[{"oa_version":"Preprint","_id":"446","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory","intvolume":" 71","abstract":[{"lang":"eng","text":"We prove that in Thomas–Fermi–Dirac–von Weizsäcker theory, a nucleus of charge Z > 0 can bind at most Z + C electrons, where C is a universal constant. This result is obtained through a comparison with Thomas-Fermi theory which, as a by-product, gives bounds on the screened nuclear potential and the radius of the minimizer. A key ingredient of the proof is a novel technique to control the particles in the exterior region, which also applies to the liquid drop model with a nuclear background potential."}],"issue":"3","type":"journal_article","date_published":"2018-03-01T00:00:00Z","publication":"Communications on Pure and Applied Mathematics","citation":{"ista":"Frank R, Nam P, Van Den Bosch H. 2018. The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory. Communications on Pure and Applied Mathematics. 71(3), 577–614.","apa":"Frank, R., Nam, P., & Van Den Bosch, H. (2018). The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory. Communications on Pure and Applied Mathematics. Wiley-Blackwell. https://doi.org/10.1002/cpa.21717","ieee":"R. Frank, P. Nam, and H. Van Den Bosch, “The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory,” Communications on Pure and Applied Mathematics, vol. 71, no. 3. Wiley-Blackwell, pp. 577–614, 2018.","ama":"Frank R, Nam P, Van Den Bosch H. The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory. Communications on Pure and Applied Mathematics. 2018;71(3):577-614. doi:10.1002/cpa.21717","chicago":"Frank, Rupert, Phan Nam, and Hanne Van Den Bosch. “The Ionization Conjecture in Thomas–Fermi–Dirac–von Weizsäcker Theory.” Communications on Pure and Applied Mathematics. Wiley-Blackwell, 2018. https://doi.org/10.1002/cpa.21717.","mla":"Frank, Rupert, et al. “The Ionization Conjecture in Thomas–Fermi–Dirac–von Weizsäcker Theory.” Communications on Pure and Applied Mathematics, vol. 71, no. 3, Wiley-Blackwell, 2018, pp. 577–614, doi:10.1002/cpa.21717.","short":"R. Frank, P. Nam, H. Van Den Bosch, Communications on Pure and Applied Mathematics 71 (2018) 577–614."},"article_type":"original","page":"577 - 614","day":"01","article_processing_charge":"No","author":[{"full_name":"Frank, Rupert","last_name":"Frank","first_name":"Rupert"},{"full_name":"Phan Thanh, Nam","last_name":"Phan Thanh","first_name":"Nam","id":"404092F4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Van Den Bosch","first_name":"Hanne","full_name":"Van Den Bosch, Hanne"}],"date_updated":"2023-09-19T10:09:40Z","date_created":"2018-12-11T11:46:31Z","volume":71,"year":"2018","acknowledgement":"We thank the referee for helpful suggestions that improved the presentation of the paper. We also acknowledge partial support by National Science Foundation Grant DMS-1363432 (R.L.F.), Austrian Science Fund (FWF) Project Nr. P 27533-N27 (P.T.N.), CONICYT (Chile) through CONICYT–PCHA/ Doctorado Nacional/2014, and Iniciativa Científica Milenio (Chile) through Millenium Nucleus RC–120002 “Física Matemática” (H.V.D.B.).\r\n","publication_status":"published","publisher":"Wiley-Blackwell","department":[{"_id":"RoSe"}],"publist_id":"7377","doi":"10.1002/cpa.21717","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000422675800004"],"arxiv":["1606.07355"]},"main_file_link":[{"url":"https://arxiv.org/abs/1606.07355","open_access":"1"}],"quality_controlled":"1","isi":1,"month":"03"},{"abstract":[{"lang":"eng","text":"In this issue of GENETICS, a new method for detecting natural selection on polygenic traits is developed and applied to sev- eral human examples ( Racimo et al. 2018 ). By de fi nition, many loci contribute to variation in polygenic traits, and a challenge for evolutionary ge neticists has been that these traits can evolve by small, nearly undetectable shifts in allele frequencies across each of many, typically unknown, loci. Recently, a helpful remedy has arisen. Genome-wide associ- ation studies (GWAS) have been illuminating sets of loci that can be interrogated jointly for c hanges in allele frequencies. By aggregating small signal s of change across many such loci, directional natural selection is now in principle detect- able using genetic data, even for highly polygenic traits. This is an exciting arena of progress – with these methods, tests can be made for selection associated with traits, and we can now study selection in what may be its most prevalent mode. The continuing fast pace of GWAS publications suggest there will be many more polygenic tests of selection in the near future, as every new GWAS is an opportunity for an accom- panying test of polygenic selection. However, it is important to be aware of complications th at arise in interpretation, especially given that these studies may easily be misinter- preted both in and outside the evolutionary genetics commu- nity. Here, we provide context for understanding polygenic tests and urge caution regarding how these results are inter- preted and reported upon more broadly."}],"issue":"4","type":"journal_article","pubrep_id":"1012","file":[{"file_name":"IST-2018-1012-v1+1_2018_Barton_Tread.pdf","access_level":"open_access","creator":"system","file_size":500129,"content_type":"application/pdf","file_id":"4958","relation":"main_file","date_created":"2018-12-12T10:12:40Z","date_updated":"2020-07-14T12:46:26Z","checksum":"3d838dc285df394376555b794b6a5ad1"}],"oa_version":"Published Version","_id":"430","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Tread lightly interpreting polygenic tests of selection","status":"public","ddc":["576"],"intvolume":" 208","day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2018-04-01T00:00:00Z","publication":"Genetics","citation":{"ieee":"J. Novembre and N. H. Barton, “Tread lightly interpreting polygenic tests of selection,” Genetics, vol. 208, no. 4. Genetics Society of America, pp. 1351–1355, 2018.","apa":"Novembre, J., & Barton, N. H. (2018). Tread lightly interpreting polygenic tests of selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.300786","ista":"Novembre J, Barton NH. 2018. Tread lightly interpreting polygenic tests of selection. Genetics. 208(4), 1351–1355.","ama":"Novembre J, Barton NH. Tread lightly interpreting polygenic tests of selection. Genetics. 2018;208(4):1351-1355. doi:10.1534/genetics.118.300786","chicago":"Novembre, John, and Nicholas H Barton. “Tread Lightly Interpreting Polygenic Tests of Selection.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.300786.","short":"J. Novembre, N.H. Barton, Genetics 208 (2018) 1351–1355.","mla":"Novembre, John, and Nicholas H. Barton. “Tread Lightly Interpreting Polygenic Tests of Selection.” Genetics, vol. 208, no. 4, Genetics Society of America, 2018, pp. 1351–55, doi:10.1534/genetics.118.300786."},"page":"1351 - 1355","file_date_updated":"2020-07-14T12:46:26Z","publist_id":"7393","author":[{"full_name":"Novembre, John","last_name":"Novembre","first_name":"John"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}],"date_updated":"2023-09-19T10:17:30Z","date_created":"2018-12-11T11:46:26Z","volume":208,"year":"2018","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Genetics Society of America","month":"04","doi":"10.1534/genetics.118.300786","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000429094400005"]},"oa":1,"isi":1,"quality_controlled":"1"},{"month":"06","external_id":{"isi":["000436494200026"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.3390/genes9060294","language":[{"iso":"eng"}],"article_number":"294","publist_id":"7714","file_date_updated":"2020-07-14T12:45:22Z","year":"2018","publisher":"MDPI AG","department":[{"_id":"BeVi"}],"publication_status":"published","author":[{"last_name":"Ma","first_name":"Wen","full_name":"Ma, Wen"},{"full_name":"Veltsos, Paris","last_name":"Veltsos","first_name":"Paris"},{"full_name":"Toups, Melissa A","last_name":"Toups","first_name":"Melissa A","orcid":"0000-0002-9752-7380","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rodrigues, Nicolas","first_name":"Nicolas","last_name":"Rodrigues"},{"full_name":"Sermier, Roberto","first_name":"Roberto","last_name":"Sermier"},{"last_name":"Jeffries","first_name":"Daniel","full_name":"Jeffries, Daniel"},{"full_name":"Perrin, Nicolas","last_name":"Perrin","first_name":"Nicolas"}],"volume":9,"date_created":"2018-12-11T11:45:09Z","date_updated":"2023-09-19T10:15:31Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"12","citation":{"ama":"Ma W, Veltsos P, Toups MA, et al. Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. Genes. 2018;9(6). doi:10.3390/genes9060294","ista":"Ma W, Veltsos P, Toups MA, Rodrigues N, Sermier R, Jeffries D, Perrin N. 2018. Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. Genes. 9(6), 294.","apa":"Ma, W., Veltsos, P., Toups, M. A., Rodrigues, N., Sermier, R., Jeffries, D., & Perrin, N. (2018). Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. Genes. MDPI AG. https://doi.org/10.3390/genes9060294","ieee":"W. Ma et al., “Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes,” Genes, vol. 9, no. 6. MDPI AG, 2018.","mla":"Ma, Wen, et al. “Tissue Specificity and Dynamics of Sex Biased Gene Expression in a Common Frog Population with Differentiated, yet Homomorphic, Sex Chromosomes.” Genes, vol. 9, no. 6, 294, MDPI AG, 2018, doi:10.3390/genes9060294.","short":"W. Ma, P. Veltsos, M.A. Toups, N. Rodrigues, R. Sermier, D. Jeffries, N. Perrin, Genes 9 (2018).","chicago":"Ma, Wen, Paris Veltsos, Melissa A Toups, Nicolas Rodrigues, Roberto Sermier, Daniel Jeffries, and Nicolas Perrin. “Tissue Specificity and Dynamics of Sex Biased Gene Expression in a Common Frog Population with Differentiated, yet Homomorphic, Sex Chromosomes.” Genes. MDPI AG, 2018. https://doi.org/10.3390/genes9060294."