---
_id: '11556'
abstract:
- lang: eng
text: "We revisit two basic Direct Simulation Monte Carlo Methods to model aggregation
kinetics and extend them for aggregation processes with collisional fragmentation
(shattering). We test the performance and accuracy of the extended methods and
compare their performance with efficient deterministic finite-difference method
applied to the same model. We validate the stochastic methods on the test problems
and apply them to verify the existence of oscillating regimes in the aggregation-fragmentation
kinetics recently detected in deterministic simulations. We confirm the emergence
of steady oscillations of densities in such systems and prove the stability of
the\r\noscillations with respect to fluctuations and noise."
acknowledgement: Zhores supercomputer of Skolkovo Institute of Science and Technology
[68] has been used in the present research. S.A.M. was supported by Moscow Center
for Fundamental and Applied Mathematics (the agreement with the Ministry of Education
and Science of the Russian Federation No. 075-15-2019-1624). A.I.O. acknowledges
RFBR project No. 20-31-90022. N.V.B. acknowledges the support of the Analytical
Center (subsidy agreement 000000D730321P5Q0002, Grant No. 70-2021-00145 02.11.2021).
article_number: '111439'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Aleksei
full_name: Kalinov, Aleksei
id: 44b7120e-eb97-11eb-a6c2-e1557aa81d02
last_name: Kalinov
orcid: 0000-0003-2189-3904
- first_name: A.I.
full_name: Osinskiy, A.I.
last_name: Osinskiy
- first_name: S.A.
full_name: Matveev, S.A.
last_name: Matveev
- first_name: W.
full_name: Otieno, W.
last_name: Otieno
- first_name: N.V.
full_name: Brilliantov, N.V.
last_name: Brilliantov
citation:
ama: Kalinov A, Osinskiy AI, Matveev SA, Otieno W, Brilliantov NV. Direct simulation
Monte Carlo for new regimes in aggregation-fragmentation kinetics. Journal
of Computational Physics. 2022;467. doi:10.1016/j.jcp.2022.111439
apa: Kalinov, A., Osinskiy, A. I., Matveev, S. A., Otieno, W., & Brilliantov,
N. V. (2022). Direct simulation Monte Carlo for new regimes in aggregation-fragmentation
kinetics. Journal of Computational Physics. Elsevier. https://doi.org/10.1016/j.jcp.2022.111439
chicago: Kalinov, Aleksei, A.I. Osinskiy, S.A. Matveev, W. Otieno, and N.V. Brilliantov.
“Direct Simulation Monte Carlo for New Regimes in Aggregation-Fragmentation Kinetics.”
Journal of Computational Physics. Elsevier, 2022. https://doi.org/10.1016/j.jcp.2022.111439.
ieee: A. Kalinov, A. I. Osinskiy, S. A. Matveev, W. Otieno, and N. V. Brilliantov,
“Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics,”
Journal of Computational Physics, vol. 467. Elsevier, 2022.
ista: Kalinov A, Osinskiy AI, Matveev SA, Otieno W, Brilliantov NV. 2022. Direct
simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics.
Journal of Computational Physics. 467, 111439.
mla: Kalinov, Aleksei, et al. “Direct Simulation Monte Carlo for New Regimes in
Aggregation-Fragmentation Kinetics.” Journal of Computational Physics,
vol. 467, 111439, Elsevier, 2022, doi:10.1016/j.jcp.2022.111439.
short: A. Kalinov, A.I. Osinskiy, S.A. Matveev, W. Otieno, N.V. Brilliantov, Journal
of Computational Physics 467 (2022).
date_created: 2022-07-11T12:19:59Z
date_published: 2022-10-15T00:00:00Z
date_updated: 2023-08-03T11:55:06Z
day: '15'
ddc:
- '518'
department:
- _id: GradSch
- _id: ChWo
doi: 10.1016/j.jcp.2022.111439
external_id:
arxiv:
- '2103.09481'
isi:
- '000917225500013'
intvolume: ' 467'
isi: 1
keyword:
- Computer Science Applications
- Physics and Astronomy (miscellaneous)
- Applied Mathematics
- Computational Mathematics
- Modeling and Simulation
- Numerical Analysis
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2103.09481
month: '10'
oa: 1
oa_version: Preprint
publication: Journal of Computational Physics
publication_identifier:
issn:
- 0021-9991
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Direct simulation Monte Carlo for new regimes in aggregation-fragmentation
kinetics
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 467
year: '2022'
...
---
_id: '10643'
abstract:
- lang: eng
text: "We prove a generalised super-adiabatic theorem for extended fermionic systems
assuming a spectral gap only in the bulk. More precisely, we assume that the infinite
system has a unique ground state and that the corresponding Gelfand–Naimark–Segal
Hamiltonian has a spectral gap above its eigenvalue zero. Moreover, we show that
a similar adiabatic theorem also holds in the bulk of finite systems up to errors
that vanish faster than any inverse power of the system size, although the corresponding
finite-volume Hamiltonians need not have a spectral gap.\r\n\r\n"
acknowledgement: J.H. acknowledges partial financial support by the ERC Advanced Grant
‘RMTBeyond’ No. 101020331. Support for publication costs from the Deutsche Forschungsgemeinschaft
and the Open Access Publishing Fund of the University of Tübingen is gratefully
acknowledged.
article_number: e4
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Sven Joscha
full_name: Henheik, Sven Joscha
id: 31d731d7-d235-11ea-ad11-b50331c8d7fb
last_name: Henheik
orcid: 0000-0003-1106-327X
- first_name: Stefan
full_name: Teufel, Stefan
last_name: Teufel
citation:
ama: 'Henheik SJ, Teufel S. Adiabatic theorem in the thermodynamic limit: Systems
with a gap in the bulk. Forum of Mathematics, Sigma. 2022;10. doi:10.1017/fms.2021.80'
apa: 'Henheik, S. J., & Teufel, S. (2022). Adiabatic theorem in the thermodynamic
limit: Systems with a gap in the bulk. Forum of Mathematics, Sigma. Cambridge
University Press. https://doi.org/10.1017/fms.2021.80'
chicago: 'Henheik, Sven Joscha, and Stefan Teufel. “Adiabatic Theorem in the Thermodynamic
Limit: Systems with a Gap in the Bulk.” Forum of Mathematics, Sigma. Cambridge
University Press, 2022. https://doi.org/10.1017/fms.2021.80.'
ieee: 'S. J. Henheik and S. Teufel, “Adiabatic theorem in the thermodynamic limit:
Systems with a gap in the bulk,” Forum of Mathematics, Sigma, vol. 10.
Cambridge University Press, 2022.'
ista: 'Henheik SJ, Teufel S. 2022. Adiabatic theorem in the thermodynamic limit:
Systems with a gap in the bulk. Forum of Mathematics, Sigma. 10, e4.'
mla: 'Henheik, Sven Joscha, and Stefan Teufel. “Adiabatic Theorem in the Thermodynamic
Limit: Systems with a Gap in the Bulk.” Forum of Mathematics, Sigma, vol.
