--- DOAJ_listed: '1' OA_place: repository OA_type: gold _id: '18655' abstract: - lang: eng text: "Let Qd be the d-dimensional binary hypercube. We say that P={v1,…,vk} is an increasing path of length k−1 in Qd, if for every i∈[k−1] the edge vivi+1 is obtained by switching some zero coordinate in vi to a one coordinate in vi+1.\r\nForm a random subgraph Qdp by retaining each edge in E(Qd) independently with probability p. We show that there is a phase transition with respect to the length of a longest increasing path around p=ed. Let α be a constant and let p=αd. When αe, whp there is a path of length d−2 in Qdp, and in fact, whether it is of length d−2,d−1, or d depends on whether the all-zero and all-one vertices percolate or not." acknowledgement: "Research supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 101034413.\r\nThe authors wish to thank Ross Pinsky for his comments on an earlier version of the paper, and for bringing reference [12] to our attention. The authors are grateful to the anonymous referees for their helpful comments and suggestions." article_number: '70' article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Michael full_name: Anastos, Michael id: 0b2a4358-bb35-11ec-b7b9-e3279b593dbb last_name: Anastos - first_name: Sahar full_name: Diskin, Sahar last_name: Diskin - first_name: Dor full_name: Elboim, Dor last_name: Elboim - first_name: Michael full_name: Krivelevich, Michael last_name: Krivelevich citation: ama: Anastos M, Diskin S, Elboim D, Krivelevich M. Climbing up a random subgraph of the hypercube. Electronic Communications in Probability. 2024;29. doi:10.1214/24-ECP639 apa: Anastos, M., Diskin, S., Elboim, D., & Krivelevich, M. (2024). Climbing up a random subgraph of the hypercube. Electronic Communications in Probability. Duke University Press. https://doi.org/10.1214/24-ECP639 chicago: Anastos, Michael, Sahar Diskin, Dor Elboim, and Michael Krivelevich. “Climbing up a Random Subgraph of the Hypercube.” Electronic Communications in Probability. Duke University Press, 2024. https://doi.org/10.1214/24-ECP639. ieee: M. Anastos, S. Diskin, D. Elboim, and M. Krivelevich, “Climbing up a random subgraph of the hypercube,” Electronic Communications in Probability, vol. 29. Duke University Press, 2024. ista: Anastos M, Diskin S, Elboim D, Krivelevich M. 2024. Climbing up a random subgraph of the hypercube. Electronic Communications in Probability. 29, 70. mla: Anastos, Michael, et al. “Climbing up a Random Subgraph of the Hypercube.” Electronic Communications in Probability, vol. 29, 70, Duke University Press, 2024, doi:10.1214/24-ECP639. short: M. Anastos, S. Diskin, D. Elboim, M. Krivelevich, Electronic Communications in Probability 29 (2024). corr_author: '1' das_tickbox: '0' date_created: 2024-12-15T23:01:51Z date_published: 2024-11-24T00:00:00Z date_updated: 2026-10-16T10:13:13Z day: '24' ddc: - '510' department: - _id: MaKw doi: 10.1214/24-ECP639 ec_funded: 1 external_id: arxiv: - '2311.16631' isi: - '001356019700001' file: - access_level: open_access checksum: 307a9d049325e6ca9bfe8b4a1f275983 content_type: application/pdf creator: dernst date_created: 2024-12-16T07:33:34Z date_updated: 2024-12-16T07:33:34Z file_id: '18657' file_name: 2024_ElectrCommProbability_Anastos.pdf file_size: 530169 relation: main_file success: 1 file_date_updated: 2024-12-16T07:33:34Z fulldoi: https://doi.org/10.1214/24-ECP639 has_accepted_license: '1' intvolume: ' 29' isi: 1 language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2311.16631 month: '11' oa: 1 oa_version: Published Version project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: Electronic Communications in Probability publication_identifier: eissn: - 1083-589X publication_status: published publisher: Duke University Press quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: yes title: Climbing up a random subgraph of the hypercube tmp: image: /images/cc_by.png 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) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 29 year: '2024' ... --- DOAJ_listed: '1' OA_place: repository OA_type: gold _id: '18951' abstract: - lang: eng text: "We consider local dynamics of the dimer model (perfect matchings) on hypercubic boxes [n] \r\nd . These consist of successively switching the dimers along alternating cycles of prescribed (small) lengths. We study the connectivity properties of the dimer configuration space equipped with these transitions. Answering a question of Freire, Klivans, Milet, and Saldanha, we show that in three dimensions any configuration admits an alternating cycle of length at most 6. We further establish that any configuration on [n] d features order n d−2 alternating cycles of length at most 4d−2. We also prove that the dynamics of dimer configurations on the unit hypercube of dimension d is ergodic when switching alternating cycles of length at most 4d−4. Finally, in the planar but non-bipartite case, we show that parallelogram-shaped boxes in the triangular lattice are ergodic for switching alternating cycles of lengths 4 and 6 only, thus improving a result of Kenyon and Rémila, which also uses 8-cycles. None of our proofs make reference to height functions." article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Ivailo full_name: Hartarsky, Ivailo last_name: Hartarsky - first_name: Lyuben full_name: Lichev, Lyuben id: 9aa8388e-d003-11ee-8458-c4c1d7447977 last_name: Lichev - first_name: Fabio Lucio full_name: Toninelli, Fabio Lucio last_name: Toninelli citation: ama: Hartarsky I, Lichev L, Toninelli FL. Local dimer dynamics in higher dimensions. Annales de l’Institut Henri Poincaré D, Combinatorics, Physics and their Interactions. 