[{"abstract":[{"lang":"eng","text":"Water adsorption and dissociation processes on pristine low-index TiO2 interfaces are important but poorly understood outside the well-studied anatase (101) and rutile (110). To understand these, we construct three sets of machine learning potentials that are simultaneously applicable to various TiO2 surfaces, based on three density-functional-theory approximations. Here we show the water dissociation free energies on seven pristine TiO2 surfaces, and predict that anatase (100), anatase (110), rutile (001), and rutile (011) favor water dissociation, anatase (101) and rutile (100) have mostly molecular adsorption, while the simulations of rutile (110) sensitively depend on the slab thickness and molecular adsorption is preferred with thick slabs. Moreover, using an automated algorithm, we reveal that these surfaces follow different types of atomistic mechanisms for proton transfer and water dissociation: one-step, two-step, or both. These mechanisms can be rationalized based on the arrangements of water molecules on the different surfaces. Our finding thus demonstrates that the different pristine TiO2 surfaces react with water in distinct ways, and cannot be represented using just the low-energy anatase (101) and rutile (110) surfaces."}],"author":[{"full_name":"Zeng, Zezhu","first_name":"Zezhu","last_name":"Zeng","orcid":"0000-0001-5126-4928","id":"54a2c730-803f-11ed-ab7e-95b29d2680e7"},{"full_name":"Wodaczek, Felix","first_name":"Felix","orcid":"0009-0000-1457-795X","id":"8b4b6a9f-32b0-11ee-9fa8-bbe85e26258e","last_name":"Wodaczek"},{"last_name":"Liu","full_name":"Liu, Keyang","first_name":"Keyang"},{"last_name":"Stein","first_name":"Frederick","full_name":"Stein, Frederick"},{"first_name":"Jürg","full_name":"Hutter, Jürg","last_name":"Hutter"},{"full_name":"Chen, Ji","first_name":"Ji","last_name":"Chen"},{"full_name":"Cheng, Bingqing","first_name":"Bingqing","last_name":"Cheng","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"}],"publisher":"Springer Nature","file_date_updated":"2023-10-16T07:34:49Z","year":"2023","acknowledgement":"F.S., J.H., and B.C. thank the Swiss National Supercomputing Centre (CSCS) for the generous allocation of CPU hours via production project s1108 at the Piz Daint supercomputer. B.C. acknowledges resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by EPSRC Tier-2 capital grant EP/P020259/1. J.C. acknowledges the Beijing Natural Science Foundation for support under grant No. JQ22001. F.S., and J.H. thank the Swiss Platform for Advanced Scientific Computing (PASC) via the 2021-2024 “Ab Initio Molecular Dynamics at the Exa-Scale” project. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101034413.","file":[{"file_id":"14432","checksum":"7d1dffd36b672ec679f08f70ce79da87","creator":"dernst","date_created":"2023-10-16T07:34:49Z","file_size":3194116,"date_updated":"2023-10-16T07:34:49Z","access_level":"open_access","content_type":"application/pdf","relation":"main_file","success":1,"file_name":"2023_NatureComm_Zeng.pdf"}],"corr_author":"1","_id":"14425","article_number":"6131","department":[{"_id":"BiCh"},{"_id":"GradSch"}],"publication":"Nature Communications","das_tickbox":"1","ddc":["540","000"],"status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["37783698"],"isi":["001084354900008"],"arxiv":["2303.07433"]},"date_updated":"2026-08-07T11:00:29Z","date_published":"2023-10-02T00:00:00Z","day":"02","intvolume":"        14","isi":1,"citation":{"short":"Z. Zeng, F. Wodaczek, K. Liu, F. Stein, J. Hutter, J. Chen, B. Cheng, Nature Communications 14 (2023).","ama":"Zeng Z, Wodaczek F, Liu K, et al. Mechanistic insight on water dissociation on pristine low-index TiO2 surfaces from machine learning molecular dynamics simulations. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-41865-8\">10.1038/s41467-023-41865-8</a>","mla":"Zeng, Zezhu, et al. “Mechanistic Insight on Water Dissociation on Pristine Low-Index TiO2 Surfaces from Machine Learning Molecular Dynamics Simulations.” <i>Nature Communications</i>, vol. 14, 6131, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-41865-8\">10.1038/s41467-023-41865-8</a>.","chicago":"Zeng, Zezhu, Felix Wodaczek, Keyang Liu, Frederick Stein, Jürg Hutter, Ji Chen, and Bingqing Cheng. “Mechanistic Insight on Water Dissociation on Pristine Low-Index TiO2 Surfaces from Machine Learning Molecular Dynamics Simulations.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-41865-8\">https://doi.org/10.1038/s41467-023-41865-8</a>.","apa":"Zeng, Z., Wodaczek, F., Liu, K., Stein, F., Hutter, J., Chen, J., &#38; Cheng, B. (2023). Mechanistic insight on water dissociation on pristine low-index TiO2 surfaces from machine learning molecular dynamics simulations. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-41865-8\">https://doi.org/10.1038/s41467-023-41865-8</a>","ieee":"Z. Zeng <i>et al.</i>, “Mechanistic insight on water dissociation on pristine low-index TiO2 surfaces from machine learning molecular dynamics simulations,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","ista":"Zeng Z, Wodaczek F, Liu K, Stein F, Hutter J, Chen J, Cheng B. 2023. Mechanistic insight on water dissociation on pristine low-index TiO2 surfaces from machine learning molecular dynamics simulations. Nature Communications. 14, 6131."},"project":[{"call_identifier":"H2020","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"article_processing_charge":"Yes","quality_controlled":"1","publication_status":"published","language":[{"iso":"eng"}],"supplementarymaterial":"yes","month":"10","dataavailabilitystatement":"The machine learning potentials, training sets, sample DFT and metadynamics input files, PYTHON data analysis scripts and other necessary source data files generated for this study are available in the SI repository (https://github.com/BingqingCheng/TiO2-water) see ref 58.\r\n58. Zeng, Z. et al. Source data for Mechanistic insight on water dissociation on pristine low-index TiO2 surfaces from machine learning molecular dynamics simulations, Zenodo, https://zenodo.org/record/8301965 (2023).","ec_funded":1,"title":"Mechanistic insight on water dissociation on pristine low-index TiO2 surfaces from machine learning molecular dynamics simulations","oa":1,"oa_version":"Published Version","has_accepted_license":"1","related_material":{"link":[{"relation":"software","url":"https://github.com/BingqingCheng/TiO2-water"}]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"eissn":["2041-1723"]},"pmid":1,"researchdata_availability":"yes","type":"journal_article","scopus_import":"1","article_type":"original","arxiv":1,"license":"https://creativecommons.org/licenses/by/4.0/","volume":14,"date_created":"2023-10-15T22:01:10Z","doi":"10.1038/s41467-023-41865-8"},{"publisher":"AIP Publishing","abstract":[{"text":"Computing the solubility of crystals in a solvent using atomistic simulations is notoriously challenging due to the complexities and convergence issues associated with free-energy methods, as well as the slow equilibration in direct-coexistence simulations. This paper introduces a molecular-dynamics workflow that simplifies and robustly computes the solubility of molecular or ionic crystals. This method is considerably more straightforward than the state-of-the-art, as we have streamlined and optimised each step of the process. Specifically, we calculate the chemical potential of the crystal using the gas-phase molecule as a reference state, and employ the S0 method to determine the concentration dependence of the chemical potential of the solute. We use this workflow to predict the solubilities of sodium chloride in water, urea polymorphs in water, and paracetamol polymorphs in both water and ethanol. Our findings indicate that the predicted solubility is sensitive to the chosen potential energy surface. Furthermore, we note that the harmonic approximation often fails for both molecular crystals and gas molecules at or above room temperature, and that the assumption of an ideal solution becomes less valid for highly soluble substances.","lang":"eng"}],"author":[{"first_name":"Aleks","full_name":"Reinhardt, Aleks","last_name":"Reinhardt"},{"last_name":"Chew","first_name":"Pin Yu","full_name":"Chew, Pin Yu"},{"last_name":"Cheng","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing","first_name":"Bingqing"}],"year":"2023","file_date_updated":"2023-11-28T08:39:06Z","corr_author":"1","acknowledgement":"A.R. and B.C. acknowledge resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by EPSRC Tier-2 capital Grant No. EP/P020259/1. P.Y.C. acknowledges support from the Ernest Oppenheimer Fund and the Winton Programme for the Physics of Sustainability.","file":[{"content_type":"application/pdf","access_level":"open_access","date_updated":"2023-11-28T08:39:06Z","file_size":6276059,"date_created":"2023-11-28T08:39:06Z","creator":"dernst","checksum":"f668ee0d07096eef81159d05bc27aabc","file_id":"14620","file_name":"2023_JourChemicalPhysics_Reinhardt.pdf","success":1,"relation":"main_file"}],"article_number":"184110","_id":"14603","department":[{"_id":"BiCh"}],"publication":"Journal of Chemical Physics","das_tickbox":"1","external_id":{"arxiv":["2308.10886"],"pmid":["37962445"],"isi":["001137066700001"]},"date_updated":"2026-08-07T11:07:46Z","ddc":["530","540"],"status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"day":"14","intvolume":"       159","date_published":"2023-11-14T00:00:00Z","quality_controlled":"1","article_processing_charge":"Yes (in subscription journal)","citation":{"ista":"Reinhardt A, Chew PY, Cheng B. 2023. A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals. Journal of Chemical Physics. 159(18), 184110.","apa":"Reinhardt, A., Chew, P. Y., &#38; Cheng, B. (2023). A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals. <i>Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0173341\">https://doi.org/10.1063/5.0173341</a>","ieee":"A. Reinhardt, P. Y. Chew, and B. Cheng, “A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals,” <i>Journal of Chemical Physics</i>, vol. 159, no. 18. AIP Publishing, 2023.","chicago":"Reinhardt, Aleks, Pin Yu Chew, and Bingqing Cheng. “A Streamlined Molecular-Dynamics Workflow for Computing Solubilities of Molecular and Ionic Crystals.” <i>Journal of Chemical Physics</i>. AIP Publishing, 2023. <a href=\"https://doi.org/10.1063/5.0173341\">https://doi.org/10.1063/5.0173341</a>.","mla":"Reinhardt, Aleks, et al. “A Streamlined Molecular-Dynamics Workflow for Computing Solubilities of Molecular and Ionic Crystals.” <i>Journal of Chemical Physics</i>, vol. 159, no. 18, 184110, AIP Publishing, 2023, doi:<a href=\"https://doi.org/10.1063/5.0173341\">10.1063/5.0173341</a>.","ama":"Reinhardt A, Chew PY, Cheng B. A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals. <i>Journal of Chemical Physics</i>. 2023;159(18). doi:<a href=\"https://doi.org/10.1063/5.0173341\">10.1063/5.0173341</a>","short":"A. Reinhardt, P.Y. Chew, B. Cheng, Journal of Chemical Physics 159 (2023)."},"isi":1,"publication_status":"published","month":"11","dataavailabilitystatement":"Simulation input files necessary to reproduce the study and Python data analysis scripts are available in the SI repository at https://github.com/BingqingCheng/solubility, and on Zenodo at http://doi.org/10.5281/zenodo.8398093.","supplementarymaterial":"no","title":"A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals","language":[{"iso":"eng"}],"has_accepted_license":"1","related_material":{"record":[{"relation":"research_data","id":"14619","status":"public"}]},"oa":1,"issue":"18","oa_version":"Published Version","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"pmid":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","researchdata_availability":"yes","scopus_import":"1","article_type":"original","volume":159,"arxiv":1,"type":"journal_article","doi":"10.1063/5.0173341","date_created":"2023-11-26T23:00:54Z"},{"author":[{"full_name":"Schörner, Maximilian","first_name":"Maximilian","last_name":"Schörner"},{"full_name":"Bethkenhagen, Mandy","first_name":"Mandy","last_name":"Bethkenhagen","orcid":"0000-0002-1838-2129","id":"201939f4-803f-11ed-ab7e-d8da4bd1517f"},{"full_name":"Döppner, Tilo","first_name":"Tilo","last_name":"Döppner"},{"last_name":"Kraus","full_name":"Kraus, Dominik","first_name":"Dominik"},{"last_name":"Fletcher","full_name":"Fletcher, Luke B.","first_name":"Luke B."},{"last_name":"Glenzer","full_name":"Glenzer, Siegfried H.","first_name":"Siegfried H."