---
_id: '9699'
abstract:
- lang: eng
  text: "We investigate the structural similarities between liquid water and 53 ices,
    including 20 known crystalline phases. We base such similarity comparison on the
    local environments that consist of atoms within a certain cutoff radius of a central
    atom. We reveal that liquid water explores the local environments of the diverse
    ice phases, by directly comparing the environments in these phases using general
    atomic descriptors, and also by demonstrating that a machine-learning potential
    trained on liquid water alone can predict the densities, the lattice energies,
    and vibrational properties of the\r\nices. The finding that the local environments
    characterising the different ice phases are found in water sheds light on water
    phase behaviors, and rationalizes the transferability of water models between
    different phases."
article_number: '2006.13316'
article_processing_charge: No
arxiv: 1
author:
- first_name: Bartomeu
  full_name: Monserrat, Bartomeu
  last_name: Monserrat
- first_name: Jan Gerit
  full_name: Brandenburg, Jan Gerit
  last_name: Brandenburg
- first_name: Edgar A.
  full_name: Engel, Edgar A.
  last_name: Engel
- first_name: Bingqing
  full_name: Cheng, Bingqing
  id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
  last_name: Cheng
  orcid: 0000-0002-3584-9632
citation:
  ama: 'Monserrat B, Brandenburg JG, Engel EA, Cheng B. Extracting ice phases from
    liquid water: Why a machine-learning water model generalizes so well. <i>arXiv</i>.
    doi:<a href="https://doi.org/10.48550/arXiv.2006.13316">10.48550/arXiv.2006.13316</a>'
  apa: 'Monserrat, B., Brandenburg, J. G., Engel, E. A., &#38; Cheng, B. (n.d.). Extracting
    ice phases from liquid water: Why a machine-learning water model generalizes so
    well. <i>arXiv</i>. <a href="https://doi.org/10.48550/arXiv.2006.13316">https://doi.org/10.48550/arXiv.2006.13316</a>'
  chicago: 'Monserrat, Bartomeu, Jan Gerit Brandenburg, Edgar A. Engel, and Bingqing
    Cheng. “Extracting Ice Phases from Liquid Water: Why a Machine-Learning Water
    Model Generalizes so Well.” <i>ArXiv</i>, n.d. <a href="https://doi.org/10.48550/arXiv.2006.13316">https://doi.org/10.48550/arXiv.2006.13316</a>.'
  ieee: 'B. Monserrat, J. G. Brandenburg, E. A. Engel, and B. Cheng, “Extracting ice
    phases from liquid water: Why a machine-learning water model generalizes so well,”
    <i>arXiv</i>. .'
  ista: 'Monserrat B, Brandenburg JG, Engel EA, Cheng B. Extracting ice phases from
    liquid water: Why a machine-learning water model generalizes so well. arXiv, 2006.13316.'
  mla: 'Monserrat, Bartomeu, et al. “Extracting Ice Phases from Liquid Water: Why
    a Machine-Learning Water Model Generalizes so Well.” <i>ArXiv</i>, 2006.13316,
    doi:<a href="https://doi.org/10.48550/arXiv.2006.13316">10.48550/arXiv.2006.13316</a>.'
  short: B. Monserrat, J.G. Brandenburg, E.A. Engel, B. Cheng, ArXiv (n.d.).
date_created: 2021-07-20T11:25:15Z
date_published: 2020-06-23T00:00:00Z
date_updated: 2024-10-14T12:05:56Z
day: '23'
doi: 10.48550/arXiv.2006.13316
extern: '1'
external_id:
  arxiv:
  - '2006.13316'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/2006.13316
month: '06'
oa: 1
oa_version: Submitted Version
publication: arXiv
publication_status: submitted
status: public
title: 'Extracting ice phases from liquid water: Why a machine-learning water model
  generalizes so well'
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '9706'
abstract:
- lang: eng
  text: 'Additional file 2: Supplementary Tables. The association of pre-adjusted
    protein levels with biological and technical covariates. Protein levels were adjusted
    for age, sex, array plate and four genetic principal components (population structure)
    prior to analyses. Significant associations are emboldened. (Table S1). pQTLs
    associated with inflammatory biomarker levels from Bayesian penalised regression
    model (Posterior Inclusion Probability > 95%). (Table S2). All pQTLs associated
    with inflammatory biomarker levels from ordinary least squares regression model
    (P < 7.14 × 10− 10). (Table S3). Summary of lambda values relating to ordinary
    least squares GWAS and EWAS performed on inflammatory protein levels (n = 70)
    in Lothian Birth Cohort 1936 study. (Table S4). Conditionally significant pQTLs
    associated with inflammatory biomarker levels from ordinary least squares regression
    model (P < 7.14 × 10− 10). (Table S5). Comparison of variance explained by ordinary
    least squares and Bayesian penalised regression models for concordantly identified
    SNPs. (Table S6). Estimate of heritability for blood protein levels as well as
    proportion of variance explained attributable to different prior mixtures. (Table
    S7). Comparison of heritability estimates from Ahsan et al. (maximum likelihood)
    and Hillary et al. (Bayesian penalised regression). (Table S8). List of concordant
    SNPs identified by linear model and Bayesian penalised regression and whether
    they have been previously identified as eQTLs. (Table S9). Bayesian tests of colocalisation
    for cis pQTLs and cis eQTLs. (Table S10). Sherlock algorithm: Genes whose expression
    are putatively associated with circulating inflammatory proteins that harbour
    pQTLs. (Table S11). CpGs associated with inflammatory protein biomarkers as identified
    by Bayesian model (Bayesian model; Posterior Inclusion Probability > 95%). (Table
    S12). CpGs associated with inflammatory protein biomarkers as identified by linear
    model (limma) at P < 5.14 × 10− 10. (Table S13). CpGs associated with inflammatory
    protein biomarkers as identified by mixed linear model (OSCA) at P < 5.14 × 10− 10.
    (Table S14). Estimate of variance explained for blood protein levels by DNA methylation
    as well as proportion of explained attributable to different prior mixtures -
    BayesR+. (Table S15). Comparison of variance in protein levels explained by genome-wide
    DNA methylation data by mixed linear model (OSCA) and Bayesian penalised regression
    model (BayesR+). (Table S16). Variance in circulating inflammatory protein biomarker
    levels explained by common genetic and methylation data (joint and conditional
    estimates from BayesR+). Ordered by combined variance explained by genetic and
    epigenetic data - smallest to largest. Significant results from t-tests comparing
    distributions for variance explained by methylation or genetics alone versus combined
    estimate are emboldened. (Table S17). Genetic and epigenetic factors identified
    by BayesR+ when conditioning on all SNPs and CpGs together. (Table S18). Mendelian
    Randomisation analyses to assess whether proteins with concordantly identified
    genetic signals are causally associated with Alzheimer’s disease risk. (Table
    S19).'
article_processing_charge: No
author:
- first_name: Robert F.
  full_name: Hillary, Robert F.
  last_name: Hillary
- first_name: Daniel
  full_name: Trejo-Banos, Daniel
  last_name: Trejo-Banos
- first_name: Athanasios
  full_name: Kousathanas, Athanasios
  last_name: Kousathanas
- first_name: Daniel L.
  full_name: McCartney, Daniel L.
  last_name: McCartney
- first_name: Sarah E.
  full_name: Harris, Sarah E.
  last_name: Harris
- first_name: Anna J.
  full_name: Stevenson, Anna J.
  last_name: Stevenson
- first_name: Marion
  full_name: Patxot, Marion
  last_name: Patxot
- first_name: Sven Erik
  full_name: Ojavee, Sven Erik
  last_name: Ojavee
- first_name: Qian
  full_name: Zhang, Qian
  last_name: Zhang
- first_name: David C.
  full_name: Liewald, David C.
  last_name: Liewald
- first_name: Craig W.
  full_name: Ritchie, Craig W.
  last_name: Ritchie
- first_name: Kathryn L.
  full_name: Evans, Kathryn L.
  last_name: Evans
- first_name: Elliot M.
  full_name: Tucker-Drob, Elliot M.
  last_name: Tucker-Drob
- first_name: Naomi R.
  full_name: Wray, Naomi R.
  last_name: Wray
- first_name: 'Allan F. '
  full_name: 'McRae, Allan F. '
  last_name: McRae
- first_name: Peter M.
  full_name: Visscher, Peter M.
  last_name: Visscher
- first_name: Ian J.
  full_name: Deary, Ian J.
  last_name: Deary
- first_name: Matthew Richard
  full_name: Robinson, Matthew Richard
  id: E5D42276-F5DA-11E9-8E24-6303E6697425
  last_name: Robinson
  orcid: 0000-0001-8982-8813
- first_name: 'Riccardo E. '
  full_name: 'Marioni, Riccardo E. '
  last_name: Marioni
citation:
  ama: Hillary RF, Trejo-Banos D, Kousathanas A, et al. Additional file 2 of multi-method
    genome- and epigenome-wide studies of inflammatory protein levels in healthy older
    adults. 2020. doi:<a href="https://doi.org/10.6084/m9.figshare.12629697.v1">10.6084/m9.figshare.12629697.v1</a>
  apa: Hillary, R. F., Trejo-Banos, D., Kousathanas, A., McCartney, D. L., Harris,
    S. E., Stevenson, A. J., … Marioni, R. E. (2020). Additional file 2 of multi-method
    genome- and epigenome-wide studies of inflammatory protein levels in healthy older
    adults. Springer Nature. <a href="https://doi.org/10.6084/m9.figshare.12629697.v1">https://doi.org/10.6084/m9.figshare.12629697.v1</a>
  chicago: Hillary, Robert F., Daniel Trejo-Banos, Athanasios Kousathanas, Daniel
    L. McCartney, Sarah E. Harris, Anna J. Stevenson, Marion Patxot, et al. “Additional
    File 2 of Multi-Method Genome- and Epigenome-Wide Studies of Inflammatory Protein
    Levels in Healthy Older Adults.” Springer Nature, 2020. <a href="https://doi.org/10.6084/m9.figshare.12629697.v1">https://doi.org/10.6084/m9.figshare.12629697.v1</a>.
  ieee: R. F. Hillary <i>et al.</i>, “Additional file 2 of multi-method genome- and
    epigenome-wide studies of inflammatory protein levels in healthy older adults.”
