[{"article_processing_charge":"No","file":[{"file_name":"FileS1.zip","checksum":"aed7ee9ca3f4dc07d8a66945f68e13cd","file_id":"5758","content_type":"application/zip","date_created":"2018-12-19T14:19:52Z","creator":"cfraisse","access_level":"open_access","date_updated":"2020-07-14T12:47:11Z","relation":"main_file","file_size":369837892},{"relation":"main_file","date_updated":"2020-07-14T12:47:11Z","file_size":84856909,"content_type":"application/zip","file_id":"5759","checksum":"3592e467b4d8206650860b612d6e12f3","creator":"cfraisse","date_created":"2018-12-19T14:19:49Z","access_level":"open_access","file_name":"FileS2.zip"},{"file_name":"FileS3.txt","file_size":881133,"date_updated":"2020-07-14T12:47:11Z","relation":"main_file","checksum":"c37ac5d5437c457338afc128c1240655","content_type":"text/plain","file_id":"5760","date_created":"2018-12-19T14:19:49Z","creator":"cfraisse","access_level":"open_access"},{"file_name":"FileS4.txt","date_created":"2018-12-19T14:19:49Z","access_level":"open_access","creator":"cfraisse","checksum":"943dfd14da61817441e33e3e3cb8cdb9","content_type":"text/plain","file_id":"5761","file_size":883742,"date_updated":"2020-07-14T12:47:11Z","relation":"main_file"},{"access_level":"open_access","creator":"cfraisse","date_created":"2018-12-19T14:19:49Z","checksum":"1c669b6c4690ec1bbca3e2da9f566d17","content_type":"text/plain","file_id":"5762","file_size":2495437,"relation":"main_file","date_updated":"2020-07-14T12:47:11Z","file_name":"FileS5.txt"},{"file_size":15913457,"relation":"main_file","date_updated":"2020-07-14T12:47:11Z","access_level":"open_access","creator":"cfraisse","date_created":"2018-12-19T14:19:50Z","content_type":"text/plain","checksum":"f40f661b987ca6fb6b47f650cbbb04e6","file_id":"5763","file_name":"FileS6.txt"},{"date_created":"2018-12-19T14:19:50Z","access_level":"open_access","creator":"cfraisse","file_id":"5764","checksum":"25f41e5b8a075669c6c88d4c6713bf6f","content_type":"text/plain","file_size":2584120,"relation":"main_file","date_updated":"2020-07-14T12:47:11Z","file_name":"FileS7.txt"},{"content_type":"text/plain","file_id":"5765","checksum":"f6c0bd3e63e14ddf5445bd69b43a9152","access_level":"open_access","creator":"cfraisse","date_created":"2018-12-19T14:19:50Z","relation":"main_file","date_updated":"2020-07-14T12:47:11Z","file_size":2446059,"file_name":"FileS8.txt"},{"file_name":"FileS9.txt","relation":"main_file","date_updated":"2020-07-14T12:47:11Z","file_size":100737,"checksum":"0fe7a58a030b11bf3b9c8ff7a7addcae","content_type":"text/plain","file_id":"5766","access_level":"open_access","date_created":"2018-12-19T14:19:50Z","creator":"cfraisse"}],"day":"19","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"}],"ec_funded":1,"date_published":"2018-12-19T00:00:00Z","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"contributor":[{"last_name":"Fraisse","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gemma","last_name":"Puixeu Sala","id":"33AB266C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.15479/at:ista:/5757","ddc":["576"],"date_created":"2018-12-19T14:22:35Z","citation":{"ista":"Fraisse C. 2018. Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster’, Institute of Science and Technology Austria, 10.15479/at:ista:/5757.","apa":"Fraisse, C. (2018). Supplementary Files for “Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.” Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:/5757","short":"C. Fraisse, (2018).","ama":"Fraisse C. Supplementary Files for “Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.” 2018. doi:10.15479/at:ista:/5757","mla":"Fraisse, Christelle. Supplementary Files for “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” Institute of Science and Technology Austria, 2018, doi:10.15479/at:ista:/5757.","chicago":"Fraisse, Christelle. “Supplementary Files for ‘Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.’” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/at:ista:/5757.","ieee":"C. Fraisse, “Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.’” Institute of Science and Technology Austria, 2018."},"_id":"5757","author":[{"last_name":"Fraisse","first_name":"Christelle","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","oa_version":"Published Version","oa":1,"related_material":{"record":[{"id":"6089","status":"public","relation":"research_paper"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Supplementary Files for \"Pleiotropy modulates the efficacy of selection in Drosophila melanogaster\"","file_date_updated":"2020-07-14T12:47:11Z","type":"research_data","keyword":["(mal)adaptation","pleiotropy","selective constraint","evo-devo","gene expression","Drosophila melanogaster"],"year":"2018","publisher":"Institute of Science and Technology Austria","month":"12","abstract":[{"text":"File S1. Variant Calling Format file of the ingroup: 197 haploid sequences of D. melanogaster from Zambia (Africa) aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S2. Variant Calling Format file of the outgroup: 1 haploid sequence of D. simulans aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S3. Annotations of each transcript in coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pn (# of non-synonymous polymorphic sites); Ds (# of synonymous divergent sites); Dn (# of non-synonymous divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S4. Annotations of each transcript in non-coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pu (# of UTR polymorphic sites); Ds (# of synonymous divergent sites); Du (# of UTR divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S5. Annotations of each transcript in coding regions with SNPGenie: Ps (# of synonymous polymorphic sites); πs (synonymous diversity); Ss_p (total # of synonymous sites in the polymorphism data); Pn (# of non-synonymous polymorphic sites); πn (non-synonymous diversity); Sn_p (total # of non-synonymous sites in the polymorphism data); Ds (# of synonymous divergent sites); ks (synonymous evolutionary rate); Ss_d (total # of synonymous sites in the divergence data); Dn (# of non-synonymous divergent sites); kn (non-synonymous evolutionary rate); Sn_d (total # of non-\r\nsynonymous sites in the divergence data); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S6. Gene expression values (RPKM summed over all transcripts) for each sample. Values were quantile-normalized across all samples.\r\n\r\nFile S7. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for coding sites, excluding variants below 5% frequency.\r\n\r\nFile S8. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for non-coding sites, excluding variants below 5%\r\nfrequency.\r\n\r\nFile S9. Final dataset with all covariates, ⍺ EWK , ωA EWK and deleterious SFS for coding sites obtained with the Eyre-Walker and Keightley method on binned data and using all variants.","lang":"eng"}],"date_updated":"2025-04-15T08:18:38Z"},{"citation":{"ama":"Gotlieb K, Lin C-Y, Serbyn M, et al. Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor. Science. 2018;362(6420):1271-1275. doi:10.1126/science.aao0980","short":"K. Gotlieb, C.-Y. Lin, M. Serbyn, W. Zhang, C.L. Smallwood, C. Jozwiak, H. Eisaki, Z. Hussain, A. Vishwanath, A. Lanzara, Science 362 (2018) 1271–1275.","ista":"Gotlieb K, Lin C-Y, Serbyn M, Zhang W, Smallwood CL, Jozwiak C, Eisaki H, Hussain Z, Vishwanath A, Lanzara A. 2018. Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor. Science. 362(6420), 1271–1275.","apa":"Gotlieb, K., Lin, C.-Y., Serbyn, M., Zhang, W., Smallwood, C. L., Jozwiak, C., … Lanzara, A. (2018). Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aao0980","chicago":"Gotlieb, Kenneth, Chiu-Yun Lin, Maksym Serbyn, Wentao Zhang, Christopher L. Smallwood, Christopher Jozwiak, Hiroshi Eisaki, Zahid Hussain, Ashvin Vishwanath, and Alessandra Lanzara. “Revealing Hidden Spin-Momentum Locking in a High-Temperature Cuprate Superconductor.” Science. American Association for the Advancement of Science, 2018. https://doi.org/10.1126/science.aao0980.","mla":"Gotlieb, Kenneth, et al. “Revealing Hidden Spin-Momentum Locking in a High-Temperature Cuprate Superconductor.” Science, vol. 362, no. 6420, American Association for the Advancement of Science, 2018, pp. 1271–75, doi:10.1126/science.aao0980.","ieee":"K. Gotlieb et al., “Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor,” Science, vol. 362, no. 6420. American Association for the Advancement of Science, pp. 1271–1275, 2018."},"volume":362,"date_created":"2018-12-19T14:53:50Z","main_file_link":[{"url":"https://doi.org/10.1126/science.aao0980","open_access":"1"}],"scopus_import":"1","day":"14","publisher":"American Association for the Advancement of Science","publication_status":"published","year":"2018","page":"1271-1275","title":"Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor","type":"journal_article","issue":"6420","isi":1,"_id":"5767","author":[{"full_name":"Gotlieb, Kenneth","first_name":"Kenneth","last_name":"Gotlieb"},{"last_name":"Lin","first_name":"Chiu-Yun","full_name":"Lin, Chiu-Yun"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn","first_name":"Maksym"},{"full_name":"Zhang, Wentao","last_name":"Zhang","first_name":"Wentao"},{"first_name":"Christopher L.","last_name":"Smallwood","full_name":"Smallwood, Christopher L."