, et al. “SCOPE Enables Type III
CRISPR-Cas Diagnostics Using Flexible Targeting and Stringent CARF Ribonuclease
Activation.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-25337-5.
ieee: J. A. Steens et al., “SCOPE enables type III CRISPR-Cas diagnostics
using flexible targeting and stringent CARF ribonuclease activation,” Nature
Communications, vol. 12. Springer Nature, 2021.
ista: Steens JA, Zhu Y, Taylor DW, Bravo JPK, Prinsen SHP, Schoen CD, Keijser BJF,
Ossendrijver M, Hofstra LM, Brouns SJJ, Shinkai A, van der Oost J, Staals RHJ.
2021. SCOPE enables type III CRISPR-Cas diagnostics using flexible targeting and
stringent CARF ribonuclease activation. Nature Communications. 12, 5033.
mla: Steens, Jurre A., et al. “SCOPE Enables Type III CRISPR-Cas Diagnostics Using
Flexible Targeting and Stringent CARF Ribonuclease Activation.” Nature Communications,
vol. 12, 5033, Springer Nature, 2021, doi:10.1038/s41467-021-25337-5.
short: J.A. Steens, Y. Zhu, D.W. Taylor, J.P.K. Bravo, S.H.P. Prinsen, C.D. Schoen,
B.J.F. Keijser, M. Ossendrijver, L.M. Hofstra, S.J.J. Brouns, A. Shinkai, J. van
der Oost, R.H.J. Staals, Nature Communications 12 (2021).
date_created: 2024-03-20T10:42:33Z
date_published: 2021-08-19T00:00:00Z
date_updated: 2024-06-04T06:11:54Z
day: '19'
doi: 10.1038/s41467-021-25337-5
extern: '1'
external_id:
pmid:
- '34413302'
intvolume: ' 12'
keyword:
- General Physics and Astronomy
- General Biochemistry
- Genetics and Molecular Biology
- General Chemistry
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41467-021-25337-5
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: SCOPE enables type III CRISPR-Cas diagnostics using flexible targeting and
stringent CARF ribonuclease activation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2021'
...
---
_id: '15138'
abstract:
- lang: eng
text: RNA viruses induce the formation of subcellular organelles that provide microenvironments
conducive to their replication. Here we show that replication factories of rotaviruses
represent protein‐RNA condensates that are formed via liquid–liquid phase separation
of the viroplasm‐forming proteins NSP5 and rotavirus RNA chaperone NSP2. Upon
mixing, these proteins readily form condensates at physiologically relevant low
micromolar concentrations achieved in the cytoplasm of virus‐infected cells. Early
infection stage condensates could be reversibly dissolved by 1,6‐hexanediol, as
well as propylene glycol that released rotavirus transcripts from these condensates.
During the early stages of infection, propylene glycol treatments reduced viral
replication and phosphorylation of the condensate‐forming protein NSP5. During
late infection, these condensates exhibited altered material properties and became
resistant to propylene glycol, coinciding with hyperphosphorylation of NSP5. Some
aspects of the assembly of cytoplasmic rotavirus replication factories mirror
the formation of other ribonucleoprotein granules. Such viral RNA‐rich condensates
that support replication of multi‐segmented genomes represent an attractive target
for developing novel therapeutic approaches.
article_number: e107711
article_processing_charge: Yes
article_type: original
author:
- first_name: Florian
full_name: Geiger, Florian
last_name: Geiger
- first_name: Julia
full_name: Acker, Julia
last_name: Acker
- first_name: Guido
full_name: Papa, Guido
last_name: Papa
- first_name: Xinyu
full_name: Wang, Xinyu
last_name: Wang
- first_name: William E
full_name: Arter, William E
last_name: Arter
- first_name: Kadi L
full_name: Saar, Kadi L
last_name: Saar
- first_name: Nadia A
full_name: Erkamp, Nadia A
last_name: Erkamp
- first_name: Runzhang
full_name: Qi, Runzhang
last_name: Qi
- first_name: Jack Peter Kelly
full_name: Bravo, Jack Peter Kelly
id: 96aecfa5-8931-11ee-af30-aa6a5d6eee0e
last_name: Bravo
orcid: 0000-0003-0456-0753
- first_name: Sebastian
full_name: Strauss, Sebastian
last_name: Strauss
- first_name: Georg
full_name: Krainer, Georg
last_name: Krainer
- first_name: Oscar R
full_name: Burrone, Oscar R
last_name: Burrone
- first_name: Ralf
full_name: Jungmann, Ralf
last_name: Jungmann
- first_name: Tuomas PJ
full_name: Knowles, Tuomas PJ
last_name: Knowles
- first_name: Hanna
full_name: Engelke, Hanna
last_name: Engelke
- first_name: Alexander
full_name: Borodavka, Alexander
last_name: Borodavka
citation:
ama: Geiger F, Acker J, Papa G, et al. Liquid–liquid phase separation underpins
the formation of replication factories in rotaviruses. The EMBO Journal.