},{"last_name":"Redmer","first_name":"Ronald","full_name":"Redmer, Ronald"}],"abstract":[{"text":"We study ab initio approaches for calculating x-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula that expresses the inelastic contribution in terms of the dielectric function. We study the electronic dynamic structure factor computed from the Mermin dielectric function using an ab initio electron-ion collision frequency in comparison to computations using a linear-response time-dependent density functional theory (LR-TDDFT) framework for hydrogen and beryllium and investigate the dispersion of free-free and bound-free contributions to the scattering signal. A separate treatment of these contributions, where only the free-free part follows the Mermin dispersion, shows good agreement with LR-TDDFT results for ambient-density beryllium, but breaks down for highly compressed matter where the bound states become pressure ionized. LR-TDDFT is used to reanalyze x-ray Thomson scattering experiments on beryllium demonstrating strong deviations from the plasma conditions inferred with traditional analytic models at small scattering angles.","lang":"eng"}],"publisher":"American Physical Society","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2301.01545"}],"year":"2023","acknowledgement":"We want to thank P. Sperling, B. Witte, M. French, G. Röpke, H. J. Lee and A. Cangi for many helpful discussions. M. S. and R. R. acknowledge support by the Deutsche Forschungsgemeinschaft (DFG) within the Research Unit FOR 2440. All simulations and analyses were performed at the North-German Supercomputing Alliance (HLRN) and the ITMZ of the University of Rostock. M. B. gratefully acknowledges support by the European Horizon 2020 programme within the Marie Sklodowska-Curie actions (xICE grant 894725) and the\r\nNOMIS foundation. The work of T. D. was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344.","_id":"13231","article_number":"065207","das_tickbox":"0","department":[{"_id":"BiCh"}],"publication":"Physical Review E","status":"public","date_updated":"2026-08-07T10:59:03Z","external_id":{"arxiv":["2301.01545"],"isi":["001020265000002"],"pmid":["37464593"]},"date_published":"2023-06-14T00:00:00Z","day":"14","intvolume":"       107","citation":{"ista":"Schörner M, Bethkenhagen M, Döppner T, Kraus D, Fletcher LB, Glenzer SH, Redmer R. 2023. X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula. Physical Review E. 107(6), 065207.","ieee":"M. Schörner <i>et al.</i>, “X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula,” <i>Physical Review E</i>, vol. 107, no. 6. American Physical Society, 2023.","apa":"Schörner, M., Bethkenhagen, M., Döppner, T., Kraus, D., Fletcher, L. B., Glenzer, S. H., &#38; Redmer, R. (2023). X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.107.065207\">https://doi.org/10.1103/PhysRevE.107.065207</a>","chicago":"Schörner, Maximilian, Mandy Bethkenhagen, Tilo Döppner, Dominik Kraus, Luke B. Fletcher, Siegfried H. Glenzer, and Ronald Redmer. “X-Ray Thomson Scattering Spectra from Density Functional Theory Molecular Dynamics Simulations Based on a Modified Chihara Formula.” <i>Physical Review E</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevE.107.065207\">https://doi.org/10.1103/PhysRevE.107.065207</a>.","mla":"Schörner, Maximilian, et al. “X-Ray Thomson Scattering Spectra from Density Functional Theory Molecular Dynamics Simulations Based on a Modified Chihara Formula.” <i>Physical Review E</i>, vol. 107, no. 6, 065207, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevE.107.065207\">10.1103/PhysRevE.107.065207</a>.","ama":"Schörner M, Bethkenhagen M, Döppner T, et al. X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula. <i>Physical Review E</i>. 2023;107(6). doi:<a href=\"https://doi.org/10.1103/PhysRevE.107.065207\">10.1103/PhysRevE.107.065207</a>","short":"M. Schörner, M. Bethkenhagen, T. Döppner, D. Kraus, L.B. Fletcher, S.H. Glenzer, R. Redmer, Physical Review E 107 (2023)."},"isi":1,"article_processing_charge":"No","quality_controlled":"1","publication_status":"published","language":[{"iso":"eng"}],"month":"06","title":"X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula","supplementarymaterial":"no","issue":"6","oa_version":"Preprint","oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"issn":["2470-0045"],"eissn":["2470-0053"]},"pmid":1,"researchdata_availability":"no","type":"journal_article","volume":107,"arxiv":1,"scopus_import":"1","article_type":"original","date_created":"2023-07-16T22:01:10Z","doi":"10.1103/PhysRevE.107.065207"},{"year":"2023","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.8398094"}],"publisher":"Zenodo","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Data underlying the publication \"A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals\" (DOI https://doi.org/10.1063/5.0173341)."}],"citation":{"ama":"Cheng B. BingqingCheng/solubility: V1.0. 2023. doi:<a href=\"https://doi.org/10.5281/ZENODO.8398094\">10.5281/ZENODO.8398094</a>","short":"B. Cheng, (2023).","apa":"Cheng, B. (2023). BingqingCheng/solubility: V1.0. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.8398094\">https://doi.org/10.5281/ZENODO.8398094</a>","ieee":"B. Cheng, “BingqingCheng/solubility: V1.0.” Zenodo, 2023.","ista":"Cheng B. 2023. BingqingCheng/solubility: V1.0, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.8398094\">10.5281/ZENODO.8398094</a>.","chicago":"Cheng, Bingqing. “BingqingCheng/Solubility: V1.0.” Zenodo, 2023. <a href=\"https://doi.org/10.5281/ZENODO.8398094\">https://doi.org/10.5281/ZENODO.8398094</a>.","mla":"Cheng, Bingqing. <i>BingqingCheng/Solubility: V1.0</i>. Zenodo, 2023, doi:<a href=\"https://doi.org/10.5281/ZENODO.8398094\">10.5281/ZENODO.8398094</a>."},"author":[{"full_name":"Cheng, Bingqing","first_name":"Bingqing","last_name":"Cheng","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"}],"has_accepted_license":"1","related_material":{"record":[{"id":"14603","status":"public","relation":"used_in_publication"}]},"oa":1,"_id":"14619","oa_version":"Published Version","month":"10","title":"BingqingCheng/solubility: V1.0","corr_author":"1","department":[{"_id":"BiCh"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.5281/ZENODO.8398094","day":"02","date_published":"2023-10-02T00:00:00Z","date_created":"2023-11-28T08:32:18Z","date_updated":"2026-08-07T11:07:45Z","ddc":["530"],"status":"public","type":"research_data_reference"},{"publisher":"American Chemical Society","abstract":[{"lang":"eng","text":"Physical catalysts often have multiple sites where reactions can take place. One prominent example is single-atom alloys, where the reactive dopant atoms can preferentially locate in the bulk or at different sites on the surface of the nanoparticle. However, ab initio modeling of catalysts usually only considers one site of the catalyst, neglecting the effects of multiple sites. Here, nanoparticles of copper doped with single-atom rhodium or palladium are modeled for the dehydrogenation of propane. Single-atom alloy nanoparticles are simulated at 400–600 K, using machine learning potentials trained on density functional theory calculations, and then the occupation of different single-atom active sites is identified using a similarity kernel. Further, the turnover frequency for all possible sites is calculated for propane dehydrogenation to propene through microkinetic modeling using density functional theory calculations. The total turnover frequencies of the whole nanoparticle are then described from both the population and the individual turnover frequency of each site. Under operating conditions, rhodium as a dopant is found to almost exclusively occupy (111) surface sites while palladium as a dopant occupies a greater variety of facets. Undercoordinated dopant surface sites are found to tend to be more reactive for propane dehydrogenation compared to the (111) surface. It is found that considering the dynamics of the single-atom alloy nanoparticle has a profound effect on the calculated catalytic activity of single-atom alloys by several orders of magnitude."}],"author":[{"full_name":"Bunting, Rhys","first_name":"Rhys","last_name":"Bunting","orcid":"0000-0001-6928-074X","id":"91deeae8-1207-11ec-b130-c194ad5b50c6"},{"first_name":"Felix","full_name":"Wodaczek, Felix","id":"8b4b6a9f-32b0-11ee-9fa8-bbe85e26258e","orcid":"0009-0000-1457-795X","last_name":"Wodaczek"},{"first_name":"Tina","full_name":"Torabi, Tina","last_name":"Torabi"},{"first_name":"Bingqing","full_name":"Cheng, Bingqing","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632"}],"year":"2023","page":"14894-14902","file_date_updated":"2023-07-12T10:22:04Z","corr_author":"1","file":[{"file_name":"2023_JACS_Bunting.pdf","relation":"main_file","success":1,"file_size":3155843,"date_updated":"2023-07-12T10:22:04Z","content_type":"application/pdf","access_level":"open_access","file_id":"13219","date_created":"2023-07-12T10:22:04Z","creator":"cchlebak","checksum":"e07d5323f9c0e5cbd1ad6453f29440ab"}],"acknowledgement":"B.C. acknowledges resources provided by the Cambridge Tier2 system operated by the University of Cambridge Research\r\nComputing Service funded by EPSRC Tier-2 capital grant EP/\r\nP020259/1.","_id":"13216","publication":"Journal of the American Chemical Society","department":[{"_id":"MaIb"},{"_id":"BiCh"}],"das_tickbox":"0","external_id":{"pmid":["37390457"],"isi":["001020623900001"]},"date_updated":"2026-08-07T11:37:26Z","ddc":["540"],"status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"intvolume":"       145","day":"30","date_published":"2023-06-30T00:00:00Z","article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","isi":1,"citation":{"ama":"Bunting R, Wodaczek F, Torabi T, Cheng B. Reactivity of single-atom alloy nanoparticles: Modeling the dehydrogenation of propane. <i>Journal of the American Chemical Society</i>. 2023;145(27):14894-14902. doi:<a href=\"https://doi.org/10.1021/jacs.3c04030\">10.1021/jacs.3c04030</a>","short":"R. Bunting, F. Wodaczek, T. Torabi, B. Cheng, Journal of the American Chemical Society 145 (2023) 14894–14902.","ista":"Bunting R, Wodaczek F, Torabi T, Cheng B. 2023. Reactivity of single-atom alloy nanoparticles: Modeling the dehydrogenation of propane. Journal of the American Chemical Society. 145(27), 14894–14902.","apa":"Bunting, R., Wodaczek, F., Torabi, T., &#38; Cheng, B. (2023). Reactivity of single-atom alloy nanoparticles: Modeling the dehydrogenation of propane. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/jacs.3c04030\">https://doi.org/10.1021/jacs.3c04030</a>","ieee":"R. Bunting, F. Wodaczek, T. Torabi, and B. Cheng, “Reactivity of single-atom alloy nanoparticles: Modeling the dehydrogenation of propane,” <i>Journal of the American Chemical Society</i>, vol. 145, no. 27. American Chemical Society, pp. 14894–14902, 2023.","mla":"Bunting, Rhys, et al. “Reactivity of Single-Atom Alloy Nanoparticles: Modeling the Dehydrogenation of Propane.” <i>Journal of the American Chemical Society</i>, vol. 145, no. 27, American Chemical Society, 2023, pp. 14894–902, doi:<a href=\"https://doi.org/10.1021/jacs.3c04030\">10.1021/jacs.3c04030</a>.","chicago":"Bunting, Rhys, Felix Wodaczek, Tina Torabi, and Bingqing Cheng. “Reactivity of Single-Atom Alloy Nanoparticles: Modeling the Dehydrogenation of Propane.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/jacs.3c04030\">https://doi.org/10.1021/jacs.3c04030</a>."},"publication_status":"published","month":"06","supplementarymaterial":"yes","title":"Reactivity of single-atom alloy nanoparticles: Modeling the dehydrogenation of propane","language":[{"iso":"eng"}],"has_accepted_license":"1","oa":1,"oa_version":"Published Version","issue":"27","publication_identifier":{"issn":["0002-7863"],"eissn":["1520-5126"]},"pmid":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","researchdata_availability":"no","article_type":"original","scopus_import":"1","volume":145,"type":"journal_article","doi":"10.1021/jacs.3c04030","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"date_created":"2023-07-12T09:16:40Z"},{"title":"Land surface modeling in the himalayas: on the importance of evaporative fluxes for the water balance of a high‐elevation catchment","month":"10","language":[{"iso":"eng"}],"oa_version":"Published Version","issue":"10","oa":1,"quality_controlled":"1","article_processing_charge":"No","citation":{"short":"P. Buri, S. Fatichi, T.E. Shaw, E.S. Miles, M.J. McCarthy, C.L. Fyffe, S. Fugger, S. Ren, M. Kneib, A. Jouberton, J. Steiner, K. Fujita, F. Pellicciotti, Water Resources Research 59 (2023).","ama":"Buri P, Fatichi S, Shaw TE, et al. Land surface modeling in the himalayas: on the importance of evaporative fluxes for the water balance of a high‐elevation catchment. <i>Water Resources Research</i>. 