10, e4, Cambridge University Press, 2022, doi:10.1017/fms.2021.80.'
short: S.J. Henheik, S. Teufel, Forum of Mathematics, Sigma 10 (2022).
date_created: 2022-01-18T16:18:51Z
date_published: 2022-01-18T00:00:00Z
date_updated: 2023-08-02T13:53:11Z
day: '18'
ddc:
- '510'
department:
- _id: GradSch
- _id: LaEr
doi: 10.1017/fms.2021.80
ec_funded: 1
external_id:
arxiv:
- '2012.15239'
isi:
- '000743615000001'
file:
- access_level: open_access
checksum: 87592a755adcef22ea590a99dc728dd3
content_type: application/pdf
creator: cchlebak
date_created: 2022-01-19T09:27:43Z
date_updated: 2022-01-19T09:27:43Z
file_id: '10646'
file_name: 2022_ForumMathSigma_Henheik.pdf
file_size: 705323
relation: main_file
success: 1
file_date_updated: 2022-01-19T09:27:43Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
keyword:
- computational mathematics
- discrete mathematics and combinatorics
- geometry and topology
- mathematical physics
- statistics and probability
- algebra and number theory
- theoretical computer science
- analysis
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 62796744-2b32-11ec-9570-940b20777f1d
call_identifier: H2020
grant_number: '101020331'
name: Random matrices beyond Wigner-Dyson-Mehta
publication: Forum of Mathematics, Sigma
publication_identifier:
eissn:
- 2050-5094
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
status: public
title: 'Adiabatic theorem in the thermodynamic limit: Systems with a gap in the bulk'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 10
year: '2022'
...
---
_id: '12148'
abstract:
- lang: eng
text: 'We prove a general local law for Wigner matrices that optimally handles observables
of arbitrary rank and thus unifies the well-known averaged and isotropic local
laws. As an application, we prove a central limit theorem in quantum unique ergodicity
(QUE): that is, we show that the quadratic forms of a general deterministic matrix
A on the bulk eigenvectors of a Wigner matrix have approximately Gaussian fluctuation.
For the bulk spectrum, we thus generalise our previous result [17] as valid for
test matrices A of large rank as well as the result of Benigni and Lopatto [7]
as valid for specific small-rank observables.'
acknowledgement: L.E. acknowledges support by ERC Advanced Grant ‘RMTBeyond’ No. 101020331.
D.S. acknowledges the support of Dr. Max Rössler, the Walter Haefner Foundation
and the ETH Zürich Foundation.
article_number: e96
article_processing_charge: No
article_type: original
author:
- first_name: Giorgio
full_name: Cipolloni, Giorgio
id: 42198EFA-F248-11E8-B48F-1D18A9856A87
last_name: Cipolloni
orcid: 0000-0002-4901-7992
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Dominik J
full_name: Schröder, Dominik J
id: 408ED176-F248-11E8-B48F-1D18A9856A87
last_name: Schröder
orcid: 0000-0002-2904-1856
citation:
ama: Cipolloni G, Erdös L, Schröder DJ. Rank-uniform local law for Wigner matrices.
Forum of Mathematics, Sigma. 2022;10. doi:10.1017/fms.2022.86
apa: Cipolloni, G., Erdös, L., & Schröder, D. J. (2022). Rank-uniform local
law for Wigner matrices. Forum of Mathematics, Sigma. Cambridge University
Press. https://doi.org/10.1017/fms.2022.86
chicago: Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Rank-Uniform
Local Law for Wigner Matrices.” Forum of Mathematics, Sigma. Cambridge
University Press, 2022. https://doi.org/10.1017/fms.2022.86.
ieee: G. Cipolloni, L. Erdös, and D. J. Schröder, “Rank-uniform local law for Wigner
matrices,” Forum of Mathematics, Sigma, vol. 10. Cambridge University Press,
2022.
ista: Cipolloni G, Erdös L, Schröder DJ. 2022. Rank-uniform local law for Wigner
matrices. Forum of Mathematics, Sigma. 10, e96.
mla: Cipolloni, Giorgio, et al. “Rank-Uniform Local Law for Wigner Matrices.” Forum
of Mathematics, Sigma, vol. 10, e96, Cambridge University Press, 2022, doi:10.1017/fms.2022.86.
short: G. Cipolloni, L. Erdös, D.J. Schröder, Forum of Mathematics, Sigma 10 (2022).
date_created: 2023-01-12T12:07:30Z
date_published: 2022-10-27T00:00:00Z
date_updated: 2023-08-04T09:00:35Z
day: '27'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1017/fms.2022.86
ec_funded: 1
external_id:
isi:
- '000873719200001'
file:
- access_level: open_access
checksum: 94a049aeb1eea5497aa097712a73c400
content_type: application/pdf
creator: dernst
date_created: 2023-01-24T10:02:40Z
date_updated: 2023-01-24T10:02:40Z
file_id: '12356'
file_name: 2022_ForumMath_Cipolloni.pdf
file_size: 817089
relation: main_file
success: 1
file_date_updated: 2023-01-24T10:02:40Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
keyword:
- Computational Mathematics
- Discrete Mathematics and Combinatorics
- Geometry and Topology
- Mathematical Physics
- Statistics and Probability
- Algebra and Number Theory
- Theoretical Computer Science
- Analysis
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 62796744-2b32-11ec-9570-940b20777f1d
call_identifier: H2020
grant_number: '101020331'
name: Random matrices beyond Wigner-Dyson-Mehta
publication: Forum of Mathematics, Sigma
publication_identifier:
issn:
- 2050-5094
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Rank-uniform local law for Wigner matrices
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 10
year: '2022'
...
---
_id: '12305'
abstract:
- lang: eng
text: This paper is concerned with the sharp interface limit for the Allen--Cahn
equation with a nonlinear Robin boundary condition in a bounded smooth domain
Ω⊂\R2. We assume that a diffuse interface already has developed and that it is
in contact with the boundary ∂Ω. The boundary condition is designed in such a
way that the limit problem is given by the mean curvature flow with constant α-contact
angle. For α close to 90° we prove a local in time convergence result for well-prepared
initial data for times when a smooth solution to the limit problem exists. Based
on the latter we construct a suitable curvilinear coordinate system and carry
out a rigorous asymptotic expansion for the Allen--Cahn equation with the nonlinear
Robin boundary condition. Moreover, we show a spectral estimate for the corresponding
linearized Allen--Cahn operator and with its aid we derive strong norm estimates
for the difference of the exact and approximate solutions using a Gronwall-type
argument.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Helmut
full_name: Abels, Helmut
last_name: Abels
- first_name: Maximilian
full_name: Moser, Maximilian
id: a60047a9-da77-11eb-85b4-c4dc385ebb8c
last_name: Moser
citation:
ama: Abels H, Moser M. Convergence of the Allen--Cahn equation with a nonlinear
Robin boundary condition to mean curvature flow with contact angle close to 90°.