2021;40(21). doi:10.15252/embj.2021107711
apa: Geiger, F., Acker, J., Papa, G., Wang, X., Arter, W. E., Saar, K. L., … Borodavka,
A. (2021). Liquid–liquid phase separation underpins the formation of replication
factories in rotaviruses. The EMBO Journal. Embo Press. https://doi.org/10.15252/embj.2021107711
chicago: Geiger, Florian, Julia Acker, Guido Papa, Xinyu Wang, William E Arter,
Kadi L Saar, Nadia A Erkamp, et al. “Liquid–Liquid Phase Separation Underpins
the Formation of Replication Factories in Rotaviruses.” The EMBO Journal.
Embo Press, 2021. https://doi.org/10.15252/embj.2021107711.
ieee: F. Geiger et al., “Liquid–liquid phase separation underpins the formation
of replication factories in rotaviruses,” The EMBO Journal, vol. 40, no.
21. Embo Press, 2021.
ista: Geiger F, Acker J, Papa G, Wang X, Arter WE, Saar KL, Erkamp NA, Qi R, Bravo
JPK, Strauss S, Krainer G, Burrone OR, Jungmann R, Knowles TP, Engelke H, Borodavka
A. 2021. Liquid–liquid phase separation underpins the formation of replication
factories in rotaviruses. The EMBO Journal. 40(21), e107711.
mla: Geiger, Florian, et al. “Liquid–Liquid Phase Separation Underpins the Formation
of Replication Factories in Rotaviruses.” The EMBO Journal, vol. 40, no.
21, e107711, Embo Press, 2021, doi:10.15252/embj.2021107711.
short: F. Geiger, J. Acker, G. Papa, X. Wang, W.E. Arter, K.L. Saar, N.A. Erkamp,
R. Qi, J.P.K. Bravo, S. Strauss, G. Krainer, O.R. Burrone, R. Jungmann, T.P. Knowles,
H. Engelke, A. Borodavka, The EMBO Journal 40 (2021).
date_created: 2024-03-20T10:42:39Z
date_published: 2021-11-02T00:00:00Z
date_updated: 2024-06-04T06:08:16Z
day: '02'
doi: 10.15252/embj.2021107711
extern: '1'
external_id:
pmid:
- '34524703'
intvolume: ' 40'
issue: '21'
keyword:
- General Immunology and Microbiology
- General Biochemistry
- Genetics and Molecular Biology
- Molecular Biology
- General Neuroscience
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.15252/embj.2021107711
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: The EMBO Journal
publication_identifier:
eissn:
- 1460-2075
issn:
- 0261-4189
publication_status: published
publisher: Embo Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Liquid–liquid phase separation underpins the formation of replication factories
in rotaviruses
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 40
year: '2021'
...
---
_id: '15139'
abstract:
- lang: eng
text: Rotavirus genomes are distributed between 11 distinct RNA molecules, all of
which must be selectively copackaged during virus assembly. This likely occurs
through sequence-specific RNA interactions facilitated by the RNA chaperone NSP2.
Here, we report that NSP2 autoregulates its chaperone activity through its C-terminal
region (CTR) that promotes RNA–RNA interactions by limiting its helix-unwinding
activity. Unexpectedly, structural proteomics data revealed that the CTR does
not directly interact with RNA, while accelerating RNA release from NSP2. Cryo–electron
microscopy reconstructions of an NSP2–RNA complex reveal a highly conserved acidic
patch on the CTR, which is poised toward the bound RNA. Virus replication was
abrogated by charge-disrupting mutations within the acidic patch but completely
restored by charge-preserving mutations. Mechanistic similarities between NSP2
and the unrelated bacterial RNA chaperone Hfq suggest that accelerating RNA dissociation
while promoting intermolecular RNA interactions may be a widespread strategy of
RNA chaperone recycling.
