[{"status":"public","date_published":"2022-09-08T00:00:00Z","publication_status":"published","type":"journal_article","file_date_updated":"2024-07-31T12:13:16Z","month":"09","year":"2022","article_processing_charge":"Yes","publisher":"IOP Publishing","abstract":[{"lang":"eng","text":"We investigate the formation of magnetic Bose polaron, an impurity atom dressed by spin-wave excitations, in a one-dimensional spinor Bose gas. Within an effective potential model, the impurity is strongly confined by the host excitations which can even overcome the impurity-medium repulsion leading to a self-localized quasi-particle state. The phase diagram of the attractive and self-bound repulsive magnetic polaron, repulsive non-magnetic (Fröhlich-type) polaron and impurity-medium phase-separation regimes is explored with respect to the Rabi-coupling between the spin components, spin–spin interactions and impurity-medium coupling. The residue of such magnetic polarons decreases substantially in both strong attractive and repulsive branches with strong impurity-spin interactions, illustrating significant dressing of the impurity. The impurity can be used to probe and maneuver the spin polarization of the magnetic medium while suppressing ferromagnetic spin–spin correlations. It is shown that mean-field theory fails as the spinor gas approaches immiscibility since the generated spin-wave excitations are prominent. Our findings illustrate that impurities can be utilized to generate controllable spin–spin correlations and magnetic polaron states which can be realized with current cold atom setups."}],"department":[{"_id":"MiLe"}],"author":[{"full_name":"Mistakidis, S I","last_name":"Mistakidis","first_name":"S I"},{"full_name":"Koutentakis, Georgios","last_name":"Koutentakis","first_name":"Georgios","id":"d7b23d3a-9e21-11ec-b482-f76739596b95"},{"first_name":"F","full_name":"Grusdt, F","last_name":"Grusdt"},{"last_name":"Schmelcher","full_name":"Schmelcher, P","first_name":"P"},{"last_name":"Sadeghpour","full_name":"Sadeghpour, H R","first_name":"H R"}],"article_type":"original","fulldoi":"https://doi.org/10.1088/1367-2630/ac836c","has_accepted_license":"1","day":"08","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)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","publication_identifier":{"issn":["1367-2630"]},"intvolume":" 24","ddc":["530"],"doi":"10.1088/1367-2630/ac836c","language":[{"iso":"eng"}],"quality_controlled":"1","date_created":"2024-05-29T06:11:35Z","article_number":"083030","issue":"8","external_id":{"arxiv":["2204.10960"]},"file":[{"creator":"dernst","checksum":"85776a9d3abe163b33b322c8e346752a","success":1,"date_updated":"2024-07-31T12:13:16Z","file_size":4201283,"file_id":"17358","relation":"main_file","file_name":"2022_NewJournPhysics_Mistakidis.pdf","content_type":"application/pdf","date_created":"2024-07-31T12:13:16Z","access_level":"open_access"}],"citation":{"ieee":"S. I. Mistakidis, G. Koutentakis, F. Grusdt, P. Schmelcher, and H. R. Sadeghpour, “Inducing spin-order with an impurity: phase diagram of the magnetic Bose polaron,” New Journal of Physics, vol. 24, no. 8. IOP Publishing, 2022.","mla":"Mistakidis, S. I., et al. “Inducing Spin-Order with an Impurity: Phase Diagram of the Magnetic Bose Polaron.” New Journal of Physics, vol. 24, no. 8, 083030, IOP Publishing, 2022, doi:10.1088/1367-2630/ac836c.","short":"S.I. Mistakidis, G. Koutentakis, F. Grusdt, P. Schmelcher, H.R. Sadeghpour, New Journal of Physics 24 (2022).","ista":"Mistakidis SI, Koutentakis G, Grusdt F, Schmelcher P, Sadeghpour HR. 2022. Inducing spin-order with an impurity: phase diagram of the magnetic Bose polaron. New Journal of Physics. 24(8), 083030.","apa":"Mistakidis, S. I., Koutentakis, G., Grusdt, F., Schmelcher, P., & Sadeghpour, H. R. (2022). Inducing spin-order with an impurity: phase diagram of the magnetic Bose polaron. New Journal of Physics. IOP Publishing. https://doi.org/10.1088/1367-2630/ac836c","ama":"Mistakidis SI, Koutentakis G, Grusdt F, Schmelcher P, Sadeghpour HR. Inducing spin-order with an impurity: phase diagram of the magnetic Bose polaron. New Journal of Physics. 2022;24(8). doi:10.1088/1367-2630/ac836c","chicago":"Mistakidis, S I, Georgios Koutentakis, F Grusdt, P Schmelcher, and H R Sadeghpour. “Inducing Spin-Order with an Impurity: Phase Diagram of the Magnetic Bose Polaron.” New Journal of Physics. IOP Publishing, 2022. https://doi.org/10.1088/1367-2630/ac836c."},"arxiv":1,"publication":"New Journal of Physics","volume":24,"_id":"17070","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","date_updated":"2024-07-31T12:14:55Z","oa":1,"title":"Inducing spin-order with an impurity: phase diagram of the magnetic Bose polaron","license":"https://creativecommons.org/licenses/by/4.0/"},{"external_id":{"pmid":["35679397"]},"pmid":1,"article_number":"abm9506","issue":"6598","acknowledgement":"We acknowledge support from the Electron Microscopy Core Facility (EMCF) and IT services of European Molecular Biology Laboratory (EMBL) Heidelberg. We thank S. Welsch at the Central Electron Microscopy Facility of the Max Planck Institute of Biophysics for technical expertise. We thank T. Hoffman and R. Alves for help with the AlphaFold installation.\r\nFunding: M.B. acknowledges funding by EMBL, the Max Planck Society, and the European Research Council (ComplexAssembly 724349). J.K. acknowledges funding from the Federal Ministry of Education and Research of Germany (FKZ 031L0100). The work by M.S. and G.H. on computer simulations was supported by the Max Planck Society. M.S. was supported by the EMBL Interdisciplinary Postdoc Programme under Marie Curie COFUND actions. M.S. and G.H. were supported by the Landes-Offensive zur Entwicklung Wissenschaftlich-ökonomischer Exzellenz (LOEWE) DynaMem program of the State of Hessen.","date_created":"2024-05-29T06:12:02Z","quality_controlled":"1","language":[{"iso":"eng"}],"doi":"10.1126/science.abm9506","intvolume":" 376","title":"AI-based structure prediction empowers integrative structural analysis of human nuclear pores","date_updated":"2024-07-31T12:10:32Z","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"17071","volume":376,"publication":"Science","citation":{"apa":"Mosalaganti, S., Obarska-Kosinska, A., Siggel, M., Taniguchi, R., Turoňová, B., Zimmerli, C. E., … Beck, M. (2022). AI-based structure prediction empowers integrative structural analysis of human nuclear pores. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.abm9506","ama":"Mosalaganti S, Obarska-Kosinska A, Siggel M, et al. AI-based structure prediction empowers integrative structural analysis of human nuclear pores. Science. 2022;376(6598). doi:10.1126/science.abm9506","chicago":"Mosalaganti, Shyamal, Agnieszka Obarska-Kosinska, Marc Siggel, Reiya Taniguchi, Beata Turoňová, Christian E. Zimmerli, Katarzyna Buczak, et al. “AI-Based Structure Prediction Empowers Integrative Structural Analysis of Human Nuclear Pores.” Science. American Association for the Advancement of Science, 2022. https://doi.org/10.1126/science.abm9506.","ieee":"S. Mosalaganti et al., “AI-based structure prediction empowers integrative structural analysis of human nuclear pores,” Science, vol. 376, no. 6598. American Association for the Advancement of Science, 2022.","mla":"Mosalaganti, Shyamal, et al. “AI-Based Structure Prediction Empowers Integrative Structural Analysis of Human Nuclear Pores.” Science, vol. 376, no. 6598, abm9506, American Association for the Advancement of Science, 2022, doi:10.1126/science.abm9506.","short":"S. Mosalaganti, A. Obarska-Kosinska, M. Siggel, R. Taniguchi, B. Turoňová, C.E. Zimmerli, K. Buczak, F. Schmidt, E. Margiotta, M.-T. Mackmull, W.J.H. Hagen, G. Hummer, J. Kosinski, M. Beck, Science 376 (2022).","ista":"Mosalaganti S, Obarska-Kosinska A, Siggel M, Taniguchi R, Turoňová B, Zimmerli CE, Buczak K, Schmidt F, Margiotta E, Mackmull M-T, Hagen WJH, Hummer G, Kosinski J, Beck M. 2022. AI-based structure prediction empowers integrative structural analysis of human nuclear pores. Science. 376(6598), abm9506."},"abstract":[{"lang":"eng","text":"The eukaryotic nucleus protects the genome and is enclosed by the two membranes of the nuclear envelope. Nuclear pore complexes (NPCs) perforate the nuclear envelope to facilitate nucleocytoplasmic transport. With a molecular weight of ∼120 MDa, the human NPC is one of the largest protein complexes. Its ~1000 proteins are taken in multiple copies from a set of about 30 distinct nucleoporins (NUPs). They can be roughly categorized into two classes. Scaffold NUPs contain folded domains and form a cylindrical scaffold architecture around a central channel. Intrinsically disordered NUPs line the scaffold and extend into the central channel, where they interact with cargo complexes. The NPC architecture is highly dynamic. It responds to changes in nuclear envelope tension with conformational breathing that manifests in dilation and constriction movements. Elucidating the scaffold architecture, ultimately at atomic resolution, will be important for gaining a more precise understanding of NPC function and dynamics but imposes a substantial challenge for structural biologists.\r\nConsiderable progress has been made toward this goal by a joint effort in the field. A synergistic combination of complementary approaches has turned out to be critical. In situ structural biology techniques were used to reveal the overall layout of the NPC scaffold that defines the spatial reference for molecular modeling. High-resolution structures of many NUPs were determined in vitro. Proteomic analysis and extensive biochemical work unraveled the interaction network of NUPs. Integrative modeling has been used to combine the different types of data, resulting in a rough outline of the NPC scaffold. Previous structural models of the human NPC, however, were patchy and limited in accuracy owing to several challenges: (i) Many of the high-resolution structures of individual NUPs have been solved from distantly related species and, consequently, do not comprehensively cover their human counterparts. (ii) The scaffold is interconnected by a set of intrinsically disordered linker NUPs that are not straightforwardly accessible to common structural biology techniques. (iii) The NPC scaffold intimately embraces the fused inner and outer nuclear membranes in a distinctive topology and cannot be studied in isolation. (iv) The conformational dynamics of scaffold NUPs limits the resolution achievable in structure determination.\r\nIn this study, we used artificial intelligence (AI)–based prediction to generate an extensive repertoire of structural models of human NUPs and their subcomplexes. The resulting models cover various domains and interfaces that so far remained structurally uncharacterized. Benchmarking against previous and unpublished x-ray and cryo–electron microscopy structures revealed unprecedented accuracy. We obtained well-resolved cryo–electron tomographic maps of both the constricted and dilated conformational states of the human NPC. Using integrative modeling, we fitted the structural models of individual NUPs into the cryo–electron microscopy maps. We explicitly included several linker NUPs and traced their trajectory through the NPC scaffold. We elucidated in great detail how membrane-associated and transmembrane NUPs are distributed across the fusion topology of both nuclear membranes. The resulting architectural model increases the structural coverage of the human NPC scaffold by about twofold. We extensively validated our model against both earlier and new experimental data. The completeness of our model has enabled microsecond-long coarse-grained molecular dynamics simulations of the NPC scaffold within an explicit membrane environment and solvent. These simulations reveal that the NPC scaffold prevents the constriction of the otherwise stable double-membrane fusion pore to small diameters in the absence of membrane tension\r\nOur 70-MDa atomically resolved model covers >90% of the human NPC scaffold. It captures conformational changes that occur during dilation and constriction. It also reveals the precise anchoring sites for intrinsically disordered NUPs, the identification of which is a prerequisite for a complete and dynamic model of the NPC. Our study exemplifies how AI-based structure prediction may accelerate the elucidation of subcellular architecture at atomic resolution."