    Springer Nature, 2020.
  ista: Hillary RF, Trejo-Banos D, Kousathanas A, McCartney DL, Harris SE, Stevenson
    AJ, Patxot M, Ojavee SE, Zhang Q, Liewald DC, Ritchie CW, Evans KL, Tucker-Drob
    EM, Wray NR, McRae AF, Visscher PM, Deary IJ, Robinson MR, Marioni RE. 2020. Additional
    file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein
    levels in healthy older adults, Springer Nature, <a href="https://doi.org/10.6084/m9.figshare.12629697.v1">10.6084/m9.figshare.12629697.v1</a>.
  mla: Hillary, Robert F., et al. <i>Additional File 2 of Multi-Method Genome- and
    Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older Adults</i>.
    Springer Nature, 2020, doi:<a href="https://doi.org/10.6084/m9.figshare.12629697.v1">10.6084/m9.figshare.12629697.v1</a>.
  short: R.F. Hillary, D. Trejo-Banos, A. Kousathanas, D.L. McCartney, S.E. Harris,
    A.J. Stevenson, M. Patxot, S.E. Ojavee, Q. Zhang, D.C. Liewald, C.W. Ritchie,
    K.L. Evans, E.M. Tucker-Drob, N.R. Wray, A.F. McRae, P.M. Visscher, I.J. Deary,
    M.R. Robinson, R.E. Marioni, (2020).
date_created: 2021-07-23T08:59:15Z
date_published: 2020-07-09T00:00:00Z
date_updated: 2026-04-02T14:28:32Z
day: '09'
department:
- _id: MaRo
doi: 10.6084/m9.figshare.12629697.v1
has_accepted_license: '1'
license: https://creativecommons.org/licenses/by/4.0/
main_file_link:
- open_access: '1'
  url: https://doi.org/10.6084/m9.figshare.12629697.v1
month: '07'
oa: 1
oa_version: Published Version
other_data_license: CC0 + CC BY (4.0)
publisher: Springer Nature
related_material:
  record:
  - id: '8133'
    relation: used_in_publication
    status: public
status: public
title: Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory
  protein levels in healthy older adults
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2020'
...
---
_id: '9708'
abstract:
- lang: eng
  text: This research data supports 'Hard antinodal gap revealed by quantum oscillations
    in the pseudogap regime of underdoped high-Tc superconductors'. A Readme file
    for plotting each figure is provided.
article_processing_charge: No
author:
- first_name: Mate
  full_name: Hartstein, Mate
  last_name: Hartstein
- first_name: Yu-Te
  full_name: Hsu, Yu-Te
  last_name: Hsu
- first_name: Kimberly A
  full_name: Modic, Kimberly A
  id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425
  last_name: Modic
  orcid: 0000-0001-9760-3147
- first_name: Juan
  full_name: Porras, Juan
  last_name: Porras
- first_name: Toshinao
  full_name: Loew, Toshinao
  last_name: Loew
- first_name: Matthieu
  full_name: Le Tacon, Matthieu
  last_name: Le Tacon
- first_name: Huakun
  full_name: Zuo, Huakun
  last_name: Zuo
- first_name: Jinhua
  full_name: Wang, Jinhua
  last_name: Wang
- first_name: Zengwei
  full_name: Zhu, Zengwei
  last_name: Zhu
- first_name: Mun
  full_name: Chan, Mun
  last_name: Chan
- first_name: Ross
  full_name: McDonald, Ross
  last_name: McDonald
- first_name: Gilbert
  full_name: Lonzarich, Gilbert
  last_name: Lonzarich
- first_name: Bernhard
  full_name: Keimer, Bernhard
  last_name: Keimer
- first_name: Suchitra
  full_name: Sebastian, Suchitra
  last_name: Sebastian
- first_name: Neil
  full_name: Harrison, Neil
  last_name: Harrison
citation:
  ama: Hartstein M, Hsu Y-T, Modic KA, et al. Accompanying dataset for “Hard antinodal
    gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc
    superconductors.” 2020. doi:<a href="https://doi.org/10.17863/cam.50169">10.17863/cam.50169</a>
  apa: Hartstein, M., Hsu, Y.-T., Modic, K. A., Porras, J., Loew, T., Le Tacon, M.,
    … Harrison, N. (2020). Accompanying dataset for “Hard antinodal gap revealed by
    quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors.”
    Apollo - University of Cambridge. <a href="https://doi.org/10.17863/cam.50169">https://doi.org/10.17863/cam.50169</a>
  chicago: Hartstein, Mate, Yu-Te Hsu, Kimberly A Modic, Juan Porras, Toshinao Loew,
    Matthieu Le Tacon, Huakun Zuo, et al. “Accompanying Dataset for ‘Hard Antinodal
    Gap Revealed by Quantum Oscillations in the Pseudogap Regime of Underdoped High-Tc
    Superconductors.’” Apollo - University of Cambridge, 2020. <a href="https://doi.org/10.17863/cam.50169">https://doi.org/10.17863/cam.50169</a>.
  ieee: M. Hartstein <i>et al.</i>, “Accompanying dataset for ‘Hard antinodal gap
    revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc
    superconductors.’” Apollo - University of Cambridge, 2020.
  ista: Hartstein M, Hsu Y-T, Modic KA, Porras J, Loew T, Le Tacon M, Zuo H, Wang
    J, Zhu Z, Chan M, McDonald R, Lonzarich G, Keimer B, Sebastian S, Harrison N.
    2020. Accompanying dataset for ‘Hard antinodal gap revealed by quantum oscillations
    in the pseudogap regime of underdoped high-Tc superconductors’, Apollo - University
    of Cambridge, <a href="https://doi.org/10.17863/cam.50169">10.17863/cam.50169</a>.
  mla: Hartstein, Mate, et al. <i>Accompanying Dataset for “Hard Antinodal Gap Revealed
    by Quantum Oscillations in the Pseudogap Regime of Underdoped High-Tc Superconductors.”</i>
    Apollo - University of Cambridge, 2020, doi:<a href="https://doi.org/10.17863/cam.50169">10.17863/cam.50169</a>.
  short: M. Hartstein, Y.-T. Hsu, K.A. Modic, J. Porras, T. Loew, M. Le Tacon, H.
    Zuo, J. Wang, Z. Zhu, M. Chan, R. McDonald, G. Lonzarich, B. Keimer, S. Sebastian,
    N. Harrison, (2020).
date_created: 2021-07-23T10:00:35Z
date_published: 2020-05-29T00:00:00Z
date_updated: 2025-07-10T11:54:51Z
day: '29'
department:
- _id: KiMo
doi: 10.17863/cam.50169
has_accepted_license: '1'
main_file_link:
- open_access: '1'
  url: https://doi.org/10.17863/CAM.50169
month: '05'
oa: 1
oa_version: Published Version
publisher: Apollo - University of Cambridge
related_material:
  record:
  - id: '7942'
    relation: used_in_publication
    status: public
status: public
title: Accompanying dataset for 'Hard antinodal gap revealed by quantum oscillations
  in the pseudogap regime of underdoped high-Tc superconductors'
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2020'
...
---
_id: '9776'
article_processing_charge: No
author:
- first_name: Rok
  full_name: Grah, Rok
  id: 483E70DE-F248-11E8-B48F-1D18A9856A87
  last_name: Grah
  orcid: 0000-0003-2539-3560
- first_name: Tamar
  full_name: Friedlander, Tamar
  last_name: Friedlander
citation:
  ama: Grah R, Friedlander T. Supporting information. 2020. doi:<a href="https://doi.org/10.1371/journal.pcbi.1007642.s001">10.1371/journal.pcbi.1007642.s001</a>
  apa: Grah, R., &#38; Friedlander, T. (2020). Supporting information. Public Library
    of Science. <a href="https://doi.org/10.1371/journal.pcbi.1007642.s001">https://doi.org/10.1371/journal.pcbi.1007642.s001</a>
  chicago: Grah, Rok, and Tamar Friedlander. “Supporting Information.” Public Library
    of Science, 2020. <a href="https://doi.org/10.1371/journal.pcbi.1007642.s001">https://doi.org/10.1371/journal.pcbi.1007642.s001</a>.
  ieee: R. Grah and T. Friedlander, “Supporting information.” Public Library of Science,
    2020.
  ista: Grah R, Friedlander T. 2020. Supporting information, Public Library of Science,
    <a href="https://doi.org/10.1371/journal.pcbi.1007642.s001">10.1371/journal.pcbi.1007642.s001</a>.
  mla: Grah, Rok, and Tamar Friedlander. <i>Supporting Information</i>. Public Library
    of Science, 2020, doi:<a href="https://doi.org/10.1371/journal.pcbi.1007642.s001">10.1371/journal.pcbi.1007642.s001</a>.
  short: R. Grah, T. Friedlander, (2020).
date_created: 2021-08-06T07:15:04Z
date_published: 2020-02-25T00:00:00Z
date_updated: 2025-06-12T06:58:06Z
day: '25'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1007642.s001
month: '02'
oa_version: Published Version
publisher: Public Library of Science
related_material:
  record:
  - id: '7569'
    relation: used_in_publication
    status: public
status: public
title: Supporting information
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2020'
...
