---
_id: '10670'
abstract:
- lang: eng
text: "Imitation learning enables high-fidelity, vision-based learning of policies
within rich, photorealistic environments. However, such techniques often rely
on traditional discrete-time neural models and face difficulties in generalizing
to domain shifts by failing to account for the causal relationships between the
agent and the environment. In this paper, we propose a theoretical and experimental
framework for learning causal representations using continuous-time neural networks,
specifically over their discrete-time counterparts. We evaluate our method in
the context of visual-control learning of drones over a series of complex tasks,
ranging from short- and long-term navigation, to chasing static and dynamic objects
through photorealistic environments. Our results demonstrate that causal continuous-time\r\ndeep
models can perform robust navigation tasks, where advanced recurrent models fail.
These models learn complex causal control representations directly from raw visual
inputs and scale to solve a variety of tasks using imitation learning."
acknowledgement: "C.V., R.H. A.A. and D.R. are partially supported by Boeing and MIT.
A.A. is supported by the National Science Foundation (NSF) Graduate Research Fellowship
Program. M.L. is supported in part by the Austrian Science Fund (FWF) under grant
Z211-N23 (Wittgenstein Award). Research was sponsored by the United States Air Force
Research Laboratory and the United States Air Force Artificial Intelligence Accelerator
and was accomplished under Cooperative Agreement Number FA8750-19-2-1000. The views
and conclusions contained in this document are those of the authors\r\nand should
not be interpreted as representing the official policies, either expressed or implied,
of the United States Air Force or the U.S. Government. The U.S. Government is authorized
to reproduce and distribute reprints for Government purposes notwithstanding any
copyright notation herein.\r\n"
alternative_title:
- ' Advances in Neural Information Processing Systems'
article_processing_charge: No
arxiv: 1
author:
- first_name: Charles J
full_name: Vorbach, Charles J
last_name: Vorbach
- first_name: Ramin
full_name: Hasani, Ramin
last_name: Hasani
- first_name: Alexander
full_name: Amini, Alexander
last_name: Amini
- first_name: Mathias
full_name: Lechner, Mathias
id: 3DC22916-F248-11E8-B48F-1D18A9856A87
last_name: Lechner
- first_name: Daniela
full_name: Rus, Daniela
last_name: Rus
citation:
ama: 'Vorbach CJ, Hasani R, Amini A, Lechner M, Rus D. Causal navigation by continuous-time
neural networks. In: 35th Conference on Neural Information Processing Systems.
Neural Information Processing Systems Foundation; 2021.'
apa: 'Vorbach, C. J., Hasani, R., Amini, A., Lechner, M., & Rus, D. (2021).
Causal navigation by continuous-time neural networks. In 35th Conference on
Neural Information Processing Systems. Virtual: Neural Information Processing
Systems Foundation.'
chicago: Vorbach, Charles J, Ramin Hasani, Alexander Amini, Mathias Lechner, and
Daniela Rus. “Causal Navigation by Continuous-Time Neural Networks.” In 35th
Conference on Neural Information Processing Systems. Neural Information Processing
Systems Foundation, 2021.
ieee: C. J. Vorbach, R. Hasani, A. Amini, M. Lechner, and D. Rus, “Causal navigation
by continuous-time neural networks,” in 35th Conference on Neural Information
Processing Systems, Virtual, 2021.
ista: 'Vorbach CJ, Hasani R, Amini A, Lechner M, Rus D. 2021. Causal navigation
by continuous-time neural networks. 35th Conference on Neural Information Processing
Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information
Processing Systems, .'
mla: Vorbach, Charles J., et al. “Causal Navigation by Continuous-Time Neural Networks.”
35th Conference on Neural Information Processing Systems, Neural Information
Processing Systems Foundation, 2021.
short: C.J. Vorbach, R. Hasani, A. Amini, M. Lechner, D. Rus, in:, 35th Conference
on Neural Information Processing Systems, Neural Information Processing Systems
Foundation, 2021.
conference:
end_date: 2021-12-10
location: Virtual
name: 'NeurIPS: Neural Information Processing Systems'
start_date: 2021-12-06
das_tickbox: '1'
date_created: 2022-01-25T15:47:50Z
date_published: 2021-12-01T00:00:00Z
date_updated: 2026-07-07T06:49:46Z
day: '01'
ddc:
- '000'
department:
- _id: GradSch
- _id: ToHe
external_id:
arxiv:
- '2106.08314'
file:
- access_level: open_access
checksum: be81f0ade174a8c9b2d4fe09590b2021
content_type: application/pdf
creator: mlechner
date_created: 2022-01-26T07:37:24Z
date_updated: 2022-01-26T07:37:24Z
file_id: '10679'
file_name: NeurIPS-2021-causal-navigation-by-continuous-time-neural-networks-Paper.pdf
file_size: 6841228
relation: main_file
success: 1
file_date_updated: 2022-01-26T07:37:24Z
has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/3.0/
main_file_link:
- open_access: '1'
url: https://proceedings.neurips.cc/paper/2021/hash/67ba02d73c54f0b83c05507b7fb7267f-Abstract.html
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
publication: 35th Conference on Neural Information Processing Systems
publication_identifier:
issn:
- 1049-5258
publication_status: published
publisher: Neural Information Processing Systems Foundation
quality_controlled: '1'
status: public
title: Causal navigation by continuous-time neural networks
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND
3.0)
short: CC BY-NC-ND (3.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '9293'
abstract:
- lang: eng
text: 'We consider planning problems for graphs, Markov Decision Processes (MDPs),
and games on graphs in an explicit state space. While graphs represent the most
basic planning model, MDPs represent interaction with nature and games on graphs
represent interaction with an adversarial environment. We consider two planning
problems with k different target sets: (a) the coverage problem asks whether there
is a plan for each individual target set; and (b) the sequential target reachability
problem asks whether the targets can be reached in a given sequence. For the coverage
problem, we present a linear-time algorithm for graphs, and quadratic conditional
lower bound for MDPs and games on graphs. For the sequential target problem, we
present a linear-time algorithm for graphs, a sub-quadratic algorithm for MDPs,
and a quadratic conditional lower bound for games on graphs. Our results with
conditional lower bounds, based on the boolean matrix multiplication (BMM) conjecture
and strong exponential time hypothesis (SETH), establish (i) model-separation
results showing that for the coverage problem MDPs and games on graphs are harder
than graphs, and for the sequential reachability problem games on graphs are harder
than MDPs and graphs; and (ii) problem-separation results showing that for MDPs
the coverage problem is harder than the sequential target problem.'
article_number: '103499'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Wolfgang
full_name: Dvořák, Wolfgang
last_name: Dvořák
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Alexander
full_name: Svozil, Alexander
last_name: Svozil
citation:
ama: Chatterjee K, Dvořák W, Henzinger M, Svozil A. Algorithms and conditional lower
bounds for planning problems. Artificial Intelligence. 2021;297(8). doi:10.1016/j.artint.2021.103499
apa: Chatterjee, K., Dvořák, W., Henzinger, M., & Svozil, A. (2021). Algorithms
and conditional lower bounds for planning problems. Artificial Intelligence.
Elsevier. https://doi.org/10.1016/j.artint.2021.103499
chicago: Chatterjee, Krishnendu, Wolfgang Dvořák, Monika Henzinger, and Alexander
Svozil. “Algorithms and Conditional Lower Bounds for Planning Problems.” Artificial
Intelligence. Elsevier, 2021. https://doi.org/10.1016/j.artint.2021.103499.
ieee: K. Chatterjee, W. Dvořák, M. Henzinger, and A. Svozil, “Algorithms and conditional
lower bounds for planning problems,” Artificial Intelligence, vol. 297,
no. 8. Elsevier, 2021.
ista: Chatterjee K, Dvořák W, Henzinger M, Svozil A. 2021. Algorithms and conditional
lower bounds for planning problems. Artificial Intelligence. 297(8), 103499.
mla: Chatterjee, Krishnendu, et al. “Algorithms and Conditional Lower Bounds for
Planning Problems.” Artificial Intelligence, vol. 297, no. 8, 103499, Elsevier,
2021, doi:10.1016/j.artint.2021.103499.
short: K. Chatterjee, W. Dvořák, M. Henzinger, A. Svozil, Artificial Intelligence
297 (2021).
corr_author: '1'
date_created: 2021-03-28T22:01:40Z
date_published: 2021-03-16T00:00:00Z
date_updated: 2026-07-07T13:36:04Z
day: '16'
department:
- _id: KrCh
doi: 10.1016/j.artint.2021.103499
external_id:
arxiv:
- '1804.07031'
isi:
- '000657537500003'
fulldoi: https://doi.org/10.1016/j.artint.2021.103499
intvolume: ' 297'
isi: 1
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1804.07031
month: '03'
oa: 1
oa_version: Preprint
publication: Artificial Intelligence
publication_identifier:
issn:
- 0004-3702
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '35'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Algorithms and conditional lower bounds for planning problems
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 297
year: '2021'
...
---
_id: '9441'
abstract:
- lang: eng
text: "Isomanifolds are the generalization of isosurfaces to arbitrary dimension
and codimension, i.e. submanifolds of ℝ^d defined as the zero set of some multivariate
multivalued smooth function f: ℝ^d → ℝ^{d-n}, where n is the intrinsic dimension
of the manifold. A natural way to approximate a smooth isomanifold M is to consider
its Piecewise-Linear (PL) approximation M̂ based on a triangulation \U0001D4AF
of the ambient space ℝ^d. In this paper, we describe a simple algorithm to trace
isomanifolds from a given starting point. The algorithm works for arbitrary dimensions
n and d, and any precision D. Our main result is that, when f (or M) has bounded
complexity, the complexity of the algorithm is polynomial in d and δ = 1/D (and
unavoidably exponential in n). Since it is known that for δ = Ω (d^{2.5}), M̂
is O(D²)-close and isotopic to M, our algorithm produces a faithful PL-approximation
of isomanifolds of bounded complexity in time polynomial in d. Combining this
algorithm with dimensionality reduction techniques, the dependency on d in the
size of M̂ can be completely removed with high probability. We also show that
the algorithm can handle isomanifolds with boundary and, more generally, isostratifolds.