}],"publisher":"American Association for the Advancement of Science","year":"2022","article_processing_charge":"No","month":"06","type":"journal_article","publication_status":"published","date_published":"2022-06-10T00:00:00Z","status":"public","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"oa_version":"None","day":"10","fulldoi":"https://doi.org/10.1126/science.abm9506","article_type":"original","author":[{"full_name":"Mosalaganti, Shyamal","last_name":"Mosalaganti","first_name":"Shyamal"},{"first_name":"Agnieszka","full_name":"Obarska-Kosinska, Agnieszka","last_name":"Obarska-Kosinska"},{"first_name":"Marc","full_name":"Siggel, Marc","last_name":"Siggel"},{"last_name":"Taniguchi","full_name":"Taniguchi, Reiya","first_name":"Reiya"},{"full_name":"Turoňová, Beata","last_name":"Turoňová","first_name":"Beata"},{"full_name":"Zimmerli, Christian E.","last_name":"Zimmerli","first_name":"Christian E."},{"first_name":"Katarzyna","last_name":"Buczak","full_name":"Buczak, Katarzyna"},{"id":"A2EF226A-AF19-11E9-924C-0525E6697425","first_name":"Florian","full_name":"Schmidt, Florian","last_name":"Schmidt"},{"last_name":"Margiotta","full_name":"Margiotta, Erica","first_name":"Erica"},{"last_name":"Mackmull","full_name":"Mackmull, Marie-Therese","first_name":"Marie-Therese"},{"last_name":"Hagen","full_name":"Hagen, Wim J. H.","first_name":"Wim J. H."},{"last_name":"Hummer","full_name":"Hummer, Gerhard","first_name":"Gerhard"},{"full_name":"Kosinski, Jan","last_name":"Kosinski","first_name":"Jan"},{"full_name":"Beck, Martin","last_name":"Beck","first_name":"Martin"}],"department":[{"_id":"MaJö"}]},{"fulldoi":"https://doi.org/10.1126/sciadv.abl6293","article_type":"original","author":[{"first_name":"Mohsin M.","last_name":"Naqvi","full_name":"Naqvi, Mohsin M."},{"id":"DC4BA84C-56E6-11EA-AD5D-348C3DDC885E","first_name":"Mario","orcid":"0000-0001-6406-524X","last_name":"Avellaneda Sarrió","full_name":"Avellaneda Sarrió, Mario"},{"first_name":"Andrew","last_name":"Roth","full_name":"Roth, Andrew"},{"first_name":"Eline J.","full_name":"Koers, Eline J.","last_name":"Koers"},{"last_name":"Roland","full_name":"Roland, Antoine","first_name":"Antoine"},{"first_name":"Vanda","full_name":"Sunderlikova, Vanda","last_name":"Sunderlikova"},{"full_name":"Kramer, Günter","last_name":"Kramer","first_name":"Günter"},{"full_name":"Rye, Hays S.","last_name":"Rye","first_name":"Hays S."},{"first_name":"Sander J.","full_name":"Tans, Sander J.","last_name":"Tans"}],"department":[{"_id":"MiSi"}],"publication_identifier":{"issn":["2375-2548"]},"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)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","day":"01","has_accepted_license":"1","file_date_updated":"2024-07-31T12:01:51Z","type":"journal_article","publication_status":"published","status":"public","date_published":"2022-03-01T00:00:00Z","abstract":[{"lang":"eng","text":"The collapse of polypeptides is thought important to protein folding, aggregation, intrinsic disorder, and phase separation. However, whether polypeptide collapse is modulated in cells to control protein states is unclear. Here, using integrated protein manipulation and imaging, we show that the chaperonin GroEL-ES can accelerate the folding of proteins by strengthening their collapse. GroEL induces contractile forces in substrate chains, which draws them into the cavity and triggers a general compaction and discrete folding transitions, even for slow-folding proteins. This collapse enhancement is strongest in the nucleotide-bound states of GroEL and is aided by GroES binding to the cavity rim and by the amphiphilic C-terminal tails at the cavity bottom. Collapse modulation is distinct from other proposed GroEL-ES folding acceleration mechanisms, including steric confinement and misfold unfolding. Given the prevalence of collapse throughout the proteome, we conjecture that collapse modulation is more generally relevant within the protein quality control machinery."}],"article_processing_charge":"Yes","year":"2022","publisher":"American Association for the Advancement of Science","month":"03","volume":8,"_id":"17072","publication":"Science Advances","file":[{"checksum":"9511579306cce7e04107d3d6389ed614","creator":"dernst","success":1,"file_name":"2022_ScienceAdv_Naqvi.pdf","relation":"main_file","content_type":"application/pdf","file_id":"17357","file_size":2404150,"date_updated":"2024-07-31T12:01:51Z","access_level":"open_access","date_created":"2024-07-31T12:01:51Z"}],"citation":{"apa":"Naqvi, M. M., Avellaneda Sarrió, M., Roth, A., Koers, E. J., Roland, A., Sunderlikova, V., … Tans, S. J. (2022). Protein chain collapse modulation and folding stimulation by GroEL-ES. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.abl6293","chicago":"Naqvi, Mohsin M., Mario Avellaneda Sarrió, Andrew Roth, Eline J. Koers, Antoine Roland, Vanda Sunderlikova, Günter Kramer, Hays S. Rye, and Sander J. Tans. “Protein Chain Collapse Modulation and Folding Stimulation by GroEL-ES.” Science Advances. American Association for the Advancement of Science, 2022. https://doi.org/10.1126/sciadv.abl6293.","ama":"Naqvi MM, Avellaneda Sarrió M, Roth A, et al. Protein chain collapse modulation and folding stimulation by GroEL-ES. Science Advances. 2022;8(9). doi:10.1126/sciadv.abl6293","mla":"Naqvi, Mohsin M., et al. “Protein Chain Collapse Modulation and Folding Stimulation by GroEL-ES.” Science Advances, vol. 8, no. 9, eabl6293, American Association for the Advancement of Science, 2022, doi:10.1126/sciadv.abl6293.","ieee":"M. M. Naqvi et al., “Protein chain collapse modulation and folding stimulation by GroEL-ES,” Science Advances, vol. 8, no. 9. American Association for the Advancement of Science, 2022.","ista":"Naqvi MM, Avellaneda Sarrió M, Roth A, Koers EJ, Roland A, Sunderlikova V, Kramer G, Rye HS, Tans SJ. 2022. Protein chain collapse modulation and folding stimulation by GroEL-ES. Science Advances. 8(9), eabl6293.","short":"M.M. Naqvi, M. Avellaneda Sarrió, A. Roth, E.J. Koers, A. Roland, V. Sunderlikova, G. Kramer, H.S. Rye, S.J. Tans, Science Advances 8 (2022)."},"oa":1,"title":"Protein chain collapse modulation and folding stimulation by GroEL-ES","scopus_import":"1","date_updated":"2024-08-05T08:30:29Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"doi":"10.1126/sciadv.abl6293","ddc":["570"],"intvolume":" 8","pmid":1,"external_id":{"pmid":["35245117"]},"issue":"9","article_number":"eabl6293","acknowledgement":"We thank A. L. Horwich, K. Chakraborty, and B. Schuler for providing plasmids, and R. van Leeuwen, M. Mayer, J. van Zon, W. Noorduin, and P. R. ten Wolde for comments and critical reading of the manuscript. Work in the group of S.J.T. was supported by the Netherlands Organization for Scientific Research (NWO). Work in the group of H.S.R. was supported by a grant from the NIH (R01GM114405).","date_created":"2024-05-29T06:12:19Z","quality_controlled":"1"},{"day":"22","place":"Cham","publication_identifier":{"eisbn":["9783030677275"],"isbn":["9783030677268"]},"oa_version":"None","author":[{"last_name":"Palacín","full_name":"Palacín, Manuel","first_name":"Manuel"},{"last_name":"Bröer","full_name":"Bröer, Stefan","first_name":"Stefan"},{"orcid":"0000-0002-7673-7178","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","last_name":"Novarino"}],"department":[{"_id":"GaNo"}],"fulldoi":"https://doi.org/10.1007/978-3-030-67727-5_18","month":"02","abstract":[{"text":"Disorders associated with the malfunction of amino acid transporters mainly affect the function of the intestine, kidney, brain, and liver. Mutations of brain amino acid transporters, for example, alter neuronal excitability (e.g., episodic ataxia due to SLC1A3 (EAAT1) defect and hyperekplexia due to SLC6A5 (GLYT2) deficiency) or brain development (SLC1A1 (EAAT3), SLC3A2/SLC7A5 (CD98hc/LAT1), and SLC1A4 (ASCT1) deficiencies). Mutations of renal and intestinal amino acid transporters SLC3A1/SLC7A9 (rBAT/b0,+AT) and SLC1A1 (EAAT3) cause renal problems (cystinuria and dicarboxylic aminoaciduria, respectively) and malabsorption that can affect whole-body homoeostasis (Hartnup disorder SLC6A19 (B0AT1), lysinuric protein intolerance SLC3A2/SLC7A7 (CD98hc/y+LAT1), and hyperdibasic aminoaciduria type 1). Mutations in the neuronal system A amino acid transporter SLC38A8 (SNAT8) cause eye developmental and visual defects. Inborn errors associated with mitochondrial SLC25 family members such as SLC25A12 (neuronal- and muscle-specific mitochondrial aspartate/glutamate transporter 1; AGC1) (global cerebral hypomyelination), SLC25A13 (aspartate/glutamate transporter 2) (citrin deficiency), SLC25A15 (ornithine-citrulline carrier 2) (homocitrullinuria, hyperornithinemia, and hyperammonemia syndrome), and SLC25A22 (mitochondrial glutamate/H+ symporter 1, GC1) (neonatal myoclonic epilepsy) will be dealt within Chap. 43 (defects of mitochondrial carriers).","lang":"eng"}],"article_processing_charge":"No","year":"2022","publisher":"Springer Nature","publication_status":"published","date_published":"2022-02-22T00:00:00Z","status":"public","type":"book_chapter","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Amino Acid Transport Defects","scopus_import":"1","date_updated":"2024-07-31T11:45:50Z","publication":"Physician's Guide to the Diagnosis, Treatment, and Follow-Up of Inherited Metabolic Diseases","citation":{"mla":"Palacín, Manuel, et al. “Amino Acid Transport Defects.” Physician’s Guide to the Diagnosis, Treatment, and Follow-Up of Inherited Metabolic Diseases, edited by Nenad Blau et al., 2nd ed., Springer Nature, 2022, pp. 291–312, doi:10.1007/978-3-030-67727-5_18.","ieee":"M. Palacín, S. Bröer, and G. Novarino, “Amino Acid Transport Defects,” in Physician’s Guide to the Diagnosis, Treatment, and Follow-Up of Inherited Metabolic Diseases, 2nd ed., N. Blau, C. D. Vici, C. R. Ferreira, C. Vianey-Saban, and C. D. M. van Karnebeek, Eds. Cham: Springer Nature, 2022, pp. 291–312.","ista":"Palacín M, Bröer S, Novarino G. 2022.Amino Acid Transport Defects. In: Physician’s Guide to the Diagnosis, Treatment, and Follow-Up of Inherited Metabolic Diseases. , 291–312.","short":"M. Palacín, S. Bröer, G. Novarino, in:, N. Blau, C.D. Vici, C.R. Ferreira, C. Vianey-Saban, C.D.M. van Karnebeek (Eds.), Physician’s Guide to the Diagnosis, Treatment, and Follow-Up of Inherited Metabolic Diseases, 2nd ed., Springer Nature, Cham, 2022, pp. 291–312.","apa":"Palacín, M., Bröer, S., & Novarino, G. (2022). Amino Acid Transport Defects. In N. Blau, C. D. Vici, C. R. Ferreira, C. Vianey-Saban, & C. D. M. van Karnebeek (Eds.), Physician’s Guide to the Diagnosis, Treatment, and Follow-Up of Inherited Metabolic Diseases (2nd ed., pp. 291–312). Cham: Springer Nature. https://doi.org/10.1007/978-3-030-67727-5_18","chicago":"Palacín, Manuel, Stefan Bröer, and Gaia Novarino. “Amino Acid Transport Defects.” In Physician’s Guide to the Diagnosis, Treatment, and Follow-Up of Inherited Metabolic Diseases, edited by Nenad Blau, Carlo Dionisi Vici, Carlos R. Ferreira, Christine Vianey-Saban, and Clara D.M. van Karnebeek, 2nd ed., 291–312. Cham: Springer Nature, 2022. https://doi.org/10.1007/978-3-030-67727-5_18.","ama":"Palacín M, Bröer S, Novarino G. Amino Acid Transport Defects. In: Blau N, Vici CD, Ferreira CR, Vianey-Saban C, van Karnebeek CDM, eds. Physician’s Guide to the Diagnosis, Treatment, and Follow-Up of Inherited Metabolic Diseases. 