SIAM Journal on Mathematical Analysis. 2022;54(1):114-172. doi:10.1137/21m1424925
apa: Abels, H., & Moser, M. (2022). Convergence of the Allen--Cahn equation
with a nonlinear Robin boundary condition to mean curvature flow with contact
angle close to 90°. SIAM Journal on Mathematical Analysis. Society for
Industrial and Applied Mathematics. https://doi.org/10.1137/21m1424925
chicago: Abels, Helmut, and Maximilian Moser. “Convergence of the Allen--Cahn Equation
with a Nonlinear Robin Boundary Condition to Mean Curvature Flow with Contact
Angle Close to 90°.” SIAM Journal on Mathematical Analysis. Society for
Industrial and Applied Mathematics, 2022. https://doi.org/10.1137/21m1424925.
ieee: H. Abels and M. Moser, “Convergence of the Allen--Cahn equation with a nonlinear
Robin boundary condition to mean curvature flow with contact angle close to 90°,”
SIAM Journal on Mathematical Analysis, vol. 54, no. 1. Society for Industrial
and Applied Mathematics, pp. 114–172, 2022.
ista: Abels H, Moser M. 2022. Convergence of the Allen--Cahn equation with a nonlinear
Robin boundary condition to mean curvature flow with contact angle close to 90°.
SIAM Journal on Mathematical Analysis. 54(1), 114–172.
mla: Abels, Helmut, and Maximilian Moser. “Convergence of the Allen--Cahn Equation
with a Nonlinear Robin Boundary Condition to Mean Curvature Flow with Contact
Angle Close to 90°.” SIAM Journal on Mathematical Analysis, vol. 54, no.
1, Society for Industrial and Applied Mathematics, 2022, pp. 114–72, doi:10.1137/21m1424925.
short: H. Abels, M. Moser, SIAM Journal on Mathematical Analysis 54 (2022) 114–172.
date_created: 2023-01-16T10:07:00Z
date_published: 2022-01-04T00:00:00Z
date_updated: 2023-08-04T10:34:56Z
day: '04'
department:
- _id: JuFi
doi: 10.1137/21m1424925
external_id:
arxiv:
- '2105.08434'
isi:
- '000762768000004'
intvolume: ' 54'
isi: 1
issue: '1'
keyword:
- Applied Mathematics
- Computational Mathematics
- Analysis
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2105.08434'
month: '01'
oa: 1
oa_version: Preprint
page: 114-172
publication: SIAM Journal on Mathematical Analysis
publication_identifier:
eissn:
- 1095-7154
issn:
- 0036-1410
publication_status: published
publisher: Society for Industrial and Applied Mathematics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Convergence of the Allen--Cahn equation with a nonlinear Robin boundary condition
to mean curvature flow with contact angle close to 90°
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 54
year: '2022'
...
---
_id: '10211'
abstract:
- lang: eng
text: "We study the problem of recovering an unknown signal \U0001D465\U0001D465
given measurements obtained from a generalized linear model with a Gaussian sensing
matrix. Two popular solutions are based on a linear estimator \U0001D465\U0001D465^L
and a spectral estimator \U0001D465\U0001D465^s. The former is a data-dependent
linear combination of the columns of the measurement matrix, and its analysis
is quite simple. The latter is the principal eigenvector of a data-dependent matrix,
and a recent line of work has studied its performance. In this paper, we show
how to optimally combine \U0001D465\U0001D465^L and \U0001D465\U0001D465^s. At
the heart of our analysis is the exact characterization of the empirical joint
distribution of (\U0001D465\U0001D465,\U0001D465\U0001D465^L,\U0001D465\U0001D465^s)
in the high-dimensional limit. This allows us to compute the Bayes-optimal combination
of \U0001D465\U0001D465^L and \U0001D465\U0001D465^s, given the limiting distribution
of the signal \U0001D465\U0001D465. When the distribution of the signal is Gaussian,
then the Bayes-optimal combination has the form \U0001D703\U0001D465\U0001D465^L+\U0001D465\U0001D465^s
and we derive the optimal combination coefficient. In order to establish the limiting
distribution of (\U0001D465\U0001D465,\U0001D465\U0001D465^L,\U0001D465\U0001D465^s),
we design and analyze an approximate message passing algorithm whose iterates
give \U0001D465\U0001D465^L and approach \U0001D465\U0001D465^s. Numerical simulations
demonstrate the improvement of the proposed combination with respect to the two
methods considered separately."
acknowledgement: M. Mondelli would like to thank Andrea Montanari for helpful discussions.
All the authors would like to thank the anonymous reviewers for their helpful comments.
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: Christos
full_name: Thrampoulidis, Christos
last_name: Thrampoulidis
- first_name: Ramji
full_name: Venkataramanan, Ramji
last_name: Venkataramanan
citation:
ama: Mondelli M, Thrampoulidis C, Venkataramanan R. Optimal combination of linear
and spectral estimators for generalized linear models. Foundations of Computational
Mathematics. 2021. doi:10.1007/s10208-021-09531-x
apa: Mondelli, M., Thrampoulidis, C., & Venkataramanan, R. (2021). Optimal combination
of linear and spectral estimators for generalized linear models. Foundations
of Computational Mathematics. Springer. https://doi.org/10.1007/s10208-021-09531-x
chicago: Mondelli, Marco, Christos Thrampoulidis, and Ramji Venkataramanan. “Optimal
Combination of Linear and Spectral Estimators for Generalized Linear Models.”
Foundations of Computational Mathematics. Springer, 2021. https://doi.org/10.1007/s10208-021-09531-x.
ieee: M. Mondelli, C. Thrampoulidis, and R. Venkataramanan, “Optimal combination
of linear and spectral estimators for generalized linear models,” Foundations
of Computational Mathematics. Springer, 2021.
ista: Mondelli M, Thrampoulidis C, Venkataramanan R. 2021. Optimal combination of
linear and spectral estimators for generalized linear models. Foundations of Computational
Mathematics.
mla: Mondelli, Marco, et al. “Optimal Combination of Linear and Spectral Estimators
for Generalized Linear Models.” Foundations of Computational Mathematics,
Springer, 2021, doi:10.1007/s10208-021-09531-x.
short: M. Mondelli, C. Thrampoulidis, R. Venkataramanan, Foundations of Computational
Mathematics (2021).
