---
_id: '10674'
abstract:
- lang: eng
  text: 'In two-player games on graphs, the players move a token through a graph to
    produce an infinite path, which determines the winner of the game. Such games
    are central in formal methods since they model the interaction between a non-terminating
    system and its environment. In bidding games the players bid for the right to
    move the token: in each round, the players simultaneously submit bids, and the
    higher bidder moves the token and pays the other player. Bidding games are known
    to have a clean and elegant mathematical structure that relies on the ability
    of the players to submit arbitrarily small bids. Many applications, however, require
    a fixed granularity for the bids, which can represent, for example, the monetary
    value expressed in cents. We study, for the first time, the combination of discrete-bidding
    and infinite-duration games. Our most important result proves that these games
    form a large determined subclass of concurrent games, where determinacy is the
    strong property that there always exists exactly one player who can guarantee
    winning the game. In particular, we show that, in contrast to non-discrete bidding
    games, the mechanism with which tied bids are resolved plays an important role
    in discrete-bidding games. We study several natural tie-breaking mechanisms and
    show that, while some do not admit determinacy, most natural mechanisms imply
    determinacy for every pair of initial budgets.'
acknowledgement: "This research was supported in part by the Austrian Science Fund
  (FWF) under grants S11402-N23 (RiSE/SHiNE), Z211-N23 (Wittgenstein Award), and M
  2369-N33 (Meitner fellowship).\r\n"
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Milad
  full_name: Aghajohari, Milad
  last_name: Aghajohari
- first_name: Guy
  full_name: Avni, Guy
  id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
  last_name: Avni
  orcid: 0000-0001-5588-8287
- first_name: Thomas A
  full_name: Henzinger, Thomas A
  id: 40876CD8-F248-11E8-B48F-1D18A9856A87
  last_name: Henzinger
  orcid: 0000-0002-2985-7724
citation:
  ama: Aghajohari M, Avni G, Henzinger TA. Determinacy in discrete-bidding infinite-duration
    games. <i>Logical Methods in Computer Science</i>. 2021;17(1):10:1-10:23. doi:<a
    href="https://doi.org/10.23638/LMCS-17(1:10)2021">10.23638/LMCS-17(1:10)2021</a>
  apa: Aghajohari, M., Avni, G., &#38; Henzinger, T. A. (2021). Determinacy in discrete-bidding
    infinite-duration games. <i>Logical Methods in Computer Science</i>. International
    Federation for Computational Logic. <a href="https://doi.org/10.23638/LMCS-17(1:10)2021">https://doi.org/10.23638/LMCS-17(1:10)2021</a>
  chicago: Aghajohari, Milad, Guy Avni, and Thomas A Henzinger. “Determinacy in Discrete-Bidding
    Infinite-Duration Games.” <i>Logical Methods in Computer Science</i>. International
    Federation for Computational Logic, 2021. <a href="https://doi.org/10.23638/LMCS-17(1:10)2021">https://doi.org/10.23638/LMCS-17(1:10)2021</a>.
  ieee: M. Aghajohari, G. Avni, and T. A. Henzinger, “Determinacy in discrete-bidding
    infinite-duration games,” <i>Logical Methods in Computer Science</i>, vol. 17,
    no. 1. International Federation for Computational Logic, p. 10:1-10:23, 2021.
  ista: Aghajohari M, Avni G, Henzinger TA. 2021. Determinacy in discrete-bidding
    infinite-duration games. Logical Methods in Computer Science. 17(1), 10:1-10:23.
  mla: Aghajohari, Milad, et al. “Determinacy in Discrete-Bidding Infinite-Duration
    Games.” <i>Logical Methods in Computer Science</i>, vol. 17, no. 1, International
    Federation for Computational Logic, 2021, p. 10:1-10:23, doi:<a href="https://doi.org/10.23638/LMCS-17(1:10)2021">10.23638/LMCS-17(1:10)2021</a>.