},{"first_name":"Christopher","last_name":"Jozwiak","full_name":"Jozwiak, Christopher"},{"first_name":"Hiroshi","last_name":"Eisaki","full_name":"Eisaki, Hiroshi"},{"full_name":"Hussain, Zahid","last_name":"Hussain","first_name":"Zahid"},{"first_name":"Ashvin","last_name":"Vishwanath","full_name":"Vishwanath, Ashvin"},{"last_name":"Lanzara","first_name":"Alessandra","full_name":"Lanzara, Alessandra"}],"publication":"Science","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"ddc":["530"],"language":[{"iso":"eng"}],"acknowledgement":" M.S. was supported by the Gordon and Betty Moore Foundation s EPiQS Initiative through grant GBMF4307","date_published":"2018-12-14T00:00:00Z","department":[{"_id":"MaSe"}],"doi":"10.1126/science.aao0980","article_processing_charge":"No","month":"12","abstract":[{"text":"Cuprate superconductors have long been thought of as having strong electronic correlations but negligible spin-orbit coupling. Using spin- and angle-resolved photoemission spectroscopy, we discovered that one of the most studied cuprate superconductors, Bi2212, has a nontrivial spin texture with a spin-momentum locking that circles the Brillouin zone center and a spin-layer locking that allows states of opposite spin to be localized in different parts of the unit cell. Our findings pose challenges for the vast majority of models of cuprates, such as the Hubbard model and its variants, where spin-orbit interaction has been mostly neglected, and open the intriguing question of how the high-temperature superconducting state emerges in the presence of this nontrivial spin texture. ","lang":"eng"}],"date_updated":"2026-06-18T18:55:21Z","external_id":{"isi":["000452994400048"]},"intvolume":" 362","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","article_type":"original","oa_version":"Published Version","quality_controlled":"1"},{"pmid":1,"intvolume":" 115","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","oa_version":"Submitted Version","quality_controlled":"1","month":"12","abstract":[{"text":"Retroviruses assemble and bud from infected cells in an immature form and require proteolytic maturation for infectivity. The CA (capsid) domains of the Gag polyproteins assemble a protein lattice as a truncated sphere in the immature virion. Proteolytic cleavage of Gag induces dramatic structural rearrangements; a subset of cleaved CA subsequently assembles into the mature core, whose architecture varies among retroviruses. Murine leukemia virus (MLV) is the prototypical γ-retrovirus and serves as the basis of retroviral vectors, but the structure of the MLV CA layer is unknown. Here we have combined X-ray crystallography with cryoelectron tomography to determine the structures of immature and mature MLV CA layers within authentic viral particles. This reveals the structural changes associated with maturation, and, by comparison with HIV-1, uncovers conserved and variable features. In contrast to HIV-1, most MLV CA is used for assembly of the mature core, which adopts variable, multilayered morphologies and does not form a closed structure. Unlike in HIV-1, there is similarity between protein–protein interfaces in the immature MLV CA layer and those in the mature CA layer, and structural maturation of MLV could be achieved through domain rotations that largely maintain hexameric interactions. Nevertheless, the dramatic architectural change on maturation indicates that extensive disassembly and reassembly are required for mature core growth. The core morphology suggests that wrapping of the genome in CA sheets may be sufficient to protect the MLV ribonucleoprotein during cell entry.","lang":"eng"}],"date_updated":"2025-06-03T11:56:09Z","external_id":{"isi":["000452866000022"],"pmid":["30478053"]},"language":[{"iso":"eng"}],"department":[{"_id":"FlSc"}],"date_published":"2018-12-11T00:00:00Z","doi":"10.1073/pnas.1811580115","article_processing_charge":"No","isi":1,"_id":"5770","author":[{"first_name":"Kun","last_name":"Qu","full_name":"Qu, Kun"},{"full_name":"Glass, Bärbel","first_name":"Bärbel","last_name":"Glass"},{"full_name":"Doležal, Michal","last_name":"Doležal","first_name":"Michal"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","last_name":"Schur","full_name":"Schur, Florian","orcid":"0000-0003-4790-8078"},{"last_name":"Murciano","first_name":"Brice","full_name":"Murciano, Brice"},{"last_name":"Rein","first_name":"Alan","full_name":"Rein, Alan"},{"last_name":"Rumlová","first_name":"Michaela","full_name":"Rumlová, Michaela"},{"last_name":"Ruml","first_name":"Tomáš","full_name":"Ruml, Tomáš"},{"first_name":"Hans-Georg","last_name":"Kräusslich","full_name":"Kräusslich, Hans-Georg"},{"last_name":"Briggs","first_name":"John A. G.","full_name":"Briggs, John A. G."}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","publication_identifier":{"issn":["0027-8424"]},"title":"Structure and architecture of immature and mature murine leukemia virus capsids","type":"journal_article","issue":"50","publisher":"National Academy of Sciences","publication_status":"published","year":"2018","page":"E11751-E11760","scopus_import":"1","day":"11","citation":{"ieee":"K. Qu et al., “Structure and architecture of immature and mature murine leukemia virus capsids,” Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 50. National Academy of Sciences, pp. E11751–E11760, 2018.","ama":"Qu K, Glass B, Doležal M, et al. Structure and architecture of immature and mature murine leukemia virus capsids. Proceedings of the National Academy of Sciences of the United States of America. 2018;115(50):E11751-E11760. doi:10.1073/pnas.1811580115","short":"K. Qu, B. Glass, M. Doležal, F.K. Schur, B. Murciano, A. Rein, M. Rumlová, T. Ruml, H.-G. Kräusslich, J.A.G. Briggs, Proceedings of the National Academy of Sciences of the United States of America 115 (2018) E11751–E11760.","ista":"Qu K, Glass B, Doležal M, Schur FK, Murciano B, Rein A, Rumlová M, Ruml T, Kräusslich H-G, Briggs JAG. 2018. Structure and architecture of immature and mature murine leukemia virus capsids. Proceedings of the National Academy of Sciences of the United States of America. 115(50), E11751–E11760.","apa":"Qu, K., Glass, B., Doležal, M., Schur, F. K., Murciano, B., Rein, A., … Briggs, J. A. G. (2018). Structure and architecture of immature and mature murine leukemia virus capsids. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1811580115","chicago":"Qu, Kun, Bärbel Glass, Michal Doležal, Florian KM Schur, Brice Murciano, Alan Rein, Michaela Rumlová, Tomáš Ruml, Hans-Georg Kräusslich, and John A. G. Briggs. “Structure and Architecture of Immature and Mature Murine Leukemia Virus Capsids.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1811580115.","mla":"Qu, Kun, et al. “Structure and Architecture of Immature and Mature Murine Leukemia Virus Capsids.” Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 50, National Academy of Sciences, 2018, pp. E11751–60, doi:10.1073/pnas.1811580115."},"volume":115,"date_created":"2018-12-20T21:09:37Z","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30478053","open_access":"1"}]},{"publication_status":"published","publisher":"National Academy of Sciences","year":"2018","page":"12728-12732","title":"Genetically encodable bioluminescent system from fungi","file_date_updated":"2020-07-14T12:47:11Z","type":"journal_article","issue":"50","citation":{"mla":"Kotlobay, Alexey A., et al. “Genetically Encodable Bioluminescent System from Fungi.” Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 50, National Academy of Sciences, 2018, pp. 12728–32, doi:10.1073/pnas.1803615115.","chicago":"Kotlobay, Alexey A., Karen Sarkisyan, Yuliana A. Mokrushina, Marina Marcet-Houben, Ekaterina O. Serebrovskaya, Nadezhda M. Markina, Louisa Gonzalez Somermeyer, et al. “Genetically Encodable Bioluminescent System from Fungi.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1803615115.","ista":"Kotlobay AA, Sarkisyan K, Mokrushina YA, Marcet-Houben M, Serebrovskaya EO, Markina NM, Gonzalez Somermeyer L, Gorokhovatsky AY, Vvedensky A, Purtov KV, Petushkov VN, Rodionova NS, Chepurnyh TV, Fakhranurova L, Guglya EB, Ziganshin R, Tsarkova AS, Kaskova ZM, Shender V, Abakumov M, Abakumova TO, Povolotskaya IS, Eroshkin FM, Zaraisky AG, Mishin AS, Dolgov SV, Mitiouchkina TY, Kopantzev EP, Waldenmaier HE, Oliveira AG, Oba Y, Barsova E, Bogdanova EA, Gabaldón T, Stevani CV, Lukyanov S, Smirnov IV, Gitelson JI, Kondrashov F, Yampolsky IV. 2018. Genetically encodable bioluminescent system from fungi. Proceedings of the National Academy of Sciences of the United States of America. 