article_number: e2100198118
article_processing_charge: No
article_type: original
author:
- first_name: Jack Peter Kelly
full_name: Bravo, Jack Peter Kelly
id: 96aecfa5-8931-11ee-af30-aa6a5d6eee0e
last_name: Bravo
orcid: 0000-0003-0456-0753
- first_name: Kira
full_name: Bartnik, Kira
last_name: Bartnik
- first_name: Luca
full_name: Venditti, Luca
last_name: Venditti
- first_name: Julia
full_name: Acker, Julia
last_name: Acker
- first_name: Emma H.
full_name: Gail, Emma H.
last_name: Gail
- first_name: Alice
full_name: Colyer, Alice
last_name: Colyer
- first_name: Chen
full_name: Davidovich, Chen
last_name: Davidovich
- first_name: Don C.
full_name: Lamb, Don C.
last_name: Lamb
- first_name: Roman
full_name: Tuma, Roman
last_name: Tuma
- first_name: Antonio N.
full_name: Calabrese, Antonio N.
last_name: Calabrese
- first_name: Alexander
full_name: Borodavka, Alexander
last_name: Borodavka
citation:
ama: Bravo JPK, Bartnik K, Venditti L, et al. Structural basis of rotavirus RNA
chaperone displacement and RNA annealing. Proceedings of the National Academy
of Sciences. 2021;118(41). doi:10.1073/pnas.2100198118
apa: Bravo, J. P. K., Bartnik, K., Venditti, L., Acker, J., Gail, E. H., Colyer,
A., … Borodavka, A. (2021). Structural basis of rotavirus RNA chaperone displacement
and RNA annealing. Proceedings of the National Academy of Sciences. Proceedings
of the National Academy of Sciences. https://doi.org/10.1073/pnas.2100198118
chicago: Bravo, Jack Peter Kelly, Kira Bartnik, Luca Venditti, Julia Acker, Emma
H. Gail, Alice Colyer, Chen Davidovich, et al. “Structural Basis of Rotavirus
RNA Chaperone Displacement and RNA Annealing.” Proceedings of the National
Academy of Sciences. Proceedings of the National Academy of Sciences, 2021.
https://doi.org/10.1073/pnas.2100198118.
ieee: J. P. K. Bravo et al., “Structural basis of rotavirus RNA chaperone
displacement and RNA annealing,” Proceedings of the National Academy of Sciences,
vol. 118, no. 41. Proceedings of the National Academy of Sciences, 2021.
ista: Bravo JPK, Bartnik K, Venditti L, Acker J, Gail EH, Colyer A, Davidovich C,
Lamb DC, Tuma R, Calabrese AN, Borodavka A. 2021. Structural basis of rotavirus
RNA chaperone displacement and RNA annealing. Proceedings of the National Academy
of Sciences. 118(41), e2100198118.
mla: Bravo, Jack Peter Kelly, et al. “Structural Basis of Rotavirus RNA Chaperone
Displacement and RNA Annealing.” Proceedings of the National Academy of Sciences,
vol. 118, no. 41, e2100198118, Proceedings of the National Academy of Sciences,
2021, doi:10.1073/pnas.2100198118.
short: J.P.K. Bravo, K. Bartnik, L. Venditti, J. Acker, E.H. Gail, A. Colyer, C.
Davidovich, D.C. Lamb, R. Tuma, A.N. Calabrese, A. Borodavka, Proceedings of the
National Academy of Sciences 118 (2021).
date_created: 2024-03-20T10:42:45Z
date_published: 2021-10-06T00:00:00Z
date_updated: 2024-06-04T06:04:07Z
day: '06'
doi: 10.1073/pnas.2100198118
extern: '1'
external_id:
pmid:
- '34615715'
intvolume: ' 118'
issue: '41'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.2100198118
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structural basis of rotavirus RNA chaperone displacement and RNA annealing
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 118
year: '2021'
...