  short: M. Aghajohari, G. Avni, T.A. Henzinger, Logical Methods in Computer Science
    17 (2021) 10:1-10:23.
date_created: 2022-01-25T16:32:13Z
date_published: 2021-02-03T00:00:00Z
date_updated: 2023-08-17T06:56:42Z
day: '03'
ddc:
- '510'
department:
- _id: ToHe
doi: 10.23638/LMCS-17(1:10)2021
external_id:
  arxiv:
  - '1905.03588'
  isi:
  - '000658724600010'
file:
- access_level: open_access
  checksum: b35586a50ed1ca8f44767de116d18d81
  content_type: application/pdf
  creator: alisjak
  date_created: 2022-01-26T08:04:50Z
  date_updated: 2022-01-26T08:04:50Z
  file_id: '10690'
  file_name: 2021_LMCS_AGHAJOHAR.pdf
  file_size: 819878
  relation: main_file
  success: 1
file_date_updated: 2022-01-26T08:04:50Z
has_accepted_license: '1'
intvolume: '        17'
isi: 1
issue: '1'
keyword:
- computer science
- computer science and game theory
- logic in computer science
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 10:1-10:23
project:
- _id: 264B3912-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: M02369
  name: Formal Methods meets Algorithmic Game Theory
- _id: 25F2ACDE-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: S11402-N23
  name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: Z211
  name: The Wittgenstein Prize
publication: Logical Methods in Computer Science
publication_identifier:
  eissn:
  - 1860-5974
publication_status: published
publisher: International Federation for Computational Logic
quality_controlled: '1'
scopus_import: '1'
status: public
title: Determinacy in discrete-bidding infinite-duration games
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 17
year: '2021'
...
---
_id: '10855'
abstract:
- lang: eng
  text: 'Consider a distributed task where the communication network is fixed but
    the local inputs given to the nodes of the distributed system may change over
    time. In this work, we explore the following question: if some of the local inputs
    change, can an existing solution be updated efficiently, in a dynamic and distributed
    manner? To address this question, we define the batch dynamic \congest model in
    which we are given a bandwidth-limited communication network and a dynamic edge
    labelling defines the problem input. The task is to maintain a solution to a graph
    problem on the labeled graph under batch changes. We investigate, when a batch
    of α edge label changes arrive, \beginitemize \item how much time as a function
    of α we need to update an existing solution, and \item how much information the
    nodes have to keep in local memory between batches in order to update the solution
    quickly. \enditemize Our work lays the foundations for the theory of input-dynamic
    distributed network algorithms. We give a general picture of the complexity landscape
    in this model, design both universal algorithms and algorithms for concrete problems,
    and present a general framework for lower bounds. In particular, we derive non-trivial
    upper bounds for two selected, contrasting problems: maintaining a minimum spanning
    tree and detecting cliques.'
acknowledgement: "We thank Jukka Suomela for discussions. We also thank our shepherd
  Mohammad Hajiesmaili\r\nand the reviewers for their time and suggestions on how
  to improve the paper. This project\r\nhas received funding from the European Research
  Council (ERC) under the European Union’s\r\nHorizon 2020 research and innovation
  programme (grant agreement No 805223 ScaleML), from the European Union’s Horizon
  2020 research and innovation programme under the Marie\r\nSk lodowska–Curie grant
  agreement No. 840605, from the Vienna Science and Technology Fund (WWTF) project
  WHATIF, ICT19-045, 2020-2024, and from the Austrian Science Fund (FWF) and netIDEE
  SCIENCE project P 33775-N."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Klaus-Tycho
  full_name: Foerster, Klaus-Tycho
  last_name: Foerster
- first_name: Janne
  full_name: Korhonen, Janne
  id: C5402D42-15BC-11E9-A202-CA2BE6697425
  last_name: Korhonen
- first_name: Ami
  full_name: Paz, Ami
  last_name: Paz
- first_name: Joel
  full_name: Rybicki, Joel
  id: 334EFD2E-F248-11E8-B48F-1D18A9856A87
  last_name: Rybicki
  orcid: 0000-0002-6432-6646
- first_name: Stefan
  full_name: Schmid, Stefan
  last_name: Schmid
citation:
  ama: Foerster K-T, Korhonen J, Paz A, Rybicki J, Schmid S. Input-dynamic distributed
    algorithms for communication networks. <i>Proceedings of the ACM on Measurement
    and Analysis of Computing Systems</i>. 2021;5(1):1-33. doi:<a href="https://doi.org/10.1145/3447384">10.1145/3447384</a>
  apa: Foerster, K.-T., Korhonen, J., Paz, A., Rybicki, J., &#38; Schmid, S. (2021).
