[{"publication_status":"published","file":[{"success":1,"creator":"dernst","date_created":"2022-06-30T07:14:48Z","access_level":"open_access","relation":"main_file","checksum":"a7706b28d24a0e32a55ea04b82a2df43","content_type":"application/pdf","date_updated":"2022-06-30T07:14:48Z","file_id":"11472","file_name":"2022_PRXQuantum_Sack.pdf","file_size":4231591}],"citation":{"ieee":"S. Sack, R. A. Medina Ramos, A. Michailidis, R. Kueng, and M. Serbyn, “Avoiding barren plateaus using classical shadows,” <i>PRX Quantum</i>, vol. 3, no. 2. American Physical Society, 2022.","chicago":"Sack, Stefan, Raimel A Medina Ramos, Alexios Michailidis, Richard Kueng, and Maksym Serbyn. “Avoiding Barren Plateaus Using Classical Shadows.” <i>PRX Quantum</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/prxquantum.3.020365\">https://doi.org/10.1103/prxquantum.3.020365</a>.","mla":"Sack, Stefan, et al. “Avoiding Barren Plateaus Using Classical Shadows.” <i>PRX Quantum</i>, vol. 3, no. 2, 020365, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/prxquantum.3.020365\">10.1103/prxquantum.3.020365</a>.","ista":"Sack S, Medina Ramos RA, Michailidis A, Kueng R, Serbyn M. 2022. Avoiding barren plateaus using classical shadows. PRX Quantum. 3(2), 020365.","apa":"Sack, S., Medina Ramos, R. A., Michailidis, A., Kueng, R., &#38; Serbyn, M. (2022). Avoiding barren plateaus using classical shadows. <i>PRX Quantum</i>. American Physical Society. <a href=\"https://doi.org/10.1103/prxquantum.3.020365\">https://doi.org/10.1103/prxquantum.3.020365</a>","ama":"Sack S, Medina Ramos RA, Michailidis A, Kueng R, Serbyn M. Avoiding barren plateaus using classical shadows. <i>PRX Quantum</i>. 2022;3(2). doi:<a href=\"https://doi.org/10.1103/prxquantum.3.020365\">10.1103/prxquantum.3.020365</a>","short":"S. Sack, R.A. Medina Ramos, A. Michailidis, R. Kueng, M. Serbyn, PRX Quantum 3 (2022)."},"status":"public","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","corr_author":"1","date_published":"2022-06-29T00:00:00Z","publisher":"American Physical Society","date_created":"2022-06-29T20:21:32Z","doi":"10.1103/prxquantum.3.020365","intvolume":"         3","author":[{"last_name":"Sack","orcid":"0000-0001-5400-8508","full_name":"Sack, Stefan","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","first_name":"Stefan"},{"last_name":"Medina Ramos","orcid":"0000-0002-5383-2869","full_name":"Medina Ramos, Raimel A","id":"CE680B90-D85A-11E9-B684-C920E6697425","first_name":"Raimel A"},{"id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","first_name":"Alexios","full_name":"Michailidis, Alexios","last_name":"Michailidis","orcid":"0000-0002-8443-1064"},{"last_name":"Kueng","full_name":"Kueng, Richard","first_name":"Richard"},{"first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn"}],"acknowledgement":"We thank Marco Cerezo, Zoe Holmes, and Nicholas Hunter-Jones for fruitful discussion and valuable feedback. We also acknowledge Adam Smith, Johannes Jakob Meyer, and Victor V. Albert for comments on the paper. The simulations were performed in the Julia programming\r\nlanguage [65] using the Yao module [66]. S.H.S., R.A.M., A.A.M. and M.S. acknowledge support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899).","keyword":["General Medicine"],"scopus_import":"1","_id":"11471","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"Variational quantum algorithms are promising algorithms for achieving quantum advantage on nearterm devices. The quantum hardware is used to implement a variational wave function and measure observables, whereas the classical computer is used to store and update the variational parameters. The optimization landscape of expressive variational ansätze is however dominated by large regions in parameter space, known as barren plateaus, with vanishing gradients, which prevents efficient optimization. In this work we propose a general algorithm to avoid barren plateaus in the initialization and throughout the optimization. To this end we define a notion of weak barren plateaus (WBPs) based on the entropies of local reduced density matrices. The presence of WBPs can be efficiently quantified using recently introduced shadow tomography of the quantum state with a classical computer. We demonstrate that avoidance of WBPs suffices to ensure sizable gradients in the initialization. In addition, we demonstrate that decreasing the gradient step size, guided by the entropies allows WBPs to be avoided during the optimization process. This paves the way for efficient barren plateau-free optimization on near-term devices. "}],"year":"2022","day":"29","article_processing_charge":"No","month":"06","isi":1,"publication":"PRX Quantum","has_accepted_license":"1","volume":3,"language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"17208","relation":"dissertation_contains"},{"relation":"dissertation_contains","id":"14622","status":"public"}]},"file_date_updated":"2022-06-30T07:14:48Z","oa_version":"Published Version","publication_identifier":{"issn":["2691-3399"]},"quality_controlled":"1","department":[{"_id":"MaSe"}],"date_updated":"2026-08-08T22:31:05Z","article_type":"original","project":[{"name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899","call_identifier":"H2020"}],"ec_funded":1,"external_id":{"isi":["000822564300001"],"arxiv":["2201.08194"]},"article_number":"020365","title":"Avoiding barren plateaus using classical shadows","ddc":["530"],"arxiv":1,"issue":"2","type":"journal_article"},{"publisher":"Elsevier","pmid":1,"doi":"10.1016/j.cub.2021.02.043","date_created":"2022-03-08T07:51:04Z","intvolume":"        31","author":[{"full_name":"Stahnke, Stephanie","last_name":"Stahnke","first_name":"Stephanie"},{"first_name":"Hermann","full_name":"Döring, Hermann","last_name":"Döring"},{"last_name":"Kusch","full_name":"Kusch, Charly","first_name":"Charly"},{"full_name":"de Gorter, David J.J.","last_name":"de Gorter","first_name":"David J.J."},{"first_name":"Sebastian","last_name":"Dütting","full_name":"Dütting, Sebastian"},{"full_name":"Guledani, Aleks","last_name":"Guledani","first_name":"Aleks"},{"first_name":"Irina","full_name":"Pleines, Irina","last_name":"Pleines"},{"first_name":"Michael","full_name":"Schnoor, Michael","last_name":"Schnoor"},{"last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Geffers","full_name":"Geffers, Robert","first_name":"Robert"},{"first_name":"Manfred","full_name":"Rohde, Manfred","last_name":"Rohde"},{"first_name":"Mathias","full_name":"Müsken, Mathias","last_name":"Müsken"},{"first_name":"Frieda","last_name":"Kage","full_name":"Kage, Frieda"},{"full_name":"Steffen, Anika","last_name":"Steffen","first_name":"Anika"},{"first_name":"Jan","full_name":"Faix, Jan","last_name":"Faix"},{"last_name":"Nieswandt","full_name":"Nieswandt, Bernhard","first_name":"Bernhard"},{"full_name":"Rottner, Klemens","last_name":"Rottner","first_name":"Klemens"},{"first_name":"Theresia E.B.","full_name":"Stradal, Theresia E.B.","last_name":"Stradal"}],"date_published":"2021-05-24T00:00:00Z","publication_status":"published","citation":{"ama":"Stahnke S, Döring H, Kusch C, et al. Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion. <i>Current Biology</i>. 2021;31(10):2051-2064.e8. doi:<a href=\"https://doi.org/10.1016/j.cub.2021.02.043\">10.1016/j.cub.2021.02.043</a>","apa":"Stahnke, S., Döring, H., Kusch, C., de Gorter, D. J. J., Dütting, S., Guledani, A., … Stradal, T. E. B. (2021). Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2021.02.043\">https://doi.org/10.1016/j.cub.2021.02.043</a>","short":"S. Stahnke, H. Döring, C. Kusch, D.J.J. de Gorter, S. Dütting, A. Guledani, I. Pleines, M. Schnoor, M.K. Sixt, R. Geffers, M. Rohde, M. Müsken, F. Kage, A. Steffen, J. Faix, B. Nieswandt, K. Rottner, T.E.B. Stradal, Current Biology 31 (2021) 2051–2064.e8.","mla":"Stahnke, Stephanie, et al. “Loss of Hem1 Disrupts Macrophage Function and Impacts Migration, Phagocytosis, and Integrin-Mediated Adhesion.” <i>Current Biology</i>, vol. 31, no. 10, Elsevier, 2021, p. 2051–2064.e8, doi:<a href=\"https://doi.org/10.1016/j.cub.2021.02.043\">10.1016/j.cub.2021.02.043</a>.","ista":"Stahnke S, Döring H, Kusch C, de Gorter DJJ, Dütting S, Guledani A, Pleines I, Schnoor M, Sixt MK, Geffers R, Rohde M, Müsken M, Kage F, Steffen A, Faix J, Nieswandt B, Rottner K, Stradal TEB. 2021. Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion. Current Biology. 31(10), 2051–2064.e8.","chicago":"Stahnke, Stephanie, Hermann Döring, Charly Kusch, David J.J. de Gorter, Sebastian Dütting, Aleks Guledani, Irina Pleines, et al. “Loss of Hem1 Disrupts Macrophage Function and Impacts Migration, Phagocytosis, and Integrin-Mediated Adhesion.” <i>Current Biology</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.cub.2021.02.043\">https://doi.org/10.1016/j.cub.2021.02.043</a>.","ieee":"S. Stahnke <i>et al.</i>, “Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion,” <i>Current Biology</i>, vol. 31, no. 10. Elsevier, p. 2051–2064.e8, 2021."},"oa":1,"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","main_file_link":[{"url":"https://doi.org/10.1101/2020.03.24.005835","open_access":"1"}],"day":"24","article_processing_charge":"No","page":"2051-2064.e8","abstract":[{"text":"Hematopoietic-specific protein 1 (Hem1) is an essential subunit of the WAVE regulatory complex (WRC) in immune cells. WRC is crucial for Arp2/3 complex activation and the protrusion of branched actin filament networks. Moreover, Hem1 loss of function in immune cells causes autoimmune diseases in humans. Here, we show that genetic removal of Hem1 in macrophages diminishes frequency and efficacy of phagocytosis as well as phagocytic cup formation in addition to defects in lamellipodial protrusion and migration. Moreover, Hem1-null macrophages displayed strong defects in cell adhesion despite unaltered podosome formation and concomitant extracellular matrix degradation. Specifically, dynamics of both adhesion and de-adhesion as well as concomitant phosphorylation of paxillin and focal adhesion kinase (FAK) were significantly compromised. Accordingly, disruption of WRC function in non-hematopoietic cells coincided with both defects in adhesion turnover and altered FAK and paxillin phosphorylation. Consistently, platelets exhibited reduced adhesion and diminished integrin αIIbβ3 activation upon WRC removal. Interestingly, adhesion phenotypes, but not lamellipodia formation, were partially rescued by small molecule activation of FAK. A full rescue of the phenotype, including lamellipodia formation, required not only the presence of WRCs but also their binding to and activation by Rac. Collectively, our results uncover that WRC impacts on integrin-dependent processes in a FAK-dependent manner, controlling formation and dismantling of adhesions, relevant for properly grabbing onto extracellular surfaces and particles during cell edge expansion, like in migration or phagocytosis.","lang":"eng"}],"year":"2021","acknowledgement":"We are grateful to Silvia Prettin, Ina Schleicher, and Petra Hagendorff for expert technical assistance; David Dettbarn for animal keeping and breeding; and Lothar Gröbe and Maria Höxter for cell sorting. We also thank Werner Tegge for peptides and Giorgio Scita for antibodies. This work was supported, in part, by the Deutsche Forschungsgemeinschaft (DFG), Priority Programm SPP1150 (to T.E.B.S., K.R., and M. Sixt), and by DFG grant GRK2223/1 (to K.R.). T.E.B.S. acknowledges support by the Helmholtz Society through HGF impulse fund W2/W3-066 and M. Schnoor by the Mexican Council for Science and Technology (CONACyT, 284292 ), Fund SEP-Cinvestav ( 108 ), and the Royal Society, UK (Newton Advanced Fellowship, NAF/R1/180017 ).","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"scopus_import":"1","_id":"10834","oa_version":"Preprint","publication_identifier":{"issn":["0960-9822"]},"language":[{"iso":"eng"}],"publication":"Current Biology","month":"05","isi":1,"volume":31,"issue":"10","type":"journal_article","external_id":{"pmid":["33711252"],"isi":["000654652200002"]},"title":"Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion","date_updated":"2023-08-17T07:01:14Z","article_type":"original","department":[{"_id":"MiSi"}],"quality_controlled":"1"},{"quality_controlled":"1","department":[{"_id":"Bio"}],"date_updated":"2023-09-05T15:58:53Z","article_type":"letter_note","external_id":{"pmid":["32990982"],"isi":["000577708800001"]},"title":"PIPE‐cloned human IgE and IgG4 antibodies: New tools for investigating cow's milk allergy and tolerance","ddc":["570"],"type":"journal_article","issue":"5","has_accepted_license":"1","volume":76,"isi":1,"publication":"Allergy","month":"05","file_date_updated":"2022-03-08T11:23:16Z","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1398-9995"],"issn":["0105-4538"]},"oa_version":"Published Version","scopus_import":"1","_id":"10836","acknowledgement":"This  work  was  supported  by  the  Austrian  Science  Fund  (FWF)  grants  MCCA  W1248-B30  and  SFB  F4606-B28  to  EJJ.  CP  received  a  short-term research fellowship of the European Federation of Immunological Societies  (EFIS-IL)  for  a  research  visit  at  Biocruces  Bizkaia  Health  Research  Institute,  Barakaldo,  Spain.  