The algorithm for isomanifolds with boundary has been implemented and experimental
results are reported, showing that it is practical and can handle cases that are
far ahead of the state-of-the-art. "
acknowledgement: We thank Dominique Attali, Guilherme de Fonseca, Arijit Ghosh, Vincent
Pilaud and Aurélien Alvarez for their comments and suggestions. We also acknowledge
the reviewers.
alternative_title:
- LIPIcs
article_processing_charge: No
author:
- first_name: Jean-Daniel
full_name: Boissonnat, Jean-Daniel
last_name: Boissonnat
- first_name: Siargey
full_name: Kachanovich, Siargey
last_name: Kachanovich
- first_name: Mathijs
full_name: Wintraecken, Mathijs
id: 307CFBC8-F248-11E8-B48F-1D18A9856A87
last_name: Wintraecken
orcid: 0000-0002-7472-2220
citation:
ama: 'Boissonnat J-D, Kachanovich S, Wintraecken M. Tracing isomanifolds in Rd in
time polynomial in d using Coxeter-Freudenthal-Kuhn triangulations. In: 37th
International Symposium on Computational Geometry. Vol 189. Leibniz International
Proceedings in Informatics (LIPIcs). Dagstuhl, Germany: Schloss Dagstuhl - Leibniz-Zentrum
für Informatik; 2021:17:1-17:16. doi:10.4230/LIPIcs.SoCG.2021.17'
apa: 'Boissonnat, J.-D., Kachanovich, S., & Wintraecken, M. (2021). Tracing
isomanifolds in Rd in time polynomial in d using Coxeter-Freudenthal-Kuhn triangulations.
In 37th International Symposium on Computational Geometry (Vol. 189, p.
17:1-17:16). Dagstuhl, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
https://doi.org/10.4230/LIPIcs.SoCG.2021.17'
chicago: 'Boissonnat, Jean-Daniel, Siargey Kachanovich, and Mathijs Wintraecken.
“Tracing Isomanifolds in Rd in Time Polynomial in d Using Coxeter-Freudenthal-Kuhn
Triangulations.” In 37th International Symposium on Computational Geometry,
189:17:1-17:16. Leibniz International Proceedings in Informatics (LIPIcs). Dagstuhl,
Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021. https://doi.org/10.4230/LIPIcs.SoCG.2021.17.'
ieee: J.-D. Boissonnat, S. Kachanovich, and M. Wintraecken, “Tracing isomanifolds
in Rd in time polynomial in d using Coxeter-Freudenthal-Kuhn triangulations,”
in 37th International Symposium on Computational Geometry, Virtual, 2021,
vol. 189, p. 17:1-17:16.
ista: 'Boissonnat J-D, Kachanovich S, Wintraecken M. 2021. Tracing isomanifolds
in Rd in time polynomial in d using Coxeter-Freudenthal-Kuhn triangulations. 37th
International Symposium on Computational Geometry. SoCG: Symposium on Computational
GeometryLeibniz International Proceedings in Informatics (LIPIcs), LIPIcs, vol.
189, 17:1-17:16.'
mla: Boissonnat, Jean-Daniel, et al. “Tracing Isomanifolds in Rd in Time Polynomial
in d Using Coxeter-Freudenthal-Kuhn Triangulations.” 37th International Symposium
on Computational Geometry, vol. 189, Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, 2021, p. 17:1-17:16, doi:10.4230/LIPIcs.SoCG.2021.17.
short: J.-D. Boissonnat, S. Kachanovich, M. Wintraecken, in:, 37th International
Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
Dagstuhl, Germany, 2021, p. 17:1-17:16.
conference:
end_date: 2021-06-11
location: Virtual
name: 'SoCG: Symposium on Computational Geometry'
start_date: 2021-06-07
das_tickbox: '1'
date_created: 2021-06-02T10:10:55Z
date_published: 2021-06-02T00:00:00Z
date_updated: 2026-07-07T13:43:40Z
day: '02'
ddc:
- '005'
- '516'
- '514'
department:
- _id: HeEd
doi: 10.4230/LIPIcs.SoCG.2021.17
ec_funded: 1
file:
- access_level: open_access
checksum: c322aa48d5d35a35877896cc565705b6
content_type: application/pdf
creator: mwintrae
date_created: 2021-06-02T10:22:33Z
date_updated: 2021-06-02T10:22:33Z
file_id: '9442'
file_name: LIPIcs-SoCG-2021-17.pdf
file_size: 1972902
relation: main_file
success: 1
file_date_updated: 2021-06-02T10:22:33Z
fulldoi: https://doi.org/10.4230/LIPIcs.SoCG.2021.17
has_accepted_license: '1'
intvolume: ' 189'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '06'
oa: 1
oa_version: Published Version
page: 17:1-17:16
place: Dagstuhl, Germany
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: 37th International Symposium on Computational Geometry
publication_identifier:
isbn:
- 978-3-95977-184-9
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
related_material:
record:
- id: '12960'
relation: later_version
status: public
scopus_import: '1'
series_title: Leibniz International Proceedings in Informatics (LIPIcs)
status: public
title: Tracing isomanifolds in Rd in time polynomial in d using Coxeter-Freudenthal-Kuhn
triangulations
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 189
year: '2021'
...
---
_id: '10041'
abstract:
- lang: eng
text: Yao’s garbling scheme is one of the most fundamental cryptographic constructions.
Lindell and Pinkas (Journal of Cryptograhy 2009) gave a formal proof of security
in the selective setting where the adversary chooses the challenge inputs before
seeing the garbled circuit assuming secure symmetric-key encryption (and hence
one-way functions). This was followed by results, both positive and negative,
concerning its security in the, stronger, adaptive setting. Applebaum et al. (Crypto
2013) showed that it cannot satisfy adaptive security as is, due to a simple incompressibility
argument. Jafargholi and Wichs (TCC 2017) considered a natural adaptation of Yao’s
scheme (where the output mapping is sent in the online phase, together with the
garbled input) that circumvents this negative result, and proved that it is adaptively
secure, at least for shallow circuits. In particular, they showed that for the
class of circuits of depth δ , the loss in security is at most exponential in δ
. The above results all concern the simulation-based notion of security. In this
work, we show that the upper bound of Jafargholi and Wichs is basically optimal
in a strong sense. As our main result, we show that there exists a family of Boolean
circuits, one for each depth δ∈N , such that any black-box reduction proving
the adaptive indistinguishability of the natural adaptation of Yao’s scheme from
any symmetric-key encryption has to lose a factor that is exponential in δ√
. Since indistinguishability is a weaker notion than simulation, our bound also
applies to adaptive simulation. To establish our results, we build on the recent
approach of Kamath et al. (Eprint 2021), which uses pebbling lower bounds in conjunction
with oracle separations to prove fine-grained lower bounds on loss in cryptographic
security.
acknowledgement: We would like to thank the anonymous reviewers of Crypto’21 whose
detailed comments helped us considerably improve the presentation of the paper.
alternative_title:
- LCNS
article_processing_charge: No
author:
- first_name: Chethan
full_name: Kamath Hosdurg, Chethan
id: 4BD3F30E-F248-11E8-B48F-1D18A9856A87
last_name: Kamath Hosdurg
orcid: 0009-0006-6812-7317
- first_name: Karen
full_name: Klein, Karen
id: 3E83A2F8-F248-11E8-B48F-1D18A9856A87
last_name: Klein
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Daniel
full_name: Wichs, Daniel
last_name: Wichs
citation:
ama: 'Kamath Hosdurg C, Klein K, Pietrzak KZ, Wichs D. Limits on the Adaptive Security
of Yao’s Garbling. In: 41st Annual International Cryptology Conference.
Vol 12826. Cham: Springer Nature; 2021:486-515. doi:10.1007/978-3-030-84245-1_17'
apa: 'Kamath Hosdurg, C., Klein, K., Pietrzak, K. Z., & Wichs, D. (2021). Limits
on the Adaptive Security of Yao’s Garbling. In 41st Annual International Cryptology
Conference (Vol. 12826, pp. 486–515). Cham: Springer Nature. https://doi.org/10.1007/978-3-030-84245-1_17'
chicago: 'Kamath Hosdurg, Chethan, Karen Klein, Krzysztof Z Pietrzak, and Daniel
Wichs. “Limits on the Adaptive Security of Yao’s Garbling.” In 41st Annual
International Cryptology Conference, 12826:486–515. Cham: Springer Nature,
2021. https://doi.org/10.1007/978-3-030-84245-1_17.'
ieee: C. Kamath Hosdurg, K. Klein, K. Z. Pietrzak, and D. Wichs, “Limits on the
Adaptive Security of Yao’s Garbling,” in 41st Annual International Cryptology
Conference, Virtual, 2021, vol. 12826, pp. 486–515.
ista: 'Kamath Hosdurg C, Klein K, Pietrzak KZ, Wichs D. 2021. Limits on the Adaptive
Security of Yao’s Garbling. 41st Annual International Cryptology Conference. CRYPTO:
Annual International Cryptology Conference, LCNS, vol. 12826, 486–515.'
mla: Kamath Hosdurg, Chethan, et al. “Limits on the Adaptive Security of Yao’s Garbling.”
41st Annual International Cryptology Conference, vol. 12826, Springer Nature,
2021, pp. 486–515, doi:10.1007/978-3-030-84245-1_17.
short: C. Kamath Hosdurg, K. Klein, K.Z. Pietrzak, D. Wichs, in:, 41st Annual International
Cryptology Conference, Springer Nature, Cham, 2021, pp. 486–515.
conference:
end_date: 2021-08-20
location: Virtual
name: 'CRYPTO: Annual International Cryptology Conference'
start_date: 2021-08-16
cryptoeprintid: 1
date_created: 2021-09-23T14:06:15Z
date_published: 2021-08-11T00:00:00Z
date_updated: 2026-07-07T13:57:01Z
day: '11'
department:
- _id: KrPi
doi: 10.1007/978-3-030-84245-1_17
ec_funded: 1
external_id:
cryptoeprintid:
- 2021/945
isi:
- '000696697800017'
fulldoi: https://doi.org/10.1007/978-3-030-84245-1_17
intvolume: ' 12826'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2021/945
month: '08'
oa: 1
oa_version: Preprint
page: 486-515
place: Cham
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication: 41st Annual International Cryptology Conference
publication_identifier:
eisbn:
- 978-3-030-84245-1
eissn:
- 1611-3349
isbn:
- 978-3-030-84244-4
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '10035'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Limits on the Adaptive Security of Yao’s Garbling
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12826
year: '2021'
...
---
_id: '11453'
abstract:
- lang: eng
text: "Neuronal computations depend on synaptic connectivity and intrinsic electrophysiological
properties. Synaptic connectivity determines which inputs from presynaptic neurons
are integrated, while cellular properties determine how inputs are filtered over
time. Unlike their biological counterparts, most computational approaches to learning
in simulated neural networks are limited to changes in synaptic connectivity.