115(50), 12728–12732.","apa":"Kotlobay, A. A., Sarkisyan, K., Mokrushina, Y. A., Marcet-Houben, M., Serebrovskaya, E. O., Markina, N. M., … Yampolsky, I. V. (2018). Genetically encodable bioluminescent system from fungi. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1803615115","short":"A.A. Kotlobay, K. Sarkisyan, Y.A. Mokrushina, M. Marcet-Houben, E.O. Serebrovskaya, N.M. Markina, L. Gonzalez Somermeyer, A.Y. Gorokhovatsky, A. Vvedensky, K.V. Purtov, V.N. Petushkov, N.S. Rodionova, T.V. Chepurnyh, L. Fakhranurova, E.B. Guglya, R. Ziganshin, A.S. Tsarkova, Z.M. Kaskova, V. Shender, M. Abakumov, T.O. Abakumova, I.S. Povolotskaya, F.M. Eroshkin, A.G. Zaraisky, A.S. Mishin, S.V. Dolgov, T.Y. Mitiouchkina, E.P. Kopantzev, H.E. Waldenmaier, A.G. Oliveira, Y. Oba, E. Barsova, E.A. Bogdanova, T. Gabaldón, C.V. Stevani, S. Lukyanov, I.V. Smirnov, J.I. Gitelson, F. Kondrashov, I.V. Yampolsky, Proceedings of the National Academy of Sciences of the United States of America 115 (2018) 12728–12732.","ama":"Kotlobay AA, Sarkisyan K, Mokrushina YA, et al. Genetically encodable bioluminescent system from fungi. Proceedings of the National Academy of Sciences of the United States of America. 2018;115(50):12728-12732. doi:10.1073/pnas.1803615115","ieee":"A. A. Kotlobay et al., “Genetically encodable bioluminescent system from fungi,” Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 50. National Academy of Sciences, pp. 12728–12732, 2018."},"volume":115,"date_created":"2018-12-23T22:59:18Z","scopus_import":"1","day":"11","abstract":[{"lang":"eng","text":"Bioluminescence is found across the entire tree of life, conferring a spectacular set of visually oriented functions from attracting mates to scaring off predators. Half a dozen different luciferins, molecules that emit light when enzymatically oxidized, are known. However, just one biochemical pathway for luciferin biosynthesis has been described in full, which is found only in bacteria. Here, we report identification of the fungal luciferase and three other key enzymes that together form the biosynthetic cycle of the fungal luciferin from caffeic acid, a simple and widespread metabolite. Introduction of the identified genes into the genome of the yeast Pichia pastoris along with caffeic acid biosynthesis genes resulted in a strain that is autoluminescent in standard media. We analyzed evolution of the enzymes of the luciferin biosynthesis cycle and found that fungal bioluminescence emerged through a series of events that included two independent gene duplications. The retention of the duplicated enzymes of the luciferin pathway in nonluminescent fungi shows that the gene duplication was followed by functional sequence divergence of enzymes of at least one gene in the biosynthetic pathway and suggests that the evolution of fungal bioluminescence proceeded through several closely related stepping stone nonluminescent biochemical reactions with adaptive roles. The availability of a complete eukaryotic luciferin biosynthesis pathway provides several applications in biomedicine and bioengineering."}],"date_updated":"2025-07-10T11:52:58Z","month":"12","external_id":{"isi":["000452866000068"]},"status":"public","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"intvolume":" 115","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"oa_version":"Published Version","quality_controlled":"1","author":[{"full_name":"Kotlobay, Alexey A.","last_name":"Kotlobay","first_name":"Alexey A."},{"last_name":"Sarkisyan","first_name":"Karen","orcid":"0000-0002-5375-6341","full_name":"Sarkisyan, Karen","id":"39A7BF80-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mokrushina, Yuliana A.","first_name":"Yuliana A.","last_name":"Mokrushina"},{"full_name":"Marcet-Houben, Marina","first_name":"Marina","last_name":"Marcet-Houben"},{"full_name":"Serebrovskaya, Ekaterina O.","first_name":"Ekaterina O.","last_name":"Serebrovskaya"},{"first_name":"Nadezhda M.","last_name":"Markina","full_name":"Markina, Nadezhda M."},{"id":"4720D23C-F248-11E8-B48F-1D18A9856A87","last_name":"Gonzalez Somermeyer","first_name":"Louisa","orcid":"0000-0001-9139-5383","full_name":"Gonzalez Somermeyer, Louisa"},{"full_name":"Gorokhovatsky, Andrey Y.","first_name":"Andrey Y.","last_name":"Gorokhovatsky"},{"last_name":"Vvedensky","first_name":"Andrey","full_name":"Vvedensky, Andrey"},{"full_name":"Purtov, Konstantin V.","first_name":"Konstantin V.","last_name":"Purtov"},{"full_name":"Petushkov, Valentin N.","last_name":"Petushkov","first_name":"Valentin N."},{"full_name":"Rodionova, Natalja S.","last_name":"Rodionova","first_name":"Natalja S."},{"full_name":"Chepurnyh, Tatiana V.","first_name":"Tatiana V.","last_name":"Chepurnyh"},{"last_name":"Fakhranurova","first_name":"Liliia","full_name":"Fakhranurova, Liliia"},{"full_name":"Guglya, Elena B.","last_name":"Guglya","first_name":"Elena B."},{"full_name":"Ziganshin, Rustam","first_name":"Rustam","last_name":"Ziganshin"},{"first_name":"Aleksandra S.","last_name":"Tsarkova","full_name":"Tsarkova, Aleksandra S."},{"last_name":"Kaskova","first_name":"Zinaida M.","full_name":"Kaskova, Zinaida M."},{"last_name":"Shender","first_name":"Victoria","full_name":"Shender, Victoria"},{"first_name":"Maxim","last_name":"Abakumov","full_name":"Abakumov, Maxim"},{"full_name":"Abakumova, Tatiana O.","last_name":"Abakumova","first_name":"Tatiana O."},{"full_name":"Povolotskaya, Inna S.","last_name":"Povolotskaya","first_name":"Inna S."},{"full_name":"Eroshkin, Fedor M.","first_name":"Fedor M.","last_name":"Eroshkin"},{"last_name":"Zaraisky","first_name":"Andrey G.","full_name":"Zaraisky, Andrey G."},{"full_name":"Mishin, Alexander S.","first_name":"Alexander S.","last_name":"Mishin"},{"full_name":"Dolgov, Sergey V.","first_name":"Sergey V.","last_name":"Dolgov"},{"full_name":"Mitiouchkina, Tatiana Y.","last_name":"Mitiouchkina","first_name":"Tatiana Y."},{"full_name":"Kopantzev, Eugene P.","first_name":"Eugene P.","last_name":"Kopantzev"},{"full_name":"Waldenmaier, Hans E.","last_name":"Waldenmaier","first_name":"Hans E."},{"last_name":"Oliveira","first_name":"Anderson G.","full_name":"Oliveira, Anderson G."},{"full_name":"Oba, Yuichi","last_name":"Oba","first_name":"Yuichi"},{"full_name":"Barsova, Ekaterina","first_name":"Ekaterina","last_name":"Barsova"},{"full_name":"Bogdanova, Ekaterina A.","first_name":"Ekaterina A.","last_name":"Bogdanova"},{"last_name":"Gabaldón","first_name":"Toni","full_name":"Gabaldón, Toni"},{"first_name":"Cassius V.","last_name":"Stevani","full_name":"Stevani, Cassius V."},{"last_name":"Lukyanov","first_name":"Sergey","full_name":"Lukyanov, Sergey"},{"first_name":"Ivan V.","last_name":"Smirnov","full_name":"Smirnov, Ivan V."},{"last_name":"Gitelson","first_name":"Josef I.","full_name":"Gitelson, Josef I."},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","first_name":"Fyodor","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor"},{"full_name":"Yampolsky, Ilia V.","last_name":"Yampolsky","first_name":"Ilia V."}],"has_accepted_license":"1","isi":1,"_id":"5780","ddc":["580"],"publication":"Proceedings of the National Academy of Sciences of the United States of America","publication_identifier":{"issn":["0027-8424"]},"department":[{"_id":"FyKo"}],"date_published":"2018-12-11T00:00:00Z","doi":"10.1073/pnas.1803615115","language":[{"iso":"eng"}],"article_processing_charge":"No","file":[{"file_name":"2018_PNAS_Kotlobay.pdf","file_size":1271988,"relation":"main_file","date_updated":"2020-07-14T12:47:11Z","file_id":"5926","content_type":"application/pdf","checksum":"46b2c12185eb2ddb598f4c7b4bd267bf","creator":"dernst","date_created":"2019-02-05T15:21:40Z","access_level":"open_access"}]},{"abstract":[{"lang":"eng","text":"Branching morphogenesis remains a subject of abiding interest. Although much is \r\nknown about the gene regulatory programs and signaling pathways that operate at \r\nthe cellular scale, it has remained unclear how the macroscopic features of branched \r\norgans, including their size, network topology and spatial patterning, are encoded. \r\nLately, it has been proposed that, these features can be explained quantitatively in \r\nseveral organs within a single unifying framework. Based on large-\r\nscale organ recon\r\n-\r\nstructions and cell lineage tracing, it has been argued that morphogenesis follows \r\nfrom the collective dynamics of sublineage- \r\nrestricted self- \r\nrenewing progenitor cells, \r\nlocalized at ductal tips, that act cooperatively to drive a serial process of ductal elon\r\n-\r\ngation and stochastic tip bifurcation. By correlating differentiation or cell cycle exit \r\nwith proximity to maturing ducts, this dynamic results in the specification of a com-\r\nplex network of defined density and statistical organization. These results suggest \r\nthat, for several mammalian tissues, branched epithelial structures develop as a self- \r\norganized process, reliant upon a strikingly simple, but generic, set of local rules, \r\nwithout recourse to a rigid and deterministic sequence of genetically programmed \r\nevents. Here, we review the basis of these findings and discuss their implications."