},"publication":"Genes","date_published":"2018-06-12T00:00:00Z","type":"journal_article","issue":"6","abstract":[{"text":"Sex-biased genes are central to the study of sexual selection, sexual antagonism, and sex chromosome evolution. We describe a comprehensive de novo assembled transcriptome in the common frog Rana temporaria based on five developmental stages and three adult tissues from both sexes, obtained from a population with karyotypically homomorphic but genetically differentiated sex chromosomes. This allows the study of sex-biased gene expression throughout development, and its effect on the rate of gene evolution while accounting for pleiotropic expression, which is known to negatively correlate with the evolutionary rate. Overall, sex-biased genes had little overlap among developmental stages and adult tissues. Late developmental stages and gonad tissues had the highest numbers of stage-or tissue-specific genes. We find that pleiotropic gene expression is a better predictor than sex bias for the evolutionary rate of genes, though it often interacts with sex bias. Although genetically differentiated, the sex chromosomes were not enriched in sex-biased genes, possibly due to a very recent arrest of XY recombination. These results extend our understanding of the developmental dynamics, tissue specificity, and genomic localization of sex-biased genes.","lang":"eng"}],"_id":"199","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 9","ddc":["570"],"title":"Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes","status":"public","file":[{"checksum":"423069beb1cd3cdd25bf3f464b38f1d7","date_created":"2019-02-01T07:52:28Z","date_updated":"2020-07-14T12:45:22Z","relation":"main_file","file_id":"5905","file_size":3985796,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2018_Genes_Ma.pdf"}],"oa_version":"Published Version"},{"oa_version":"Submitted Version","status":"public","title":"Toward a unified theory of efficient, predictive, and sparse coding","intvolume":" 115","_id":"543","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"A central goal in theoretical neuroscience is to predict the response properties of sensory neurons from first principles. To this end, “efficient coding” posits that sensory neurons encode maximal information about their inputs given internal constraints. There exist, however, many variants of efficient coding (e.g., redundancy reduction, different formulations of predictive coding, robust coding, sparse coding, etc.), differing in their regimes of applicability, in the relevance of signals to be encoded, and in the choice of constraints. It is unclear how these types of efficient coding relate or what is expected when different coding objectives are combined. Here we present a unified framework that encompasses previously proposed efficient coding models and extends to unique regimes. We show that optimizing neural responses to encode predictive information can lead them to either correlate or decorrelate their inputs, depending on the stimulus statistics; in contrast, at low noise, efficiently encoding the past always predicts decorrelation. Later, we investigate coding of naturalistic movies and show that qualitatively different types of visual motion tuning and levels of response sparsity are predicted, depending on whether the objective is to recover the past or predict the future. Our approach promises a way to explain the observed diversity of sensory neural responses, as due to multiple functional goals and constraints fulfilled by different cell types and/or circuits."}],"issue":"1","type":"journal_article","date_published":"2018-01-02T00:00:00Z","page":"186 - 191","publication":"PNAS","citation":{"apa":"Chalk, M. J., Marre, O., & Tkačik, G. (2018). Toward a unified theory of efficient, predictive, and sparse coding. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1711114115","ieee":"M. J. Chalk, O. Marre, and G. Tkačik, “Toward a unified theory of efficient, predictive, and sparse coding,” PNAS, vol. 115, no. 1. National Academy of Sciences, pp. 186–191, 2018.","ista":"Chalk MJ, Marre O, Tkačik G. 2018. Toward a unified theory of efficient, predictive, and sparse coding. PNAS. 115(1), 186–191.","ama":"Chalk MJ, Marre O, Tkačik G. Toward a unified theory of efficient, predictive, and sparse coding. PNAS. 2018;115(1):186-191. doi:10.1073/pnas.1711114115","chicago":"Chalk, Matthew J, Olivier Marre, and Gašper Tkačik. “Toward a Unified Theory of Efficient, Predictive, and Sparse Coding.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1711114115.","short":"M.J. Chalk, O. Marre, G. Tkačik, PNAS 115 (2018) 186–191.","mla":"Chalk, Matthew J., et al. “Toward a Unified Theory of Efficient, Predictive, and Sparse Coding.” PNAS, vol. 115, no. 1, National Academy of Sciences, 2018, pp. 186–91, doi:10.1073/pnas.1711114115."},"day":"02","article_processing_charge":"No","scopus_import":"1","date_updated":"2023-09-19T10:16:35Z","date_created":"2018-12-11T11:47:04Z","volume":115,"author":[{"id":"2BAAC544-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7782-4436","first_name":"Matthew J","last_name":"Chalk","full_name":"Chalk, Matthew J"},{"full_name":"Marre, Olivier","last_name":"Marre","first_name":"Olivier"},{"last_name":"Tkacik","first_name":"Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper"}],"publication_status":"published","department":[{"_id":"GaTk"}],"publisher":"National Academy of Sciences","year":"2018","publist_id":"7273","language":[{"iso":"eng"}],"doi":"10.1073/pnas.1711114115","quality_controlled":"1","isi":1,"project":[{"_id":"254D1A94-B435-11E9-9278-68D0E5697425","grant_number":"P 25651-N26","call_identifier":"FWF","name":"Sensitivity to higher-order statistics in natural scenes"}],"external_id":{"isi":["000419128700049"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/152660 "}],"oa":1,"month":"01"},{"intvolume":" 114","status":"public","title":"Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients","_id":"421","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Submitted Version","type":"journal_article","issue":"4","abstract":[{"text":"Cell shape is determined by a balance of intrinsic properties of the cell as well as its mechanochemical environment. Inhomogeneous shape changes underlie many morphogenetic events and involve spatial gradients in active cellular forces induced by complex chemical signaling. Here, we introduce a mechanochemical model based on the notion that cell shape changes may be induced by external diffusible biomolecules that influence cellular contractility (or equivalently, adhesions) in a concentration-dependent manner—and whose spatial profile in turn is affected by cell shape. We map out theoretically the possible interplay between chemical concentration and cellular structure. Besides providing a direct route to spatial gradients in cell shape profiles in tissues, we show that the dependence on cell shape helps create robust mechanochemical gradients.","lang":"eng"}],"page":"968 - 977","citation":{"chicago":"Dasbiswas, Kinjal, Edouard B Hannezo, and Nir Gov. “Theory of Eppithelial Cell Shape Transitions Induced by Mechanoactive Chemical Gradients.” Biophysical Journal. Biophysical Society, 2018. https://doi.org/10.1016/j.bpj.2017.12.022.","mla":"Dasbiswas, Kinjal, et al. “Theory of Eppithelial Cell Shape Transitions Induced by Mechanoactive Chemical Gradients.” Biophysical Journal, vol. 114, no. 4, Biophysical Society, 2018, pp. 968–77, doi:10.1016/j.bpj.2017.12.022.","short":"K. Dasbiswas, E.B. Hannezo, N. Gov, Biophysical Journal 114 (2018) 968–977.","ista":"Dasbiswas K, Hannezo EB, Gov N. 2018. Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients. Biophysical Journal. 114(4), 968–977.","ieee":"K. Dasbiswas, E. B. Hannezo, and N. Gov, “Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients,” Biophysical Journal, vol. 114, no. 4. Biophysical Society, pp. 968–977, 2018.","apa":"Dasbiswas, K., Hannezo, E. B., & Gov, N. (2018). Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients. Biophysical Journal. Biophysical Society. https://doi.org/10.1016/j.bpj.2017.12.022","ama":"Dasbiswas K, Hannezo EB, Gov N. Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients. Biophysical Journal. 2018;114(4):968-977. doi:10.1016/j.bpj.2017.12.022"},"publication":"Biophysical Journal","date_published":"2018-02-27T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"27","department":[{"_id":"EdHa"}],"publisher":"Biophysical Society","publication_status":"published","year":"2018","volume":114,"date_updated":"2023-09-19T10:13:55Z","date_created":"2018-12-11T11:46:23Z","author":[{"first_name":"Kinjal","last_name":"Dasbiswas","full_name":"Dasbiswas, Kinjal"},{"full_name":"Hannezo, Claude-Edouard B","first_name":"Claude-Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"},{"full_name":"Gov, Nir","first_name":"Nir","last_name":"Gov"}],"publist_id":"7403","quality_controlled":"1","isi":1,"external_id":{"isi":["000428016700021"],"arxiv":["1709.01486"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1709.01486"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.bpj.2017.12.022","month":"02"},{"month":"10","isi":1,"quality_controlled":"1","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000448656700018"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.3390/genes9100480","article_number":"480","file_date_updated":"2020-07-14T12:47:27Z","ec_funded":1,"publist_id":"7991","publication_status":"published","department":[{"_id":"BeVi"}],"publisher":"MDPI AG","year":"2018","acknowledgement":"NSF DEB-1830753 and ISTPlus Fellowship","date_updated":"2023-09-19T10:37:03Z","date_created":"2018-12-11T11:44:26Z","volume":9,"author":[{"id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9638-1220","first_name":"William J","last_name":"Gammerdinger","full_name":"Gammerdinger, William J"},{"last_name":"Kocher","first_name":"Thomas","full_name":"Kocher, Thomas"}],"scopus_import":"1","day":"04","article_processing_charge":"No","has_accepted_license":"1","publication":"Genes","citation":{"mla":"Gammerdinger, William J., and Thomas Kocher. “Unusual Diversity of Sex Chromosomes in African Cichlid Fishes.” Genes, vol. 9, no. 10, 480, MDPI AG, 2018, doi:10.3390/genes9100480.","short":"W.J. Gammerdinger, T. Kocher, Genes 9 (2018).","chicago":"Gammerdinger, William J, and Thomas Kocher. “Unusual Diversity of Sex Chromosomes in African Cichlid Fishes.” Genes. MDPI AG, 2018. https://doi.org/10.3390/genes9100480.","ama":"Gammerdinger WJ, Kocher T. Unusual diversity of sex chromosomes in African cichlid fishes. Genes. 