2024. doi:10.4171/aihpd/200 apa: Hartarsky, I., Lichev, L., & Toninelli, F. L. (2024). Local dimer dynamics in higher dimensions. Annales de l’Institut Henri Poincaré D, Combinatorics, Physics and Their Interactions. EMS Press. https://doi.org/10.4171/aihpd/200 chicago: Hartarsky, Ivailo, Lyuben Lichev, and Fabio Lucio Toninelli. “Local Dimer Dynamics in Higher Dimensions.” Annales de l’Institut Henri Poincaré D, Combinatorics, Physics and Their Interactions. EMS Press, 2024. https://doi.org/10.4171/aihpd/200. ieee: I. Hartarsky, L. Lichev, and F. L. Toninelli, “Local dimer dynamics in higher dimensions,” Annales de l’Institut Henri Poincaré D, Combinatorics, Physics and their Interactions. EMS Press, 2024. ista: Hartarsky I, Lichev L, Toninelli FL. 2024. Local dimer dynamics in higher dimensions. Annales de l’Institut Henri Poincaré D, Combinatorics, Physics and their Interactions. mla: Hartarsky, Ivailo, et al. “Local Dimer Dynamics in Higher Dimensions.” Annales de l’Institut Henri Poincaré D, Combinatorics, Physics and Their Interactions, EMS Press, 2024, doi:10.4171/aihpd/200. short: I. Hartarsky, L. Lichev, F.L. Toninelli, Annales de l’Institut Henri Poincaré D, Combinatorics, Physics and Their Interactions (2024). das_tickbox: '1' date_created: 2025-01-29T10:57:09Z date_published: 2024-08-26T00:00:00Z date_updated: 2026-10-16T10:14:21Z day: '26' department: - _id: MaKw doi: 10.4171/aihpd/200 external_id: arxiv: - '2304.10930' fulldoi: https://doi.org/10.4171/aihpd/200 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2304.10930 mathsc: - 05B50 - 05C70 - 82C20 month: '08' oa: 1 oa_version: Preprint publication: Annales de l’Institut Henri Poincaré D, Combinatorics, Physics and their Interactions publication_identifier: eissn: - 2308-5835 issn: - 2308-5827 publication_status: epub_ahead publisher: EMS Press quality_controlled: '1' researchdata_availability: unclear scopus_import: '1' status: public supplementarymaterial: unclear title: Local dimer dynamics in higher dimensions type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- OA_place: repository OA_type: green _id: '18559' abstract: - lang: eng text: We prove a 1973 conjecture due to Erdős on the existence of Steiner triple systems with arbitrarily high girth. acknowledgement: Sah and Sawhney were supported by NSF Graduate Research Fellowship Program DGE1745302. Sah was supported by the PD Soros Fellowship. Simkin was supported by the Center of Mathematical Sciences and Applications at Harvard University. article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Matthew Alan full_name: Kwan, Matthew Alan id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3 last_name: Kwan orcid: 0000-0002-4003-7567 - first_name: Ashwin full_name: Sah, Ashwin last_name: Sah - first_name: Mehtaab full_name: Sawhney, Mehtaab last_name: Sawhney - first_name: Michael full_name: Simkin, Michael last_name: Simkin citation: ama: Kwan MA, Sah A, Sawhney M, Simkin M. High-girth Steiner triple systems. Annals of Mathematics. 2024;200(3):1059-1156. doi:10.4007/annals.2024.200.3.4 apa: Kwan, M. A., Sah, A., Sawhney, M., & Simkin, M. (2024). High-girth Steiner triple systems. Annals of Mathematics. Princeton University. https://doi.org/10.4007/annals.2024.200.3.4 chicago: Kwan, Matthew Alan, Ashwin Sah, Mehtaab Sawhney, and Michael Simkin. “High-Girth Steiner Triple Systems.” Annals of Mathematics. Princeton University, 2024. https://doi.org/10.4007/annals.2024.200.3.4. ieee: M. A. Kwan, A. Sah, M. Sawhney, and M. Simkin, “High-girth Steiner triple systems,” Annals of Mathematics, vol. 200, no. 3. Princeton University, pp. 1059–1156, 2024. ista: Kwan MA, Sah A, Sawhney M, Simkin M. 2024. High-girth Steiner triple systems. Annals of Mathematics. 200(3), 1059–1156. mla: Kwan, Matthew Alan, et al. “High-Girth Steiner Triple Systems.” Annals of Mathematics, vol. 200, no. 3, Princeton University, 2024, pp. 1059–156, doi:10.4007/annals.2024.200.3.4. short: M.A. Kwan, A. Sah, M. Sawhney, M. Simkin, Annals of Mathematics 200 (2024) 1059–1156. corr_author: '1' das_tickbox: '0' date_created: 2024-11-17T23:01:48Z date_published: 2024-11-01T00:00:00Z date_updated: 2026-10-16T10:12:22Z day: '01' department: - _id: MaKw doi: 10.4007/annals.2024.200.3.4 external_id: arxiv: - '2201.04554' isi: - '001366233800004' fulldoi: https://doi.org/10.4007/annals.2024.200.3.4 intvolume: ' 200' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2201.04554 month: '11' oa: 1 oa_version: Preprint page: 1059-1156 publication: Annals of Mathematics publication_identifier: eissn: - 1939-8980 issn: - 0003-486X publication_status: published publisher: Princeton University quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: yes title: High-girth Steiner triple systems type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 200 year: '2024' ... --- OA_place: publisher OA_type: hybrid _id: '18938' abstract: - lang: eng text: The synthesis of proteins as encoded in the genome depends critically on translational fidelity. Nevertheless, errors inevitably occur, and those that result in reading frame shifts are particularly consequential because the resulting polypeptides are typically nonfunctional. Despite the generally maladaptive impact of such errors, the proper decoding of certain mRNAs, including many viral mRNAs, depends on a process known as programmed ribosomal frameshifting. The fact that these programmed events, commonly involving a shift to the –1 frame, occur at specific evolutionarily optimized “slippery” sites has facilitated mechanistic investigation. By contrast, less is known about the scope and nature of error (i.e., nonprogrammed) frameshifting. Here, we examine error frameshifting by monitoring spontaneous frameshift events that suppress the effects of single base pair deletions affecting two unrelated test proteins. To map the precise sites of frameshifting, we developed a