---
_id: '9777'
article_processing_charge: No
author:
- first_name: Rok
  full_name: Grah, Rok
  id: 483E70DE-F248-11E8-B48F-1D18A9856A87
  last_name: Grah
  orcid: 0000-0003-2539-3560
- first_name: Tamar
  full_name: Friedlander, Tamar
  last_name: Friedlander
citation:
  ama: Grah R, Friedlander T. Maximizing crosstalk. 2020. doi:<a href="https://doi.org/10.1371/journal.pcbi.1007642.s002">10.1371/journal.pcbi.1007642.s002</a>
  apa: Grah, R., &#38; Friedlander, T. (2020). Maximizing crosstalk. Public Library
    of Science. <a href="https://doi.org/10.1371/journal.pcbi.1007642.s002">https://doi.org/10.1371/journal.pcbi.1007642.s002</a>
  chicago: Grah, Rok, and Tamar Friedlander. “Maximizing Crosstalk.” Public Library
    of Science, 2020. <a href="https://doi.org/10.1371/journal.pcbi.1007642.s002">https://doi.org/10.1371/journal.pcbi.1007642.s002</a>.
  ieee: R. Grah and T. Friedlander, “Maximizing crosstalk.” Public Library of Science,
    2020.
  ista: Grah R, Friedlander T. 2020. Maximizing crosstalk, Public Library of Science,
    <a href="https://doi.org/10.1371/journal.pcbi.1007642.s002">10.1371/journal.pcbi.1007642.s002</a>.
  mla: Grah, Rok, and Tamar Friedlander. <i>Maximizing Crosstalk</i>. Public Library
    of Science, 2020, doi:<a href="https://doi.org/10.1371/journal.pcbi.1007642.s002">10.1371/journal.pcbi.1007642.s002</a>.
  short: R. Grah, T. Friedlander, (2020).
date_created: 2021-08-06T07:21:51Z
date_published: 2020-02-25T00:00:00Z
date_updated: 2025-06-12T06:58:06Z
day: '25'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1007642.s002
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1371/journal.pcbi.1007642.s002
month: '02'
oa: 1
oa_version: None
publisher: Public Library of Science
related_material:
  record:
  - id: '7569'
    relation: used_in_publication
    status: public
status: public
title: Maximizing crosstalk
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '9779'
article_processing_charge: No
author:
- first_name: Rok
  full_name: Grah, Rok
  id: 483E70DE-F248-11E8-B48F-1D18A9856A87
  last_name: Grah
  orcid: 0000-0003-2539-3560
- first_name: Tamar
  full_name: Friedlander, Tamar
  last_name: Friedlander
citation:
  ama: Grah R, Friedlander T. Distribution of crosstalk values. 2020. doi:<a href="https://doi.org/10.1371/journal.pcbi.1007642.s003">10.1371/journal.pcbi.1007642.s003</a>
  apa: Grah, R., &#38; Friedlander, T. (2020). Distribution of crosstalk values. Public
    Library of Science. <a href="https://doi.org/10.1371/journal.pcbi.1007642.s003">https://doi.org/10.1371/journal.pcbi.1007642.s003</a>
  chicago: Grah, Rok, and Tamar Friedlander. “Distribution of Crosstalk Values.” Public
    Library of Science, 2020. <a href="https://doi.org/10.1371/journal.pcbi.1007642.s003">https://doi.org/10.1371/journal.pcbi.1007642.s003</a>.
  ieee: R. Grah and T. Friedlander, “Distribution of crosstalk values.” Public Library
    of Science, 2020.
  ista: Grah R, Friedlander T. 2020. Distribution of crosstalk values, Public Library
    of Science, <a href="https://doi.org/10.1371/journal.pcbi.1007642.s003">10.1371/journal.pcbi.1007642.s003</a>.
  mla: Grah, Rok, and Tamar Friedlander. <i>Distribution of Crosstalk Values</i>.
    Public Library of Science, 2020, doi:<a href="https://doi.org/10.1371/journal.pcbi.1007642.s003">10.1371/journal.pcbi.1007642.s003</a>.
  short: R. Grah, T. Friedlander, (2020).
date_created: 2021-08-06T07:24:37Z
date_published: 2020-02-25T00:00:00Z
date_updated: 2025-06-12T06:58:06Z
day: '25'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1007642.s003
month: '02'
oa_version: Published Version
publisher: Public Library of Science
related_material:
  record:
  - id: '7569'
    relation: used_in_publication
    status: public
status: public
title: Distribution of crosstalk values
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2020'
...
---
_id: '9780'
abstract:
- lang: eng
  text: "PADREV : 4,4'-dimethoxy[1,1'-biphenyl]-2,2',5,5'-tetrol\r\nSpace Group: C
    2 (5), Cell: a 24.488(16)Å b 5.981(4)Å c 3.911(3)Å, α 90° β 91.47(3)° γ 90°"
article_processing_charge: No
author:
- first_name: Werner
  full_name: Schlemmer, Werner
  last_name: Schlemmer
- first_name: Philipp
  full_name: Nothdurft, Philipp
  last_name: Nothdurft
- first_name: Alina
  full_name: Petzold, Alina
  last_name: Petzold
- first_name: Gisbert
  full_name: Riess, Gisbert
  last_name: Riess
- first_name: Philipp
  full_name: Frühwirt, Philipp
  last_name: Frühwirt
- first_name: Max
  full_name: Schmallegger, Max
  last_name: Schmallegger
- first_name: Georg
  full_name: Gescheidt-Demner, Georg
  last_name: Gescheidt-Demner
- first_name: Roland
  full_name: Fischer, Roland
  last_name: Fischer
- first_name: Stefan Alexander
  full_name: Freunberger, Stefan Alexander
  id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
  last_name: Freunberger
  orcid: 0000-0003-2902-5319
- first_name: Wolfgang
  full_name: Kern, Wolfgang
  last_name: Kern
- first_name: Stefan
  full_name: Spirk, Stefan
  last_name: Spirk
citation:
  ama: 'Schlemmer W, Nothdurft P, Petzold A, et al. CCDC 1991959: Experimental Crystal
    Structure Determination. 2020. doi:<a href="https://doi.org/10.5517/ccdc.csd.cc24vsrk">10.5517/ccdc.csd.cc24vsrk</a>'
  apa: 'Schlemmer, W., Nothdurft, P., Petzold, A., Riess, G., Frühwirt, P., Schmallegger,
    M., … Spirk, S. (2020). CCDC 1991959: Experimental Crystal Structure Determination.
    CCDC. <a href="https://doi.org/10.5517/ccdc.csd.cc24vsrk">https://doi.org/10.5517/ccdc.csd.cc24vsrk</a>'
  chicago: 'Schlemmer, Werner, Philipp Nothdurft, Alina Petzold, Gisbert Riess, Philipp
    Frühwirt, Max Schmallegger, Georg Gescheidt-Demner, et al. “CCDC 1991959: Experimental
    Crystal Structure Determination.” CCDC, 2020. <a href="https://doi.org/10.5517/ccdc.csd.cc24vsrk">https://doi.org/10.5517/ccdc.csd.cc24vsrk</a>.'
  ieee: 'W. Schlemmer <i>et al.</i>, “CCDC 1991959: Experimental Crystal Structure
    Determination.” CCDC, 2020.'
  ista: 'Schlemmer W, Nothdurft P, Petzold A, Riess G, Frühwirt P, Schmallegger M,
    Gescheidt-Demner G, Fischer R, Freunberger SA, Kern W, Spirk S. 2020. CCDC 1991959:
    Experimental Crystal Structure Determination, CCDC, <a href="https://doi.org/10.5517/ccdc.csd.cc24vsrk">10.5517/ccdc.csd.cc24vsrk</a>.'
  mla: 'Schlemmer, Werner, et al. <i>CCDC 1991959: Experimental Crystal Structure
    Determination</i>. CCDC, 2020, doi:<a href="https://doi.org/10.5517/ccdc.csd.cc24vsrk">10.5517/ccdc.csd.cc24vsrk</a>.'
  short: W. Schlemmer, P. Nothdurft, A. Petzold, G. Riess, P. Frühwirt, M. Schmallegger,
    G. Gescheidt-Demner, R. Fischer, S.A. Freunberger, W. Kern, S. Spirk, (2020).
date_created: 2021-08-06T07:41:07Z
date_published: 2020-03-22T00:00:00Z
date_updated: 2026-06-18T19:32:35Z
day: '22'
department:
- _id: StFr
doi: 10.5517/ccdc.csd.cc24vsrk
main_file_link:
- open_access: '1'
  url: https://dx.doi.org/10.5517/ccdc.csd.cc24vsrk
month: '03'
oa: 1
oa_version: Published Version
publisher: CCDC
related_material:
  record:
  - id: '8329'
    relation: used_in_publication
    status: public
status: public
title: 'CCDC 1991959: Experimental Crystal Structure Determination'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2020'
...
---
OA_place: publisher
OA_type: hybrid
_id: '9798'
abstract:
- lang: eng
  text: Fitness interactions between mutations can influence a population’s evolution
    in many different ways. While epistatic effects are difficult to measure precisely,
    important information is captured by the mean and variance of log fitnesses for
    individuals carrying different numbers of mutations. We derive predictions for
    these quantities from a class of simple fitness landscapes, based on models of
    optimizing selection on quantitative traits. We also explore extensions to the
    models, including modular pleiotropy, variable effect sizes, mutational bias and
    maladaptation of the wild type. We illustrate our approach by reanalysing a large
    dataset of mutant effects in a yeast snoRNA. Though characterized by some large
    epistatic effects, these data give a good overall fit to the non-epistatic null
    model, suggesting that epistasis might have limited influence on the evolutionary
    dynamics in this system. We also show how the amount of epistasis depends on both
    the underlying fitness landscape and the distribution of mutations, and so is
    expected to vary in consistent ways between new mutations, standing variation
    and fixed mutations.
article_processing_charge: No
author:
- first_name: Christelle
  full_name: Fraisse, Christelle
  id: 32DF5794-F248-11E8-B48F-1D18A9856A87
  last_name: Fraisse
  orcid: 0000-0001-8441-5075
- first_name: John J.
  full_name: Welch, John J.
  last_name: Welch
citation:
  ama: Fraisse C, Welch JJ. Simulation code for Fig S2 from the distribution of epistasis
    on simple fitness landscapes. 2020. doi:<a href="https://doi.org/10.6084/m9.figshare.7957472.v1">10.6084/m9.figshare.7957472.v1</a>
  apa: Fraisse, C., &#38; Welch, J. J. (2020). Simulation code for Fig S2 from the
    distribution of epistasis on simple fitness landscapes. Royal Society of London.
    <a href="https://doi.org/10.6084/m9.figshare.7957472.v1">https://doi.org/10.6084/m9.figshare.7957472.v1</a>
  chicago: Fraisse, Christelle, and John J. Welch. “Simulation Code for Fig S2 from
    the Distribution of Epistasis on Simple Fitness Landscapes.” Royal Society of
    London, 2020. <a href="https://doi.org/10.6084/m9.figshare.7957472.v1">https://doi.org/10.6084/m9.figshare.7957472.v1</a>.
  ieee: C. Fraisse and J. J. Welch, “Simulation code for Fig S2 from the distribution
    of epistasis on simple fitness landscapes.” Royal Society of London, 2020.
  ista: Fraisse C, Welch JJ. 2020. Simulation code for Fig S2 from the distribution
    of epistasis on simple fitness landscapes, Royal Society of London, <a href="https://doi.org/10.6084/m9.figshare.7957472.v1">10.6084/m9.figshare.7957472.v1</a>.
  mla: Fraisse, Christelle, and John J. Welch. <i>Simulation Code for Fig S2 from
    the Distribution of Epistasis on Simple Fitness Landscapes</i>. Royal Society
    of London, 2020, doi:<a href="https://doi.org/10.6084/m9.figshare.7957472.v1">10.6084/m9.figshare.7957472.v1</a>.
  short: C. Fraisse, J.J. Welch, (2020).
date_created: 2021-08-06T11:18:15Z
date_published: 2020-10-15T00:00:00Z
date_updated: 2026-06-18T19:05:02Z
day: '15'
department:
- _id: BeVi
- _id: NiBa
doi: 10.6084/m9.figshare.7957472.v1
main_file_link:
- open_access: '1'
  url: https://doi.org/10.6084/m9.figshare.7957472.v1
month: '10'
oa: 1
oa_version: Published Version
publisher: Royal Society of London
related_material:
  record:
  - id: '6467'
    relation: used_in_publication
    status: public
status: public
title: Simulation code for Fig S2 from the distribution of epistasis on simple fitness
  landscapes
type: research_data_reference
user_id: 0043cee0-e5fc-11ee-9736-f83bc23afbf0
year: '2020'
...