    Input-dynamic distributed algorithms for communication networks. <i>Proceedings
    of the ACM on Measurement and Analysis of Computing Systems</i>. Association for
    Computing Machinery. <a href="https://doi.org/10.1145/3447384">https://doi.org/10.1145/3447384</a>
  chicago: Foerster, Klaus-Tycho, Janne Korhonen, Ami Paz, Joel Rybicki, and Stefan
    Schmid. “Input-Dynamic Distributed Algorithms for Communication Networks.” <i>Proceedings
    of the ACM on Measurement and Analysis of Computing Systems</i>. Association for
    Computing Machinery, 2021. <a href="https://doi.org/10.1145/3447384">https://doi.org/10.1145/3447384</a>.
  ieee: K.-T. Foerster, J. Korhonen, A. Paz, J. Rybicki, and S. Schmid, “Input-dynamic
    distributed algorithms for communication networks,” <i>Proceedings of the ACM
    on Measurement and Analysis of Computing Systems</i>, vol. 5, no. 1. Association
    for Computing Machinery, pp. 1–33, 2021.
  ista: Foerster K-T, Korhonen J, Paz A, Rybicki J, Schmid S. 2021. Input-dynamic
    distributed algorithms for communication networks. Proceedings of the ACM on Measurement
    and Analysis of Computing Systems. 5(1), 1–33.
  mla: Foerster, Klaus-Tycho, et al. “Input-Dynamic Distributed Algorithms for Communication
    Networks.” <i>Proceedings of the ACM on Measurement and Analysis of Computing
    Systems</i>, vol. 5, no. 1, Association for Computing Machinery, 2021, pp. 1–33,
    doi:<a href="https://doi.org/10.1145/3447384">10.1145/3447384</a>.
  short: K.-T. Foerster, J. Korhonen, A. Paz, J. Rybicki, S. Schmid, Proceedings of
    the ACM on Measurement and Analysis of Computing Systems 5 (2021) 1–33.
date_created: 2022-03-18T09:10:27Z
date_published: 2021-03-01T00:00:00Z
date_updated: 2023-09-26T10:40:55Z
day: '01'
department:
- _id: DaAl
doi: 10.1145/3447384
ec_funded: 1
external_id:
  arxiv:
  - '2005.07637'
intvolume: '         5'
issue: '1'
keyword:
- Computer Networks and Communications
- Hardware and Architecture
- Safety
- Risk
- Reliability and Quality
- Computer Science (miscellaneous)
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/2005.07637
month: '03'
oa: 1
oa_version: Preprint
page: 1-33
project:
- _id: 26A5D39A-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '840605'
  name: Coordination in constrained and natural distributed systems
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '805223'
  name: Elastic Coordination for Scalable Machine Learning
publication: Proceedings of the ACM on Measurement and Analysis of Computing Systems
publication_identifier:
  issn:
  - 2476-1249
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
  record:
  - id: '10854'
    relation: shorter_version
    status: public
scopus_import: '1'
status: public
title: Input-dynamic distributed algorithms for communication networks
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2021'
...
---
_id: '11446'
abstract:
- lang: eng
  text: Suppose that n is not a prime power and not twice a prime power. We prove
    that for any Hausdorff compactum X with a free action of the symmetric group Sn,
    there exists an Sn-equivariant map X→Rn whose image avoids the diagonal {(x,x,…,x)∈Rn∣x∈R}.