targeted mass spectrometry–based method called “translational tiling proteomics” for interrogating the full set of possible –1 slippage events that could produce the observed frameshift suppression. Surprisingly, such events occur at many sites along the transcripts, involving up to one half of the available codons. Only a subset of these resembled canonical “slippery” sites, implicating alternative mechanisms potentially involving noncognate mispairing events. Additionally, the aggregate frequency of these events (ranging from 1 to 10% in our test cases) was higher than we might have anticipated. Our findings point to an unexpected degree of mechanistic diversity among ribosomal frameshifting events and suggest that frameshifted products may contribute more significantly to the proteome than generally assumed. acknowledgement: We thank S. L. Dove for valuable discussion and comments on the manuscript and R. Hellmiss for artwork. This work was supported by NIH grants GM136247 to A.H., AG011085 to J.W.H., and GM132129 to J.A.P. article_number: e2317453121 article_processing_charge: No article_type: original author: - first_name: Benjamin L full_name: Springstein, Benjamin L id: b4eb62ef-ac72-11ed-9503-ed3b4d66c083 last_name: Springstein orcid: 0000-0002-3461-5391 - first_name: Joao A. full_name: Paulo, Joao A. last_name: Paulo - first_name: Hankum full_name: Park, Hankum last_name: Park - first_name: Kemardo full_name: Henry, Kemardo last_name: Henry - first_name: Eleanor full_name: Fleming, Eleanor last_name: Fleming - first_name: Zoë full_name: Feder, Zoë last_name: Feder - first_name: J. Wade full_name: Harper, J. Wade last_name: Harper - first_name: Ann full_name: Hochschild, Ann last_name: Hochschild citation: ama: Springstein BL, Paulo JA, Park H, et al. Systematic analysis of nonprogrammed frameshift suppression in E.coli via translational tiling proteomics. Proceedings of the National Academy of Sciences of the United States of America. 2024;121(6). doi:10.1073/pnas.2317453121 apa: Springstein, B. L., Paulo, J. A., Park, H., Henry, K., Fleming, E., Feder, Z., … Hochschild, A. (2024). Systematic analysis of nonprogrammed frameshift suppression in E.coli via translational tiling proteomics. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2317453121 chicago: Springstein, Benjamin L, Joao A. Paulo, Hankum Park, Kemardo Henry, Eleanor Fleming, Zoë Feder, J. Wade Harper, and Ann Hochschild. “Systematic Analysis of Nonprogrammed Frameshift Suppression in E.Coli via Translational Tiling Proteomics.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2317453121. ieee: B. L. Springstein et al., “Systematic analysis of nonprogrammed frameshift suppression in E.coli via translational tiling proteomics,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 6. National Academy of Sciences, 2024. ista: Springstein BL, Paulo JA, Park H, Henry K, Fleming E, Feder Z, Harper JW, Hochschild A. 2024. Systematic analysis of nonprogrammed frameshift suppression in E.coli via translational tiling proteomics. Proceedings of the National Academy of Sciences of the United States of America. 121(6), e2317453121. mla: Springstein, Benjamin L., et al. “Systematic Analysis of Nonprogrammed Frameshift Suppression in E.Coli via Translational Tiling Proteomics.” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 6, e2317453121, National Academy of Sciences, 2024, doi:10.1073/pnas.2317453121. short: B.L. Springstein, J.A. Paulo, H. Park, K. Henry, E. Fleming, Z. Feder, J.W. Harper, A. Hochschild, Proceedings of the National Academy of Sciences of the United States of America 121 (2024). das_tickbox: '1' dataavailabilitystatement: Key plasmids developed in this work will be deposited with Addgene; all other plasmids developed in this work will be made available upon request with no restrictions. Proteomic data (.RAW files) and SDRF (sample and data relationship format) files are available via ProteomeXchange with identifier PXD047675 date_created: 2025-01-29T08:39:27Z date_published: 2024-02-06T00:00:00Z date_updated: 2026-10-16T10:37:18Z day: '06' ddc: - '570' department: - _id: MaLo doi: 10.1073/pnas.2317453121 external_id: pmid: - '38289956' file: - access_level: open_access checksum: 5bd62c7cb4287e3706a1d45d6ef61fd1 content_type: application/pdf creator: dernst date_created: 2025-01-29T08:43:16Z date_updated: 2025-01-29T08:43:16Z file_id: '18939' file_name: 2024_PNAS_Springstein.pdf file_size: 720902 relation: main_file success: 1 file_date_updated: 2025-01-29T08:43:16Z fulldoi: https://doi.org/10.1073/pnas.2317453121 has_accepted_license: '1' intvolume: ' 121' issue: '6' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '02' oa: 1 oa_version: Published Version pmid: 1 publication: Proceedings of the National Academy of Sciences of the United States of America publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: Systematic analysis of nonprogrammed frameshift suppression in E.coli via translational tiling proteomics tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 121 year: '2024' ... --- OA_place: publisher OA_type: gold _id: '18073' abstract: - lang: eng text: Conserved signaling cascades monitor protein-folding homeostasis to ensure proper cellular function. One of the evolutionary conserved key players is IRE1, which maintains endoplasmic reticulum (ER) homeostasis through the unfolded protein response (UPR). Upon accumulation of misfolded proteins in the ER, IRE1 forms clusters on the ER membrane to initiate UPR signaling. What regulates IRE1 cluster formation is not fully understood. Here, we show that the ER lumenal domain (LD) of human IRE1α forms biomolecular condensates in vitro. IRE1α LD condensates were stabilized both by binding to unfolded polypeptides as well as by tethering to model