---
OA_place: publisher
OA_type: hybrid
_id: '9799'
abstract:
- lang: eng
  text: Fitness interactions between mutations can influence a population’s evolution
    in many different ways. While epistatic effects are difficult to measure precisely,
    important information is captured by the mean and variance of log fitnesses for
    individuals carrying different numbers of mutations. We derive predictions for
    these quantities from a class of simple fitness landscapes, based on models of
    optimizing selection on quantitative traits. We also explore extensions to the
    models, including modular pleiotropy, variable effect sizes, mutational bias and
    maladaptation of the wild type. We illustrate our approach by reanalysing a large
    dataset of mutant effects in a yeast snoRNA. Though characterized by some large
    epistatic effects, these data give a good overall fit to the non-epistatic null
    model, suggesting that epistasis might have limited influence on the evolutionary
    dynamics in this system. We also show how the amount of epistasis depends on both
    the underlying fitness landscape and the distribution of mutations, and so is
    expected to vary in consistent ways between new mutations, standing variation
    and fixed mutations.
article_processing_charge: No
author:
- first_name: Christelle
  full_name: Fraisse, Christelle
  id: 32DF5794-F248-11E8-B48F-1D18A9856A87
  last_name: Fraisse
  orcid: 0000-0001-8441-5075
- first_name: John J.
  full_name: Welch, John J.
  last_name: Welch
citation:
  ama: Fraisse C, Welch JJ. Simulation code for Fig S1 from the distribution of epistasis
    on simple fitness landscapes. 2020. doi:<a href="https://doi.org/10.6084/m9.figshare.7957469.v1">10.6084/m9.figshare.7957469.v1</a>
  apa: Fraisse, C., &#38; Welch, J. J. (2020). Simulation code for Fig S1 from the
    distribution of epistasis on simple fitness landscapes. Royal Society of London.
    <a href="https://doi.org/10.6084/m9.figshare.7957469.v1">https://doi.org/10.6084/m9.figshare.7957469.v1</a>
  chicago: Fraisse, Christelle, and John J. Welch. “Simulation Code for Fig S1 from
    the Distribution of Epistasis on Simple Fitness Landscapes.” Royal Society of
    London, 2020. <a href="https://doi.org/10.6084/m9.figshare.7957469.v1">https://doi.org/10.6084/m9.figshare.7957469.v1</a>.
  ieee: C. Fraisse and J. J. Welch, “Simulation code for Fig S1 from the distribution
    of epistasis on simple fitness landscapes.” Royal Society of London, 2020.
  ista: Fraisse C, Welch JJ. 2020. Simulation code for Fig S1 from the distribution
    of epistasis on simple fitness landscapes, Royal Society of London, <a href="https://doi.org/10.6084/m9.figshare.7957469.v1">10.6084/m9.figshare.7957469.v1</a>.
  mla: Fraisse, Christelle, and John J. Welch. <i>Simulation Code for Fig S1 from
    the Distribution of Epistasis on Simple Fitness Landscapes</i>. Royal Society
    of London, 2020, doi:<a href="https://doi.org/10.6084/m9.figshare.7957469.v1">10.6084/m9.figshare.7957469.v1</a>.
  short: C. Fraisse, J.J. Welch, (2020).
date_created: 2021-08-06T11:26:57Z
date_published: 2020-10-15T00:00:00Z
date_updated: 2026-06-18T19:05:02Z
day: '15'
department:
- _id: BeVi
- _id: NiBa
doi: 10.6084/m9.figshare.7957469.v1
main_file_link:
- open_access: '1'
  url: https://doi.org/10.6084/m9.figshare.7957469.v1
month: '10'
oa: 1
oa_version: Published Version
publisher: Royal Society of London
related_material:
  record:
  - id: '6467'
    relation: used_in_publication
    status: public
status: public
title: Simulation code for Fig S1 from the distribution of epistasis on simple fitness
  landscapes
type: research_data_reference
user_id: 0043cee0-e5fc-11ee-9736-f83bc23afbf0
year: '2020'
...
---
_id: '6488'
abstract:
- lang: eng
  text: We prove a central limit theorem for the difference of linear eigenvalue statistics
    of a sample covariance matrix W˜ and its minor W. We find that the fluctuation
    of this difference is much smaller than those of the individual linear statistics,
    as a consequence of the strong correlation between the eigenvalues of W˜ and W.
    Our result identifies the fluctuation of the spatial derivative of the approximate
    Gaussian field in the recent paper by Dumitru and Paquette. Unlike in a similar
    result for Wigner matrices, for sample covariance matrices, the fluctuation may
    entirely vanish.
article_number: '2050006'
article_processing_charge: No
article_type: original
arxiv: 1
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
citation:
  ama: 'Cipolloni G, Erdös L. Fluctuations for differences of linear eigenvalue statistics
    for sample covariance matrices. <i>Random Matrices: Theory and Application</i>.
    2020;9(3). doi:<a href="https://doi.org/10.1142/S2010326320500069">10.1142/S2010326320500069</a>'
  apa: 'Cipolloni, G., &#38; Erdös, L. (2020). Fluctuations for differences of linear
    eigenvalue statistics for sample covariance matrices. <i>Random Matrices: Theory
    and Application</i>. World Scientific Publishing. <a href="https://doi.org/10.1142/S2010326320500069">https://doi.org/10.1142/S2010326320500069</a>'
  chicago: 'Cipolloni, Giorgio, and László Erdös. “Fluctuations for Differences of
    Linear Eigenvalue Statistics for Sample Covariance Matrices.” <i>Random Matrices:
    Theory and Application</i>. World Scientific Publishing, 2020. <a href="https://doi.org/10.1142/S2010326320500069">https://doi.org/10.1142/S2010326320500069</a>.'
  ieee: 'G. Cipolloni and L. Erdös, “Fluctuations for differences of linear eigenvalue
    statistics for sample covariance matrices,” <i>Random Matrices: Theory and Application</i>,
    vol. 9, no. 3. World Scientific Publishing, 2020.'
  ista: 'Cipolloni G, Erdös L. 2020. Fluctuations for differences of linear eigenvalue
    statistics for sample covariance matrices. Random Matrices: Theory and Application.
    9(3), 2050006.'
  mla: 'Cipolloni, Giorgio, and László Erdös. “Fluctuations for Differences of Linear
    Eigenvalue Statistics for Sample Covariance Matrices.” <i>Random Matrices: Theory
    and Application</i>, vol. 9, no. 3, 2050006, World Scientific Publishing, 2020,
    doi:<a href="https://doi.org/10.1142/S2010326320500069">10.1142/S2010326320500069</a>.'
  short: 'G. Cipolloni, L. Erdös, Random Matrices: Theory and Application 9 (2020).'
date_created: 2019-05-26T21:59:14Z
date_published: 2020-07-01T00:00:00Z
date_updated: 2025-07-10T11:53:26Z
day: '01'
department:
- _id: LaEr
doi: 10.1142/S2010326320500069
ec_funded: 1
external_id:
  arxiv:
  - '1806.08751'
  isi:
  - '000547464400001'
intvolume: '         9'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1806.08751
month: '07'
oa: 1
oa_version: Preprint
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '338804'
  name: Random matrices, universality and disordered quantum systems
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '665385'
  name: International IST Doctoral Program
publication: 'Random Matrices: Theory and Application'
publication_identifier:
  eissn:
  - 2010-3271
  issn:
  - 2010-3263
publication_status: published
publisher: World Scientific Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fluctuations for differences of linear eigenvalue statistics for sample covariance
  matrices
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2020'
...
---
_id: '6563'
abstract:
- lang: eng
  text: "This paper presents two algorithms. The first decides the existence of a
    pointed homotopy between given simplicial maps \U0001D453,\U0001D454:\U0001D44B→\U0001D44C,
    and the second computes the group [\U0001D6F4\U0001D44B,\U0001D44C]∗ of pointed
    homotopy classes of maps from a suspension; in both cases, the target Y is assumed
    simply connected. More generally, these algorithms work relative to \U0001D434⊆\U0001D44B."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Marek
  full_name: Filakovský, Marek
  id: 3E8AF77E-F248-11E8-B48F-1D18A9856A87
  last_name: Filakovský
- first_name: Lukas
  full_name: Vokřínek, Lukas
  last_name: Vokřínek
citation:
  ama: Filakovský M, Vokřínek L. Are two given maps homotopic? An algorithmic viewpoint.
    <i>Foundations of Computational Mathematics</i>. 2020;20:311-330. doi:<a href="https://doi.org/10.1007/s10208-019-09419-x">10.1007/s10208-019-09419-x</a>
  apa: Filakovský, M., &#38; Vokřínek, L. (2020). Are two given maps homotopic? An
    algorithmic viewpoint. <i>Foundations of Computational Mathematics</i>. Springer
    Nature. <a href="https://doi.org/10.1007/s10208-019-09419-x">https://doi.org/10.1007/s10208-019-09419-x</a>
  chicago: Filakovský, Marek, and Lukas Vokřínek. “Are Two given Maps Homotopic? An
    Algorithmic Viewpoint.” <i>Foundations of Computational Mathematics</i>. Springer
    Nature, 2020. <a href="https://doi.org/10.1007/s10208-019-09419-x">https://doi.org/10.1007/s10208-019-09419-x</a>.
  ieee: M. Filakovský and L. Vokřínek, “Are two given maps homotopic? An algorithmic
    viewpoint,” <i>Foundations of Computational Mathematics</i>, vol. 20. Springer
    Nature, pp. 311–330, 2020.
  ista: Filakovský M, Vokřínek L. 2020. Are two given maps homotopic? An algorithmic
    viewpoint. Foundations of Computational Mathematics. 20, 311–330.
  mla: Filakovský, Marek, and Lukas Vokřínek. “Are Two given Maps Homotopic? An Algorithmic
    Viewpoint.” <i>Foundations of Computational Mathematics</i>, vol. 20, Springer
    Nature, 2020, pp. 311–30, doi:<a href="https://doi.org/10.1007/s10208-019-09419-x">10.1007/s10208-019-09419-x</a>.
  short: M. Filakovský, L. Vokřínek, Foundations of Computational Mathematics 20 (2020)
    311–330.
date_created: 2019-06-16T21:59:14Z
date_published: 2020-04-01T00:00:00Z
date_updated: 2025-07-10T11:53:32Z
day: '01'
department:
- _id: UlWa
doi: 10.1007/s10208-019-09419-x
external_id:
  arxiv:
  - '1312.2337'
  isi:
  - '000522437400004'
intvolume: '        20'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1312.2337
month: '04'
oa: 1
oa_version: Preprint
page: 311-330
project:
- _id: 26611F5C-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: P31312
  name: Algorithms for Embeddings and Homotopy Theory
publication: Foundations of Computational Mathematics
publication_identifier:
  eissn:
  - 1615-3383
  issn:
  - 1615-3375
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Are two given maps homotopic? An algorithmic viewpoint
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 20
year: '2020'
...