---
_id: '15140'
abstract:
- lang: eng
text: Remdesivir is a nucleoside analog approved by the US FDA for treatment of
COVID-19. Here, we present a 3.9-Å-resolution cryo-EM reconstruction of a remdesivir-stalled
RNA-dependent RNA polymerase complex, revealing full incorporation of 3 copies
of remdesivir monophosphate (RMP) and a partially incorporated fourth RMP in the
active site. The structure reveals that RMP blocks RNA translocation after incorporation
of 3 bases following RMP, resulting in delayed chain termination, which can guide
the rational design of improved antiviral drugs.
article_processing_charge: No
article_type: original
author:
- first_name: Jack Peter Kelly
full_name: Bravo, Jack Peter Kelly
id: 96aecfa5-8931-11ee-af30-aa6a5d6eee0e
last_name: Bravo
orcid: 0000-0003-0456-0753
- first_name: Tyler L.
full_name: Dangerfield, Tyler L.
last_name: Dangerfield
- first_name: David W.
full_name: Taylor, David W.
last_name: Taylor
- first_name: Kenneth A.
full_name: Johnson, Kenneth A.
last_name: Johnson
citation:
ama: Bravo JPK, Dangerfield TL, Taylor DW, Johnson KA. Remdesivir is a delayed translocation
inhibitor of SARS-CoV-2 replication. Molecular Cell. 2021;81(7):1548-1552.e4.
doi:10.1016/j.molcel.2021.01.035
apa: Bravo, J. P. K., Dangerfield, T. L., Taylor, D. W., & Johnson, K. A. (2021).
Remdesivir is a delayed translocation inhibitor of SARS-CoV-2 replication. Molecular
Cell. Elsevier. https://doi.org/10.1016/j.molcel.2021.01.035
chicago: Bravo, Jack Peter Kelly, Tyler L. Dangerfield, David W. Taylor, and Kenneth
A. Johnson. “Remdesivir Is a Delayed Translocation Inhibitor of SARS-CoV-2 Replication.”
Molecular Cell. Elsevier, 2021. https://doi.org/10.1016/j.molcel.2021.01.035.
ieee: J. P. K. Bravo, T. L. Dangerfield, D. W. Taylor, and K. A. Johnson, “Remdesivir
is a delayed translocation inhibitor of SARS-CoV-2 replication,” Molecular
Cell, vol. 81, no. 7. Elsevier, p. 1548–1552.e4, 2021.
ista: Bravo JPK, Dangerfield TL, Taylor DW, Johnson KA. 2021. Remdesivir is a delayed
translocation inhibitor of SARS-CoV-2 replication. Molecular Cell. 81(7), 1548–1552.e4.
mla: Bravo, Jack Peter Kelly, et al. “Remdesivir Is a Delayed Translocation Inhibitor
of SARS-CoV-2 Replication.” Molecular Cell, vol. 81, no. 7, Elsevier, 2021,
p. 1548–1552.e4, doi:10.1016/j.molcel.2021.01.035.
short: J.P.K. Bravo, T.L. Dangerfield, D.W. Taylor, K.A. Johnson, Molecular Cell
81 (2021) 1548–1552.e4.
date_created: 2024-03-20T10:42:53Z
date_published: 2021-04-01T00:00:00Z
date_updated: 2024-06-04T06:00:56Z
day: '01'
doi: 10.1016/j.molcel.2021.01.035
extern: '1'
external_id:
pmid:
- '33631104'
intvolume: ' 81'
issue: '7'
keyword:
- Cell Biology
- Molecular Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: 'https://doi.org/10.1101/2020.12.14.422718 '
month: '04'
oa: 1
oa_version: Preprint
page: 1548-1552.e4
pmid: 1
publication: Molecular Cell
publication_identifier:
issn:
- 1097-2765
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Remdesivir is a delayed translocation inhibitor of SARS-CoV-2 replication
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 81
year: '2021'
...
---
_id: '15141'
abstract:
- lang: eng
text: We reveal the cryo-electron microscopy structure of a type IV-B CRISPR ribonucleoprotein
(RNP) complex (Csf) at 3.9-Å resolution. The complex best resembles the type III-A
CRISPR Csm effector complex, consisting of a Cas7-like (Csf2) filament intertwined
with a small subunit (Cas11) filament, but the complex lacks subunits for RNA
processing and target DNA cleavage. Surprisingly, instead of assembling around
a CRISPR-derived RNA (crRNA), the complex assembles upon heterogeneous RNA of
a regular length arranged in a pseudo-A-form configuration. These findings provide
a high-resolution glimpse into the assembly and function of enigmatic type IV
CRISPR systems, expanding our understanding of class I CRISPR-Cas system architecture,
and suggesting a function for type IV-B RNPs that may be distinct from other class
1 CRISPR-associated systems.
article_number: '102201'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Yi
full_name: Zhou, Yi
last_name: Zhou
- first_name: Jack Peter Kelly
full_name: Bravo, Jack Peter Kelly
id: 96aecfa5-8931-11ee-af30-aa6a5d6eee0e
last_name: Bravo
orcid: 0000-0003-0456-0753
- first_name: Hannah N.