2nd ed. Cham: Springer Nature; 2022:291-312. doi:10.1007/978-3-030-67727-5_18"},"_id":"17075","page":"291-312","acknowledgement":"The authors thank Dr. Christian Lueck (Canberra Hospital) for clarification of differential diagnosis in cases of episodic ataxia. The authors thank Dr. Rafael Artuch (Hospital San Joan de Deu, Barcelona) for reference values of plasma amino acid concentration. The authors also thank Lisa Kraus (Institute of Science and Technology-Austria) and Dr. Susanna Bodoy (IRB-Barcelona) that helped in preparing tables and bibliography.","date_created":"2024-05-29T06:13:04Z","quality_controlled":"1","editor":[{"full_name":"Blau, Nenad","last_name":"Blau","first_name":"Nenad"},{"last_name":"Vici","full_name":"Vici, Carlo Dionisi","first_name":"Carlo Dionisi"},{"first_name":"Carlos R. ","last_name":"Ferreira","full_name":"Ferreira, Carlos R. "},{"first_name":"Christine","last_name":"Vianey-Saban","full_name":"Vianey-Saban, Christine"},{"last_name":"van Karnebeek","full_name":"van Karnebeek, Clara D.M.","first_name":"Clara D.M."}],"language":[{"iso":"eng"}],"doi":"10.1007/978-3-030-67727-5_18","edition":"2"},{"external_id":{"arxiv":["2105.13337"]},"issue":"10","acknowledgement":"We thank the referees for extensive comments which helped improve the paper substantially.\r\nThe first author was supported in part by NSF grants DMS-1954395 and DMS-1953799. The second author was supported by NSF grant DMS-1953990. The third author was supported by NSF grant DMS180052. The fourth and fifth authors were both supported by NSF Graduate Research Fellowship Program DGE-1745302.","date_created":"2024-05-29T06:13:37Z","quality_controlled":"1","language":[{"iso":"eng"}],"doi":"10.1090/cams/13","ddc":["500"],"intvolume":" 2","license":"https://creativecommons.org/licenses/by/3.0/","title":"Friendly bisections of random graphs","oa":1,"date_updated":"2024-07-15T08:06:05Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":2,"_id":"17077","page":"380-416","publication":"Communications of the American Mathematical Society","citation":{"short":"A. Ferber, M.A. Kwan, B. Narayanan, A. Sah, M. Sawhney, Communications of the American Mathematical Society 2 (2022) 380–416.","ista":"Ferber A, Kwan MA, Narayanan B, Sah A, Sawhney M. 2022. Friendly bisections of random graphs. Communications of the American Mathematical Society. 2(10), 380–416.","mla":"Ferber, Asaf, et al. “Friendly Bisections of Random Graphs.” Communications of the American Mathematical Society, vol. 2, no. 10, American Mathematical Society, 2022, pp. 380–416, doi:10.1090/cams/13.","ieee":"A. Ferber, M. A. Kwan, B. Narayanan, A. Sah, and M. Sawhney, “Friendly bisections of random graphs,” Communications of the American Mathematical Society, vol. 2, no. 10. American Mathematical Society, pp. 380–416, 2022.","ama":"Ferber A, Kwan MA, Narayanan B, Sah A, Sawhney M. Friendly bisections of random graphs. Communications of the American Mathematical Society. 2022;2(10):380-416. doi:10.1090/cams/13","chicago":"Ferber, Asaf, Matthew Alan Kwan, Bhargav Narayanan, Ashwin Sah, and Mehtaab Sawhney. “Friendly Bisections of Random Graphs.” Communications of the American Mathematical Society. American Mathematical Society, 2022. https://doi.org/10.1090/cams/13.","apa":"Ferber, A., Kwan, M. A., Narayanan, B., Sah, A., & Sawhney, M. (2022). Friendly bisections of random graphs. Communications of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/cams/13"},"arxiv":1,"file":[{"date_updated":"2024-07-12T12:55:02Z","file_size":335965,"file_id":"17230","file_name":"2022_CommAMS_Ferber.pdf","content_type":"application/pdf","relation":"main_file","date_created":"2024-07-12T12:55:02Z","access_level":"open_access","creator":"cchlebak","checksum":"719861e76f5bce3d0362d8171daa26fc","success":1}],"abstract":[{"text":"Resolving a conjecture of Füredi from 1988, we prove that with high probability, the random graph 𝔾(𝑛, 1/2) admits a friendly bisection of its vertex set, i.e., a\r\npartition of its vertex set into two parts whose sizes differ by at most one in which\r\n𝑛 − 𝑜(𝑛) vertices have more neighbours in their own part as across. Our proof is constructive, and in the process, we develop a new method to study stochastic processes\r\ndriven by degree information in random graphs; this involves combining enumeration\r\ntechniques with an abstract second moment argument.","lang":"eng"}],"publisher":"American Mathematical Society","year":"2022","article_processing_charge":"No","month":"12","file_date_updated":"2024-07-12T12:55:02Z","type":"journal_article","publication_status":"published","status":"public","date_published":"2022-12-20T00:00:00Z","publication_identifier":{"issn":["2692-3688"]},"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","short":"CC BY (3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode"},"oa_version":"Published Version","has_accepted_license":"1","day":"20","fulldoi":"https://doi.org/10.1090/cams/13","corr_author":"1","article_type":"original","department":[{"_id":"MaKw"}],"author":[{"full_name":"Ferber, Asaf","last_name":"Ferber","first_name":"Asaf"},{"first_name":"Matthew Alan","orcid":"0000-0002-4003-7567","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","last_name":"Kwan","full_name":"Kwan, Matthew Alan"},{"first_name":"Bhargav","full_name":"Narayanan, Bhargav","last_name":"Narayanan"},{"full_name":"Sah, Ashwin","last_name":"Sah","first_name":"Ashwin"},{"first_name":"Mehtaab","full_name":"Sawhney, Mehtaab","last_name":"Sawhney"}]},{"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","year":"2022","article_processing_charge":"Yes","abstract":[{"text":"Given a graph where every vertex has exactly one labeled token, how can we most quickly execute a given permutation on the tokens? In (sequential) token swapping, the goal is to use the shortest possible sequence of swaps, each of which exchanges the tokens at the two endpoints of an edge of the graph. In parallel token swapping, the goal is to use the fewest rounds, each of which consists of one or more swaps on the edges of a matching. We prove that both of these problems remain NP-hard when the graph is restricted to be a tree. These token swapping problems have been studied by disparate groups of researchers in discrete mathematics, theoretical computer science, robot motion planning, game theory, and engineering. Previous work establishes NP-completeness on general graphs (for both problems), constant-factor approximation algorithms, and some poly-time exact algorithms for simple graph classes such as cliques, stars, paths, and cycles. Sequential and parallel token swapping on trees were first studied over thirty years ago (as \"sorting with a transposition tree\") and over twenty-five years ago (as \"routing permutations via matchings\"), yet their complexities were previously unknown. We also show limitations on approximation of sequential token swapping on trees: we identify a broad class of algorithms that encompass all three known polynomial-time algorithms that achieve the best known approximation factor (which is 2) and show that no such algorithm can achieve an approximation factor less than 2.","lang":"eng"}],"project":[{"grant_number":"Z00342","_id":"268116B8-B435-11E9-9278-68D0E5697425","name":"Mathematics, Computer Science","call_identifier":"FWF"}],"conference":{"end_date":"2022-09-09","start_date":"2022-09-05","location":"Berlin/Potsdam, Germany","name":"ESA: European Symposium on Algorithms"},"month":"09","type":"conference","file_date_updated":"2024-08-12T08:51:44Z","date_published":"2022-09-01T00:00:00Z","status":"public","publication_status":"published","oa_version":"Published Version","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)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"day":"01","has_accepted_license":"1","fulldoi":"https://doi.org/10.4230/LIPIcs.ESA.2022.3","corr_author":"1","department":[{"_id":"HeEd"},{"_id":"UlWa"}],"author":[{"full_name":"Aichholzer, Oswin","last_name":"Aichholzer","first_name":"Oswin"},{"first_name":"Erik D.","full_name":"Demaine, Erik D.","last_name":"Demaine"},{"first_name":"Matias","last_name":"Korman","full_name":"Korman, Matias"},{"full_name":"Lubiw, Anna","last_name":"Lubiw","first_name":"Anna"},{"first_name":"Jayson","last_name":"Lynch","full_name":"Lynch, Jayson"},{"full_name":"Masárová, Zuzana","last_name":"Masárová","id":"45CFE238-F248-11E8-B48F-1D18A9856A87","first_name":"Zuzana","orcid":"0000-0002-6660-1322"},{"first_name":"Mikhail","last_name":"Rudoy","full_name":"Rudoy, Mikhail"},{"first_name":"Virginia","last_name":"Vassilevska Williams","full_name":"Vassilevska Williams, Virginia"},{"first_name":"Nicole","last_name":"Wein","full_name":"Wein, Nicole"}],"alternative_title":["LIPIcs"],"article_number":"3","external_id":{"arxiv":["2103.06707"]},"quality_controlled":"1","date_created":"2024-05-29T06:27:16Z","acknowledgement":"g Anna Lubiw: Supported by the Natural Sciences and Engineering Research Council of\r\nCanada (NSERC). Jayson Lynch: Supported by the Natural Sciences and Engineering Research Council of Canada (NSERC). Zuzana Masárová: Supported by Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31. Virginia Vassilevska Williams: Supported by an NSF CAREER Award, NSF Grants CCF-1528078, CCF-1514339 and CCF-1909429, a BSF Grant BSF:2012338, a Google Research Fellowship and a Sloan Research Fellowship.\r\nNicole Wein: Supported by a grant to DIMACS from the Simons Foundation (820931). This work was done while the author was at MIT.\r\nThis research was initiated at the 34th Bellairs Winter Workshop on Computational Geometry, co-organized by Erik Demaine and Godfried Toussaint, held on March 22–29,\r\n2019 in Holetown, Barbados. We thank the other participants of that workshop for providing a\r\nstimulating research environment.","doi":"10.4230/LIPIcs.ESA.2022.3","language":[{"iso":"eng"}],"intvolume":" 244","ddc":["510"],"date_updated":"2025-04-15T07:16:56Z","scopus_import":"1","oa":1,"title":"Hardness of token swapping on trees","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":244,"_id":"17084","file":[{"date_updated":"2024-08-12T08:51:44Z","file_name":"2022_LIPIcS_Aichholzer.pdf","content_type":"application/pdf","relation":"main_file","file_id":"17420","file_size":1406071,"access_level":"open_access","date_created":"2024-08-12T08:51:44Z","creator":"dernst","checksum":"a1fbd3e7baad510fbcb998cf4a7d9f7f","success":1}],"arxiv":1,"citation":{"apa":"Aichholzer, O., Demaine, E. D., Korman, M., Lubiw, A., Lynch, J., Masárová, Z., … Wein, N. (2022). Hardness of token swapping on trees. In 30th Annual European Symposium on Algorithms (Vol. 244). Berlin/Potsdam, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ESA.2022.3","chicago":"Aichholzer, Oswin, Erik D. Demaine, Matias Korman, Anna Lubiw, Jayson Lynch, Zuzana Masárová, Mikhail Rudoy, Virginia Vassilevska Williams, and Nicole Wein. “Hardness of Token Swapping on Trees.” In 30th Annual European Symposium on Algorithms, Vol. 244. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022. https://doi.org/10.4230/LIPIcs.ESA.2022.3.","ama":"Aichholzer O, Demaine ED, Korman M, et al. Hardness of token swapping on trees. In: 30th Annual European Symposium on Algorithms. Vol 244. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2022. doi:10.4230/LIPIcs.ESA.2022.3","ieee":"O. Aichholzer et al., “Hardness of token swapping on trees,” in 30th Annual European Symposium on Algorithms, Berlin/Potsdam, Germany, 2022, vol. 244.","mla":"Aichholzer, Oswin, et al. “Hardness of Token Swapping on Trees.” 30th Annual European Symposium on Algorithms, vol. 244, 3, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022, doi:10.4230/LIPIcs.ESA.2022.3.","ista":"Aichholzer O, Demaine ED, Korman M, Lubiw A, Lynch J, Masárová Z, Rudoy M, Vassilevska Williams V, Wein N. 2022. Hardness of token swapping on trees. 30th Annual European Symposium on Algorithms. ESA: European Symposium on Algorithms, LIPIcs, vol. 244, 3.","short":"O. Aichholzer, E.D. Demaine, M. Korman, A. Lubiw, J. Lynch, Z. Masárová, M. Rudoy, V. Vassilevska Williams, N. Wein, in:, 30th Annual European Symposium on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022."