    Previously, the special cases of this statement for certain X were usually proved
    using the equivartiant obstruction theory. Such calculations are difficult and
    may become infeasible past the first (primary) obstruction. We take a different
    approach which allows us to prove the vanishing of all obstructions simultaneously.
    The essential step in the proof is classifying the possible degrees of Sn-equivariant
    maps from the boundary ∂Δn−1 of (n−1)-simplex to itself. Existence of equivariant
    maps between spaces is important for many questions arising from discrete mathematics
    and geometry, such as Kneser’s conjecture, the Square Peg conjecture, the Splitting
    Necklace problem, and the Topological Tverberg conjecture, etc. We demonstrate
    the utility of our result applying it to one such question, a specific instance
    of envy-free division problem.
acknowledgement: S. Avvakumov has received funding from the European Research Council
  under the European Union’s Seventh Framework Programme ERC Grant agreement ERC StG
  716424–CASe. S. Kudrya was supported by the Austrian Academic Exchange Service (OeAD),
  ICM-2019-13577.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Sergey
  full_name: Avvakumov, Sergey
  id: 3827DAC8-F248-11E8-B48F-1D18A9856A87
  last_name: Avvakumov
- first_name: Sergey
  full_name: Kudrya, Sergey
  id: ecf01965-d252-11ea-95a5-8ada5f6c6a67
  last_name: Kudrya
citation:
  ama: Avvakumov S, Kudrya S. Vanishing of all equivariant obstructions and the mapping
    degree. <i>Discrete &#38; Computational Geometry</i>. 2021;66(3):1202-1216. doi:<a
    href="https://doi.org/10.1007/s00454-021-00299-z">10.1007/s00454-021-00299-z</a>
  apa: Avvakumov, S., &#38; Kudrya, S. (2021). Vanishing of all equivariant obstructions
    and the mapping degree. <i>Discrete &#38; Computational Geometry</i>. Springer
    Nature. <a href="https://doi.org/10.1007/s00454-021-00299-z">https://doi.org/10.1007/s00454-021-00299-z</a>
  chicago: Avvakumov, Sergey, and Sergey Kudrya. “Vanishing of All Equivariant Obstructions
    and the Mapping Degree.” <i>Discrete &#38; Computational Geometry</i>. Springer
    Nature, 2021. <a href="https://doi.org/10.1007/s00454-021-00299-z">https://doi.org/10.1007/s00454-021-00299-z</a>.
  ieee: S. Avvakumov and S. Kudrya, “Vanishing of all equivariant obstructions and
    the mapping degree,” <i>Discrete &#38; Computational Geometry</i>, vol. 66, no.
    3. Springer Nature, pp. 1202–1216, 2021.
  ista: Avvakumov S, Kudrya S. 2021. Vanishing of all equivariant obstructions and
    the mapping degree. Discrete &#38; Computational Geometry. 66(3), 1202–1216.
  mla: Avvakumov, Sergey, and Sergey Kudrya. “Vanishing of All Equivariant Obstructions
    and the Mapping Degree.” <i>Discrete &#38; Computational Geometry</i>, vol. 66,
    no. 3, Springer Nature, 2021, pp. 1202–16, doi:<a href="https://doi.org/10.1007/s00454-021-00299-z">10.1007/s00454-021-00299-z</a>.
  short: S. Avvakumov, S. Kudrya, Discrete &#38; Computational Geometry 66 (2021)
    1202–1216.