}],"date_updated":"2025-07-10T11:52:59Z","month":"12","external_id":{"isi":["000453555100002"]},"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":" 60","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"oa_version":"Published Version","quality_controlled":"1","author":[{"orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Simons","first_name":"Benjamin D.","full_name":"Simons, Benjamin D."}],"has_accepted_license":"1","isi":1,"_id":"5787","publication_identifier":{"issn":["0012-1592"]},"ddc":["570"],"publication":"Development Growth and Differentiation","date_published":"2018-12-09T00:00:00Z","department":[{"_id":"EdHa"}],"doi":"10.1111/dgd.12570","language":[{"iso":"eng"}],"article_processing_charge":"No","file":[{"access_level":"open_access","creator":"dernst","date_created":"2019-02-06T10:40:46Z","file_id":"5933","checksum":"a6d30b0785db902c734a84fecb2eadd9","content_type":"application/pdf","relation":"main_file","date_updated":"2020-07-14T12:47:11Z","file_size":1313606,"file_name":"2018_DevGrowh_Hannezo.pdf"}],"publisher":"Wiley","page":"512-521","year":"2018","file_date_updated":"2020-07-14T12:47:11Z","title":"Statistical theory of branching morphogenesis","type":"journal_article","issue":"9","citation":{"ista":"Hannezo EB, Simons BD. 2018. Statistical theory of branching morphogenesis. Development Growth and Differentiation. 60(9), 512–521.","apa":"Hannezo, E. B., & Simons, B. D. (2018). Statistical theory of branching morphogenesis. Development Growth and Differentiation. Wiley. https://doi.org/10.1111/dgd.12570","ama":"Hannezo EB, Simons BD. Statistical theory of branching morphogenesis. Development Growth and Differentiation. 2018;60(9):512-521. doi:10.1111/dgd.12570","short":"E.B. Hannezo, B.D. Simons, Development Growth and Differentiation 60 (2018) 512–521.","mla":"Hannezo, Edouard B., and Benjamin D. Simons. “Statistical Theory of Branching Morphogenesis.” Development Growth and Differentiation, vol. 60, no. 9, Wiley, 2018, pp. 512–21, doi:10.1111/dgd.12570.","chicago":"Hannezo, Edouard B, and Benjamin D. Simons. “Statistical Theory of Branching Morphogenesis.” Development Growth and Differentiation. Wiley, 2018. https://doi.org/10.1111/dgd.12570.","ieee":"E. B. Hannezo and B. D. Simons, “Statistical theory of branching morphogenesis,” Development Growth and Differentiation, vol. 60, no. 9. Wiley, pp. 512–521, 2018."},"volume":60,"date_created":"2018-12-30T22:59:14Z","scopus_import":"1","day":"09"},{"citation":{"ieee":"G. Avni, T. A. Henzinger, and R. Ibsen-Jensen, “Infinite-duration poorman-bidding games,” presented at the 14th International Conference on Web and Internet Economics, WINE, Oxford, UK, 2018, vol. 11316, pp. 21–36.","chicago":"Avni, Guy, Thomas A Henzinger, and Rasmus Ibsen-Jensen. “Infinite-Duration Poorman-Bidding Games,” 11316:21–36. Springer, 2018. https://doi.org/10.1007/978-3-030-04612-5_2.","mla":"Avni, Guy, et al. Infinite-Duration Poorman-Bidding Games. Vol. 11316, Springer, 2018, pp. 21–36, doi:10.1007/978-3-030-04612-5_2.","ama":"Avni G, Henzinger TA, Ibsen-Jensen R. Infinite-duration poorman-bidding games. In: Vol 11316. Springer; 2018:21-36. doi:10.1007/978-3-030-04612-5_2","short":"G. Avni, T.A. Henzinger, R. Ibsen-Jensen, in:, Springer, 2018, pp. 21–36.","apa":"Avni, G., Henzinger, T. A., & Ibsen-Jensen, R. (2018). Infinite-duration poorman-bidding games (Vol. 11316, pp. 21–36). Presented at the 14th International Conference on Web and Internet Economics, WINE, Oxford, UK: Springer. https://doi.org/10.1007/978-3-030-04612-5_2","ista":"Avni G, Henzinger TA, Ibsen-Jensen R. 2018. Infinite-duration poorman-bidding games. 14th International Conference on Web and Internet Economics, WINE, LNCS, vol. 11316, 21–36."},"volume":11316,"date_created":"2018-12-30T22:59:14Z","main_file_link":[{"url":"https://arxiv.org/abs/1804.04372","open_access":"1"}],"scopus_import":"1","day":"21","conference":{"start_date":"2018-12-15","location":"Oxford, UK","name":"14th International Conference on Web and Internet Economics, WINE","end_date":"2018-12-17"},"publisher":"Springer","page":"21-36","year":"2018","title":"Infinite-duration poorman-bidding games","type":"conference","alternative_title":["LNCS"],"isi":1,"_id":"5788","author":[{"orcid":"0000-0001-5588-8287","full_name":"Avni, Guy","last_name":"Avni","first_name":"Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A"},{"last_name":"Ibsen-Jensen","first_name":"Rasmus","orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"isbn":["9783030046118"],"issn":["0302-9743"]},"language":[{"iso":"eng"}],"date_published":"2018-11-21T00:00:00Z","department":[{"_id":"ToHe"}],"doi":"10.1007/978-3-030-04612-5_2","article_processing_charge":"No","project":[{"call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"},{"grant_number":"M02369","call_identifier":"FWF","_id":"264B3912-B435-11E9-9278-68D0E5697425","name":"Formal Methods meets Algorithmic Game Theory"}],"month":"11","date_updated":"2026-04-16T09:54:39Z","abstract":[{"lang":"eng","text":"In two-player games on graphs, the players move a token through a graph to produce an infinite path, which determines the winner or payoff of the game. Such games are central in formal verification since they model the interaction between a non-terminating system and its environment. We study bidding games in which the players bid for the right to move the token. Two bidding rules have been defined. In Richman bidding, in each round, the players simultaneously submit bids, and the higher bidder moves the token and pays the other player. Poorman bidding is similar except that the winner of the bidding pays the “bank” rather than the other player. While poorman reachability games have been studied before, we present, for the first time, results on infinite-duration poorman games. A central quantity in these games is the ratio between the two players’ initial budgets. The questions we study concern a necessary and sufficient ratio with which a player can achieve a goal. For reachability objectives, such threshold ratios are known to exist for both bidding rules. We show that the properties of poorman reachability games extend to complex qualitative objectives such as parity, similarly to the Richman case. Our most interesting results concern quantitative poorman games, namely poorman mean-payoff games, where we construct optimal strategies depending on the initial ratio, by showing a connection with random-turn based games. The connection in itself is interesting, because it does not hold for reachability poorman games. We also solve the complexity problems that arise in poorman bidding games."}],"external_id":{"arxiv":["1804.04372"],"isi":["000865933000002"]},"intvolume":" 11316","oa":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","status":"public","arxiv":1,"oa_version":"Preprint","quality_controlled":"1"},{"month":"12","date_updated":"2025-07-10T11:53:00Z","abstract":[{"lang":"eng","text":"Due to data compression or low resolution, nearby vertices and edges of a graph drawing may be bundled to a common node or arc. We model such a “compromised” drawing by a piecewise linear map φ:G → ℝ. We wish to perturb φ by an arbitrarily small ε>0 into a proper drawing (in which the vertices are distinct points, any two edges intersect in finitely many points, and no three edges have a common interior point) that minimizes the number of crossings. An ε-perturbation, for every ε>0, is given by a piecewise linear map (Formula Presented), where with ||·|| is the uniform norm (i.e., sup norm). We present a polynomial-time solution for this optimization problem when G is a cycle and the map φ has no spurs (i.e., no two adjacent edges are mapped to overlapping arcs). We also show that the problem becomes NP-complete (i) when G is an arbitrary graph and φ has no spurs, and (ii) when φ may have spurs and G is a cycle or a union of disjoint paths."