},"publication":"30th Annual European Symposium on Algorithms"},{"oa_version":"Published Version","publication_identifier":{"isbn":["9781839697500"]},"day":"23","fulldoi":"https://doi.org/10.5772/intechopen.100535","ec_funded":1,"author":[{"first_name":"Jordi","full_name":"Floriach-Clark, Jordi","last_name":"Floriach-Clark"},{"full_name":"Tang, Han","last_name":"Tang","first_name":"Han","orcid":"0000-0001-6152-6637","id":"19BDF720-25A0-11EA-AC6E-928F3DDC885E"},{"first_name":"Viola","full_name":"Willemsen, Viola","last_name":"Willemsen"}],"department":[{"_id":"JiFr"}],"year":"2022","article_processing_charge":"No","publisher":"IntechOpen","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"}],"abstract":[{"lang":"eng","text":"Mosses are a cosmopolitan group of land plants, sister to vascular plants, with a high potential for molecular and cell biological research. The species Physcomitrium patens has helped gaining better understanding of the biological processes of the plant cell, and it has become a central system to understand water-to-land plant transition through 2D-to-3D growth transition, regulation of asymmetric cell division, shoot apical cell establishment and maintenance, phyllotaxis and regeneration. P. patens was the first fully sequenced moss in 2008, with the latest annotated release in 2018. It has been shown that many gene functions and networks are conserved in mosses when compared to angiosperms. Importantly, this model organism has a simplified and accessible body structure that facilitates close tracking in time and space with the support of live cell imaging set-ups and multiple reporter lines. This has become possible thanks to its fully established molecular toolkit, with highly efficient PEG-assisted, CRISPR/Cas9 and RNAi transformation and silencing protocols, among others. Here we provide examples on how mosses exhibit advantages over vascular plants to study several processes and their future potential to answer some other outstanding questions in plant cell biology."}],"month":"06","type":"book_chapter","date_published":"2022-06-23T00:00:00Z","status":"public","publication_status":"published","date_updated":"2026-06-18T17:52:59Z","oa":1,"title":"Mosses: Accessible Systems for Plant Development Studies","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5772/intechopen.100535"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"17085","citation":{"mla":"Floriach-Clark, Jordi, et al. “Mosses: Accessible Systems for Plant Development Studies.” Model Organisms in Plant Genetics, edited by Ibrokhim Y. Abdurakhmonov, IntechOpen, 2022, doi:10.5772/intechopen.100535.","ieee":"J. Floriach-Clark, H. Tang, and V. Willemsen, “Mosses: Accessible Systems for Plant Development Studies,” in Model Organisms in Plant Genetics, I. Y. Abdurakhmonov, Ed. IntechOpen, 2022.","short":"J. Floriach-Clark, H. Tang, V. Willemsen, in:, I.Y. Abdurakhmonov (Ed.), Model Organisms in Plant Genetics, IntechOpen, 2022.","ista":"Floriach-Clark J, Tang H, Willemsen V. 2022.Mosses: Accessible Systems for Plant Development Studies. In: Model Organisms in Plant Genetics. .","apa":"Floriach-Clark, J., Tang, H., & Willemsen, V. (2022). Mosses: Accessible Systems for Plant Development Studies. In I. Y. Abdurakhmonov (Ed.), Model Organisms in Plant Genetics. IntechOpen. https://doi.org/10.5772/intechopen.100535","ama":"Floriach-Clark J, Tang H, Willemsen V. Mosses: Accessible Systems for Plant Development Studies. In: Abdurakhmonov IY, ed. Model Organisms in Plant Genetics. IntechOpen; 2022. doi:10.5772/intechopen.100535","chicago":"Floriach-Clark, Jordi, Han Tang, and Viola Willemsen. “Mosses: Accessible Systems for Plant Development Studies.” In Model Organisms in Plant Genetics, edited by Ibrokhim Y. Abdurakhmonov. IntechOpen, 2022. https://doi.org/10.5772/intechopen.100535."},"publication":"Model Organisms in Plant Genetics","quality_controlled":"1","editor":[{"first_name":"Ibrokhim Y.","last_name":"Abdurakhmonov","full_name":"Abdurakhmonov, Ibrokhim Y."}],"date_created":"2024-05-29T06:35:13Z","acknowledgement":"The authors would like to thank Dr. Jeroen de Keijzer and Dr. Tijs Ketelaar for their thoughtful and detailed review of the manuscript. Also, the funding agencies Technology, Knowledge and Innovation, division Horticulture and Propagating Material (TKI T&U) and the Dutch Research Council (NWO) (reference number: TKILWV20.390) for funding JFC and the ERC grant to Prof. J. Friml (reference number: PR1023ERC02) for funding HT. The authors would like to sincerely apologise for the literature not cited that may be relevant for this chapter and is not present due to space constraints.","doi":"10.5772/intechopen.100535","language":[{"iso":"eng"}],"ddc":["580"]},{"corr_author":"1","alternative_title":["NeurIPS"],"author":[{"last_name":"Zhang","full_name":"Zhang, Yihan","orcid":"0000-0002-6465-6258","first_name":"Yihan","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c"},{"first_name":"Nir","last_name":"Weinberger","full_name":"Weinberger, Nir"}],"department":[{"_id":"MaMo"}],"publication_identifier":{"isbn":["9781713871088"]},"oa_version":"Published Version","day":"01","has_accepted_license":"1","file_date_updated":"2024-08-05T09:44:49Z","type":"conference","publication_status":"published","date_published":"2022-12-01T00:00:00Z","status":"public","conference":{"name":"NeurIPS: Neural Information Processing Systems","location":"New Orleans, LA, United States","end_date":"2022-12-09","start_date":"2022-11-28"},"abstract":[{"lang":"eng","text":"We consider a high-dimensional mean estimation problem over a binary hidden Markov model, which illuminates the interplay between memory in data, sample size, dimension, and signal strength in statistical inference. In this model, an estimator observes n samples of a d-dimensional parameter vector θ∗∈Rd, multiplied by a random sign Si (1≤i≤n), and corrupted by isotropic standard Gaussian noise. The sequence of signs {Si}i∈[n]∈{−1,1}n is drawn from a stationary homogeneous Markov chain with flip probability δ∈[0,1/2]. As δ varies, this model smoothly interpolates two well-studied models: the Gaussian Location Model for which δ=0 and the Gaussian Mixture Model for which δ=1/2. Assuming that the estimator knows δ, we establish a nearly minimax optimal (up to logarithmic factors) estimation error rate, as a function of ∥θ∗∥,δ,d,n. We then provide an upper bound to the case of estimating δ, assuming a (possibly inaccurate) knowledge of θ∗. The bound is proved to be tight when θ∗ is an accurately known constant. These results are then combined to an algorithm which estimates θ∗ with δ unknown a priori, and theoretical guarantees on its error are stated."}],"article_processing_charge":"No","year":"2022","publisher":"ML Research Press","month":"12","volume":35,"_id":"17086","publication":"36th Conference on Neural Information Processing Systems","arxiv":1,"citation":{"ieee":"Y. Zhang and N. Weinberger, “Mean estimation in high-dimensional binary Markov Gaussian mixture models,” in 36th Conference on Neural Information Processing Systems, New Orleans, LA, United States, 2022, vol. 35.","mla":"Zhang, Yihan, and Nir Weinberger. “Mean Estimation in High-Dimensional Binary Markov Gaussian Mixture Models.” 36th Conference on Neural Information Processing Systems, vol. 35, ML Research Press, 2022.","short":"Y. Zhang, N. Weinberger, in:, 36th Conference on Neural Information Processing Systems, ML Research Press, 2022.","ista":"Zhang Y, Weinberger N. 2022. Mean estimation in high-dimensional binary Markov Gaussian mixture models. 36th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, NeurIPS, vol. 35.","apa":"Zhang, Y., & Weinberger, N. (2022). Mean estimation in high-dimensional binary Markov Gaussian mixture models. In 36th Conference on Neural Information Processing Systems (Vol. 35). New Orleans, LA, United States: ML Research Press.","ama":"Zhang Y, Weinberger N. Mean estimation in high-dimensional binary Markov Gaussian mixture models. In: 36th Conference on Neural Information Processing Systems. Vol 35. ML Research Press; 2022.","chicago":"Zhang, Yihan, and Nir Weinberger. “Mean Estimation in High-Dimensional Binary Markov Gaussian Mixture Models.” In 36th Conference on Neural Information Processing Systems, Vol. 35. ML Research Press, 2022."},"file":[{"file_size":476307,"file_id":"17392","relation":"main_file","content_type":"application/pdf","file_name":"2022_NeurIPS_Zhang.pdf","date_updated":"2024-08-05T09:44:49Z","date_created":"2024-08-05T09:44:49Z","access_level":"open_access","checksum":"05f6f9f8fc34e224e0cad045b9489030","creator":"dernst","success":1}],"title":"Mean estimation in high-dimensional binary Markov Gaussian mixture models","oa":1,"scopus_import":"1","date_updated":"2024-08-05T09:48:58Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"ddc":["000"],"intvolume":" 35","external_id":{"arxiv":["2206.02455"]},"acknowledgement":"Part of this work was done when YZ was a postdoc at Technion where he received funding from\r\nthe European Union’s Horizon 2020 research and innovation programme under grant agreement No 682203-ERC-[Inf-Speed-Tradeoff]. The work of of NW was supported in part by the Israel Science Foundation (ISF) under Grant 1782/22. NW is grateful to Guy Bresler for introducing him to this problem, for the initial ideas that led to this research, and for many helpful discussions on the topic.","date_created":"2024-05-29T06:37:16Z","quality_controlled":"1"},{"doi":"10.18653/v1/2022.emnlp-main.279","language":[{"iso":"eng"}],"ddc":["000"],"external_id":{"arxiv":["2203.07259"]},"quality_controlled":"1","date_created":"2024-05-29T06:40:55Z","page":"4163-4181","_id":"17088","file":[{"access_level":"open_access","date_created":"2024-07-31T11:03:34Z","file_name":"2022_EMNLP_Kurtic.pdf","content_type":"application/pdf","relation":"main_file","file_size":522563,"file_id":"17354","date_updated":"2024-07-31T11:03:34Z","success":1,"checksum":"c47b9edd8a9f743ac77a593de6d2e84a","creator":"dernst"}],"citation":{"ama":"Kurtic E, Campos D, Nguyen T, et al. The optimal BERT surgeon: Scalable and accurate second-order pruning for large language models. In: Proceedings of the 2022 Conference on Empirical Methods in Natural Language Processing. Association for Computational Linguistics; 2022:4163-4181. doi:10.18653/v1/2022.emnlp-main.279","chicago":"Kurtic, Eldar, Daniel Campos, Tuan Nguyen, Elias Frantar, Mark Kurtz, Benjamin Fineran, Michael Goin, and Dan-Adrian Alistarh. “The Optimal BERT Surgeon: Scalable and Accurate Second-Order Pruning for Large Language Models.” In Proceedings of the 2022 Conference on Empirical Methods in Natural Language Processing, 4163–81. Association for Computational Linguistics, 2022. https://doi.org/10.18653/v1/2022.emnlp-main.279.","apa":"Kurtic, E., Campos, D., Nguyen, T., Frantar, E., Kurtz, M., Fineran, B., … Alistarh, D.-A. (2022). The optimal BERT surgeon: Scalable and accurate second-order pruning for large language models. In Proceedings of the 2022 Conference on Empirical Methods in Natural Language Processing (pp. 4163–4181). Abu Dhabi, United Arab Emirates: Association for Computational Linguistics. https://doi.org/10.18653/v1/2022.emnlp-main.279","short":"E. Kurtic, D. Campos, T. Nguyen, E. Frantar, M. Kurtz, B. Fineran, M. Goin, D.-A. Alistarh, in:, Proceedings of the 2022 Conference on Empirical Methods in Natural Language Processing, Association for Computational Linguistics, 2022, pp. 4163–4181.","ista":"Kurtic E, Campos D, Nguyen T, Frantar E, Kurtz M, Fineran B, Goin M, Alistarh D-A. 2022. The optimal BERT surgeon: Scalable and accurate second-order pruning for large language models. Proceedings of the 2022 Conference on Empirical Methods in Natural Language Processing. EMNLP: Conference on Empirical Methods in Natural Language Processing, 4163–4181.","ieee":"E. Kurtic et al., “The optimal BERT surgeon: Scalable and accurate second-order pruning for large language models,” in Proceedings of the 2022 Conference on Empirical Methods in Natural Language Processing, Abu Dhabi, United Arab Emirates, 2022, pp. 4163–4181.","mla":"Kurtic, Eldar, et al. “The Optimal BERT Surgeon: Scalable and Accurate Second-Order Pruning for Large Language Models.” Proceedings of the 2022 Conference on Empirical Methods in Natural Language Processing, Association for Computational Linguistics, 2022, pp. 4163–81, doi:10.18653/v1/2022.emnlp-main.279."