However, if intrinsic parameters change, neural computations are altered drastically.
Here, we include the parameters that determine the intrinsic properties,\r\ne.g.,
time constants and reset potential, into the learning paradigm. Using sparse feedback
signals that indicate target spike times, and gradient-based parameter updates,
we show that the intrinsic parameters can be learned along with the synaptic weights
to produce specific input-output functions. Specifically, we use a teacher-student
paradigm in which a randomly initialised leaky integrate-and-fire or resonate-and-fire
neuron must recover the parameters of a teacher neuron. We show that complex temporal
functions can be learned online and without backpropagation through time, relying
on event-based updates only. Our results are a step towards online learning of
neural computations from ungraded and unsigned sparse feedback signals with a
biologically inspired learning mechanism."
acknowledgement: We would like to thank Professor Dr. Henning Sprekeler for his valuable
suggestions and Dr. Andrew Saxe, Milan Klöwer and Anna Wallis for their constructive
feedback on the manuscript. Lukas Braun was supported by the Network of European
Neuroscience Schools through their NENS Exchange Grant program, by the European
Union through their European Community Action Scheme for the Mobility of University
Students, the Woodward Scholarship awarded by Wadham College, Oxford and the Medical
Research Council [MR/N013468/1]. Tim P. Vogels was supported by a Wellcome Trust
Senior Research Fellowship [214316/Z/18/Z].
alternative_title:
- Advances in Neural Information Processing Systems
article_processing_charge: No
author:
- first_name: Lukas
full_name: Braun, Lukas
last_name: Braun
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
citation:
ama: 'Braun L, Vogels TP. Online learning of neural computations from sparse temporal
feedback. In: 35th Conference on Neural Information Processing Systems.
Vol 20. Neural Information Processing Systems Foundation; 2021:16437-16450.'
apa: 'Braun, L., & Vogels, T. P. (2021). Online learning of neural computations
from sparse temporal feedback. In 35th Conference on Neural Information Processing
Systems (Vol. 20, pp. 16437–16450). Virtual, Online: Neural Information Processing
Systems Foundation.'
chicago: Braun, Lukas, and Tim P Vogels. “Online Learning of Neural Computations
from Sparse Temporal Feedback.” In 35th Conference on Neural Information Processing
Systems, 20:16437–50. Neural Information Processing Systems Foundation, 2021.
ieee: L. Braun and T. P. Vogels, “Online learning of neural computations from sparse
temporal feedback,” in 35th Conference on Neural Information Processing Systems,
Virtual, Online, 2021, vol. 20, pp. 16437–16450.
ista: 'Braun L, Vogels TP. 2021. Online learning of neural computations from sparse
temporal feedback. 35th Conference on Neural Information Processing Systems. NeurIPS:
Neural Information Processing Systems, Advances in Neural Information Processing
Systems, vol. 20, 16437–16450.'
mla: Braun, Lukas, and Tim P. Vogels. “Online Learning of Neural Computations from
Sparse Temporal Feedback.” 35th Conference on Neural Information Processing
Systems, vol. 20, Neural Information Processing Systems Foundation, 2021,
pp. 16437–50.
short: L. Braun, T.P. Vogels, in:, 35th Conference on Neural Information Processing
Systems, Neural Information Processing Systems Foundation, 2021, pp. 16437–16450.
conference:
end_date: 2021-12-14
location: Virtual, Online
name: 'NeurIPS: Neural Information Processing Systems'
start_date: 2021-12-06
corr_author: '1'
das_tickbox: '1'
date_created: 2022-06-19T22:01:59Z
date_published: 2021-12-01T00:00:00Z
date_updated: 2026-07-08T05:45:00Z
day: '01'
ddc:
- '000'
- '570'
department:
- _id: TiVo
intvolume: ' 20'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://proceedings.neurips.cc/paper/2021/file/88e1ce84f9feef5a08d0df0334c53468-Paper.pdf
month: '12'
oa: 1
oa_version: Published Version
page: 16437-16450
project:
- _id: c084a126-5a5b-11eb-8a69-d75314a70a87
grant_number: 214316/Z/18/Z
name: "Whatâ\x80\x99s in a memory? Spatiotemporal dynamics in strongly coupled recurrent
neuronal networks."
publication: 35th Conference on Neural Information Processing Systems
publication_identifier:
isbn:
- '9781713845393'
issn:
- 1049-5258
publication_status: published
publisher: Neural Information Processing Systems Foundation
quality_controlled: '1'
scopus_import: '1'
status: public
title: Online learning of neural computations from sparse temporal feedback
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 20
year: '2021'
...
---
_id: '11452'
abstract:
- lang: eng
text: We study efficient distributed algorithms for the fundamental problem of principal
component analysis and leading eigenvector computation on the sphere, when the
data are randomly distributed among a set of computational nodes. We propose a
new quantized variant of Riemannian gradient descent to solve this problem, and
prove that the algorithm converges with high probability under a set of necessary
spherical-convexity properties. We give bounds on the number of bits transmitted
by the algorithm under common initialization schemes, and investigate the dependency
on the problem dimension in each case.
acknowledgement: We would like to thank the anonymous reviewers for helpful comments
and suggestions. We also thank Aurelien Lucchi and Antonio Orvieto for fruitful
discussions at an early stage of this work. FA is partially supported by the SNSF
under research project No. 192363 and conducted part of this work while at IST Austria
under the European Union’s Horizon 2020 research and innovation programme (grant
agreement No. 805223 ScaleML). PD partly conducted this work while at IST Austria
and was supported by the European Union’s Horizon 2020 programme under the Marie
Skłodowska-Curie grant agreement No. 754411.
alternative_title:
- Advances in Neural Information Processing Systems
article_processing_charge: No
arxiv: 1
author:
- first_name: Foivos
full_name: Alimisis, Foivos
last_name: Alimisis
- first_name: Peter
full_name: Davies, Peter
id: 11396234-BB50-11E9-B24C-90FCE5697425
last_name: Davies
orcid: 0000-0002-5646-9524
- first_name: Bart
full_name: Vandereycken, Bart
last_name: Vandereycken
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
citation:
ama: 'Alimisis F, Davies P, Vandereycken B, Alistarh D-A. Distributed principal
component analysis with limited communication. In: 35th Conference on Neural
Information Processing Systems. Vol 4. Neural Information Processing Systems
Foundation; 2021:2823-2834.'
apa: 'Alimisis, F., Davies, P., Vandereycken, B., & Alistarh, D.-A. (2021).
Distributed principal component analysis with limited communication. In 35th
Conference on Neural Information Processing Systems (Vol. 4, pp. 2823–2834).
Virtual, Online: Neural Information Processing Systems Foundation.'
chicago: Alimisis, Foivos, Peter Davies, Bart Vandereycken, and Dan-Adrian Alistarh.
“Distributed Principal Component Analysis with Limited Communication.” In 35th
Conference on Neural Information Processing Systems, 4:2823–34. Neural Information
Processing Systems Foundation, 2021.
ieee: F. Alimisis, P. Davies, B. Vandereycken, and D.-A. Alistarh, “Distributed
principal component analysis with limited communication,” in 35th Conference
on Neural Information Processing Systems, Virtual, Online, 2021, vol. 4, pp.
2823–2834.
ista: 'Alimisis F, Davies P, Vandereycken B, Alistarh D-A. 2021. Distributed principal
component analysis with limited communication. 35th Conference on Neural Information
Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in
Neural Information Processing Systems, vol. 4, 2823–2834.'
mla: Alimisis, Foivos, et al. “Distributed Principal Component Analysis with Limited
Communication.” 35th Conference on Neural Information Processing Systems,
vol. 4, Neural Information Processing Systems Foundation, 2021, pp. 2823–34.
short: F. Alimisis, P. Davies, B. Vandereycken, D.-A. Alistarh, in:, 35th Conference
on Neural Information Processing Systems, Neural Information Processing Systems
Foundation, 2021, pp. 2823–2834.
conference:
end_date: 2021-12-14
location: Virtual, Online
name: 'NeurIPS: Neural Information Processing Systems'
start_date: 2021-12-06
corr_author: '1'
das_tickbox: '1'
date_created: 2022-06-19T22:01:58Z
date_published: 2021-12-01T00:00:00Z
date_updated: 2026-07-08T05:44:33Z
day: '01'
ddc:
- '000'
department:
- _id: DaAl
ec_funded: 1
external_id:
arxiv:
- '2110.14391'
intvolume: ' 4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://proceedings.neurips.cc/paper/2021/file/1680e9fa7b4dd5d62ece800239bb53bd-Paper.pdf
month: '12'
oa: 1
oa_version: Published Version
page: 2823-2834
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: 35th Conference on Neural Information Processing Systems
publication_identifier:
isbn:
- '9781713845393'
issn:
- 1049-5258
publication_status: published
publisher: Neural Information Processing Systems Foundation
quality_controlled: '1'
scopus_import: '1'
status: public
title: Distributed principal component analysis with limited communication
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2021'
...
---
_id: '9331'
abstract:
- lang: eng
text: 'Quantum entanglement has been generated and verified in cold-atom experiments
and used to make atom-interferometric measurements below the shot-noise limit.