}],"external_id":{"isi":["000672802500016"],"arxiv":["1808.07608"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"status":"public","arxiv":1,"oa_version":"Preprint","quality_controlled":"1","alternative_title":["LNCS"],"isi":1,"_id":"5791","author":[{"full_name":"Fulek, Radoslav","orcid":"0000-0001-8485-1774","first_name":"Radoslav","last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tóth, Csaba D.","first_name":"Csaba D.","last_name":"Tóth"}],"publication_identifier":{"isbn":["9783030044138"]},"language":[{"iso":"eng"}],"date_published":"2018-12-18T00:00:00Z","department":[{"_id":"UlWa"}],"doi":"10.1007/978-3-030-04414-5_16","article_processing_charge":"No","publisher":"Springer","publication_status":"published","page":"229-241","year":"2018","title":"Crossing minimization in perturbed drawings","type":"conference","citation":{"ieee":"R. Fulek and C. D. Tóth, “Crossing minimization in perturbed drawings,” presented at the GD: Graph Drawing and Network Visualization, Barcelona, Spain, 2018, vol. 11282, pp. 229–241.","chicago":"Fulek, Radoslav, and Csaba D. Tóth. “Crossing Minimization in Perturbed Drawings,” 11282:229–41. Springer, 2018. https://doi.org/10.1007/978-3-030-04414-5_16.","mla":"Fulek, Radoslav, and Csaba D. Tóth. Crossing Minimization in Perturbed Drawings. Vol. 11282, Springer, 2018, pp. 229–41, doi:10.1007/978-3-030-04414-5_16.","short":"R. Fulek, C.D. Tóth, in:, Springer, 2018, pp. 229–241.","ama":"Fulek R, Tóth CD. Crossing minimization in perturbed drawings. In: Vol 11282. Springer; 2018:229-241. doi:10.1007/978-3-030-04414-5_16","ista":"Fulek R, Tóth CD. 2018. Crossing minimization in perturbed drawings. GD: Graph Drawing and Network Visualization, LNCS, vol. 11282, 229–241.","apa":"Fulek, R., & Tóth, C. D. (2018). Crossing minimization in perturbed drawings (Vol. 11282, pp. 229–241). Presented at the GD: Graph Drawing and Network Visualization, Barcelona, Spain: Springer. https://doi.org/10.1007/978-3-030-04414-5_16"},"volume":"11282 ","date_created":"2018-12-30T22:59:15Z","main_file_link":[{"url":"https://arxiv.org/abs/1808.07608","open_access":"1"}],"scopus_import":"1","day":"18","conference":{"location":"Barcelona, Spain","start_date":"2018-09-26","name":"GD: Graph Drawing and Network Visualization","end_date":"2018-09-28"}},{"scopus_import":"1","ec_funded":1,"day":"17","citation":{"ista":"Yakaboylu E, Shkolnikov M, Lemeshko M. 2018. Quantum groups as hidden symmetries of quantum impurities. Physical Review Letters. 121(25), 255302.","apa":"Yakaboylu, E., Shkolnikov, M., & Lemeshko, M. (2018). Quantum groups as hidden symmetries of quantum impurities. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.121.255302","ama":"Yakaboylu E, Shkolnikov M, Lemeshko M. Quantum groups as hidden symmetries of quantum impurities. Physical Review Letters. 2018;121(25). doi:10.1103/PhysRevLett.121.255302","short":"E. Yakaboylu, M. Shkolnikov, M. Lemeshko, Physical Review Letters 121 (2018).","mla":"Yakaboylu, Enderalp, et al. “Quantum Groups as Hidden Symmetries of Quantum Impurities.” Physical Review Letters, vol. 121, no. 25, 255302, American Physical Society, 2018, doi:10.1103/PhysRevLett.121.255302.","chicago":"Yakaboylu, Enderalp, Mikhail Shkolnikov, and Mikhail Lemeshko. “Quantum Groups as Hidden Symmetries of Quantum Impurities.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.121.255302.","ieee":"E. Yakaboylu, M. Shkolnikov, and M. Lemeshko, “Quantum groups as hidden symmetries of quantum impurities,” Physical Review Letters, vol. 121, no. 25. American Physical Society, 2018."},"article_number":"255302","volume":121,"date_created":"2019-01-06T22:59:12Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1809.00222"}],"title":"Quantum groups as hidden symmetries of quantum impurities","type":"journal_article","issue":"25","publisher":"American Physical Society","publication_status":"published","year":"2018","language":[{"iso":"eng"}],"date_published":"2018-12-17T00:00:00Z","department":[{"_id":"MiLe"}],"doi":"10.1103/PhysRevLett.121.255302","article_processing_charge":"No","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"},{"_id":"26031614-B435-11E9-9278-68D0E5697425","name":"Quantum rotations in the presence of a many-body environment","call_identifier":"FWF","grant_number":"P29902"}],"isi":1,"_id":"5794","author":[{"id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5973-0874","full_name":"Yakaboylu, Enderalp","first_name":"Enderalp","last_name":"Yakaboylu"},{"last_name":"Shkolnikov","first_name":"Mikhail","orcid":"0000-0002-4310-178X","full_name":"Shkolnikov, Mikhail","id":"35084A62-F248-11E8-B48F-1D18A9856A87"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802"}],"publication_identifier":{"issn":["00319007"]},"publication":"Physical Review Letters","intvolume":" 121","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","article_type":"original","arxiv":1,"oa_version":"Preprint","quality_controlled":"1","month":"12","abstract":[{"lang":"eng","text":"We present an approach to interacting quantum many-body systems based on the notion of quantum groups, also known as q-deformed Lie algebras. In particular, we show that, if the symmetry of a free quantum particle corresponds to a Lie group G, in the presence of a many-body environment this particle can be described by a deformed group, Gq. Crucially, the single deformation parameter, q, contains all the information about the many-particle interactions in the system. We exemplify our approach by considering a quantum rotor interacting with a bath of bosons, and demonstrate that extracting the value of q from closed-form solutions in the perturbative regime allows one to predict the behavior of the system for arbitrary values of the impurity-bath coupling strength, in good agreement with nonperturbative calculations. Furthermore, the value of the deformation parameter allows one to predict at which coupling strengths rotor-bath interactions result in a formation of a stable quasiparticle. The approach based on quantum groups does not only allow for a drastic simplification of impurity problems, but also provides valuable insights into hidden symmetries of interacting many-particle systems."}],"date_updated":"2025-04-15T06:50:24Z","external_id":{"arxiv":["1809.00222"],"isi":["000454178600009"]}},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"pmid":1,"intvolume":" 5","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"status":"public","quality_controlled":"1","oa_version":"Published Version","month":"12","abstract":[{"text":"The emergence of syntax during childhood is a remarkable example of how complex correlations unfold in nonlinear ways through development. In particular, rapid transitions seem to occur as children reach the age of two, which seems to separate a two-word, tree-like network of syntactic relations among words from the scale-free graphs associated with the adult, complex grammar. Here, we explore the evolution of syntax networks through language acquisition using the chromatic number, which captures the transition and provides a natural link to standard theories on syntactic structures. The data analysis is compared to a null model of network growth dynamics which is shown to display non-trivial and sensible differences. At a more general level, we observe that the chromatic classes define independent regions of the graph, and thus, can be interpreted as the footprints of incompatibility relations, somewhat as opposed to modularity considerations.","lang":"eng"}],"date_updated":"2023-10-18T06:41:12Z","external_id":{"pmid":["30662738"],"isi":["000456566500027"]},"language":[{"iso":"eng"}],"acknowledgement":"This work was supported by the James McDonnell Foundation (B.C-M., S.V. and R.S.)","doi":"10.1098/rsos.181286","date_published":"2018-12-12T00:00:00Z","department":[{"_id":"EdHa"}],"file":[{"date_updated":"2020-07-14T12:47:13Z","relation":"main_file","file_size":646732,"checksum":"9664d4417f6b792242e31eea77ce9501","content_type":"application/pdf","file_id":"5924","creator":"dernst","access_level":"open_access","date_created":"2019-02-05T14:38:09Z","file_name":"2018_RoyalSocOS_Corominas.pdf"}],"article_processing_charge":"No","_id":"5859","isi":1,"has_accepted_license":"1","author":[{"id":"43BE2298-F248-11E8-B48F-1D18A9856A87","first_name":"Bernat","last_name":"Corominas-Murtra","orcid":"0000-0001-9806-5643","full_name":"Corominas-Murtra, Bernat"},{"full_name":"Fibla, Martí Sànchez","first_name":"Martí Sànchez","last_name":"Fibla"},{"first_name":"Sergi","last_name":"Valverde","full_name":"Valverde, Sergi"},{"full_name":"Solé, Ricard","last_name":"Solé","first_name":"Ricard"}],"publication":"Royal Society Open Science","publication_identifier":{"issn":["2054-5703"]},"ddc":["570"],"type":"journal_article","file_date_updated":"2020-07-14T12:47:13Z","title":"Chromatic transitions in the emergence of syntax networks","issue":"12","publisher":"The Royal Society","publication_status":"published","year":"2018","scopus_import":"1","day":"12","article_number":"181286","citation":{"mla":"Corominas-Murtra, Bernat, et al. “Chromatic Transitions in the Emergence of Syntax Networks.” Royal Society Open Science, vol. 5, no. 12, 181286, The Royal Society, 2018, doi:10.1098/rsos.181286.","chicago":"Corominas-Murtra, Bernat, Martí Sànchez Fibla, Sergi Valverde, and Ricard Solé. “Chromatic Transitions in the Emergence of Syntax Networks.” Royal Society Open Science. The Royal Society, 2018. https://doi.org/10.1098/rsos.181286.","apa":"Corominas-Murtra, B., Fibla, M. S., Valverde, S., & Solé, R. (2018). Chromatic transitions in the emergence of syntax networks. Royal Society Open Science. The Royal Society. https://doi.org/10.1098/rsos.181286","ista":"Corominas-Murtra B, Fibla MS, Valverde S, Solé R. 2018. Chromatic transitions in the emergence of syntax networks. Royal Society Open Science. 