2023;59(10). doi:<a href=\"https://doi.org/10.1029/2022wr033841\">10.1029/2022wr033841</a>","mla":"Buri, Pascal, et al. “Land Surface Modeling in the Himalayas: On the Importance of Evaporative Fluxes for the Water Balance of a High‐elevation Catchment.” <i>Water Resources Research</i>, vol. 59, no. 10, e2022WR033841, American Geophysical Union, 2023, doi:<a href=\"https://doi.org/10.1029/2022wr033841\">10.1029/2022wr033841</a>.","chicago":"Buri, Pascal, Simone Fatichi, Thomas E. Shaw, Evan S. Miles, Michael J. McCarthy, Catriona L. Fyffe, Stefan Fugger, et al. “Land Surface Modeling in the Himalayas: On the Importance of Evaporative Fluxes for the Water Balance of a High‐elevation Catchment.” <i>Water Resources Research</i>. American Geophysical Union, 2023. <a href=\"https://doi.org/10.1029/2022wr033841\">https://doi.org/10.1029/2022wr033841</a>.","ista":"Buri P, Fatichi S, Shaw TE, Miles ES, McCarthy MJ, Fyffe CL, Fugger S, Ren S, Kneib M, Jouberton A, Steiner J, Fujita K, Pellicciotti F. 2023. Land surface modeling in the himalayas: on the importance of evaporative fluxes for the water balance of a high‐elevation catchment. Water Resources Research. 59(10), e2022WR033841.","apa":"Buri, P., Fatichi, S., Shaw, T. E., Miles, E. S., McCarthy, M. J., Fyffe, C. L., … Pellicciotti, F. (2023). Land surface modeling in the himalayas: on the importance of evaporative fluxes for the water balance of a high‐elevation catchment. <i>Water Resources Research</i>. American Geophysical Union. <a href=\"https://doi.org/10.1029/2022wr033841\">https://doi.org/10.1029/2022wr033841</a>","ieee":"P. Buri <i>et al.</i>, “Land surface modeling in the himalayas: on the importance of evaporative fluxes for the water balance of a high‐elevation catchment,” <i>Water Resources Research</i>, vol. 59, no. 10. American Geophysical Union, 2023."},"publication_status":"published","volume":59,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","scopus_import":"1","article_type":"original","type":"journal_article","doi":"10.1029/2022wr033841","date_created":"2026-07-27T12:30:24Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_identifier":{"eissn":["1944-7973"],"issn":["0043-1397"]},"OA_place":"publisher","article_number":"e2022WR033841","extern":"1","_id":"22505","publisher":"American Geophysical Union","author":[{"last_name":"Buri","full_name":"Buri, Pascal","first_name":"Pascal"},{"first_name":"Simone","full_name":"Fatichi, Simone","id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6","last_name":"Fatichi"},{"first_name":"Thomas E.","full_name":"Shaw, Thomas E.","last_name":"Shaw"},{"last_name":"Miles","full_name":"Miles, Evan S.","first_name":"Evan S."},{"full_name":"McCarthy, Michael J.","first_name":"Michael J.","last_name":"McCarthy"},{"last_name":"Fyffe","first_name":"Catriona L.","full_name":"Fyffe, Catriona L."},{"last_name":"Fugger","first_name":"Stefan","full_name":"Fugger, Stefan"},{"full_name":"Ren, Shaoting","first_name":"Shaoting","last_name":"Ren"},{"last_name":"Kneib","first_name":"Marin","full_name":"Kneib, Marin"},{"last_name":"Jouberton","full_name":"Jouberton, Achille","first_name":"Achille"},{"full_name":"Steiner, Jakob","first_name":"Jakob","last_name":"Steiner"},{"last_name":"Fujita","full_name":"Fujita, Koji","first_name":"Koji"},{"full_name":"Pellicciotti, Francesca","first_name":"Francesca","last_name":"Pellicciotti"}],"abstract":[{"lang":"eng","text":"High Mountain Asia (HMA) is among the most vulnerable water towers globally and yet future projections of water availability in and from its high-mountain catchments remain uncertain, as their hydrologic response to ongoing environmental changes is complex. Mechanistic modeling approaches incorporating cryospheric, hydrological, and vegetation processes in high spatial, temporal, and physical detail have never been applied for high-elevation catchments of HMA. We use a land surface model at high spatial and temporal resolution (100 m and hourly) to simulate the coupled dynamics of energy, water, and vegetation for the 350 km2 Langtang catchment (Nepal). We compare our model outputs for one hydrological year against a large set of observations to gain insight into the partitioning of the water balance at the subseasonal scale and across elevation bands. During the simulated hydrological year, we find that evapotranspiration is a key component of the total water balance, as it causes about the equivalent of 20% of all the available precipitation or 154% of the water production from glacier melt in the basin to return directly to the atmosphere. The depletion of the cryospheric water budget is dominated by snow melt, but at high elevations is primarily dictated by snow and ice sublimation. Snow sublimation is the dominant vapor flux (49%) at the catchment scale, accounting for the equivalent of 11% of snowfall, 17% of snowmelt, and 75% of ice melt, respectively. We conclude that simulations should consider sublimation and other evaporative fluxes explicitly, as otherwise water balance estimates can be ill-quantified."}],"year":"2023","main_file_link":[{"url":"https://doi.org/10.1029/2022WR033841","open_access":"1"}],"OA_type":"hybrid","date_updated":"2026-08-11T05:45:52Z","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"status":"public","intvolume":"        59","day":"01","date_published":"2023-10-01T00:00:00Z","das_tickbox":"1","publication":"Water Resources Research"},{"article_type":"original","scopus_import":"1","volume":11,"type":"journal_article","doi":"10.1109/access.2023.3237897","keyword":["General Engineering","General Materials Science","General Computer Science","Electrical and Electronic Engineering"],"date_created":"2023-08-09T12:09:57Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2169-3536"]},"title":"Practical limitations of Ethereum’s layer-2","month":"08","language":[{"iso":"eng"}],"has_accepted_license":"1","oa":1,"oa_version":"Published Version","quality_controlled":"1","article_processing_charge":"Yes","citation":{"ieee":"R. Neiheiser, G. Inacio, L. Rech, C. Montez, M. Matos, and L. Rodrigues, “Practical limitations of Ethereum’s layer-2,” <i>IEEE Access</i>, vol. 11. IEEE, pp. 8651–8662, 2023.","apa":"Neiheiser, R., Inacio, G., Rech, L., Montez, C., Matos, M., &#38; Rodrigues, L. (2023). Practical limitations of Ethereum’s layer-2. <i>IEEE Access</i>. IEEE. <a href=\"https://doi.org/10.1109/access.2023.3237897\">https://doi.org/10.1109/access.2023.3237897</a>","ista":"Neiheiser R, Inacio G, Rech L, Montez C, Matos M, Rodrigues L. 2023. Practical limitations of Ethereum’s layer-2. IEEE Access. 11, 8651–8662.","chicago":"Neiheiser, Ray, Gustavo Inacio, Luciana Rech, Carlos Montez, Miguel Matos, and Luis Rodrigues. “Practical Limitations of Ethereum’s Layer-2.” <i>IEEE Access</i>. IEEE, 2023. <a href=\"https://doi.org/10.1109/access.2023.3237897\">https://doi.org/10.1109/access.2023.3237897</a>.","mla":"Neiheiser, Ray, et al. “Practical Limitations of Ethereum’s Layer-2.” <i>IEEE Access</i>, vol. 11, IEEE, 2023, pp. 8651–62, doi:<a href=\"https://doi.org/10.1109/access.2023.3237897\">10.1109/access.2023.3237897</a>.","ama":"Neiheiser R, Inacio G, Rech L, Montez C, Matos M, Rodrigues L. Practical limitations of Ethereum’s layer-2. <i>IEEE Access</i>. 2023;11:8651-8662. doi:<a href=\"https://doi.org/10.1109/access.2023.3237897\">10.1109/access.2023.3237897</a>","short":"R. Neiheiser, G. Inacio, L. Rech, C. Montez, M. Matos, L. Rodrigues, IEEE Access 11 (2023) 8651–8662."},"isi":1,"publication_status":"published","date_updated":"2026-08-12T06:33:48Z","external_id":{"isi":["000927831000001"]},"ddc":["000"],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"status":"public","intvolume":"        11","day":"01","date_published":"2023-08-01T00:00:00Z","department":[{"_id":"ElKo"}],"publication":"IEEE Access","corr_author":"1","file":[{"file_id":"14166","date_created":"2023-08-22T06:37:48Z","creator":"dernst","checksum":"4b80b0ff212edf7e5842fbdd53784432","file_size":1289285,"date_updated":"2023-08-22T06:37:48Z","content_type":"application/pdf","access_level":"open_access","relation":"main_file","success":1,"file_name":"2023_IEEEAccess_Neiheiser.pdf"}],"acknowledgement":"This work was supported in part by the Coordenação de Aperfeiçoamento de Pessoal de Nivel Superior (CAPES)—Brazil (CAPES), in part by the Fundação para a Ciência e Tecnologia (FCT) under Project UIDB/50021/2020 and Grant 2020.05270.BD, in part by the Project COSMOS (via the Orçamento de Estado (OE) with ref. PTDC/EEI-COM/29271/2017 and via the ‘‘Programa Operacional Regional de Lisboa na sua componente Fundo Europeu de Desenvolvimento Regional (FEDER)’’ with ref. Lisboa-01-0145-FEDER-029271), and in part by the project Angainor with reference LISBOA-01-0145-FEDER-031456 as well as supported by Meta Platforms for the project key Transparency at Scale.","_id":"13988","publisher":"IEEE","abstract":[{"lang":"eng","text":"Most permissionless blockchains inherently suffer from throughput limitations. Layer-2 systems, such as side-chains or Rollups, have been proposed as a possible strategy to overcome this limitation. Layer-2 systems interact with the main-chain in two ways. First, users can move funds from/to the main-chain to/from the layer-2. Second, layer-2 systems periodically synchronize with the main-chain to keep some form of log of their activity on the main-chain - this log is key for security. Due to this interaction with the main-chain, which is necessary and recurrent, layer-2 systems impose some load on the main-chain. The impact of such load on the main-chain has been, so far, poorly understood. In addition to that, layer-2 approaches typically sacrifice decentralization and security in favor of higher throughput. This paper presents an experimental study that analyzes the current state of Ethereum layer-2 projects. Our goal is to assess the load they impose on Ethereum and to understand their scalability potential in the long-run. Our analysis shows that the impact of any given layer-2 on the main-chain is the result of both technical aspects (how state is logged on the main-chain) and user behavior (how often users decide to transfer funds between the layer-2 and the main-chain). Based on our observations, we infer that without efficient mechanisms that allow users to transfer funds in a secure and fast manner directly from one layer-2 project to another, current layer-2 systems will not be able to scale Ethereum effectively, regardless of their technical solutions. Furthermore, from our results, we conclude that the layer-2 systems that offer similar security guarantees as Ethereum have limited scalability potential, while approaches that offer better performance, sacrifice security and lead to an increase in centralization which runs against the end-goals of permissionless blockchains."}],"author":[{"full_name":"Neiheiser, Ray","first_name":"Ray","last_name":"Neiheiser","orcid":"0000-0001-7227-8309","id":"f09651b9-fec0-11ec-b5d8-934aff0e52a4"},{"last_name":"Inacio","full_name":"Inacio, Gustavo","first_name":"Gustavo"},{"last_name":"Rech","first_name":"Luciana","full_name":"Rech, Luciana"},{"first_name":"Carlos","full_name":"Montez, Carlos","last_name":"Montez"},{"last_name":"Matos","first_name":"Miguel","full_name":"Matos, Miguel"},{"first_name":"Luis","full_name":"Rodrigues, Luis","last_name":"Rodrigues"}],"page":"8651-8662","year":"2023","file_date_updated":"2023-08-22T06:37:48Z"},{"status":"public","ddc":["000"],"date_updated":"2026-08-12T06:34:07Z","date_published":"2023-05-23T00:00:00Z","day":"23","department":[{"_id":"GradSch"},{"_id":"DaAl"},{"_id":"ChLa"}],"OA_place":"publisher","file":[{"file_name":"PhD_Thesis_Alexandra_Peste_final.pdf","success":1,"relation":"main_file","content_type":"application/pdf","access_level":"open_access","date_updated":"2023-05-24T16:11:16Z","file_size":2152072,"creator":"epeste","date_created":"2023-05-24T16:11:16Z","checksum":"6b3354968403cb9d48cc5a83611fb571","file_id":"13087"},{"relation":"source_file","file_name":"PhD_Thesis_APeste.zip","checksum":"8d0df94bbcf4db72c991f22503b3fd60","date_created":"2023-05-24T16:12:59Z","creator":"epeste","file_id":"13088","access_level":"closed","content_type":"application/zip","date_updated":"2023-05-24T16:12:59Z","file_size":1658293}],"degree_awarded":"PhD","corr_author":"1","_id":"13074","author":[{"first_name":"Elena-Alexandra","full_name":"Peste, Elena-Alexandra","id":"32D78294-F248-11E8-B48F-1D18A9856A87","last_name":"Peste"}],"abstract":[{"lang":"eng","text":"Deep learning has become an integral part of a large number of important applications, and many of the recent breakthroughs have been enabled by the ability to train very large models, capable to capture complex patterns and relationships from the data. At the same time, the massive sizes of modern deep learning models have made their deployment to smaller devices more challenging; this is particularly important, as in many applications the users rely on accurate deep learning predictions, but they only have access to devices with limited memory and compute power. One solution to this problem is to prune neural networks, by setting as many of their parameters as possible to zero, to obtain accurate sparse models with lower memory footprint. Despite the great research progress in obtaining sparse models that preserve accuracy, while satisfying memory and computational constraints, there are still many challenges associated with efficiently training sparse models, as well as understanding their generalization properties.