full_name: Taylor, Hannah N.
last_name: Taylor
- first_name: Jurre A.
full_name: Steens, Jurre A.
last_name: Steens
- first_name: Ryan N.
full_name: Jackson, Ryan N.
last_name: Jackson
- first_name: Raymond H.J.
full_name: Staals, Raymond H.J.
last_name: Staals
- first_name: David W.
full_name: Taylor, David W.
last_name: Taylor
citation:
ama: Zhou Y, Bravo JPK, Taylor HN, et al. Structure of a type IV CRISPR-Cas ribonucleoprotein
complex. iScience. 2021;24(3). doi:10.1016/j.isci.2021.102201
apa: Zhou, Y., Bravo, J. P. K., Taylor, H. N., Steens, J. A., Jackson, R. N., Staals,
R. H. J., & Taylor, D. W. (2021). Structure of a type IV CRISPR-Cas ribonucleoprotein
complex. IScience. Elsevier. https://doi.org/10.1016/j.isci.2021.102201
chicago: Zhou, Yi, Jack Peter Kelly Bravo, Hannah N. Taylor, Jurre A. Steens, Ryan
N. Jackson, Raymond H.J. Staals, and David W. Taylor. “Structure of a Type IV
CRISPR-Cas Ribonucleoprotein Complex.” IScience. Elsevier, 2021. https://doi.org/10.1016/j.isci.2021.102201.
ieee: Y. Zhou et al., “Structure of a type IV CRISPR-Cas ribonucleoprotein
complex,” iScience, vol. 24, no. 3. Elsevier, 2021.
ista: Zhou Y, Bravo JPK, Taylor HN, Steens JA, Jackson RN, Staals RHJ, Taylor DW.
2021. Structure of a type IV CRISPR-Cas ribonucleoprotein complex. iScience. 24(3),
102201.
mla: Zhou, Yi, et al. “Structure of a Type IV CRISPR-Cas Ribonucleoprotein Complex.”
IScience, vol. 24, no. 3, 102201, Elsevier, 2021, doi:10.1016/j.isci.2021.102201.
short: Y. Zhou, J.P.K. Bravo, H.N. Taylor, J.A. Steens, R.N. Jackson, R.H.J. Staals,
D.W. Taylor, IScience 24 (2021).
date_created: 2024-03-20T10:43:00Z
date_published: 2021-03-19T00:00:00Z
date_updated: 2024-06-04T05:56:45Z
day: '19'
doi: 10.1016/j.isci.2021.102201
extern: '1'
external_id:
pmid:
- '33733066'
intvolume: ' 24'
issue: '3'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.isci.2021.102201
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: iScience
publication_identifier:
issn:
- 2589-0042
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Structure of a type IV CRISPR-Cas ribonucleoprotein complex
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2021'
...
---
_id: '15151'
abstract:
- lang: eng
text: Eukaryotic DNA-binding proteins operate in the context of chromatin, where
nucleosomes are the elementary building blocks. Nucleosomal DNA is wrapped around
a histone core, thereby rendering a large fraction of the DNA surface inaccessible
to DNA-binding proteins. Nevertheless, first responders in DNA repair and sequence-specific
transcription factors bind DNA target sites obstructed by chromatin. While early
studies examined protein binding to histone-free DNA, it is only now beginning
to emerge how DNA sequences are interrogated on nucleosomes. These readout strategies
range from the release of nucleosomal DNA from histones, to rotational/translation
register shifts of the DNA motif, and nucleosome-specific DNA binding modes that
differ from those observed on naked DNA. Since DNA motif engagement on nucleosomes
strongly depends on position and orientation, we argue that motif location and
nucleosome positioning co-determine protein access to DNA in transcription and
DNA repair.
article_processing_charge: No
article_type: review
author:
- first_name: Alicia
full_name: Michael, Alicia
id: 6437c950-2a03-11ee-914d-d6476dd7b75c
last_name: Michael
orcid: 0000-0002-6080-839X
- first_name: Nicolas H.
full_name: Thomä, Nicolas H.
last_name: Thomä
citation:
ama: Michael AK, Thomä NH. Reading the chromatinized genome. Cell. 2021;184(14):3599-3611.
doi:10.1016/j.cell.2021.05.029
apa: Michael, A. K., & Thomä, N. H. (2021). Reading the chromatinized genome.