2018;9(10). doi:10.3390/genes9100480","ista":"Gammerdinger WJ, Kocher T. 2018. Unusual diversity of sex chromosomes in African cichlid fishes. Genes. 9(10), 480.","apa":"Gammerdinger, W. J., & Kocher, T. (2018). Unusual diversity of sex chromosomes in African cichlid fishes. Genes. MDPI AG. https://doi.org/10.3390/genes9100480","ieee":"W. J. Gammerdinger and T. Kocher, “Unusual diversity of sex chromosomes in African cichlid fishes,” Genes, vol. 9, no. 10. MDPI AG, 2018."},"date_published":"2018-10-04T00:00:00Z","type":"journal_article","abstract":[{"text":"African cichlids display a remarkable assortment of jaw morphologies, pigmentation patterns, and mating behaviors. In addition to this previously documented diversity, recent studies have documented a rich diversity of sex chromosomes within these fishes. Here we review the known sex-determination network within vertebrates, and the extraordinary number of sex chromosomes systems segregating in African cichlids. We also propose a model for understanding the unusual number of sex chromosome systems within this clade.","lang":"eng"}],"issue":"10","ddc":["570"],"status":"public","title":"Unusual diversity of sex chromosomes in African cichlid fishes","intvolume":" 9","_id":"63","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"file_id":"5743","relation":"main_file","checksum":"bec527692e2c9b56919c0429634ff337","date_updated":"2020-07-14T12:47:27Z","date_created":"2018-12-18T09:54:46Z","access_level":"open_access","file_name":"2018_Genes_Gammerdinger.pdf","creator":"dernst","file_size":1415791,"content_type":"application/pdf"}],"oa_version":"Published Version"},{"scopus_import":"1","day":"14","article_processing_charge":"No","publication":"Nature Physics","citation":{"chicago":"Turner, Christopher, Alexios Michailidis, Dmitry Abanin, Maksym Serbyn, and Zlatko Papić. “Weak Ergodicity Breaking from Quantum Many-Body Scars.” Nature Physics. Nature Publishing Group, 2018. https://doi.org/10.1038/s41567-018-0137-5.","short":"C. Turner, A. Michailidis, D. Abanin, M. Serbyn, Z. Papić, Nature Physics 14 (2018) 745–749.","mla":"Turner, Christopher, et al. “Weak Ergodicity Breaking from Quantum Many-Body Scars.” Nature Physics, vol. 14, Nature Publishing Group, 2018, pp. 745–49, doi:10.1038/s41567-018-0137-5.","ieee":"C. Turner, A. Michailidis, D. Abanin, M. Serbyn, and Z. Papić, “Weak ergodicity breaking from quantum many-body scars,” Nature Physics, vol. 14. Nature Publishing Group, pp. 745–749, 2018.","apa":"Turner, C., Michailidis, A., Abanin, D., Serbyn, M., & Papić, Z. (2018). Weak ergodicity breaking from quantum many-body scars. Nature Physics. Nature Publishing Group. https://doi.org/10.1038/s41567-018-0137-5","ista":"Turner C, Michailidis A, Abanin D, Serbyn M, Papić Z. 2018. Weak ergodicity breaking from quantum many-body scars. Nature Physics. 14, 745–749.","ama":"Turner C, Michailidis A, Abanin D, Serbyn M, Papić Z. Weak ergodicity breaking from quantum many-body scars. Nature Physics. 2018;14:745-749. doi:10.1038/s41567-018-0137-5"},"article_type":"original","page":"745 - 749","date_published":"2018-05-14T00:00:00Z","type":"journal_article","abstract":[{"text":"The thermodynamic description of many-particle systems rests on the assumption of ergodicity, the ability of a system to explore all allowed configurations in the phase space. Recent studies on many-body localization have revealed the existence of systems that strongly violate ergodicity in the presence of quenched disorder. Here, we demonstrate that ergodicity can be weakly broken by a different mechanism, arising from the presence of special eigenstates in the many-body spectrum that are reminiscent of quantum scars in chaotic non-interacting systems. In the single-particle case, quantum scars correspond to wavefunctions that concentrate in the vicinity of unstable periodic classical trajectories. We show that many-body scars appear in the Fibonacci chain, a model with a constrained local Hilbert space that has recently been experimentally realized in a Rydberg-atom quantum simulator. The quantum scarred eigenstates are embedded throughout the otherwise thermalizing many-body spectrum but lead to direct experimental signatures, as we show for periodic recurrences that reproduce those observed in the experiment. Our results suggest that scarred many-body bands give rise to a new universality class of quantum dynamics, opening up opportunities for the creation of novel states with long-lived coherence in systems that are now experimentally realizable.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"296","status":"public","title":"Weak ergodicity breaking from quantum many-body scars","intvolume":" 14","oa_version":"Submitted Version","month":"05","main_file_link":[{"url":"http://eprints.whiterose.ac.uk/130860/","open_access":"1"}],"external_id":{"isi":["000438253600028"]},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1038/s41567-018-0137-5","language":[{"iso":"eng"}],"publist_id":"7585","acknowledgement":"C.J.T., A.M. and Z.P. acknowledge support from EPSRC grants EP/P009409/1 and EP/M50807X/1, and Royal Society Research Grant RG160635. D.A. acknowledges support from the Swiss National Science Foundation.","year":"2018","publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"MaSe"}],"author":[{"full_name":"Turner, Christopher","last_name":"Turner","first_name":"Christopher"},{"full_name":"Michailidis, Alexios","last_name":"Michailidis","first_name":"Alexios","orcid":"0000-0002-8443-1064","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Abanin, Dmitry","first_name":"Dmitry","last_name":"Abanin"},{"orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","first_name":"Maksym","full_name":"Serbyn, Maksym"},{"first_name":"Zlatko","last_name":"Papić","full_name":"Papić, Zlatko"}],"date_created":"2018-12-11T11:45:40Z","date_updated":"2023-09-19T10:37:55Z","volume":14},{"oa_version":"Submitted Version","_id":"607","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Well posedness and maximum entropy approximation for the dynamics of quantitative traits","abstract":[{"lang":"eng","text":"We study the Fokker-Planck equation derived in the large system limit of the Markovian process describing the dynamics of quantitative traits. The Fokker-Planck equation is posed on a bounded domain and its transport and diffusion coefficients vanish on the domain's boundary. We first argue that, despite this degeneracy, the standard no-flux boundary condition is valid. We derive the weak formulation of the problem and prove the existence and uniqueness of its solutions by constructing the corresponding contraction semigroup on a suitable function space. Then, we prove that for the parameter regime with high enough mutation rate the problem exhibits a positive spectral gap, which implies exponential convergence to equilibrium.Next, we provide a simple derivation of the so-called Dynamic Maximum Entropy (DynMaxEnt) method for approximation of observables (moments) of the Fokker-Planck solution, which can be interpreted as a nonlinear Galerkin approximation. The limited applicability of the DynMaxEnt method inspires us to introduce its modified version that is valid for the whole range of admissible parameters. Finally, we present several numerical experiments to demonstrate the performance of both the original and modified DynMaxEnt methods. We observe that in the parameter regimes where both methods are valid, the modified one exhibits slightly better approximation properties compared to the original one."}],"type":"journal_article","date_published":"2018-08-01T00:00:00Z","publication":"Physica D: Nonlinear Phenomena","citation":{"ieee":"K. Bodova, J. Haskovec, and P. Markowich, “Well posedness and maximum entropy approximation for the dynamics of quantitative traits,” Physica D: Nonlinear Phenomena, vol. 376–377. Elsevier, pp. 108–120, 2018.","apa":"Bodova, K., Haskovec, J., & Markowich, P. (2018). Well posedness and maximum entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena. Elsevier. https://doi.org/10.1016/j.physd.2017.10.015","ista":"Bodova K, Haskovec J, Markowich P. 2018. Well posedness and maximum entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena. 376–377, 108–120.","ama":"Bodova K, Haskovec J, Markowich P. Well posedness and maximum entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena. 2018;376-377:108-120. doi:10.1016/j.physd.2017.10.015","chicago":"Bodova, Katarina, Jan Haskovec, and Peter Markowich. “Well Posedness and Maximum Entropy Approximation for the Dynamics of Quantitative Traits.” Physica D: Nonlinear Phenomena. Elsevier, 2018. https://doi.org/10.1016/j.physd.2017.10.015.","short":"K. Bodova, J. Haskovec, P. Markowich, Physica D: Nonlinear Phenomena 376–377 (2018) 108–120.","mla":"Bodova, Katarina, et al. “Well Posedness and Maximum Entropy Approximation for the Dynamics of Quantitative Traits.” Physica D: Nonlinear Phenomena, vol. 376–377, Elsevier, 2018, pp. 108–20, doi:10.1016/j.physd.2017.10.015."},"page":"108-120","day":"01","article_processing_charge":"No","scopus_import":"1","author":[{"full_name":"Bodova, Katarina","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7214-0171","first_name":"Katarina","last_name":"Bodova"},{"last_name":"Haskovec","first_name":"Jan","full_name":"Haskovec, Jan"},{"first_name":"Peter","last_name":"Markowich","full_name":"Markowich, Peter"}],"date_created":"2018-12-11T11:47:28Z","date_updated":"2023-09-19T10:38:34Z","volume":"376-377","year":"2018","acknowledgement":"JH and PM are funded by KAUST baseline funds and grant no. 1000000193 .