date_created: 2021-11-03T10:59:08Z
date_published: 2021-08-17T00:00:00Z
date_updated: 2023-09-05T14:13:57Z
day: '17'
ddc:
- '510'
department:
- _id: MaMo
doi: 10.1007/s10208-021-09531-x
external_id:
arxiv:
- '2008.03326'
isi:
- '000685721000001'
file:
- access_level: open_access
checksum: 9ea12dd8045a0678000a3a59295221cb
content_type: application/pdf
creator: alisjak
date_created: 2021-12-13T15:47:54Z
date_updated: 2021-12-13T15:47:54Z
file_id: '10542'
file_name: 2021_Springer_Mondelli.pdf
file_size: 2305731
relation: main_file
success: 1
file_date_updated: 2021-12-13T15:47:54Z
has_accepted_license: '1'
isi: 1
keyword:
- Applied Mathematics
- Computational Theory and Mathematics
- Computational Mathematics
- Analysis
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Foundations of Computational Mathematics
publication_identifier:
eissn:
- 1615-3383
issn:
- 1615-3375
publication_status: published
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
status: public
title: Optimal combination of linear and spectral estimators for generalized linear
models
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '14125'
abstract:
- lang: eng
text: "Motivation: Recent technological advances have led to an increase in the
production and availability of single-cell data. The ability to integrate a set
of multi-technology measurements would allow the identification of biologically
or clinically meaningful observations through the unification of the perspectives
afforded by each technology. In most cases, however, profiling technologies consume
the used cells and thus pairwise correspondences between datasets are lost. Due
to the sheer size single-cell datasets can acquire, scalable algorithms that are
able to universally match single-cell measurements carried out in one cell to
its corresponding sibling in another technology are needed.\r\nResults: We propose
Single-Cell data Integration via Matching (SCIM), a scalable approach to recover
such correspondences in two or more technologies. SCIM assumes that cells share
a common (low-dimensional) underlying structure and that the underlying cell distribution
is approximately constant across technologies. It constructs a technology-invariant
latent space using an autoencoder framework with an adversarial objective. Multi-modal
datasets are integrated by pairing cells across technologies using a bipartite
matching scheme that operates on the low-dimensional latent representations. We
evaluate SCIM on a simulated cellular branching process and show that the cell-to-cell
matches derived by SCIM reflect the same pseudotime on the simulated dataset.
Moreover, we apply our method to two real-world scenarios, a melanoma tumor sample
and a human bone marrow sample, where we pair cells from a scRNA dataset to their
sibling cells in a CyTOF dataset achieving 90% and 78% cell-matching accuracy
for each one of the samples, respectively."
article_processing_charge: No
article_type: original
author:
- first_name: Stefan G
full_name: Stark, Stefan G
last_name: Stark
- first_name: Joanna
full_name: Ficek, Joanna
last_name: Ficek
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Ximena
full_name: Bonilla, Ximena
last_name: Bonilla
- first_name: Stéphane
full_name: Chevrier, Stéphane
last_name: Chevrier
- first_name: Franziska
full_name: Singer, Franziska
last_name: Singer
- first_name: Rudolf
full_name: Aebersold, Rudolf
last_name: Aebersold
- first_name: Faisal S
full_name: Al-Quaddoomi, Faisal S
last_name: Al-Quaddoomi
- first_name: Jonas
full_name: Albinus, Jonas
last_name: Albinus
- first_name: Ilaria
full_name: Alborelli, Ilaria
last_name: Alborelli
- first_name: Sonali
full_name: Andani, Sonali
last_name: Andani
- first_name: Per-Olof
full_name: Attinger, Per-Olof
last_name: Attinger
- first_name: Marina
full_name: Bacac, Marina
last_name: Bacac
- first_name: Daniel
full_name: Baumhoer, Daniel
last_name: Baumhoer
- first_name: Beatrice
full_name: Beck-Schimmer, Beatrice
last_name: Beck-Schimmer
- first_name: Niko
full_name: Beerenwinkel, Niko
last_name: Beerenwinkel
- first_name: Christian
full_name: Beisel, Christian
last_name: Beisel
- first_name: Lara
full_name: Bernasconi, Lara
last_name: Bernasconi
- first_name: Anne
full_name: Bertolini, Anne
last_name: Bertolini
- first_name: Bernd
full_name: Bodenmiller, Bernd
last_name: Bodenmiller
- first_name: Ximena
full_name: Bonilla, Ximena
last_name: Bonilla
- first_name: Ruben
full_name: Casanova, Ruben
last_name: Casanova
- first_name: Stéphane
full_name: Chevrier, Stéphane
last_name: Chevrier
- first_name: Natalia
full_name: Chicherova, Natalia
last_name: Chicherova
- first_name: Maya
full_name: D'Costa, Maya
last_name: D'Costa
- first_name: Esther
full_name: Danenberg, Esther
last_name: Danenberg
- first_name: Natalie
full_name: Davidson, Natalie
last_name: Davidson
- first_name: Monica-Andreea Dră
full_name: gan, Monica-Andreea Dră
last_name: gan
- first_name: Reinhard
full_name: Dummer, Reinhard
last_name: Dummer
- first_name: Stefanie
full_name: Engler, Stefanie
last_name: Engler
- first_name: Martin
full_name: Erkens, Martin
last_name: Erkens
- first_name: Katja
full_name: Eschbach, Katja
last_name: Eschbach
- first_name: Cinzia
full_name: Esposito, Cinzia
last_name: Esposito
- first_name: André
full_name: Fedier, André
last_name: Fedier
- first_name: Pedro
full_name: Ferreira, Pedro
last_name: Ferreira
- first_name: Joanna
full_name: Ficek, Joanna
last_name: Ficek
- first_name: Anja L
full_name: Frei, Anja L
last_name: Frei
- first_name: Bruno
full_name: Frey, Bruno
last_name: Frey
- first_name: Sandra
full_name: Goetze, Sandra
last_name: Goetze
- first_name: Linda
full_name: Grob, Linda
last_name: Grob
- first_name: Gabriele
full_name: Gut, Gabriele
last_name: Gut
- first_name: Detlef
full_name: Günther, Detlef
last_name: Günther
- first_name: Martina
full_name: Haberecker, Martina
last_name: Haberecker
- first_name: Pirmin
full_name: Haeuptle, Pirmin
last_name: Haeuptle
- first_name: Viola
full_name: Heinzelmann-Schwarz, Viola
last_name: Heinzelmann-Schwarz
- first_name: Sylvia
full_name: Herter, Sylvia
last_name: Herter
- first_name: Rene
full_name: Holtackers, Rene
last_name: Holtackers
- first_name: Tamara
full_name: Huesser, Tamara
last_name: Huesser
- first_name: Anja
full_name: Irmisch, Anja
last_name: Irmisch
- first_name: Francis
full_name: Jacob, Francis
last_name: Jacob
- first_name: Andrea
full_name: Jacobs, Andrea
last_name: Jacobs
- first_name: Tim M
full_name: Jaeger, Tim M