date_created: 2022-06-17T08:45:15Z
date_published: 2021-10-01T00:00:00Z
date_updated: 2023-02-23T13:26:41Z
day: '01'
doi: 10.1007/s00454-021-00299-z
extern: '1'
external_id:
  arxiv:
  - '1910.12628'
intvolume: '        66'
issue: '3'
keyword:
- Computational Theory and Mathematics
- Discrete Mathematics and Combinatorics
- Geometry and Topology
- Theoretical Computer Science
language:
- iso: eng
month: '10'
oa_version: Preprint
page: 1202-1216
publication: Discrete & Computational Geometry
publication_identifier:
  eissn:
  - 1432-0444
  issn:
  - 0179-5376
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
  record:
  - id: '8182'
    relation: earlier_version
    status: public
scopus_import: '1'
status: public
title: Vanishing of all equivariant obstructions and the mapping degree
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 66
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. <i>Bioinformatics</i>. 2020;36(Supplement_2):i919-i927.
    doi:<a href="https://doi.org/10.1093/bioinformatics/btaa843">10.1093/bioinformatics/btaa843</a>'
  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. <i>Bioinformatics</i>. Oxford University Press. <a href="https://doi.org/10.1093/bioinformatics/btaa843">https://doi.org/10.1093/bioinformatics/btaa843</a>'
  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.” <i>Bioinformatics</i>. Oxford University
    Press, 2020. <a href="https://doi.org/10.1093/bioinformatics/btaa843">https://doi.org/10.1093/bioinformatics/btaa843</a>.'
  ieee: 'S. G. Stark <i>et al.</i>, “SCIM: Universal single-cell matching with unpaired
    feature sets,” <i>Bioinformatics</i>, 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.” <i>Bioinformatics</i>, vol. 36, no. Supplement_2, Oxford University
    Press, 2020, pp. i919–27, doi:<a href="https://doi.org/10.1093/bioinformatics/btaa843">10.1093/bioinformatics/btaa843</a>.'
  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: '11657'
abstract:
- lang: eng
  text: The minimum cut problem for an undirected edge-weighted graph asks us to divide
    its set of nodes into two blocks while minimizing the weight sum of the cut edges.
    Here, we introduce a linear-time algorithm to compute near-minimum cuts. Our algorithm
    is based on cluster contraction using label propagation and Padberg and Rinaldi’s
    contraction heuristics [SIAM Review, 1991]. We give both sequential and shared-memory
    parallel implementations of our algorithm. Extensive experiments on both real-world
    and generated instances show that our algorithm finds the optimal cut on nearly
    all instances significantly faster than other state-of-the-art exact algorithms,
    and our error rate is lower than that of other heuristic algorithms. In addition,
    our parallel algorithm runs a factor 7.5× faster on average when using 32 threads.
    To further speed up computations, we also give a version of our algorithm that
    performs random edge contractions as preprocessing. This version achieves a lower
    running time and better parallel scalability at the expense of a higher error
    rate.
article_processing_charge: No
article_type: original
arxiv: 1
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: Alexander
  full_name: Noe, Alexander
  last_name: Noe
- first_name: Christian
  full_name: Schulz, Christian
  last_name: Schulz
- first_name: Darren
  full_name: Strash, Darren
  last_name: Strash
citation:
  ama: Henzinger MH, Noe A, Schulz C, Strash D. Practical minimum cut algorithms.
    <i>ACM Journal of Experimental Algorithmics</i>. 2018;23:1-22. doi:<a href="https://doi.org/10.1145/3274662">10.1145/3274662</a>
  apa: Henzinger, M. H., Noe, A., Schulz, C., &#38; Strash, D. (2018). Practical minimum
    cut algorithms. <i>ACM Journal of Experimental Algorithmics</i>. Association for
    Computing Machinery. <a href="https://doi.org/10.1145/3274662">https://doi.org/10.1145/3274662</a>
  chicago: Henzinger, Monika H, Alexander Noe, Christian Schulz, and Darren Strash.
    “Practical Minimum Cut Algorithms.” <i>ACM Journal of Experimental Algorithmics</i>.