---
_id: '6593'
abstract:
- lang: eng
  text: 'We consider the monotone variational inequality problem in a Hilbert space
    and describe a projection-type method with inertial terms under the following
    properties: (a) The method generates a strongly convergent iteration sequence;
    (b) The method requires, at each iteration, only one projection onto the feasible
    set and two evaluations of the operator; (c) The method is designed for variational
    inequality for which the underline operator is monotone and uniformly continuous;
    (d) The method includes an inertial term. The latter is also shown to speed up
    the convergence in our numerical results. A comparison with some related methods
    is given and indicates that the new method is promising.'
acknowledgement: The research of this author is supported by the ERC grant at the
  IST.
article_processing_charge: No
article_type: original
author:
- first_name: Yekini
  full_name: Shehu, Yekini
  id: 3FC7CB58-F248-11E8-B48F-1D18A9856A87
  last_name: Shehu
  orcid: 0000-0001-9224-7139
- first_name: Xiao-Huan
  full_name: Li, Xiao-Huan
  last_name: Li
- first_name: Qiao-Li
  full_name: Dong, Qiao-Li
  last_name: Dong
citation:
  ama: Shehu Y, Li X-H, Dong Q-L. An efficient projection-type method for monotone
    variational inequalities in Hilbert spaces. <i>Numerical Algorithms</i>. 2020;84:365-388.
    doi:<a href="https://doi.org/10.1007/s11075-019-00758-y">10.1007/s11075-019-00758-y</a>
  apa: Shehu, Y., Li, X.-H., &#38; Dong, Q.-L. (2020). An efficient projection-type
    method for monotone variational inequalities in Hilbert spaces. <i>Numerical Algorithms</i>.
    Springer Nature. <a href="https://doi.org/10.1007/s11075-019-00758-y">https://doi.org/10.1007/s11075-019-00758-y</a>
  chicago: Shehu, Yekini, Xiao-Huan Li, and Qiao-Li Dong. “An Efficient Projection-Type
    Method for Monotone Variational Inequalities in Hilbert Spaces.” <i>Numerical
    Algorithms</i>. Springer Nature, 2020. <a href="https://doi.org/10.1007/s11075-019-00758-y">https://doi.org/10.1007/s11075-019-00758-y</a>.
  ieee: Y. Shehu, X.-H. Li, and Q.-L. Dong, “An efficient projection-type method for
    monotone variational inequalities in Hilbert spaces,” <i>Numerical Algorithms</i>,
    vol. 84. Springer Nature, pp. 365–388, 2020.
  ista: Shehu Y, Li X-H, Dong Q-L. 2020. An efficient projection-type method for monotone
    variational inequalities in Hilbert spaces. Numerical Algorithms. 84, 365–388.
  mla: Shehu, Yekini, et al. “An Efficient Projection-Type Method for Monotone Variational
    Inequalities in Hilbert Spaces.” <i>Numerical Algorithms</i>, vol. 84, Springer
    Nature, 2020, pp. 365–88, doi:<a href="https://doi.org/10.1007/s11075-019-00758-y">10.1007/s11075-019-00758-y</a>.
  short: Y. Shehu, X.-H. Li, Q.-L. Dong, Numerical Algorithms 84 (2020) 365–388.
corr_author: '1'
date_created: 2019-06-27T20:09:33Z
date_published: 2020-05-01T00:00:00Z
date_updated: 2024-11-04T13:52:40Z
day: '01'
ddc:
- '000'
department:
- _id: VlKo
doi: 10.1007/s11075-019-00758-y
ec_funded: 1
external_id:
  isi:
  - '000528979000015'
file:
- access_level: open_access
  checksum: bb1a1eb3ebb2df380863d0db594673ba
  content_type: application/pdf
  creator: kschuh
  date_created: 2019-10-01T13:14:10Z
  date_updated: 2020-07-14T12:47:34Z
  file_id: '6927'
  file_name: ExtragradientMethodPaper.pdf
  file_size: 359654
  relation: main_file
file_date_updated: 2020-07-14T12:47:34Z
has_accepted_license: '1'
intvolume: '        84'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Submitted Version
page: 365-388
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '616160'
  name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication: Numerical Algorithms
publication_identifier:
  eissn:
  - 1572-9265
  issn:
  - 1017-1398
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: An efficient projection-type method for monotone variational inequalities in
  Hilbert spaces
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 84
year: '2020'
...
---
_id: '6649'
abstract:
- lang: eng
  text: "While Hartree–Fock theory is well established as a fundamental approximation
    for interacting fermions, it has been unclear how to describe corrections to it
    due to many-body correlations. In this paper we start from the Hartree–Fock state
    given by plane waves and introduce collective particle–hole pair excitations.
    These pairs can be approximately described by a bosonic quadratic Hamiltonian.
    We use Bogoliubov theory to construct a trial state yielding a rigorous Gell-Mann–Brueckner–type
    upper bound to the ground state energy. Our result justifies the random-phase
    approximation in the mean-field scaling regime, for repulsive, regular interaction
    potentials.\r\n"
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Niels P
  full_name: Benedikter, Niels P
  id: 3DE6C32A-F248-11E8-B48F-1D18A9856A87
  last_name: Benedikter
  orcid: 0000-0002-1071-6091
- first_name: Phan Thành
  full_name: Nam, Phan Thành
  last_name: Nam
- first_name: Marcello
  full_name: Porta, Marcello
  last_name: Porta
- first_name: Benjamin
  full_name: Schlein, Benjamin
  last_name: Schlein
- first_name: Robert
  full_name: Seiringer, Robert
  id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
  last_name: Seiringer
  orcid: 0000-0002-6781-0521
citation:
  ama: Benedikter NP, Nam PT, Porta M, Schlein B, Seiringer R. Optimal upper bound
    for the correlation energy of a Fermi gas in the mean-field regime. <i>Communications
    in Mathematical Physics</i>. 2020;374:2097–2150. doi:<a href="https://doi.org/10.1007/s00220-019-03505-5">10.1007/s00220-019-03505-5</a>
  apa: Benedikter, N. P., Nam, P. T., Porta, M., Schlein, B., &#38; Seiringer, R.
    (2020). Optimal upper bound for the correlation energy of a Fermi gas in the mean-field
    regime. <i>Communications in Mathematical Physics</i>. Springer Nature. <a href="https://doi.org/10.1007/s00220-019-03505-5">https://doi.org/10.1007/s00220-019-03505-5</a>
  chicago: Benedikter, Niels P, Phan Thành Nam, Marcello Porta, Benjamin Schlein,
    and Robert Seiringer. “Optimal Upper Bound for the Correlation Energy of a Fermi
    Gas in the Mean-Field Regime.” <i>Communications in Mathematical Physics</i>.
    Springer Nature, 2020. <a href="https://doi.org/10.1007/s00220-019-03505-5">https://doi.org/10.1007/s00220-019-03505-5</a>.
  ieee: N. P. Benedikter, P. T. Nam, M. Porta, B. Schlein, and R. Seiringer, “Optimal
    upper bound for the correlation energy of a Fermi gas in the mean-field regime,”
    <i>Communications in Mathematical Physics</i>, vol. 374. Springer Nature, pp.
    2097–2150, 2020.
  ista: Benedikter NP, Nam PT, Porta M, Schlein B, Seiringer R. 2020. Optimal upper
    bound for the correlation energy of a Fermi gas in the mean-field regime. Communications
    in Mathematical Physics. 374, 2097–2150.
  mla: Benedikter, Niels P., et al. “Optimal Upper Bound for the Correlation Energy
    of a Fermi Gas in the Mean-Field Regime.” <i>Communications in Mathematical Physics</i>,
    vol. 374, Springer Nature, 2020, pp. 2097–2150, doi:<a href="https://doi.org/10.1007/s00220-019-03505-5">10.1007/s00220-019-03505-5</a>.
  short: N.P. Benedikter, P.T. Nam, M. Porta, B. Schlein, R. Seiringer, Communications
    in Mathematical Physics 374 (2020) 2097–2150.
corr_author: '1'
date_created: 2019-07-18T13:30:04Z
date_published: 2020-03-01T00:00:00Z
date_updated: 2025-04-14T07:27:00Z
day: '01'
ddc:
- '530'
department:
- _id: RoSe
doi: 10.1007/s00220-019-03505-5
ec_funded: 1
external_id:
  arxiv:
  - '1809.01902'
  isi:
  - '000527910700019'
file:
- access_level: open_access
  checksum: f9dd6dd615a698f1d3636c4a092fed23
  content_type: application/pdf
  creator: dernst
  date_created: 2019-07-24T07:19:10Z
  date_updated: 2020-07-14T12:47:35Z
  file_id: '6668'
  file_name: 2019_CommMathPhysics_Benedikter.pdf
  file_size: 853289
  relation: main_file
file_date_updated: 2020-07-14T12:47:35Z
has_accepted_license: '1'
intvolume: '       374'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 2097–2150
project:
- _id: 3AC91DDA-15DF-11EA-824D-93A3E7B544D1
  call_identifier: FWF
  name: FWF Open Access Fund
- _id: 25C878CE-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: P27533_N27
  name: Structure of the Excitation Spectrum for Many-Body Quantum Systems
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '694227'
  name: Analysis of quantum many-body systems
publication: Communications in Mathematical Physics
publication_identifier:
  eissn:
  - 1432-0916
  issn:
  - 0010-3616
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Optimal upper bound for the correlation energy of a Fermi gas in the mean-field
  regime
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: 374
year: '2020'
...