5(12), 181286.","ama":"Corominas-Murtra B, Fibla MS, Valverde S, Solé R. Chromatic transitions in the emergence of syntax networks. Royal Society Open Science. 2018;5(12). doi:10.1098/rsos.181286","short":"B. Corominas-Murtra, M.S. Fibla, S. Valverde, R. Solé, Royal Society Open Science 5 (2018).","ieee":"B. Corominas-Murtra, M. S. Fibla, S. Valverde, and R. Solé, “Chromatic transitions in the emergence of syntax networks,” Royal Society Open Science, vol. 5, no. 12. The Royal Society, 2018."},"date_created":"2019-01-20T22:59:18Z","volume":5},{"doi":"10.7554/eLife.37888","department":[{"_id":"MiSi"}],"date_published":"2018-06-06T00:00:00Z","language":[{"iso":"eng"}],"file":[{"file_name":"2018_eLife_Alanko.pdf","access_level":"open_access","creator":"dernst","date_created":"2019-02-13T10:52:11Z","file_id":"5973","checksum":"f1c7ec2a809408d763c4b529a98f9a3b","content_type":"application/pdf","date_updated":"2020-07-14T12:47:13Z","relation":"main_file","file_size":358141}],"article_processing_charge":"No","has_accepted_license":"1","author":[{"id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","full_name":"Alanko, Jonna H","orcid":"0000-0002-7698-3061","first_name":"Jonna H","last_name":"Alanko"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","first_name":"Michael K"}],"_id":"5861","isi":1,"publication":"eLife","ddc":["570"],"publication_identifier":{"issn":["2050-084X"]},"article_type":"original","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"intvolume":" 7","quality_controlled":"1","oa_version":"Published Version","abstract":[{"text":"In zebrafish larvae, it is the cell type that determines how the cell responds to a chemokine signal.","lang":"eng"}],"date_updated":"2025-07-10T11:53:05Z","month":"06","external_id":{"isi":["000434375000001"]},"scopus_import":"1","day":"06","citation":{"ieee":"J. H. Alanko and M. K. Sixt, “The cell sets the tone,” eLife, vol. 7. eLife Sciences Publications, 2018.","short":"J.H. Alanko, M.K. Sixt, ELife 7 (2018).","ama":"Alanko JH, Sixt MK. The cell sets the tone. eLife. 2018;7. doi:10.7554/eLife.37888","ista":"Alanko JH, Sixt MK. 2018. The cell sets the tone. eLife. 7, e37888.","apa":"Alanko, J. H., & Sixt, M. K. (2018). The cell sets the tone. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.37888","chicago":"Alanko, Jonna H, and Michael K Sixt. “The Cell Sets the Tone.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.37888.","mla":"Alanko, Jonna H., and Michael K. Sixt. “The Cell Sets the Tone.” ELife, vol. 7, e37888, eLife Sciences Publications, 2018, doi:10.7554/eLife.37888."},"article_number":"e37888","date_created":"2019-01-20T22:59:19Z","volume":7,"type":"journal_article","file_date_updated":"2020-07-14T12:47:13Z","title":"The cell sets the tone","publication_status":"published","publisher":"eLife Sciences Publications","corr_author":"1","year":"2018"},{"scopus_import":"1","day":"07","article_number":"100","citation":{"ieee":"D.-C. Tarlungeanu and G. Novarino, “Genomics in neurodevelopmental disorders: an avenue to personalized medicine,” Experimental & Molecular Medicine, vol. 50, no. 8. Springer Nature, 2018.","mla":"Tarlungeanu, Dora-Clara, and Gaia Novarino. “Genomics in Neurodevelopmental Disorders: An Avenue to Personalized Medicine.” Experimental & Molecular Medicine, vol. 50, no. 8, 100, Springer Nature, 2018, doi:10.1038/s12276-018-0129-7.","chicago":"Tarlungeanu, Dora-Clara, and Gaia Novarino. “Genomics in Neurodevelopmental Disorders: An Avenue to Personalized Medicine.” Experimental & Molecular Medicine. Springer Nature, 2018. https://doi.org/10.1038/s12276-018-0129-7.","apa":"Tarlungeanu, D.-C., & Novarino, G. (2018). Genomics in neurodevelopmental disorders: an avenue to personalized medicine. Experimental & Molecular Medicine. Springer Nature. https://doi.org/10.1038/s12276-018-0129-7","ista":"Tarlungeanu D-C, Novarino G. 2018. Genomics in neurodevelopmental disorders: an avenue to personalized medicine. Experimental & Molecular Medicine. 50(8), 100.","ama":"Tarlungeanu D-C, Novarino G. Genomics in neurodevelopmental disorders: an avenue to personalized medicine. Experimental & Molecular Medicine. 2018;50(8). doi:10.1038/s12276-018-0129-7","short":"D.-C. Tarlungeanu, G. Novarino, Experimental & Molecular Medicine 50 (2018)."},"date_created":"2019-01-27T22:59:11Z","volume":50,"type":"journal_article","file_date_updated":"2020-07-14T12:47:13Z","title":"Genomics in neurodevelopmental disorders: an avenue to personalized medicine","issue":"8","publication_status":"published","publisher":"Springer Nature","year":"2018","doi":"10.1038/s12276-018-0129-7","department":[{"_id":"GaNo"}],"date_published":"2018-08-07T00:00:00Z","language":[{"iso":"eng"}],"file":[{"file_size":1237482,"relation":"main_file","date_updated":"2020-07-14T12:47:13Z","access_level":"open_access","creator":"dernst","date_created":"2019-01-28T15:18:02Z","content_type":"application/pdf","checksum":"4498301c8c53097c9a1a8ef990936eb5","file_id":"5893","file_name":"2018_EMM_Tarlungeanu.pdf"}],"article_processing_charge":"No","has_accepted_license":"1","author":[{"id":"2ABCE612-F248-11E8-B48F-1D18A9856A87","last_name":"Tarlungeanu","first_name":"Dora-Clara","full_name":"Tarlungeanu, Dora-Clara"},{"full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}],"_id":"5888","isi":1,"ddc":["570"],"publication_identifier":{"issn":["2092-6413"]},"publication":"Experimental & Molecular Medicine","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"intvolume":" 50","pmid":1,"quality_controlled":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Despite the remarkable number of scientific breakthroughs of the last 100 years, the treatment of neurodevelopmental\r\ndisorders (e.g., autism spectrum disorder, intellectual disability) remains a great challenge. Recent advancements in\r\ngenomics, such as whole-exome or whole-genome sequencing, have enabled scientists to identify numerous\r\nmutations underlying neurodevelopmental disorders. Given the few hundred risk genes that have been discovered,\r\nthe etiological variability and the heterogeneous clinical presentation, the need for genotype — along with phenotype-\r\nbased diagnosis of individual patients has become a requisite. In this review we look at recent advancements in\r\ngenomic analysis and their translation into clinical practice."}],"date_updated":"2023-09-11T14:04:41Z","month":"08","external_id":{"pmid":["30089840"],"isi":["000441266700006"]}},{"scopus_import":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-10575-8_27","date_published":"2018-05-19T00:00:00Z","department":[{"_id":"KrCh"}],"day":"19","_id":"59","citation":{"chicago":"Bloem, Roderick, Krishnendu Chatterjee, and Barbara Jobstmann. “Graph Games and Reactive Synthesis.” In Handbook of Model Checking, edited by Thomas A Henzinger, Edmund M. Clarke, Helmut Veith, and Roderick Bloem, 1st ed., 921–62. Springer, 2018. https://doi.org/10.1007/978-3-319-10575-8_27.","mla":"Bloem, Roderick, et al. “Graph Games and Reactive Synthesis.” Handbook of Model Checking, edited by Thomas A Henzinger et al., 1st ed., Springer, 2018, pp. 921–62, doi:10.1007/978-3-319-10575-8_27.","ama":"Bloem R, Chatterjee K, Jobstmann B. Graph games and reactive synthesis. In: Henzinger TA, Clarke EM, Veith H, Bloem R, eds. Handbook of Model Checking. 1st ed. Springer; 2018:921-962. doi:10.1007/978-3-319-10575-8_27","short":"R. Bloem, K. Chatterjee, B. Jobstmann, in:, T.A. Henzinger, E.M. Clarke, H. Veith, R. Bloem (Eds.), Handbook of Model Checking, 1st ed., Springer, 2018, pp. 921–962.","apa":"Bloem, R., Chatterjee, K., & Jobstmann, B. (2018). Graph games and reactive synthesis. In T. A. Henzinger, E. M. Clarke, H. Veith, & R. Bloem (Eds.), Handbook of Model Checking (1st ed., pp. 921–962). Springer. https://doi.org/10.1007/978-3-319-10575-8_27","ista":"Bloem R, Chatterjee K, Jobstmann B. 2018.Graph games and reactive synthesis. In: Handbook of Model Checking. , 921–962.","ieee":"R. Bloem, K. Chatterjee, and B. Jobstmann, “Graph games and reactive synthesis,” in Handbook of Model Checking, 1st ed., T. A. Henzinger, E. M. Clarke, H. Veith, and R. Bloem, Eds. Springer, 2018, pp. 921–962."