    Association for Computing Machinery, 2018. <a href="https://doi.org/10.1145/3274662">https://doi.org/10.1145/3274662</a>.
  ieee: M. H. Henzinger, A. Noe, C. Schulz, and D. Strash, “Practical minimum cut
    algorithms,” <i>ACM Journal of Experimental Algorithmics</i>, vol. 23. Association
    for Computing Machinery, pp. 1–22, 2018.
  ista: Henzinger MH, Noe A, Schulz C, Strash D. 2018. Practical minimum cut algorithms.
    ACM Journal of Experimental Algorithmics. 23, 1–22.
  mla: Henzinger, Monika H., et al. “Practical Minimum Cut Algorithms.” <i>ACM Journal
    of Experimental Algorithmics</i>, vol. 23, Association for Computing Machinery,
    2018, pp. 1–22, doi:<a href="https://doi.org/10.1145/3274662">10.1145/3274662</a>.
  short: M.H. Henzinger, A. Noe, C. Schulz, D. Strash, ACM Journal of Experimental
    Algorithmics 23 (2018) 1–22.
date_created: 2022-07-27T08:28:26Z
date_published: 2018-10-01T00:00:00Z
date_updated: 2022-09-09T11:32:52Z
day: '01'
doi: 10.1145/3274662
extern: '1'
external_id:
  arxiv:
  - '1708.06127'
intvolume: '        23'
keyword:
- Theoretical Computer Science
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1708.06127
month: '10'
oa: 1
oa_version: Preprint
page: 1-22
publication: ACM Journal of Experimental Algorithmics
publication_identifier:
  eissn:
  - 1084-6654
  issn:
  - 1084-6654
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Practical minimum cut algorithms
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 23
year: '2018'
...
---
_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. <i>ACM Transactions on Economics and Computation</i>. 2015;4(1). doi:<a href="https://doi.org/10.1145/2716312">10.1145/2716312</a>
  apa: Dütting, P., Henzinger, M. H., &#38; Weber, I. (2015). An expressive mechanism
    for auctions on the web. <i>ACM Transactions on Economics and Computation</i>.
    Association for Computing Machinery. <a href="https://doi.org/10.1145/2716312">https://doi.org/10.1145/2716312</a>
  chicago: Dütting, Paul, Monika H Henzinger, and Ingmar Weber. “An Expressive Mechanism
    for Auctions on the Web.” <i>ACM Transactions on Economics and Computation</i>.
    Association for Computing Machinery, 2015. <a href="https://doi.org/10.1145/2716312">https://doi.org/10.1145/2716312</a>.
  ieee: P. Dütting, M. H. Henzinger, and I. Weber, “An expressive mechanism for auctions
    on the web,” <i>ACM Transactions on Economics and Computation</i>, 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.” <i>ACM
    Transactions on Economics and Computation</i>, vol. 4, no. 1, 1, Association for
    Computing Machinery, 2015, doi:<a href="https://doi.org/10.1145/2716312">10.1145/2716312</a>.
  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. <i>Bioinformatics</i>.
    2014;30(15):2219-2220. doi:<a href="https://doi.org/10.1093/bioinformatics/btu166">10.1093/bioinformatics/btu166</a>'
  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. <i>Bioinformatics</i>. Oxford
    University Press. <a href="https://doi.org/10.1093/bioinformatics/btu166">https://doi.org/10.1093/bioinformatics/btu166</a>'
  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.” <i>Bioinformatics</i>.
    Oxford University Press, 2014. <a href="https://doi.org/10.1093/bioinformatics/btu166">https://doi.org/10.1093/bioinformatics/btu166</a>.'
  ieee: 'S. Morin <i>et al.</i>, “Relax: The analysis of biomolecular kinetics and
    thermodynamics using NMR relaxation dispersion data,” <i>Bioinformatics</i>, 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.” <i>Bioinformatics</i>, vol.
    30, no. 15, Oxford University Press, 2014, pp. 2219–20, doi:<a href="https://doi.org/10.1093/bioinformatics/btu166">10.1093/bioinformatics/btu166</a>.'