membranes, suggesting their role in assembling IRE1α into signaling-competent stable clusters. Molecular dynamics simulations indicated that weak multivalent interactions drive IRE1α LD clustering. Mutagenesis experiments identified disordered regions in IRE1α LD to control its clustering in vitro and in cells. Importantly, dysregulated clustering of IRE1α mutants led to defects in IRE1α signaling. Our results revealed that disordered regions in IRE1α LD control its clustering and suggest their role as a common strategy in regulating protein assembly on membranes. acknowledgement: We thank late Thomas Peterbauer at the Max Perutz Labs Biooptics Light Microscopy Facility for his help and support. We are grateful to Kitti Csalyi and Thomas Sauer at Max Perutz Labs Biooptics FACS facility for their help. We thank Grzegorz Scibisz and Sertan Atilla for their support with the expression and purification of mCherry-IRE1α LD-10His. We are grateful to Aleksandra S Anisimova with her help in the generation of stable cell lines and the statistical analyses of the data. We thank Venja Vieweger for her help with the characterization of the WLLI and D123P IRE1 mutants in cells. We are thankful to Monika Kubickova for the help with the AUC experiments. We acknowledge CF BIC of CIISB, Instruct-CZ Centre, supported by MEYS CR (LM2023042)) and European Regional Development Fund-Project, UP CIISB“ (No. CZ.02.1.01/0.0/0.0/18_046/0015974). We thank the members of the Karagöz lab for the critical reading and editing of the manuscript. We are thankful to our colleagues Diego Acosta-Alvear, Vladislav Belyy, Jirka Peschek, Yasin Dagdas, Javier Martinez, Sascha Martens and Alwin Köhler for their invaluable input on the manuscript. We are grateful to Life Science Editors, especially Katrina Woolcock for her useful edits and comments on the manuscript. We acknowledge funding from Austrian Science Fund (FWF-SFB F79 and FWF-W 1261) to GEK. PK acknowledges the support of the Max Perutz PhD fellowship. GAV is funded by Stand-Alone grants (P30231-B, P30415-B, P36572), Special Research Grant (SFB grant F79), and Doctoral School grant (DK grant W1261) from the Austrian Science Fund (FWF). ES and RC acknowledge support and funding by the Frankfurt Institute of Advanced Studies, the LOEWE Center for Multiscale Modelling in Life Sciences of the state of Hesse, the Collaborative Research Center 1507 “Membrane-associated Protein Assemblies, Machineries, and Supercomplexes” (Project ID 450648163), and the International Max Planck Research School on Cellular Biophysics (to RC), the Center for Scientific Computing of the Goethe University and the Jülich Supercomputing Centre for computational resources and support. article_processing_charge: Yes article_type: original author: - first_name: Paulina full_name: Kettel, Paulina last_name: Kettel - first_name: Laura full_name: Marosits, Laura last_name: Marosits - first_name: Elena full_name: Spinetti, Elena last_name: Spinetti - first_name: Michael full_name: Rechberger, Michael last_name: Rechberger - first_name: Caterina full_name: Giannini, Caterina id: e3fdddd5-f6e0-11ea-865d-ca99ee6367f4 last_name: Giannini - first_name: Philipp full_name: Radler, Philipp id: 40136C2A-F248-11E8-B48F-1D18A9856A87 last_name: Radler orcid: '0000-0001-9198-2182 ' - first_name: Isabell full_name: Niedermoser, Isabell last_name: Niedermoser - first_name: Irmgard full_name: Fischer, Irmgard last_name: Fischer - first_name: Gijs A. full_name: Versteeg, Gijs A. last_name: Versteeg - first_name: Martin full_name: Loose, Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 - first_name: Roberto full_name: Covino, Roberto last_name: Covino - first_name: G. Elif full_name: Karagöz, G. Elif last_name: Karagöz citation: ama: Kettel P, Marosits L, Spinetti E, et al. Disordered regions in the IRE1α ER lumenal domain mediate its stress-induced clustering. EMBO Journal. 2024;43(20):4668-4698. doi:10.1038/s44318-024-00207-0 apa: Kettel, P., Marosits, L., Spinetti, E., Rechberger, M., Giannini, C., Radler, P., … Karagöz, G. E. (2024). Disordered regions in the IRE1α ER lumenal domain mediate its stress-induced clustering. EMBO Journal. Embo Press. https://doi.org/10.1038/s44318-024-00207-0 chicago: Kettel, Paulina, Laura Marosits, Elena Spinetti, Michael Rechberger, Caterina Giannini, Philipp Radler, Isabell Niedermoser, et al. “Disordered Regions in the IRE1α ER Lumenal Domain Mediate Its Stress-Induced Clustering.” EMBO Journal. Embo Press, 2024. https://doi.org/10.1038/s44318-024-00207-0. ieee: P. Kettel et al., “Disordered regions in the IRE1α ER lumenal domain mediate its stress-induced clustering,” EMBO Journal, vol. 43, no. 20. Embo Press, pp. 4668–4698, 2024. ista: Kettel P, Marosits L, Spinetti E, Rechberger M, Giannini C, Radler P, Niedermoser I, Fischer I, Versteeg GA, Loose M, Covino R, Karagöz GE. 2024. Disordered regions in the IRE1α ER lumenal domain mediate its stress-induced clustering. EMBO Journal. 