},"author":[{"full_name":"Bloem, Roderick","last_name":"Bloem","first_name":"Roderick"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"last_name":"Jobstmann","first_name":"Barbara","full_name":"Jobstmann, Barbara"}],"date_created":"2018-12-11T11:44:24Z","publication":"Handbook of Model Checking","publication_identifier":{"isbn":["978-3-319-10574-1"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"book_chapter","title":"Graph games and reactive synthesis","status":"public","edition":"1","editor":[{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Clarke, Edmund M.","first_name":"Edmund M.","last_name":"Clarke"},{"full_name":"Veith, Helmut","last_name":"Veith","first_name":"Helmut"},{"full_name":"Bloem, Roderick","first_name":"Roderick","last_name":"Bloem"}],"quality_controlled":"1","oa_version":"None","month":"05","publisher":"Springer","abstract":[{"text":"Graph-based games are an important tool in computer science. They have applications in synthesis, verification, refinement, and far beyond. We review graphbased games with objectives on infinite plays. We give definitions and algorithms to solve the games and to give a winning strategy. The objectives we consider are mostly Boolean, but we also look at quantitative graph-based games and their objectives. Synthesis aims to turn temporal logic specifications into correct reactive systems. We explain the reduction of synthesis to graph-based games (or equivalently tree automata) using synthesis of LTL specifications as an example. We treat the classical approach that uses determinization of parity automata and more modern approaches.","lang":"eng"}],"date_updated":"2021-01-12T08:05:10Z","publication_status":"published","publist_id":"7995","page":"921 - 962","year":"2018"},{"type":"conference","file_date_updated":"2020-07-14T12:47:13Z","title":"Keynote: The first-order logic of signals","page":"1-10","year":"2018","publication_status":"published","publisher":"IEEE","conference":{"end_date":"2018-10-05","name":"EMSOFT: Embedded Software","location":"Turin, Italy","start_date":"2018-09-30"},"day":"30","scopus_import":"1","date_created":"2019-02-13T09:19:28Z","citation":{"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","ista":"Bakhirkin A, Ferrere T, Henzinger TA, Nickovicl D. 2018. Keynote: The first-order logic of signals. 2018 International Conference on Embedded Software. EMSOFT: Embedded Software, 1–10.","short":"A. Bakhirkin, T. Ferrere, T.A. Henzinger, D. Nickovicl, in:, 2018 International Conference on Embedded Software, IEEE, 2018, pp. 1–10.","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","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.","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.","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."},"quality_controlled":"1","oa_version":"Published Version","status":"public","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000492828500005"]},"date_updated":"2025-07-10T11:53:06Z","abstract":[{"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.","lang":"eng"}],"month":"09","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"},{"name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF"}],"file":[{"file_name":"2018_EMSOFT_Bakhirkin.pdf","checksum":"234a33ad9055b3458fcdda6af251b33a","content_type":"application/pdf","file_id":"7839","access_level":"open_access","date_created":"2020-05-14T16:01:29Z","creator":"dernst","relation":"main_file","date_updated":"2020-07-14T12:47:13Z","file_size":338006}],"article_processing_charge":"No","doi":"10.1109/emsoft.2018.8537203","department":[{"_id":"ToHe"}],"date_published":"2018-09-30T00:00:00Z","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781538655603"]},"publication":"2018 International Conference on Embedded Software","ddc":["000"],"has_accepted_license":"1","author":[{"last_name":"Bakhirkin","first_name":"Alexey","full_name":"Bakhirkin, Alexey"},{"id":"40960E6E-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Ferrere","orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"last_name":"Nickovicl","first_name":"Deian","full_name":"Nickovicl, Deian"}],"_id":"5959","isi":1},{"day":"24","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1712.01341"}],"volume":37,"date_created":"2019-02-13T09:36:20Z","citation":{"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.","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.","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","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.","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","short":"S. Rohou, P. Franek, C. Aubry, L. Jaulin, The International Journal of Robotics Research 37 (2018) 1500–1516.","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."},"issue":"12","title":"Proving the existence of loops in robot trajectories","type":"journal_article","year":"2018","page":"1500-1516","publication_status":"published","publisher":"SAGE Publications","article_processing_charge":"No","date_published":"2018-10-24T00:00:00Z","department":[{"_id":"UlWa"}],"doi":"10.1177/0278364918808367","language":[{"iso":"eng"}],"publication":"The International Journal of Robotics Research","publication_identifier":{"issn":["0278-3649"],"eissn":["1741-3176"]},"author":[{"full_name":"Rohou, Simon","first_name":"Simon","last_name":"Rohou"},{"first_name":"Peter","last_name":"Franek","orcid":"0000-0001-8878-8397","full_name":"Franek, Peter","id":"473294AE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Aubry, Clément","first_name":"Clément","last_name":"Aubry"},{"full_name":"Jaulin, Luc","first_name":"Luc","last_name":"Jaulin"}],"isi":1,"_id":"5960","oa_version":"Preprint","quality_controlled":"1","arxiv":1,"status":"public","intvolume":" 37","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"arxiv":["1712.01341"],"isi":["000456881100004"]},"date_updated":"2023-09-19T10:41:59Z","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"}],"month":"10"},{"isi":1,"citation":{"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.","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. 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, 2018, pp. 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; 2018:487-488. doi:10.1145/3212734.3212798","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, 2018, pp. 487–88, doi:10.1145/3212734.3212798.","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, 2018. https://doi.org/10.1145/3212734.3212798."},"_id":"5961","author":[{"last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"isbn":["9781450357951"]},"publication":"Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC '18","date_created":"2019-02-13T09:48:55Z","language":[{"iso":"eng"}],"scopus_import":"1","department":[{"_id":"DaAl"}],"date_published":"2018-07-27T00:00:00Z","doi":"10.1145/3212734.3212798","article_processing_charge":"No","day":"27","conference":{"end_date":"2018-07-27","name":"PODC: Principles of Distributed Computing","location":"Egham, United Kingdom","start_date":"2018-07-23"},"publisher":"ACM","month":"07","publication_status":"published","date_updated":"2025-06-03T11:56:33Z","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"}],"page":"487-488","year":"2018","external_id":{"isi":["000458186900063"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"A brief tutorial on distributed and concurrent machine learning","type":"conference","oa_version":"None","quality_controlled":"1"},{"page":"169-178","year":"2018","publisher":"ACM","publication_status":"published","title":"The convergence of stochastic gradient descent in asynchronous shared memory","type":"conference","date_created":"2019-02-13T09:58:58Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.08841"}],"citation":{"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.","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, 2018. 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, 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, 2018, pp. 169–178.","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; 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.","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. https://doi.org/10.1145/3212734.3212763"},"day":"23","conference":{"location":"Egham, United Kingdom","name":"PODC: Principles of Distributed Computing","start_date":"2018-07-23","end_date":"2018-07-27"},"scopus_import":"1","external_id":{"arxiv":["1803.08841"],"isi":["000458186900022"]},"month":"07","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"}],"date_updated":"2025-06-03T11:56:41Z","arxiv":1,"oa_version":"Preprint","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"status":"public","publication":"Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC '18","publication_identifier":{"isbn":["9781450357951"]},"isi":1,"_id":"5962","author":[{"last_name":"Alistarh","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"De Sa, Christopher","first_name":"Christopher","last_name":"De Sa"},{"id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87","full_name":"Konstantinov, Nikola H","first_name":"Nikola H","last_name":"Konstantinov"}],"article_processing_charge":"No","language":[{"iso":"eng"}],"department":[{"_id":"DaAl"}],"date_published":"2018-07-23T00:00:00Z","doi":"10.1145/3212734.3212763"},{"language":[{"iso":"eng"}],"doi":"10.1145/3212734.3212756","date_published":"2018-07-23T00:00:00Z","department":[{"_id":"DaAl"}],"article_processing_charge":"No","_id":"5963","isi":1,"author":[{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Trevor A","last_name":"Brown","full_name":"Brown, Trevor A","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kopinsky, Justin","first_name":"Justin","last_name":"Kopinsky"},{"full_name":"Nadiradze, Giorgi","last_name":"Nadiradze","first_name":"Giorgi"}],"publication_identifier":{"isbn":["9781450357951"]},"publication":"Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC '18","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"status":"public","arxiv":1,"quality_controlled":"1","oa_version":"Preprint","month":"07","date_updated":"2025-06-03T11:56:49Z","abstract":[{"lang":"eng","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."