\r\nWe thank Nicholas Barton (IST Austria) for his useful comments and suggestions. \r\n\r\n","publication_status":"published","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"publisher":"Elsevier","publist_id":"7198","doi":"10.1016/j.physd.2017.10.015","language":[{"iso":"eng"}],"external_id":{"isi":["000437962900012"],"arxiv":["1704.08757"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1704.08757"}],"quality_controlled":"1","isi":1,"month":"08"},{"intvolume":" 97","status":"public","title":"Two-photon processes based on quantum commutators","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"294","oa_version":"Submitted Version","type":"journal_article","issue":"4","abstract":[{"text":"We developed a method to calculate two-photon processes in quantum mechanics that replaces the infinite summation over the intermediate states by a perturbation expansion. This latter consists of a series of commutators that involve position, momentum, and Hamiltonian quantum operators. We analyzed several single- and many-particle cases for which a closed-form solution to the perturbation expansion exists, as well as more complicated cases for which a solution is found by convergence. Throughout the article, Rayleigh and Raman scattering are taken as examples of two-photon processes. The present method provides a clear distinction between the Thomson scattering, regarded as classical scattering, and quantum contributions. Such a distinction lets us derive general results concerning light scattering. Finally, possible extensions to the developed formalism are discussed.","lang":"eng"}],"citation":{"mla":"Fratini, Filippo, et al. “Two-Photon Processes Based on Quantum Commutators.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 4, American Physical Society, 2018, doi:10.1103/PhysRevA.97.043842.","short":"F. Fratini, L. Safari, P. Amaro, J. Santos, Physical Review A - Atomic, Molecular, and Optical Physics 97 (2018).","chicago":"Fratini, Filippo, Laleh Safari, Pedro Amaro, and José Santos. “Two-Photon Processes Based on Quantum Commutators.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2018. https://doi.org/10.1103/PhysRevA.97.043842.","ama":"Fratini F, Safari L, Amaro P, Santos J. Two-photon processes based on quantum commutators. Physical Review A - Atomic, Molecular, and Optical Physics. 2018;97(4). doi:10.1103/PhysRevA.97.043842","ista":"Fratini F, Safari L, Amaro P, Santos J. 2018. Two-photon processes based on quantum commutators. Physical Review A - Atomic, Molecular, and Optical Physics. 97(4).","apa":"Fratini, F., Safari, L., Amaro, P., & Santos, J. (2018). Two-photon processes based on quantum commutators. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.97.043842","ieee":"F. Fratini, L. Safari, P. Amaro, and J. Santos, “Two-photon processes based on quantum commutators,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 4. American Physical Society, 2018."},"publication":"Physical Review A - Atomic, Molecular, and Optical Physics","date_published":"2018-04-18T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"18","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","publication_status":"published","year":"2018","volume":97,"date_updated":"2023-09-19T10:17:56Z","date_created":"2018-12-11T11:45:40Z","author":[{"full_name":"Fratini, Filippo","first_name":"Filippo","last_name":"Fratini"},{"full_name":"Safari, Laleh","first_name":"Laleh","last_name":"Safari","id":"3C325E5E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Pedro","last_name":"Amaro","full_name":"Amaro, Pedro"},{"first_name":"José","last_name":"Santos","full_name":"Santos, José"}],"ec_funded":1,"publist_id":"7587","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1801.06892","open_access":"1"}],"oa":1,"external_id":{"isi":["000430296800008"],"arxiv":["1801.06892"]},"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevA.97.043842","month":"04"},{"scopus_import":"1","article_processing_charge":"No","day":"01","page":"1267-1319","citation":{"chicago":"Duerinckx, Mitia, and Julian L Fischer. “Well-Posedness for Mean-Field Evolutions Arising in Superconductivity.” Annales de l’Institut Henri Poincare (C) Non Linear Analysis. Elsevier, 2018. https://doi.org/10.1016/j.anihpc.2017.11.004.","mla":"Duerinckx, Mitia, and Julian L. Fischer. “Well-Posedness for Mean-Field Evolutions Arising in Superconductivity.” Annales de l’Institut Henri Poincare (C) Non Linear Analysis, vol. 35, no. 5, Elsevier, 2018, pp. 1267–319, doi:10.1016/j.anihpc.2017.11.004.","short":"M. Duerinckx, J.L. Fischer, Annales de l’Institut Henri Poincare (C) Non Linear Analysis 35 (2018) 1267–1319.","ista":"Duerinckx M, Fischer JL. 2018. Well-posedness for mean-field evolutions arising in superconductivity. Annales de l’Institut Henri Poincare (C) Non Linear Analysis. 35(5), 1267–1319.","apa":"Duerinckx, M., & Fischer, J. L. (2018). Well-posedness for mean-field evolutions arising in superconductivity. Annales de l’Institut Henri Poincare (C) Non Linear Analysis. Elsevier. https://doi.org/10.1016/j.anihpc.2017.11.004","ieee":"M. Duerinckx and J. L. Fischer, “Well-posedness for mean-field evolutions arising in superconductivity,” Annales de l’Institut Henri Poincare (C) Non Linear Analysis, vol. 35, no. 5. Elsevier, pp. 1267–1319, 2018.","ama":"Duerinckx M, Fischer JL. Well-posedness for mean-field evolutions arising in superconductivity. Annales de l’Institut Henri Poincare (C) Non Linear Analysis. 2018;35(5):1267-1319. doi:10.1016/j.anihpc.2017.11.004"},"publication":"Annales de l'Institut Henri Poincare (C) Non Linear Analysis","date_published":"2018-08-01T00:00:00Z","type":"journal_article","issue":"5","abstract":[{"text":"We establish the existence of a global solution for a new family of fluid-like equations, which are obtained in certain regimes in as the mean-field evolution of the supercurrent density in a (2D section of a) type-II superconductor with pinning and with imposed electric current. We also consider general vortex-sheet initial data, and investigate the uniqueness and regularity properties of the solution. For some choice of parameters, the equation under investigation coincides with the so-called lake equation from 2D shallow water fluid dynamics, and our analysis then leads to a new existence result for rough initial data.","lang":"eng"}],"intvolume":" 35","status":"public","title":"Well-posedness for mean-field evolutions arising in superconductivity","_id":"606","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Submitted Version","month":"08","isi":1,"quality_controlled":"1","external_id":{"arxiv":["1607.00268"],"isi":["000437975500005"]},"main_file_link":[{"url":"https://arxiv.org/abs/1607.00268","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.anihpc.2017.11.004","publist_id":"7199","publisher":"Elsevier","department":[{"_id":"JuFi"}],"publication_status":"published","acknowledgement":"The work of the author is supported by F.R.S.-FNRS ( Fonds de la Recherche Scientifique - FNRS ) through a Research Fellowship.\r\n\r\n","year":"2018","volume":35,"date_created":"2018-12-11T11:47:27Z","date_updated":"2023-09-19T10:39:09Z","author":[{"full_name":"Duerinckx, Mitia","first_name":"Mitia","last_name":"Duerinckx"},{"full_name":"Fischer, Julian L","last_name":"Fischer","first_name":"Julian L","orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87"}]},{"abstract":[{"lang":"eng","text":"Formalizing properties of systems with continuous dynamics is a challenging task. In this paper, we propose a formal framework for specifying and monitoring rich temporal properties of real-valued signals. We introduce signal first-order logic (SFO) as a specification language that combines first-order logic with linear-real arithmetic and unary function symbols interpreted as piecewise-linear signals. We first show that while the satisfiability problem for SFO is undecidable, its membership and monitoring problems are decidable. We develop an offline monitoring procedure for SFO that has polynomial complexity in the size of the input trace and the specification, for a fixed number of quantifiers and function symbols. We show that the algorithm has computation time linear in the size of the input trace for the important fragment of bounded-response specifications interpreted over input traces with finite variability. We can use our results to extend signal temporal logic with first-order quantifiers over time and value parameters, while preserving its efficient monitoring. We finally demonstrate the practical appeal of our logic through a case study in the micro-electronics domain."}],"type":"conference","file":[{"file_name":"2018_EMSOFT_Bakhirkin.pdf","access_level":"open_access","file_size":338006,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"7839","date_updated":"2020-07-14T12:47:13Z","date_created":"2020-05-14T16:01:29Z","checksum":"234a33ad9055b3458fcdda6af251b33a"}],"oa_version":"Published Version","_id":"5959","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["000"],"status":"public","title":"Keynote: The first-order logic of signals","day":"30","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2018-09-30T00:00:00Z","publication":"2018 International Conference on Embedded Software","citation":{"ama":"Bakhirkin A, Ferrere T, Henzinger TA, Nickovicl D. Keynote: The first-order logic of signals. In: 2018 International Conference on Embedded Software. IEEE; 2018:1-10. doi:10.1109/emsoft.2018.8537203","ista":"Bakhirkin A, Ferrere T, Henzinger TA, Nickovicl D. 2018. Keynote: The first-order logic of signals. 2018 International Conference on Embedded Software. EMSOFT: International Conference on Embedded Software, 1–10.","ieee":"A. Bakhirkin, T. Ferrere, T. A. Henzinger, and D. Nickovicl, “Keynote: The first-order logic of signals,” in 2018 International Conference on Embedded Software, Turin, Italy, 2018, pp. 1–10.","apa":"Bakhirkin, A., Ferrere, T., Henzinger, T. A., & Nickovicl, D. (2018). Keynote: The first-order logic of signals. In 2018 International Conference on Embedded Software (pp. 1–10). Turin, Italy: IEEE. https://doi.org/10.1109/emsoft.2018.8537203","mla":"Bakhirkin, Alexey, et al. “Keynote: The First-Order Logic of Signals.” 