---
_id: '6748'
abstract:
- lang: eng
  text: "Fitting a function by using linear combinations of a large number N of `simple'
    components is one of the most fruitful ideas in statistical learning. This idea
    lies at the core of a variety of methods, from two-layer neural networks to kernel
    regression, to boosting. In general, the resulting risk minimization problem is
    non-convex and is solved by gradient descent or its variants. Unfortunately, little
    is known about global convergence properties of these approaches.\r\nHere we consider
    the problem of learning a concave function f on a compact convex domain Ω⊆ℝd,
    using linear combinations of `bump-like' components (neurons). The parameters
    to be fitted are the centers of N bumps, and the resulting empirical risk minimization
    problem is highly non-convex. We prove that, in the limit in which the number
    of neurons diverges, the evolution of gradient descent converges to a Wasserstein
    gradient flow in the space of probability distributions over Ω. Further, when
    the bump width δ tends to 0, this gradient flow has a limit which is a viscous
    porous medium equation. Remarkably, the cost function optimized by this gradient
    flow exhibits a special property known as displacement convexity, which implies
    exponential convergence rates for N→∞, δ→0. Surprisingly, this asymptotic theory
    appears to capture well the behavior for moderate values of δ,N. Explaining this
    phenomenon, and understanding the dependence on δ,N in a quantitative manner remains
    an outstanding challenge."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Adel
  full_name: Javanmard, Adel
  last_name: Javanmard
- first_name: Marco
  full_name: Mondelli, Marco
  id: 27EB676C-8706-11E9-9510-7717E6697425
  last_name: Mondelli
  orcid: 0000-0002-3242-7020
- first_name: Andrea
  full_name: Montanari, Andrea
  last_name: Montanari
citation:
  ama: Javanmard A, Mondelli M, Montanari A. Analysis of a two-layer neural network
    via displacement convexity. <i>Annals of Statistics</i>. 2020;48(6):3619-3642.
    doi:<a href="https://doi.org/10.1214/20-AOS1945">10.1214/20-AOS1945</a>
  apa: Javanmard, A., Mondelli, M., &#38; Montanari, A. (2020). Analysis of a two-layer
    neural network via displacement convexity. <i>Annals of Statistics</i>. Institute
    of Mathematical Statistics. <a href="https://doi.org/10.1214/20-AOS1945">https://doi.org/10.1214/20-AOS1945</a>
  chicago: Javanmard, Adel, Marco Mondelli, and Andrea Montanari. “Analysis of a Two-Layer
    Neural Network via Displacement Convexity.” <i>Annals of Statistics</i>. Institute
    of Mathematical Statistics, 2020. <a href="https://doi.org/10.1214/20-AOS1945">https://doi.org/10.1214/20-AOS1945</a>.
  ieee: A. Javanmard, M. Mondelli, and A. Montanari, “Analysis of a two-layer neural
    network via displacement convexity,” <i>Annals of Statistics</i>, vol. 48, no.
    6. Institute of Mathematical Statistics, pp. 3619–3642, 2020.
  ista: Javanmard A, Mondelli M, Montanari A. 2020. Analysis of a two-layer neural
    network via displacement convexity. Annals of Statistics. 48(6), 3619–3642.
  mla: Javanmard, Adel, et al. “Analysis of a Two-Layer Neural Network via Displacement
    Convexity.” <i>Annals of Statistics</i>, vol. 48, no. 6, Institute of Mathematical
    Statistics, 2020, pp. 3619–42, doi:<a href="https://doi.org/10.1214/20-AOS1945">10.1214/20-AOS1945</a>.
  short: A. Javanmard, M. Mondelli, A. Montanari, Annals of Statistics 48 (2020) 3619–3642.
date_created: 2019-07-31T09:39:42Z
date_published: 2020-12-11T00:00:00Z
date_updated: 2024-10-21T06:02:33Z
day: '11'
department:
- _id: MaMo
doi: 10.1214/20-AOS1945
external_id:
  arxiv:
  - '1901.01375'
  isi:
  - '000598369200021'
intvolume: '        48'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1901.01375
month: '12'
oa: 1
oa_version: Preprint
page: 3619-3642
publication: Annals of Statistics
publication_identifier:
  eissn:
  - 1941-7330
  issn:
  - 1932-6157
publication_status: published
publisher: Institute of Mathematical Statistics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Analysis of a two-layer neural network via displacement convexity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 48
year: '2020'
...
---
_id: '6761'
abstract:
- lang: eng
  text: In resource allocation games, selfish players share resources that are needed
    in order to fulfill their objectives. The cost of using a resource depends on
    the load on it. In the traditional setting, the players make their choices concurrently
    and in one-shot. That is, a strategy for a player is a subset of the resources.
    We introduce and study dynamic resource allocation games. In this setting, the
    game proceeds in phases. In each phase each player chooses one resource. A scheduler
    dictates the order in which the players proceed in a phase, possibly scheduling
    several players to proceed concurrently. The game ends when each player has collected
    a set of resources that fulfills his objective. The cost for each player then
    depends on this set as well as on the load on the resources in it – we consider
    both congestion and cost-sharing games. We argue that the dynamic setting is the
    suitable setting for many applications in practice. We study the stability of
    dynamic resource allocation games, where the appropriate notion of stability is
    that of subgame perfect equilibrium, study the inefficiency incurred due to selfish
    behavior, and also study problems that are particular to the dynamic setting,
    like constraints on the order in which resources can be chosen or the problem
    of finding a scheduler that achieves stability.
article_processing_charge: No
article_type: original
author:
- 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
- first_name: Orna
  full_name: Kupferman, Orna
  last_name: Kupferman
citation:
  ama: Avni G, Henzinger TA, Kupferman O. Dynamic resource allocation games. <i>Theoretical
    Computer Science</i>. 2020;807:42-55. doi:<a href="https://doi.org/10.1016/j.tcs.2019.06.031">10.1016/j.tcs.2019.06.031</a>
  apa: Avni, G., Henzinger, T. A., &#38; Kupferman, O. (2020). Dynamic resource allocation
    games. <i>Theoretical Computer Science</i>. Elsevier. <a href="https://doi.org/10.1016/j.tcs.2019.06.031">https://doi.org/10.1016/j.tcs.2019.06.031</a>
  chicago: Avni, Guy, Thomas A Henzinger, and Orna Kupferman. “Dynamic Resource Allocation
    Games.” <i>Theoretical Computer Science</i>. Elsevier, 2020. <a href="https://doi.org/10.1016/j.tcs.2019.06.031">https://doi.org/10.1016/j.tcs.2019.06.031</a>.
  ieee: G. Avni, T. A. Henzinger, and O. Kupferman, “Dynamic resource allocation games,”
    <i>Theoretical Computer Science</i>, vol. 807. Elsevier, pp. 42–55, 2020.
  ista: Avni G, Henzinger TA, Kupferman O. 2020. Dynamic resource allocation games.
    Theoretical Computer Science. 807, 42–55.
  mla: Avni, Guy, et al. “Dynamic Resource Allocation Games.” <i>Theoretical Computer
    Science</i>, vol. 807, Elsevier, 2020, pp. 42–55, doi:<a href="https://doi.org/10.1016/j.tcs.2019.06.031">10.1016/j.tcs.2019.06.031</a>.
  short: G. Avni, T.A. Henzinger, O. Kupferman, Theoretical Computer Science 807 (2020)
    42–55.
date_created: 2019-08-04T21:59:20Z
date_published: 2020-02-06T00:00:00Z
date_updated: 2026-04-16T09:35:15Z
day: '06'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1016/j.tcs.2019.06.031
external_id:
  isi:
  - '000512219400004'
file:
- access_level: open_access
  checksum: e86635417f45eb2cd75778f91382f737
  content_type: application/pdf
  creator: dernst
  date_created: 2020-10-09T06:31:22Z
  date_updated: 2020-10-09T06:31:22Z
  file_id: '8639'
  file_name: 2020_TheoreticalCS_Avni.pdf
  file_size: 1413001
  relation: main_file
  success: 1
file_date_updated: 2020-10-09T06:31:22Z
has_accepted_license: '1'
intvolume: '       807'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Submitted Version
page: 42-55
project:
- _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: Formal methods for the design and analysis of complex systems
- _id: 264B3912-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: M02369
  name: Formal Methods meets Algorithmic Game Theory
publication: Theoretical Computer Science
publication_identifier:
  issn:
  - 0304-3975
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
  record:
  - id: '1341'
    relation: earlier_version
    status: public
scopus_import: '1'
status: public
title: Dynamic resource allocation games
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 807
year: '2020'
...
---
_id: '6796'
abstract:
- lang: eng
  text: Nearby grid cells have been observed to express a remarkable degree of long-rangeorder,
    which is often idealized as extending potentially to infinity. Yet their strict
    peri-odic firing and ensemble coherence are theoretically possible only in flat
    environments, much unlike the burrows which rodents usually live in. Are the symmetrical,
    coherent grid maps inferred in the lab relevant to chart their way in their natural
    habitat? We consider spheres as simple models of curved environments and waiting
    for the appropriate experiments to be performed, we use our adaptation model to
    predict what grid maps would emerge in a network with the same type of recurrent
    connections, which on the plane produce coherence among the units. We find that
    on the sphere such connections distort the maps that single grid units would express
    on their own, and aggregate them into clusters. When remapping to a different
    spherical environment, units in each cluster maintain only partial coherence,
    similar to what is observed in disordered materials, such as spin glasses.
article_processing_charge: No
article_type: original
author:
- first_name: Federico
  full_name: Stella, Federico
  id: 39AF1E74-F248-11E8-B48F-1D18A9856A87
  last_name: Stella
  orcid: 0000-0001-9439-3148
- first_name: Eugenio
  full_name: Urdapilleta, Eugenio
  last_name: Urdapilleta
- first_name: Yifan
  full_name: Luo, Yifan
  last_name: Luo
- first_name: Alessandro
  full_name: Treves, Alessandro
  last_name: Treves
citation:
  ama: Stella F, Urdapilleta E, Luo Y, Treves A. Partial coherence and frustration
    in self-organizing spherical grids. <i>Hippocampus</i>. 2020;30(4):302-313. doi:<a
    href="https://doi.org/10.1002/hipo.23144">10.1002/hipo.23144</a>
  apa: Stella, F., Urdapilleta, E., Luo, Y., &#38; Treves, A. (2020). Partial coherence
    and frustration in self-organizing spherical grids. <i>Hippocampus</i>. Wiley.