}],"external_id":{"arxiv":["1808.04155"],"isi":["000458186900048"]},"scopus_import":"1","day":"23","conference":{"location":"Egham, United Kingdom","start_date":"2018-07-23","name":"PODC: Principles of Distributed Computing","end_date":"2018-07-27"},"citation":{"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, 2018. 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, 2018, pp. 377–86, doi:10.1145/3212734.3212756.","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; 2018:377-386. 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, 2018, pp. 377–386.","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.","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. https://doi.org/10.1145/3212734.3212756","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."},"date_created":"2019-02-13T10:03:25Z","main_file_link":[{"url":"https://arxiv.org/abs/1808.04155","open_access":"1"}],"type":"conference","title":"Relaxed schedulers can efficiently parallelize iterative algorithms","publisher":"ACM","publication_status":"published","year":"2018","page":"377-386"},{"main_file_link":[{"open_access":"1","url":"https://hal-univ-lyon3.archives-ouvertes.fr/INRIA/hal-01887733v1"}],"date_created":"2019-02-13T10:08:19Z","citation":{"ieee":"V. Aksenov, D.-A. Alistarh, and P. Kuznetsov, “Brief Announcement: Performance prediction for coarse-grained locking,” in Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, Egham, United Kingdom, 2018, pp. 411–413.","chicago":"Aksenov, Vitaly, Dan-Adrian Alistarh, and Petr Kuznetsov. “Brief Announcement: Performance Prediction for Coarse-Grained Locking.” In Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, 411–13. ACM, 2018. https://doi.org/10.1145/3212734.3212785.","mla":"Aksenov, Vitaly, et al. “Brief Announcement: Performance Prediction for Coarse-Grained Locking.” Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, ACM, 2018, pp. 411–13, doi:10.1145/3212734.3212785.","short":"V. Aksenov, D.-A. Alistarh, P. Kuznetsov, in:, Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, ACM, 2018, pp. 411–413.","ama":"Aksenov V, Alistarh D-A, Kuznetsov P. Brief Announcement: Performance prediction for coarse-grained locking. In: Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18. ACM; 2018:411-413. doi:10.1145/3212734.3212785","ista":"Aksenov V, Alistarh D-A, Kuznetsov P. 2018. Brief Announcement: Performance prediction for coarse-grained locking. Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18. PODC: Principles of Distributed Computing, 411–413.","apa":"Aksenov, V., Alistarh, D.-A., & Kuznetsov, P. (2018). Brief Announcement: Performance prediction for coarse-grained locking. In Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18 (pp. 411–413). Egham, United Kingdom: ACM. https://doi.org/10.1145/3212734.3212785"},"conference":{"end_date":"2018-07-27","name":"PODC: Principles of Distributed Computing","start_date":"2018-07-23","location":"Egham, United Kingdom"},"day":"23","scopus_import":"1","year":"2018","page":"411-413","publication_status":"published","publisher":"ACM","type":"conference","title":"Brief Announcement: Performance prediction for coarse-grained locking","publication":"Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC '18","publication_identifier":{"isbn":["9781450357951"]},"author":[{"first_name":"Vitaly","last_name":"Aksenov","full_name":"Aksenov, Vitaly"},{"first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kuznetsov, Petr","last_name":"Kuznetsov","first_name":"Petr"}],"_id":"5964","isi":1,"article_processing_charge":"No","doi":"10.1145/3212734.3212785","date_published":"2018-07-23T00:00:00Z","department":[{"_id":"DaAl"}],"language":[{"iso":"eng"}],"external_id":{"isi":["000458186900052"]},"date_updated":"2025-06-03T11:58:00Z","abstract":[{"text":"A standard design pattern found in many concurrent data structures, such as hash tables or ordered containers, is an alternation of parallelizable sections that incur no data conflicts and critical sections that must run sequentially and are protected with locks. A lock can be viewed as a queue that arbitrates the order in which the critical sections are executed, and a natural question is whether we can use stochastic analysis to predict the resulting throughput. As a preliminary evidence to the affirmative, we describe a simple model that can be used to predict the throughput of coarse-grained lock-based algorithms. We show that our model works well for CLH lock, and we expect it to work for other popular lock designs such as TTAS, MCS, etc.","lang":"eng"}],"month":"07","quality_controlled":"1","oa_version":"Submitted Version","status":"public","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"month":"07","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"}],"date_updated":"2026-04-08T07:00:45Z","external_id":{"isi":["000545269600016"],"arxiv":["1804.01018"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10429"}]},"status":"public","arxiv":1,"oa_version":"Preprint","quality_controlled":"1","isi":1,"_id":"5965","author":[{"first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Brown, Trevor A","first_name":"Trevor A","last_name":"Brown","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kopinsky","first_name":"Justin","full_name":"Kopinsky, Justin"},{"full_name":"Li, Jerry Z.","last_name":"Li","first_name":"Jerry Z."},{"full_name":"Nadiradze, Giorgi","first_name":"Giorgi","last_name":"Nadiradze"}],"publication":"Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA '18","publication_identifier":{"isbn":["9781450357999"]},"language":[{"iso":"eng"}],"department":[{"_id":"DaAl"}],"date_published":"2018-07-16T00:00:00Z","doi":"10.1145/3210377.3210411","article_processing_charge":"No","publisher":"ACM","publication_status":"published","page":"133-142","year":"2018","title":"Distributionally linearizable data structures","type":"conference","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, 2018, pp. 133–142.","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; 2018:133-142. doi:10.1145/3210377.3210411","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. 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.","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, 2018. https://doi.org/10.1145/3210377.3210411.","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, 2018, pp. 133–42, 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."},"date_created":"2019-02-13T10:17:19Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.01018"}],"scopus_import":"1","day":"16","conference":{"end_date":"2018-07-18","location":"Vienna, Austria","start_date":"2018-07-16","name":"SPAA: Symposium on Parallelism in Algorithms and Architectures"}},{"publication_status":"published","publisher":"ACM","page":"383-392","year":"2018","type":"conference","title":"The transactional conflict problem","citation":{"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; 2018:383-392. 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, 2018, pp. 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. https://doi.org/10.1145/3210377.3210406","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.","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, 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, 2018, pp. 383–92, doi: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."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.00947"}],"date_created":"2019-02-13T10:26:07Z","scopus_import":"1","conference":{"location":"Vienna, Austria","name":"SPAA: Symposium on Parallelism in Algorithms and Architectures","start_date":"2018-07-16","end_date":"2018-07-18"},"day":"16","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."}],"date_updated":"2025-06-03T11:58:22Z","month":"07","external_id":{"isi":["000545269600046"],"arxiv":["1804.00947"]},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","oa_version":"Preprint","arxiv":1,"author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian","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"}],"_id":"5966","isi":1,"publication_identifier":{"isbn":["9781450357999"]},"publication":"Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA '18","doi":"10.1145/3210377.3210406","date_published":"2018-07-16T00:00:00Z","department":[{"_id":"DaAl"}],"language":[{"iso":"eng"}],"article_processing_charge":"No"}]