last_name: Jaeger
- first_name: Katharina
full_name: Jahn, Katharina
last_name: Jahn
- first_name: Alva R
full_name: James, Alva R
last_name: James
- first_name: Philip M
full_name: Jermann, Philip M
last_name: Jermann
- first_name: André
full_name: Kahles, André
last_name: Kahles
- first_name: Abdullah
full_name: Kahraman, Abdullah
last_name: Kahraman
- first_name: Viktor H
full_name: Koelzer, Viktor H
last_name: Koelzer
- first_name: Werner
full_name: Kuebler, Werner
last_name: Kuebler
- first_name: Jack
full_name: Kuipers, Jack
last_name: Kuipers
- first_name: Christian P
full_name: Kunze, Christian P
last_name: Kunze
- first_name: Christian
full_name: Kurzeder, Christian
last_name: Kurzeder
- first_name: Kjong-Van
full_name: Lehmann, Kjong-Van
last_name: Lehmann
- first_name: Mitchell
full_name: Levesque, Mitchell
last_name: Levesque
- first_name: Sebastian
full_name: Lugert, Sebastian
last_name: Lugert
- first_name: Gerd
full_name: Maass, Gerd
last_name: Maass
- first_name: Markus
full_name: Manz, Markus
last_name: Manz
- first_name: Philipp
full_name: Markolin, Philipp
last_name: Markolin
- first_name: Julien
full_name: Mena, Julien
last_name: Mena
- first_name: Ulrike
full_name: Menzel, Ulrike
last_name: Menzel
- first_name: Julian M
full_name: Metzler, Julian M
last_name: Metzler
- first_name: Nicola
full_name: Miglino, Nicola
last_name: Miglino
- first_name: Emanuela S
full_name: Milani, Emanuela S
last_name: Milani
- first_name: Holger
full_name: Moch, Holger
last_name: Moch
- first_name: Simone
full_name: Muenst, Simone
last_name: Muenst
- first_name: Riccardo
full_name: Murri, Riccardo
last_name: Murri
- first_name: Charlotte KY
full_name: Ng, Charlotte KY
last_name: Ng
- first_name: Stefan
full_name: Nicolet, Stefan
last_name: Nicolet
- first_name: Marta
full_name: Nowak, Marta
last_name: Nowak
- first_name: Patrick GA
full_name: Pedrioli, Patrick GA
last_name: Pedrioli
- first_name: Lucas
full_name: Pelkmans, Lucas
last_name: Pelkmans
- first_name: Salvatore
full_name: Piscuoglio, Salvatore
last_name: Piscuoglio
- first_name: Michael
full_name: Prummer, Michael
last_name: Prummer
- first_name: Mathilde
full_name: Ritter, Mathilde
last_name: Ritter
- first_name: Christian
full_name: Rommel, Christian
last_name: Rommel
- first_name: María L
full_name: Rosano-González, María L
last_name: Rosano-González
- first_name: Gunnar
full_name: Rätsch, Gunnar
last_name: Rätsch
- first_name: Natascha
full_name: Santacroce, Natascha
last_name: Santacroce
- first_name: Jacobo Sarabia del
full_name: Castillo, Jacobo Sarabia del
last_name: Castillo
- first_name: Ramona
full_name: Schlenker, Ramona
last_name: Schlenker
- first_name: Petra C
full_name: Schwalie, Petra C
last_name: Schwalie
- first_name: Severin
full_name: Schwan, Severin
last_name: Schwan
- first_name: Tobias
full_name: Schär, Tobias
last_name: Schär
- first_name: Gabriela
full_name: Senti, Gabriela
last_name: Senti
- first_name: Franziska
full_name: Singer, Franziska
last_name: Singer
- first_name: Sujana
full_name: Sivapatham, Sujana
last_name: Sivapatham
- first_name: Berend
full_name: Snijder, Berend
last_name: Snijder
- first_name: Bettina
full_name: Sobottka, Bettina
last_name: Sobottka
- first_name: Vipin T
full_name: Sreedharan, Vipin T
last_name: Sreedharan
- first_name: Stefan
full_name: Stark, Stefan
last_name: Stark
- first_name: Daniel J
full_name: Stekhoven, Daniel J
last_name: Stekhoven
- first_name: Alexandre PA
full_name: Theocharides, Alexandre PA
last_name: Theocharides
- first_name: Tinu M
full_name: Thomas, Tinu M
last_name: Thomas
- first_name: Markus
full_name: Tolnay, Markus
last_name: Tolnay
- first_name: Vinko
full_name: Tosevski, Vinko
last_name: Tosevski
- first_name: Nora C
full_name: Toussaint, Nora C
last_name: Toussaint
- first_name: Mustafa A
full_name: Tuncel, Mustafa A
last_name: Tuncel
- first_name: Marina
full_name: Tusup, Marina
last_name: Tusup
- first_name: Audrey Van
full_name: Drogen, Audrey Van
last_name: Drogen
- first_name: Marcus
full_name: Vetter, Marcus
last_name: Vetter
- first_name: Tatjana
full_name: Vlajnic, Tatjana
last_name: Vlajnic
- first_name: Sandra
full_name: Weber, Sandra
last_name: Weber
- first_name: Walter P
full_name: Weber, Walter P
last_name: Weber
- first_name: Rebekka
full_name: Wegmann, Rebekka
last_name: Wegmann
- first_name: Michael
full_name: Weller, Michael
last_name: Weller
- first_name: Fabian
full_name: Wendt, Fabian
last_name: Wendt
- first_name: Norbert
full_name: Wey, Norbert
last_name: Wey
- first_name: Andreas
full_name: Wicki, Andreas
last_name: Wicki
- first_name: Bernd
full_name: Wollscheid, Bernd
last_name: Wollscheid
- first_name: Shuqing
full_name: Yu, Shuqing
last_name: Yu
- first_name: Johanna
full_name: Ziegler, Johanna
last_name: Ziegler
- first_name: Marc
full_name: Zimmermann, Marc
last_name: Zimmermann
- first_name: Martin
full_name: Zoche, Martin
last_name: Zoche
- first_name: Gregor
full_name: Zuend, Gregor
last_name: Zuend
- first_name: Gunnar
full_name: Rätsch, Gunnar
last_name: Rätsch
- first_name: Kjong-Van
full_name: Lehmann, Kjong-Van
last_name: Lehmann
citation:
ama: 'Stark SG, Ficek J, Locatello F, et al. SCIM: Universal single-cell matching
with unpaired feature sets. Bioinformatics. 2020;36(Supplement_2):i919-i927.
doi:10.1093/bioinformatics/btaa843'
apa: 'Stark, S. G., Ficek, J., Locatello, F., Bonilla, X., Chevrier, S., Singer,
F., … Lehmann, K.-V. (2020). SCIM: Universal single-cell matching with unpaired
feature sets. Bioinformatics. Oxford University Press. https://doi.org/10.1093/bioinformatics/btaa843'
chicago: 'Stark, Stefan G, Joanna Ficek, Francesco Locatello, Ximena Bonilla, Stéphane
Chevrier, Franziska Singer, Rudolf Aebersold, et al. “SCIM: Universal Single-Cell
Matching with Unpaired Feature Sets.” Bioinformatics. Oxford University
Press, 2020. https://doi.org/10.1093/bioinformatics/btaa843.'
ieee: 'S. G. Stark et al., “SCIM: Universal single-cell matching with unpaired
feature sets,” Bioinformatics, vol. 36, no. Supplement_2. Oxford University
Press, pp. i919–i927, 2020.'
ista: 'Stark SG et al. 2020. SCIM: Universal single-cell matching with unpaired
feature sets. Bioinformatics. 36(Supplement_2), i919–i927.'
mla: 'Stark, Stefan G., et al. “SCIM: Universal Single-Cell Matching with Unpaired
Feature Sets.” Bioinformatics, vol. 36, no. Supplement_2, Oxford University
Press, 2020, pp. i919–27, doi:10.1093/bioinformatics/btaa843.'
short: S.G. Stark, J. Ficek, F. Locatello, X. Bonilla, S. Chevrier, F. Singer, R.