2018 International Conference on Embedded Software, IEEE, 2018, pp. 1–10, doi:10.1109/emsoft.2018.8537203.","short":"A. Bakhirkin, T. Ferrere, T.A. Henzinger, D. Nickovicl, in:, 2018 International Conference on Embedded Software, IEEE, 2018, pp. 1–10.","chicago":"Bakhirkin, Alexey, Thomas Ferrere, Thomas A Henzinger, and Deian Nickovicl. “Keynote: The First-Order Logic of Signals.” In 2018 International Conference on Embedded Software, 1–10. IEEE, 2018. https://doi.org/10.1109/emsoft.2018.8537203."},"page":"1-10","file_date_updated":"2020-07-14T12:47:13Z","author":[{"full_name":"Bakhirkin, Alexey","last_name":"Bakhirkin","first_name":"Alexey"},{"full_name":"Ferrere, Thomas","first_name":"Thomas","last_name":"Ferrere","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5199-3143"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Deian","last_name":"Nickovicl","full_name":"Nickovicl, Deian"}],"date_updated":"2023-09-19T10:41:29Z","date_created":"2019-02-13T09:19:28Z","year":"2018","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"IEEE","month":"09","publication_identifier":{"isbn":["9781538655603"]},"conference":{"end_date":"2018-10-05","location":"Turin, Italy","start_date":"2018-09-30","name":"EMSOFT: International Conference on Embedded Software"},"doi":"10.1109/emsoft.2018.8537203","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000492828500005"]},"quality_controlled":"1","isi":1,"project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF"}]},{"year":"2018","publication_status":"published","department":[{"_id":"DaAl"}],"publisher":"ACM Press","author":[{"full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh"},{"full_name":"De Sa, Christopher","first_name":"Christopher","last_name":"De Sa"},{"full_name":"Konstantinov, Nikola H","id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87","first_name":"Nikola H","last_name":"Konstantinov"}],"date_updated":"2023-09-19T10:42:53Z","date_created":"2019-02-13T09:58:58Z","month":"07","publication_identifier":{"isbn":["9781450357951"]},"oa":1,"external_id":{"arxiv":["1803.08841"],"isi":["000458186900022"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.08841"}],"quality_controlled":"1","isi":1,"conference":{"name":"PODC: Principles of Distributed Computing","end_date":"2018-07-27","start_date":"2018-07-23","location":"Egham, United Kingdom"},"doi":"10.1145/3212734.3212763","language":[{"iso":"eng"}],"type":"conference","abstract":[{"text":"Stochastic Gradient Descent (SGD) is a fundamental algorithm in machine learning, representing the optimization backbone for training several classic models, from regression to neural networks. Given the recent practical focus on distributed machine learning, significant work has been dedicated to the convergence properties of this algorithm under the inconsistent and noisy updates arising from execution in a distributed environment. However, surprisingly, the convergence properties of this classic algorithm in the standard shared-memory model are still not well-understood. In this work, we address this gap, and provide new convergence bounds for lock-free concurrent stochastic gradient descent, executing in the classic asynchronous shared memory model, against a strong adaptive adversary. Our results give improved upper and lower bounds on the \"price of asynchrony'' when executing the fundamental SGD algorithm in a concurrent setting. They show that this classic optimization tool can converge faster and with a wider range of parameters than previously known under asynchronous iterations. At the same time, we exhibit a fundamental trade-off between the maximum delay in the system and the rate at which SGD can converge, which governs the set of parameters under which this algorithm can still work efficiently.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5962","title":"The convergence of stochastic gradient descent in asynchronous shared memory","status":"public","oa_version":"Preprint","scopus_import":"1","day":"23","article_processing_charge":"No","publication":"Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC '18","citation":{"ama":"Alistarh D-A, De Sa C, Konstantinov NH. The convergence of stochastic gradient descent in asynchronous shared memory. In: Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18. ACM Press; 2018:169-178. doi:10.1145/3212734.3212763","ista":"Alistarh D-A, De Sa C, Konstantinov NH. 2018. The convergence of stochastic gradient descent in asynchronous shared memory. Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18. PODC: Principles of Distributed Computing, 169–178.","ieee":"D.-A. Alistarh, C. De Sa, and N. H. Konstantinov, “The convergence of stochastic gradient descent in asynchronous shared memory,” in Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, Egham, United Kingdom, 2018, pp. 169–178.","apa":"Alistarh, D.-A., De Sa, C., & Konstantinov, N. H. (2018). The convergence of stochastic gradient descent in asynchronous shared memory. In Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18 (pp. 169–178). Egham, United Kingdom: ACM Press. https://doi.org/10.1145/3212734.3212763","mla":"Alistarh, Dan-Adrian, et al. “The Convergence of Stochastic Gradient Descent in Asynchronous Shared Memory.” Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, ACM Press, 2018, pp. 169–78, doi:10.1145/3212734.3212763.","short":"D.-A. Alistarh, C. De Sa, N.H. Konstantinov, in:, Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, ACM Press, 2018, pp. 169–178.","chicago":"Alistarh, Dan-Adrian, Christopher De Sa, and Nikola H Konstantinov. “The Convergence of Stochastic Gradient Descent in Asynchronous Shared Memory.” In Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, 169–78. ACM Press, 2018. https://doi.org/10.1145/3212734.3212763."},"page":"169-178","date_published":"2018-07-23T00:00:00Z"},{"status":"public","title":"Zipf's Law, unbounded complexity and open-ended evolution","intvolume":" 15","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5860","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"A major problem for evolutionary theory is understanding the so-called open-ended nature of evolutionary change, from its definition to its origins. Open-ended evolution (OEE) refers to the unbounded increase in complexity that seems to characterize evolution on multiple scales. This property seems to be a characteristic feature of biological and technological evolution and is strongly tied to the generative potential associated with combinatorics, which allows the system to grow and expand their available state spaces. Interestingly, many complex systems presumably displaying OEE, from language to proteins, share a common statistical property: the presence of Zipf's Law. Given an inventory of basic items (such as words or protein domains) required to build more complex structures (sentences or proteins) Zipf's Law tells us that most of these elements are rare whereas a few of them are extremely common. Using algorithmic information theory, in this paper we provide a fundamental definition for open-endedness, which can be understood as postulates. Its statistical counterpart, based on standard Shannon information theory, has the structure of a variational problem which is shown to lead to Zipf's Law as the expected consequence of an evolutionary process displaying OEE. We further explore the problem of information conservation through an OEE process and we conclude that statistical information (standard Shannon information) is not conserved, resulting in the paradoxical situation in which the increase of information content has the effect of erasing itself. We prove that this paradox is solved if we consider non-statistical forms of information. This last result implies that standard information theory may not be a suitable theoretical framework to explore the persistence and increase of the information content in OEE systems.","lang":"eng"}],"issue":"149","publication":"Journal of the Royal Society Interface","citation":{"ama":"Corominas-Murtra B, Seoane LF, Solé R. Zipf’s Law, unbounded complexity and open-ended evolution. Journal of the Royal Society Interface. 2018;15(149). doi:10.1098/rsif.2018.0395","apa":"Corominas-Murtra, B., Seoane, L. F., & Solé, R. (2018). Zipf’s Law, unbounded complexity and open-ended evolution. Journal of the Royal Society Interface. Royal Society Publishing. https://doi.org/10.1098/rsif.2018.0395","ieee":"B. Corominas-Murtra, L. F. Seoane, and R. Solé, “Zipf’s Law, unbounded complexity and open-ended evolution,” Journal of the Royal Society Interface, vol. 15, no. 149. Royal Society Publishing, 2018.","ista":"Corominas-Murtra B, Seoane LF, Solé R. 2018. Zipf’s Law, unbounded complexity and open-ended evolution. Journal of the Royal Society Interface. 15(149), 20180395.","short":"B. Corominas-Murtra, L.F. Seoane, R. Solé, Journal of the Royal Society Interface 15 (2018).","mla":"Corominas-Murtra, Bernat, et al. “Zipf’s Law, Unbounded Complexity and Open-Ended Evolution.” Journal of the Royal Society Interface, vol. 15, no. 149, 20180395, Royal Society Publishing, 2018, doi:10.1098/rsif.2018.0395.","chicago":"Corominas-Murtra, Bernat, Luís F. Seoane, and Ricard Solé. “Zipf’s Law, Unbounded Complexity and Open-Ended Evolution.” Journal of the Royal Society Interface. Royal Society Publishing, 2018. https://doi.org/10.1098/rsif.2018.0395."