43(20), 4668–4698. mla: Kettel, Paulina, et al. “Disordered Regions in the IRE1α ER Lumenal Domain Mediate Its Stress-Induced Clustering.” EMBO Journal, vol. 43, no. 20, Embo Press, 2024, pp. 4668–98, doi:10.1038/s44318-024-00207-0. short: P. Kettel, L. Marosits, E. Spinetti, M. Rechberger, C. Giannini, P. Radler, I. Niedermoser, I. Fischer, G.A. Versteeg, M. Loose, R. Covino, G.E. Karagöz, EMBO Journal 43 (2024) 4668–4698. das_tickbox: '1' dataavailabilitystatement: 'All the raw data in this work has been deposited to Biostudies with the accession number: S-BIAD1023. One can access the data through the link below: https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD1023?key=426953ee-3da4-4cf4-a496-e607ce240aff. The source data of this paper are collected in the following database record: biostudies:S-SCDT-10_1038-S44318-024-00207-0.' date_created: 2024-09-15T22:01:42Z date_published: 2024-10-15T00:00:00Z date_updated: 2026-10-16T10:37:47Z day: '15' ddc: - '570' department: - _id: MaLo - _id: JiFr doi: 10.1038/s44318-024-00207-0 external_id: isi: - '001306286100002' pmid: - '39232130' file: - access_level: open_access checksum: 04f4df1a561083f2846676442fc4eb3c content_type: application/pdf creator: dernst date_created: 2025-01-13T08:43:20Z date_updated: 2025-01-13T08:43:20Z file_id: '18827' file_name: 2024_Embo_Kettel.pdf file_size: 10080854 relation: main_file success: 1 file_date_updated: 2025-01-13T08:43:20Z fulldoi: https://doi.org/10.1038/s44318-024-00207-0 has_accepted_license: '1' intvolume: ' 43' isi: 1 issue: '20' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 4668-4698 pmid: 1 publication: EMBO Journal publication_identifier: eissn: - 1460-2075 issn: - 0261-4189 publication_status: published publisher: Embo Press quality_controlled: '1' researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: Disordered regions in the IRE1α ER lumenal domain mediate its stress-induced clustering tmp: image: /images/cc_by.png 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) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 43 year: '2024' ... --- _id: '14834' abstract: - lang: eng text: Bacteria divide by binary fission. The protein machine responsible for this process is the divisome, a transient assembly of more than 30 proteins in and on the surface of the cytoplasmic membrane. Together, they constrict the cell envelope and remodel the peptidoglycan layer to eventually split the cell into two. For Escherichia coli, most molecular players involved in this process have probably been identified, but obtaining the quantitative information needed for a mechanistic understanding can often not be achieved from experiments in vivo alone. Since the discovery of the Z-ring more than 30 years ago, in vitro reconstitution experiments have been crucial to shed light on molecular processes normally hidden in the complex environment of the living cell. In this review, we summarize how rebuilding the divisome from purified components – or at least parts of it - have been instrumental to obtain the detailed mechanistic understanding of the bacterial cell division machinery that we have today. acknowledgement: We acknowledge members of the Loose laboratory at ISTA for helpful discussions—in particular M. Kojic for his insightful comments. This work was supported by the Austrian Science Fund (FWF P34607) to M.L. article_number: '151380' article_processing_charge: Yes article_type: review author: - first_name: Philipp full_name: Radler, Philipp id: 40136C2A-F248-11E8-B48F-1D18A9856A87 last_name: Radler orcid: '0000-0001-9198-2182 ' - first_name: Martin full_name: Loose, Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 citation: ama: 'Radler P, Loose M. A dynamic duo: Understanding the roles of FtsZ and FtsA for Escherichia coli cell division through in vitro approaches. European Journal of Cell Biology. 2024;103(1). doi:10.1016/j.ejcb.2023.151380' apa: 'Radler, P., & Loose, M. (2024). A dynamic duo: Understanding the roles of FtsZ and FtsA for Escherichia coli cell division through in vitro approaches. European Journal of Cell Biology. Elsevier. https://doi.org/10.1016/j.ejcb.2023.151380' chicago: 'Radler, Philipp, and Martin Loose. “A Dynamic Duo: Understanding the Roles of FtsZ and FtsA for Escherichia Coli Cell Division through in Vitro Approaches.” European Journal of Cell Biology. Elsevier, 2024. https://doi.org/10.1016/j.ejcb.2023.151380.' ieee: 'P. Radler and M. Loose, “A dynamic duo: Understanding the roles of FtsZ and FtsA for Escherichia coli cell division through in vitro approaches,” European Journal of Cell Biology, vol. 103, no. 1. Elsevier, 2024.' ista: 'Radler P, Loose M. 2024. A dynamic duo: Understanding the roles of FtsZ and FtsA for Escherichia coli cell division through in vitro approaches. European Journal of Cell Biology. 103(1), 151380.' mla: 'Radler, Philipp, and Martin Loose. “A Dynamic Duo: Understanding the Roles of FtsZ and FtsA for Escherichia Coli Cell Division through in Vitro Approaches.” European Journal of Cell Biology, vol. 103, no. 1, 151380, Elsevier, 2024, doi:10.1016/j.ejcb.2023.151380.' short: P. Radler, M. Loose, European Journal of Cell Biology 103 (2024). corr_author: '1' das_tickbox: '0' date_created: 2024-01-18T08:16:43Z date_published: 2024-03-01T00:00:00Z date_updated: 2026-10-16T10:15:15Z day: '01' ddc: - '570' department: - _id: MaLo doi: 10.1016/j.ejcb.2023.151380 external_id: isi: - '001166216800001' pmid: - '38218128' file: - access_level: open_access checksum: 5d170abbc87585205c010657e4552360 content_type: application/pdf creator: dernst date_created: 2024-07-16T12:07:20Z date_updated: 2024-07-16T12:07:20Z file_id: '17265' file_name: 2024_EJCB_Radler.pdf file_size: 9995304 relation: main_file success: 1 file_date_updated: 2024-07-16T12:07:20Z fulldoi: https://doi.org/10.1016/j.ejcb.2023.151380 has_accepted_license: '1' intvolume: ' 103' isi: 1 issue: '1' keyword: - Cell Biology - General Medicine - Histology - Pathology and Forensic Medicine language: - iso: eng month: '03' oa: 1 oa_version: Published Version pmid: 1 project: - _id: fc38323b-9c52-11eb-aca3-ff8afb4a011d grant_number: P34607 name: In vitro reconstitution of bacterial cell division publication: European Journal of Cell Biology publication_identifier: issn: - 0171-9335 publication_status: published publisher: Elsevier quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: 'A dynamic duo: Understanding the roles of FtsZ and FtsA for Escherichia coli cell division through in vitro approaches' tmp: image: /images/cc_by.png 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) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 