\r\n\r\nThe focus of this thesis is to investigate how the training process of sparse models can be made more efficient, and to understand the differences between sparse and dense models in terms of how well they can generalize to changes in the data distribution. We first study a method for co-training sparse and dense models, at a lower cost compared to regular training. With our method we can obtain very accurate sparse networks, and dense models that can recover the baseline accuracy. Furthermore, we are able to more easily analyze the differences, at prediction level, between the sparse-dense model pairs. Next, we investigate the generalization properties of sparse neural networks in more detail, by studying how well different sparse models trained on a larger task can adapt to smaller, more specialized tasks, in a transfer learning scenario. Our analysis across multiple pruning methods and sparsity levels reveals that sparse models provide features that can transfer similarly to or better than the dense baseline. However, the choice of the pruning method plays an important role, and can influence the results when the features are fixed (linear finetuning), or when they are allowed to adapt to the new task (full finetuning). Using sparse models with fixed masks for finetuning on new tasks has an important practical advantage, as it enables training neural networks on smaller devices. However, one drawback of current pruning methods is that the entire training cycle has to be repeated to obtain the initial sparse model, for every sparsity target; in consequence, the entire training process is costly and also multiple models need to be stored. In the last part of the thesis we propose a method that can train accurate dense models that are compressible in a single step, to multiple sparsity levels, without additional finetuning. Our method results in sparse models that can be competitive with existing pruning methods, and which can also successfully generalize to new tasks."}],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2023-05-24T16:12:59Z","year":"2023","page":"147","type":"dissertation","date_created":"2023-05-23T17:07:53Z","doi":"10.15479/at:ista:13074","acknowledged_ssus":[{"_id":"ScienComp"}],"publication_identifier":{"issn":["2663-337X"]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","language":[{"iso":"eng"}],"title":"Efficiency and generalization of sparse neural networks","month":"05","ec_funded":1,"oa_version":"Published Version","oa":1,"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"13053"},{"id":"11458","status":"public","relation":"part_of_dissertation"},{"id":"12299","status":"public","relation":"part_of_dissertation"}]},"alternative_title":["ISTA Thesis"],"has_accepted_license":"1","project":[{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385"},{"grant_number":"805223","call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425","name":"Elastic Coordination for Scalable Machine Learning"}],"citation":{"ama":"Krumes A. Efficiency and generalization of sparse neural networks. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:13074\">10.15479/at:ista:13074</a>","short":"A. Krumes, Efficiency and Generalization of Sparse Neural Networks, Institute of Science and Technology Austria, 2023.","ista":"Krumes A. 2023. Efficiency and generalization of sparse neural networks. Institute of Science and Technology Austria.","apa":"Krumes, A. (2023). <i>Efficiency and generalization of sparse neural networks</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:13074\">https://doi.org/10.15479/at:ista:13074</a>","ieee":"A. Krumes, “Efficiency and generalization of sparse neural networks,” Institute of Science and Technology Austria, 2023.","mla":"Krumes, Alexandra. <i>Efficiency and Generalization of Sparse Neural Networks</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:13074\">10.15479/at:ista:13074</a>.","chicago":"Krumes, Alexandra. “Efficiency and Generalization of Sparse Neural Networks.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:13074\">https://doi.org/10.15479/at:ista:13074</a>."},"article_processing_charge":"No","supervisor":[{"last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","full_name":"Lampert, Christoph"},{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh"}],"publication_status":"published"},{"file_date_updated":"2023-02-14T07:58:26Z","year":"2023","abstract":[{"text":"The limited exchange between human communities is a key factor in preventing the spread of COVID-19. This paper introduces a digital framework that combines an integration of real mobility data at the country scale with a series of modeling techniques and visual capabilities that highlight mobility patterns before and during the pandemic. The findings not only significantly exhibit mobility trends and different degrees of similarities at regional and local levels but also provide potential insight into the emergence of a pandemic on human behavior patterns and their likely socio-economic impacts.","lang":"eng"}],"author":[{"first_name":"Mohammad","full_name":"Forghani, Mohammad","last_name":"Forghani"},{"first_name":"Christophe","full_name":"Claramunt, Christophe","last_name":"Claramunt"},{"first_name":"Farid","full_name":"Karimipour, Farid","last_name":"Karimipour","id":"2A2BCDC4-CF62-11E9-BE5E-3B1EE6697425","orcid":"0000-0001-6746-4174"},{"full_name":"Heiler, Georg","first_name":"Georg","last_name":"Heiler"}],"publisher":"IEEE","_id":"12548","article_number":"00093","file":[{"file_name":"Visual Analysis_Mobility_COVID19 - SocDM2022.pdf","relation":"main_file","success":1,"date_updated":"2023-02-14T07:58:26Z","file_size":1183339,"content_type":"application/pdf","access_level":"open_access","file_id":"12549","creator":"fkarimip","date_created":"2023-02-14T07:58:26Z","checksum":"c253bee25e6dfe484f96662daa119cb6"}],"conference":{"name":"ICDMW: Conference on Data Mining Workshops","start_date":"2022-11-28","location":"Orlando, FL, United States","end_date":"2022-12-01"},"publication":"2022 IEEE International Conference on Data Mining Workshops","department":[{"_id":"HeEd"}],"date_published":"2023-02-08T00:00:00Z","day":"08","ddc":["600"],"status":"public","date_updated":"2026-08-12T06:34:58Z","external_id":{"isi":["000971492200145"]},"publication_status":"published","citation":{"mla":"Forghani, Mohammad, et al. “Visual Analytics of Mobility Network Changes Observed Using Mobile Phone Data during COVID-19 Pandemic.” <i>2022 IEEE International Conference on Data Mining Workshops</i>, 00093, IEEE, 2023, doi:<a href=\"https://doi.org/10.1109/icdmw58026.2022.00093\">10.1109/icdmw58026.2022.00093</a>.","chicago":"Forghani, Mohammad, Christophe Claramunt, Farid Karimipour, and Georg Heiler. “Visual Analytics of Mobility Network Changes Observed Using Mobile Phone Data during COVID-19 Pandemic.” In <i>2022 IEEE International Conference on Data Mining Workshops</i>. IEEE, 2023. <a href=\"https://doi.org/10.1109/icdmw58026.2022.00093\">https://doi.org/10.1109/icdmw58026.2022.00093</a>.","ieee":"M. Forghani, C. Claramunt, F. Karimipour, and G. Heiler, “Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic,” in <i>2022 IEEE International Conference on Data Mining Workshops</i>, Orlando, FL, United States, 2023.","apa":"Forghani, M., Claramunt, C., Karimipour, F., &#38; Heiler, G. (2023). Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic. In <i>2022 IEEE International Conference on Data Mining Workshops</i>. Orlando, FL, United States: IEEE. <a href=\"https://doi.org/10.1109/icdmw58026.2022.00093\">https://doi.org/10.1109/icdmw58026.2022.00093</a>","ista":"Forghani M, Claramunt C, Karimipour F, Heiler G. 2023. Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic. 2022 IEEE International Conference on Data Mining Workshops. ICDMW: Conference on Data Mining Workshops, 00093.","short":"M. Forghani, C. Claramunt, F. Karimipour, G. Heiler, in:, 2022 IEEE International Conference on Data Mining Workshops, IEEE, 2023.","ama":"Forghani M, Claramunt C, Karimipour F, Heiler G. Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic. In: <i>2022 IEEE International Conference on Data Mining Workshops</i>. IEEE; 2023. doi:<a href=\"https://doi.org/10.1109/icdmw58026.2022.00093\">10.1109/icdmw58026.2022.00093</a>"},"isi":1,"quality_controlled":"1","article_processing_charge":"No","oa":1,"oa_version":"Submitted Version","has_accepted_license":"1","language":[{"iso":"eng"}],"month":"02","title":"Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic","publication_identifier":{"eisbn":["9798350346091"],"eissn":["2375-9259"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-02-14T07:56:21Z","doi":"10.1109/icdmw58026.2022.00093","type":"conference","scopus_import":"1"},{"publication_status":"published","quality_controlled":"1","article_processing_charge":"No","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"isi":1,"citation":{"mla":"Xu, Yizhou, et al. “Approximate Message Passing for Multi-Layer Estimation in Rotationally Invariant Models.” <i>2023 IEEE Information Theory Workshop</i>, IEEE, 2023, pp. 294–98, doi:<a href=\"https://doi.org/10.1109/ITW55543.2023.10160238\">10.1109/ITW55543.2023.10160238</a>.","chicago":"Xu, Yizhou, Tian Qi Hou, Shan Suo Liang, and Marco Mondelli. “Approximate Message Passing for Multi-Layer Estimation in Rotationally Invariant Models.” In <i>2023 IEEE Information Theory Workshop</i>, 294–98. IEEE, 2023. <a href=\"https://doi.org/10.1109/ITW55543.2023.10160238\">https://doi.org/10.1109/ITW55543.2023.10160238</a>.","ista":"Xu Y, Hou TQ, Liang SS, Mondelli M. 2023. Approximate message passing for multi-layer estimation in rotationally invariant models. 2023 IEEE Information Theory Workshop. ITW: Information Theory Workshop, 294–298.","apa":"Xu, Y., Hou, T. Q., Liang, S. S., &#38; Mondelli, M. (2023). Approximate message passing for multi-layer estimation in rotationally invariant models. In <i>2023 IEEE Information Theory Workshop</i> (pp. 294–298). Saint-Malo, France: IEEE. <a href=\"https://doi.org/10.1109/ITW55543.2023.10160238\">https://doi.org/10.1109/ITW55543.2023.10160238</a>","ieee":"Y. Xu, T. Q. Hou, S. S. Liang, and M. Mondelli, “Approximate message passing for multi-layer estimation in rotationally invariant models,” in <i>2023 IEEE Information Theory Workshop</i>, Saint-Malo, France, 2023, pp. 294–298.","short":"Y. Xu, T.Q. Hou, S.S. Liang, M. Mondelli, in:, 2023 IEEE Information Theory Workshop, IEEE, 2023, pp. 294–298.","ama":"Xu Y, Hou TQ, Liang SS, Mondelli M. Approximate message passing for multi-layer estimation in rotationally invariant models. In: <i>2023 IEEE Information Theory Workshop</i>. IEEE; 2023:294-298. doi:<a href=\"https://doi.org/10.1109/ITW55543.2023.10160238\">10.1109/ITW55543.2023.10160238</a>"},"oa_version":"Preprint","oa":1,"month":"05","title":"Approximate message passing for multi-layer estimation in rotationally invariant models","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9798350301496"],"eissn":["2475-4218"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1109/ITW55543.2023.10160238","date_created":"2023-07-30T22:01:04Z","arxiv":1,"scopus_import":"1","type":"conference","page":"294-298","year":"2023","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2212.01572"}],"publisher":"IEEE","author":[{"last_name":"Xu","full_name":"Xu, Yizhou","first_name":"Yizhou"},{"full_name":"Hou, Tian Qi","first_name":"Tian Qi","last_name":"Hou"},{"first_name":"Shan Suo","full_name":"Liang, Shan Suo","last_name":"Liang"},{"id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","last_name":"Mondelli","first_name":"Marco","full_name":"Mondelli, Marco"}],"abstract":[{"text":"We consider the problem of reconstructing the signal and the hidden variables from observations coming from a multi-layer network with rotationally invariant weight matrices. The multi-layer structure models inference from deep generative priors, and the rotational invariance imposed on the weights generalizes the i.i.d. Gaussian assumption by allowing for a complex correlation structure, which is typical in applications. In this work, we present a new class of approximate message passing (AMP) algorithms and give a state evolution recursion which precisely characterizes their performance in the large system limit. In contrast