},"date_published":"2018-12-12T00:00:00Z","scopus_import":"1","day":"12","article_processing_charge":"No","publication_status":"published","department":[{"_id":"EdHa"}],"publisher":"Royal Society Publishing","year":"2018","date_created":"2019-01-20T22:59:19Z","date_updated":"2023-09-19T10:40:38Z","volume":15,"author":[{"id":"43BE2298-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9806-5643","first_name":"Bernat","last_name":"Corominas-Murtra","full_name":"Corominas-Murtra, Bernat"},{"full_name":"Seoane, Luís F.","first_name":"Luís F.","last_name":"Seoane"},{"last_name":"Solé","first_name":"Ricard","full_name":"Solé, Ricard"}],"article_number":"20180395","quality_controlled":"1","isi":1,"external_id":{"arxiv":["1612.01605"],"isi":["000456783800002"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1612.01605","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1098/rsif.2018.0395","month":"12","publication_identifier":{"issn":["17425689"]}},{"language":[{"iso":"eng"}],"conference":{"end_date":"2018-07-27","start_date":"2018-07-23","location":"Egham, United Kingdom","name":"PODC: Principles of Distributed Computing"},"date_published":"2018-07-27T00:00:00Z","doi":"10.1145/3212734.3212798","quality_controlled":"1","isi":1,"page":"487-488","publication":"Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC '18","citation":{"chicago":"Alistarh, Dan-Adrian. “A Brief Tutorial on Distributed and Concurrent Machine Learning.” In Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, 487–88. ACM Press, 2018. https://doi.org/10.1145/3212734.3212798.","short":"D.-A. Alistarh, in:, Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, ACM Press, 2018, pp. 487–488.","mla":"Alistarh, Dan-Adrian. “A Brief Tutorial on Distributed and Concurrent Machine Learning.” Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, ACM Press, 2018, pp. 487–88, doi:10.1145/3212734.3212798.","apa":"Alistarh, D.-A. (2018). A brief tutorial on distributed and concurrent machine learning. In Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18 (pp. 487–488). Egham, United Kingdom: ACM Press. https://doi.org/10.1145/3212734.3212798","ieee":"D.-A. Alistarh, “A brief tutorial on distributed and concurrent machine learning,” in Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, Egham, United Kingdom, 2018, pp. 487–488.","ista":"Alistarh D-A. 2018. A brief tutorial on distributed and concurrent machine learning. Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18. PODC: Principles of Distributed Computing, 487–488.","ama":"Alistarh D-A. A brief tutorial on distributed and concurrent machine learning. In: Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18. ACM Press; 2018:487-488. doi:10.1145/3212734.3212798"},"external_id":{"isi":["000458186900063"]},"month":"07","day":"27","article_processing_charge":"No","publication_identifier":{"isbn":["9781450357951"]},"scopus_import":"1","date_updated":"2023-09-19T10:42:28Z","date_created":"2019-02-13T09:48:55Z","oa_version":"None","author":[{"full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh"}],"title":"A brief tutorial on distributed and concurrent machine learning","publication_status":"published","status":"public","department":[{"_id":"DaAl"}],"publisher":"ACM Press","year":"2018","_id":"5961","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"The area of machine learning has made considerable progress over the past decade, enabled by the widespread availability of large datasets, as well as by improved algorithms and models. Given the large computational demands of machine learning workloads, parallelism, implemented either through single-node concurrency or through multi-node distribution, has been a third key ingredient to advances in machine learning.\r\nThe goal of this tutorial is to provide the audience with an overview of standard distribution techniques in machine learning, with an eye towards the intriguing trade-offs between synchronization and communication costs of distributed machine learning algorithms, on the one hand, and their convergence, on the other.The tutorial will focus on parallelization strategies for the fundamental stochastic gradient descent (SGD) algorithm, which is a key tool when training machine learning models, from classical instances such as linear regression, to state-of-the-art neural network architectures.\r\nThe tutorial will describe the guarantees provided by this algorithm in the sequential case, and then move on to cover both shared-memory and message-passing parallelization strategies, together with the guarantees they provide, and corresponding trade-offs. The presentation will conclude with a broad overview of ongoing research in distributed and concurrent machine learning. The tutorial will assume no prior knowledge beyond familiarity with basic concepts in algebra and analysis.\r\n","lang":"eng"}],"type":"conference"},{"type":"journal_article","abstract":[{"text":"In this paper we present a reliable method to verify the existence of loops along the uncertain trajectory of a robot, based on proprioceptive measurements only, within a bounded-error context. The loop closure detection is one of the key points in simultaneous localization and mapping (SLAM) methods, especially in homogeneous environments with difficult scenes recognitions. The proposed approach is generic and could be coupled with conventional SLAM algorithms to reliably reduce their computing burden, thus improving the localization and mapping processes in the most challenging environments such as unexplored underwater extents. To prove that a robot performed a loop whatever the uncertainties in its evolution, we employ the notion of topological degree that originates in the field of differential topology. We show that a verification tool based on the topological degree is an optimal method for proving robot loops. This is demonstrated both on datasets from real missions involving autonomous underwater vehicles and by a mathematical discussion.","lang":"eng"}],"issue":"12","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5960","status":"public","title":"Proving the existence of loops in robot trajectories","intvolume":" 37","oa_version":"Preprint","scopus_import":"1","day":"24","article_processing_charge":"No","publication":"The International Journal of Robotics Research","citation":{"chicago":"Rohou, Simon, Peter Franek, Clément Aubry, and Luc Jaulin. “Proving the Existence of Loops in Robot Trajectories.” The International Journal of Robotics Research. SAGE Publications, 2018. https://doi.org/10.1177/0278364918808367.","mla":"Rohou, Simon, et al. “Proving the Existence of Loops in Robot Trajectories.” The International Journal of Robotics Research, vol. 37, no. 12, SAGE Publications, 2018, pp. 1500–16, doi:10.1177/0278364918808367.","short":"S. Rohou, P. Franek, C. Aubry, L. Jaulin, The International Journal of Robotics Research 37 (2018) 1500–1516.","ista":"Rohou S, Franek P, Aubry C, Jaulin L. 2018. Proving the existence of loops in robot trajectories. The International Journal of Robotics Research. 37(12), 1500–1516.","apa":"Rohou, S., Franek, P., Aubry, C., & Jaulin, L. (2018). Proving the existence of loops in robot trajectories. The International Journal of Robotics Research. SAGE Publications. https://doi.org/10.1177/0278364918808367","ieee":"S. Rohou, P. Franek, C. Aubry, and L. Jaulin, “Proving the existence of loops in robot trajectories,” The International Journal of Robotics Research, vol. 37, no. 12. SAGE Publications, pp. 1500–1516, 2018.","ama":"Rohou S, Franek P, Aubry C, Jaulin L. Proving the existence of loops in robot trajectories. The International Journal of Robotics Research. 2018;37(12):1500-1516. doi:10.1177/0278364918808367"},"page":"1500-1516","date_published":"2018-10-24T00:00:00Z","year":"2018","publication_status":"published","department":[{"_id":"UlWa"}],"publisher":"SAGE Publications","author":[{"last_name":"Rohou","first_name":"Simon","full_name":"Rohou, Simon"},{"full_name":"Franek, Peter","orcid":"0000-0001-8878-8397","id":"473294AE-F248-11E8-B48F-1D18A9856A87","last_name":"Franek","first_name":"Peter"},{"last_name":"Aubry","first_name":"Clément","full_name":"Aubry, Clément"},{"last_name":"Jaulin","first_name":"Luc","full_name":"Jaulin, Luc"}],"date_updated":"2023-09-19T10:41:59Z","date_created":"2019-02-13T09:36:20Z","volume":37,"month":"10","publication_identifier":{"issn":["0278-3649"],"eissn":["1741-3176"]},"external_id":{"arxiv":["1712.01341"],"isi":["000456881100004"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1712.01341","open_access":"1"}],"isi":1,"quality_controlled":"1","doi":"10.1177/0278364918808367","language":[{"iso":"eng"}]},{"oa_version":"Preprint","status":"public","title":"Relaxed schedulers can efficiently parallelize iterative algorithms","_id":"5963","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"There has been significant progress in understanding the parallelism inherent to iterative sequential algorithms: for many classic algorithms, the depth of the dependence structure is now well understood, and scheduling techniques have been developed to exploit this shallow dependence structure for efficient parallel implementations. A related, applied research strand has studied methods by which certain iterative task-based algorithms can be efficiently parallelized via relaxed concurrent priority schedulers. These allow for high concurrency when inserting and removing tasks, at the cost of executing superfluous work due to the relaxed semantics of the scheduler. In this work, we take a step towards unifying these two research directions, by showing that there exists a family of relaxed priority schedulers that can efficiently and deterministically execute classic iterative algorithms such as greedy maximal independent set (MIS) and matching. Our primary result shows that, given a randomized scheduler with an expected relaxation factor of k in terms of the maximum allowed priority inversions on a task, and any graph on n vertices, the scheduler is able to execute greedy MIS with only an additive factor of \\poly(k) expected additional iterations compared to an exact (but not scalable) scheduler. This counter-intuitive result demonstrates that the overhead of relaxation when computing MIS is not dependent on the input size or structure of the input graph. Experimental results show that this overhead can be clearly offset by the gain in performance due to the highly scalable scheduler. In sum, we present an efficient method to deterministically parallelize iterative sequential algorithms, with provable runtime guarantees in terms of the number of executed tasks to completion.","lang":"eng"}],"type":"conference","date_published":"2018-07-23T00:00:00Z","page":"377-386","citation":{"ama":"Alistarh D-A, Brown TA, Kopinsky J, Nadiradze G. Relaxed schedulers can efficiently parallelize iterative algorithms. In: Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18. ACM Press; 2018:377-386. doi:10.1145/3212734.3212756","ista":"Alistarh D-A, Brown TA, Kopinsky J, Nadiradze G. 2018. Relaxed schedulers can efficiently parallelize iterative algorithms. Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18. PODC: Principles of Distributed Computing, 377–386.","ieee":"D.-A. Alistarh, T. A. Brown, J. Kopinsky, and G. Nadiradze, “Relaxed schedulers can efficiently parallelize iterative algorithms,” in Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, Egham, United Kingdom, 2018, pp. 377–386.","apa":"Alistarh, D.-A., Brown, T. A., Kopinsky, J., & Nadiradze, G. (2018). Relaxed schedulers can efficiently parallelize iterative algorithms. In Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18 (pp. 377–386). Egham, United Kingdom: ACM Press. https://doi.org/10.1145/3212734.3212756","mla":"Alistarh, Dan-Adrian, et al. “Relaxed Schedulers Can Efficiently Parallelize Iterative Algorithms.” Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, ACM Press, 2018, pp. 377–86, doi:10.1145/3212734.3212756.","short":"D.-A. Alistarh, T.A. Brown, J. Kopinsky, G. Nadiradze, in:, Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, ACM Press, 2018, pp. 377–386.","chicago":"Alistarh, Dan-Adrian, Trevor A Brown, Justin Kopinsky, and Giorgi Nadiradze. “Relaxed Schedulers Can Efficiently Parallelize Iterative Algorithms.” In Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, 377–86. ACM Press, 2018. https://doi.org/10.1145/3212734.3212756."},"publication":"Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC '18","article_processing_charge":"No","day":"23","scopus_import":"1","date_updated":"2023-09-19T10:43:21Z","date_created":"2019-02-13T10:03:25Z","author":[{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian"},{"first_name":"Trevor A","last_name":"Brown","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","full_name":"Brown, Trevor A"},{"last_name":"Kopinsky","first_name":"Justin","full_name":"Kopinsky, Justin"},{"first_name":"Giorgi","last_name":"Nadiradze","full_name":"Nadiradze, Giorgi"}],"department":[{"_id":"DaAl"}],"publisher":"ACM Press","publication_status":"published","year":"2018","language":[{"iso":"eng"}],"doi":"10.1145/3212734.3212756","conference":{"name":"PODC: Principles of Distributed Computing","end_date":"2018-07-27","location":"Egham, United Kingdom","start_date":"2018-07-23"},"quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://arxiv.org/abs/1808.04155","open_access":"1"}],"external_id":{"isi":["000458186900048"],"arxiv":["1808.04155"]},"oa":1,"publication_identifier":{"isbn":["9781450357951"]},"month":"07"},{"isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1804.01018","open_access":"1"}],"external_id":{"isi":["000545269600016"],"arxiv":["1804.01018"]},"language":[{"iso":"eng"}],"conference":{"name":"SPAA: Symposium on Parallelism in Algorithms and Architectures","start_date":"2018-07-16","location":"Vienna, Austria","end_date":"2018-07-18"},"doi":"10.1145/3210377.3210411","month":"07","publication_identifier":{"isbn":["9781450357999"]},"publication_status":"published","department":[{"_id":"DaAl"}],"publisher":"ACM Press","year":"2018","date_updated":"2023-09-19T10:44:13Z","date_created":"2019-02-13T10:17:19Z","author":[{"first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"},{"full_name":"Brown, Trevor A","first_name":"Trevor A","last_name":"Brown","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kopinsky, Justin","last_name":"Kopinsky","first_name":"Justin"},{"full_name":"Li, Jerry Z.","first_name":"Jerry Z.","last_name":"Li"},{"first_name":"Giorgi","last_name":"Nadiradze","full_name":"Nadiradze, Giorgi"}],"related_material":{"record":[{"id":"10429","status":"public","relation":"dissertation_contains"}]},"page":"133-142","publication":"Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA '18","citation":{"short":"D.-A. Alistarh, T.A. Brown, J. Kopinsky, J.Z. Li, G. Nadiradze, in:, Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA ’18, ACM Press, 2018, pp. 133–142.","mla":"Alistarh, Dan-Adrian, et al. “Distributionally Linearizable Data Structures.” Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA ’18, ACM Press, 2018, pp. 133–42, doi:10.1145/3210377.3210411.","chicago":"Alistarh, Dan-Adrian, Trevor A Brown, Justin Kopinsky, Jerry Z. Li, and Giorgi Nadiradze. “Distributionally Linearizable Data Structures.” In Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA ’18, 133–42. ACM Press, 2018. https://doi.org/10.1145/3210377.3210411.","ama":"Alistarh D-A, Brown TA, Kopinsky J, Li JZ, Nadiradze G. Distributionally linearizable data structures. In: Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA ’18. ACM Press; 2018:133-142. doi:10.1145/3210377.3210411","ieee":"D.-A. Alistarh, T. A. Brown, J. Kopinsky, J. Z. Li, and G. Nadiradze, “Distributionally linearizable data structures,” in Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA ’18, Vienna, Austria, 2018, pp. 133–142.","apa":"Alistarh, D.-A., Brown, T. A., Kopinsky, J., Li, J. Z., & Nadiradze, G. (2018). Distributionally linearizable data structures. In Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA ’18 (pp. 133–142). Vienna, Austria: ACM Press. https://doi.org/10.1145/3210377.3210411","ista":"Alistarh D-A, Brown TA, Kopinsky J, Li JZ, Nadiradze G. 2018. Distributionally linearizable data structures. Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA ’18. SPAA: Symposium on Parallelism in Algorithms and Architectures, 133–142."},"date_published":"2018-07-16T00:00:00Z","scopus_import":"1","day":"16","article_processing_charge":"No","title":"Distributionally linearizable data structures","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5965","oa_version":"Preprint","type":"conference","abstract":[{"text":"Relaxed concurrent data structures have become increasingly popular, due to their scalability in graph processing and machine learning applications (\\citeNguyen13, gonzalez2012powergraph ). Despite considerable interest, there exist families of natural, high performing randomized relaxed concurrent data structures, such as the popular MultiQueue~\\citeMQ pattern for implementing relaxed priority queue data structures, for which no guarantees are known in the concurrent setting~\\citeAKLN17. Our main contribution is in showing for the first time that, under a set of analytic assumptions, a family of relaxed concurrent data structures, including variants of MultiQueues, but also a new approximate counting algorithm we call the MultiCounter, provides strong probabilistic guarantees on the degree of relaxation with respect to the sequential specification, in arbitrary concurrent executions. We formalize these guarantees via a new correctness condition called distributional linearizability, tailored to concurrent implementations with randomized relaxations. Our result is based on a new analysis of an asynchronous variant of the classic power-of-two-choices load balancing algorithm, in which placement choices can be based on inconsistent, outdated information (this result may be of independent interest). We validate our results empirically, showing that the MultiCounter algorithm can implement scalable relaxed timestamps.","lang":"eng"}]},{"publication":"Proceedings of the 2018 ACM Conference on Economics and Computation - EC '18","citation":{"chicago":"Hansen, Kristoffer Arnsfelt, Rasmus Ibsen-Jensen, and Abraham Neyman. “The Big Match with a Clock and a Bit of Memory.” In Proceedings of the 2018 ACM Conference on Economics and Computation - EC ’18, 149–50. ACM Press, 2018. https://doi.org/10.1145/3219166.3219198.","short":"K.A. Hansen, R. Ibsen-Jensen, A. Neyman, in:, Proceedings of the 2018 ACM Conference on Economics and Computation - EC ’18, ACM Press, 2018, pp. 149–150.","mla":"Hansen, Kristoffer Arnsfelt, et al. “The Big Match with a Clock and a Bit of Memory.” Proceedings of the 2018 ACM Conference on Economics and Computation - EC ’18, ACM Press, 2018, pp. 149–50, doi:10.1145/3219166.3219198.","ieee":"K. A. Hansen, R. Ibsen-Jensen, and A. Neyman, “The Big Match with a clock and a bit of memory,” in Proceedings of the 2018 ACM Conference on Economics and Computation - EC ’18, Ithaca, NY, United States, 2018, pp. 149–150.","apa":"Hansen, K. A., Ibsen-Jensen, R., & Neyman, A. (2018). The Big Match with a clock and a bit of memory. In Proceedings of the 2018 ACM Conference on Economics and Computation - EC ’18 (pp. 149–150). Ithaca, NY, United States: ACM Press. https://doi.org/10.1145/3219166.3219198","ista":"Hansen KA, Ibsen-Jensen R, Neyman A. 2018. The Big Match with a clock and a bit of memory. Proceedings of the 2018 ACM Conference on Economics and Computation - EC ’18. EC: Conference on Economics and Computation, 149–150.","ama":"Hansen KA, Ibsen-Jensen R, Neyman A. The Big Match with a clock and a bit of memory. In: Proceedings of the 2018 ACM Conference on Economics and Computation - EC ’18. ACM Press; 2018:149-150. doi:10.1145/3219166.3219198"},"page":"149-150","date_published":"2018-06-18T00:00:00Z","scopus_import":"1","day":"18","has_accepted_license":"1","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5967","ddc":["000"],"status":"public","title":"The Big Match with a clock and a bit of memory","file":[{"creator":"dernst","file_size":302539,"content_type":"application/pdf","file_name":"2018_EC18_Hansen.