    <a href="https://doi.org/10.1002/hipo.23144">https://doi.org/10.1002/hipo.23144</a>
  chicago: Stella, Federico, Eugenio Urdapilleta, Yifan Luo, and Alessandro Treves.
    “Partial Coherence and Frustration in Self-Organizing Spherical Grids.” <i>Hippocampus</i>.
    Wiley, 2020. <a href="https://doi.org/10.1002/hipo.23144">https://doi.org/10.1002/hipo.23144</a>.
  ieee: F. Stella, E. Urdapilleta, Y. Luo, and A. Treves, “Partial coherence and frustration
    in self-organizing spherical grids,” <i>Hippocampus</i>, vol. 30, no. 4. Wiley,
    pp. 302–313, 2020.
  ista: Stella F, Urdapilleta E, Luo Y, Treves A. 2020. Partial coherence and frustration
    in self-organizing spherical grids. Hippocampus. 30(4), 302–313.
  mla: Stella, Federico, et al. “Partial Coherence and Frustration in Self-Organizing
    Spherical Grids.” <i>Hippocampus</i>, vol. 30, no. 4, Wiley, 2020, pp. 302–13,
    doi:<a href="https://doi.org/10.1002/hipo.23144">10.1002/hipo.23144</a>.
  short: F. Stella, E. Urdapilleta, Y. Luo, A. Treves, Hippocampus 30 (2020) 302–313.
date_created: 2019-08-11T21:59:24Z
date_published: 2020-04-01T00:00:00Z
date_updated: 2025-05-22T11:13:25Z
day: '01'
ddc:
- '570'
department:
- _id: JoCs
doi: 10.1002/hipo.23144
external_id:
  isi:
  - '000477299600001'
  pmid:
  - '31339190'
file:
- access_level: open_access
  checksum: 7b54d22bfbfc0d1188a9ea24d985bfb2
  content_type: application/pdf
  creator: dernst
  date_created: 2019-08-12T07:53:33Z
  date_updated: 2020-07-14T12:47:40Z
  file_id: '6800'
  file_name: 2019_Hippocampus_Stella.pdf
  file_size: 2370658
  relation: main_file
file_date_updated: 2020-07-14T12:47:40Z
has_accepted_license: '1'
intvolume: '        30'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 302-313
pmid: 1
publication: Hippocampus
publication_identifier:
  eissn:
  - 1098-1063
  issn:
  - 1050-9631
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Partial coherence and frustration in self-organizing spherical grids
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: 9947682f-b9fa-11ee-9c4a-b3ffaafe6614
volume: 30
year: '2020'
...
---
_id: '6808'
abstract:
- lang: eng
  text: Super-resolution fluorescence microscopy has become an important catalyst
    for discovery in the life sciences. In STimulated Emission Depletion (STED) microscopy,
    a pattern of light drives fluorophores from a signal-emitting on-state to a non-signalling
    off-state. Only emitters residing in a sub-diffraction volume around an intensity
    minimum are allowed to fluoresce, rendering them distinguishable from the nearby,
    but dark fluorophores. STED routinely achieves resolution in the few tens of nanometers
    range in biological samples and is suitable for live imaging. Here, we review
    the working principle of STED and provide general guidelines for successful STED
    imaging. The strive for ever higher resolution comes at the cost of increased
    light burden. We discuss techniques to reduce light exposure and mitigate its
    detrimental effects on the specimen. These include specialized illumination strategies
    as well as protecting fluorophores from photobleaching mediated by high-intensity
    STED light. This opens up the prospect of volumetric imaging in living cells and
    tissues with diffraction-unlimited resolution in all three spatial dimensions.
article_processing_charge: No
article_type: original
author:
- first_name: Wiebke
  full_name: Jahr, Wiebke
  id: 425C1CE8-F248-11E8-B48F-1D18A9856A87
  last_name: Jahr
- first_name: Philipp
  full_name: Velicky, Philipp
  id: 39BDC62C-F248-11E8-B48F-1D18A9856A87
  last_name: Velicky
  orcid: 0000-0002-2340-7431
- first_name: Johann G
  full_name: Danzl, Johann G
  id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
  last_name: Danzl
  orcid: 0000-0001-8559-3973
citation:
  ama: Jahr W, Velicky P, Danzl JG. Strategies to maximize performance in STimulated
    Emission Depletion (STED) nanoscopy of biological specimens. <i>Methods</i>. 2020;174(3):27-41.
    doi:<a href="https://doi.org/10.1016/j.ymeth.2019.07.019">10.1016/j.ymeth.2019.07.019</a>
  apa: Jahr, W., Velicky, P., &#38; Danzl, J. G. (2020). Strategies to maximize performance
    in STimulated Emission Depletion (STED) nanoscopy of biological specimens. <i>Methods</i>.
    Elsevier. <a href="https://doi.org/10.1016/j.ymeth.2019.07.019">https://doi.org/10.1016/j.ymeth.2019.07.019</a>
  chicago: Jahr, Wiebke, Philipp Velicky, and Johann G Danzl. “Strategies to Maximize
    Performance in STimulated Emission Depletion (STED) Nanoscopy of Biological Specimens.”
    <i>Methods</i>. Elsevier, 2020. <a href="https://doi.org/10.1016/j.ymeth.2019.07.019">https://doi.org/10.1016/j.ymeth.2019.07.019</a>.
  ieee: W. Jahr, P. Velicky, and J. G. Danzl, “Strategies to maximize performance
    in STimulated Emission Depletion (STED) nanoscopy of biological specimens,” <i>Methods</i>,
    vol. 174, no. 3. Elsevier, pp. 27–41, 2020.
  ista: Jahr W, Velicky P, Danzl JG. 2020. Strategies to maximize performance in STimulated
    Emission Depletion (STED) nanoscopy of biological specimens. Methods. 174(3),
    27–41.
  mla: Jahr, Wiebke, et al. “Strategies to Maximize Performance in STimulated Emission
    Depletion (STED) Nanoscopy of Biological Specimens.” <i>Methods</i>, vol. 174,
    no. 3, Elsevier, 2020, pp. 27–41, doi:<a href="https://doi.org/10.1016/j.ymeth.2019.07.019">10.1016/j.ymeth.2019.07.019</a>.
  short: W. Jahr, P. Velicky, J.G. Danzl, Methods 174 (2020) 27–41.
date_created: 2019-08-12T16:36:32Z
date_published: 2020-03-01T00:00:00Z
date_updated: 2025-04-14T09:39:25Z
day: '01'
department:
- _id: JoDa
doi: 10.1016/j.ymeth.2019.07.019
external_id:
  isi:
  - '000525860400005'
  pmid:
  - '31344404'
intvolume: '       174'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7100895/
month: '03'
oa: 1
oa_version: Submitted Version
page: 27-41
pmid: 1
project:
- _id: 265CB4D0-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: I03600
  name: Optical control of synaptic function via adhesion molecules
- _id: 2668BFA0-B435-11E9-9278-68D0E5697425
  grant_number: LT00057
  name: High-speed 3D-nanoscopy to study the role of adhesion during 3D cell migration
publication: Methods
publication_identifier:
  issn:
  - 1046-2023
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Strategies to maximize performance in STimulated Emission Depletion (STED)
  nanoscopy of biological specimens
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 174
year: '2020'
...
---
_id: '6906'
abstract:
- lang: eng
  text: We consider systems of bosons trapped in a box, in the Gross–Pitaevskii regime.
    We show that low-energy states exhibit complete Bose–Einstein condensation with
    an optimal bound on the number of orthogonal excitations. This extends recent
    results obtained in Boccato et al. (Commun Math Phys 359(3):975–1026, 2018), removing
    the assumption of small interaction potential.
acknowledgement: "We would like to thank P. T. Nam and R. Seiringer for several useful
  discussions and\r\nfor suggesting us to use the localization techniques from [9].
  C. Boccato has received funding from the\r\nEuropean Research Council (ERC) under
  the programme Horizon 2020 (Grant Agreement 694227). B. Schlein gratefully acknowledges
  support from the NCCR SwissMAP and from the Swiss National Foundation of Science
  (Grant No. 200020_1726230) through the SNF Grant “Dynamical and energetic properties
  of Bose–Einstein condensates”."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Chiara
  full_name: Boccato, Chiara
  id: 342E7E22-F248-11E8-B48F-1D18A9856A87
  last_name: Boccato
- first_name: Christian
  full_name: Brennecke, Christian
  last_name: Brennecke
- first_name: Serena
  full_name: Cenatiempo, Serena
  last_name: Cenatiempo
- first_name: Benjamin
  full_name: Schlein, Benjamin
  last_name: Schlein
citation:
  ama: Boccato C, Brennecke C, Cenatiempo S, Schlein B. Optimal rate for Bose-Einstein
    condensation in the Gross-Pitaevskii regime. <i>Communications in Mathematical
    Physics</i>. 2020;376:1311-1395. doi:<a href="https://doi.org/10.1007/s00220-019-03555-9">10.1007/s00220-019-03555-9</a>
  apa: Boccato, C., Brennecke, C., Cenatiempo, S., &#38; Schlein, B. (2020). Optimal
    rate for Bose-Einstein condensation in the Gross-Pitaevskii regime. <i>Communications
    in Mathematical Physics</i>. Springer. <a href="https://doi.org/10.1007/s00220-019-03555-9">https://doi.org/10.1007/s00220-019-03555-9</a>
  chicago: Boccato, Chiara, Christian Brennecke, Serena Cenatiempo, and Benjamin Schlein.
    “Optimal Rate for Bose-Einstein Condensation in the Gross-Pitaevskii Regime.”
    <i>Communications in Mathematical Physics</i>. Springer, 2020. <a href="https://doi.org/10.1007/s00220-019-03555-9">https://doi.org/10.1007/s00220-019-03555-9</a>.
  ieee: C. Boccato, C. Brennecke, S. Cenatiempo, and B. Schlein, “Optimal rate for
    Bose-Einstein condensation in the Gross-Pitaevskii regime,” <i>Communications
    in Mathematical Physics</i>, vol. 376. Springer, pp. 1311–1395, 2020.
  ista: Boccato C, Brennecke C, Cenatiempo S, Schlein B. 2020. Optimal rate for Bose-Einstein
    condensation in the Gross-Pitaevskii regime. Communications in Mathematical Physics.