with the existing multi-layer VAMP (ML-VAMP) approach, our proposed AMP – dubbed multilayer rotationally invariant generalized AMP (ML-RI-GAMP) – provides a natural generalization beyond Gaussian designs, in the sense that it recovers the existing Gaussian AMP as a special case. Furthermore, ML-RI-GAMP exhibits a significantly lower complexity than ML-VAMP, as the computationally intensive singular value decomposition is replaced by an estimation of the moments of the design matrices. Finally, our numerical results show that this complexity gain comes at little to no cost in the performance of the algorithm.","lang":"eng"}],"_id":"13321","corr_author":"1","acknowledgement":"Marco Mondelli was partially supported by the 2019 Lopez-Loreta prize.","conference":{"name":"ITW: Information Theory Workshop","start_date":"2023-04-23","end_date":"2023-04-28","location":"Saint-Malo, France"},"department":[{"_id":"MaMo"}],"publication":"2023 IEEE Information Theory Workshop","day":"01","date_published":"2023-05-01T00:00:00Z","date_updated":"2026-08-12T06:38:51Z","external_id":{"arxiv":["2212.01572"],"isi":["001031733100053"]},"status":"public"},{"ddc":["000"],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"status":"public","external_id":{"isi":["000936534100012"],"arxiv":["2204.07373"]},"date_updated":"2026-08-12T06:40:15Z","date_published":"2023-03-01T00:00:00Z","intvolume":"         8","day":"01","publication":"IEEE Robotics and Automation Letters","department":[{"_id":"ToHe"}],"file":[{"file_name":"2023_IEEERobAutLetters_Lechner.pdf","success":1,"relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_size":944052,"date_updated":"2023-03-07T12:22:23Z","creator":"cchlebak","date_created":"2023-03-07T12:22:23Z","checksum":"5a75dcd326ea66685de2b1aaec259e85","file_id":"12714"}],"acknowledgement":"We thank Christoph Lampert for inspiring this work. The\r\nviews and conclusions contained in this document are those of\r\nthe authors and should not be interpreted as representing the\r\nofficial policies, either expressed or implied, of the United States\r\nAir Force or the U.S. Government. The U.S. Government is\r\nauthorized to reproduce and distribute reprints for Government\r\npurposes notwithstanding any copyright notation herein.","_id":"12704","abstract":[{"lang":"eng","text":"Adversarial training (i.e., training on adversarially perturbed input data) is a well-studied method for making neural networks robust to potential adversarial attacks during inference. However, the improved robustness does not come for free but rather is accompanied by a decrease in overall model accuracy and performance. Recent work has shown that, in practical robot learning applications, the effects of adversarial training do not pose a fair trade-off but inflict a net loss when measured in holistic robot performance. This work revisits the robustness-accuracy trade-off in robot learning by systematically analyzing if recent advances in robust training methods and theory in conjunction with adversarial robot learning, are capable of making adversarial training suitable for real-world robot applications. We evaluate three different robot learning tasks ranging from autonomous driving in a high-fidelity environment amenable to sim-to-real deployment to mobile robot navigation and gesture recognition. Our results demonstrate that, while these techniques make incremental improvements on the trade-off on a relative scale, the negative impact on the nominal accuracy caused by adversarial training still outweighs the improved robustness by an order of magnitude. We conclude that although progress is happening, further advances in robust learning methods are necessary before they can benefit robot learning tasks in practice."}],"author":[{"full_name":"Lechner, Mathias","first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","last_name":"Lechner"},{"last_name":"Amini","full_name":"Amini, Alexander","first_name":"Alexander"},{"first_name":"Daniela","full_name":"Rus, Daniela","last_name":"Rus"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"}],"publisher":"IEEE","file_date_updated":"2023-03-07T12:22:23Z","year":"2023","page":"1595-1602","type":"journal_article","scopus_import":"1","article_type":"original","arxiv":1,"volume":8,"date_created":"2023-03-05T23:01:04Z","doi":"10.1109/LRA.2023.3240930","publication_identifier":{"eissn":["2377-3766"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"month":"03","title":"Revisiting the adversarial robustness-accuracy tradeoff in robot learning","oa":1,"issue":"3","oa_version":"Published Version","has_accepted_license":"1","related_material":{"record":[{"status":"public","id":"11366","relation":"earlier_version"}]},"citation":{"mla":"Lechner, Mathias, et al. “Revisiting the Adversarial Robustness-Accuracy Tradeoff in Robot Learning.” <i>IEEE Robotics and Automation Letters</i>, vol. 8, no. 3, IEEE, 2023, pp. 1595–602, doi:<a href=\"https://doi.org/10.1109/LRA.2023.3240930\">10.1109/LRA.2023.3240930</a>.","chicago":"Lechner, Mathias, Alexander Amini, Daniela Rus, and Thomas A Henzinger. “Revisiting the Adversarial Robustness-Accuracy Tradeoff in Robot Learning.” <i>IEEE Robotics and Automation Letters</i>. IEEE, 2023. <a href=\"https://doi.org/10.1109/LRA.2023.3240930\">https://doi.org/10.1109/LRA.2023.3240930</a>.","ista":"Lechner M, Amini A, Rus D, Henzinger TA. 2023. Revisiting the adversarial robustness-accuracy tradeoff in robot learning. IEEE Robotics and Automation Letters. 8(3), 1595–1602.","apa":"Lechner, M., Amini, A., Rus, D., &#38; Henzinger, T. A. (2023). Revisiting the adversarial robustness-accuracy tradeoff in robot learning. <i>IEEE Robotics and Automation Letters</i>. IEEE. <a href=\"https://doi.org/10.1109/LRA.2023.3240930\">https://doi.org/10.1109/LRA.2023.3240930</a>","ieee":"M. Lechner, A. Amini, D. Rus, and T. A. Henzinger, “Revisiting the adversarial robustness-accuracy tradeoff in robot learning,” <i>IEEE Robotics and Automation Letters</i>, vol. 8, no. 3. IEEE, pp. 1595–1602, 2023.","short":"M. Lechner, A. Amini, D. Rus, T.A. Henzinger, IEEE Robotics and Automation Letters 8 (2023) 1595–1602.","ama":"Lechner M, Amini A, Rus D, Henzinger TA. Revisiting the adversarial robustness-accuracy tradeoff in robot learning. <i>IEEE Robotics and Automation Letters</i>. 2023;8(3):1595-1602. doi:<a href=\"https://doi.org/10.1109/LRA.2023.3240930\">10.1109/LRA.2023.3240930</a>"},"isi":1,"article_processing_charge":"No","quality_controlled":"1","publication_status":"published"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"isbn":["9798350335873"],"issn":["1043-6871"]},"type":"conference","scopus_import":"1","volume":2023,"arxiv":1,"date_created":"2023-08-06T22:01:10Z","doi":"10.1109/LICS56636.2023.10175771","isi":1,"citation":{"short":"J. Kretinsky, T. Meggendorfer, M. Weininger, in:, 38th Annual ACM/IEEE Symposium on Logic in Computer Science, IEEE, 2023.","ama":"Kretinsky J, Meggendorfer T, Weininger M. Stopping criteria for value iteration on stochastic games with quantitative objectives. In: <i>38th Annual ACM/IEEE Symposium on Logic in Computer Science</i>. Vol 2023. IEEE; 2023. doi:<a href=\"https://doi.org/10.1109/LICS56636.2023.10175771\">10.1109/LICS56636.2023.10175771</a>","mla":"Kretinsky, Jan, et al. “Stopping Criteria for Value Iteration on Stochastic Games with Quantitative Objectives.” <i>38th Annual ACM/IEEE Symposium on Logic in Computer Science</i>, vol. 2023, IEEE, 2023, doi:<a href=\"https://doi.org/10.1109/LICS56636.2023.10175771\">10.1109/LICS56636.2023.10175771</a>.","chicago":"Kretinsky, Jan, Tobias Meggendorfer, and Maximilian Weininger. “Stopping Criteria for Value Iteration on Stochastic Games with Quantitative Objectives.” In <i>38th Annual ACM/IEEE Symposium on Logic in Computer Science</i>, Vol. 2023. IEEE, 2023. <a href=\"https://doi.org/10.1109/LICS56636.2023.10175771\">https://doi.org/10.1109/LICS56636.2023.10175771</a>.","ista":"Kretinsky J, Meggendorfer T, Weininger M. 2023. Stopping criteria for value iteration on stochastic games with quantitative objectives. 38th Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Logic in Computer Science vol. 2023.","ieee":"J. Kretinsky, T. Meggendorfer, and M. Weininger, “Stopping criteria for value iteration on stochastic games with quantitative objectives,” in <i>38th Annual ACM/IEEE Symposium on Logic in Computer Science</i>, Boston, MA, United States, 2023, vol. 2023.","apa":"Kretinsky, J., Meggendorfer, T., &#38; Weininger, M. (2023). Stopping criteria for value iteration on stochastic games with quantitative objectives. In <i>38th Annual ACM/IEEE Symposium on Logic in Computer Science</i> (Vol. 2023). Boston, MA, United States: IEEE. <a href=\"https://doi.org/10.1109/LICS56636.2023.10175771\">https://doi.org/10.1109/LICS56636.2023.10175771</a>"},"quality_controlled":"1","article_processing_charge":"No","publication_status":"published","language":[{"iso":"eng"}],"title":"Stopping criteria for value iteration on stochastic games with quantitative objectives","month":"07","oa":1,"oa_version":"Preprint","department":[{"_id":"KrCh"}],"publication":"38th Annual ACM/IEEE Symposium on Logic in Computer Science","conference":{"end_date":"2023-06-29","location":"Boston, MA, United States","start_date":"2023-06-26","name":"LICS: Logic in Computer Science"},"status":"public","external_id":{"isi":["001036707700042"],"arxiv":["2304.09930"]},"date_updated":"2026-08-12T06:39:58Z","date_published":"2023-07-01T00:00:00Z","day":"01","intvolume":"      2023","abstract":[{"lang":"eng","text":"A classic solution technique for Markov decision processes (MDP) and stochastic games (SG) is value iteration (VI). Due to its good practical performance, this approximative approach is typically preferred over exact techniques, even though no practical bounds on the imprecision of the result could be given until recently. As a consequence, even the most used model checkers could return arbitrarily wrong results. Over the past decade, different works derived stopping criteria, indicating when the precision reaches the desired level, for various settings, in particular MDP with reachability, total reward, and mean payoff, and SG with reachability.In this paper, we provide the first stopping criteria for VI on SG with total reward and mean payoff, yielding the first anytime algorithms in these settings. To this end, we provide the solution in two flavours: First through a reduction to the MDP case and second directly on SG. The former is simpler and automatically utilizes any advances on MDP. The latter allows for more local computations, heading towards better practical efficiency.Our solution unifies the previously mentioned approaches for MDP and SG and their underlying ideas. To achieve this, we isolate objective-specific subroutines as well as identify objective-independent concepts. These structural concepts, while surprisingly simple, form the very essence of the unified solution."}],"author":[{"full_name":"Kretinsky, Jan","first_name":"Jan","orcid":"0000-0002-8122-2881","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","last_name":"Kretinsky"},{"first_name":"Tobias","full_name":"Meggendorfer, Tobias","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","orcid":"0000-0002-1712-2165","last_name":"Meggendorfer"},{"full_name":"Weininger, Maximilian","first_name":"Maximilian","last_name":"Weininger","orcid":"0000-0002-0163-2152","id":"02ab0197-cc70-11ed-ab61-918e71f56881"}],"publisher":"IEEE","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2304.09930","open_access":"1"}],"year":"2023","acknowledgement":"This research was funded in part by DFG projects 383882557 “SUV” and 427755713 “GOPro”.","corr_author":"1","_id":"13967"},{"publisher":"IEEE","author":[{"orcid":"0000-0002-6465-6258","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","last_name":"Zhang","full_name":"Zhang, Yihan","first_name":"Yihan"}],"abstract":[{"text":"We consider zero-error communication over a two-transmitter deterministic adversarial multiple access channel (MAC) governed by an adversary who has access to the transmissions of both senders (hence called omniscient ) and aims to maliciously corrupt the communication. None of the encoders, jammer and decoder is allowed to randomize using private or public randomness. This enforces a combinatorial nature of the problem. Our model covers a large family of channels studied in the literature, including all deterministic discrete memoryless noisy or noiseless MACs. In this work, given an arbitrary two-transmitter deterministic omniscient adversarial MAC, we characterize when the capacity region: 1) has nonempty interior (in particular, is two-dimensional); 2) consists of two line segments (in particular, has empty interior); 3) consists of one line segment (in particular, is one-dimensional); 4) or only contains (0,0) (in particular, is zero-dimensional). This extends a recent result by Wang et al. (201 9) from the point-to-point setting to the multiple access setting. Indeed, our converse arguments build upon their generalized Plotkin bound and involve delicate case analysis. One of the technical challenges is to take care of both “joint confusability” and “marginal confusability”. In particular, the treatment of marginal confusability does not follow from the point-to-point results by Wang et al. Our achievability results follow from random coding with expurgation.","lang":"eng"}],"page":"4093-4127","year":"2023","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2101.12426","open_access":"1"}],"corr_author":"1","acknowledgement":"The author would like to thank Amitalok J. Budkuley and Sidharth Jaggi for many helpful discussions at the early stage of this work. He would also like to thank Nir Ailon, Qi Cao, and Chandra Nair for discussions on a related problem regarding zero-error binary adder MACs.