VKK  received  an  EFIS-IL  short-term  research  fellowship  for  a  research  visit  at  King’s  College  London.  The research was funded by the National Institute for Health Research (NIHR) Biomedical Research Centre (BRC) based at Guy's and St Thomas' NHS Foundation Trust and King's College London (IS-BRC-1215-20006) (SNK).  The  authors  acknowledge  support  by  the  Medical  Research  Council (MR/L023091/1) (SNK); Breast Cancer Now (147; KCL-BCN-Q3)(SNK); Cancer Research UK (C30122/A11527; C30122/A15774) (SNK); Cancer  Research  UK  King's  Health  Partners  Centre  at  King's  College  London   (C604/A25135)   (SNK);   CRUK/NIHR   in   England/DoH   for   Scotland,  Wales  and  Northern  Ireland  Experimental  Cancer  Medicine  Centre  (C10355/A15587)  (SNK).  The  views  expressed  are  those  of  the  author(s)  and  not  necessarily  those  of  the  NHS,  the  NIHR  or  the  Department  of  Health.  Additionally,  this  work  was  funded  by  Instituto  de  Salud  Carlos  III  through  the  project  \"PI16/01223\"  (Co-funded  by  European Regional Development Fund; “A way to make Europe”) to FB and  by  the  Department  of  Health,  Basque  Government  through  the  project “2019111031” to OZ. OZ is recipient of a Sara Borrell 2017 post-doctoral contract “CD17/00128” funded by Instituto de Salud Carlos III (Co-funded by European Social Fund; “Investing in your future”).","keyword":["Immunology","Immunology and Allergy"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"year":"2021","page":"1553-1556","article_processing_charge":"No","day":"01","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Pranger CL, Singer J, Köhler VK, Pali‐Schöll I, Fiocchi A, Karagiannis SN, Zenarruzabeitia O, Borrego F, Jensen‐Jarolim E. 2021. PIPE‐cloned human IgE and IgG4 antibodies: New tools for investigating cow’s milk allergy and tolerance. Allergy. 76(5), 1553–1556.","mla":"Pranger, Christina L., et al. “PIPE‐cloned Human IgE and IgG4 Antibodies: New Tools for Investigating Cow’s Milk Allergy and Tolerance.” <i>Allergy</i>, vol. 76, no. 5, Wiley, 2021, pp. 1553–56, doi:<a href=\"https://doi.org/10.1111/all.14604\">10.1111/all.14604</a>.","chicago":"Pranger, Christina L., Judit Singer, Verena K. Köhler, Isabella Pali‐Schöll, Alessandro Fiocchi, Sophia N. Karagiannis, Olatz Zenarruzabeitia, Francisco Borrego, and Erika Jensen‐Jarolim. “PIPE‐cloned Human IgE and IgG4 Antibodies: New Tools for Investigating Cow’s Milk Allergy and Tolerance.” <i>Allergy</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/all.14604\">https://doi.org/10.1111/all.14604</a>.","ieee":"C. L. Pranger <i>et al.</i>, “PIPE‐cloned human IgE and IgG4 antibodies: New tools for investigating cow’s milk allergy and tolerance,” <i>Allergy</i>, vol. 76, no. 5. Wiley, pp. 1553–1556, 2021.","apa":"Pranger, C. L., Singer, J., Köhler, V. K., Pali‐Schöll, I., Fiocchi, A., Karagiannis, S. N., … Jensen‐Jarolim, E. (2021). PIPE‐cloned human IgE and IgG4 antibodies: New tools for investigating cow’s milk allergy and tolerance. <i>Allergy</i>. Wiley. <a href=\"https://doi.org/10.1111/all.14604\">https://doi.org/10.1111/all.14604</a>","ama":"Pranger CL, Singer J, Köhler VK, et al. PIPE‐cloned human IgE and IgG4 antibodies: New tools for investigating cow’s milk allergy and tolerance. <i>Allergy</i>. 2021;76(5):1553-1556. doi:<a href=\"https://doi.org/10.1111/all.14604\">10.1111/all.14604</a>","short":"C.L. Pranger, J. Singer, V.K. Köhler, I. Pali‐Schöll, A. Fiocchi, S.N. Karagiannis, O. Zenarruzabeitia, F. Borrego, E. Jensen‐Jarolim, Allergy 76 (2021) 1553–1556."},"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"9526f9554112fc027c9f7fa540c488cd","date_created":"2022-03-08T11:23:16Z","creator":"dernst","success":1,"file_size":626081,"file_name":"2021_Allergy_Pranger.pdf","date_updated":"2022-03-08T11:23:16Z","file_id":"10837"}],"oa":1,"status":"public","date_published":"2021-05-01T00:00:00Z","intvolume":"        76","author":[{"last_name":"Pranger","full_name":"Pranger, Christina L.","first_name":"Christina L."},{"id":"36432834-F248-11E8-B48F-1D18A9856A87","first_name":"Judit","full_name":"Fazekas-Singer, Judit","last_name":"Fazekas-Singer","orcid":"0000-0002-8777-3502"},{"first_name":"Verena K.","full_name":"Köhler, Verena K.","last_name":"Köhler"},{"first_name":"Isabella","full_name":"Pali‐Schöll, Isabella","last_name":"Pali‐Schöll"},{"full_name":"Fiocchi, Alessandro","last_name":"Fiocchi","first_name":"Alessandro"},{"first_name":"Sophia N.","full_name":"Karagiannis, Sophia N.","last_name":"Karagiannis"},{"first_name":"Olatz","full_name":"Zenarruzabeitia, Olatz","last_name":"Zenarruzabeitia"},{"last_name":"Borrego","full_name":"Borrego, Francisco","first_name":"Francisco"},{"first_name":"Erika","full_name":"Jensen‐Jarolim, Erika","last_name":"Jensen‐Jarolim"}],"publisher":"Wiley","pmid":1,"date_created":"2022-03-08T11:19:05Z","doi":"10.1111/all.14604"},{"quality_controlled":"1","department":[{"_id":"BeVi"}],"date_updated":"2024-10-09T21:01:47Z","article_type":"original","external_id":{"pmid":["33638231"],"isi":["000669439700001"]},"title":"Using replicate hybrid zones to understand the genomic basis of adaptive divergence","ddc":["570"],"issue":"15","type":"journal_article","publication":"Molecular Ecology","isi":1,"month":"08","volume":30,"has_accepted_license":"1","language":[{"iso":"eng"}],"file_date_updated":"2022-03-08T11:31:30Z","oa_version":"Published Version","publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"acknowledgement":"We thank everyone who helped with fieldwork, snail processing and DNA extractions, particularly Laura Brettell, Mårten Duvetorp, Juan Galindo, Anne-Lise Liabot, Mark Ravinet, Irena Senčić and Zuzanna Zagrodzka. We are also grateful to Edinburgh Genomics for library preparation and sequencing, to Stuart Baird and Mark Ravinet for helpful discussions, and to three anonymous reviewers for their constructive comments. This work was supported by the Natural Environment Research Council (NE/K014021/1), the European Research Council (AdG-693030-BARRIERS), Swedish Research Councils Formas and Vetenskapsrådet through a Linnaeus grant to the Centre for Marine Evolutionary Biology (217-2008-1719), the European Regional Development Fund (POCI-01-0145-FEDER-030628), and the Fundação para a iência e a Tecnologia,\r\nPortugal (PTDC/BIA-EVL/\r\n30628/2017). A.M.W. and R.F. were\r\nfunded by the European Union’s Horizon 2020 research and innovation\r\nprogramme under Marie Skłodowska-Curie\r\ngrant agreements\r\nno. 754411/797747 and no. 706376, respectively.","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"scopus_import":"1","_id":"10838","page":"3797-3814","abstract":[{"text":"Combining hybrid zone analysis with genomic data is a promising approach to understanding the genomic basis of adaptive divergence. It allows for the identification of genomic regions underlying barriers to gene flow. It also provides insights into spatial patterns of allele frequency change, informing about the interplay between environmental factors, dispersal and selection. However, when only a single hybrid zone is analysed, it is difficult to separate patterns generated by selection from those resulting from chance. Therefore, it is beneficial to look for repeatable patterns across replicate hybrid zones in the same system. We applied this approach to the marine snail Littorina saxatilis, which contains two ecotypes, adapted to wave-exposed rocks vs. high-predation boulder fields. The existence of numerous hybrid zones between ecotypes offered the opportunity to test for the repeatability of genomic architectures and spatial patterns of divergence. We sampled and phenotyped snails from seven replicate hybrid zones on the Swedish west coast and genotyped them for thousands of single nucleotide polymorphisms. Shell shape and size showed parallel clines across all zones. Many genomic regions showing steep clines and/or high differentiation were shared among hybrid zones, consistent with a common evolutionary history and extensive gene flow between zones, and supporting the importance of these regions for divergence. In particular, we found that several large putative inversions contribute to divergence in all locations. Additionally, we found evidence for consistent displacement of clines from the boulder–rock transition. Our results demonstrate patterns of spatial variation that would not be accessible without continuous spatial sampling, a large genomic data set and replicate hybrid zones.","lang":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"year":"2021","day":"01","article_processing_charge":"No","citation":{"mla":"Westram, Anja M., et al. “Using Replicate Hybrid Zones to Understand the Genomic Basis of Adaptive Divergence.” <i>Molecular Ecology</i>, vol. 30, no. 15, Wiley, 2021, pp. 3797–814, doi:<a href=\"https://doi.org/10.1111/mec.15861\">10.1111/mec.15861</a>.","ista":"Westram AM, Faria R, Johannesson K, Butlin R. 2021. Using replicate hybrid zones to understand the genomic basis of adaptive divergence. Molecular Ecology. 30(15), 3797–3814.","ieee":"A. M. Westram, R. Faria, K. Johannesson, and R. Butlin, “Using replicate hybrid zones to understand the genomic basis of adaptive divergence,” <i>Molecular Ecology</i>, vol. 30, no. 15. Wiley, pp. 3797–3814, 2021.","chicago":"Westram, Anja M, Rui Faria, Kerstin Johannesson, and Roger Butlin. “Using Replicate Hybrid Zones to Understand the Genomic Basis of Adaptive Divergence.” <i>Molecular Ecology</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/mec.15861\">https://doi.org/10.1111/mec.15861</a>.","ama":"Westram AM, Faria R, Johannesson K, Butlin R. Using replicate hybrid zones to understand the genomic basis of adaptive divergence. <i>Molecular Ecology</i>. 2021;30(15):3797-3814. doi:<a href=\"https://doi.org/10.1111/mec.15861\">10.1111/mec.15861</a>","short":"A.M. Westram, R. Faria, K. Johannesson, R. Butlin, Molecular Ecology 30 (2021) 3797–3814.","apa":"Westram, A. M., Faria, R., Johannesson, K., &#38; Butlin, R. (2021). Using replicate hybrid zones to understand the genomic basis of adaptive divergence. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.15861\">https://doi.org/10.1111/mec.15861</a>"},"publication_status":"published","file":[{"access_level":"open_access","checksum":"d5611f243ceb63a0e091d6662ebd9cda","relation":"main_file","content_type":"application/pdf","success":1,"creator":"dernst","date_created":"2022-03-08T11:31:30Z","file_id":"10839","date_updated":"2022-03-08T11:31:30Z","file_size":1726548,"file_name":"2021_MolecularEcology_Westram.pdf"}],"oa":1,"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2021-08-01T00:00:00Z","corr_author":"1","publisher":"Wiley","pmid":1,"date_created":"2022-03-08T11:28:32Z","doi":"10.1111/mec.15861","intvolume":"        30","author":[{"last_name":"Westram","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M"},{"last_name":"Faria","full_name":"Faria, Rui","first_name":"Rui"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"last_name":"Butlin","full_name":"Butlin, Roger","first_name":"Roger"}]},{"type":"conference","conference":{"location":"Virtual, Online","end_date":"2021-08-27","start_date":"2021-08-19","name":"IJCAI: International Joint Conferences on Artificial Intelligence"},"ddc":["000"],"title":"Solving partially observable stochastic shortest-path games","ec_funded":1,"date_updated":"2026-06-18T10:41:02Z","project":[{"call_identifier":"H2020","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"quality_controlled":"1","department":[{"_id":"KrCh"}],"oa_version":"Published Version","publication_identifier":{"isbn":["9780999241196"],"issn":["1045-0823"]},"language":[{"iso":"eng"}],"month":"09","publication":"30th International Joint Conference on Artificial Intelligence","article_processing_charge":"No","day":"01","abstract":[{"lang":"eng","text":"We study the two-player zero-sum extension of the partially observable stochastic shortest-path problem where one agent has only partial information about the environment. We formulate this problem as a partially observable stochastic game (POSG): given a set of target states and negative rewards for each transition, the player with imperfect information maximizes the expected undiscounted total reward until a target state is reached. The second player with the perfect information aims for the opposite. We base our formalism on POSGs with one-sided observability (OS-POSGs) and give the following contributions: (1) we introduce a novel heuristic search value iteration algorithm that iteratively solves depth-limited variants of the game, (2) we derive the bound on the depth guaranteeing an arbitrary precision, (3) we propose a novel upper-bound estimation that allows early terminations, and (4) we experimentally evaluate the algorithm on a pursuit-evasion game."