},"arxiv":1,"publication":"Proceedings of the 2022 Conference on Empirical Methods in Natural Language Processing","date_updated":"2024-07-31T11:05:32Z","scopus_import":"1","oa":1,"title":"The optimal BERT surgeon: Scalable and accurate second-order pruning for large language models","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","file_date_updated":"2024-07-31T11:03:34Z","status":"public","date_published":"2022-12-01T00:00:00Z","publication_status":"published","publisher":"Association for Computational Linguistics","year":"2022","article_processing_charge":"Yes","abstract":[{"lang":"eng","text":"In this paper, we consider the problem of sparsifying BERT models, which are a key building block for natural language processing, in order to reduce their storage and computational cost. We introduce the Optimal BERT Surgeon (oBERT), an efficient and accurate pruning method based on approximate second-order information, which we show to yield state-of-the-art results in both stages of language tasks: pre-training and fine-tuning. Specifically, oBERT extends existing work on second-order pruning by allowing for pruning weight blocks, and is the first such method that is applicable at BERT scale. Second, we investigate compounding compression approaches to obtain highly compressed but accurate models for deployment on edge devices. These models significantly push boundaries of the current state-of-the-art sparse BERT models with respect to all metrics: model size, inference speed and task accuracy. For example, relative to the dense BERT-base, we obtain 10x model size compression with < 1% accuracy drop, 10x CPU-inference speedup with < 2% accuracy drop, and 29x CPU-inference speedup with < 7.5% accuracy drop. Our code, fully integrated with Transformers and SparseML, is available at https://github.com/neuralmagic/sparseml/tree/main/research/optimal_BERT_surgeon_oBERT."}],"conference":{"location":"Abu Dhabi, United Arab Emirates","end_date":"2022-12-11","start_date":"2022-12-07","name":"EMNLP: Conference on Empirical Methods in Natural Language Processing"},"month":"12","fulldoi":"https://doi.org/10.18653/v1/2022.emnlp-main.279","corr_author":"1","author":[{"last_name":"Kurtic","full_name":"Kurtic, Eldar","id":"47beb3a5-07b5-11eb-9b87-b108ec578218","first_name":"Eldar"},{"full_name":"Campos, Daniel","last_name":"Campos","first_name":"Daniel"},{"first_name":"Tuan","last_name":"Nguyen","full_name":"Nguyen, Tuan"},{"full_name":"Frantar, Elias","last_name":"Frantar","first_name":"Elias","id":"09a8f98d-ec99-11ea-ae11-c063a7b7fe5f"},{"first_name":"Mark","last_name":"Kurtz","full_name":"Kurtz, Mark"},{"last_name":"Fineran","full_name":"Fineran, Benjamin","first_name":"Benjamin"},{"first_name":"Michael","last_name":"Goin","full_name":"Goin, Michael"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian"}],"department":[{"_id":"DaAl"}],"related_material":{"link":[{"url":"https://github.com/neuralmagic/sparseml/tree/main/research/optimal_BERT_surgeon_oBERT","relation":"software"}]},"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)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","has_accepted_license":"1","day":"01"},{"citation":{"ama":"O’Brien RE, Bravo JPK, Ramos D, Hibshman GN, Wright JT, Taylor DW. Modes of inhibition used by phage anti-CRISPRs to evade type I-C Cascade. bioRxiv. 2022. doi:10.1101/2022.06.15.496202","chicago":"O’Brien, Roisin E., Jack Peter Kelly Bravo, Delisa Ramos, Grace N. Hibshman, Jacquelyn T. Wright, and David W. Taylor. “Modes of Inhibition Used by Phage Anti-CRISPRs to Evade Type I-C Cascade.” BioRxiv. Cold Spring Harbor Laboratory, 2022. https://doi.org/10.1101/2022.06.15.496202.","apa":"O’Brien, R. E., Bravo, J. P. K., Ramos, D., Hibshman, G. N., Wright, J. T., & Taylor, D. W. (2022). Modes of inhibition used by phage anti-CRISPRs to evade type I-C Cascade. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2022.06.15.496202","short":"R.E. O’Brien, J.P.K. Bravo, D. Ramos, G.N. Hibshman, J.T. Wright, D.W. Taylor, BioRxiv (2022).","ista":"O’Brien RE, Bravo JPK, Ramos D, Hibshman GN, Wright JT, Taylor DW. 2022. Modes of inhibition used by phage anti-CRISPRs to evade type I-C Cascade. bioRxiv, 10.1101/2022.06.15.496202.","ieee":"R. E. O’Brien, J. P. K. Bravo, D. Ramos, G. N. Hibshman, J. T. Wright, and D. W. Taylor, “Modes of inhibition used by phage anti-CRISPRs to evade type I-C Cascade,” bioRxiv. Cold Spring Harbor Laboratory, 2022.","mla":"O’Brien, Roisin E., et al. “Modes of Inhibition Used by Phage Anti-CRISPRs to Evade Type I-C Cascade.” BioRxiv, Cold Spring Harbor Laboratory, 2022, doi:10.1101/2022.06.15.496202."},"author":[{"full_name":"O’Brien, Roisin E.","last_name":"O’Brien","first_name":"Roisin E."},{"last_name":"Bravo","full_name":"Bravo, Jack Peter Kelly","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","orcid":"0000-0003-0456-0753","first_name":"Jack Peter Kelly"},{"last_name":"Ramos","full_name":"Ramos, Delisa","first_name":"Delisa"},{"first_name":"Grace N.","full_name":"Hibshman, Grace N.","last_name":"Hibshman"},{"first_name":"Jacquelyn T.","last_name":"Wright","full_name":"Wright, Jacquelyn T."},{"full_name":"Taylor, David W.","last_name":"Taylor","first_name":"David W."}],"publication":"bioRxiv","fulldoi":"https://doi.org/10.1101/2022.06.15.496202","_id":"17115","main_file_link":[{"url":"https://doi.org/10.1101/2022.06.15.496202","open_access":"1"}],"extern":"1","day":"15","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","date_updated":"2024-06-04T07:03:02Z","oa":1,"title":"Modes of inhibition used by phage anti-CRISPRs to evade type I-C Cascade","date_published":"2022-06-15T00:00:00Z","status":"public","publication_status":"published","doi":"10.1101/2022.06.15.496202","type":"preprint","language":[{"iso":"eng"}],"month":"06","date_created":"2024-06-04T06:43:30Z","year":"2022","article_processing_charge":"No","publisher":"Cold Spring Harbor Laboratory","abstract":[{"lang":"eng","text":"Cascades are RNA-guided multi-subunit CRISPR-Cas surveillances complexes that target foreign nucleic acids for destruction. Here, we present a 2.9-Å resolution cryo-electron (cryo-EM) structure of the D. vulgaris type I-C Cascade bound to a double-stranded (ds)DNA target. Our data shows how the 5’-TTC-3’ protospacer adjacent motif (PAM) sequence is recognized, and provides a unique mechanism through which the displaced, single-stranded non-target strand (NTS) is stabilized via stacking interactions with protein subunits in order to favor R-loop formation and prevent dsDNA re-annealing. Additionally, we provide structural insights into how diverse anti-CRISPR (Acr) proteins utilize distinct strategies to achieve a shared mechanism of type I-C Cascade inhibition by blocking initial DNA binding. These observations provide a structural basis for directional R-loop formation and reveal how divergent Acr proteins have converged upon common molecular mechanisms to efficiently shut down CRISPR immunity."}]},{"author":[{"last_name":"Schwartz","full_name":"Schwartz, Evan A.","first_name":"Evan A."},{"orcid":"0000-0003-0456-0753","first_name":"Jack Peter Kelly","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","full_name":"Bravo, Jack Peter Kelly","last_name":"Bravo"},{"last_name":"Macias","full_name":"Macias, Luis A.","first_name":"Luis A."},{"first_name":"Caitlyn L.","full_name":"McCafferty, Caitlyn L.","last_name":"McCafferty"},{"first_name":"Tyler L.","last_name":"Dangerfield","full_name":"Dangerfield, Tyler L."},{"first_name":"Jada N.","last_name":"Walker","full_name":"Walker, Jada N."},{"first_name":"Jennifer S.","last_name":"Brodbelt","full_name":"Brodbelt, Jennifer S."},{"last_name":"Fineran","full_name":"Fineran, Peter C.","first_name":"Peter C."},{"first_name":"Robert D.","full_name":"Fagerlund, Robert D.","last_name":"Fagerlund"},{"last_name":"Taylor","full_name":"Taylor, David W.","first_name":"David W."}],"citation":{"apa":"Schwartz, E. A., Bravo, J. P. K., Macias, L. A., McCafferty, C. L., Dangerfield, T. L., Walker, J. N., … Taylor, D. W. (n.d.). Assembly of multi-subunit fusion proteins into the RNA-targeting type III-D CRISPR-Cas effector complex. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2022.06.13.496011","ama":"Schwartz EA, Bravo JPK, Macias LA, et al. Assembly of multi-subunit fusion proteins into the RNA-targeting type III-D CRISPR-Cas effector complex. bioRxiv. doi:10.1101/2022.06.13.496011","chicago":"Schwartz, Evan A., Jack Peter Kelly Bravo, Luis A. Macias, Caitlyn L. McCafferty, Tyler L. Dangerfield, Jada N. Walker, Jennifer S. Brodbelt, Peter C. Fineran, Robert D. Fagerlund, and David W. Taylor. “Assembly of Multi-Subunit Fusion Proteins into the RNA-Targeting Type III-D CRISPR-Cas Effector Complex.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2022.06.13.496011.","mla":"Schwartz, Evan A., et al. “Assembly of Multi-Subunit Fusion Proteins into the RNA-Targeting Type III-D CRISPR-Cas Effector Complex.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2022.06.13.496011.","ieee":"E. A. Schwartz et al., “Assembly of multi-subunit fusion proteins into the RNA-targeting type III-D CRISPR-Cas effector complex,” bioRxiv. Cold Spring Harbor Laboratory.","short":"E.A. Schwartz, J.P.K. Bravo, L.A. Macias, C.L. McCafferty, T.L. Dangerfield, J.N. Walker, J.S. Brodbelt, P.C. Fineran, R.D. Fagerlund, D.W. Taylor, BioRxiv (n.d.).","ista":"Schwartz EA, Bravo JPK, Macias LA, McCafferty CL, Dangerfield TL, Walker JN, Brodbelt JS, Fineran PC, Fagerlund RD, Taylor DW. Assembly of multi-subunit fusion proteins into the RNA-targeting type III-D CRISPR-Cas effector complex. bioRxiv, 10.1101/2022.06.13.496011."},"publication":"bioRxiv","fulldoi":"https://doi.org/10.1101/2022.06.13.496011","_id":"17116","main_file_link":[{"url":"https://doi.org/10.1101/2022.06.13.496011","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"14","extern":"1","date_updated":"2024-06-04T06:58:41Z","oa_version":"Preprint","oa":1,"title":"Assembly of multi-subunit fusion proteins into the RNA-targeting type III-D CRISPR-Cas effector complex","date_published":"2022-06-14T00:00:00Z","status":"public","publication_status":"submitted","type":"preprint","doi":"10.1101/2022.06.13.496011","language":[{"iso":"eng"}],"month":"06","date_created":"2024-06-04T06:44:16Z","publisher":"Cold Spring Harbor Laboratory","year":"2022","article_processing_charge":"No","abstract":[{"text":"CRISPR (Clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) systems are a type of adaptive immune response in bacteria and archaea that utilize crRNA (CRISPR RNA)-guided effector complexes to target complementary RNA or DNA for destruction. The prototypical type III-A and III-B CRISPR-Cas systems utilize multi-subunit effector complexes composed of individual proteins to cleave ssRNA targets at 6-nt intervals, as well as non-specifically degrading ssDNA and activating cyclic oligoadenylate (cOA) synthesis. Recent studies have shown that type III systems can contain subunit fusions yet maintain canonical type III RNA-targeting capabilities. To understand how a multi-subunit fusion effector functions, we determine structures of a variant type III-D effector and biochemically characterize how it cleaves RNA targets. These findings provide insights into how multi-subunit fusion proteins are tethered together and assemble into an active and programmable RNA endonuclease, how the effector utilizes a novel mechanism for target RNA seeding, and the structural basis for the evolution of type III effector complexes. Furthermore, our results provide a blueprint for fusing subunits in class 1 effectors for design of user-defined effector complexes with disparate activities.Important noteWhile this manuscript was in preparation, a manuscript describing the structure of the type III-E effector was published1. We reference these important findings; however, a careful comparison of the structures will follow once the coordinates have been released by the PDB.","lang":"eng"}]},{"fulldoi":"https://doi.org/10.1101/2022.06.13.495754","_id":"17117","author":[{"full_name":"Bravo, Jack Peter Kelly","last_name":"Bravo","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","orcid":"0000-0003-0456-0753","first_name":"Jack Peter Kelly"},{"full_name":"Hallmark, Thom","last_name":"Hallmark","first_name":"Thom"},{"first_name":"Bronson","full_name":"Naegle, Bronson","last_name":"Naegle"},{"full_name":"Beisel, Chase L.","last_name":"Beisel","first_name":"Chase L."