However, current state-of-the-art cold-atom devices exploit separable (i.e., unentangled)
atomic states. This perspective piece asks the question: can entanglement usefully
improve cold-atom sensors, in the sense that it gives new sensing capabilities
unachievable with current state-of-the-art devices? We briefly review the state-of-the-art
in precision cold-atom sensing, focusing on clocks and inertial sensors, identifying
the potential benefits entanglement could bring to these devices, and the challenges
that need to be overcome to realize these benefits. We survey demonstrated methods
of generating metrologically useful entanglement in cold-atom systems, note their
relative strengths and weaknesses, and assess their prospects for near-to-medium
term quantum-enhanced cold-atom sensing.'
acknowledgement: We acknowledge fruitful discussions with John Close, Chris Freier,
Kyle Hardman, Joseph Hope, and Paul Wigley, and insightful suggestions made by Franck
Pereira dos Santos on behalf of the Atom Interferometry and Inertial Sensors team
at SYRTE. S.S.S. was supported by an Australian Research Council Discovery Early
Career Researcher Award (DECRA), Project No. DE200100495. O.H. was supported by
IST Austria.
article_number: '140501'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Stuart S.
full_name: Szigeti, Stuart S.
last_name: Szigeti
- first_name: Onur
full_name: Hosten, Onur
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
- first_name: Simon A.
full_name: Haine, Simon A.
last_name: Haine
citation:
ama: 'Szigeti SS, Hosten O, Haine SA. Improving cold-atom sensors with quantum entanglement:
Prospects and challenges. Applied Physics Letters. 2021;118(14). doi:10.1063/5.0050235'
apa: 'Szigeti, S. S., Hosten, O., & Haine, S. A. (2021). Improving cold-atom
sensors with quantum entanglement: Prospects and challenges. Applied Physics
Letters. AIP Publishing. https://doi.org/10.1063/5.0050235'
chicago: 'Szigeti, Stuart S., Onur Hosten, and Simon A. Haine. “Improving Cold-Atom
Sensors with Quantum Entanglement: Prospects and Challenges.” Applied Physics
Letters. AIP Publishing, 2021. https://doi.org/10.1063/5.0050235.'
ieee: 'S. S. Szigeti, O. Hosten, and S. A. Haine, “Improving cold-atom sensors with
quantum entanglement: Prospects and challenges,” Applied Physics Letters,
vol. 118, no. 14. AIP Publishing, 2021.'
ista: 'Szigeti SS, Hosten O, Haine SA. 2021. Improving cold-atom sensors with quantum
entanglement: Prospects and challenges. Applied Physics Letters. 118(14), 140501.'
mla: 'Szigeti, Stuart S., et al. “Improving Cold-Atom Sensors with Quantum Entanglement:
Prospects and Challenges.” Applied Physics Letters, vol. 118, no. 14, 140501,
AIP Publishing, 2021, doi:10.1063/5.0050235.'
short: S.S. Szigeti, O. Hosten, S.A. Haine, Applied Physics Letters 118 (2021).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: The data that support the findings of this study are available
from the corresponding author upon reasonable request.
date_created: 2021-04-18T22:01:40Z
date_published: 2021-04-07T00:00:00Z
date_updated: 2026-07-08T08:53:45Z
day: '07'
department:
- _id: OnHo
doi: 10.1063/5.0050235
external_id:
arxiv:
- '2010.09168'
isi:
- '000637702100001'
fulldoi: https://doi.org/10.1063/5.0050235
intvolume: ' 118'
isi: 1
issue: '14'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2010.09168
month: '04'
oa: 1
oa_version: Preprint
publication: Applied Physics Letters
publication_identifier:
issn:
- 0003-6951
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
researchdata_availability: upon request
scopus_import: '1'
status: public
supplementarymaterial: no
title: 'Improving cold-atom sensors with quantum entanglement: Prospects and challenges'
type: journal_article
user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d
volume: 118
year: '2021'
...
---
OA_place: publisher
OA_type: free access
_id: '9168'
abstract:
- lang: eng
text: Interspecific crossing experiments have shown that sex chromosomes play a
major role in reproductive isolation between many pairs of species. However, their
ability to act as reproductive barriers, which hamper interspecific genetic exchange,
has rarely been evaluated quantitatively compared to Autosomes. This genome-wide
limitation of gene flow is essential for understanding the complete separation
of species, and thus speciation. Here, we develop a mainland-island model of secondary
contact between hybridizing species of an XY (or ZW) sexual system. We obtain
theoretical predictions for the frequency of introgressed alleles, and the strength
of the barrier to neutral gene flow for the two types of chromosomes carrying
multiple interspecific barrier loci. Theoretical predictions are obtained for
scenarios where introgressed alleles are rare. We show that the same analytical
expressions apply for sex chromosomes and autosomes, but with different sex-averaged
effective parameters. The specific features of sex chromosomes (hemizygosity and
absence of recombination in the heterogametic sex) lead to reduced levels of introgression
on the X (or Z) compared to autosomes. This effect can be enhanced by certain
types of sex-biased forces, but it remains overall small (except when alleles
causing incompatibilities are recessive). We discuss these predictions in the
light of empirical data comprising model-based tests of introgression and cline
surveys in various biological systems.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "The computations were performed with the IST Austria High-Performance
Computing (HPC) Cluster and the Institut Français de Bioinformatique (IFB) Core
Cluster. We are grateful to Nick Barton and Beatriz Vicoso for critical comments
on the model and the manuscript. We also thank Brian Charlesworth, Stuart Baird,
and an anonymous reviewer for insightful comments.\r\nC.F. was supported by an Austrian
Science Foundation FWF grant (Project M 2463-B29)."
article_number: iyaa025
article_processing_charge: No
article_type: original
author:
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Himani
full_name: Sachdeva, Himani
id: 42377A0A-F248-11E8-B48F-1D18A9856A87
last_name: Sachdeva
citation:
ama: 'Fraisse C, Sachdeva H. The rates of introgression and barriers to genetic
exchange between hybridizing species: Sex chromosomes vs autosomes. Genetics.
2021;217(2). doi:10.1093/genetics/iyaa025'
apa: 'Fraisse, C., & Sachdeva, H. (2021). The rates of introgression and barriers
to genetic exchange between hybridizing species: Sex chromosomes vs autosomes.
Genetics. Genetics Society of America. https://doi.org/10.1093/genetics/iyaa025'
chicago: 'Fraisse, Christelle, and Himani Sachdeva. “The Rates of Introgression
and Barriers to Genetic Exchange between Hybridizing Species: Sex Chromosomes
vs Autosomes.” Genetics. Genetics Society of America, 2021. https://doi.org/10.1093/genetics/iyaa025.'
ieee: 'C. Fraisse and H. Sachdeva, “The rates of introgression and barriers to genetic
exchange between hybridizing species: Sex chromosomes vs autosomes,” Genetics,
vol. 217, no. 2. Genetics Society of America, 2021.'
ista: 'Fraisse C, Sachdeva H. 2021. The rates of introgression and barriers to genetic
exchange between hybridizing species: Sex chromosomes vs autosomes. Genetics.
217(2), iyaa025.'
mla: 'Fraisse, Christelle, and Himani Sachdeva. “The Rates of Introgression and
Barriers to Genetic Exchange between Hybridizing Species: Sex Chromosomes vs Autosomes.”
Genetics, vol. 217, no. 2, iyaa025, Genetics Society of America, 2021,
doi:10.1093/genetics/iyaa025.'
short: C. Fraisse, H. Sachdeva, Genetics 217 (2021).
corr_author: '1'
date_created: 2021-02-18T14:41:30Z
date_published: 2021-02-01T00:00:00Z
date_updated: 2026-07-28T12:39:03Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1093/genetics/iyaa025
external_id:
isi:
- '000637218100005'
pmid:
- '33724409'
fulldoi: https://doi.org/10.1093/genetics/iyaa025
intvolume: ' 217'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1093/genetics/iyaa025
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2662AADE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02463
name: Sex chromosomes and species barriers
publication: Genetics
publication_identifier:
issn:
- 1943-2631
publication_status: published
publisher: Genetics Society of America
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The rates of introgression and barriers to genetic exchange between hybridizing
species: Sex chromosomes vs autosomes'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 217
year: '2021'
...
---
OA_place: publisher
OA_type: free access
_id: '9793'
abstract:
- lang: eng
text: Astrocytes extensively infiltrate the neuropil to regulate critical aspects
of synaptic development and function. This process is regulated by transcellular
interactions between astrocytes and neurons via cell adhesion molecules. How astrocytes
coordinate developmental processes among one another to parse out the synaptic
neuropil and form non-overlapping territories is unknown. Here we identify a molecular
mechanism regulating astrocyte-astrocyte interactions during development to coordinate
astrocyte morphogenesis and gap junction coupling. We show that hepaCAM, a disease-linked,
astrocyte-enriched cell adhesion molecule, regulates astrocyte competition for
territory and morphological complexity in the developing mouse cortex. Furthermore,
conditional deletion of Hepacam from developing astrocytes significantly impairs
gap junction coupling between astrocytes and disrupts the balance between synaptic
excitation and inhibition. Mutations in HEPACAM cause megalencephalic leukoencephalopathy
with subcortical cysts in humans. Therefore, our findings suggest that disruption
of astrocyte self-organization mechanisms could be an underlying cause of neural
pathology.
acknowledgement: This work was supported by the National Institutes of Health (R01
DA047258 and R01 NS102237 to C.E., F32 NS100392 to K.T.B.) and the Holland-Trice
Brain Research Award (to C.E.). K.T.B. was supported by postdoctoral fellowships
from the Foerster-Bernstein Family and The Hartwell Foundation. The Hippenmeyer
lab was supported by the European Research Council (ERC) under the European Union’s
Horizon 2020 research and innovations program (725780 LinPro) to S.H. R.E. was supported
by Ministerio de Ciencia y Tecnología (RTI2018-093493-B-I00). We thank the Duke
Light Microscopy Core Facility, the Duke Transgenic Mouse Facility, Dr. U. Schulte
for assistance with proteomic experiments, and Dr. D. Silver for critical review
of the manuscript. Cartoon elements of figure panels were created using BioRender.com.
article_processing_charge: No
article_type: original
author:
- first_name: Katherine T.
full_name: Baldwin, Katherine T.
last_name: Baldwin
- first_name: Christabel X.
full_name: Tan, Christabel X.
last_name: Tan
- first_name: Samuel T.
full_name: Strader, Samuel T.
last_name: Strader
- first_name: Changyu
full_name: Jiang, Changyu
last_name: Jiang
- first_name: Justin T.
full_name: Savage, Justin T.
last_name: Savage
- first_name: Xabier
full_name: Elorza-Vidal, Xabier
last_name: Elorza-Vidal
- first_name: Ximena
full_name: Contreras, Ximena
id: 475990FE-F248-11E8-B48F-1D18A9856A87
last_name: Contreras
- first_name: Thomas
full_name: Rülicke, Thomas
last_name: Rülicke
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Raúl
full_name: Estévez, Raúl
last_name: Estévez
- first_name: Ru-Rong
full_name: Ji, Ru-Rong
last_name: Ji
- first_name: Cagla
full_name: Eroglu, Cagla
last_name: Eroglu
citation:
ama: Baldwin KT, Tan CX, Strader ST, et al. HepaCAM controls astrocyte self-organization
and coupling. Neuron. 2021;109(15):2427-2442.e10. doi:10.1016/j.neuron.2021.05.025
apa: Baldwin, K. T., Tan, C. X., Strader, S. T., Jiang, C., Savage, J. T., Elorza-Vidal,
X., … Eroglu, C. (2021). HepaCAM controls astrocyte self-organization and coupling.
Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2021.05.025
chicago: Baldwin, Katherine T., Christabel X. Tan, Samuel T. Strader, Changyu Jiang,
Justin T. Savage, Xabier Elorza-Vidal, Ximena Contreras, et al. “HepaCAM Controls
Astrocyte Self-Organization and Coupling.” Neuron. Elsevier, 2021. https://doi.org/10.1016/j.neuron.2021.05.025.
ieee: K. T. Baldwin et al., “HepaCAM controls astrocyte self-organization
and coupling,” Neuron, vol. 109, no. 15. Elsevier, p. 2427–2442.e10, 2021.
ista: Baldwin KT, Tan CX, Strader ST, Jiang C, Savage JT, Elorza-Vidal X, Contreras
X, Rülicke T, Hippenmeyer S, Estévez R, Ji R-R, Eroglu C. 2021. HepaCAM controls
astrocyte self-organization and coupling. Neuron. 109(15), 2427–2442.e10.
mla: Baldwin, Katherine T., et al. “HepaCAM Controls Astrocyte Self-Organization
and Coupling.” Neuron, vol. 109, no. 15, Elsevier, 2021, p. 2427–2442.e10,
doi:10.1016/j.neuron.2021.05.025.
short: K.T. Baldwin, C.X. Tan, S.T. Strader, C. Jiang, J.T. Savage, X. Elorza-Vidal,
X. Contreras, T. Rülicke, S. Hippenmeyer, R. Estévez, R.-R. Ji, C. Eroglu, Neuron
109 (2021) 2427–2442.e10.
date_created: 2021-08-06T09:08:25Z
date_published: 2021-08-04T00:00:00Z
date_updated: 2026-07-28T12:30:05Z
day: '04'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1016/j.neuron.2021.05.025
ec_funded: 1
external_id:
isi:
- '000692851900010'
pmid:
- '34171291'
fulldoi: https://doi.org/10.1016/j.neuron.2021.05.025
intvolume: ' 109'
isi: 1
issue: '15'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.neuron.2021.05.025
month: '08'
oa: 1
oa_version: Published Version
page: 2427-2442.e10
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
publication: Neuron
publication_identifier:
eissn:
- 1097-4199
issn:
- 0896-6273
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: HepaCAM controls astrocyte self-organization and coupling
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 109
year: '2021'
...
---
OA_place: publisher
OA_type: free access
_id: '10363'
abstract:
- lang: eng
text: Erythropoietin enhances oxygen delivery and reduces hypoxia-induced cell death,
but its pro-thrombotic activity is problematic for use of erythropoietin in treating
hypoxia. We constructed a fusion protein that stimulates red blood cell production
and neuroprotection without triggering platelet production, a marker for thrombosis.
The protein consists of an anti-glycophorin A nanobody and an erythropoietin mutant
(L108A). The mutation reduces activation of erythropoietin receptor homodimers
that induce erythropoiesis and thrombosis, but maintains the tissue-protective
signaling. The binding of the nanobody element to glycophorin A rescues homodimeric
erythropoietin receptor activation on red blood cell precursors. In a cell proliferation
assay, the fusion protein is active at 10−14 M, allowing an estimate of the number
of receptor–ligand complexes needed for signaling. This fusion protein stimulates
erythroid cell proliferation in vitro and in mice, and shows neuroprotective activity
in vitro. Our erythropoietin fusion protein presents a novel molecule for treating
hypoxia.
acknowledgement: This work was supported by funds from the Wyss Institute for Biologically
Inspired Engineering and the Boston Biomedical Innovation Center (Pilot Award 112475;
Drive Award U54HL119145). J.L., K.M.K., D.R.B., J.C.W. and P.A.S. were supported
by the Harvard Medical School Department of Systems Biology. J.C.W. was further
supported by the Harvard Medical School Laboratory of Systems Pharmacology. A.V.,
D.R.B. and P.A.S. were further supported by the Wyss Institute for Biologically
Inspired Engineering. N.G.G. was sponsored by the Army Research Office under Grant
Number W911NF-17-2-0092. The views and conclusions contained in this document are
those of the authors and should not be interpreted as representing the official
policies, either expressed or implied, of the Army Research Office or the U.S. Government.
The U.S. Government is authorized to reproduce and distribute reprints for Government
purposes notwithstanding any copyright notation herein. We sincerely thank Amanda
Graveline and the Wyss Institute at Harvard for their scientific support.
article_number: gzab025
article_processing_charge: No
article_type: original
author:
- first_name: Jungmin
full_name: Lee, Jungmin
last_name: Lee
- first_name: Andyna
full_name: Vernet, Andyna
last_name: Vernet
- first_name: Nathalie
full_name: Gruber, Nathalie
id: 2C9C8316-AA17-11E9-B5C2-8BC2E5697425
last_name: Gruber
- first_name: Kasia M.
full_name: Kready, Kasia M.
last_name: Kready
- first_name: Devin R.
full_name: Burrill, Devin R.
last_name: Burrill
- first_name: Jeffrey C.
full_name: Way, Jeffrey C.
last_name: Way
- first_name: Pamela A.
full_name: Silver, Pamela A.
last_name: Silver
citation:
ama: Lee J, Vernet A, Gruber N, et al. Rational engineering of an erythropoietin
fusion protein to treat hypoxia. Protein Engineering, Design and Selection.
2021;34. doi:10.1093/protein/gzab025
apa: Lee, J., Vernet, A., Gruber, N., Kready, K. M., Burrill, D. R., Way, J. C.,
& Silver, P. A. (2021). Rational engineering of an erythropoietin fusion protein
to treat hypoxia. Protein Engineering, Design and Selection. Oxford University
Press. https://doi.org/10.1093/protein/gzab025
chicago: Lee, Jungmin, Andyna Vernet, Nathalie Gruber, Kasia M. Kready, Devin R.
Burrill, Jeffrey C. Way, and Pamela A. Silver. “Rational Engineering of an Erythropoietin
Fusion Protein to Treat Hypoxia.” Protein Engineering, Design and Selection.
Oxford University Press, 2021. https://doi.org/10.1093/protein/gzab025.
ieee: J. Lee et al., “Rational engineering of an erythropoietin fusion protein
to treat hypoxia,” Protein Engineering, Design and Selection, vol. 34.
Oxford University Press, 2021.
ista: Lee J, Vernet A, Gruber N, Kready KM, Burrill DR, Way JC, Silver PA. 2021.
Rational engineering of an erythropoietin fusion protein to treat hypoxia. Protein
Engineering, Design and Selection. 34, gzab025.
mla: Lee, Jungmin, et al. “Rational Engineering of an Erythropoietin Fusion Protein
to Treat Hypoxia.” Protein Engineering, Design and Selection, vol. 34,
gzab025, Oxford University Press, 2021, doi:10.1093/protein/gzab025.
short: J. Lee, A. Vernet, N. Gruber, K.M. Kready, D.R. Burrill, J.C. Way, P.A. Silver,
Protein Engineering, Design and Selection 34 (2021).
date_created: 2021-11-28T23:01:28Z
date_published: 2021-11-01T00:00:00Z
date_updated: 2026-07-28T12:27:59Z
day: '01'
ddc:
- '570'
department:
- _id: CaGu
doi: 10.1093/protein/gzab025
external_id:
isi:
- '000746596900001'
pmid:
- '34725710'
fulldoi: https://doi.org/10.1093/protein/gzab025
intvolume: ' 34'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1093/protein/gzab025
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: Protein Engineering, Design and Selection
publication_identifier:
eissn:
- 1741-0134
issn:
- 1741-0126
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Rational engineering of an erythropoietin fusion protein to treat hypoxia
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2021'
...
---
OA_type: closed access
_id: '10809'
abstract:
- lang: eng
text: Thermoelectric materials are engines that convert heat into an electrical
current. Intuitively, the efficiency of this process depends on how many electrons
(charge carriers) can move and how easily they do so, how much energy those moving
electrons transport, and how easily the temperature gradient is maintained. In
terms of material properties, an excellent thermoelectric material requires a
high electrical conductivity σ, a high Seebeck coefficient S (a measure of the
induced thermoelectric voltage as a function of temperature gradient), and a low
thermal conductivity κ. The challenge is that these three properties are strongly
interrelated in a conflicting manner (1). On page 722 of this issue, Roychowdhury
et al. (2) have found a way to partially break these ties in silver antimony telluride
(AgSbTe2) with the addition of cadmium (Cd) cations, which increase the ordering
in this inherently disordered thermoelectric material.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Yu
full_name: Liu, Yu
id: 2A70014E-F248-11E8-B48F-1D18A9856A87
last_name: Liu
orcid: 0000-0001-7313-6740
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
citation:
ama: Liu Y, Ibáñez M. Tidying up the mess. Science. 2021;371(6530):678-679.
doi:10.1126/science.abg0886
apa: Liu, Y., & Ibáñez, M. (2021). Tidying up the mess. Science. American
Association for the Advancement of Science. https://doi.org/10.1126/science.abg0886
chicago: Liu, Yu, and Maria Ibáñez. “Tidying up the Mess.” Science. American
Association for the Advancement of Science, 2021. https://doi.org/10.1126/science.abg0886.
ieee: Y. Liu and M. Ibáñez, “Tidying up the mess,” Science, vol. 371, no.
6530. American Association for the Advancement of Science, pp. 678–679, 2021.
ista: Liu Y, Ibáñez M. 2021. Tidying up the mess. Science. 371(6530), 678–679.
mla: Liu, Yu, and Maria Ibáñez. “Tidying up the Mess.” Science, vol. 371,
no. 6530, American Association for the Advancement of Science, 2021, pp. 678–79,
doi:10.1126/science.abg0886.
short: Y. Liu, M. Ibáñez, Science 371 (2021) 678–679.
corr_author: '1'
date_created: 2022-03-03T09:51:48Z
date_published: 2021-02-12T00:00:00Z
date_updated: 2026-07-28T12:16:17Z
day: '12'
department:
- _id: MaIb
doi: 10.1126/science.abg0886
external_id:
isi:
- '000617551600027'
pmid:
- '33574201'
fulldoi: https://doi.org/10.1126/science.abg0886
intvolume: ' 371'
isi: 1
issue: '6530'
language:
- iso: eng
month: '02'
oa_version: None
page: 678-679
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tidying up the mess
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 371
year: '2021'
...