    376, 1311–1395.
  mla: Boccato, Chiara, et al. “Optimal Rate for Bose-Einstein Condensation in the
    Gross-Pitaevskii Regime.” <i>Communications in Mathematical Physics</i>, vol.
    376, Springer, 2020, pp. 1311–95, doi:<a href="https://doi.org/10.1007/s00220-019-03555-9">10.1007/s00220-019-03555-9</a>.
  short: C. Boccato, C. Brennecke, S. Cenatiempo, B. Schlein, Communications in Mathematical
    Physics 376 (2020) 1311–1395.
date_created: 2019-09-24T17:30:59Z
date_published: 2020-06-01T00:00:00Z
date_updated: 2025-04-14T07:27:00Z
day: '01'
department:
- _id: RoSe
doi: 10.1007/s00220-019-03555-9
ec_funded: 1
external_id:
  arxiv:
  - '1812.03086'
  isi:
  - '000536053300012'
intvolume: '       376'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1812.03086
month: '06'
oa: 1
oa_version: Preprint
page: 1311-1395
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '694227'
  name: Analysis of quantum many-body systems
publication: Communications in Mathematical Physics
publication_identifier:
  eissn:
  - 1432-0916
  issn:
  - 0010-3616
publication_status: published
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
status: public
title: Optimal rate for Bose-Einstein condensation in the Gross-Pitaevskii regime
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 376
year: '2020'
...
---
_id: '6944'
abstract:
- lang: eng
  text: 'We study the problem of automatically detecting if a given multi-class classifier
    operates outside of its specifications (out-of-specs), i.e. on input data from
    a different distribution than what it was trained for. This is an important problem
    to solve on the road towards creating reliable computer vision systems for real-world
    applications, because the quality of a classifier’s predictions cannot be guaranteed
    if it operates out-of-specs. Previously proposed methods for out-of-specs detection
    make decisions on the level of single inputs. This, however, is insufficient to
    achieve low false positive rate and high false negative rates at the same time.
    In this work, we describe a new procedure named KS(conf), based on statistical
    reasoning. Its main component is a classical Kolmogorov–Smirnov test that is applied
    to the set of predicted confidence values for batches of samples. Working with
    batches instead of single samples allows increasing the true positive rate without
    negatively affecting the false positive rate, thereby overcoming a crucial limitation
    of single sample tests. We show by extensive experiments using a variety of convolutional
    network architectures and datasets that KS(conf) reliably detects out-of-specs
    situations even under conditions where other tests fail. It furthermore has a
    number of properties that make it an excellent candidate for practical deployment:
    it is easy to implement, adds almost no overhead to the system, works with any
    classifier that outputs confidence scores, and requires no a priori knowledge
    about how the data distribution could change.'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Rémy
  full_name: Sun, Rémy
  last_name: Sun
- first_name: Christoph
  full_name: Lampert, Christoph
  id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
  last_name: Lampert
  orcid: 0000-0001-8622-7887
citation:
  ama: 'Sun R, Lampert C. KS(conf): A light-weight test if a multiclass classifier
    operates outside of its specifications. <i>International Journal of Computer Vision</i>.
    2020;128(4):970-995. doi:<a href="https://doi.org/10.1007/s11263-019-01232-x">10.1007/s11263-019-01232-x</a>'
  apa: 'Sun, R., &#38; Lampert, C. (2020). KS(conf): A light-weight test if a multiclass
    classifier operates outside of its specifications. <i>International Journal of
    Computer Vision</i>. Springer Nature. <a href="https://doi.org/10.1007/s11263-019-01232-x">https://doi.org/10.1007/s11263-019-01232-x</a>'
  chicago: 'Sun, Rémy, and Christoph Lampert. “KS(Conf): A Light-Weight Test If a
    Multiclass Classifier Operates Outside of Its Specifications.” <i>International
    Journal of Computer Vision</i>. Springer Nature, 2020. <a href="https://doi.org/10.1007/s11263-019-01232-x">https://doi.org/10.1007/s11263-019-01232-x</a>.'
  ieee: 'R. Sun and C. Lampert, “KS(conf): A light-weight test if a multiclass classifier
    operates outside of its specifications,” <i>International Journal of Computer
    Vision</i>, vol. 128, no. 4. Springer Nature, pp. 970–995, 2020.'
  ista: 'Sun R, Lampert C. 2020. KS(conf): A light-weight test if a multiclass classifier
    operates outside of its specifications. International Journal of Computer Vision.
    128(4), 970–995.'
  mla: 'Sun, Rémy, and Christoph Lampert. “KS(Conf): A Light-Weight Test If a Multiclass
    Classifier Operates Outside of Its Specifications.” <i>International Journal of
    Computer Vision</i>, vol. 128, no. 4, Springer Nature, 2020, pp. 970–95, doi:<a
    href="https://doi.org/10.1007/s11263-019-01232-x">10.1007/s11263-019-01232-x</a>.'
  short: R. Sun, C. Lampert, International Journal of Computer Vision 128 (2020) 970–995.
corr_author: '1'
date_created: 2019-10-14T09:14:28Z
date_published: 2020-04-01T00:00:00Z
date_updated: 2025-04-15T07:10:25Z
day: '01'
ddc:
- '004'
department:
- _id: ChLa
doi: 10.1007/s11263-019-01232-x
ec_funded: 1
external_id:
  isi:
  - '000494406800001'
file:
- access_level: open_access
  checksum: 155e63edf664dcacb3bdc1c2223e606f
  content_type: application/pdf
  creator: dernst
  date_created: 2019-11-26T10:30:02Z
  date_updated: 2020-07-14T12:47:45Z
  file_id: '7110'
  file_name: 2019_IJCV_Sun.pdf
  file_size: 1715072
  relation: main_file
file_date_updated: 2020-07-14T12:47:45Z
has_accepted_license: '1'
intvolume: '       128'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 970-995
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '308036'
  name: Lifelong Learning of Visual Scene Understanding
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
  name: IST Austria Open Access Fund
publication: International Journal of Computer Vision
publication_identifier:
  eissn:
  - 1573-1405
  issn:
  - 0920-5691
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
  link:
  - relation: erratum
    url: https://doi.org/10.1007/s11263-019-01262-5
  record:
  - id: '6482'
    relation: earlier_version
    status: public
scopus_import: '1'
status: public
title: 'KS(conf): A light-weight test if a multiclass classifier operates outside
  of its specifications'
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 128
year: '2020'
...
---
_id: '6976'
abstract:
- lang: eng
  text: Origami is rapidly transforming the design of robots1,2, deployable structures3,4,5,6
    and metamaterials7,8,9,10,11,12,13,14. However, as foldability requires a large
    number of complex compatibility conditions that are difficult to satisfy, the
    design of crease patterns is limited to heuristics and computer optimization.
    Here we introduce a systematic strategy that enables intuitive and effective design
    of complex crease patterns that are guaranteed to fold. First, we exploit symmetries
    to construct 140 distinct foldable motifs, and represent these as jigsaw puzzle
    pieces. We then show that when these pieces are fitted together they encode foldable
    crease patterns. This maps origami design to solving combinatorial problems, which
    allows us to systematically create, count and classify a vast number of crease
    patterns. We show that all of these crease patterns are pluripotent—capable of
    folding into multiple shapes—and solve exactly for the number of possible shapes
    for each pattern. Finally, we employ our framework to rationally design a crease
    pattern that folds into two independently defined target shapes, and fabricate
    such pluripotent origami. Our results provide physicists, mathematicians and engineers
    with a powerful new design strategy.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Peter
  full_name: Dieleman, Peter
  last_name: Dieleman
- first_name: Niek
  full_name: Vasmel, Niek
  last_name: Vasmel
- first_name: Scott R
  full_name: Waitukaitis, Scott R
  id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
  last_name: Waitukaitis
  orcid: 0000-0002-2299-3176
- first_name: Martin
  full_name: van Hecke, Martin
  last_name: van Hecke
citation:
  ama: Dieleman P, Vasmel N, Waitukaitis SR, van Hecke M. Jigsaw puzzle design of
    pluripotent origami. <i>Nature Physics</i>. 2020;16(1):63–68. doi:<a href="https://doi.org/10.1038/s41567-019-0677-3">10.1038/s41567-019-0677-3</a>
  apa: Dieleman, P., Vasmel, N., Waitukaitis, S. R., &#38; van Hecke, M. (2020). Jigsaw
    puzzle design of pluripotent origami. <i>Nature Physics</i>. Springer Nature.
    <a href="https://doi.org/10.1038/s41567-019-0677-3">https://doi.org/10.1038/s41567-019-0677-3</a>
  chicago: Dieleman, Peter, Niek Vasmel, Scott R Waitukaitis, and Martin van Hecke.
    “Jigsaw Puzzle Design of Pluripotent Origami.” <i>Nature Physics</i>. Springer
    Nature, 2020. <a href="https://doi.org/10.1038/s41567-019-0677-3">https://doi.org/10.1038/s41567-019-0677-3</a>.
  ieee: P. Dieleman, N. Vasmel, S. R. Waitukaitis, and M. van Hecke, “Jigsaw puzzle
    design of pluripotent origami,” <i>Nature Physics</i>, vol. 16, no. 1. Springer
    Nature, pp. 63–68, 2020.
  ista: Dieleman P, Vasmel N, Waitukaitis SR, van Hecke M. 2020. Jigsaw puzzle design
    of pluripotent origami. Nature Physics. 16(1), 63–68.
  mla: Dieleman, Peter, et al. “Jigsaw Puzzle Design of Pluripotent Origami.” <i>Nature
    Physics</i>, vol. 16, no. 1, Springer Nature, 2020, pp. 63–68, doi:<a href="https://doi.org/10.1038/s41567-019-0677-3">10.1038/s41567-019-0677-3</a>.
  short: P. Dieleman, N. Vasmel, S.R. Waitukaitis, M. van Hecke, Nature Physics 16
    (2020) 63–68.
date_created: 2019-10-31T07:51:44Z
date_published: 2020-01-01T00:00:00Z
date_updated: 2021-01-12T08:11:16Z
day: '01'
doi: 10.1038/s41567-019-0677-3
extern: '1'
intvolume: '        16'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 63–68
publication: Nature Physics
publication_identifier:
  eissn:
  - 1745-2481
  issn:
  - 1745-2473
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Jigsaw puzzle design of pluripotent origami
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 16
year: '2020'
...