103 year: '2024' ... --- OA_place: repository OA_type: green _id: '18702' abstract: - lang: eng text: 'In this work we prove lower bounds on the (communication) cost of maintaining a shared key among a dynamic group of users. Being “dynamic” means one can add and remove users from the group. This captures important protocols like multicast encryption (ME) and continuous group-key agreement (CGKA), which is the primitive underlying many group messaging applications. We prove our bounds in a combinatorial setting where the state of the protocol progresses in rounds. The state of the protocol in each round is captured by a set system, with each of its elements specifying a set of users who share a secret key. We show this combinatorial model implies bounds in symbolic models for ME and CGKA that capture, as building blocks, PRGs, PRFs, dual PRFs, secret sharing, and symmetric encryption in the setting of ME, and PRGs, PRFs, dual PRFs, secret sharing, public-key encryption, and key-updatable public-key encryption in the setting of CGKA. The models are related to the ones used by Micciancio and Panjwani (Eurocrypt’04) and Bienstock et al. (TCC’20) to analyze ME and CGKA, respectively. We prove – using the Bollobás’ Set Pairs Inequality – that the cost (number of uploaded ciphertexts) for replacing a set of d users in a group of size n is Ω(dln(n/d)). Our lower bound is asymptotically tight and both improves on a bound of Ω(d) by Bienstock et al. (TCC’20), and generalizes a result by Micciancio and Panjwani (Eurocrypt’04), who proved a lower bound of Ω(log(n)) for d=1. ' alternative_title: - LNCS article_processing_charge: No author: - first_name: Michael full_name: Anastos, Michael id: 0b2a4358-bb35-11ec-b7b9-e3279b593dbb last_name: Anastos - first_name: Benedikt full_name: Auerbach, Benedikt id: D33D2B18-E445-11E9-ABB7-15F4E5697425 last_name: Auerbach orcid: 0000-0002-7553-6606 - first_name: Mirza Ahad full_name: Baig, Mirza Ahad id: 3EDE6DE4-AA5A-11E9-986D-341CE6697425 last_name: Baig - first_name: Miguel full_name: Cueto Noval, Miguel id: ffc563a3-f6e0-11ea-865d-e3cce03d17cc last_name: Cueto Noval orcid: 0000-0002-2505-4246 - first_name: Matthew Alan full_name: Kwan, Matthew Alan id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3 last_name: Kwan orcid: 0000-0002-4003-7567 - first_name: Guillermo full_name: Pascual Perez, Guillermo id: 2D7ABD02-F248-11E8-B48F-1D18A9856A87 last_name: Pascual Perez orcid: 0000-0001-8630-415X - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 citation: ama: 'Anastos M, Auerbach B, Baig MA, et al. The cost of maintaining keys in dynamic groups with applications to multicast encryption and group messaging. In: 22nd International Conference on Theory of Cryptography. Vol 15364. Springer Nature; 2024:413-443. doi:10.1007/978-3-031-78011-0_14' apa: 'Anastos, M., Auerbach, B., Baig, M. A., Cueto Noval, M., Kwan, M. A., Pascual Perez, G., & Pietrzak, K. Z. (2024). The cost of maintaining keys in dynamic groups with applications to multicast encryption and group messaging. In 22nd International Conference on Theory of Cryptography (Vol. 15364, pp. 413–443). Milan, Italy: Springer Nature. https://doi.org/10.1007/978-3-031-78011-0_14' chicago: Anastos, Michael, Benedikt Auerbach, Mirza Ahad Baig, Miguel Cueto Noval, Matthew Alan Kwan, Guillermo Pascual Perez, and Krzysztof Z Pietrzak. “The Cost of Maintaining Keys in Dynamic Groups with Applications to Multicast Encryption and Group Messaging.” In 22nd International Conference on Theory of Cryptography, 15364:413–43. Springer Nature, 2024. https://doi.org/10.1007/978-3-031-78011-0_14. ieee: M. Anastos et al., “The cost of maintaining keys in dynamic groups with applications to multicast encryption and group messaging,” in 22nd International Conference on Theory of Cryptography, Milan, Italy, 2024, vol. 15364, pp. 413–443. ista: 'Anastos M, Auerbach B, Baig MA, Cueto Noval M, Kwan MA, Pascual Perez G, Pietrzak KZ. 2024. The cost of maintaining keys in dynamic groups with applications to multicast encryption and group messaging. 22nd International Conference on Theory of Cryptography. TCC: Theory of Cryptography, LNCS, vol. 15364, 413–443.' mla: Anastos, Michael, et al. “The Cost of Maintaining Keys in Dynamic Groups with Applications to Multicast Encryption and Group Messaging.” 22nd International Conference on Theory of Cryptography, vol. 15364, Springer Nature, 2024, pp. 413–43, doi:10.1007/978-3-031-78011-0_14. short: M. Anastos, B. Auerbach, M.A. Baig, M. Cueto Noval, M.A. Kwan, G. Pascual Perez, K.Z. Pietrzak, in:, 22nd International Conference on Theory of Cryptography, Springer Nature, 2024, pp. 413–443. conference: end_date: 2024-12-06 location: Milan, Italy name: 'TCC: Theory of Cryptography' start_date: 2024-12-02 corr_author: '1' das_tickbox: '0' date_created: 2024-12-22T23:01:47Z date_published: 2024-12-02T00:00:00Z date_updated: 2026-10-16T10:14:41Z day: '02' department: - _id: MaKw - _id: KrPi doi: 10.1007/978-3-031-78011-0_14 external_id: isi: - '001545628900014' fulldoi: https://doi.org/10.1007/978-3-031-78011-0_14 intvolume: ' 15364' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2024/1097 month: '12' oa: 1 oa_version: Preprint page: 413-443 publication: 22nd International Conference on Theory of Cryptography publication_identifier: eissn: - 1611-3349 isbn: - '9783031780103' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '22664' relation: dissertation_contains status: public researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: The cost of maintaining keys in dynamic groups with applications to multicast encryption and group messaging type: conference user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 15364 year: '2024' ... --- _id: '17475' abstract: - lang: eng text: "As a discrete analogue of Kac’s celebrated question on ‘hearing the shape of a drum’ and towards a practical\r\ngraph isomorphism test, it is of interest to understand which graphs are determined up to isomorphism by\r\ntheir spectrum (of their adjacency matrix). A striking conjecture in this area, due to van Dam and Haemers,\r\nis that ‘almost all graphs are determined by their spectrum’, meaning that the fraction of unlabelled n-vertex\r\ngraphs which are determined by their spectrum converges to 1 as n → ∞.