Aebersold, F.S. Al-Quaddoomi, J. Albinus, I. Alborelli, S. Andani, P.-O. Attinger,
M. Bacac, D. Baumhoer, B. Beck-Schimmer, N. Beerenwinkel, C. Beisel, L. Bernasconi,
A. Bertolini, B. Bodenmiller, X. Bonilla, R. Casanova, S. Chevrier, N. Chicherova,
M. D’Costa, E. Danenberg, N. Davidson, M.-A.D. gan, R. Dummer, S. Engler, M. Erkens,
K. Eschbach, C. Esposito, A. Fedier, P. Ferreira, J. Ficek, A.L. Frei, B. Frey,
S. Goetze, L. Grob, G. Gut, D. Günther, M. Haberecker, P. Haeuptle, V. Heinzelmann-Schwarz,
S. Herter, R. Holtackers, T. Huesser, A. Irmisch, F. Jacob, A. Jacobs, T.M. Jaeger,
K. Jahn, A.R. James, P.M. Jermann, A. Kahles, A. Kahraman, V.H. Koelzer, W. Kuebler,
J. Kuipers, C.P. Kunze, C. Kurzeder, K.-V. Lehmann, M. Levesque, S. Lugert, G.
Maass, M. Manz, P. Markolin, J. Mena, U. Menzel, J.M. Metzler, N. Miglino, E.S.
Milani, H. Moch, S. Muenst, R. Murri, C.K. Ng, S. Nicolet, M. Nowak, P.G. Pedrioli,
L. Pelkmans, S. Piscuoglio, M. Prummer, M. Ritter, C. Rommel, M.L. Rosano-González,
G. Rätsch, N. Santacroce, J.S. del Castillo, R. Schlenker, P.C. Schwalie, S. Schwan,
T. Schär, G. Senti, F. Singer, S. Sivapatham, B. Snijder, B. Sobottka, V.T. Sreedharan,
S. Stark, D.J. Stekhoven, A.P. Theocharides, T.M. Thomas, M. Tolnay, V. Tosevski,
N.C. Toussaint, M.A. Tuncel, M. Tusup, A.V. Drogen, M. Vetter, T. Vlajnic, S.
Weber, W.P. Weber, R. Wegmann, M. Weller, F. Wendt, N. Wey, A. Wicki, B. Wollscheid,
S. Yu, J. Ziegler, M. Zimmermann, M. Zoche, G. Zuend, G. Rätsch, K.-V. Lehmann,
Bioinformatics 36 (2020) i919–i927.
date_created: 2023-08-21T12:28:20Z
date_published: 2020-12-01T00:00:00Z
date_updated: 2023-09-11T10:21:00Z
day: '01'
department:
- _id: FrLo
doi: 10.1093/bioinformatics/btaa843
extern: '1'
external_id:
pmid:
- '33381818'
intvolume: ' 36'
issue: Supplement_2
keyword:
- Computational Mathematics
- Computational Theory and Mathematics
- Computer Science Applications
- Molecular Biology
- Biochemistry
- Statistics and Probability
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1093/bioinformatics/btaa843
month: '12'
oa: 1
oa_version: Published Version
page: i919-i927
pmid: 1
publication: Bioinformatics
publication_identifier:
eissn:
- 1367-4811
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/ratschlab/scim
scopus_import: '1'
status: public
title: 'SCIM: Universal single-cell matching with unpaired feature sets'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 36
year: '2020'
...
---
_id: '9781'
abstract:
- lang: eng
text: We consider the Pekar functional on a ball in ℝ3. We prove uniqueness of minimizers,
and a quadratic lower bound in terms of the distance to the minimizer. The latter
follows from nondegeneracy of the Hessian at the minimum.
acknowledgement: We are grateful for the hospitality at the Mittag-Leffler Institute,
where part of this work has been done. The work of the authors was supported by
the European Research Council (ERC)under the European Union's Horizon 2020 research
and innovation programme grant 694227.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Dario
full_name: Feliciangeli, Dario
id: 41A639AA-F248-11E8-B48F-1D18A9856A87
last_name: Feliciangeli
orcid: 0000-0003-0754-8530
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Feliciangeli D, Seiringer R. Uniqueness and nondegeneracy of minimizers of
the Pekar functional on a ball. SIAM Journal on Mathematical Analysis.
2020;52(1):605-622. doi:10.1137/19m126284x
apa: Feliciangeli, D., & Seiringer, R. (2020). Uniqueness and nondegeneracy
of minimizers of the Pekar functional on a ball. SIAM Journal on Mathematical
Analysis. Society for Industrial & Applied Mathematics . https://doi.org/10.1137/19m126284x
chicago: Feliciangeli, Dario, and Robert Seiringer. “Uniqueness and Nondegeneracy
of Minimizers of the Pekar Functional on a Ball.” SIAM Journal on Mathematical
Analysis. Society for Industrial & Applied Mathematics , 2020. https://doi.org/10.1137/19m126284x.
ieee: D. Feliciangeli and R. Seiringer, “Uniqueness and nondegeneracy of minimizers
of the Pekar functional on a ball,” SIAM Journal on Mathematical Analysis,
vol. 52, no. 1. Society for Industrial & Applied Mathematics , pp. 605–622,
2020.
ista: Feliciangeli D, Seiringer R. 2020. Uniqueness and nondegeneracy of minimizers
of the Pekar functional on a ball. SIAM Journal on Mathematical Analysis. 52(1),
605–622.
mla: Feliciangeli, Dario, and Robert Seiringer. “Uniqueness and Nondegeneracy of
Minimizers of the Pekar Functional on a Ball.” SIAM Journal on Mathematical
Analysis, vol. 52, no. 1, Society for Industrial & Applied Mathematics
, 2020, pp. 605–22, doi:10.1137/19m126284x.
short: D. Feliciangeli, R. Seiringer, SIAM Journal on Mathematical Analysis 52 (2020)
605–622.
date_created: 2021-08-06T07:34:16Z
date_published: 2020-02-12T00:00:00Z
date_updated: 2023-09-07T13:30:11Z
day: '12'
ddc:
- '510'
department:
- _id: RoSe
doi: 10.1137/19m126284x
ec_funded: 1
external_id:
arxiv:
- '1904.08647 '
isi:
- '000546967700022'
has_accepted_license: '1'
intvolume: ' 52'
isi: 1
issue: '1'
keyword:
- Applied Mathematics
- Computational Mathematics
- Analysis
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1904.08647
month: '02'
oa: 1
oa_version: Preprint
page: 605-622
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication: SIAM Journal on Mathematical Analysis
publication_identifier:
eissn:
- 1095-7154
issn:
- 0036-1410
publication_status: published
publisher: 'Society for Industrial & Applied Mathematics '
quality_controlled: '1'
related_material:
record:
- id: '9733'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 52
year: '2020'
...