},{"last_name":"Jackson","full_name":"Jackson, Ryan N.","first_name":"Ryan N."},{"first_name":"David W.","full_name":"Taylor, David W.","last_name":"Taylor"}],"citation":{"apa":"Bravo, J. P. K., Hallmark, T., Naegle, B., Beisel, C. L., Jackson, R. N., & Taylor, D. W. (2022). Large-scale structural rearrangements unleash indiscriminate nuclease activity of CRISPR-Cas12a2. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2022.06.13.495754","chicago":"Bravo, Jack Peter Kelly, Thom Hallmark, Bronson Naegle, Chase L. Beisel, Ryan N. Jackson, and David W. Taylor. “Large-Scale Structural Rearrangements Unleash Indiscriminate Nuclease Activity of CRISPR-Cas12a2.” BioRxiv. Cold Spring Harbor Laboratory, 2022. https://doi.org/10.1101/2022.06.13.495754.","ama":"Bravo JPK, Hallmark T, Naegle B, Beisel CL, Jackson RN, Taylor DW. Large-scale structural rearrangements unleash indiscriminate nuclease activity of CRISPR-Cas12a2. bioRxiv. 2022. doi:10.1101/2022.06.13.495754","mla":"Bravo, Jack Peter Kelly, et al. “Large-Scale Structural Rearrangements Unleash Indiscriminate Nuclease Activity of CRISPR-Cas12a2.” BioRxiv, Cold Spring Harbor Laboratory, 2022, doi:10.1101/2022.06.13.495754.","ieee":"J. P. K. Bravo, T. Hallmark, B. Naegle, C. L. Beisel, R. N. Jackson, and D. W. Taylor, “Large-scale structural rearrangements unleash indiscriminate nuclease activity of CRISPR-Cas12a2,” bioRxiv. Cold Spring Harbor Laboratory, 2022.","ista":"Bravo JPK, Hallmark T, Naegle B, Beisel CL, Jackson RN, Taylor DW. 2022. Large-scale structural rearrangements unleash indiscriminate nuclease activity of CRISPR-Cas12a2. bioRxiv, 10.1101/2022.06.13.495754.","short":"J.P.K. Bravo, T. Hallmark, B. Naegle, C.L. Beisel, R.N. Jackson, D.W. Taylor, BioRxiv (2022)."},"publication":"bioRxiv","oa_version":"Preprint","date_updated":"2024-06-04T06:55:16Z","oa":1,"title":"Large-scale structural rearrangements unleash indiscriminate nuclease activity of CRISPR-Cas12a2","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2022.06.13.495754"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"13","extern":"1","type":"preprint","doi":"10.1101/2022.06.13.495754","language":[{"iso":"eng"}],"date_published":"2022-06-13T00:00:00Z","status":"public","publication_status":"published","publisher":"Cold Spring Harbor Laboratory","year":"2022","article_processing_charge":"No","abstract":[{"text":"Cas12a2 is a CRISPR-associated nuclease that performs RNA-guided degradation of non-specific single-stranded (ss)RNA, ssDNA and double-stranded (ds)DNA upon recognition of a complementary RNA target, culminating in abortive infection (Dmytrenko 2022). Here, we report structures of Cas12a2 in binary, ternary, and quaternary complexes to reveal a complete activation pathway. Our structures reveal that Cas12a2 is autoinhibited until binding a cognate RNA target, which exposes the RuvC active site within a large, positively charged cleft. Double-stranded DNA substrates are captured through duplex distortion and local melting, stabilized by pairs of ‘aromatic clamp’ residues that are crucial for dsDNA degradation and in vivo immune system function. Our work provides a structural basis for this unprecedented mechanism of abortive infection to achieve population-level immunity, which can be leveraged to create rational mutants that degrade a spectrum of collateral substrates.","lang":"eng"}],"month":"06","date_created":"2024-06-04T06:44:59Z"},{"article_number":"2212.11836","year":"2022","article_processing_charge":"No","abstract":[{"text":"An action of a complex reductive group G on a smooth projective variety X is regular when all regular unipotent elements in G act with finitely many fixed points. Then the complex G-equivariant cohomology ring of X is isomorphic to the coordinate ring of a certain regular fixed point scheme. Examples include partial flag varieties, smooth Schubert varieties and Bott-Samelson varieties. We also show that a more general version of the fixed point scheme allows a generalisation to GKM spaces, such as toric varieties.","lang":"eng"}],"external_id":{"arxiv":["2212.11836"]},"month":"12","date_created":"2024-06-23T15:01:27Z","doi":"10.48550/arXiv.2212.11836","type":"preprint","language":[{"iso":"eng"}],"status":"public","date_published":"2022-12-22T00:00:00Z","publication_status":"draft","oa_version":"Preprint","date_updated":"2026-04-07T12:55:46Z","title":"Spectrum of equivariant cohomology as a fixed point scheme","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2212.11836"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"22","fulldoi":"https://doi.org/10.48550/arXiv.2212.11836","OA_place":"repository","_id":"17157","related_material":{"record":[{"relation":"later_version","id":"19071","status":"public"},{"id":"17156","relation":"dissertation_contains","status":"public"}]},"citation":{"apa":"Hausel, T., & Rychlewicz, K. P. (n.d.). Spectrum of equivariant cohomology as a fixed point scheme. arXiv. https://doi.org/10.48550/arXiv.2212.11836","chicago":"Hausel, Tamás, and Kamil P Rychlewicz. “Spectrum of Equivariant Cohomology as a Fixed Point Scheme.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2212.11836.","ama":"Hausel T, Rychlewicz KP. Spectrum of equivariant cohomology as a fixed point scheme. arXiv. doi:10.48550/arXiv.2212.11836","mla":"Hausel, Tamás, and Kamil P. Rychlewicz. “Spectrum of Equivariant Cohomology as a Fixed Point Scheme.” ArXiv, 2212.11836, doi:10.48550/arXiv.2212.11836.","ieee":"T. Hausel and K. P. Rychlewicz, “Spectrum of equivariant cohomology as a fixed point scheme,” arXiv. .","ista":"Hausel T, Rychlewicz KP. Spectrum of equivariant cohomology as a fixed point scheme. arXiv, 2212.11836.","short":"T. Hausel, K.P. Rychlewicz, ArXiv (n.d.)."},"arxiv":1,"author":[{"last_name":"Hausel","full_name":"Hausel, Tamás","orcid":"0000-0002-9582-2634","first_name":"Tamás","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Rychlewicz","full_name":"Rychlewicz, Kamil P","first_name":"Kamil P","id":"85A07246-A8BF-11E9-B4FA-D9E3E5697425"}],"department":[{"_id":"GradSch"},{"_id":"TaHa"}],"publication":"arXiv"},{"file_date_updated":"2024-12-11T09:22:19Z","type":"journal_article","publication_status":"published","date_published":"2022-08-01T00:00:00Z","status":"public","abstract":[{"lang":"eng","text":"Shear thickening is an intriguing rheological behaviour which consists in a brutal increase in the viscosity above a critical shear rate. It is famously encountered in suspensions of corn starch in water. Despite having been discovered in the early 1930's, its underlying mechanisms remained a mystery for a long time. In 2013–14, numerical and theoretical works [[1], [2], [3]] put forward a frictional transition scenario to explain this phenomenon.\r\nIn this talk, I will present experimental work investigating this frictional transition scenario. In order to test the ideas of this model, one has to go further than standard rheological techniques, since they do not provide access to the frictional state of the measured suspension. I will thus focus on the techniques that we developed in order to evidence the frictional transition and link it to the presence of a shear-thickening behaviour."}],"publisher":"Elsevier","article_processing_charge":"No","year":"2022","month":"08","OA_place":"publisher","fulldoi":"https://doi.org/10.1016/j.sctalk.2022.100038","corr_author":"1","article_type":"original","department":[{"_id":"ScWa"}],"author":[{"orcid":"0000-0002-1843-3803","first_name":"Cécile","id":"5f654c5d-04a1-11eb-ab36-ba9ffec58bd8","full_name":"Clavaud, Cécile","last_name":"Clavaud"}],"publication_identifier":{"eissn":["2772-5693"]},"oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"day":"01","has_accepted_license":"1","language":[{"iso":"eng"}],"doi":"10.1016/j.sctalk.2022.100038","ddc":["530"],"intvolume":" 3","article_number":"100038","date_created":"2024-12-01T23:01:55Z","acknowledgement":"This talk presents parts of my PhD work, conducted at IUSTI in Marseille under the supervision of Yoël Forterre and Bloen Metzger. It aslo benefited from contributions from Antoine Bérut, and some of the data was acquired by Pauline Dame as part of a summer internship.\r\nThis work was supported by the European Research Council (ERC) under the European Union Horizon 2020 Research and Innovation program (ERC Grant 647384) and by the Labex MEC (ANR-10-LABX-0092) under the 647384) and by the A*MIDEX project (ANR-11-IDEX-0001-02) funded by the French government program Investissements d'Avenir, and by ANR ScienceFriction (No. ANR-18-CE30-0024).","quality_controlled":"1","_id":"18606","volume":3,"publication":"Science Talks","citation":{"ista":"Clavaud C. 2022. Shear thickening in dense suspensions: an experimental study. Science Talks. 3, 100038.","short":"C. Clavaud, Science Talks 3 (2022).","mla":"Clavaud, Cécile. “Shear Thickening in Dense Suspensions: An Experimental Study.” Science Talks, vol. 3, 100038, Elsevier, 2022, doi:10.1016/j.sctalk.2022.100038.","ieee":"C. Clavaud, “Shear thickening in dense suspensions: an experimental study,” Science Talks, vol. 3. Elsevier, 2022.","chicago":"Clavaud, Cécile. “Shear Thickening in Dense Suspensions: An Experimental Study.” Science Talks. Elsevier, 2022. https://doi.org/10.1016/j.sctalk.2022.100038.","ama":"Clavaud C. Shear thickening in dense suspensions: an experimental study. Science Talks. 2022;3. doi:10.1016/j.sctalk.2022.100038","apa":"Clavaud, C. (2022). Shear thickening in dense suspensions: an experimental study. Science Talks. Elsevier. https://doi.org/10.1016/j.sctalk.2022.100038"},"file":[{"checksum":"379a5f0b2684cd5393a23be374591484","creator":"dernst","success":1,"file_size":1128564,"file_id":"18607","content_type":"application/pdf","file_name":"2022_ScienceTalks_Clavaud.pdf","relation":"main_file","date_updated":"2024-12-03T08:41:48Z","date_created":"2024-12-03T08:41:48Z","access_level":"open_access"},{"checksum":"666c0bd9af8432437554d0c75c540809","creator":"dernst","success":1,"content_type":"video/mp4","relation":"main_file","file_name":"2024_ScienceTalk_Clavaud_Video.mp4","file_id":"18646","file_size":93265727,"date_updated":"2024-12-11T09:22:13Z","access_level":"open_access","date_created":"2024-12-11T09:22:13Z"},{"checksum":"8fd0d6224d7a0125fcf7d9ca0d80d700","creator":"dernst","file_id":"18647","file_size":58282147,"content_type":"video/mp4","file_name":"2024_ScienceTalk__Clavaud_QA.mp4","relation":"supplementary_material","date_updated":"2024-12-11T09:22:19Z","date_created":"2024-12-11T09:22:19Z","access_level":"open_access"}],"DOAJ_listed":"1","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","title":"Shear thickening in dense suspensions: an experimental study","oa":1,"OA_type":"gold","date_updated":"2024-12-11T09:24:57Z","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"date_published":"2022-12-01T00:00:00Z","status":"public","publication_status":"published","type":"conference","file_date_updated":"2025-01-24T19:13:32Z","month":"12","publisher":"Neural Information Processing Systems Foundation","article_processing_charge":"No","year":"2022","abstract":[{"lang":"eng","text":"Convolutional neural networks were the standard for solving many computer vision tasks until recently, when Transformers of MLP-based architectures have started to show competitive performance. These architectures typically have a vast number of weights and need to be trained on massive datasets; hence, they are not suitable for their use in low-data regimes. In this work, we propose a simple yet effective framework to improve generalization from small amounts of data. We augment modern CNNs with fully-connected (FC) layers and show the massive impact this architectural change has in low-data regimes. We further present an online joint knowledge-distillation method to utilize the extra FC layers at train time but avoid them during test time. This allows us to improve the generalization of a CNN-based model without any increase in the number of weights at test time. We perform classification experiments for a large range of network backbones and several standard datasets on supervised learning and active learning. Our experiments significantly outperform the networks without fully-connected layers, reaching a relative improvement of up to 16% validation accuracy in the supervised setting without adding any extra parameters during inference."