}],"year":"2021","page":"4182-4189","scopus_import":"1","_id":"10847","acknowledgement":"This research was supported by the Czech Science Foundation (no. 19-24384Y), by the OP VVV MEYS funded project CZ.02.1.01/0.0/0.0/16 019/0000765 “Research Center for Informatics”, by the ERC CoG 863818 (ForM-SMArt), and by the Combat Capabilities Development Command Army Research Laboratory and was accomplished under Cooperative\r\nAgreement Number W911NF-13-2-0045 (ARL Cyber Security CRA). The views and conclusions contained in this document are those of the authors and should not be interpreted as\r\nrepresenting the official policies, either expressed or implied, of the Combat Capabilities Development Command Army Research Laboratory or the U.S. Government. The U.S. Government is authorized to reproduce and distribute reprints for Government purposes not withstanding any copyright notation here on. ","author":[{"last_name":"Tomášek","full_name":"Tomášek, Petr","first_name":"Petr"},{"full_name":"Horák, Karel","last_name":"Horák","first_name":"Karel"},{"full_name":"Aradhye, Aditya","last_name":"Aradhye","first_name":"Aditya"},{"first_name":"Branislav","last_name":"Bošanský","full_name":"Bošanský, Branislav"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"}],"publisher":"International Joint Conferences on Artificial Intelligence","doi":"10.24963/ijcai.2021/575","date_created":"2022-03-13T23:01:47Z","date_published":"2021-09-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://doi.org/10.24963/ijcai.2021/575","open_access":"1"}],"publication_status":"published","citation":{"chicago":"Tomášek, Petr, Karel Horák, Aditya Aradhye, Branislav Bošanský, and Krishnendu Chatterjee. “Solving Partially Observable Stochastic Shortest-Path Games.” In <i>30th International Joint Conference on Artificial Intelligence</i>, 4182–89. International Joint Conferences on Artificial Intelligence, 2021. <a href=\"https://doi.org/10.24963/ijcai.2021/575\">https://doi.org/10.24963/ijcai.2021/575</a>.","ieee":"P. Tomášek, K. Horák, A. Aradhye, B. Bošanský, and K. Chatterjee, “Solving partially observable stochastic shortest-path games,” in <i>30th International Joint Conference on Artificial Intelligence</i>, Virtual, Online, 2021, pp. 4182–4189.","mla":"Tomášek, Petr, et al. “Solving Partially Observable Stochastic Shortest-Path Games.” <i>30th International Joint Conference on Artificial Intelligence</i>, International Joint Conferences on Artificial Intelligence, 2021, pp. 4182–89, doi:<a href=\"https://doi.org/10.24963/ijcai.2021/575\">10.24963/ijcai.2021/575</a>.","ista":"Tomášek P, Horák K, Aradhye A, Bošanský B, Chatterjee K. 2021. Solving partially observable stochastic shortest-path games. 30th International Joint Conference on Artificial Intelligence. IJCAI: International Joint Conferences on Artificial Intelligence, 4182–4189.","apa":"Tomášek, P., Horák, K., Aradhye, A., Bošanský, B., &#38; Chatterjee, K. (2021). Solving partially observable stochastic shortest-path games. In <i>30th International Joint Conference on Artificial Intelligence</i> (pp. 4182–4189). Virtual, Online: International Joint Conferences on Artificial Intelligence. <a href=\"https://doi.org/10.24963/ijcai.2021/575\">https://doi.org/10.24963/ijcai.2021/575</a>","ama":"Tomášek P, Horák K, Aradhye A, Bošanský B, Chatterjee K. Solving partially observable stochastic shortest-path games. In: <i>30th International Joint Conference on Artificial Intelligence</i>. International Joint Conferences on Artificial Intelligence; 2021:4182-4189. doi:<a href=\"https://doi.org/10.24963/ijcai.2021/575\">10.24963/ijcai.2021/575</a>","short":"P. Tomášek, K. Horák, A. Aradhye, B. Bošanský, K. Chatterjee, in:, 30th International Joint Conference on Artificial Intelligence, International Joint Conferences on Artificial Intelligence, 2021, pp. 4182–4189."},"oa":1,"status":"public"},{"language":[{"iso":"eng"}],"volume":33,"publication":"Reviews in Mathematical Physics","isi":1,"month":"02","oa_version":"Preprint","publication_identifier":{"eissn":["1793-6659"],"issn":["0129-055X"]},"article_type":"original","project":[{"call_identifier":"H2020","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems"}],"date_updated":"2025-04-14T07:26:58Z","quality_controlled":"1","department":[{"_id":"RoSe"}],"type":"journal_article","issue":"01","title":"The polaron at strong coupling","arxiv":1,"external_id":{"isi":["000613313200013"],"arxiv":["1912.12509"]},"article_number":"2060012","ec_funded":1,"date_published":"2021-02-01T00:00:00Z","corr_author":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.12509"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","oa":1,"publication_status":"published","citation":{"short":"R. Seiringer, Reviews in Mathematical Physics 33 (2021).","ama":"Seiringer R. The polaron at strong coupling. <i>Reviews in Mathematical Physics</i>. 2021;33(01). doi:<a href=\"https://doi.org/10.1142/s0129055x20600120\">10.1142/s0129055x20600120</a>","apa":"Seiringer, R. (2021). The polaron at strong coupling. <i>Reviews in Mathematical Physics</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1142/s0129055x20600120\">https://doi.org/10.1142/s0129055x20600120</a>","mla":"Seiringer, Robert. “The Polaron at Strong Coupling.” <i>Reviews in Mathematical Physics</i>, vol. 33, no. 01, 2060012, World Scientific Publishing, 2021, doi:<a href=\"https://doi.org/10.1142/s0129055x20600120\">10.1142/s0129055x20600120</a>.","ista":"Seiringer R. 2021. The polaron at strong coupling. Reviews in Mathematical Physics. 33(01), 2060012.","chicago":"Seiringer, Robert. “The Polaron at Strong Coupling.” <i>Reviews in Mathematical Physics</i>. World Scientific Publishing, 2021. <a href=\"https://doi.org/10.1142/s0129055x20600120\">https://doi.org/10.1142/s0129055x20600120</a>.","ieee":"R. Seiringer, “The polaron at strong coupling,” <i>Reviews in Mathematical Physics</i>, vol. 33, no. 01. World Scientific Publishing, 2021."},"author":[{"last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"intvolume":"        33","date_created":"2022-03-18T08:11:34Z","doi":"10.1142/s0129055x20600120","publisher":"World Scientific Publishing","year":"2021","abstract":[{"lang":"eng","text":" We review old and new results on the Fröhlich polaron model. The discussion includes the validity of the (classical) Pekar approximation in the strong coupling limit, quantum corrections to this limit, as well as the divergence of the effective polaron mass."}],"_id":"10852","scopus_import":"1","keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"acknowledgement":"This work was supported by the European Research Council (ERC) under the Euro-pean Union’s Horizon 2020 research and innovation programme (grant agreementNo. 694227).","article_processing_charge":"No","day":"01"},{"oa_version":"Preprint","publication_identifier":{"isbn":["9781450380706"]},"month":"07","publication":"Proceedings of the 33rd ACM Symposium on Parallelism in Algorithms and Architectures","language":[{"iso":"eng"}],"arxiv":1,"conference":{"name":"SPAA: Symposium on Parallelism in Algorithms and Architectures","end_date":"2021-07-08","start_date":"2021-07-06","location":"Virtual, Online"},"external_id":{"arxiv":["2105.08098"]},"title":"A scalable concurrent algorithm for dynamic connectivity","type":"conference","quality_controlled":"1","department":[{"_id":"DaAl"}],"date_updated":"2022-03-18T08:45:46Z","publisher":"Association for Computing Machinery","doi":"10.1145/3409964.3461810","date_created":"2022-03-18T08:21:47Z","author":[{"first_name":"Alexander","last_name":"Fedorov","full_name":"Fedorov, Alexander"},{"full_name":"Koval, Nikita","last_name":"Koval","first_name":"Nikita"},{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"citation":{"short":"A. Fedorov, N. Koval, D.-A. Alistarh, in:, Proceedings of the 33rd ACM Symposium on Parallelism in Algorithms and Architectures, Association for Computing Machinery, 2021, pp. 208–220.","ama":"Fedorov A, Koval N, Alistarh D-A. A scalable concurrent algorithm for dynamic connectivity. In: <i>Proceedings of the 33rd ACM Symposium on Parallelism in Algorithms and Architectures</i>. Association for Computing Machinery; 2021:208-220. doi:<a href=\"https://doi.org/10.1145/3409964.3461810\">10.1145/3409964.3461810</a>","apa":"Fedorov, A., Koval, N., &#38; Alistarh, D.-A. (2021). A scalable concurrent algorithm for dynamic connectivity. In <i>Proceedings of the 33rd ACM Symposium on Parallelism in Algorithms and Architectures</i> (pp. 208–220). Virtual, Online: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3409964.3461810\">https://doi.org/10.1145/3409964.3461810</a>","ieee":"A. Fedorov, N. Koval, and D.-A. Alistarh, “A scalable concurrent algorithm for dynamic connectivity,” in <i>Proceedings of the 33rd ACM Symposium on Parallelism in Algorithms and Architectures</i>, Virtual, Online, 2021, pp. 208–220.","chicago":"Fedorov, Alexander, Nikita Koval, and Dan-Adrian Alistarh. “A Scalable Concurrent Algorithm for Dynamic Connectivity.” In <i>Proceedings of the 33rd ACM Symposium on Parallelism in Algorithms and Architectures</i>, 208–20. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3409964.3461810\">https://doi.org/10.1145/3409964.3461810</a>.","ista":"Fedorov A, Koval N, Alistarh D-A. 2021. A scalable concurrent algorithm for dynamic connectivity. Proceedings of the 33rd ACM Symposium on Parallelism in Algorithms and Architectures. SPAA: Symposium on Parallelism in Algorithms and Architectures, 208–220.","mla":"Fedorov, Alexander, et al. “A Scalable Concurrent Algorithm for Dynamic Connectivity.” <i>Proceedings of the 33rd ACM Symposium on Parallelism in Algorithms and Architectures</i>, Association for Computing Machinery, 2021, pp. 208–20, doi:<a href=\"https://doi.org/10.1145/3409964.3461810\">10.1145/3409964.3461810</a>."},"publication_status":"published","status":"public","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2105.08098"}],"date_published":"2021-07-01T00:00:00Z","article_processing_charge":"No","day":"01","scopus_import":"1","_id":"10853","page":"208-220","abstract":[{"lang":"eng","text":"Dynamic Connectivity is a fundamental algorithmic graph problem, motivated by a wide range of applications to social and communication networks and used as a building block in various other algorithms, such as the bi-connectivity and the dynamic minimal spanning tree problems. In brief, we wish to maintain the connected components of the graph under dynamic edge insertions and deletions. In the sequential case, the problem has been well-studied from both theoretical and practical perspectives. However, much less is known about efficient concurrent solutions to this problem. This is the gap we address in this paper. We start from one of the classic data structures used to solve this problem, the Euler Tour Tree. Our first contribution is a non-blocking single-writer implementation of it. We leverage this data structure to obtain the first truly concurrent generalization of dynamic connectivity, which preserves the time complexity of its sequential counterpart, but is also scalable in practice. To achieve this, we rely on three main techniques. The first is to ensure that connectivity queries, which usually dominate real-world workloads, are non-blocking. The second non-trivial technique expands the above idea by making all queries that do not change the connectivity structure non-blocking. The third ingredient is applying fine-grained locking for updating the connected components, which allows operations on disjoint components to occur in parallel. We evaluate the resulting algorithm on various workloads, executing on both real and synthetic graphs. The results show the efficiency of each of the proposed optimizations; the most efficient variant improves the performance of a coarse-grained based implementation on realistic scenarios up to 6x on average and up to 30x when connectivity queries dominate."}],"year":"2021"},{"day":"01","article_processing_charge":"No","acknowledgement":"We thank Jukka Suomela for discussions. We also thank our shepherd Mohammad Hajiesmaili and the reviewers for their time and suggestions on how to improve the paper. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML), from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska–Curie grant agreement No. 840605, from the Vienna Science and Technology Fund (WWTF) project WHATIF, ICT19-045, 2020-2024, and from the Austrian Science Fund (FWF) and netIDEE SCIENCE project P 33775-N.","_id":"10854","scopus_import":"1","page":"71-72","year":"2021","abstract":[{"text":"Consider a distributed task where the communication network is fixed but the local inputs given to the nodes of the distributed system may change over time. In this work, we explore the following question: if some of the local inputs change, can an existing solution be updated efficiently, in a dynamic and distributed manner?\r\nTo address this question, we define the batch dynamic CONGEST model in which we are given a bandwidth-limited communication network and a dynamic edge labelling defines the problem input. The task is to maintain a solution to a graph problem on the labelled graph under batch changes. We investigate, when a batch of alpha edge label changes arrive, - how much time as a function of alpha we need to update an existing solution, and - how much information the nodes have to keep in local memory between batches in order to update the solution quickly.