---
_id: '11670'
abstract:
- lang: eng
text: Auctions are widely used on the Web. Applications range from sponsored search
to platforms such as eBay. In these and in many other applications the auctions
in use are single-/multi-item auctions with unit demand. The main drawback of
standard mechanisms for this type of auctions, such as VCG and GSP, is the limited
expressiveness that they offer to the bidders. The General Auction Mechanism (GAM)
of Aggarwal et al. [2009] takes a first step toward addressing the problem of
limited expressiveness by computing a bidder optimal, envy-free outcome for linear
utility functions with identical slopes and a single discontinuity per bidder-item
pair. We show that in many practical situations this does not suffice to adequately
model the preferences of the bidders, and we overcome this problem by presenting
the first mechanism for piecewise linear utility functions with nonidentical slopes
and multiple discontinuities. Our mechanism runs in polynomial time. Like GAM
it is incentive compatible for inputs that fulfill a certain nondegeneracy assumption,
but our requirement is more general than the requirement of GAM. For discontinuous
utility functions that are nondegenerate as well as for continuous utility functions
the outcome of our mechanism is a competitive equilibrium. We also show how our
mechanism can be used to compute approximately bidder optimal, envy-free outcomes
for a general class of continuous utility functions via piecewise linear approximation.
Finally, we prove hardness results for even more expressive settings.
acknowledgement: We would like to thank Veronika Loitzenbauer and the anonymous referees
for their valuable feedback.
article_number: '1'
article_processing_charge: No
article_type: original
author:
- first_name: Paul
full_name: Dütting, Paul
last_name: Dütting
- 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: Ingmar
full_name: Weber, Ingmar
last_name: Weber
citation:
ama: Dütting P, Henzinger MH, Weber I. An expressive mechanism for auctions on the
web. ACM Transactions on Economics and Computation. 2015;4(1). doi:10.1145/2716312
apa: Dütting, P., Henzinger, M. H., & Weber, I. (2015). An expressive mechanism
for auctions on the web. ACM Transactions on Economics and Computation.
Association for Computing Machinery. https://doi.org/10.1145/2716312
chicago: Dütting, Paul, Monika H Henzinger, and Ingmar Weber. “An Expressive Mechanism
for Auctions on the Web.” ACM Transactions on Economics and Computation.
Association for Computing Machinery, 2015. https://doi.org/10.1145/2716312.
ieee: P. Dütting, M. H. Henzinger, and I. Weber, “An expressive mechanism for auctions
on the web,” ACM Transactions on Economics and Computation, vol. 4, no.
1. Association for Computing Machinery, 2015.
ista: Dütting P, Henzinger MH, Weber I. 2015. An expressive mechanism for auctions
on the web. ACM Transactions on Economics and Computation. 4(1), 1.
mla: Dütting, Paul, et al. “An Expressive Mechanism for Auctions on the Web.” ACM
Transactions on Economics and Computation, vol. 4, no. 1, 1, Association for
Computing Machinery, 2015, doi:10.1145/2716312.
short: P. Dütting, M.H. Henzinger, I. Weber, ACM Transactions on Economics and Computation
4 (2015).
date_created: 2022-07-27T12:43:18Z
date_published: 2015-12-02T00:00:00Z
date_updated: 2023-02-09T10:08:41Z
day: '02'
doi: 10.1145/2716312
extern: '1'
intvolume: ' 4'
issue: '1'
keyword:
- Computational Mathematics
- Marketing
- Economics and Econometrics
- Statistics and Probability
- Computer Science (miscellaneous)
language:
- iso: eng
month: '12'
oa_version: None
publication: ACM Transactions on Economics and Computation
publication_identifier:
eissn:
- 2167-8383
issn:
- 2167-8375
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: An expressive mechanism for auctions on the web
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2015'
...
---
_id: '8459'
abstract:
- lang: eng
text: Nuclear magnetic resonance (NMR) is a powerful tool for observing the motion
of biomolecules at the atomic level. One technique, the analysis of relaxation
dispersion phenomenon, is highly suited for studying the kinetics and thermodynamics
of biological processes. Built on top of the relax computational environment for
NMR dynamics is a new dispersion analysis designed to be comprehensive, accurate
and easy-to-use. The software supports more models, both numeric and analytic,
than current solutions. An automated protocol, available for scripting and driving
the graphical user interface (GUI), is designed to simplify the analysis of dispersion
data for NMR spectroscopists. Decreases in optimization time are granted by parallelization
for running on computer clusters and by skipping an initial grid search by using
parameters from one solution as the starting point for another —using analytic
model results for the numeric models, taking advantage of model nesting, and using
averaged non-clustered results for the clustered analysis.
article_processing_charge: No
article_type: original
author:
- first_name: Sébastien
full_name: Morin, Sébastien
last_name: Morin
- first_name: Troels E
full_name: Linnet, Troels E
last_name: Linnet
- first_name: Mathilde
full_name: Lescanne, Mathilde
last_name: Lescanne
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Gary S
full_name: Thompson, Gary S
last_name: Thompson
- first_name: Martin
full_name: Tollinger, Martin
last_name: Tollinger
- first_name: Kaare
full_name: Teilum, Kaare
last_name: Teilum
- first_name: Stéphane
full_name: Gagné, Stéphane
last_name: Gagné
- first_name: Dominique
full_name: Marion, Dominique
last_name: Marion
- first_name: Christian
full_name: Griesinger, Christian
last_name: Griesinger
- first_name: Martin
full_name: Blackledge, Martin
last_name: Blackledge
- first_name: Edward J
full_name: d’Auvergne, Edward J
last_name: d’Auvergne
citation:
ama: 'Morin S, Linnet TE, Lescanne M, et al. Relax: The analysis of biomolecular
kinetics and thermodynamics using NMR relaxation dispersion data. Bioinformatics.
2014;30(15):2219-2220. doi:10.1093/bioinformatics/btu166'
apa: 'Morin, S., Linnet, T. E., Lescanne, M., Schanda, P., Thompson, G. S., Tollinger,
M., … d’Auvergne, E. J. (2014). Relax: The analysis of biomolecular kinetics and
thermodynamics using NMR relaxation dispersion data. Bioinformatics. Oxford
University Press. https://doi.org/10.1093/bioinformatics/btu166'
chicago: 'Morin, Sébastien, Troels E Linnet, Mathilde Lescanne, Paul Schanda, Gary
S Thompson, Martin Tollinger, Kaare Teilum, et al. “Relax: The Analysis of Biomolecular
Kinetics and Thermodynamics Using NMR Relaxation Dispersion Data.” Bioinformatics.
Oxford University Press, 2014. https://doi.org/10.1093/bioinformatics/btu166.'
ieee: 'S. Morin et al., “Relax: The analysis of biomolecular kinetics and
thermodynamics using NMR relaxation dispersion data,” Bioinformatics, vol.
30, no. 15. Oxford University Press, pp. 2219–2220, 2014.'
ista: 'Morin S, Linnet TE, Lescanne M, Schanda P, Thompson GS, Tollinger M, Teilum
K, Gagné S, Marion D, Griesinger C, Blackledge M, d’Auvergne EJ. 2014. Relax:
The analysis of biomolecular kinetics and thermodynamics using NMR relaxation
dispersion data. Bioinformatics. 30(15), 2219–2220.'
mla: 'Morin, Sébastien, et al. “Relax: The Analysis of Biomolecular Kinetics and
Thermodynamics Using NMR Relaxation Dispersion Data.” Bioinformatics, vol.