\r\nThe work of Yihan Zhang was supported by the European Union’s Horizon 2020 Research and Innovation Programme under Grant 682203-ERC-[Inf-Speed-Tradeoff]","_id":"14751","publication":"IEEE Transactions on Information Theory","department":[{"_id":"MaMo"}],"external_id":{"arxiv":["2101.12426"],"isi":["001017307000001"]},"date_updated":"2026-08-12T06:41:37Z","status":"public","day":"01","intvolume":"        69","date_published":"2023-07-01T00:00:00Z","article_processing_charge":"No","quality_controlled":"1","isi":1,"citation":{"apa":"Zhang, Y. (2023). Zero-error communication over adversarial MACs. <i>IEEE Transactions on Information Theory</i>. IEEE. <a href=\"https://doi.org/10.1109/tit.2023.3257239\">https://doi.org/10.1109/tit.2023.3257239</a>","ieee":"Y. Zhang, “Zero-error communication over adversarial MACs,” <i>IEEE Transactions on Information Theory</i>, vol. 69, no. 7. IEEE, pp. 4093–4127, 2023.","ista":"Zhang Y. 2023. Zero-error communication over adversarial MACs. IEEE Transactions on Information Theory. 69(7), 4093–4127.","chicago":"Zhang, Yihan. “Zero-Error Communication over Adversarial MACs.” <i>IEEE Transactions on Information Theory</i>. IEEE, 2023. <a href=\"https://doi.org/10.1109/tit.2023.3257239\">https://doi.org/10.1109/tit.2023.3257239</a>.","mla":"Zhang, Yihan. “Zero-Error Communication over Adversarial MACs.” <i>IEEE Transactions on Information Theory</i>, vol. 69, no. 7, IEEE, 2023, pp. 4093–127, doi:<a href=\"https://doi.org/10.1109/tit.2023.3257239\">10.1109/tit.2023.3257239</a>.","ama":"Zhang Y. Zero-error communication over adversarial MACs. <i>IEEE Transactions on Information Theory</i>. 2023;69(7):4093-4127. doi:<a href=\"https://doi.org/10.1109/tit.2023.3257239\">10.1109/tit.2023.3257239</a>","short":"Y. Zhang, IEEE Transactions on Information Theory 69 (2023) 4093–4127."},"publication_status":"published","title":"Zero-error communication over adversarial MACs","month":"07","language":[{"iso":"eng"}],"oa_version":"Preprint","issue":"7","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["1557-9654"],"issn":["0018-9448"]},"arxiv":1,"volume":69,"scopus_import":"1","article_type":"original","type":"journal_article","doi":"10.1109/tit.2023.3257239","date_created":"2024-01-08T13:04:54Z","keyword":["Computer Science Applications","Information Systems"]},{"external_id":{"isi":["001069680100011"],"arxiv":["2105.01427"]},"date_updated":"2026-08-12T06:41:54Z","status":"public","day":"04","intvolume":"        69","date_published":"2023-07-04T00:00:00Z","publication":"IEEE Transactions on Information Theory","department":[{"_id":"MaMo"}],"corr_author":"1","acknowledgement":"Nikita Polyanskii’s research was conducted in part during October 2020 - December 2021 with the Technical University of Munich and the Skolkovo Institute of Science and Technology. His work was supported by the German Research Foundation (Deutsche Forschungsgemeinschaft, DFG) under Grant No. WA3907/1-1 and the Russian Foundation for Basic Research (RFBR)\r\nunder Grant No. 20-01-00559.\r\nYihan Zhang is supported by funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 682203-ERC-[Inf-Speed-Tradeoff].","_id":"13269","publisher":"IEEE","abstract":[{"lang":"eng","text":"This paper is a collection of results on combinatorial properties of codes for the Z-channel . A Z-channel with error fraction τ takes as input a length- n binary codeword and injects in an adversarial manner up to n τ asymmetric errors, i.e., errors that only zero out bits but do not flip 0’s to 1’s. It is known that the largest ( L - 1)-list-decodable code for the Z-channel with error fraction τ has exponential size (in n ) if τ is less than a critical value that we call the ( L - 1)- list-decoding Plotkin point and has constant size if τ is larger than the threshold. The ( L -1)-list-decoding Plotkin point is known to be L -1/L-1 – L -L/ L-1 , which equals 1/4 for unique-decoding with L -1 = 1. In this paper, we derive various results for the size of the largest codes above and below the list-decoding Plotkin point. In particular, we show that the largest ( L -1)-list-decodable code ε-above the Plotkin point, for any given sufficiently small positive constant ε > 0, has size Θ L (ε -3/2 ) for any L - 1 ≥ 1. We also devise upper and lower bounds on the exponential size of codes below the list-decoding Plotkin point."}],"author":[{"last_name":"Polyanskii","full_name":"Polyanskii, Nikita","first_name":"Nikita"},{"id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","orcid":"0000-0002-6465-6258","last_name":"Zhang","first_name":"Yihan","full_name":"Zhang, Yihan"}],"year":"2023","page":"6340-6357","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2105.01427"}],"article_type":"original","scopus_import":"1","arxiv":1,"volume":69,"type":"journal_article","doi":"10.1109/TIT.2023.3292219","date_created":"2023-07-23T22:01:14Z","publication_identifier":{"issn":["0018-9448"],"eissn":["1557-9654"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Codes for the Z-channel","month":"07","language":[{"iso":"eng"}],"oa":1,"issue":"10","oa_version":"Preprint","quality_controlled":"1","article_processing_charge":"No","citation":{"short":"N. Polyanskii, Y. Zhang, IEEE Transactions on Information Theory 69 (2023) 6340–6357.","ama":"Polyanskii N, Zhang Y. Codes for the Z-channel. <i>IEEE Transactions on Information Theory</i>. 2023;69(10):6340-6357. doi:<a href=\"https://doi.org/10.1109/TIT.2023.3292219\">10.1109/TIT.2023.3292219</a>","chicago":"Polyanskii, Nikita, and Yihan Zhang. “Codes for the Z-Channel.” <i>IEEE Transactions on Information Theory</i>. IEEE, 2023. <a href=\"https://doi.org/10.1109/TIT.2023.3292219\">https://doi.org/10.1109/TIT.2023.3292219</a>.","mla":"Polyanskii, Nikita, and Yihan Zhang. “Codes for the Z-Channel.” <i>IEEE Transactions on Information Theory</i>, vol. 69, no. 10, IEEE, 2023, pp. 6340–57, doi:<a href=\"https://doi.org/10.1109/TIT.2023.3292219\">10.1109/TIT.2023.3292219</a>.","apa":"Polyanskii, N., &#38; Zhang, Y. (2023). Codes for the Z-channel. <i>IEEE Transactions on Information Theory</i>. IEEE. <a href=\"https://doi.org/10.1109/TIT.2023.3292219\">https://doi.org/10.1109/TIT.2023.3292219</a>","ieee":"N. Polyanskii and Y. Zhang, “Codes for the Z-channel,” <i>IEEE Transactions on Information Theory</i>, vol. 69, no. 10. IEEE, pp. 6340–6357, 2023.","ista":"Polyanskii N, Zhang Y. 2023. Codes for the Z-channel. IEEE Transactions on Information Theory. 69(10), 6340–6357."},"isi":1,"publication_status":"published"},{"abstract":[{"text":"Investigating modifications in the hydrological cycle is essential to understand the impacts of climate change on ecosystems. This study assesses the change in the velocity of the water cycle over land at the global scale, whereas previous studies have mostly focused on changes in the atmospheric water cycle. The hydrological acceleration is quantified by a decrease in average residence time (RT) of water in the first meter of soil. The soil water RT is shown to be sensitive to the soil texture and seasonality of hydroclimatic variables. Despite substantial local variability, most of the RTs are in the range of 50–300 days. The global mean soil water RT declined at a rate of −2.30 and −0.36 days decade−1 (−1.6 to 1.0 days decade−1 the range of nine models) from 2001 to 2020 as measured by reanalysis and CMIP6 simulations for the historical scenario, respectively, which corresponds to −6.8 and −1.1 days °C−1 when expressed per degree of global warming over land. This acceleration is projected to continue at a rate of −1.35 days decade−1 (−3.4 to 0.0 days decade−1 the range of nine models) or −2.2 days °C−1 during the period 2015–2100 under the most extreme emission scenario: SSP 585. Changes in precipitation dominantly drive the acceleration of the terrestrial water cycle compared to changes in evapotranspiration. Rising temperatures and increasing carbon dioxide have opposite effects on the speed of the terrestrial water cycle with compensatory roles keeping RT relatively unchanged in the absence of PR trends.","lang":"eng"}],"author":[{"first_name":"Y.","full_name":"Wang, Y.","last_name":"Wang"},{"full_name":"Meili, N.","first_name":"N.","last_name":"Meili"},{"first_name":"Simone","full_name":"Fatichi, Simone","last_name":"Fatichi","id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6"}],"publisher":"American Geophysical Union","main_file_link":[{"url":"https://doi.org/10.1029/2022WR033970","open_access":"1"}],"OA_type":"hybrid","year":"2023","OA_place":"publisher","_id":"22554","extern":"1","article_number":"e2022WR033970","publication":"Water Resources Research","das_tickbox":"1","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"date_updated":"2026-08-12T08:32:38Z","date_published":"2023-08-01T00:00:00Z","intvolume":"        59","day":"01","citation":{"short":"Y. Wang, N. Meili, S. Fatichi, Water Resources Research 59 (2023).","ama":"Wang Y, Meili N, Fatichi S. Evidence and controls of the acceleration of the hydrological cycle over land. <i>Water Resources Research</i>. 2023;59(8). doi:<a href=\"https://doi.org/10.1029/2022wr033970\">10.1029/2022wr033970</a>","chicago":"Wang, Y., N. Meili, and Simone Fatichi. “Evidence and Controls of the Acceleration of the Hydrological Cycle over Land.” <i>Water Resources Research</i>. American Geophysical Union, 2023. <a href=\"https://doi.org/10.1029/2022wr033970\">https://doi.org/10.1029/2022wr033970</a>.","mla":"Wang, Y., et al. “Evidence and Controls of the Acceleration of the Hydrological Cycle over Land.” <i>Water Resources Research</i>, vol. 59, no. 8, e2022WR033970, American Geophysical Union, 2023, doi:<a href=\"https://doi.org/10.1029/2022wr033970\">10.1029/2022wr033970</a>.","ieee":"Y. Wang, N. Meili, and S. Fatichi, “Evidence and controls of the acceleration of the hydrological cycle over land,” <i>Water Resources Research</i>, vol. 59, no. 8. American Geophysical Union, 2023.","apa":"Wang, Y., Meili, N., &#38; Fatichi, S. (2023). Evidence and controls of the acceleration of the hydrological cycle over land. <i>Water Resources Research</i>. American Geophysical Union. <a href=\"https://doi.org/10.1029/2022wr033970\">https://doi.org/10.1029/2022wr033970</a>","ista":"Wang Y, Meili N, Fatichi S. 2023. Evidence and controls of the acceleration of the hydrological cycle over land. Water Resources Research. 59(8), e2022WR033970."