---
_id: '8317'
abstract:
- lang: eng
text: When can a polyomino piece of paper be folded into a unit cube? Prior work
studied tree-like polyominoes, but polyominoes with holes remain an intriguing
open problem. We present sufficient conditions for a polyomino with one or several
holes to fold into a cube, and conditions under which cube folding is impossible.
In particular, we show that all but five special “basic” holes guarantee foldability.
acknowledgement: This research was performed in part at the 33rd Bellairs Winter Workshop
on Computational Geometry. We thank all other participants for a fruitful atmosphere.
H. Akitaya was supported by NSF CCF-1422311 & 1423615. Z. Masárová was partially
funded by Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31.
article_number: '101700'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Oswin
full_name: Aichholzer, Oswin
last_name: Aichholzer
- first_name: Hugo A.
full_name: Akitaya, Hugo A.
last_name: Akitaya
- first_name: Kenneth C.
full_name: Cheung, Kenneth C.
last_name: Cheung
- first_name: Erik D.
full_name: Demaine, Erik D.
last_name: Demaine
- first_name: Martin L.
full_name: Demaine, Martin L.
last_name: Demaine
- first_name: Sándor P.
full_name: Fekete, Sándor P.
last_name: Fekete
- first_name: Linda
full_name: Kleist, Linda
last_name: Kleist
- first_name: Irina
full_name: Kostitsyna, Irina
last_name: Kostitsyna
- first_name: Maarten
full_name: Löffler, Maarten
last_name: Löffler
- first_name: Zuzana
full_name: Masárová, Zuzana
id: 45CFE238-F248-11E8-B48F-1D18A9856A87
last_name: Masárová
orcid: 0000-0002-6660-1322
- first_name: Klara
full_name: Mundilova, Klara
last_name: Mundilova
- first_name: Christiane
full_name: Schmidt, Christiane
last_name: Schmidt
citation:
ama: 'Aichholzer O, Akitaya HA, Cheung KC, et al. Folding polyominoes with holes
into a cube. Computational Geometry: Theory and Applications. 2021;93.
doi:10.1016/j.comgeo.2020.101700'
apa: 'Aichholzer, O., Akitaya, H. A., Cheung, K. C., Demaine, E. D., Demaine, M.
L., Fekete, S. P., … Schmidt, C. (2021). Folding polyominoes with holes into a
cube. Computational Geometry: Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2020.101700'
chicago: 'Aichholzer, Oswin, Hugo A. Akitaya, Kenneth C. Cheung, Erik D. Demaine,
Martin L. Demaine, Sándor P. Fekete, Linda Kleist, et al. “Folding Polyominoes
with Holes into a Cube.” Computational Geometry: Theory and Applications.
Elsevier, 2021. https://doi.org/10.1016/j.comgeo.2020.101700.'
ieee: 'O. Aichholzer et al., “Folding polyominoes with holes into a cube,”
Computational Geometry: Theory and Applications, vol. 93. Elsevier, 2021.'
ista: 'Aichholzer O, Akitaya HA, Cheung KC, Demaine ED, Demaine ML, Fekete SP, Kleist
L, Kostitsyna I, Löffler M, Masárová Z, Mundilova K, Schmidt C. 2021. Folding
polyominoes with holes into a cube. Computational Geometry: Theory and Applications.
93, 101700.'
mla: 'Aichholzer, Oswin, et al. “Folding Polyominoes with Holes into a Cube.” Computational
Geometry: Theory and Applications, vol. 93, 101700, Elsevier, 2021, doi:10.1016/j.comgeo.2020.101700.'
short: 'O. Aichholzer, H.A. Akitaya, K.C. Cheung, E.D. Demaine, M.L. Demaine, S.P.
Fekete, L. Kleist, I. Kostitsyna, M. Löffler, Z. Masárová, K. Mundilova, C. Schmidt,
Computational Geometry: Theory and Applications 93 (2021).'
corr_author: '1'
date_created: 2020-08-30T22:01:09Z
date_published: 2021-02-01T00:00:00Z
date_updated: 2026-07-28T13:08:48Z
day: '01'
department:
- _id: HeEd
doi: 10.1016/j.comgeo.2020.101700
external_id:
arxiv:
- '1910.09917'
isi:
- '000579185100004'
fulldoi: https://doi.org/10.1016/j.comgeo.2020.101700
intvolume: ' 93'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1910.09917v3
month: '02'
oa: 1
oa_version: Preprint
project:
- _id: 268116B8-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00342
name: Mathematics, Computer Science
publication: 'Computational Geometry: Theory and Applications'
publication_identifier:
eissn:
- 1879-081X
issn:
- 0925-7721
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '6989'
relation: shorter_version
status: public
scopus_import: '1'
status: public
title: Folding polyominoes with holes into a cube
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 93
year: '2021'
...
---
OA_place: repository
OA_type: green
_id: '10912'
abstract:
- lang: eng
text: Brain dynamics display collective phenomena as diverse as neuronal oscillations
and avalanches. Oscillations are rhythmic, with fluctuations occurring at a characteristic
scale, whereas avalanches are scale-free cascades of neural activity. Here we
show that such antithetic features can coexist in a very generic class of adaptive
neural networks. In the most simple yet fully microscopic model from this class
we make direct contact with human brain resting-state activity recordings via
tractable inference of the model's two essential parameters. The inferred model
quantitatively captures the dynamics over a broad range of scales, from single
sensor fluctuations, collective behaviors of nearly-synchronous extreme events
on multiple sensors, to neuronal avalanches unfolding over multiple sensors across
multiple time-bins. Importantly, the inferred parameters correlate with model-independent
signatures of "closeness to criticality", suggesting that the coexistence of scale-specific
(neural oscillations) and scale-free (neuronal avalanches) dynamics in brain activity
occurs close to a non-equilibrium critical point at the onset of self-sustained
oscillations.
acknowledgement: "FL acknowledges support from the European Union’s Horizon 2020 research
and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411.
GT\r\nacknowledges the support of the Austrian Science Fund (FWF) under Stand-Alone
Grant\r\nNo. P34015."
article_number: '2108.06686'
article_processing_charge: No
arxiv: 1
author:
- first_name: Fabrizio
full_name: Lombardi, Fabrizio
id: A057D288-3E88-11E9-986D-0CF4E5697425
last_name: Lombardi
orcid: 0000-0003-2623-5249
- first_name: Selver
full_name: Pepic, Selver
id: F93245C4-C3CA-11E9-B4F0-C6F4E5697425
last_name: Pepic
- first_name: Oren
full_name: Shriki, Oren
last_name: Shriki
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Daniele
full_name: De Martino, Daniele
last_name: De Martino
citation:
ama: Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. Quantifying the coexistence
of neuronal oscillations and avalanches. doi:10.48550/ARXIV.2108.06686
apa: Lombardi, F., Pepic, S., Shriki, O., Tkačik, G., & De Martino, D. (n.d.).
Quantifying the coexistence of neuronal oscillations and avalanches. arXiv. https://doi.org/10.48550/ARXIV.2108.06686
chicago: Lombardi, Fabrizio, Selver Pepic, Oren Shriki, Gašper Tkačik, and Daniele
De Martino. “Quantifying the Coexistence of Neuronal Oscillations and Avalanches.”
arXiv, n.d. https://doi.org/10.48550/ARXIV.2108.06686.
ieee: F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, and D. De Martino, “Quantifying
the coexistence of neuronal oscillations and avalanches.” arXiv.
ista: Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. Quantifying the coexistence
of neuronal oscillations and avalanches. 2108.06686.
mla: Lombardi, Fabrizio, et al. Quantifying the Coexistence of Neuronal Oscillations
and Avalanches. 2108.06686, arXiv, doi:10.48550/ARXIV.2108.06686.
short: F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, D. De Martino, (n.d.).
date_created: 2022-03-21T11:41:28Z
date_published: 2021-08-17T00:00:00Z
date_updated: 2026-07-29T06:53:41Z
day: '17'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.48550/ARXIV.2108.06686
ec_funded: 1
external_id:
arxiv:
- '2108.06686'
fulldoi: https://doi.org/10.48550/ARXIV.2108.06686
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2108.06686
month: '08'
oa: 1
oa_version: Preprint
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 626c45b5-2b32-11ec-9570-e509828c1ba6
grant_number: P34015
name: Efficient coding with biophysical realism
publication_status: submitted
publisher: arXiv
related_material:
record:
- id: '12762'
relation: later_version
status: public
status: public
title: Quantifying the coexistence of neuronal oscillations and avalanches
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '10080'
abstract:
- lang: eng
text: Hippocampal and neocortical neural activity is modulated by the position of
the individual in space. While hippocampal neurons provide the basis for a spatial
map, prefrontal cortical neurons generalize over environmental features. Whether
these generalized representations result from a bidirectional interaction with,
or are mainly derived from hippocampal spatial representations is not known. By
examining simultaneously recorded hippocampal and medial prefrontal neurons, we
observed that prefrontal spatial representations show a delayed coherence with
hippocampal ones. We also identified subpopulations of cells in the hippocampus
and medial prefrontal cortex that formed functional cross-area couplings; these
resembled the optimal connections predicted by a probabilistic model of spatial
information transfer and generalization. Moreover, cross-area couplings were strongest
and had the shortest delay preceding spatial decision-making. Our results suggest
that generalized spatial coding in the medial prefrontal cortex is inherited from
spatial representations in the hippocampus, and that the routing of information
can change dynamically with behavioral demands.
acknowledgement: We thank Federico Stella for invaluable suggestions and discussions.
We thank Yosman BapatDhar and Andrea Cumpelik for comments, help and suggestions
on the exposure of the text. We thank Predrag Živadinović and Juliana Couras for
comments on the text and the figures. This work was supported by the EU-FP7 MC-ITN
IN-SENS (grant 607616).
article_processing_charge: No
author:
- first_name: Michele
full_name: Nardin, Michele
id: 30BD0376-F248-11E8-B48F-1D18A9856A87
last_name: Nardin
orcid: 0000-0001-8849-6570
- first_name: Karola
full_name: Käfer, Karola
id: 2DAA49AA-F248-11E8-B48F-1D18A9856A87
last_name: Käfer
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
biorxivid: 1
citation:
ama: Nardin M, Käfer K, Csicsvari JL. The generalized spatial representation in
the prefrontal cortex is inherited from the hippocampus. bioRxiv. doi:10.1101/2021.09.30.462269
apa: Nardin, M., Käfer, K., & Csicsvari, J. L. (n.d.). The generalized spatial
representation in the prefrontal cortex is inherited from the hippocampus. bioRxiv.
https://doi.org/10.1101/2021.09.30.462269
chicago: Nardin, Michele, Karola Käfer, and Jozsef L Csicsvari. “The Generalized
Spatial Representation in the Prefrontal Cortex Is Inherited from the Hippocampus.”