}],"conference":{"name":"NeurIPS: Neural Information Processing Systems","end_date":"2022-12-09","start_date":"2022-11-28","location":"New Orleans, LA, United States"},"author":[{"first_name":"Peter","last_name":"Kocsis","full_name":"Kocsis, Peter"},{"full_name":"Súkeník, Peter","last_name":"Súkeník","id":"d64d6a8d-eb8e-11eb-b029-96fd216dec3c","first_name":"Peter"},{"first_name":"Guillem","full_name":"Brasó, Guillem","last_name":"Brasó"},{"first_name":"Matthias","full_name":"Niessner, Matthias","last_name":"Niessner"},{"first_name":"Laura","last_name":"Leal-Taixé","full_name":"Leal-Taixé, Laura"},{"full_name":"Elezi, Ismail","last_name":"Elezi","first_name":"Ismail"}],"alternative_title":["Advances in Neural Information Processing Systems"],"OA_place":"publisher","has_accepted_license":"1","day":"01","extern":"1","oa_version":"Published Version","publication_identifier":{"issn":["1049-5258"]},"intvolume":" 35","ddc":["000"],"language":[{"iso":"eng"}],"quality_controlled":"1","acknowledgement":"This work was supported by a Sofja Kovalevskaja Award, a postdoc fellowship\r\nfrom the Humboldt Foundation, the ERC Starting Grant Scan2CAD (804724), and the German\r\nResearch Foundation (DFG) Research Unit \"Learning and Simulation in Visual Computing\".","date_created":"2025-01-24T19:16:01Z","external_id":{"arxiv":["2210.05657"]},"arxiv":1,"file":[{"date_updated":"2025-01-24T19:13:32Z","file_name":"NeurIPS-2022-the-unreasonable-effectiveness-of-fully-connected-layers-for-low-data-regimes-Paper-Conference.pdf","content_type":"application/pdf","relation":"main_file","file_id":"18877","file_size":444819,"access_level":"open_access","date_created":"2025-01-24T19:13:32Z","creator":"psukenik","checksum":"2a14e59ef8b34d9a1a27a7adbc6f83ff","success":1}],"citation":{"ista":"Kocsis P, Súkeník P, Brasó G, Niessner M, Leal-Taixé L, Elezi I. 2022. The unreasonable effectiveness of fully-connected layers for low-data regimes. 36th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 35, 1896–1908.","short":"P. Kocsis, P. Súkeník, G. Brasó, M. Niessner, L. Leal-Taixé, I. Elezi, in:, 36th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2022, pp. 1896–1908.","mla":"Kocsis, Peter, et al. “The Unreasonable Effectiveness of Fully-Connected Layers for Low-Data Regimes.” 36th Conference on Neural Information Processing Systems, vol. 35, Neural Information Processing Systems Foundation, 2022, pp. 1896–908.","ieee":"P. Kocsis, P. Súkeník, G. Brasó, M. Niessner, L. Leal-Taixé, and I. Elezi, “The unreasonable effectiveness of fully-connected layers for low-data regimes,” in 36th Conference on Neural Information Processing Systems, New Orleans, LA, United States, 2022, vol. 35, pp. 1896–1908.","chicago":"Kocsis, Peter, Peter Súkeník, Guillem Brasó, Matthias Niessner, Laura Leal-Taixé, and Ismail Elezi. “The Unreasonable Effectiveness of Fully-Connected Layers for Low-Data Regimes.” In 36th Conference on Neural Information Processing Systems, 35:1896–1908. Neural Information Processing Systems Foundation, 2022.","ama":"Kocsis P, Súkeník P, Brasó G, Niessner M, Leal-Taixé L, Elezi I. The unreasonable effectiveness of fully-connected layers for low-data regimes. In: 36th Conference on Neural Information Processing Systems. Vol 35. Neural Information Processing Systems Foundation; 2022:1896-1908.","apa":"Kocsis, P., Súkeník, P., Brasó, G., Niessner, M., Leal-Taixé, L., & Elezi, I. (2022). The unreasonable effectiveness of fully-connected layers for low-data regimes. In 36th Conference on Neural Information Processing Systems (Vol. 35, pp. 1896–1908). New Orleans, LA, United States: Neural Information Processing Systems Foundation."},"publication":"36th Conference on Neural Information Processing Systems","page":"1896-1908","_id":"18876","volume":35,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-07-10T11:51:28Z","scopus_import":"1","title":"The unreasonable effectiveness of fully-connected layers for low-data regimes","oa":1,"OA_type":"gold"},{"publication_identifier":{"issn":["0002-9947"],"eissn":["1088-6850"]},"oa_version":"Preprint","day":"01","extern":"1","OA_place":"repository","fulldoi":"https://doi.org/10.1090/tran/8732","article_type":"original","author":[{"full_name":"Chan, Yik Tung","last_name":"Chan","id":"c4c0afc8-9262-11ed-9231-d8b0bc743af1","orcid":"0000-0001-8467-4106","first_name":"Yik Tung"}],"abstract":[{"text":"Abstract. We study integral points on the quadratic twists ED : y2 = x3 −\r\nD2x of the congruent number curve. We give upper bounds on the number of\r\nintegral points in each coset of 2ED(Q) in ED(Q) and show that their total is\r\n (3.8)rank ED(Q). We further show that the average number of non-torsion\r\nintegral points in this family is bounded above by 2. As an application we also\r\ndeduce from our upper bounds that the system of simultaneous Pell equations\r\naX2 − bY 2 = d, bY 2 − cZ2 = d for pairwise coprime positive integers a, b, c, d,\r\nhas at most (3.6)ω(abcd) integer solutions.","lang":"eng"}],"publisher":"American Mathematical Society","year":"2022","article_processing_charge":"No","month":"09","type":"journal_article","publication_status":"published","date_published":"2022-09-01T00:00:00Z","status":"public","title":"Integral points on the congruent number curve","oa":1,"OA_type":"green","date_updated":"2025-07-10T11:51:47Z","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2004.03331"}],"_id":"19490","volume":375,"page":"6675-6700","publication":"Transactions of the American Mathematical Society","arxiv":1,"citation":{"ieee":"S. Chan, “Integral points on the congruent number curve,” Transactions of the American Mathematical Society, vol. 375, no. 9. American Mathematical Society, pp. 6675–6700, 2022.","mla":"Chan, Stephanie. “Integral Points on the Congruent Number Curve.” Transactions of the American Mathematical Society, vol. 375, no. 9, American Mathematical Society, 2022, pp. 6675–700, doi:10.1090/tran/8732.","short":"S. Chan, Transactions of the American Mathematical Society 375 (2022) 6675–6700.","ista":"Chan S. 2022. Integral points on the congruent number curve. Transactions of the American Mathematical Society. 375(9), 6675–6700.","apa":"Chan, S. (2022). Integral points on the congruent number curve. Transactions of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/tran/8732","ama":"Chan S. Integral points on the congruent number curve. Transactions of the American Mathematical Society. 2022;375(9):6675-6700. doi:10.1090/tran/8732","chicago":"Chan, Stephanie. “Integral Points on the Congruent Number Curve.” Transactions of the American Mathematical Society. American Mathematical Society, 2022. https://doi.org/10.1090/tran/8732."},"external_id":{"arxiv":["2004.03331"]},"issue":"9","date_created":"2025-04-05T10:50:56Z","quality_controlled":"1","language":[{"iso":"eng"}],"doi":"10.1090/tran/8732","intvolume":" 375"},{"arxiv":1,"citation":{"short":"S. Chan, P. Koymans, D. Milovic, C. Pagano, Forum of Mathematics, Sigma 10 (2022).","ista":"Chan S, Koymans P, Milovic D, Pagano C. 2022. The 8-rank of the narrow class group and the negative Pell equation. Forum of Mathematics, Sigma. 10, e46.","ieee":"S. Chan, P. Koymans, D. Milovic, and C. Pagano, “The 8-rank of the narrow class group and the negative Pell equation,” Forum of Mathematics, Sigma, vol. 10. Cambridge University Press, 2022.","mla":"Chan, Stephanie, et al. “The 8-Rank of the Narrow Class Group and the Negative Pell Equation.” Forum of Mathematics, Sigma, vol. 10, e46, Cambridge University Press, 2022, doi:10.1017/fms.2022.40.","ama":"Chan S, Koymans P, Milovic D, Pagano C. The 8-rank of the narrow class group and the negative Pell equation. Forum of Mathematics, Sigma. 2022;10. doi:10.1017/fms.2022.40","chicago":"Chan, Stephanie, Peter Koymans, Djordjo Milovic, and Carlo Pagano. “The 8-Rank of the Narrow Class Group and the Negative Pell Equation.” Forum of Mathematics, Sigma. Cambridge University Press, 2022. https://doi.org/10.1017/fms.2022.40.","apa":"Chan, S., Koymans, P., Milovic, D., & Pagano, C. (2022). The 8-rank of the narrow class group and the negative Pell equation. Forum of Mathematics, Sigma. Cambridge University Press. https://doi.org/10.1017/fms.2022.40"},"publication":"Forum of Mathematics, Sigma","volume":10,"_id":"19491","main_file_link":[{"url":"https://doi.org/10.1017/fms.2022.40","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","date_updated":"2025-07-10T11:51:47Z","OA_type":"gold","oa":1,"title":"The 8-rank of the narrow class group and the negative Pell equation","DOAJ_listed":"1","intvolume":" 10","ddc":["510"],"doi":"10.1017/fms.2022.40","language":[{"iso":"eng"}],"quality_controlled":"1","date_created":"2025-04-05T10:51:00Z","article_number":"e46","external_id":{"arxiv":["1908.01752"]},"author":[{"full_name":"Chan, Yik Tung","last_name":"Chan","id":"c4c0afc8-9262-11ed-9231-d8b0bc743af1","orcid":"0000-0001-8467-4106","first_name":"Yik Tung"},{"first_name":"Peter","full_name":"Koymans, Peter","last_name":"Koymans"},{"first_name":"Djordjo","full_name":"Milovic, Djordjo","last_name":"Milovic"},{"last_name":"Pagano","full_name":"Pagano, Carlo","first_name":"Carlo"}],"article_type":"original","fulldoi":"https://doi.org/10.1017/fms.2022.40","OA_place":"publisher","extern":"1","has_accepted_license":"1","day":"17","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)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","publication_identifier":{"issn":["2050-5094"]},"date_published":"2022-05-17T00:00:00Z","status":"public","publication_status":"published","type":"journal_article","month":"05","article_processing_charge":"Yes","year":"2022","publisher":"Cambridge University Press","abstract":[{"lang":"eng","text":"Using a recent breakthrough of Smith [18], we improve the results of Fouvry and Klüners [4, 5] on the solubility of the negative Pell equation. Let D denote the set of positive squarefree integers having no prime factors congruent to 3 modulo 4 . Stevenhagen [19] conjectured that the density of d in D such that the negative Pell equation x2−dy2=−1 is solvable with x,y∈Z is 58.1% , to the nearest tenth of a percent. By studying the distribution of the 8 -rank of narrow class groups Cl+(d) of Q(√d) , we prove that the infimum of this density is at least 53.8% ."}]},{"type":"journal_article","date_published":"2022-02-11T00:00:00Z","status":"public","publication_status":"published","article_processing_charge":"Yes","year":"2022","publisher":"Springer Nature","abstract":[{"text":">Controlling spin wave excitations in magnetic materials underpins the burgeoning field of magnonics. Yet, little is known about how magnons interact with the conduction electrons of itinerant magnets, or how this interplay can be controlled. Via a surface-sensitive spectroscopic approach, we demonstrate a strong electron–magnon coupling at the Pd-terminated surface of the delafossite oxide PdCoO2, where a polar surface charge mediates a Stoner transition to itinerant surface ferromagnetism. We show how the coupling is enhanced sevenfold with increasing surface disorder, and concomitant charge carrier doping, becoming sufficiently strong to drive the system into a polaronic regime, accompanied by a significant quasiparticle mass enhancement. Our study thus sheds light on electron–magnon interactions in solid-state materials, and the ways in which these can be controlled.","lang":"eng"}],"month":"02","fulldoi":"https://doi.org/10.1038/s41535-022-00428-8","OA_place":"publisher","author":[{"first_name":"F.","last_name":"Mazzola","full_name":"Mazzola, F."