\r\nOur work lays the foundations for the theory of input-dynamic distributed network algorithms. We give a general picture of the complexity landscape in this model, design both universal algorithms and algorithms for concrete problems, and present a general framework for lower bounds. The diverse time complexity of our model spans from constant time, through time polynomial in alpha, and to alpha time, which we show to be enough for any task.","lang":"eng"}],"date_created":"2022-03-18T08:48:41Z","doi":"10.1145/3410220.3453923","publisher":"Association for Computing Machinery","author":[{"last_name":"Foerster","full_name":"Foerster, Klaus-Tycho","first_name":"Klaus-Tycho"},{"first_name":"Janne","id":"C5402D42-15BC-11E9-A202-CA2BE6697425","last_name":"Korhonen","full_name":"Korhonen, Janne"},{"full_name":"Paz, Ami","last_name":"Paz","first_name":"Ami"},{"orcid":"0000-0002-6432-6646","last_name":"Rybicki","full_name":"Rybicki, Joel","first_name":"Joel","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schmid, Stefan","last_name":"Schmid","first_name":"Stefan"}],"oa":1,"status":"public","citation":{"ama":"Foerster K-T, Korhonen J, Paz A, Rybicki J, Schmid S. Input-dynamic distributed algorithms for communication networks. In: <i>Abstract Proceedings of the 2021 ACM SIGMETRICS / International Conference on Measurement and Modeling of Computer Systems</i>. Association for Computing Machinery; 2021:71-72. doi:<a href=\"https://doi.org/10.1145/3410220.3453923\">10.1145/3410220.3453923</a>","short":"K.-T. Foerster, J. Korhonen, A. Paz, J. Rybicki, S. Schmid, in:, Abstract Proceedings of the 2021 ACM SIGMETRICS / International Conference on Measurement and Modeling of Computer Systems, Association for Computing Machinery, 2021, pp. 71–72.","apa":"Foerster, K.-T., Korhonen, J., Paz, A., Rybicki, J., &#38; Schmid, S. (2021). Input-dynamic distributed algorithms for communication networks. In <i>Abstract Proceedings of the 2021 ACM SIGMETRICS / International Conference on Measurement and Modeling of Computer Systems</i> (pp. 71–72). Virtual, Online: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3410220.3453923\">https://doi.org/10.1145/3410220.3453923</a>","chicago":"Foerster, Klaus-Tycho, Janne Korhonen, Ami Paz, Joel Rybicki, and Stefan Schmid. “Input-Dynamic Distributed Algorithms for Communication Networks.” In <i>Abstract Proceedings of the 2021 ACM SIGMETRICS / International Conference on Measurement and Modeling of Computer Systems</i>, 71–72. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3410220.3453923\">https://doi.org/10.1145/3410220.3453923</a>.","ieee":"K.-T. Foerster, J. Korhonen, A. Paz, J. Rybicki, and S. Schmid, “Input-dynamic distributed algorithms for communication networks,” in <i>Abstract Proceedings of the 2021 ACM SIGMETRICS / International Conference on Measurement and Modeling of Computer Systems</i>, Virtual, Online, 2021, pp. 71–72.","mla":"Foerster, Klaus-Tycho, et al. “Input-Dynamic Distributed Algorithms for Communication Networks.” <i>Abstract Proceedings of the 2021 ACM SIGMETRICS / International Conference on Measurement and Modeling of Computer Systems</i>, Association for Computing Machinery, 2021, pp. 71–72, doi:<a href=\"https://doi.org/10.1145/3410220.3453923\">10.1145/3410220.3453923</a>.","ista":"Foerster K-T, Korhonen J, Paz A, Rybicki J, Schmid S. 2021. Input-dynamic distributed algorithms for communication networks. Abstract Proceedings of the 2021 ACM SIGMETRICS / International Conference on Measurement and Modeling of Computer Systems. SIGMETRICS: International Conference on Measurement and Modeling of Computer Systems, 71–72."},"publication_status":"published","main_file_link":[{"url":"https://arxiv.org/abs/2005.07637","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-05-01T00:00:00Z","ec_funded":1,"external_id":{"arxiv":["2005.07637"]},"conference":{"end_date":"2021-06-18","start_date":"2021-06-14","location":"Virtual, Online","name":"SIGMETRICS: International Conference on Measurement and Modeling of Computer Systems"},"title":"Input-dynamic distributed algorithms for communication networks","arxiv":1,"type":"conference","quality_controlled":"1","department":[{"_id":"DaAl"}],"project":[{"grant_number":"805223","call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning","_id":"268A44D6-B435-11E9-9278-68D0E5697425"},{"grant_number":"840605","call_identifier":"H2020","_id":"26A5D39A-B435-11E9-9278-68D0E5697425","name":"Coordination in constrained and natural distributed systems"}],"date_updated":"2025-04-14T13:52:09Z","oa_version":"Preprint","publication_identifier":{"isbn":["9781450380720"]},"month":"05","publication":"Abstract Proceedings of the 2021 ACM SIGMETRICS / International Conference on Measurement and Modeling of Computer Systems","language":[{"iso":"eng"}],"related_material":{"record":[{"id":"10855","relation":"extended_version","status":"public"}]}},{"publisher":"Association for Computing Machinery","date_created":"2022-03-18T09:10:27Z","doi":"10.1145/3447384","intvolume":"         5","author":[{"first_name":"Klaus-Tycho","full_name":"Foerster, Klaus-Tycho","last_name":"Foerster"},{"last_name":"Korhonen","full_name":"Korhonen, Janne","id":"C5402D42-15BC-11E9-A202-CA2BE6697425","first_name":"Janne"},{"first_name":"Ami","full_name":"Paz, Ami","last_name":"Paz"},{"first_name":"Joel","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","full_name":"Rybicki, Joel","orcid":"0000-0002-6432-6646","last_name":"Rybicki"},{"full_name":"Schmid, Stefan","last_name":"Schmid","first_name":"Stefan"}],"citation":{"chicago":"Foerster, Klaus-Tycho, Janne Korhonen, Ami Paz, Joel Rybicki, and Stefan Schmid. “Input-Dynamic Distributed Algorithms for Communication Networks.” <i>Proceedings of the ACM on Measurement and Analysis of Computing Systems</i>. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3447384\">https://doi.org/10.1145/3447384</a>.","ieee":"K.-T. Foerster, J. Korhonen, A. Paz, J. Rybicki, and S. Schmid, “Input-dynamic distributed algorithms for communication networks,” <i>Proceedings of the ACM on Measurement and Analysis of Computing Systems</i>, vol. 5, no. 1. Association for Computing Machinery, pp. 1–33, 2021.","ista":"Foerster K-T, Korhonen J, Paz A, Rybicki J, Schmid S. 2021. Input-dynamic distributed algorithms for communication networks. Proceedings of the ACM on Measurement and Analysis of Computing Systems. 5(1), 1–33.","mla":"Foerster, Klaus-Tycho, et al. “Input-Dynamic Distributed Algorithms for Communication Networks.” <i>Proceedings of the ACM on Measurement and Analysis of Computing Systems</i>, vol. 5, no. 1, Association for Computing Machinery, 2021, pp. 1–33, doi:<a href=\"https://doi.org/10.1145/3447384\">10.1145/3447384</a>.","short":"K.-T. Foerster, J. Korhonen, A. Paz, J. Rybicki, S. Schmid, Proceedings of the ACM on Measurement and Analysis of Computing Systems 5 (2021) 1–33.","ama":"Foerster K-T, Korhonen J, Paz A, Rybicki J, Schmid S. Input-dynamic distributed algorithms for communication networks. <i>Proceedings of the ACM on Measurement and Analysis of Computing Systems</i>. 2021;5(1):1-33. doi:<a href=\"https://doi.org/10.1145/3447384\">10.1145/3447384</a>","apa":"Foerster, K.-T., Korhonen, J., Paz, A., Rybicki, J., &#38; Schmid, S. (2021). Input-dynamic distributed algorithms for communication networks. <i>Proceedings of the ACM on Measurement and Analysis of Computing Systems</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3447384\">https://doi.org/10.1145/3447384</a>"},"publication_status":"published","oa":1,"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://arxiv.org/abs/2005.07637","open_access":"1"}],"date_published":"2021-03-01T00:00:00Z","day":"01","article_processing_charge":"No","acknowledgement":"We thank Jukka Suomela for discussions. We also thank our shepherd Mohammad Hajiesmaili\r\nand the reviewers for their time and suggestions on how to improve the paper. This project\r\nhas received funding from the European Research Council (ERC) under the European Union’s\r\nHorizon 2020 research and innovation programme (grant agreement No 805223 ScaleML), from the European Union’s Horizon 2020 research and innovation programme under the Marie\r\nSk lodowska–Curie grant agreement No. 840605, from the Vienna Science and Technology Fund (WWTF) project WHATIF, ICT19-045, 2020-2024, and from the Austrian Science Fund (FWF) and netIDEE SCIENCE project P 33775-N.","keyword":["Computer Networks and Communications","Hardware and Architecture","Safety","Risk","Reliability and Quality","Computer Science (miscellaneous)"],"scopus_import":"1","_id":"10855","page":"1-33","abstract":[{"text":"Consider a distributed task where the communication network is fixed but the local inputs given to the nodes of the distributed system may change over time. In this work, we explore the following question: if some of the local inputs change, can an existing solution be updated efficiently, in a dynamic and distributed manner? To address this question, we define the batch dynamic \\congest model in which we are given a bandwidth-limited communication network and a dynamic edge labelling defines the problem input. The task is to maintain a solution to a graph problem on the labeled graph under batch changes. We investigate, when a batch of α edge label changes arrive, \\beginitemize \\item how much time as a function of α we need to update an existing solution, and \\item how much information the nodes have to keep in local memory between batches in order to update the solution quickly. \\enditemize Our work lays the foundations for the theory of input-dynamic distributed network algorithms. We give a general picture of the complexity landscape in this model, design both universal algorithms and algorithms for concrete problems, and present a general framework for lower bounds. In particular, we derive non-trivial upper bounds for two selected, contrasting problems: maintaining a minimum spanning tree and detecting cliques.","lang":"eng"}],"year":"2021","publication_identifier":{"issn":["2476-1249"]},"oa_version":"Preprint","month":"03","publication":"Proceedings of the ACM on Measurement and Analysis of Computing Systems","volume":5,"language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","relation":"shorter_version","id":"10854"}]},"ec_funded":1,"arxiv":1,"title":"Input-dynamic distributed algorithms for communication networks","external_id":{"arxiv":["2005.07637"]},"issue":"1","type":"journal_article","quality_controlled":"1","department":[{"_id":"DaAl"}],"date_updated":"2025-04-14T13:52:09Z","project":[{"_id":"26A5D39A-B435-11E9-9278-68D0E5697425","name":"Coordination in constrained and natural distributed systems","grant_number":"840605","call_identifier":"H2020"},{"grant_number":"805223","call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425","name":"Elastic Coordination for Scalable Machine Learning"}],"article_type":"original"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Ivanov, Grigory, and Igor Tsiutsiurupa. “On the Volume of Sections of the Cube.” <i>Analysis and Geometry in Metric Spaces</i>, vol. 9, no. 1, De Gruyter, 2021, pp. 1–18, doi:<a href=\"https://doi.org/10.1515/agms-2020-0103\">10.1515/agms-2020-0103</a>.","ista":"Ivanov G, Tsiutsiurupa I. 2021. On the volume of sections of the cube. Analysis and Geometry in Metric Spaces. 9(1), 1–18.","chicago":"Ivanov, Grigory, and Igor Tsiutsiurupa. “On the Volume of Sections of the Cube.” <i>Analysis and Geometry in Metric Spaces</i>. De Gruyter, 2021. <a href=\"https://doi.org/10.1515/agms-2020-0103\">https://doi.org/10.1515/agms-2020-0103</a>.","ieee":"G. Ivanov and I. Tsiutsiurupa, “On the volume of sections of the cube,” <i>Analysis and Geometry in Metric Spaces</i>, vol. 9, no. 1. De Gruyter, pp. 1–18, 2021.","apa":"Ivanov, G., &#38; Tsiutsiurupa, I. (2021). On the volume of sections of the cube. <i>Analysis and Geometry in Metric Spaces</i>. De Gruyter. <a href=\"https://doi.org/10.1515/agms-2020-0103\">https://doi.org/10.1515/agms-2020-0103</a>","ama":"Ivanov G, Tsiutsiurupa I. On the volume of sections of the cube. <i>Analysis and Geometry in Metric Spaces</i>. 2021;9(1):1-18. doi:<a href=\"https://doi.org/10.1515/agms-2020-0103\">10.1515/agms-2020-0103</a>","short":"G. Ivanov, I. Tsiutsiurupa, Analysis and Geometry in Metric Spaces 9 (2021) 1–18."},"publication_status":"published","file":[{"date_created":"2022-03-18T09:31:59Z","success":1,"creator":"dernst","content_type":"application/pdf","checksum":"7e615ac8489f5eae580b6517debfdc53","relation":"main_file","access_level":"open_access","file_name":"2021_AnalysisMetricSpaces_Ivanov.pdf","file_size":789801,"file_id":"10857","date_updated":"2022-03-18T09:31:59Z"}],"oa":1,"status":"public","date_published":"2021-01-29T00:00:00Z","intvolume":"         9","author":[{"first_name":"Grigory","id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E","last_name":"Ivanov","full_name":"Ivanov, Grigory"},{"full_name":"Tsiutsiurupa, Igor","last_name":"Tsiutsiurupa","first_name":"Igor"}],"publisher":"De Gruyter","date_created":"2022-03-18T09:25:14Z","doi":"10.1515/agms-2020-0103","scopus_import":"1","_id":"10856","acknowledgement":"The authors acknowledge the support of the grant of the Russian Government N 075-15-\r\n2019-1926. G.I.was supported also by the SwissNational Science Foundation grant 200021-179133. The authors are very grateful to the anonymous reviewer for valuable remarks.","keyword":["Applied Mathematics","Geometry and Topology","Analysis"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"We study the properties of the maximal volume k-dimensional sections of the n-dimensional cube [−1, 1]n. We obtain a first order necessary condition for a k-dimensional subspace to be a local maximizer of the volume of such sections, which we formulate in a geometric way. We estimate the length of the projection of a vector of the standard basis of Rn onto a k-dimensional subspace that maximizes the volume of the intersection. We \u001cnd the optimal upper bound on the volume of a planar section of the cube [−1, 1]n , n ≥ 2."