\r\nIn this paper, we make a step towards this conjecture, showing that there are exponentially many n-vertex\r\ngraphs which are determined by their spectrum. This improves on previous bounds (of shape e\r\nc\r\n√\r\nn\r\n). We also\r\npropose a number of further directions of research.\r\n" acknowledgement: Matthew Kwan was supported by ERC Starting Grant ‘RANDSTRUCT’ No. 101076777. article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Illya full_name: Koval, Illya id: 2eed1f3b-896a-11ed-bdf8-93c7c4bf159e last_name: Koval - first_name: Matthew Alan full_name: Kwan, Matthew Alan id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3 last_name: Kwan orcid: 0000-0002-4003-7567 citation: ama: Koval I, Kwan MA. Exponentially many graphs are determined by their spectrum. Quarterly Journal of Mathematics. 2024;75(3):869-899. doi:10.1093/qmath/haae030 apa: Koval, I., & Kwan, M. A. (2024). Exponentially many graphs are determined by their spectrum. Quarterly Journal of Mathematics. Oxford University Press. https://doi.org/10.1093/qmath/haae030 chicago: Koval, Illya, and Matthew Alan Kwan. “Exponentially Many Graphs Are Determined by Their Spectrum.” Quarterly Journal of Mathematics. Oxford University Press, 2024. https://doi.org/10.1093/qmath/haae030. ieee: I. Koval and M. A. Kwan, “Exponentially many graphs are determined by their spectrum,” Quarterly Journal of Mathematics, vol. 75, no. 3. Oxford University Press, pp. 869–899, 2024. ista: Koval I, Kwan MA. 2024. Exponentially many graphs are determined by their spectrum. Quarterly Journal of Mathematics. 75(3), 869–899. mla: Koval, Illya, and Matthew Alan Kwan. “Exponentially Many Graphs Are Determined by Their Spectrum.” Quarterly Journal of Mathematics, vol. 75, no. 3, Oxford University Press, 2024, pp. 869–99, doi:10.1093/qmath/haae030. short: I. Koval, M.A. Kwan, Quarterly Journal of Mathematics 75 (2024) 869–899. corr_author: '1' das_tickbox: '0' date_created: 2024-09-01T22:01:07Z date_published: 2024-06-19T00:00:00Z date_updated: 2026-10-16T10:14:59Z day: '19' ddc: - '500' department: - _id: MaKw - _id: VaKa doi: 10.1093/qmath/haae030 external_id: arxiv: - '2309.09788' isi: - '001249741500001' file: - access_level: open_access checksum: abf200d37ad69e6f2c0750a30296ad97 content_type: application/pdf creator: cchlebak date_created: 2024-09-06T12:23:57Z date_updated: 2024-09-06T12:23:57Z file_id: '17851' file_name: 2024_QuJofMath_Koval.pdf file_size: 946411 relation: main_file success: 1 file_date_updated: 2024-09-06T12:23:57Z fulldoi: https://doi.org/10.1093/qmath/haae030 has_accepted_license: '1' intvolume: ' 75' isi: 1 issue: '3' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 869-899 project: - _id: bd95085b-d553-11ed-ba76-e55d3349be45 grant_number: '101076777' name: Randomness and structure in combinatorics publication: Quarterly Journal of Mathematics publication_identifier: eissn: - 1464-3847 issn: - 0033-5606 publication_status: published publisher: Oxford University Press quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: Exponentially many graphs are determined by their spectrum tmp: image: /images/cc_by.png 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) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 75 year: '2024' ... --- _id: '15118' abstract: - lang: eng text: Cell division in all domains of life requires the orchestration of many proteins, but in Archaea most of the machinery remains poorly characterized. Here we investigate the FtsZ-based cell division mechanism in Haloferax volcanii and find proteins containing photosynthetic reaction centre (PRC) barrel domains that play an essential role in archaeal cell division. We rename these proteins cell division protein B 1 (CdpB1) and CdpB2. Depletions and deletions in their respective genes cause severe cell division defects, generating drastically enlarged cells. Fluorescence microscopy of tagged FtsZ1, FtsZ2 and SepF in CdpB1 and CdpB2 mutant strains revealed an unusually disordered divisome that is not organized into a distinct ring-like structure. Biochemical analysis shows that SepF forms a tripartite complex with CdpB1/2 and crystal structures suggest that these two proteins might form filaments, possibly aligning SepF and the FtsZ2 ring during cell division. Overall our results indicate that PRC-domain proteins play essential roles in FtsZ-based cell division in Archaea. acknowledged_ssus: - _id: LifeSc acknowledgement: We thank X. Ye (ISTA) for providing the His–SUMO expression plasmid pSVA13429. pCDB302 was a gift from C. Bahl (Addgene plasmid number 113673; http://n2t.net/addgene:113673; RRID Addgene_113673). We thank B. Ahsan, G. Sharov, G. Cannone and S. Chen from the Medical Research Council (MRC) LMB Electron Microscopy Facility for help and support. We thank Scientific Computing at the MRC LMB for their support. We thank L. Trübestein and N. Krasnici of the protein service unit of the ISTA Lab Support Facility for help with the SEC coupled with multi-angle light scattering experiments. We thank D. Grohmann and R. Reichelt from the Archaea Centre at the University of Regensburg for providing the P. furiosus cell material. P.N. and S.-V.A. were supported by a Momentum grant from the Volkswagen (VW) Foundation (grant number 94933). D.K.