BioRxiv, n.d. https://doi.org/10.1101/2021.09.30.462269.
ieee: M. Nardin, K. Käfer, and J. L. Csicsvari, “The generalized spatial representation
in the prefrontal cortex is inherited from the hippocampus,” bioRxiv. .
ista: Nardin M, Käfer K, Csicsvari JL. The generalized spatial representation in
the prefrontal cortex is inherited from the hippocampus. bioRxiv, 10.1101/2021.09.30.462269.
mla: Nardin, Michele, et al. “The Generalized Spatial Representation in the Prefrontal
Cortex Is Inherited from the Hippocampus.” BioRxiv, doi:10.1101/2021.09.30.462269.
short: M. Nardin, K. Käfer, J.L. Csicsvari, BioRxiv (n.d.).
das_tickbox: '1'
date_created: 2021-10-04T06:28:32Z
date_published: 2021-10-02T00:00:00Z
date_updated: 2026-07-29T06:33:53Z
day: '02'
department:
- _id: GradSch
- _id: JoCs
doi: 10.1101/2021.09.30.462269
ec_funded: 1
external_id:
biorxivid:
- 10.1101/2021.09.30.462269
fulldoi: https://doi.org/10.1101/2021.09.30.462269
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2021.09.30.462269
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: 257BBB4C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '607616'
name: inter-and intracellular signalling in schizophrenia
publication: bioRxiv
publication_status: submitted
status: public
title: The generalized spatial representation in the prefrontal cortex is inherited
from the hippocampus
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '9905'
abstract:
- lang: eng
text: Vaccines are thought to be the best available solution for controlling the
ongoing SARS-CoV-2 pandemic. However, the emergence of vaccine-resistant strains
may come too rapidly for current vaccine developments to alleviate the health,
economic and social consequences of the pandemic. To quantify and characterize
the risk of such a scenario, we created a SIR-derived model with initial stochastic
dynamics of the vaccine-resistant strain to study the probability of its emergence
and establishment. Using parameters realistically resembling SARS-CoV-2 transmission,
we model a wave-like pattern of the pandemic and consider the impact of the rate
of vaccination and the strength of non-pharmaceutical intervention measures on
the probability of emergence of a resistant strain. As expected, we found that
a fast rate of vaccination decreases the probability of emergence of a resistant
strain. Counterintuitively, when a relaxation of non-pharmaceutical interventions
happened at a time when most individuals of the population have already been vaccinated
the probability of emergence of a resistant strain was greatly increased. Consequently,
we show that a period of transmission reduction close to the end of the vaccination
campaign can substantially reduce the probability of resistant strain establishment.
Our results suggest that policymakers and individuals should consider maintaining
non-pharmaceutical interventions and transmission-reducing behaviours throughout
the entire vaccination period.
acknowledgement: We thank Alexey Kondrashov, Nick Machnik, Raimundo Julian Saona Urmeneta,
Gasper Tkacik and Nick Barton for fruitful discussions. We also thank participants
of EvoLunch seminar at IST Austria and the internal seminar at the Banco de España
for useful comments. The opinions expressed in this document are exclusively of
the authors and, therefore, do not necessarily coincide with those of the Banco
de España or the Eurosystem. ETD is supported by the Swiss National Science and
Louis Jeantet Foundation. The work of FAK was in part supported by the ERC Consolidator
Grant (771209-CharFL).
article_number: '15729'
article_processing_charge: Yes
article_type: original
author:
- first_name: Simon
full_name: Rella, Simon
id: B4765ACA-AA38-11E9-AC9A-0930E6697425
last_name: Rella
- first_name: Yuliya A.
full_name: Kulikova, Yuliya A.
last_name: Kulikova
- first_name: Emmanouil T.
full_name: Dermitzakis, Emmanouil T.
last_name: Dermitzakis
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Rella S, Kulikova YA, Dermitzakis ET, Kondrashov F. Rates of SARS-CoV-2 transmission
and vaccination impact the fate of vaccine-resistant strains. Scientific Reports.
2021;11(1). doi:10.1038/s41598-021-95025-3
apa: Rella, S., Kulikova, Y. A., Dermitzakis, E. T., & Kondrashov, F. (2021).
Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant
strains. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-021-95025-3
chicago: Rella, Simon, Yuliya A. Kulikova, Emmanouil T. Dermitzakis, and Fyodor
Kondrashov. “Rates of SARS-CoV-2 Transmission and Vaccination Impact the Fate
of Vaccine-Resistant Strains.” Scientific Reports. Springer Nature, 2021.
https://doi.org/10.1038/s41598-021-95025-3.
ieee: S. Rella, Y. A. Kulikova, E. T. Dermitzakis, and F. Kondrashov, “Rates of
SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains,”
Scientific Reports, vol. 11, no. 1. Springer Nature, 2021.
ista: Rella S, Kulikova YA, Dermitzakis ET, Kondrashov F. 2021. Rates of SARS-CoV-2
transmission and vaccination impact the fate of vaccine-resistant strains. Scientific
Reports. 11(1), 15729.
mla: Rella, Simon, et al. “Rates of SARS-CoV-2 Transmission and Vaccination Impact
the Fate of Vaccine-Resistant Strains.” Scientific Reports, vol. 11, no.
1, 15729, Springer Nature, 2021, doi:10.1038/s41598-021-95025-3.
short: S. Rella, Y.A. Kulikova, E.T. Dermitzakis, F. Kondrashov, Scientific Reports
11 (2021).
date_created: 2021-08-15T22:01:26Z
date_published: 2021-07-30T00:00:00Z
date_updated: 2026-07-29T12:57:49Z
day: '30'
ddc:
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department:
- _id: FyKo
doi: 10.1038/s41598-021-95025-3
ec_funded: 1
external_id:
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issue: '1'
language:
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month: '07'
oa: 1
oa_version: Published Version
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project:
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call_identifier: H2020
grant_number: '771209'
name: Characterizing the fitness landscape on population and global scales
publication: Scientific Reports
publication_identifier:
eissn:
- 2045-2322
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
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relation: press_release
url: https://ist.ac.at/en/news/counterintuitive-dynamics-threaten-the-end-of-the-pandemic/
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relation: dissertation_contains
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scopus_import: '1'
status: public
title: Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant
strains
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 11
year: '2021'
...
---
OA_place: publisher
_id: '9418'
abstract:
- lang: eng
text: "Deep learning is best known for its empirical success across a wide range
of applications\r\nspanning computer vision, natural language processing and speech.
Of equal significance,\r\nthough perhaps less known, are its ramifications for
learning theory: deep networks have\r\nbeen observed to perform surprisingly well
in the high-capacity regime, aka the overfitting\r\nor underspecified regime.
Classically, this regime on the far right of the bias-variance curve\r\nis associated
with poor generalisation; however, recent experiments with deep networks\r\nchallenge
this view.\r\n\r\nThis thesis is devoted to investigating various aspects of underspecification
in deep learning.\r\nFirst, we argue that deep learning models are underspecified
on two levels: a) any given\r\ntraining dataset can be fit by many different functions,
and b) any given function can be\r\nexpressed by many different parameter configurations.
We refer to the second kind of\r\nunderspecification as parameterisation redundancy
and we precisely characterise its extent.\r\nSecond, we characterise the implicit
criteria (the inductive bias) that guide learning in the\r\nunderspecified regime.
Specifically, we consider a nonlinear but tractable classification\r\nsetting,
and show that given the choice, neural networks learn classifiers with a large
margin.\r\nThird, we consider learning scenarios where the inductive bias is not
by itself sufficient to\r\ndeal with underspecification. We then study different
ways of ‘tightening the specification’: i)\r\nIn the setting of representation
learning with variational autoencoders, we propose a hand-\r\ncrafted regulariser
based on mutual information. ii) In the setting of binary classification, we\r\nconsider
soft-label (real-valued) supervision. We derive a generalisation bound for linear\r\nnetworks
supervised in this way and verify that soft labels facilitate fast learning. Finally,
we\r\nexplore an application of soft-label supervision to the training of multi-exit
models."
acknowledged_ssus:
- _id: ScienComp
- _id: CampIT
- _id: E-Lib
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Phuong
full_name: Bui Thi Mai, Phuong
id: 3EC6EE64-F248-11E8-B48F-1D18A9856A87
last_name: Bui Thi Mai
citation:
ama: Phuong M. Underspecification in deep learning. 2021. doi:10.15479/AT:ISTA:9418
apa: Phuong, M. (2021). Underspecification in deep learning. Institute of
Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9418
chicago: Phuong, Mary. “Underspecification in Deep Learning.” Institute of Science
and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9418.
ieee: M. Phuong, “Underspecification in deep learning,” Institute of Science and
Technology Austria, 2021.
ista: Phuong M. 2021. Underspecification in deep learning. Institute of Science
and Technology Austria.
mla: Phuong, Mary. Underspecification in Deep Learning. Institute of Science
and Technology Austria, 2021, doi:10.15479/AT:ISTA:9418.
short: M. Phuong, Underspecification in Deep Learning, Institute of Science and
Technology Austria, 2021.
corr_author: '1'
date_created: 2021-05-24T13:06:23Z
date_published: 2021-05-30T00:00:00Z
date_updated: 2026-07-30T05:33:52Z
day: '30'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: GradSch
- _id: ChLa
doi: 10.15479/AT:ISTA:9418
doi_confirm: '1'
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month: '05'
oa: 1
oa_version: Published Version
page: '125'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
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relation: part_of_dissertation
status: deleted
- id: '7481'
relation: part_of_dissertation
status: public
- id: '9416'
relation: part_of_dissertation
status: public
- id: '7479'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
title: Underspecification in deep learning
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2021'
...