}],"year":"2021","page":"1-18","article_processing_charge":"No","day":"29","has_accepted_license":"1","volume":9,"isi":1,"month":"01","publication":"Analysis and Geometry in Metric Spaces","file_date_updated":"2022-03-18T09:31:59Z","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2299-3274"]},"oa_version":"Published Version","department":[{"_id":"UlWa"}],"quality_controlled":"1","date_updated":"2023-08-17T07:07:58Z","article_type":"original","external_id":{"isi":["000734286800001"],"arxiv":["2004.02674"]},"arxiv":1,"ddc":["510"],"title":"On the volume of sections of the cube","type":"journal_article","issue":"1"},{"language":[{"iso":"eng"}],"file_date_updated":"2022-03-18T09:53:15Z","isi":1,"publication":"Nanomaterials","month":"07","has_accepted_license":"1","volume":11,"publication_identifier":{"issn":["2079-4991"]},"oa_version":"Published Version","date_updated":"2025-06-12T06:42:18Z","article_type":"original","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411"}],"quality_controlled":"1","department":[{"_id":"MaIb"}],"issue":"7","type":"journal_article","ec_funded":1,"article_number":"1827","external_id":{"pmid":["34361214"],"isi":["000676570000001"]},"title":"Enhanced thermoelectric performance of n-type Bi2Se3 nanosheets through Sn doping","ddc":["540"],"date_published":"2021-07-14T00:00:00Z","corr_author":"1","file":[{"file_size":4867547,"file_name":"2021_Nanomaterials_Li.pdf","file_id":"10859","date_updated":"2022-03-18T09:53:15Z","checksum":"f28a8b5cf80f5605828359bb398463b0","access_level":"open_access","relation":"main_file","content_type":"application/pdf","success":1,"creator":"dernst","date_created":"2022-03-18T09:53:15Z"}],"citation":{"short":"M. Li, Y. Zhang, T. Zhang, Y. Zuo, K. Xiao, J. Arbiol, J. Llorca, Y. Liu, A. Cabot, Nanomaterials 11 (2021).","ama":"Li M, Zhang Y, Zhang T, et al. Enhanced thermoelectric performance of n-type Bi2Se3 nanosheets through Sn doping. <i>Nanomaterials</i>. 2021;11(7). doi:<a href=\"https://doi.org/10.3390/nano11071827\">10.3390/nano11071827</a>","apa":"Li, M., Zhang, Y., Zhang, T., Zuo, Y., Xiao, K., Arbiol, J., … Cabot, A. (2021). Enhanced thermoelectric performance of n-type Bi2Se3 nanosheets through Sn doping. <i>Nanomaterials</i>. MDPI. <a href=\"https://doi.org/10.3390/nano11071827\">https://doi.org/10.3390/nano11071827</a>","mla":"Li, Mengyao, et al. “Enhanced Thermoelectric Performance of N-Type Bi2Se3 Nanosheets through Sn Doping.” <i>Nanomaterials</i>, vol. 11, no. 7, 1827, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/nano11071827\">10.3390/nano11071827</a>.","ista":"Li M, Zhang Y, Zhang T, Zuo Y, Xiao K, Arbiol J, Llorca J, Liu Y, Cabot A. 2021. Enhanced thermoelectric performance of n-type Bi2Se3 nanosheets through Sn doping. Nanomaterials. 11(7), 1827.","ieee":"M. Li <i>et al.</i>, “Enhanced thermoelectric performance of n-type Bi2Se3 nanosheets through Sn doping,” <i>Nanomaterials</i>, vol. 11, no. 7. MDPI, 2021.","chicago":"Li, Mengyao, Yu Zhang, Ting Zhang, Yong Zuo, Ke Xiao, Jordi Arbiol, Jordi Llorca, Yu Liu, and Andreu Cabot. “Enhanced Thermoelectric Performance of N-Type Bi2Se3 Nanosheets through Sn Doping.” <i>Nanomaterials</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/nano11071827\">https://doi.org/10.3390/nano11071827</a>."},"publication_status":"published","status":"public","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"MDPI","pmid":1,"doi":"10.3390/nano11071827","date_created":"2022-03-18T09:45:02Z","intvolume":"        11","author":[{"first_name":"Mengyao","last_name":"Li","full_name":"Li, Mengyao"},{"first_name":"Yu","last_name":"Zhang","full_name":"Zhang, Yu"},{"full_name":"Zhang, Ting","last_name":"Zhang","first_name":"Ting"},{"full_name":"Zuo, Yong","last_name":"Zuo","first_name":"Yong"},{"last_name":"Xiao","full_name":"Xiao, Ke","first_name":"Ke"},{"full_name":"Arbiol, Jordi","last_name":"Arbiol","first_name":"Jordi"},{"full_name":"Llorca, Jordi","last_name":"Llorca","first_name":"Jordi"},{"full_name":"Liu, Yu","last_name":"Liu","orcid":"0000-0001-7313-6740","first_name":"Yu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Cabot, Andreu","last_name":"Cabot","first_name":"Andreu"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"abstract":[{"text":"The cost-effective conversion of low-grade heat into electricity using thermoelectric devices requires developing alternative materials and material processing technologies able to reduce the currently high device manufacturing costs. In this direction, thermoelectric materials that do not rely on rare or toxic elements such as tellurium or lead need to be produced using high-throughput technologies not involving high temperatures and long processes. Bi2Se3 is an obvious possible Te-free alternative to Bi2Te3 for ambient temperature thermoelectric applications, but its performance is still low for practical applications, and additional efforts toward finding proper dopants are required. Here, we report a scalable method to produce Bi2Se3 nanosheets at low synthesis temperatures. We studied the influence of different dopants on the thermoelectric properties of this material. Among the elements tested, we demonstrated that Sn doping resulted in the best performance. Sn incorporation resulted in a significant improvement to the Bi2Se3 Seebeck coefficient and a reduction in the thermal conductivity in the direction of the hot-press axis, resulting in an overall 60% improvement in the thermoelectric figure of merit of Bi2Se3.","lang":"eng"}],"year":"2021","acknowledgement":"M.L., Y.Z., T.Z. and K.X. thank the China Scholarship Council for their scholarship\r\nsupport. Y.L. acknowledges funding from the European Union’s Horizon 2020 research and\r\ninnovation program under the Marie Sklodowska-Curie grant agreement No. 754411. J.L. thanks the ICREA Academia program and projects MICINN/FEDER RTI2018-093996-B-C31 and G.C. 2017 SGR 128. ICN2 acknowledges funding from the Generalitat de Catalunya 2017 SGR 327 and the Spanish MINECO ENE2017-85087-C3.","keyword":["General Materials Science","General Chemical Engineering"],"scopus_import":"1","_id":"10858","article_processing_charge":"No","day":"14"},{"date_updated":"2024-10-09T21:01:50Z","article_type":"original","department":[{"_id":"UlWa"}],"quality_controlled":"1","type":"journal_article","issue":"4","external_id":{"isi":["000730165300021"],"arxiv":["1804.10055"]},"arxiv":1,"title":"Tight frames and related geometric problems","language":[{"iso":"eng"}],"volume":64,"publication":"Canadian Mathematical Bulletin","month":"12","isi":1,"publication_identifier":{"issn":["0008-4395"],"eissn":["1496-4287"]},"oa_version":"Preprint","abstract":[{"lang":"eng","text":"A tight frame is the orthogonal projection of some orthonormal basis of Rn onto Rk. We show that a set of vectors is a tight frame if and only if the set of all cross products of these vectors is a tight frame. We reformulate a range of problems on the volume of projections (or sections) of regular polytopes in terms of tight frames and write a first-order necessary condition for local extrema of these problems. As applications, we prove new results for the problem of maximization of the volume of zonotopes."}],"year":"2021","page":"942-963","scopus_import":"1","_id":"10860","acknowledgement":"The author was supported by the Swiss National Science Foundation grant 200021_179133. The author acknowledges the financial support from the Ministry of Education and Science of the Russian Federation in the framework of MegaGrant no. 075-15-2019-1926.","keyword":["General Mathematics","Tight frame","Grassmannian","zonotope"],"day":"18","article_processing_charge":"No","date_published":"2021-12-18T00:00:00Z","corr_author":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","main_file_link":[{"url":"https://arxiv.org/abs/1804.10055","open_access":"1"}],"publication_status":"published","citation":{"ieee":"G. Ivanov, “Tight frames and related geometric problems,” <i>Canadian Mathematical Bulletin</i>, vol. 64, no. 4. Canadian Mathematical Society, pp. 942–963, 2021.","chicago":"Ivanov, Grigory. “Tight Frames and Related Geometric Problems.” <i>Canadian Mathematical Bulletin</i>. Canadian Mathematical Society, 2021. <a href=\"https://doi.org/10.4153/s000843952000096x\">https://doi.org/10.4153/s000843952000096x</a>.","ista":"Ivanov G. 2021. Tight frames and related geometric problems. Canadian Mathematical Bulletin. 64(4), 942–963.","mla":"Ivanov, Grigory. “Tight Frames and Related Geometric Problems.” <i>Canadian Mathematical Bulletin</i>, vol. 64, no. 4, Canadian Mathematical Society, 2021, pp. 942–63, doi:<a href=\"https://doi.org/10.4153/s000843952000096x\">10.4153/s000843952000096x</a>.","apa":"Ivanov, G. (2021). Tight frames and related geometric problems. <i>Canadian Mathematical Bulletin</i>. Canadian Mathematical Society. <a href=\"https://doi.org/10.4153/s000843952000096x\">https://doi.org/10.4153/s000843952000096x</a>","short":"G. Ivanov, Canadian Mathematical Bulletin 64 (2021) 942–963.","ama":"Ivanov G. Tight frames and related geometric problems. <i>Canadian Mathematical Bulletin</i>. 2021;64(4):942-963. doi:<a href=\"https://doi.org/10.4153/s000843952000096x\">10.4153/s000843952000096x</a>"},"oa":1,"status":"public","intvolume":"        64","author":[{"id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E","first_name":"Grigory","last_name":"Ivanov","full_name":"Ivanov, Grigory"}],"publisher":"Canadian Mathematical Society","doi":"10.4153/s000843952000096x","date_created":"2022-03-18T09:55:59Z"},{"date_published":"2021-11-08T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Krishna, S., Arrojo e Drigo, R., Capitanio, J. S., Ramachandra, R., Ellisman, M., &#38; Hetzer, M. (2021). Identification of long-lived proteins in the mitochondria reveals increased stability of the electron transport chain. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2021.10.008\">https://doi.org/10.1016/j.devcel.2021.10.008</a>","short":"S. Krishna, R. Arrojo e Drigo, J.S. Capitanio, R. Ramachandra, M. Ellisman, M. Hetzer, Developmental Cell 56 (2021) P2952–2965.e9.","ama":"Krishna S, Arrojo e Drigo R, Capitanio JS, Ramachandra R, Ellisman M, Hetzer M. Identification of long-lived proteins in the mitochondria reveals increased stability of the electron transport chain. <i>Developmental Cell</i>. 2021;56(21):P2952-2965.e9. doi:<a href=\"https://doi.org/10.1016/j.devcel.2021.10.008\">10.1016/j.devcel.2021.10.008</a>","chicago":"Krishna, Shefali, Rafael Arrojo e Drigo, Juliana S. Capitanio, Ranjan Ramachandra, Mark Ellisman, and Martin Hetzer. “Identification of Long-Lived Proteins in the Mitochondria Reveals Increased Stability of the Electron Transport Chain.” <i>Developmental Cell</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.devcel.2021.10.008\">https://doi.org/10.1016/j.devcel.2021.10.008</a>.","ieee":"S. Krishna, R. Arrojo e Drigo, J. S. Capitanio, R. Ramachandra, M. Ellisman, and M. Hetzer, “Identification of long-lived proteins in the mitochondria reveals increased stability of the electron transport chain,” <i>Developmental Cell</i>, vol. 56, no. 21. Elsevier, p. P2952–2965.e9, 2021.","ista":"Krishna S, Arrojo e Drigo R, Capitanio JS, Ramachandra R, Ellisman M, Hetzer M. 2021. Identification of long-lived proteins in the mitochondria reveals increased stability of the electron transport chain. Developmental Cell. 56(21), P2952–2965.e9.","mla":"Krishna, Shefali, et al. “Identification of Long-Lived Proteins in the Mitochondria Reveals Increased Stability of the Electron Transport Chain.” <i>Developmental Cell</i>, vol. 56, no. 21, Elsevier, 2021, p. P2952–2965.e9, doi:<a href=\"https://doi.org/10.1016/j.devcel.2021.10.008\">10.1016/j.devcel.2021.10.008</a>."},"publication_status":"published","status":"public","intvolume":"        56","author":[{"last_name":"Krishna","full_name":"Krishna, Shefali","first_name":"Shefali"},{"first_name":"Rafael","last_name":"Arrojo e Drigo","full_name":"Arrojo e Drigo, Rafael"},{"first_name":"Juliana S.","last_name":"Capitanio","full_name":"Capitanio, Juliana S."