Cell. Elsevier. https://doi.org/10.1016/j.cell.2021.05.029
chicago: Michael, Alicia K., and Nicolas H. Thomä. “Reading the Chromatinized Genome.”
Cell. Elsevier, 2021. https://doi.org/10.1016/j.cell.2021.05.029.
ieee: A. K. Michael and N. H. Thomä, “Reading the chromatinized genome,” Cell,
vol. 184, no. 14. Elsevier, pp. 3599–3611, 2021.
ista: Michael AK, Thomä NH. 2021. Reading the chromatinized genome. Cell. 184(14),
3599–3611.
mla: Michael, Alicia K., and Nicolas H. Thomä. “Reading the Chromatinized Genome.”
Cell, vol. 184, no. 14, Elsevier, 2021, pp. 3599–611, doi:10.1016/j.cell.2021.05.029.
short: A.K. Michael, N.H. Thomä, Cell 184 (2021) 3599–3611.
date_created: 2024-03-21T07:54:19Z
date_published: 2021-07-08T00:00:00Z
date_updated: 2024-03-25T12:31:39Z
day: '08'
doi: 10.1016/j.cell.2021.05.029
extern: '1'
intvolume: ' 184'
issue: '14'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cell.2021.05.029
month: '07'
oa: 1
oa_version: Published Version
page: 3599-3611
publication: Cell
publication_identifier:
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Reading the chromatinized genome
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 184
year: '2021'
...
---
_id: '15215'
abstract:
- lang: eng
text: AT2019wey (SRGA J043520.9+552226, SRGE J043523.3+552234) is a transient first
reported by the ATLAS optical survey in 2019 December. It rose to prominence upon
detection, three months later, by the Spektrum-Roentgen-Gamma (SRG) mission in
its first all-sky survey. X-ray observations reported in Yao et al. suggest that
AT2019wey is a Galactic low-mass X-ray binary (LMXB) with a black hole (BH) or
neutron star (NS) accretor. Here we present ultraviolet, optical, near-infrared,
and radio observations of this object. We show that the companion is a short-period
(P ≲ 16 hr) low-mass (<1 M⊙) star. We consider AT2019wey to be a candidate BH
system since its locations on the Lradio–LX and Lopt–LX diagrams are closer to
BH binaries than NS binaries. We demonstrate that from 2020 June to August, despite
the more than 10 times brightening at radio and X-ray wavelengths, the optical
luminosity of AT2019wey only increased by 1.3–1.4 times. We interpret the UV/optical
emission before the brightening as thermal emission from a truncated disk in a
hot accretion flow and the UV/optical emission after the brightening as reprocessing
of the X-ray emission in the outer accretion disk. AT2019wey demonstrates that
combining current wide-field optical surveys and SRG provides a way to discover
the emerging population of short-period BH LMXB systems with faint X-ray outbursts.
article_number: '120'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Yuhan
full_name: Yao, Yuhan
last_name: Yao
- first_name: S. R.
full_name: Kulkarni, S. R.
last_name: Kulkarni
- first_name: Kevin B.
full_name: Burdge, Kevin B.
last_name: Burdge
- first_name: Ilaria
full_name: Caiazzo, Ilaria
id: 8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d
last_name: Caiazzo
orcid: 0000-0002-4770-5388
- first_name: Kishalay
full_name: De, Kishalay
last_name: De
- first_name: Dillon
full_name: Dong, Dillon
last_name: Dong
- first_name: C.
full_name: Fremling, C.
last_name: Fremling
- first_name: Mansi M.
full_name: Kasliwal, Mansi M.
last_name: Kasliwal
- first_name: Thomas
full_name: Kupfer, Thomas
last_name: Kupfer
- first_name: Jan
full_name: van Roestel, Jan
last_name: van Roestel
- first_name: Jesper
full_name: Sollerman, Jesper
last_name: Sollerman
- first_name: Ashot
full_name: Bagdasaryan, Ashot
last_name: Bagdasaryan
- first_name: Eric C.
full_name: Bellm, Eric C.
last_name: Bellm
- first_name: S. Bradley
full_name: Cenko, S. Bradley
last_name: Cenko
- first_name: Andrew J.