},{"first_name":"C. -M.","full_name":"Yim, C. -M.","last_name":"Yim"},{"full_name":"Sunko, Veronika","last_name":"Sunko","id":"23cb1cf6-2c7a-11ef-91a4-f72fc19f20b3","first_name":"Veronika","orcid":"0000-0003-2724-3523"},{"full_name":"Khim, S.","last_name":"Khim","first_name":"S."},{"last_name":"Kushwaha","full_name":"Kushwaha, P.","first_name":"P."},{"first_name":"O. J.","last_name":"Clark","full_name":"Clark, O. J."},{"last_name":"Bawden","full_name":"Bawden, L.","first_name":"L."},{"first_name":"I.","last_name":"Marković","full_name":"Marković, I."},{"first_name":"D.","full_name":"Chakraborti, D.","last_name":"Chakraborti"},{"first_name":"T. K.","full_name":"Kim, T. K.","last_name":"Kim"},{"last_name":"Hoesch","full_name":"Hoesch, M.","first_name":"M."},{"first_name":"A. P.","last_name":"Mackenzie","full_name":"Mackenzie, A. P."},{"last_name":"Wahl","full_name":"Wahl, P.","first_name":"P."},{"first_name":"P. D. C.","last_name":"King","full_name":"King, P. D. C."}],"article_type":"original","oa_version":"Published Version","publication_identifier":{"eissn":["2397-4648"]},"extern":"1","day":"11","doi":"10.1038/s41535-022-00428-8","language":[{"iso":"eng"}],"intvolume":" 7","article_number":"20","external_id":{"arxiv":["2112.04869"]},"quality_controlled":"1","date_created":"2025-06-10T09:20:49Z","_id":"19822","volume":7,"citation":{"ieee":"F. Mazzola et al., “Tuneable electron–magnon coupling of ferromagnetic surface states in PdCoO2,” npj Quantum Materials, vol. 7. Springer Nature, 2022.","mla":"Mazzola, F., et al. “Tuneable Electron–Magnon Coupling of Ferromagnetic Surface States in PdCoO2.” Npj Quantum Materials, vol. 7, 20, Springer Nature, 2022, doi:10.1038/s41535-022-00428-8.","ista":"Mazzola F, Yim C-M, Sunko V, Khim S, Kushwaha P, Clark OJ, Bawden L, Marković I, Chakraborti D, Kim TK, Hoesch M, Mackenzie AP, Wahl P, King PDC. 2022. Tuneable electron–magnon coupling of ferromagnetic surface states in PdCoO2. npj Quantum Materials. 7, 20.","short":"F. Mazzola, C.-M. Yim, V. Sunko, S. Khim, P. Kushwaha, O.J. Clark, L. Bawden, I. Marković, D. Chakraborti, T.K. Kim, M. Hoesch, A.P. Mackenzie, P. Wahl, P.D.C. King, Npj Quantum Materials 7 (2022).","apa":"Mazzola, F., Yim, C.-M., Sunko, V., Khim, S., Kushwaha, P., Clark, O. J., … King, P. D. C. (2022). Tuneable electron–magnon coupling of ferromagnetic surface states in PdCoO2. Npj Quantum Materials. Springer Nature. https://doi.org/10.1038/s41535-022-00428-8","chicago":"Mazzola, F., C. -M. Yim, Veronika Sunko, S. Khim, P. Kushwaha, O. J. Clark, L. Bawden, et al. “Tuneable Electron–Magnon Coupling of Ferromagnetic Surface States in PdCoO2.” Npj Quantum Materials. Springer Nature, 2022. https://doi.org/10.1038/s41535-022-00428-8.","ama":"Mazzola F, Yim C-M, Sunko V, et al. Tuneable electron–magnon coupling of ferromagnetic surface states in PdCoO2. npj Quantum Materials. 2022;7. doi:10.1038/s41535-022-00428-8"},"arxiv":1,"publication":"npj Quantum Materials","scopus_import":"1","date_updated":"2025-06-10T13:13:32Z","oa":1,"title":"Tuneable electron–magnon coupling of ferromagnetic surface states in PdCoO2","OA_type":"gold","DOAJ_listed":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41535-022-00428-8"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"has_accepted_license":"1","day":"15","oa_version":"Published Version","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)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_identifier":{"isbn":["9783985470587"],"eisbn":["9783985475582"]},"author":[{"id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9582-2634","first_name":"Tamás","last_name":"Hausel","full_name":"Hausel, Tamás"}],"department":[{"_id":"TaHa"}],"fulldoi":"https://doi.org/10.4171/icm2022/164","corr_author":"1","OA_place":"publisher","month":"07","publisher":"EMS Press","article_processing_charge":"No","year":"2022","abstract":[{"lang":"eng","text":"The first part of this paper is a survey of mathematical results on mirror symmetry phenomena between Hitchin systems for Langlands dual groups. The second part introduces\r\nand discusses multiplicity algebras of the Hitchin system on Lagrangians, and considers\r\ncorresponding conjectural structures on their mirror."}],"conference":{"location":"virtuel","start_date":"2022-07-06","end_date":"2022-07-14","name":"ICM: International Congress of Mathematicians"},"date_published":"2022-07-15T00:00:00Z","status":"public","publication_status":"published","type":"book_chapter","file_date_updated":"2025-09-24T09:05:05Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-09-24T09:12:13Z","title":"Enhanced mirror symmetry for Langlands dual Hitchin systems","OA_type":"gold","oa":1,"file":[{"date_updated":"2025-09-24T09:05:05Z","content_type":"application/pdf","file_name":"2022_ICM_Hausel.pdf","relation":"main_file","file_id":"20387","file_size":655370,"access_level":"open_access","date_created":"2025-09-24T09:05:05Z","creator":"dernst","checksum":"d2b9d4cf51c854f1082d8dc18c5853b1","success":1}],"citation":{"mla":"Hausel, Tamás. “Enhanced Mirror Symmetry for Langlands Dual Hitchin Systems.” International Congress of Mathematicians, EMS Press, 2022, pp. 2228–49, doi:10.4171/icm2022/164.","ieee":"T. Hausel, “Enhanced mirror symmetry for Langlands dual Hitchin systems,” in International Congress of Mathematicians, EMS Press, 2022, pp. 2228–2249.","short":"T. Hausel, in:, International Congress of Mathematicians, EMS Press, 2022, pp. 2228–2249.","ista":"Hausel T. 2022.Enhanced mirror symmetry for Langlands dual Hitchin systems. In: International Congress of Mathematicians. , 2228–2249.","apa":"Hausel, T. (2022). Enhanced mirror symmetry for Langlands dual Hitchin systems. In International Congress of Mathematicians (pp. 2228–2249). virtuel: EMS Press. https://doi.org/10.4171/icm2022/164","ama":"Hausel T. Enhanced mirror symmetry for Langlands dual Hitchin systems. In: International Congress of Mathematicians. EMS Press; 2022:2228-2249. doi:10.4171/icm2022/164","chicago":"Hausel, Tamás. “Enhanced Mirror Symmetry for Langlands Dual Hitchin Systems.” In International Congress of Mathematicians, 2228–49. EMS Press, 2022. https://doi.org/10.4171/icm2022/164."},"arxiv":1,"publication":"International Congress of Mathematicians","page":"2228-2249","_id":"19984","quality_controlled":"1","date_created":"2025-07-10T13:13:36Z","acknowledgement":"The author thanks Nigel Hitchin for introducing him to Higgs bundles during 1995–1998,\r\nsuggesting the SYZ picture for Langlands dual Hitchin systems in 1996, and for the\r\nmore recent collaborations [29, 30]. He also thanks David Ben-Zvi, Pierre-Henri Chaudouard, Pierre Deligne, Ron Donagi, Sergei Gukov, Jochen Heinloth, Vadim Kaloshin,\r\nJoel Kamnitzer, Gérard Laumon, Anton Mellit, David Nadler, Andy Neitzke, Ngô Bao\r\nChâu, Michael Thaddeus, Tony Pantev, Du Pei, Richárd Rimányi, Leonid Rybnikov, Vivek\r\nShende, Balázs Szendrői, András Szenes, Fernando Rodriguez-Villegas, Edward Witten,\r\nand Zhiwei Yun for discussions about the subjects in this paper over the years. Thanks are\r\nalso due to Hülya Argüz, Jakub Löwit, Balázs Szendrői, and Nigel Hitchin for the careful\r\nreading of the paper.","external_id":{"arxiv":["2112.09455"]},"ddc":["510"],"doi":"10.4171/icm2022/164","language":[{"iso":"eng"}]},{"page":"292-305","volume":13660,"_id":"20062","citation":{"chicago":"Henzinger, Monika. “Fine-Grained Complexity Lower Bounds for Problems in Computer Aided Verification.” In Principles of Systems Design, edited by Jean-François Raskin, Krishnendu Chatterjee, Laurent Doyen, and Rupak Majumdar, 13660:292–305. LNCS. Cham: Springer Nature Switzerland, 2022. https://doi.org/10.1007/978-3-031-22337-2_14.","ama":"Henzinger M. Fine-Grained Complexity Lower Bounds for Problems in Computer Aided Verification. In: Raskin J-F, Chatterjee K, Doyen L, Majumdar R, eds. Principles of Systems Design. Vol 13660. LNCS. Cham: Springer Nature Switzerland; 2022:292-305. doi:10.1007/978-3-031-22337-2_14","apa":"Henzinger, M. (2022). Fine-Grained Complexity Lower Bounds for Problems in Computer Aided Verification. In J.-F. Raskin, K. Chatterjee, L. Doyen, & R. Majumdar (Eds.), Principles of Systems Design (Vol. 13660, pp. 292–305). Cham: Springer Nature Switzerland. https://doi.org/10.1007/978-3-031-22337-2_14","ista":"Henzinger M. 2022.Fine-Grained Complexity Lower Bounds for Problems in Computer Aided Verification. In: Principles of Systems Design. vol. 13660, 292–305.","short":"M. Henzinger, in:, J.-F. Raskin, K. Chatterjee, L. Doyen, R. Majumdar (Eds.), Principles of Systems Design, Springer Nature Switzerland, Cham, 2022, pp. 292–305.","ieee":"M. Henzinger, “Fine-Grained Complexity Lower Bounds for Problems in Computer Aided Verification,” in Principles of Systems Design, vol. 13660, J.-F. Raskin, K. Chatterjee, L. Doyen, and R. Majumdar, Eds. Cham: Springer Nature Switzerland, 2022, pp. 292–305.","mla":"Henzinger, Monika. “Fine-Grained Complexity Lower Bounds for Problems in Computer Aided Verification.” Principles of Systems Design, edited by Jean-François Raskin et al., vol. 13660, Springer Nature Switzerland, 2022, pp. 292–305, doi:10.1007/978-3-031-22337-2_14."},"series_title":"LNCS","publication":"Principles of Systems Design","date_updated":"2025-07-22T06:23:55Z","scopus_import":"1","title":"Fine-Grained Complexity Lower Bounds for Problems in Computer Aided Verification","OA_type":"closed access","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/978-3-031-22337-2_14","language":[{"iso":"eng"}],"intvolume":" 13660","editor":[{"first_name":"Jean-François","last_name":"Raskin","full_name":"Raskin, Jean-François"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"last_name":"Doyen","full_name":"Doyen, Laurent","first_name":"Laurent"},{"first_name":"Rupak","last_name":"Majumdar","full_name":"Majumdar, Rupak"}],"quality_controlled":"1","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No. 101019564 “The Design of Modern Fully Dynamic Data Structures (MoDynStruct)” and from the Austrian Science Fund (FWF) project “Fast Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024.","date_created":"2025-07-22T06:19:50Z","fulldoi":"https://doi.org/10.1007/978-3-031-22337-2_14","author":[{"full_name":"Henzinger, Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","first_name":"Monika H"}],"oa_version":"None","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031223365"],"eisbn":["9783031223372"],"issn":["0302-9743"]},"place":"Cham","day":"29","extern":"1","type":"book_chapter","date_published":"2022-12-29T00:00:00Z","status":"public","publication_status":"published","publisher":"Springer Nature Switzerland","article_processing_charge":"No","year":"2022","abstract":[{"text":"This article presents two fine-grained complexity lower bounds with relevance to algorithmic problems in computer aided verification. We have chosen these lower bounds as the proofs are relatively simple, but the techniques can be extended to give lower bounds for many more algorithmic problems. The goal is to present the bounds with minimal notation, making the results accessible to a broad community and stimulating further research in the area.\r\n\r\nSpecifically, we first describe a lower bound on the symbolic complexity of computing strongly connected components, which can be extended to show lower bounds for fundamental model-checking questions in graphs, published in [CDHL16b]. Second we present a conditional lower bound for disjunctive safety problems on graphs from [CDHL18] in the RAM model of computation. This bound can be modified to give conditional lower bounds for disjunctive objectives for reachability, Büchi, coBüchi and Rabin objectives in MDPs. We also present various open questions.","lang":"eng"}],"month":"12"}]