},{"full_name":"Ramachandra, Ranjan","last_name":"Ramachandra","first_name":"Ranjan"},{"first_name":"Mark","full_name":"Ellisman, Mark","last_name":"Ellisman"},{"orcid":"0000-0002-2111-992X","last_name":"HETZER","full_name":"HETZER, Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W"}],"publisher":"Elsevier","doi":"10.1016/j.devcel.2021.10.008","pmid":1,"date_created":"2022-04-07T07:43:14Z","abstract":[{"text":"In order to combat molecular damage, most cellular proteins undergo rapid turnover. We have previously identified large nuclear protein assemblies that can persist for years in post-mitotic tissues and are subject to age-related decline. Here, we report that mitochondria can be long lived in the mouse brain and reveal that specific mitochondrial proteins have half-lives longer than the average proteome. These mitochondrial long-lived proteins (mitoLLPs) are core components of the electron transport chain (ETC) and display increased longevity in respiratory supercomplexes. We find that COX7C, a mitoLLP that forms a stable contact site between complexes I and IV, is required for complex IV and supercomplex assembly. Remarkably, even upon depletion of COX7C transcripts, ETC function is maintained for days, effectively uncoupling mitochondrial function from ongoing transcription of its mitoLLPs. Our results suggest that modulating protein longevity within the ETC is critical for mitochondrial proteome maintenance and the robustness of mitochondrial function.","lang":"eng"}],"year":"2021","extern":"1","page":"P2952-2965.e9","scopus_import":"1","_id":"11052","keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"article_processing_charge":"No","day":"08","language":[{"iso":"eng"}],"volume":56,"publication":"Developmental Cell","month":"11","publication_identifier":{"issn":["1534-5807"]},"oa_version":"None","date_updated":"2025-12-15T10:01:56Z","article_type":"original","department":[{"_id":"MaHe"}],"quality_controlled":"1","type":"journal_article","issue":"21","external_id":{"pmid":["34715012"]},"title":"Identification of long-lived proteins in the mitochondria reveals increased stability of the electron transport chain"},{"date_created":"2022-06-05T22:01:52Z","publisher":"AAAI Press","author":[{"last_name":"Kungurtsev","full_name":"Kungurtsev, Vyacheslav","first_name":"Vyacheslav"},{"first_name":"Malcolm","full_name":"Egan, Malcolm","last_name":"Egan"},{"full_name":"Chatterjee, Bapi","orcid":"0000-0002-2742-4028","last_name":"Chatterjee","id":"3C41A08A-F248-11E8-B48F-1D18A9856A87","first_name":"Bapi"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian"}],"intvolume":"        35","date_published":"2021-05-18T00:00:00Z","oa":1,"status":"public","citation":{"chicago":"Kungurtsev, Vyacheslav, Malcolm Egan, Bapi Chatterjee, and Dan-Adrian Alistarh. “Asynchronous Optimization Methods for Efficient Training of Deep Neural Networks with Guarantees.” In <i>35th AAAI Conference on Artificial Intelligence, AAAI 2021</i>, 35:8209–16. AAAI Press, 2021.","ieee":"V. Kungurtsev, M. Egan, B. Chatterjee, and D.-A. Alistarh, “Asynchronous optimization methods for efficient training of deep neural networks with guarantees,” in <i>35th AAAI Conference on Artificial Intelligence, AAAI 2021</i>, Virtual, Online, 2021, vol. 35, no. 9B, pp. 8209–8216.","mla":"Kungurtsev, Vyacheslav, et al. “Asynchronous Optimization Methods for Efficient Training of Deep Neural Networks with Guarantees.” <i>35th AAAI Conference on Artificial Intelligence, AAAI 2021</i>, vol. 35, no. 9B, AAAI Press, 2021, pp. 8209–16.","ista":"Kungurtsev V, Egan M, Chatterjee B, Alistarh D-A. 2021. Asynchronous optimization methods for efficient training of deep neural networks with guarantees. 35th AAAI Conference on Artificial Intelligence, AAAI 2021. AAAI: Conference on Artificial Intelligence vol. 35, 8209–8216.","short":"V. Kungurtsev, M. Egan, B. Chatterjee, D.-A. Alistarh, in:, 35th AAAI Conference on Artificial Intelligence, AAAI 2021, AAAI Press, 2021, pp. 8209–8216.","apa":"Kungurtsev, V., Egan, M., Chatterjee, B., &#38; Alistarh, D.-A. (2021). Asynchronous optimization methods for efficient training of deep neural networks with guarantees. In <i>35th AAAI Conference on Artificial Intelligence, AAAI 2021</i> (Vol. 35, pp. 8209–8216). Virtual, Online: AAAI Press.","ama":"Kungurtsev V, Egan M, Chatterjee B, Alistarh D-A. Asynchronous optimization methods for efficient training of deep neural networks with guarantees. In: <i>35th AAAI Conference on Artificial Intelligence, AAAI 2021</i>. Vol 35. AAAI Press; 2021:8209-8216."},"publication_status":"published","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.1905.11845","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"18","article_processing_charge":"No","page":"8209-8216","year":"2021","abstract":[{"text":"Asynchronous distributed algorithms are a popular way to reduce synchronization costs in large-scale optimization, and in particular for neural network training. However, for nonsmooth and nonconvex objectives, few convergence guarantees exist beyond cases where closed-form proximal operator solutions are available. As training most popular deep neural networks corresponds to optimizing nonsmooth and nonconvex objectives, there is a pressing need for such convergence guarantees. In this paper, we analyze for the first time the convergence of stochastic asynchronous optimization for this general class of objectives. In particular, we focus on stochastic subgradient methods allowing for block variable partitioning, where the shared model is asynchronously updated by concurrent processes. To this end, we use a probabilistic model which captures key features of real asynchronous scheduling between concurrent processes. Under this model, we establish convergence with probability one to an invariant set for stochastic subgradient methods with momentum. From a practical perspective, one issue with the family of algorithms that we consider is that they are not efficiently supported by machine learning frameworks, which mostly focus on distributed data-parallel strategies. To address this, we propose a new implementation strategy for shared-memory based training of deep neural networks for a partitioned but shared model in single- and multi-GPU settings. Based on this implementation, we achieve on average1.2x speed-up in comparison to state-of-the-art training methods for popular image classification tasks, without compromising accuracy.","lang":"eng"}],"acknowledgement":"Vyacheslav Kungurtsev was supported by the OP VVV project CZ.02.1.01/0.0/0.0/16 019/0000765 “Research Center for Informatics. Bapi Chatterjee was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 754411 (ISTPlus). Dan Alistarh has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML).","_id":"11436","scopus_import":"1","oa_version":"Preprint","publication_identifier":{"eissn":["2374-3468"],"isbn":["9781713835974"],"issn":["2159-5399"]},"language":[{"iso":"eng"}],"month":"05","publication":"35th AAAI Conference on Artificial Intelligence, AAAI 2021","volume":35,"issue":"9B","type":"conference","ec_funded":1,"title":"Asynchronous optimization methods for efficient training of deep neural networks with guarantees","arxiv":1,"external_id":{"arxiv":["1905.11845"]},"conference":{"end_date":"2021-02-09","start_date":"2021-02-02","location":"Virtual, Online","name":"AAAI: Conference on Artificial Intelligence"},"project":[{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","name":"Elastic Coordination for Scalable Machine Learning","grant_number":"805223","call_identifier":"H2020"}],"date_updated":"2025-04-14T07:43:57Z","quality_controlled":"1","department":[{"_id":"DaAl"}]},{"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML), and a CNRS PEPS grant. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp). We would also like to thank Christoph Lampert for his feedback on an earlier version of this work, as well as for providing hardware for the Transformer-XL experiments.","scopus_import":"1","_id":"11458","page":"8557-8570","abstract":[{"text":"The increasing computational requirements of deep neural networks (DNNs) have led to significant interest in obtaining DNN models that are sparse, yet accurate. Recent work has investigated the even harder case of sparse training, where the DNN weights are, for as much as possible, already sparse to reduce computational costs during training. Existing sparse training methods are often empirical and can have lower accuracy relative to the dense baseline. In this paper, we present a general approach called Alternating Compressed/DeCompressed (AC/DC) training of DNNs, demonstrate convergence for a variant of the algorithm, and show that AC/DC outperforms existing sparse training methods in accuracy at similar computational budgets; at high sparsity levels, AC/DC even outperforms existing methods that rely on accurate pre-trained dense models. An important property of AC/DC is that it allows co-training of dense and sparse models, yielding accurate sparse–dense model pairs at the end of the training process. This is useful in practice, where compressed variants may be desirable for deployment in resource-constrained settings without re-doing the entire training flow, and also provides us with insights into the accuracy gap between dense and compressed models. The code is available at: https://github.com/IST-DASLab/ACDC.","lang":"eng"}],"year":"2021","day":"06","article_processing_charge":"No","citation":{"ista":"Krumes A, Iofinova EB, Vladu A, Alistarh D-A. 2021. AC/DC: Alternating Compressed/DeCompressed training of deep neural networks. 35th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 34, 8557–8570.","mla":"Krumes, Alexandra, et al. “AC/DC: Alternating Compressed/DeCompressed Training of Deep Neural Networks.” <i>35th Conference on Neural Information Processing Systems</i>, vol. 34, Neural Information Processing Systems Foundation, 2021, pp. 8557–70.","chicago":"Krumes, Alexandra, Eugenia B Iofinova, Adrian Vladu, and Dan-Adrian Alistarh. “AC/DC: Alternating Compressed/DeCompressed Training of Deep Neural Networks.” In <i>35th Conference on Neural Information Processing Systems</i>, 34:8557–70. Neural Information Processing Systems Foundation, 2021.","ieee":"A. Krumes, E. B. Iofinova, A. Vladu, and D.-A. Alistarh, “AC/DC: Alternating Compressed/DeCompressed training of deep neural networks,” in <i>35th Conference on Neural Information Processing Systems</i>, Virtual, Online, 2021, vol. 34, pp. 8557–8570.","apa":"Krumes, A., Iofinova, E. B., Vladu, A., &#38; Alistarh, D.-A. (2021). AC/DC: Alternating Compressed/DeCompressed training of deep neural networks. In <i>35th Conference on Neural Information Processing Systems</i> (Vol. 34, pp. 8557–8570). Virtual, Online: Neural Information Processing Systems Foundation.","short":"A. Krumes, E.B. Iofinova, A. Vladu, D.-A. Alistarh, in:, 35th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2021, pp. 8557–8570.","ama":"Krumes A, Iofinova EB, Vladu A, Alistarh D-A. AC/DC: Alternating Compressed/DeCompressed training of deep neural networks. In: <i>35th Conference on Neural Information Processing Systems</i>. Vol 34. Neural Information Processing Systems Foundation; 2021:8557-8570."},"publication_status":"published","status":"public","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://proceedings.neurips.cc/paper/2021/file/48000647b315f6f00f913caa757a70b3-Paper.pdf","open_access":"1"}],"corr_author":"1","date_published":"2021-12-06T00:00:00Z","acknowledged_ssus":[{"_id":"ScienComp"}],"publisher":"Neural Information Processing Systems Foundation","date_created":"2022-06-20T12:11:53Z","intvolume":"        34","author":[{"last_name":"Peste","full_name":"Peste, Elena-Alexandra","id":"32D78294-F248-11E8-B48F-1D18A9856A87","first_name":"Elena-Alexandra"},{"orcid":"0000-0002-7778-3221","last_name":"Iofinova","full_name":"Iofinova, Eugenia B","first_name":"Eugenia B","id":"f9a17499-f6e0-11ea-865d-fdf9a3f77117"},{"last_name":"Vladu","full_name":"Vladu, Adrian","first_name":"Adrian"},{"first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","orcid":"0000-0003-3650-940X"}],"quality_controlled":"1","department":[{"_id":"GradSch"},{"_id":"DaAl"}],"alternative_title":["Advances in Neural Information Processing Systems"],"date_updated":"2026-06-18T17:18:20Z","project":[{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020","grant_number":"805223"}],"ec_funded":1,"arxiv":1,"title":"AC/DC: Alternating Compressed/DeCompressed training of deep neural networks","external_id":{"arxiv":["2106.12379"]},"conference":{"start_date":"2021-12-06","location":"Virtual, Online","end_date":"2021-12-14","name":"NeurIPS: Neural Information Processing Systems"},"ddc":["000"],"type":"conference","month":"12","publication":"35th Conference on Neural Information Processing Systems","volume":34,"language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"13074"}]},"oa_version":"Published Version","publication_identifier":{"issn":["1049-5258"],"isbn":["9781713845393"]}},{"year":"2021","abstract":[{"lang":"eng","text":"Efficiently approximating local curvature information of the loss function is a key tool for optimization and compression of deep neural networks. Yet, most existing methods to approximate second-order information have high computational\r\nor storage costs, which limits their practicality. In this work, we investigate matrix-free, linear-time approaches for estimating Inverse-Hessian Vector Products (IHVPs) for the case when the Hessian can be approximated as a sum of rank-one matrices, as in the classic approximation of the Hessian by the empirical Fisher matrix. We propose two new algorithms: the first is tailored towards network compression and can compute the IHVP for dimension d, if the Hessian is given as a sum of m rank-one matrices, using O(dm2) precomputation, O(dm) cost for computing the IHVP, and query cost O(m) for any single element of the inverse Hessian. The second algorithm targets an optimization setting, where we wish to compute the product between the inverse Hessian, estimated over a sliding window of optimization steps, and a given gradient direction, as required for preconditioned SGD. We give an algorithm with cost O(dm + m2) for computing the IHVP and O(dm + m3) for adding or removing any gradient from the sliding window. These\r\ntwo algorithms yield state-of-the-art results for network pruning and optimization with lower computational overhead relative to existing second-order methods. Implementations are available at [9] and [17]."