30, no. 15, Oxford University Press, 2014, pp. 2219–20, doi:10.1093/bioinformatics/btu166.'
short: S. Morin, T.E. Linnet, M. Lescanne, P. Schanda, G.S. Thompson, M. Tollinger,
K. Teilum, S. Gagné, D. Marion, C. Griesinger, M. Blackledge, E.J. d’Auvergne,
Bioinformatics 30 (2014) 2219–2220.
date_created: 2020-09-18T10:08:07Z
date_published: 2014-08-01T00:00:00Z
date_updated: 2021-01-12T08:19:25Z
day: '01'
doi: 10.1093/bioinformatics/btu166
extern: '1'
intvolume: ' 30'
issue: '15'
keyword:
- Statistics and Probability
- Computational Theory and Mathematics
- Biochemistry
- Molecular Biology
- Computational Mathematics
- Computer Science Applications
language:
- iso: eng
month: '08'
oa_version: None
page: 2219-2220
publication: Bioinformatics
publication_identifier:
issn:
- 1367-4803
- 1460-2059
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1093/bioinformatics/btz397
status: public
title: 'Relax: The analysis of biomolecular kinetics and thermodynamics using NMR
relaxation dispersion data'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2014'
...
---
_id: '8509'
abstract:
- lang: eng
text: The goal of this paper is to present to nonspecialists what is perhaps the
simplest possible geometrical picture explaining the mechanism of Arnold diffusion.
We choose to speak of a specific model—that of geometric rays in a periodic optical
medium. This model is equivalent to that of a particle in a periodic potential
in ${\mathbb R}^{n}$ with energy prescribed and to the geodesic flow in a Riemannian
metric on ${\mathbb R}^{n} $.
article_processing_charge: No
article_type: original
author:
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: Mark
full_name: Levi, Mark
last_name: Levi
citation:
ama: Kaloshin V, Levi M. Geometry of Arnold diffusion. SIAM Review. 2008;50(4):702-720.
doi:10.1137/070703235
apa: Kaloshin, V., & Levi, M. (2008). Geometry of Arnold diffusion. SIAM
Review. Society for Industrial & Applied Mathematics. https://doi.org/10.1137/070703235
chicago: Kaloshin, Vadim, and Mark Levi. “Geometry of Arnold Diffusion.” SIAM
Review. Society for Industrial & Applied Mathematics, 2008. https://doi.org/10.1137/070703235.
ieee: V. Kaloshin and M. Levi, “Geometry of Arnold diffusion,” SIAM Review,
vol. 50, no. 4. Society for Industrial & Applied Mathematics, pp. 702–720,
2008.
ista: Kaloshin V, Levi M. 2008. Geometry of Arnold diffusion. SIAM Review. 50(4),
702–720.
mla: Kaloshin, Vadim, and Mark Levi. “Geometry of Arnold Diffusion.” SIAM Review,
vol. 50, no. 4, Society for Industrial & Applied Mathematics, 2008, pp. 702–20,
doi:10.1137/070703235.
short: V. Kaloshin, M. Levi, SIAM Review 50 (2008) 702–720.
date_created: 2020-09-18T10:48:12Z
date_published: 2008-11-05T00:00:00Z
date_updated: 2021-01-12T08:19:46Z
day: '05'
doi: 10.1137/070703235
extern: '1'
intvolume: ' 50'
issue: '4'
keyword:
- Theoretical Computer Science
- Applied Mathematics
- Computational Mathematics
language:
- iso: eng
month: '11'
oa_version: None
page: 702-720
publication: SIAM Review
publication_identifier:
issn:
- 0036-1445
- 1095-7200
publication_status: published
publisher: Society for Industrial & Applied Mathematics
quality_controlled: '1'
status: public
title: Geometry of Arnold diffusion
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 50
year: '2008'
...
---
_id: '11683'
abstract:
- lang: eng
text: The vertex connectivity κ of a graph is the smallest number of vertices whose
deletion separates the graph or makes it trivial. We present the fastest known
deterministic algorithm for finding the vertex connectivity and a corresponding
separator. The time for a digraph having n vertices and m edges is O(min{κ3 +
n, κn}m); for an undirected graph the term m can be replaced by κn. A randomized
algorithm finds κ with error probability 1/2 in time O(nm). If the vertices have
nonnegative weights the weighted vertex connectivity is found in time O(κ1nmlog(n2/m))
where κ1 ≤ m/n is the unweighted vertex connectivity or in expected time O(nmlog(n2/m))
with error probability 1/2. The main algorithm combines two previous vertex connectivity
algorithms and a generalization of the preflow-push algorithm of Hao and Orlin
(1994, J. Algorithms17, 424–446) that computes edge connectivity.
article_processing_charge: No
article_type: original
author:
- 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: Satish
full_name: Rao, Satish
last_name: Rao
- first_name: Harold N.
full_name: Gabow, Harold N.
last_name: Gabow
citation:
ama: 'Henzinger MH, Rao S, Gabow HN. Computing vertex connectivity: New bounds from
old techniques. Journal of Algorithms. 2000;34(2):222-250. doi:10.1006/jagm.1999.1055'
apa: 'Henzinger, M. H., Rao, S., & Gabow, H. N. (2000). Computing vertex connectivity:
New bounds from old techniques. Journal of Algorithms. Elsevier. https://doi.org/10.1006/jagm.1999.1055'
chicago: 'Henzinger, Monika H, Satish Rao, and Harold N. Gabow. “Computing Vertex
Connectivity: New Bounds from Old Techniques.” Journal of Algorithms. Elsevier,
2000. https://doi.org/10.1006/jagm.1999.1055.'
ieee: 'M. H. Henzinger, S. Rao, and H. N. Gabow, “Computing vertex connectivity:
New bounds from old techniques,” Journal of Algorithms, vol. 34, no. 2.
Elsevier, pp. 222–250, 2000.'
ista: 'Henzinger MH, Rao S, Gabow HN. 2000. Computing vertex connectivity: New bounds
from old techniques. Journal of Algorithms. 34(2), 222–250.'
mla: 'Henzinger, Monika H., et al. “Computing Vertex Connectivity: New Bounds from
Old Techniques.” Journal of Algorithms, vol. 34, no. 2, Elsevier, 2000,
pp. 222–50, doi:10.1006/jagm.1999.1055.'
short: M.H. Henzinger, S. Rao, H.N. Gabow, Journal of Algorithms 34 (2000) 222–250.
date_created: 2022-07-28T08:56:10Z
date_published: 2000-02-01T00:00:00Z
date_updated: 2022-09-12T09:06:48Z
day: '01'
doi: 10.1006/jagm.1999.1055
extern: '1'
intvolume: ' 34'
issue: '2'
keyword:
- Computational Theory and Mathematics
- Computational Mathematics
- Control and Optimization
language:
- iso: eng
month: '02'
oa_version: None
page: 222-250
publication: Journal of Algorithms
publication_identifier:
issn:
- 0196-6774
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Computing vertex connectivity: New bounds from old techniques'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2000'
...