---
_id: '9416'
abstract:
- lang: eng
text: 'We study the inductive bias of two-layer ReLU networks trained by gradient
flow. We identify a class of easy-to-learn (`orthogonally separable'') datasets,
and characterise the solution that ReLU networks trained on such datasets converge
to. Irrespective of network width, the solution turns out to be a combination
of two max-margin classifiers: one corresponding to the positive data subset and
one corresponding to the negative data subset. The proof is based on the recently
introduced concept of extremal sectors, for which we prove a number of properties
in the context of orthogonal separability. In particular, we prove stationarity
of activation patterns from some time onwards, which enables a reduction of the
ReLU network to an ensemble of linear subnetworks.'
article_processing_charge: No
author:
- first_name: Phuong
full_name: Bui Thi Mai, Phuong
id: 3EC6EE64-F248-11E8-B48F-1D18A9856A87
last_name: Bui Thi Mai
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Phuong M, Lampert C. The inductive bias of ReLU networks on orthogonally separable
data. In: 9th International Conference on Learning Representations. ; 2021.'
apa: Phuong, M., & Lampert, C. (2021). The inductive bias of ReLU networks on
orthogonally separable data. In 9th International Conference on Learning Representations.
Virtual.
chicago: Phuong, Mary, and Christoph Lampert. “The Inductive Bias of ReLU Networks
on Orthogonally Separable Data.” In 9th International Conference on Learning
Representations, 2021.
ieee: M. Phuong and C. Lampert, “The inductive bias of ReLU networks on orthogonally
separable data,” in 9th International Conference on Learning Representations,
Virtual, 2021.
ista: 'Phuong M, Lampert C. 2021. The inductive bias of ReLU networks on orthogonally
separable data. 9th International Conference on Learning Representations. ICLR:
International Conference on Learning Representations.'
mla: Phuong, Mary, and Christoph Lampert. “The Inductive Bias of ReLU Networks on
Orthogonally Separable Data.” 9th International Conference on Learning Representations,
2021.
short: M. Phuong, C. Lampert, in:, 9th 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
corr_author: '1'
date_created: 2021-05-24T11:16:46Z
date_published: 2021-05-01T00:00:00Z
date_updated: 2026-07-30T05:33:51Z
day: '01'
ddc:
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department:
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- _id: ChLa
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url: https://openreview.net/pdf?id=krz7T0xU9Z_
month: '05'
oa: 1
oa_version: Published Version
publication: 9th International Conference on Learning Representations
publication_status: published
quality_controlled: '1'
related_material:
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- id: '9418'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: The inductive bias of ReLU networks on orthogonally separable data
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '10579'
abstract:
- lang: eng
text: 'We consider a totally asymmetric simple exclusion process (TASEP) consisting
of particles on a lattice that require binding by a "token" to move. Using a combination
of theory and simulations, we address the following questions: (i) How token binding
kinetics affects the current-density relation; (ii) How the current-density relation
depends on the scarcity of tokens; (iii) How tokens propagate the effects of the
locally-imposed disorder (such a slow site) over the entire lattice; (iv) How
a shared pool of tokens couples concurrent TASEPs running on multiple lattices;
(v) How our results translate to TASEPs with open boundaries that exchange particles
with the reservoir. Since real particle motion (including in systems that inspired
the standard TASEP model, e.g., protein synthesis or movement of molecular motors)
is often catalyzed, regulated, actuated, or otherwise mediated, the token-driven
TASEP dynamics analyzed in this paper should allow for a better understanding
of real systems and enable a closer match between TASEP theory and experimental
observations.'
acknowledgement: B.K. thanks Stefano Elefante, Simon Rella, and Michal Hledík for
their help with the usage of the cluster. B.K. additionally thanks Călin Guet and
his group for help and advice. We thank M. Hennessey-Wesen for constructive comments
on the manuscript. We thank Ankita Gupta (Indian Institute of Technology) for spotting
a typographical error in Eq. (49) in the preprint version of this paper.
article_number: '2112.13558'
article_processing_charge: No
arxiv: 1
author:
- first_name: Bor
full_name: Kavcic, Bor
id: 350F91D2-F248-11E8-B48F-1D18A9856A87
last_name: Kavcic
orcid: 0000-0001-6041-254X
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Kavcic B, Tkačik G. Token-driven totally asymmetric simple exclusion process.
arXiv. doi:10.48550/arXiv.2112.13558
apa: Kavcic, B., & Tkačik, G. (n.d.). Token-driven totally asymmetric simple
exclusion process. arXiv. https://doi.org/10.48550/arXiv.2112.13558
chicago: Kavcic, Bor, and Gašper Tkačik. “Token-Driven Totally Asymmetric Simple
Exclusion Process.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2112.13558.
ieee: B. Kavcic and G. Tkačik, “Token-driven totally asymmetric simple exclusion
process,” arXiv. .
ista: Kavcic B, Tkačik G. Token-driven totally asymmetric simple exclusion process.
arXiv, 2112.13558.
mla: Kavcic, Bor, and Gašper Tkačik. “Token-Driven Totally Asymmetric Simple Exclusion
Process.” ArXiv, 2112.13558, doi:10.48550/arXiv.2112.13558.
short: B. Kavcic, G. Tkačik, ArXiv (n.d.).
corr_author: '1'
date_created: 2021-12-28T06:52:09Z
date_published: 2021-12-27T00:00:00Z
date_updated: 2026-08-04T08:34:23Z
day: '27'
ddc:
- '530'
department:
- _id: GaTk
doi: 10.48550/arXiv.2112.13558
external_id:
arxiv:
- '2112.13558'
fulldoi: https://doi.org/10.48550/arXiv.2112.13558
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language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
main_file_link:
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month: '12'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
related_material:
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relation: later_version
status: public
status: public
title: Token-driven totally asymmetric simple exclusion process
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
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short: CC BY-NC-ND (4.0)
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '15279'
abstract:
- lang: eng
text: We formulate and prove an analog of Poonen’s finite-field Bertini theorem
with Taylor conditions that holds in the Grothendieck ring of varieties. This
gives a broad generalization of the work of Vakil and Wood, who treated the case
of smooth hypersurface sections, and is made possible by the use of motivic Euler
products to write down candidate motivic probabilities. As applications, we give
motivic analogs of many results in arithmetic statistics that have been proven
using Poonen’s sieve, including work of Bucur and Kedlaya on complete intersections
and Erman and Wood on semiample Bertini theorems.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Margaret
full_name: Bilu, Margaret
id: 98C47862-10D5-11EA-BEDD-0F6F3DDC885E
last_name: Bilu
- first_name: Sean
full_name: Howe, Sean
last_name: Howe
citation:
ama: Bilu M, Howe S. Motivic Euler products in motivic statistics. Algebra &
Number Theory. 2021;15(9):2195-2259. doi:10.2140/ant.2021.15.2195
apa: Bilu, M., & Howe, S. (2021). Motivic Euler products in motivic statistics.
Algebra & Number Theory. Mathematical Sciences Publishers. https://doi.org/10.2140/ant.2021.15.2195
chicago: Bilu, Margaret, and Sean Howe. “Motivic Euler Products in Motivic Statistics.”
Algebra & Number Theory. Mathematical Sciences Publishers, 2021. https://doi.org/10.2140/ant.2021.15.2195.
ieee: M. Bilu and S. Howe, “Motivic Euler products in motivic statistics,” Algebra
& Number Theory, vol. 15, no. 9. Mathematical Sciences Publishers, pp.
2195–2259, 2021.
ista: Bilu M, Howe S. 2021. Motivic Euler products in motivic statistics. Algebra
& Number Theory. 15(9), 2195–2259.
mla: Bilu, Margaret, and Sean Howe. “Motivic Euler Products in Motivic Statistics.”
Algebra & Number Theory, vol. 15, no. 9, Mathematical Sciences Publishers,
2021, pp. 2195–259, doi:10.2140/ant.2021.15.2195.
short: M. Bilu, S. Howe, Algebra & Number Theory 15 (2021) 2195–2259.
corr_author: '1'
das_tickbox: '0'
date_created: 2024-04-03T08:12:59Z
date_published: 2021-12-23T00:00:00Z
date_updated: 2026-08-06T11:10:09Z
day: '23'
department:
- _id: TiBr
doi: 10.2140/ant.2021.15.2195
external_id:
arxiv:
- '1910.05207'
fulldoi: https://doi.org/10.2140/ant.2021.15.2195
intvolume: ' 15'
issue: '9'
keyword:
- Algebra and Number Theory
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1910.05207
month: '12'
oa: 1
oa_version: Preprint
page: 2195-2259
publication: Algebra & Number Theory
publication_identifier:
eissn:
- 1944-7833
issn:
- 1937-0652
publication_status: published
publisher: Mathematical Sciences Publishers
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: Motivic Euler products in motivic statistics
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 15
year: '2021'
...
---
_id: '12076'
abstract:
- lang: eng
text: We find an asymptotic formula for the number of primitive vectors $(z_1,\ldots,z_4)\in
(\mathbb{Z}_{\neq 0})^4$ such that $z_1,\ldots, z_4$ are all squareful and bounded
by $B$, and $z_1+\cdots + z_4 = 0$. Our result agrees in the power of $B$ and
$\log B$ with the Campana-Manin conjecture of Pieropan, Smeets, Tanimoto and V\'{a}rilly-Alvarado.
article_number: '2104.06966'
article_processing_charge: No
arxiv: 1
author:
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full_name: Shute, Alec L
id: 440EB050-F248-11E8-B48F-1D18A9856A87
last_name: Shute
orcid: 0000-0002-1812-2810
citation:
ama: Shute AL. Sums of four squareful numbers. arXiv. doi:10.48550/arXiv.2104.06966
apa: Shute, A. L. (n.d.). Sums of four squareful numbers. arXiv. https://doi.org/10.48550/arXiv.2104.06966
chicago: Shute, Alec L. “Sums of Four Squareful Numbers.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2104.06966.
ieee: A. L. Shute, “Sums of four squareful numbers,” arXiv. .
ista: Shute AL. Sums of four squareful numbers. arXiv, 2104.06966.
mla: Shute, Alec L. “Sums of Four Squareful Numbers.” ArXiv, 2104.06966,
doi:10.48550/arXiv.2104.06966.
short: A.L. Shute, ArXiv (n.d.).
corr_author: '1'
das_tickbox: '0'
date_created: 2022-09-09T10:42:51Z
date_published: 2021-04-15T00:00:00Z
date_updated: 2026-08-06T11:08:48Z
day: '15'
department:
- _id: TiBr
doi: 10.48550/arXiv.2104.06966
external_id:
arxiv:
- '2104.06966'
fulldoi: https://doi.org/10.48550/arXiv.2104.06966
language:
- iso: eng
main_file_link:
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url: https://doi.org/10.48550/arXiv.2104.06966
month: '04'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: draft
related_material:
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- id: '12072'
relation: dissertation_contains
status: public
researchdata_availability: no
status: public
supplementarymaterial: no
title: Sums of four squareful numbers
type: preprint
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2021'
...