full_name: Drake, Andrew J.
last_name: Drake
- first_name: Dmitry A.
full_name: Duev, Dmitry A.
last_name: Duev
- first_name: Matthew J.
full_name: Graham, Matthew J.
last_name: Graham
- first_name: Stephen
full_name: Kaye, Stephen
last_name: Kaye
- first_name: Frank J.
full_name: Masci, Frank J.
last_name: Masci
- first_name: Nicolas
full_name: Miranda, Nicolas
last_name: Miranda
- first_name: Thomas A.
full_name: Prince, Thomas A.
last_name: Prince
- first_name: Reed
full_name: Riddle, Reed
last_name: Riddle
- first_name: Ben
full_name: Rusholme, Ben
last_name: Rusholme
- first_name: Maayane T.
full_name: Soumagnac, Maayane T.
last_name: Soumagnac
citation:
ama: 'Yao Y, Kulkarni SR, Burdge KB, et al. Multi-wavelength observations of AT2019wey:
A new candidate black hole low-mass X-ray binary. The Astrophysical Journal.
2021;920(2). doi:10.3847/1538-4357/ac15f9'
apa: 'Yao, Y., Kulkarni, S. R., Burdge, K. B., Caiazzo, I., De, K., Dong, D., …
Soumagnac, M. T. (2021). Multi-wavelength observations of AT2019wey: A new candidate
black hole low-mass X-ray binary. The Astrophysical Journal. American Astronomical
Society. https://doi.org/10.3847/1538-4357/ac15f9'
chicago: 'Yao, Yuhan, S. R. Kulkarni, Kevin B. Burdge, Ilaria Caiazzo, Kishalay
De, Dillon Dong, C. Fremling, et al. “Multi-Wavelength Observations of AT2019wey:
A New Candidate Black Hole Low-Mass X-Ray Binary.” The Astrophysical Journal.
American Astronomical Society, 2021. https://doi.org/10.3847/1538-4357/ac15f9.'
ieee: 'Y. Yao et al., “Multi-wavelength observations of AT2019wey: A new
candidate black hole low-mass X-ray binary,” The Astrophysical Journal,
vol. 920, no. 2. American Astronomical Society, 2021.'
ista: 'Yao Y, Kulkarni SR, Burdge KB, Caiazzo I, De K, Dong D, Fremling C, Kasliwal
MM, Kupfer T, van Roestel J, Sollerman J, Bagdasaryan A, Bellm EC, Cenko SB, Drake
AJ, Duev DA, Graham MJ, Kaye S, Masci FJ, Miranda N, Prince TA, Riddle R, Rusholme
B, Soumagnac MT. 2021. Multi-wavelength observations of AT2019wey: A new candidate
black hole low-mass X-ray binary. The Astrophysical Journal. 920(2), 120.'
mla: 'Yao, Yuhan, et al. “Multi-Wavelength Observations of AT2019wey: A New Candidate
Black Hole Low-Mass X-Ray Binary.” The Astrophysical Journal, vol. 920,
no. 2, 120, American Astronomical Society, 2021, doi:10.3847/1538-4357/ac15f9.'
short: Y. Yao, S.R. Kulkarni, K.B. Burdge, I. Caiazzo, K. De, D. Dong, C. Fremling,
M.M. Kasliwal, T. Kupfer, J. van Roestel, J. Sollerman, A. Bagdasaryan, E.C. Bellm,
S.B. Cenko, A.J. Drake, D.A. Duev, M.J. Graham, S. Kaye, F.J. Masci, N. Miranda,
T.A. Prince, R. Riddle, B. Rusholme, M.T. Soumagnac, The Astrophysical Journal
920 (2021).
date_created: 2024-03-26T10:32:06Z
date_published: 2021-10-21T00:00:00Z
date_updated: 2024-04-02T07:28:22Z
day: '21'
doi: 10.3847/1538-4357/ac15f9
extern: '1'
external_id:
arxiv:
- '2012.00169'
intvolume: ' 920'
issue: '2'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2012.00169
month: '10'
oa: 1
oa_version: Preprint
publication: The Astrophysical Journal
publication_identifier:
eissn:
- 1538-4357
issn:
- 0004-637X
publication_status: published
publisher: American Astronomical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Multi-wavelength observations of AT2019wey: A new candidate black hole low-mass
X-ray binary'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 920
year: '2021'
...