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:14Z","date_created":"2019-11-19T08:24:24Z","checksum":"bb52683e349cfd864f4769a8f38f2798","file_id":"7054","relation":"main_file"}],"oa_version":"Submitted Version","type":"conference","abstract":[{"lang":"eng","text":"The Big Match is a multi-stage two-player game. In each stage Player 1 hides one or two pebbles in his hand, and his opponent has to guess that number; Player 1 loses a point if Player 2 is correct, and otherwise he wins a point. As soon as Player 1 hides one pebble, the players cannot change their choices in any future stage.\r\nBlackwell and Ferguson (1968) give an ε-optimal strategy for Player 1 that hides, in each stage, one pebble with a probability that depends on the entire past history. Any strategy that depends just on the clock or on a finite memory is worthless. The long-standing natural open problem has been whether every strategy that depends just on the clock and a finite memory is worthless. We prove that there is such a strategy that is ε-optimal. In fact, we show that just two states of memory are sufficient.\r\n"}],"external_id":{"isi":["000492755100020"]},"oa":1,"quality_controlled":"1","isi":1,"conference":{"name":"EC: Conference on Economics and Computation","location":"Ithaca, NY, United States","start_date":"2018-06-18","end_date":"2018-06-22"},"doi":"10.1145/3219166.3219198","language":[{"iso":"eng"}],"month":"06","publication_identifier":{"isbn":["9781450358293"]},"year":"2018","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"ACM Press","author":[{"first_name":"Kristoffer Arnsfelt","last_name":"Hansen","full_name":"Hansen, Kristoffer Arnsfelt"},{"full_name":"Ibsen-Jensen, Rasmus","last_name":"Ibsen-Jensen","first_name":"Rasmus","orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Neyman, Abraham","last_name":"Neyman","first_name":"Abraham"}],"date_created":"2019-02-13T10:31:41Z","date_updated":"2023-09-19T10:45:15Z","file_date_updated":"2020-07-14T12:47:14Z"},{"publication_identifier":{"isbn":["9781450357999"]},"month":"07","isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1804.00947","open_access":"1"}],"external_id":{"isi":["000545269600046"],"arxiv":["1804.00947"]},"language":[{"iso":"eng"}],"doi":"10.1145/3210377.3210406","conference":{"name":"SPAA: Symposium on Parallelism in Algorithms and Architectures","end_date":"2018-07-18","start_date":"2018-07-16","location":"Vienna, Austria"},"department":[{"_id":"DaAl"}],"publisher":"ACM Press","publication_status":"published","year":"2018","date_created":"2019-02-13T10:26:07Z","date_updated":"2023-09-19T10:44:49Z","author":[{"first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"},{"full_name":"Haider, Syed Kamran","first_name":"Syed Kamran","last_name":"Haider"},{"full_name":"Kübler, Raphael","last_name":"Kübler","first_name":"Raphael"},{"full_name":"Nadiradze, Giorgi","last_name":"Nadiradze","first_name":"Giorgi"}],"scopus_import":"1","article_processing_charge":"No","day":"16","page":"383-392","citation":{"chicago":"Alistarh, Dan-Adrian, Syed Kamran Haider, Raphael Kübler, and Giorgi Nadiradze. “The Transactional Conflict Problem.” In Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA ’18, 383–92. ACM Press, 2018. https://doi.org/10.1145/3210377.3210406.","mla":"Alistarh, Dan-Adrian, et al. “The Transactional Conflict Problem.” Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA ’18, ACM Press, 2018, pp. 383–92, doi:10.1145/3210377.3210406.","short":"D.-A. Alistarh, S.K. Haider, R. Kübler, G. Nadiradze, in:, Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA ’18, ACM Press, 2018, pp. 383–392.","ista":"Alistarh D-A, Haider SK, Kübler R, Nadiradze G. 2018. The transactional conflict problem. Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA ’18. SPAA: Symposium on Parallelism in Algorithms and Architectures, 383–392.","apa":"Alistarh, D.-A., Haider, S. K., Kübler, R., & Nadiradze, G. (2018). The transactional conflict problem. In Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA ’18 (pp. 383–392). Vienna, Austria: ACM Press. https://doi.org/10.1145/3210377.3210406","ieee":"D.-A. Alistarh, S. K. Haider, R. Kübler, and G. Nadiradze, “The transactional conflict problem,” in Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA ’18, Vienna, Austria, 2018, pp. 383–392.","ama":"Alistarh D-A, Haider SK, Kübler R, Nadiradze G. The transactional conflict problem. In: Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA ’18. ACM Press; 2018:383-392. doi:10.1145/3210377.3210406"},"publication":"Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA '18","date_published":"2018-07-16T00:00:00Z","type":"conference","abstract":[{"lang":"eng","text":"The transactional conflict problem arises in transactional systems whenever two or more concurrent transactions clash on a data item. While the standard solution to such conflicts is to immediately abort one of the transactions, some practical systems consider the alternative of delaying conflict resolution for a short interval, which may allow one of the transactions to commit. The challenge in the transactional conflict problem is to choose the optimal length of this delay interval so as to minimize the overall running time penalty for the conflicting transactions. In this paper, we propose a family of optimal online algorithms for the transactional conflict problem. Specifically, we consider variants of this problem which arise in different implementations of transactional systems, namely \"requestor wins'' and \"requestor aborts'' implementations: in the former, the recipient of a coherence request is aborted, whereas in the latter, it is the requestor which has to abort. Both strategies are implemented by real systems. We show that the requestor aborts case can be reduced to a classic instance of the ski rental problem, while the requestor wins case leads to a new version of this classical problem, for which we derive optimal deterministic and randomized algorithms. Moreover, we prove that, under a simplified adversarial model, our algorithms are constant-competitive with the offline optimum in terms of throughput. We validate our algorithmic results empirically through a hardware simulation of hardware transactional memory (HTM), showing that our algorithms can lead to non-trivial performance improvements for classic concurrent data structures."}],"title":"The transactional conflict problem","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5966","oa_version":"Preprint"},{"scopus_import":"1","day":"08","article_processing_charge":"No","page":"2029-2056","publication":"SIAM Journal on Computing","citation":{"chicago":"Kolmogorov, Vladimir. “Commutativity in the Algorithmic Lovász Local Lemma.” SIAM Journal on Computing. Society for Industrial & Applied Mathematics (SIAM), 2018. https://doi.org/10.1137/16m1093306.","short":"V. Kolmogorov, SIAM Journal on Computing 47 (2018) 2029–2056.","mla":"Kolmogorov, Vladimir. “Commutativity in the Algorithmic Lovász Local Lemma.” SIAM Journal on Computing, vol. 47, no. 6, Society for Industrial & Applied Mathematics (SIAM), 2018, pp. 2029–56, doi:10.1137/16m1093306.","apa":"Kolmogorov, V. (2018). Commutativity in the algorithmic Lovász local lemma. SIAM Journal on Computing. Society for Industrial & Applied Mathematics (SIAM). https://doi.org/10.1137/16m1093306","ieee":"V. Kolmogorov, “Commutativity in the algorithmic Lovász local lemma,” SIAM Journal on Computing, vol. 47, no. 6. Society for Industrial & Applied Mathematics (SIAM), pp. 2029–2056, 2018.","ista":"Kolmogorov V. 2018. Commutativity in the algorithmic Lovász local lemma. SIAM Journal on Computing. 47(6), 2029–2056.","ama":"Kolmogorov V. Commutativity in the algorithmic Lovász local lemma. SIAM Journal on Computing. 2018;47(6):2029-2056. doi:10.1137/16m1093306"},"date_published":"2018-11-08T00:00:00Z","type":"journal_article","abstract":[{"text":"We consider the recent formulation of the algorithmic Lov ́asz Local Lemma [N. Har-vey and J. Vondr ́ak, inProceedings of FOCS, 2015, pp. 1327–1345; D. Achlioptas and F. Iliopoulos,inProceedings of SODA, 2016, pp. 2024–2038; D. Achlioptas, F. Iliopoulos, and V. Kolmogorov,ALocal Lemma for Focused Stochastic Algorithms, arXiv preprint, 2018] for finding objects that avoid“bad features,” or “flaws.” It extends the Moser–Tardos resampling algorithm [R. A. Moser andG. Tardos,J. ACM, 57 (2010), 11] to more general discrete spaces. At each step the method picks aflaw present in the current state and goes to a new state according to some prespecified probabilitydistribution (which depends on the current state and the selected flaw). However, the recent formu-lation is less flexible than the Moser–Tardos method since it requires a specific flaw selection rule,whereas the algorithm of Moser and Tardos allows an arbitrary rule (and thus can potentially beimplemented more efficiently). We formulate a new “commutativity” condition and prove that it issufficient for an arbitrary rule to work. It also enables an efficient parallelization under an additionalassumption. We then show that existing resampling oracles for perfect matchings and permutationsdo satisfy this condition.","lang":"eng"}],"issue":"6","status":"public","title":"Commutativity in the algorithmic Lovász local lemma","intvolume":" 47","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5975","oa_version":"Preprint","month":"11","publication_identifier":{"issn":["0097-5397"],"eissn":["1095-7111"]},"quality_controlled":"1","isi":1,"project":[{"grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"external_id":{"arxiv":["1506.08547"],"isi":["000453785100001"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1506.08547","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1137/16m1093306","ec_funded":1,"publication_status":"published","publisher":"Society for Industrial & Applied Mathematics (SIAM)","department":[{"_id":"VlKo"}],"year":"2018","date_created":"2019-02-13T12:59:33Z","date_updated":"2023-09-19T14:24:58Z","volume":47,"author":[{"first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir"}],"related_material":{"record":[{"id":"1193","status":"public","relation":"earlier_version"}]}}]