}],"page":"14873-14886","_id":"11463","scopus_import":"1","acknowledgement":"We gratefully acknowledge funding the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML), as well as computational support from Amazon Web Services (AWS) EC2.","day":"06","article_processing_charge":"No","corr_author":"1","date_published":"2021-12-06T00:00:00Z","main_file_link":[{"url":"https://proceedings.neurips.cc/paper/2021/file/7cfd5df443b4eb0d69886a583b33de4c-Paper.pdf","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"status":"public","publication_status":"published","citation":{"short":"E. Frantar, E. Kurtic, D.-A. Alistarh, in:, 35th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2021, pp. 14873–14886.","apa":"Frantar, E., Kurtic, E., &#38; Alistarh, D.-A. (2021). M-FAC: Efficient matrix-free approximations of second-order information. In <i>35th Conference on Neural Information Processing Systems</i> (Vol. 34, pp. 14873–14886). Virtual, Online: Neural Information Processing Systems Foundation.","ama":"Frantar E, Kurtic E, Alistarh D-A. M-FAC: Efficient matrix-free approximations of second-order information. In: <i>35th Conference on Neural Information Processing Systems</i>. Vol 34. Neural Information Processing Systems Foundation; 2021:14873-14886.","mla":"Frantar, Elias, et al. “M-FAC: Efficient Matrix-Free Approximations of Second-Order Information.” <i>35th Conference on Neural Information Processing Systems</i>, vol. 34, Neural Information Processing Systems Foundation, 2021, pp. 14873–86.","ista":"Frantar E, Kurtic E, Alistarh D-A. 2021. M-FAC: Efficient matrix-free approximations of second-order information. 35th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 34, 14873–14886.","chicago":"Frantar, Elias, Eldar Kurtic, and Dan-Adrian Alistarh. “M-FAC: Efficient Matrix-Free Approximations of Second-Order Information.” In <i>35th Conference on Neural Information Processing Systems</i>, 34:14873–86. Neural Information Processing Systems Foundation, 2021.","ieee":"E. Frantar, E. Kurtic, and D.-A. Alistarh, “M-FAC: Efficient matrix-free approximations of second-order information,” in <i>35th Conference on Neural Information Processing Systems</i>, Virtual, Online, 2021, vol. 34, pp. 14873–14886."},"author":[{"full_name":"Frantar, Elias","last_name":"Frantar","first_name":"Elias","id":"09a8f98d-ec99-11ea-ae11-c063a7b7fe5f"},{"last_name":"Kurtic","full_name":"Kurtic, Eldar","first_name":"Eldar","id":"47beb3a5-07b5-11eb-9b87-b108ec578218"},{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"}],"intvolume":"        34","date_created":"2022-06-26T22:01:35Z","publisher":"Neural Information Processing Systems Foundation","project":[{"call_identifier":"H2020","grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"date_updated":"2026-06-18T17:18:44Z","alternative_title":["Advances in Neural Information Processing Systems"],"department":[{"_id":"DaAl"}],"quality_controlled":"1","type":"conference","arxiv":1,"external_id":{"arxiv":["2010.08222"]},"ddc":["000"],"conference":{"location":"Virtual, Online","end_date":"2021-12-14","start_date":"2021-12-06","name":"NeurIPS: Neural Information Processing Systems"},"title":"M-FAC: Efficient matrix-free approximations of second-order information","ec_funded":1,"language":[{"iso":"eng"}],"volume":34,"publication":"35th Conference on Neural Information Processing Systems","month":"12","oa_version":"Published Version","publication_identifier":{"isbn":["9781713845393"],"issn":["1049-5258"]}},{"quality_controlled":"1","department":[{"_id":"DaAl"}],"date_updated":"2026-06-18T17:19:18Z","project":[{"call_identifier":"H2020","grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"alternative_title":["Advances in Neural Information Processing Systems"],"arxiv":1,"external_id":{"arxiv":["2010.08222"]},"conference":{"start_date":"2021-12-06","location":"Virtual, Online","end_date":"2021-12-14","name":"NeurIPS: Neural Information Processing Systems"},"ddc":["000"],"title":"Towards tight communication lower bounds for distributed optimisation","ec_funded":1,"type":"conference","volume":34,"month":"12","publication":"35th Conference on Neural Information Processing Systems","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1049-5258"],"isbn":["9781713845393"]},"oa_version":"Published Version","scopus_import":"1","_id":"11464","acknowledgement":"We thank the NeurIPS reviewers for insightful comments that helped us improve the positioning of our results, as well as for pointing out the subsampling approach for complementing the randomised lower bound. We also thank Foivos Alimisis and Peter Davies for useful discussions. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML).","abstract":[{"lang":"eng","text":"We consider a standard distributed optimisation setting where N machines, each holding a d-dimensional function\r\nfi, aim to jointly minimise the sum of the functions ∑Ni=1fi(x). This problem arises naturally in large-scale distributed optimisation, where a standard solution is to apply variants of (stochastic) gradient descent. We focus on the communication complexity of this problem: our main result provides the first fully unconditional bounds on total number of bits which need to be sent and received by the N machines to solve this problem under point-to-point communication, within a given error-tolerance. Specifically, we show that Ω(Ndlogd/Nε) total bits need to be communicated between the machines to find an additive ϵ-approximation to the minimum of ∑Ni=1fi(x). The result holds for both deterministic and randomised algorithms, and, importantly, requires no assumptions on the algorithm structure. The lower bound is tight under certain restrictions on parameter values, and is matched within constant factors for quadratic objectives by a new variant of quantised gradient descent, which we describe and analyse. Our results bring over tools from communication complexity to distributed optimisation, which has potential for further applications."}],"year":"2021","page":"7254-7266","article_processing_charge":"No","day":"06","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://proceedings.neurips.cc/paper/2021/file/3b92d18aa7a6176dd37d372bc2f1eb71-Paper.pdf"}],"citation":{"chicago":"Alistarh, Dan-Adrian, and Janne Korhonen. “Towards Tight Communication Lower Bounds for Distributed Optimisation.” In <i>35th Conference on Neural Information Processing Systems</i>, 34:7254–66. Neural Information Processing Systems Foundation, 2021.","ieee":"D.-A. Alistarh and J. Korhonen, “Towards tight communication lower bounds for distributed optimisation,” in <i>35th Conference on Neural Information Processing Systems</i>, Virtual, Online, 2021, vol. 34, pp. 7254–7266.","ista":"Alistarh D-A, Korhonen J. 2021. Towards tight communication lower bounds for distributed optimisation. 35th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 34, 7254–7266.","mla":"Alistarh, Dan-Adrian, and Janne Korhonen. “Towards Tight Communication Lower Bounds for Distributed Optimisation.” <i>35th Conference on Neural Information Processing Systems</i>, vol. 34, Neural Information Processing Systems Foundation, 2021, pp. 7254–66.","apa":"Alistarh, D.-A., &#38; Korhonen, J. (2021). Towards tight communication lower bounds for distributed optimisation. In <i>35th Conference on Neural Information Processing Systems</i> (Vol. 34, pp. 7254–7266). Virtual, Online: Neural Information Processing Systems Foundation.","short":"D.-A. Alistarh, J. Korhonen, in:, 35th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2021, pp. 7254–7266.","ama":"Alistarh D-A, Korhonen J. Towards tight communication lower bounds for distributed optimisation. In: <i>35th Conference on Neural Information Processing Systems</i>. Vol 34. Neural Information Processing Systems Foundation; 2021:7254-7266."},"publication_status":"published","status":"public","oa":1,"date_published":"2021-12-06T00:00:00Z","corr_author":"1","intvolume":"        34","author":[{"full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"id":"C5402D42-15BC-11E9-A202-CA2BE6697425","first_name":"Janne","last_name":"Korhonen","full_name":"Korhonen, Janne"}],"publisher":"Neural Information Processing Systems Foundation","date_created":"2022-06-26T22:01:35Z"},{"department":[{"_id":"XiFe"}],"quality_controlled":"1","date_updated":"2023-05-08T11:01:18Z","article_type":"original","external_id":{"pmid":["34387350"]},"title":"Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors","issue":"22","type":"journal_article","publication":"Journal of Experimental Botany","month":"08","volume":72,"language":[{"iso":"eng"}],"oa_version":"None","publication_identifier":{"issn":["0022-0957","1460-2431"]},"acknowledgement":"We thank the Gatsby Foundation (UK) for funding to the JDGJ laboratory. PD acknowledges support from the European Union’s Horizon 2020 Research and Innovation Program under Marie Skłodowska Curie Actions (grant agreement: 656243) and a Future Leader Fellowship from the Biotechnology and Biological Sciences Research Council (BBSRC) (grant agreement: BB/R012172/1). TS, RKS, DM, and JDGJ were supported by the Gatsby Foundation funding to the\r\nSainsbury Laboratory. NMP and KV were supported by a BOF grant from Ghent University (grant agreement: BOF24Y2019001901). WG and RZ were supported by the Scottish Government Rural and Environment Science and Analytical Services division (RESAS), and RZ also acknowledges the support from a BBSRC Bioinformatics and Biological Resources Fund (grant agreement: BB/S020160/1).BPMN was supported by the Norwich Research Park (NRP) Biosciences Doctoral Training Partnership (DTP) funded by the BBSRC (grant agreement: BB/M011216/1). SH and XF were supported by a BBSRC Responsive Mode grant (grant agreement: BB/S009620/1) and a European Research Council Starting grant ‘SexMeth’ (grant agreement: 804981). CL was supported by Deutsche Forschungsgemeinschaft (grant agreement: LI 2862/4). ","keyword":["Plant Science","Physiology"],"scopus_import":"1","_id":"12186","extern":"1","page":"7927-7941","abstract":[{"text":"Activation of cell-surface and intracellular receptor-mediated immunity results in rapid transcriptional reprogramming that underpins disease resistance. However, the mechanisms by which co-activation of both immune systems lead to transcriptional changes are not clear. Here, we combine RNA-seq and ATAC-seq to define changes in gene expression and chromatin accessibility. Activation of cell-surface or intracellular receptor-mediated immunity, or both, increases chromatin accessibility at induced defence genes. Analysis of ATAC-seq and RNA-seq data combined with publicly available information on transcription factor DNA-binding motifs enabled comparison of individual gene regulatory networks activated by cell-surface or intracellular receptor-mediated immunity, or by both. These results and analyses reveal overlapping and conserved transcriptional regulatory mechanisms between the two immune systems.","lang":"eng"}],"year":"2021","day":"13","article_processing_charge":"No","citation":{"ieee":"P. Ding <i>et al.</i>, “Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors,” <i>Journal of Experimental Botany</i>, vol. 72, no. 22. Oxford University Press, pp. 7927–7941, 2021.","chicago":"Ding, Pingtao, Toshiyuki Sakai, Ram Krishna Shrestha, Nicolas Manosalva Perez, Wenbin Guo, Bruno Pok Man Ngou, Shengbo He, et al. “Chromatin Accessibility Landscapes Activated by Cell-Surface and Intracellular Immune Receptors.” <i>Journal of Experimental Botany</i>. Oxford University Press, 2021. <a href=\"https://doi.org/10.1093/jxb/erab373\">https://doi.org/10.1093/jxb/erab373</a>.","mla":"Ding, Pingtao, et al. “Chromatin Accessibility Landscapes Activated by Cell-Surface and Intracellular Immune Receptors.” <i>Journal of Experimental Botany</i>, vol. 72, no. 22, Oxford University Press, 2021, pp. 7927–41, doi:<a href=\"https://doi.org/10.1093/jxb/erab373\">10.1093/jxb/erab373</a>.","ista":"Ding P, Sakai T, Krishna Shrestha R, Manosalva Perez N, Guo W, Ngou BPM, He S, Liu C, Feng X, Zhang R, Vandepoele K, MacLean D, Jones JDG. 2021. Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors. Journal of Experimental Botany. 72(22), 7927–7941.","short":"P. Ding, T. Sakai, R. Krishna Shrestha, N. Manosalva Perez, W. Guo, B.P.M. Ngou, S. He, C. Liu, X. Feng, R. Zhang, K. Vandepoele, D. MacLean, J.D.G. Jones, Journal of Experimental Botany 72 (2021) 7927–7941.","apa":"Ding, P., Sakai, T., Krishna Shrestha, R., Manosalva Perez, N., Guo, W., Ngou, B. P. M., … Jones, J. D. G. (2021). Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors. <i>Journal of Experimental Botany</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jxb/erab373\">https://doi.org/10.1093/jxb/erab373</a>","ama":"Ding P, Sakai T, Krishna Shrestha R, et al. Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors. <i>Journal of Experimental Botany</i>. 2021;72(22):7927-7941. doi:<a href=\"https://doi.org/10.1093/jxb/erab373\">10.1093/jxb/erab373</a>"},"publication_status":"published","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-08-13T00:00:00Z","publisher":"Oxford University Press","pmid":1,"doi":"10.1093/jxb/erab373","date_created":"2023-01-16T09:14:35Z","intvolume":"        72","author":[{"last_name":"Ding","full_name":"Ding, Pingtao","first_name":"Pingtao"},{"full_name":"Sakai, Toshiyuki","last_name":"Sakai","first_name":"Toshiyuki"},{"first_name":"Ram","last_name":"Krishna Shrestha","full_name":"Krishna Shrestha, Ram"},{"full_name":"Manosalva Perez, Nicolas","last_name":"Manosalva Perez","first_name":"Nicolas"},{"first_name":"Wenbin","full_name":"Guo, Wenbin","last_name":"Guo"},{"first_name":"Bruno Pok Man","last_name":"Ngou","full_name":"Ngou, Bruno Pok Man"},{"full_name":"He, Shengbo","last_name":"He","first_name":"Shengbo"},{"first_name":"Chang","full_name":"Liu, Chang","last_name":"Liu"},{"first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","full_name":"Feng, Xiaoqi","last_name":"Feng","orcid":"0000-0002-4008-1234"},{"first_name":"Runxuan","full_name":"Zhang, Runxuan","last_name":"Zhang"},{"first_name":"Klaas","last_name":"Vandepoele","full_name":"Vandepoele, Klaas"},{"last_name":"MacLean","full_name":"MacLean, Dan","first_name":"Dan"},{"first_name":"Jonathan D G","last_name":"Jones","full_name":"Jones, Jonathan D G"}]},{"oa_version":"Preprint","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"volume":373,"publication":"Science","month":"07","language":[{"iso":"eng"}],"external_id":{"pmid":["34210850"]},"title":"Nurse cell-derived small RNAs define paternal epigenetic inheritance in Arabidopsis","type":"journal_article","issue":"6550","department":[{"_id":"XiFe"}],"quality_controlled":"1","article_type":"original","date_updated":"2026-03-19T10:52:21Z","OA_place":"repository","author":[{"first_name":"Jincheng","last_name":"Long","full_name":"Long, Jincheng"},{"full_name":"Walker, James","last_name":"Walker","first_name":"James"},{"first_name":"Wenjing","full_name":"She, Wenjing","last_name":"She"},{"full_name":"Aldridge, Billy","last_name":"Aldridge","first_name":"Billy"},{"first_name":"Hongbo","full_name":"Gao, Hongbo","last_name":"Gao"},{"full_name":"Deans, Samuel","last_name":"Deans","first_name":"Samuel"},{"last_name":"Vickers","full_name":"Vickers, Martin","first_name":"Martin"},{"first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234","last_name":"Feng"}],"intvolume":"       373","pmid":1,"date_created":"2023-01-16T09:15:14Z","doi":"10.1126/science.abh0556","publisher":"American Association for the Advancement of Science","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2021.01.25.428150"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa":1,"status":"public","citation":{"short":"J. Long, J. Walker, W. She, B. Aldridge, H. Gao, S. Deans, M. Vickers, X. Feng, Science 373 (2021).","apa":"Long, J., Walker, J., She, W., Aldridge, B., Gao, H., Deans, S., … Feng, X. (2021). Nurse cell-derived small RNAs define paternal epigenetic inheritance in Arabidopsis. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.abh0556\">https://doi.org/10.1126/science.abh0556</a>","ama":"Long J, Walker J, She W, et al. Nurse cell-derived small RNAs define paternal epigenetic inheritance in Arabidopsis. <i>Science</i>. 2021;373(6550). doi:<a href=\"https://doi.org/10.1126/science.abh0556\">10.1126/science.abh0556</a>","chicago":"Long, Jincheng, James Walker, Wenjing She, Billy Aldridge, Hongbo Gao, Samuel Deans, Martin Vickers, and Xiaoqi Feng. “Nurse Cell-Derived Small RNAs Define Paternal Epigenetic Inheritance in Arabidopsis.” <i>Science</i>. American Association for the Advancement of Science, 2021. <a href=\"https://doi.org/10.1126/science.abh0556\">https://doi.org/10.1126/science.abh0556</a>.","ieee":"J. Long <i>et al.</i>, “Nurse cell-derived small RNAs define paternal epigenetic inheritance in Arabidopsis,” <i>Science</i>, vol. 373, no. 6550. American Association for the Advancement of Science, 2021.","mla":"Long, Jincheng, et al. “Nurse Cell-Derived Small RNAs Define Paternal Epigenetic Inheritance in Arabidopsis.” <i>Science</i>, vol. 373, no. 6550, American Association for the Advancement of Science, 2021, doi:<a href=\"https://doi.org/10.1126/science.abh0556\">10.1126/science.abh0556</a>.","ista":"Long J, Walker J, She W, Aldridge B, Gao H, Deans S, Vickers M, Feng X. 2021. Nurse cell-derived small RNAs define paternal epigenetic inheritance in Arabidopsis. Science. 373(6550)."},"publication_status":"published","date_published":"2021-07-02T00:00:00Z","article_processing_charge":"No","day":"02","_id":"12187","OA_type":"green","scopus_import":"1","keyword":["Multidisciplinary"],"acknowledgement":"We thank the John Innes Centre Bioimaging Facility (S. Lopez, E. Wegel, and K. Findlay) for their assistance with microscopy and the Norwich BioScience Institute Partnership Computing Infrastructure for Science Group for high-performance computing resources. Funding: This work was funded by a European Research Council Starting Grant (“SexMeth” 804981; J.L., J.W., and X.F.), a Sainsbury Charitable Foundation studentship (J.W.), two Biotechnology and Biological Sciences Research Council (BBSRC) grants (BBS0096201 and BBP0135111; W.S., M.V., and X.F.), two John Innes Foundation studentships (B.A. and S.D.), and a BBSRC David Phillips Fellowship (BBL0250431; H.G. and X.F.). Author contributions: J.L., J.W., and X.F. designed the study and wrote the manuscript; J.L., W.S., B.A., H.G., and S.D. performed the experiments; and J.L., J.W., B.A., H.G., S.D., M.V., and X.F. analyzed the data. Competing interests: The authors declare no competing interests. Data and material availability: All sequencing data have been deposited in the Gene Expression Omnibus (GEO) under accession no. GSE161625. Accession nos. of published datasets used in this study are listed in table S6. Published software used in this study include Bowtie v1.2.2 (https://doi.org/10.1002/0471250953.bi1107s32), Bismark v0.22.2 (https://doi.org/10.1093/bioinformatics/btr167), Kallisto v0.43.0 (https://doi.org/10.1038/nbt0816-888d), Shortstack v3.8.5 (https://doi.org/10.1534/g3.116.030452), and Cutadapt v1.15 (https://doi.org/10.1089/cmb.2017.0096). TrimGalore v0.4.1 and MarkDuplicates v1.141 are available from https://github.com/FelixKrueger/TrimGalore and https://github.com/broadinstitute/picard, respectively. All remaining data are in the main paper or the supplementary materials.","year":"2021","abstract":[{"lang":"eng","text":"Genomes of germ cells present an existential vulnerability to organisms because germ cell mutations will propagate to future generations. Transposable elements are one source of such mutations. In the small flowering plant Arabidopsis, Long et al. found that genome methylation in the male germline is directed by small interfering RNAs (siRNAs) imperfectly transcribed from transposons (see the Perspective by Mosher). These germline siRNAs silence germline transposons and establish inherited methylation patterns in sperm, thus maintaining the integrity of the plant genome across generations."}],"extern":"1"},{"publisher":"Springer Nature","doi":"10.1007/978-3-030-72016-2_2","date_created":"2023-03-26T22:01:09Z","intvolume":"     12651","author":[{"full_name":"Bansal, Suguman","last_name":"Bansal","first_name":"Suguman"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Vardi, Moshe Y.","last_name":"Vardi","first_name":"Moshe Y."}],"date_published":"2021-03-21T00:00:00Z","publication_status":"published","file":[{"file_size":747418,"file_name":"2021_LNCS_Bansal.pdf","date_updated":"2023-03-28T11:00:33Z","file_id":"12777","content_type":"application/pdf","checksum":"b020b78b23587ce7610b1aafb4e63438","access_level":"open_access","relation":"main_file","date_created":"2023-03-28T11:00:33Z","success":1,"creator":"dernst"}],"citation":{"short":"S. Bansal, K. Chatterjee, M.Y. Vardi, in:, 27th International Conference on Tools and Algorithms for the Construction and Analysis of Systems, Springer Nature, 2021, pp. 20–37.","ama":"Bansal S, Chatterjee K, Vardi MY. On satisficing in quantitative games. In: <i>27th International Conference on Tools and Algorithms for the Construction and Analysis of Systems</i>. Vol 12651. Springer Nature; 2021:20-37. doi:<a href=\"https://doi.org/10.1007/978-3-030-72016-2_2\">10.1007/978-3-030-72016-2_2</a>","apa":"Bansal, S., Chatterjee, K., &#38; Vardi, M. Y. (2021). On satisficing in quantitative games. In <i>27th International Conference on Tools and Algorithms for the Construction and Analysis of Systems</i> (Vol. 12651, pp. 20–37). Luxembourg City, Luxembourg: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-72016-2_2\">https://doi.org/10.1007/978-3-030-72016-2_2</a>","ieee":"S. Bansal, K. Chatterjee, and M. Y. Vardi, “On satisficing in quantitative games,” in <i>27th International Conference on Tools and Algorithms for the Construction and Analysis of Systems</i>, Luxembourg City, Luxembourg, 2021, vol. 12651, pp. 20–37.","chicago":"Bansal, Suguman, Krishnendu Chatterjee, and Moshe Y. Vardi. “On Satisficing in Quantitative Games.” In <i>27th International Conference on Tools and Algorithms for the Construction and Analysis of Systems</i>, 12651:20–37. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-030-72016-2_2\">https://doi.org/10.1007/978-3-030-72016-2_2</a>.","mla":"Bansal, Suguman, et al. “On Satisficing in Quantitative Games.” <i>27th International Conference on Tools and Algorithms for the Construction and Analysis of Systems</i>, vol. 12651, Springer Nature, 2021, pp. 20–37, doi:<a href=\"https://doi.org/10.1007/978-3-030-72016-2_2\">10.1007/978-3-030-72016-2_2</a>.","ista":"Bansal S, Chatterjee K, Vardi MY. 2021. On satisficing in quantitative games. 27th International Conference on Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 12651, 20–37."},"oa":1,"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"21","article_processing_charge":"No","page":"20-37","abstract":[{"text":"Several problems in planning and reactive synthesis can be reduced to the analysis of two-player quantitative graph games. Optimization is one form of analysis. We argue that in many cases it may be better to replace the optimization problem with the satisficing problem, where instead of searching for optimal solutions, the goal is to search for solutions that adhere to a given threshold bound.\r\nThis work defines and investigates the satisficing problem on a two-player graph game with the discounted-sum cost model. We show that while the satisficing problem can be solved using numerical methods just like the optimization problem, this approach does not render compelling benefits over optimization. When the discount factor is, however, an integer, we present another approach to satisficing, which is purely based on automata methods. We show that this approach is algorithmically more performant – both theoretically and empirically – and demonstrates the broader applicability of satisficing over optimization.","lang":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"year":"2021","acknowledgement":"We thank anonymous reviewers for valuable inputs. This work is supported in part by NSF grant 2030859 to the CRA for the CIFellows Project, NSF grants IIS-1527668, CCF-1704883, IIS-1830549, the ERC CoG 863818 (ForM-SMArt), and an award from the Maryland Procurement Office.","scopus_import":"1","_id":"12767","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783030720155"],"issn":["0302-9743"]},"oa_version":"Published Version","language":[{"iso":"eng"}],"file_date_updated":"2023-03-28T11:00:33Z","publication":"27th International Conference on Tools and Algorithms for the Construction and Analysis of Systems","month":"03","has_accepted_license":"1","volume":12651,"type":"conference","ec_funded":1,"arxiv":1,"external_id":{"arxiv":["2101.02594"]},"conference":{"start_date":"2021-03-27","end_date":"2021-04-01","location":"Luxembourg City, Luxembourg","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"title":"On satisficing in quantitative games","ddc":["000"],"alternative_title":["LNCS"],"date_updated":"2025-07-10T13:18:02Z","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","call_identifier":"H2020"}],"department":[{"_id":"KrCh"}],"quality_controlled":"1"}]