  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: '9145'
abstract:
- lang: eng
  text: "We have found a new way to express the solutions of the RSM (Reynolds Stress
    Model) equations that allows us to present the turbulent diffusivities for heat,
    salt and momentum in a way that is considerably simpler and thus easier to implement
    than in previous work. The RSM provides the dimensionless mixing efficiencies
    Γα (α stands for heat, salt and momentum). However, to compute the diffusivities,
    one needs additional information, specifically, the dissipation ε. Since a dynamic
    equation for the latter that includes the physical processes relevant to the ocean
    is still not available, one must resort to different sources of information outside
    the RSM to obtain a complete Mixing Scheme usable in OGCMs.\r\nAs for the RSM
    results, we show that the Γα’s are functions of both Ri and Rρ (Richardson number
    and density ratio representing double diffusion, DD); the Γα are different for
    heat, salt and momentum; in the case of heat, the traditional value Γh = 0.2 is
    valid only in the presence of strong shear (when DD is inoperative) while when
    shear subsides, NATRE data show that Γh can be three times as large, a result
    that we reproduce. The salt Γs is given in terms of Γh. The momentum Γm has thus
    far been guessed with different prescriptions while the RSM provides a well defined
    expression for Γm(Ri, Rρ). Having tested Γh, we then test the momentum Γm by showing
    that the turbulent Prandtl number Γm/Γh vs. Ri reproduces the available data quite
    well.\r\n\r\nAs for the dissipation ε, we use different representations, one for
    the mixed layer (ML), one for the thermocline and one for the ocean’s bottom.
    For the ML, we adopt a procedure analogous to the one successfully used in PB
    (planetary boundary layer) studies; for the thermocline, we employ an expression
    for the variable εN−2 from studies of the internal gravity waves spectra which
    includes a latitude dependence; for the ocean bottom, we adopt the enhanced bottom
    diffusivity expression used by previous authors but with a state of the art internal
    tidal energy formulation and replace the fixed Γα = 0.2 with the RSM result that
    brings into the problem the Ri, Rρ dependence of the Γα; the unresolved bottom
    drag, which has thus far been either ignored or modeled with heuristic relations,
    is modeled using a formalism we previously developed and tested in PBL studies.\r\nWe
    carried out several tests without an OGCM. Prandtl and flux Richardson numbers
    vs. Ri. The RSM model reproduces both types of data satisfactorily. DD and Mixing
    efficiency Γh(Ri, Rρ). The RSM model reproduces well the NATRE data. Bimodal ε-distribution.
    NATRE data show that ε(Ri < 1) ≈ 10ε(Ri > 1), which our model reproduces. Heat
    to salt flux ratio. In the Ri ≫ 1 regime, the RSM predictions reproduce the data
    satisfactorily. NATRE mass diffusivity. The z-profile of the mass diffusivity
    reproduces well the measurements at NATRE. The local form of the mixing scheme
    is algebraic with one cubic equation to solve."
article_processing_charge: No
article_type: original
author:
- first_name: V.M.
  full_name: Canuto, V.M.
  last_name: Canuto
- first_name: A.M.
  full_name: Howard, A.M.
  last_name: Howard
- first_name: Y.
  full_name: Cheng, Y.
  last_name: Cheng
- first_name: Caroline J
  full_name: Muller, Caroline J
  id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
  last_name: Muller
  orcid: 0000-0001-5836-5350
- first_name: A.
  full_name: Leboissetier, A.
  last_name: Leboissetier
- first_name: S.R.
  full_name: Jayne, S.R.
  last_name: Jayne
citation:
  ama: 'Canuto VM, Howard AM, Cheng Y, Muller CJ, Leboissetier A, Jayne SR. Ocean
    turbulence, III: New GISS vertical mixing scheme. <i>Ocean Modelling</i>. 2010;34(3-4):70-91.
    doi:<a href="https://doi.org/10.1016/j.ocemod.2010.04.006">10.1016/j.ocemod.2010.04.006</a>'
  apa: 'Canuto, V. M., Howard, A. M., Cheng, Y., Muller, C. J., Leboissetier, A.,
    &#38; Jayne, S. R. (2010). Ocean turbulence, III: New GISS vertical mixing scheme.