},"article_processing_charge":"No","quality_controlled":"1","publication_status":"published","language":[{"iso":"eng"}],"month":"08","title":"Evidence and controls of the acceleration of the hydrological cycle over land","oa":1,"oa_version":"Published Version","issue":"8","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_identifier":{"issn":["0043-1397"],"eissn":["1944-7973"]},"type":"journal_article","article_type":"original","scopus_import":"1","volume":59,"date_created":"2026-07-27T12:30:24Z","doi":"10.1029/2022wr033970"},{"publication":"34th International Conference on Concurrency Theory","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"conference":{"name":"CONCUR: Conference on Concurrency Theory","start_date":"2023-09-18","end_date":"2023-09-23","location":"Antwerp, Belgium"},"date_updated":"2026-08-12T08:46:04Z","external_id":{"isi":["001570542500017"],"arxiv":["2307.06016"]},"status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"ddc":["000"],"intvolume":"       279","day":"01","date_published":"2023-09-01T00:00:00Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","author":[{"last_name":"Boker","id":"31E297B6-F248-11E8-B48F-1D18A9856A87","first_name":"Udi","full_name":"Boker, Udi"},{"last_name":"Henzinger","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","first_name":"Thomas A"},{"id":"b26baa86-3308-11ec-87b0-8990f34baa85","last_name":"Mazzocchi","full_name":"Mazzocchi, Nicolas Adrien","first_name":"Nicolas Adrien"},{"full_name":"Sarac, Naci E","first_name":"Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","last_name":"Sarac"}],"abstract":[{"lang":"eng","text":"The safety-liveness dichotomy is a fundamental concept in formal languages which plays a key role in verification. Recently, this dichotomy has been lifted to quantitative properties, which are arbitrary functions from infinite words to partially-ordered domains. We look into harnessing the dichotomy for the specific classes of quantitative properties expressed by quantitative automata. These automata contain finitely many states and rational-valued transition weights, and their common value functions Inf, Sup, LimInf, LimSup, LimInfAvg, LimSupAvg, and DSum map infinite words into the totallyordered domain of real numbers. In this automata-theoretic setting, we establish a connection between quantitative safety and topological continuity and provide an alternative characterization of quantitative safety and liveness in terms of their boolean counterparts. For all common value functions, we show how the safety closure of a quantitative automaton can be constructed in PTime, and we provide PSpace-complete checks of whether a given quantitative automaton is safe or live, with the exception of LimInfAvg and LimSupAvg automata, for which the safety check is in ExpSpace. Moreover, for deterministic Sup, LimInf, and LimSup automata, we give PTime decompositions into safe and live automata. These decompositions enable the separation of techniques for safety and liveness verification for quantitative specifications."}],"year":"2023","file_date_updated":"2023-07-14T12:03:48Z","corr_author":"1","file":[{"file_name":"CONCUR23.pdf","success":1,"relation":"main_file","content_type":"application/pdf","access_level":"open_access","date_updated":"2023-07-14T12:03:48Z","file_size":755529,"creator":"esarac","date_created":"2023-07-14T12:03:48Z","checksum":"d40e57a04448ea5c77d7e1cfb9590a81","file_id":"13224"}],"acknowledgement":"We thank Christof Löding for pointing us to some results on PSpace-hardess of universality problems and the anonymous reviewers for their helpful comments. This work was supported in part by the ERC-2020-AdG 101020093 and the Israel Science Foundation grant 2410/22.","article_number":"17","_id":"13221","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["1868-8969"],"isbn":["9783959772990"]},"volume":279,"arxiv":1,"scopus_import":"1","type":"conference","doi":"10.4230/LIPIcs.CONCUR.2023.17","date_created":"2023-07-14T10:00:15Z","quality_controlled":"1","article_processing_charge":"No","project":[{"call_identifier":"H2020","grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"isi":1,"citation":{"short":"U. Boker, T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, in:, 34th International Conference on Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","ama":"Boker U, Henzinger TA, Mazzocchi NA, Sarac NE. Safety and liveness of quantitative automata. In: <i>34th International Conference on Concurrency Theory</i>. Vol 279. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2023.17\">10.4230/LIPIcs.CONCUR.2023.17</a>","mla":"Boker, Udi, et al. “Safety and Liveness of Quantitative Automata.” <i>34th International Conference on Concurrency Theory</i>, vol. 279, 17, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2023.17\">10.4230/LIPIcs.CONCUR.2023.17</a>.","chicago":"Boker, Udi, Thomas A Henzinger, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Safety and Liveness of Quantitative Automata.” In <i>34th International Conference on Concurrency Theory</i>, Vol. 279. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2023.17\">https://doi.org/10.4230/LIPIcs.CONCUR.2023.17</a>.","apa":"Boker, U., Henzinger, T. A., Mazzocchi, N. A., &#38; Sarac, N. E. (2023). Safety and liveness of quantitative automata. In <i>34th International Conference on Concurrency Theory</i> (Vol. 279). Antwerp, Belgium: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2023.17\">https://doi.org/10.4230/LIPIcs.CONCUR.2023.17</a>","ieee":"U. Boker, T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “Safety and liveness of quantitative automata,” in <i>34th International Conference on Concurrency Theory</i>, Antwerp, Belgium, 2023, vol. 279.","ista":"Boker U, Henzinger TA, Mazzocchi NA, Sarac NE. 2023. Safety and liveness of quantitative automata. 34th International Conference on Concurrency Theory. CONCUR: Conference on Concurrency Theory, LIPIcs, vol. 279, 17."},"publication_status":"published","month":"09","ec_funded":1,"title":"Safety and liveness of quantitative automata","language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"20147","relation":"dissertation_contains"},{"relation":"later_version","id":"20342","status":"public"}]},"has_accepted_license":"1","alternative_title":["LIPIcs"],"oa_version":"Published Version","oa":1},{"publication":"Current Opinion in Genetics & Development","department":[{"_id":"DaZi"}],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"status":"public","ddc":["570"],"external_id":{"isi":["001047020200001"],"pmid":["37441873"]},"date_updated":"2026-08-12T09:55:32Z","date_published":"2023-08-01T00:00:00Z","day":"01","intvolume":"        81","author":[{"first_name":"Elizabeth","full_name":"Hollwey, Elizabeth","id":"b8c4f54b-e484-11eb-8fdc-a54df64ef6dd","last_name":"Hollwey"},{"first_name":"Amy","full_name":"Briffa, Amy","last_name":"Briffa"},{"last_name":"Howard","first_name":"Martin","full_name":"Howard, Martin"},{"last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","first_name":"Daniel","full_name":"Zilberman, Daniel"}],"abstract":[{"lang":"eng","text":"Many modes and mechanisms of epigenetic inheritance have been elucidated in eukaryotes. Most of them are relatively short-term, generally not exceeding one or a few organismal generations. However, emerging evidence indicates that one mechanism, cytosine DNA methylation, can mediate epigenetic inheritance over much longer timescales, which are mostly or completely inaccessible in the laboratory. Here we discuss the evidence for, and mechanisms and implications of, such long-term epigenetic inheritance. We argue that compelling evidence supports the long-term epigenetic inheritance of gene body methylation, at least in the model angiosperm Arabidopsis thaliana, and that variation in such methylation can therefore serve as an epigenetic basis for phenotypic variation in natural populations."}],"publisher":"Elsevier","file_date_updated":"2023-08-07T08:32:26Z","year":"2023","file":[{"file_name":"2023_CurrentOpinionGenetics_Hollwey.pdf","relation":"main_file","success":1,"date_updated":"2023-08-07T08:32:26Z","file_size":2568632,"access_level":"open_access","content_type":"application/pdf","file_id":"13980","checksum":"a294cd9506b80ed6ef218ef44ed32765","date_created":"2023-08-07T08:32:26Z","creator":"dernst"}],"corr_author":"1","_id":"13965","article_number":"102087","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["1879-0380"],"issn":["0959-437X"]},"type":"journal_article","volume":81,"scopus_import":"1","article_type":"original","date_created":"2023-08-06T22:01:10Z","doi":"10.1016/j.gde.2023.102087","isi":1,"citation":{"short":"E. Hollwey, A. Briffa, M. Howard, D. Zilberman, Current Opinion in Genetics &#38; Development 81 (2023).","ama":"Hollwey E, Briffa A, Howard M, Zilberman D. Concepts, mechanisms and implications of long-term epigenetic inheritance. <i>Current Opinion in Genetics &#38; Development</i>. 2023;81(8). doi:<a href=\"https://doi.org/10.1016/j.gde.2023.102087\">10.1016/j.gde.2023.102087</a>","chicago":"Hollwey, Elizabeth, Amy Briffa, Martin Howard, and Daniel Zilberman. “Concepts, Mechanisms and Implications of Long-Term Epigenetic Inheritance.” <i>Current Opinion in Genetics &#38; Development</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.gde.2023.102087\">https://doi.org/10.1016/j.gde.2023.102087</a>.","mla":"Hollwey, Elizabeth, et al. “Concepts, Mechanisms and Implications of Long-Term Epigenetic Inheritance.” <i>Current Opinion in Genetics &#38; Development</i>, vol. 81, no. 8, 102087, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.gde.2023.102087\">10.1016/j.gde.2023.102087</a>.","apa":"Hollwey, E., Briffa, A., Howard, M., &#38; Zilberman, D. (2023). Concepts, mechanisms and implications of long-term epigenetic inheritance. <i>Current Opinion in Genetics &#38; Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.gde.2023.102087\">https://doi.org/10.1016/j.gde.2023.102087</a>","ieee":"E. Hollwey, A. Briffa, M. Howard, and D. Zilberman, “Concepts, mechanisms and implications of long-term epigenetic inheritance,” <i>Current Opinion in Genetics &#38; Development</i>, vol. 81, no. 8. Elsevier, 2023.","ista":"Hollwey E, Briffa A, Howard M, Zilberman D. 2023. Concepts, mechanisms and implications of long-term epigenetic inheritance. Current Opinion in Genetics &#38; Development. 81(8), 102087."},"article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","language":[{"iso":"eng"}],"title":"Concepts, mechanisms and implications of long-term epigenetic inheritance","month":"08","oa_version":"Published Version","issue":"8","oa":1,"has_accepted_license":"1"},{"ddc":["570"],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"status":"public","date_updated":"2026-08-12T09:59:59Z","external_id":{"pmid":["37665167"],"isi":["001097449100002"]},"date_published":"2023-10-01T00:00:00Z","intvolume":"       150","day":"01","publication":"Development","department":[{"_id":"AnKi"}],"file":[{"file_size":12836306,"date_updated":"2024-01-10T12:41:13Z","access_level":"open_access","content_type":"application/pdf","file_id":"14790","checksum":"2d6f52dc33260a9b2352b8f28374ba5f","date_created":"2024-01-10T12:41:13Z","creator":"dernst","file_name":"2023_Development_Harish.pdf","relation":"main_file","success":1}],"acknowledgement":"We thank members of the Brand lab, as well as Justina Stark (Ivo Sbalzarini group, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany) for project-related discussions; Darren Gilmour (University of Zurich), Karuna Sampath (University of Warwick) and Gokul Kesavan (Vowels Lifesciences Private Limited, Bangalore) for comments on the manuscript; personnel of the CMCB technology platform, TU Dresden for imaging and image analysis-related support; and Maurizio Abbate (Technical support, Arivis) for help with image analysis. We are also grateful to Stapornwongkul and Briscoe for commenting on a preprint version of our work (Stapornwongkul and Briscoe, 2022).\r\nThis work was supported by the Deutsche Forschungsgemeinschaft (BR 1746/6-2, BR 1746/11-1 and BR 1746/3 to M.B.), by a Cluster of Excellence ‘Physics of Life’ seed grant and by institutional funds from Technische Universitat Dresden (to M.B.). Open Access funding provided by Technische Universitat Dresden. Deposited in PMC for immediate release.","_id":"14774","article_number":"dev201559","abstract":[{"text":"Morphogen gradients impart positional information to cells in a homogenous tissue field. Fgf8a, a highly conserved growth factor, has been proposed to act as a morphogen during zebrafish gastrulation. However, technical limitations have so far prevented direct visualization of the endogenous Fgf8a gradient and confirmation of its morphogenic activity. Here, we monitor Fgf8a propagation in the developing neural plate using a CRISPR/Cas9-mediated EGFP knock-in at the endogenous fgf8a locus. By combining sensitive imaging with single-molecule fluorescence correlation spectroscopy, we demonstrate that Fgf8a, which is produced at the embryonic margin, propagates by diffusion through the extracellular space and forms a graded distribution towards the animal pole. Overlaying the Fgf8a gradient curve with expression profiles of its downstream targets determines the precise input-output relationship of Fgf8a-mediated patterning. Manipulation of the extracellular Fgf8a levels alters the signaling outcome, thus establishing Fgf8a as a bona fide morphogen during zebrafish gastrulation. Furthermore, by hindering Fgf8a diffusion, we demonstrate that extracellular diffusion of the protein from the source is crucial for it to achieve its morphogenic potential.","lang":"eng"}],"author":[{"id":"1bae78aa-ee0e-11ec-9b76-bc42990f409d","last_name":"Harish","first_name":"Rohit K","full_name":"Harish, Rohit K"},{"last_name":"Gupta","first_name":"Mansi","full_name":"Gupta, Mansi"},{"last_name":"Zöller","full_name":"Zöller, Daniela","first_name":"Daniela"},{"last_name":"Hartmann","full_name":"Hartmann, Hella","first_name":"Hella"},{"full_name":"Gheisari, Ali","first_name":"Ali","last_name":"Gheisari"},{"last_name":"Machate","full_name":"Machate, Anja","first_name":"Anja"},{"last_name":"Hans","full_name":"Hans, Stefan","first_name":"Stefan"},{"last_name":"Brand","first_name":"Michael","full_name":"Brand, Michael"}],"publisher":"Company of Biologists","file_date_updated":"2024-01-10T12:41:13Z","year":"2023","type":"journal_article","article_type":"original","volume":150,"keyword":["Developmental Biology","Molecular Biology"],"date_created":"2024-01-10T09:18:54Z","doi":"10.1242/dev.201559","publication_identifier":{"eissn":["1477-9129"],"issn":["0950-1991"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"language":[{"iso":"eng"}],"month":"10","title":"Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation","oa":1,"oa_version":"Published Version","issue":"19","has_accepted_license":"1","isi":1,"citation":{"chicago":"Harish, Rohit K, Mansi Gupta, Daniela Zöller, Hella Hartmann, Ali Gheisari, Anja Machate, Stefan Hans, and Michael Brand. “Real-Time Monitoring of an Endogenous Fgf8a Gradient Attests to Its Role as a Morphogen during Zebrafish Gastrulation.” <i>Development</i>. Company of Biologists, 2023. <a href=\"https://doi.org/10.1242/dev.201559\">https://doi.org/10.1242/dev.201559</a>.","mla":"Harish, Rohit K., et al. “Real-Time Monitoring of an Endogenous Fgf8a Gradient Attests to Its Role as a Morphogen during Zebrafish Gastrulation.” <i>Development</i>, vol. 150, no. 19, dev201559, Company of Biologists, 2023, doi:<a href=\"https://doi.org/10.1242/dev.201559\">10.1242/dev.201559</a>.","ista":"Harish RK, Gupta M, Zöller D, Hartmann H, Gheisari A, Machate A, Hans S, Brand M. 2023. Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation. Development. 150(19), dev201559.","apa":"Harish, R. K., Gupta, M., Zöller, D., Hartmann, H., Gheisari, A., Machate, A., … Brand, M. (2023). Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.201559\">https://doi.org/10.1242/dev.201559</a>","ieee":"R. K. Harish <i>et al.</i>, “Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation,” <i>Development</i>, vol. 150, no. 19. Company of Biologists, 2023.","short":"R.K. Harish, M. Gupta, D. Zöller, H. Hartmann, A. Gheisari, A. Machate, S. Hans, M. Brand, Development 150 (2023).","ama":"Harish RK, Gupta M, Zöller D, et al. Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation. <i>Development</i>. 2023;150(19). doi:<a href=\"https://doi.org/10.1242/dev.201559\">10.1242/dev.201559</a>"},"article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","publication_status":"published"},{"title":"Evolutionary dynamics of mutants that modify population structure","month":"11","ec_funded":1,"language":[{"iso":"eng"}],"has_accepted_license":"1","issue":"208","oa_version":"Published Version","oa":1,"quality_controlled":"1","article_processing_charge":"Yes (in subscription journal)","project":[{"grant_number":"863818","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"isi":1,"citation":{"mla":"Tkadlec, Josef, et al. “Evolutionary Dynamics of Mutants That Modify Population Structure.” <i>Journal of the Royal Society Interface</i>, vol. 20, no. 208, 20230355, Royal Society, 2023, doi:<a href=\"https://doi.org/10.1098/rsif.2023.0355\">10.1098/rsif.2023.0355</a>.","chicago":"Tkadlec, Josef, Kamran Kaveh, Krishnendu Chatterjee, and Martin A. Nowak. “Evolutionary Dynamics of Mutants That Modify Population Structure.” <i>Journal of the Royal Society Interface</i>. Royal Society, 2023. <a href=\"https://doi.org/10.1098/rsif.2023.0355\">https://doi.org/10.1098/rsif.2023.0355</a>.","apa":"Tkadlec, J., Kaveh, K., Chatterjee, K., &#38; Nowak, M. A. (2023). Evolutionary dynamics of mutants that modify population structure. <i>Journal of the Royal Society Interface</i>. Royal Society. <a href=\"https://doi.org/10.1098/rsif.2023.0355\">https://doi.org/10.1098/rsif.2023.0355</a>","ieee":"J. Tkadlec, K. Kaveh, K. Chatterjee, and M. A. Nowak, “Evolutionary dynamics of mutants that modify population structure,” <i>Journal of the Royal Society Interface</i>, vol. 20, no. 208. Royal Society, 2023.","ista":"Tkadlec J, Kaveh K, Chatterjee K, Nowak MA. 2023. Evolutionary dynamics of mutants that modify population structure. Journal of the Royal Society Interface. 20(208), 20230355.","short":"J. Tkadlec, K. Kaveh, K. Chatterjee, M.A. Nowak, Journal of the Royal Society Interface 20 (2023).","ama":"Tkadlec J, Kaveh K, Chatterjee K, Nowak MA. Evolutionary dynamics of mutants that modify population structure. <i>Journal of the Royal Society Interface</i>. 2023;20(208). doi:<a href=\"https://doi.org/10.1098/rsif.2023.0355\">10.1098/rsif.2023.0355</a>"},"publication_status":"published","volume":20,"scopus_import":"1","article_type":"original","type":"journal_article","doi":"10.1098/rsif.2023.0355","date_created":"2023-12-10T23:00:58Z","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["1742-5662"]},"acknowledgement":"K.C. acknowledges support from the ERC CoG 863818(ForM-SMArt). J.T. is supported by Center for Foundations ofModern Computer Science (Charles Univ. project UNCE/SCI/004).","file":[{"file_size":1720243,"date_updated":"2023-12-11T11:10:32Z","access_level":"open_access","content_type":"application/pdf","file_id":"14673","checksum":"2eefab13127c7786dbd33303c482a004","date_created":"2023-12-11T11:10:32Z","creator":"dernst","file_name":"2023_RoyalInterface_Tkadlec.pdf","relation":"main_file","success":1}],"article_number":"20230355","_id":"14657","publisher":"Royal Society","author":[{"first_name":"Josef","full_name":"Tkadlec, Josef","last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1097-9684"},{"first_name":"Kamran","full_name":"Kaveh, Kamran","last_name":"Kaveh"},{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Nowak, Martin A.","first_name":"Martin A.","last_name":"Nowak"}],"abstract":[{"text":"Natural selection is usually studied between mutants that differ in reproductive rate, but are subject to the same population structure. Here we explore how natural selection acts on mutants that have the same reproductive rate, but different population structures. In our framework, population structure is given by a graph that specifies where offspring can disperse. The invading mutant disperses offspring on a different graph than the resident wild-type. We find that more densely connected dispersal graphs tend to increase the invader’s fixation probability, but the exact relationship between structure and fixation probability is subtle. We present three main results. First, we prove that if both invader and resident are on complete dispersal graphs, then removing a single edge in the invader’s dispersal graph reduces its fixation probability. Second, we show that for certain island models higher invader’s connectivity increases its fixation probability, but the magnitude of the effect depends on the exact layout of the connections. Third, we show that for lattices the effect of different connectivity is comparable to that of different fitness: for large population size, the invader’s fixation probability is either constant or exponentially small, depending on whether it is more or less connected than the resident.","lang":"eng"}],"year":"2023","file_date_updated":"2023-12-11T11:10:32Z","external_id":{"pmid":["38016637"],"isi":["001124419300002"]},"date_updated":"2026-08-12T14:05:25Z","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"ddc":["000","570"],"intvolume":"        20","day":"29","date_published":"2023-11-29T00:00:00Z","department":[{"_id":"KrCh"}],"publication":"Journal of the Royal Society Interface"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["1049-5258"],"isbn":["9781713899921"]},"researchdata_availability":"no","type":"conference","arxiv":1,"volume":36,"scopus_import":"1","date_created":"2024-02-07T15:11:11Z","doi":"10.52202/075280-0147","citation":{"mla":"Zhu, Zhenyu, et al. “Sample Complexity Bounds for Score-Matching: Causal Discovery and Generative Modeling.” <i>37th Conference on Neural Information Processing Systems</i>, vol. 36, Neural Information Processing Systems Foundation, 2023, pp. 3325–37, doi:<a href=\"https://doi.org/10.52202/075280-0147\">10.52202/075280-0147</a>.","chicago":"Zhu, Zhenyu, Francesco Locatello, and Volkan Cevher. “Sample Complexity Bounds for Score-Matching: Causal Discovery and Generative Modeling.” In <i>37th Conference on Neural Information Processing Systems</i>, 36:3325–37. Neural Information Processing Systems Foundation, 2023. <a href=\"https://doi.org/10.52202/075280-0147\">https://doi.org/10.52202/075280-0147</a>.","ista":"Zhu Z, Locatello F, Cevher V. 2023. Sample complexity bounds for score-matching: Causal discovery and generative modeling. 37th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 36, 3325–3337.","apa":"Zhu, Z., Locatello, F., &#38; Cevher, V. (2023). Sample complexity bounds for score-matching: Causal discovery and generative modeling. In <i>37th Conference on Neural Information Processing Systems</i> (Vol. 36, pp. 3325–3337). New Orleans, LO, United States: Neural Information Processing Systems Foundation. <a href=\"https://doi.org/10.52202/075280-0147\">https://doi.org/10.52202/075280-0147</a>","ieee":"Z. Zhu, F. Locatello, and V. Cevher, “Sample complexity bounds for score-matching: Causal discovery and generative modeling,” in <i>37th Conference on Neural Information Processing Systems</i>, New Orleans, LO, United States, 2023, vol. 36, pp. 3325–3337.","short":"Z. Zhu, F. Locatello, V. Cevher, in:, 37th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2023, pp. 3325–3337.","ama":"Zhu Z, Locatello F, Cevher V. Sample complexity bounds for score-matching: Causal discovery and generative modeling. In: <i>37th Conference on Neural Information Processing Systems</i>. Vol 36. Neural Information Processing Systems Foundation; 2023:3325-3337. doi:<a href=\"https://doi.org/10.52202/075280-0147\">10.52202/075280-0147</a>"},"article_processing_charge":"No","quality_controlled":"1","publication_status":"published","language":[{"iso":"eng"}],"supplementarymaterial":"yes","title":"Sample complexity bounds for score-matching: Causal discovery and generative modeling","month":"10","oa_version":"Published Version","oa":1,"alternative_title":["Advances in Neural Information Processing Systems"],"has_accepted_license":"1","das_tickbox":"0","department":[{"_id":"FrLo"}],"publication":"37th Conference on Neural Information Processing Systems","conference":{"location":"New Orleans, LO, United States","end_date":"2023-12-16","name":"NeurIPS: Neural Information Processing Systems","start_date":"2023-12-12"},"status":"public","ddc":["000"],"date_updated":"2026-08-13T07:09:06Z","external_id":{"arxiv":["2310.18123"]},"date_published":"2023-10-27T00:00:00Z","day":"27","intvolume":"        36","author":[{"first_name":"Zhenyu","full_name":"Zhu, Zhenyu","last_name":"Zhu"},{"last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","first_name":"Francesco","full_name":"Locatello, Francesco"},{"last_name":"Cevher","first_name":"Volkan","full_name":"Cevher, Volkan"}],"abstract":[{"lang":"eng","text":"This paper provides statistical sample complexity bounds for score-matching and\r\nits applications in causal discovery. We demonstrate that accurate estimation of the\r\nscore function is achievable by training a standard deep ReLU neural network using\r\nstochastic gradient descent. We establish bounds on the error rate of recovering\r\ncausal relationships using the score-matching-based causal discovery method of\r\nRolland et al. [2022], assuming a sufficiently good estimation of the score function.\r\nFinally, we analyze the upper bound of score-matching estimation within the scorebased generative modeling, which has been applied for causal discovery but is also\r\nof independent interest within the domain of generative models.y"}],"publisher":"Neural Information Processing Systems Foundation","file_date_updated":"2026-08-13T07:02:51Z","OA_type":"gold","year":"2023","page":"3325-3337","OA_place":"publisher","acknowledgement":"We are thankful to the reviewers for providing constructive feedback and Kun Zhang and Dominik\r\nJanzing for helpful discussion on the special case of deterministic children. This work was supported\r\nby Hasler Foundation Program: Hasler Responsible AI (project number 21043). This work was\r\nsupported by the Swiss National Science Foundation (SNSF) under grant number 200021_205011.\r\nFrancesco Locatello did not contribute to this work at Amazon. ","file":[{"file_name":"2023_Neurips_Zhu.pdf","success":1,"relation":"main_file","content_type":"application/pdf","access_level":"open_access","date_updated":"2026-08-13T07:02:51Z","file_size":305362,"creator":"dernst","date_created":"2026-08-13T07:02:51Z","checksum":"6f10adadefceb3bb50ad0b2637493381","file_id":"22700"}],"corr_author":"1","_id":"14953"}]