    <i>Ocean Modelling</i>. Elsevier. <a href="https://doi.org/10.1016/j.ocemod.2010.04.006">https://doi.org/10.1016/j.ocemod.2010.04.006</a>'
  chicago: 'Canuto, V.M., A.M. Howard, Y. Cheng, Caroline J Muller, A. Leboissetier,
    and S.R. Jayne. “Ocean Turbulence, III: New GISS Vertical Mixing Scheme.” <i>Ocean
    Modelling</i>. Elsevier, 2010. <a href="https://doi.org/10.1016/j.ocemod.2010.04.006">https://doi.org/10.1016/j.ocemod.2010.04.006</a>.'
  ieee: 'V. M. Canuto, A. M. Howard, Y. Cheng, C. J. Muller, A. Leboissetier, and
    S. R. Jayne, “Ocean turbulence, III: New GISS vertical mixing scheme,” <i>Ocean
    Modelling</i>, vol. 34, no. 3–4. Elsevier, pp. 70–91, 2010.'
  ista: 'Canuto VM, Howard AM, Cheng Y, Muller CJ, Leboissetier A, Jayne SR. 2010.
    Ocean turbulence, III: New GISS vertical mixing scheme. Ocean Modelling. 34(3–4),
    70–91.'
  mla: 'Canuto, V. M., et al. “Ocean Turbulence, III: New GISS Vertical Mixing Scheme.”
    <i>Ocean Modelling</i>, vol. 34, no. 3–4, Elsevier, 2010, pp. 70–91, doi:<a href="https://doi.org/10.1016/j.ocemod.2010.04.006">10.1016/j.ocemod.2010.04.006</a>.'
  short: V.M. Canuto, A.M. Howard, Y. Cheng, C.J. Muller, A. Leboissetier, S.R. Jayne,
    Ocean Modelling 34 (2010) 70–91.
date_created: 2021-02-15T14:40:19Z
date_published: 2010-05-12T00:00:00Z
date_updated: 2022-01-24T13:51:35Z
day: '12'
doi: 10.1016/j.ocemod.2010.04.006
extern: '1'
intvolume: '        34'
issue: 3-4
keyword:
- Computer Science (miscellaneous)
- Geotechnical Engineering and Engineering Geology
- Atmospheric Science
- Oceanography
language:
- iso: eng
month: '05'
oa_version: None
page: 70-91
publication: Ocean Modelling
publication_identifier:
  issn:
  - 1463-5003
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: 'Ocean turbulence, III: New GISS vertical mixing scheme'
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 34
year: '2010'
...
---
_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. <i>SIAM Review</i>. 2008;50(4):702-720.
    doi:<a href="https://doi.org/10.1137/070703235">10.1137/070703235</a>
  apa: Kaloshin, V., &#38; Levi, M. (2008). Geometry of Arnold diffusion. <i>SIAM
    Review</i>. Society for Industrial &#38; Applied Mathematics. <a href="https://doi.org/10.1137/070703235">https://doi.org/10.1137/070703235</a>
  chicago: Kaloshin, Vadim, and Mark Levi. “Geometry of Arnold Diffusion.” <i>SIAM
    Review</i>. Society for Industrial &#38; Applied Mathematics, 2008. <a href="https://doi.org/10.1137/070703235">https://doi.org/10.1137/070703235</a>.
  ieee: V. Kaloshin and M. Levi, “Geometry of Arnold diffusion,” <i>SIAM Review</i>,
    vol. 50, no. 4. Society for Industrial &#38; 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.” <i>SIAM Review</i>,
    vol. 50, no. 4, Society for Industrial &#38; Applied Mathematics, 2008, pp. 702–20,
    doi:<a href="https://doi.org/10.1137/070703235">10.1137/070703235</a>.
  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'
...