-C. and D.B. were supported by the VW Stiftung ‘Life?’ programme (to J.L.; grant number Az 96727) and by the MRC, as part of UK Research and Innovation (UKRI), MRC file reference number U105184326 (to J.L.). N.T. and S.G. acknowledge support from the French Government’s Investissement d’Avenir program, Laboratoire d’Excellence ‘Integrative Biology of Emerging Infectious Diseases’ (grant number ANR-10-LABX-62-IBEID), and the computational and storage services (Maestro cluster) provided by the IT department at Institut Pasteur. M.K. and M.L. were supported by the Austrian Science Fund (FWF) Stand-Alone P34607. For the purpose of open access, the MRC Laboratory of Molecular Biology has applied a CC BY public copyright licence to any author accepted manuscript version arising. article_processing_charge: No article_type: original author: - first_name: Phillip full_name: Nußbaum, Phillip last_name: Nußbaum - first_name: Danguole full_name: Kureisaite-Ciziene, Danguole last_name: Kureisaite-Ciziene - first_name: Dom full_name: Bellini, Dom last_name: Bellini - first_name: Chris full_name: Van Der Does, Chris last_name: Van Der Does - first_name: Marko full_name: Kojic, Marko id: 73e7ecd4-dc85-11ea-9058-88a16394b160 last_name: Kojic orcid: 0000-0001-7244-8128 - first_name: Najwa full_name: Taib, Najwa last_name: Taib - first_name: Anna full_name: Yeates, Anna last_name: Yeates - first_name: Maxime full_name: Tourte, Maxime last_name: Tourte - first_name: Simonetta full_name: Gribaldo, Simonetta last_name: Gribaldo - first_name: Martin full_name: Loose, Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 - first_name: Jan full_name: Löwe, Jan last_name: Löwe - first_name: Sonja Verena full_name: Albers, Sonja Verena last_name: Albers citation: ama: Nußbaum P, Kureisaite-Ciziene D, Bellini D, et al. Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division. Nature Microbiology. 2024;9(3):698-711. doi:10.1038/s41564-024-01600-5 apa: Nußbaum, P., Kureisaite-Ciziene, D., Bellini, D., Van Der Does, C., Kojic, M., Taib, N., … Albers, S. V. (2024). Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division. Nature Microbiology. Springer Nature. https://doi.org/10.1038/s41564-024-01600-5 chicago: Nußbaum, Phillip, Danguole Kureisaite-Ciziene, Dom Bellini, Chris Van Der Does, Marko Kojic, Najwa Taib, Anna Yeates, et al. “Proteins Containing Photosynthetic Reaction Centre Domains Modulate FtsZ-Based Archaeal Cell Division.” Nature Microbiology. Springer Nature, 2024. https://doi.org/10.1038/s41564-024-01600-5. ieee: P. Nußbaum et al., “Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division,” Nature Microbiology, vol. 9, no. 3. Springer Nature, pp. 698–711, 2024. ista: Nußbaum P, Kureisaite-Ciziene D, Bellini D, Van Der Does C, Kojic M, Taib N, Yeates A, Tourte M, Gribaldo S, Loose M, Löwe J, Albers SV. 2024. Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division. Nature Microbiology. 9(3), 698–711. mla: Nußbaum, Phillip, et al. “Proteins Containing Photosynthetic Reaction Centre Domains Modulate FtsZ-Based Archaeal Cell Division.” Nature Microbiology, vol. 9, no. 3, Springer Nature, 2024, pp. 698–711, doi:10.1038/s41564-024-01600-5. short: P. Nußbaum, D. Kureisaite-Ciziene, D. Bellini, C. Van Der Does, M. Kojic, N. Taib, A. Yeates, M. Tourte, S. Gribaldo, M. Loose, J. Löwe, S.V. Albers, Nature Microbiology 9 (2024) 698–711. das_tickbox: '1' dataavailabilitystatement: The data that support the findings of this study are available in the Source Data. Source data are provided with this paper. Coordinates have been submitted to the Protein Data Bank (PDB) with accession code 8QZO. date_created: 2024-03-17T23:00:58Z date_published: 2024-03-04T00:00:00Z date_updated: 2026-10-16T10:35:48Z day: '04' department: - _id: MaLo doi: 10.1038/s41564-024-01600-5 external_id: isi: - '001183270800021' pmid: - '38443575' fulldoi: https://doi.org/10.1038/s41564-024-01600-5 intvolume: ' 9' isi: 1 issue: '3' language: - iso: eng month: '03' oa_version: None page: 698-711 pmid: 1 project: - _id: fc38323b-9c52-11eb-aca3-ff8afb4a011d grant_number: P34607 name: In vitro reconstitution of bacterial cell division publication: Nature Microbiology publication_identifier: eissn: - 2058-5276 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '20741' relation: dissertation_contains status: public researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 9 year: '2024' ... --- OA_place: publisher OA_type: hybrid _id: '15330' abstract: - lang: eng text: Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth and development by controlling plasma membrane protein composition and cargo uptake. CME relies on the precise recruitment of regulators for vesicle maturation and release. Homologues of components of mammalian vesicle scission are strong candidates to be part of the scission machinery in plants, but the precise roles of these proteins in this process are not fully understood. Here, we characterised the roles of Plant Dynamin-Related Proteins 2 (DRP2s) and SH3-domain containing protein 2 (SH3P2), the plant homologue to Dynamins’ recruiters, like Endophilin and Amphiphysin, in the CME by combining high-resolution imaging of endocytic events in vivo and characterisation of the purified proteins in vitro. Although DRP2s and SH3P2 arrive similarly late during CME and physically interact, genetic analysis of the sh3p123 triple-mutant and complementation assays with non-SH3P2-interacting DRP2 variants suggests that SH3P2 does not directly recruit DRP2s to the site of endocytosis. These observations imply that despite the presence of many well-conserved endocytic components, plants have acquired a distinct mechanism for CME. acknowledged_ssus: - _id: EM-Fac - _id: LifeSc - _id: Bio acknowledgement: "Nataliia Gnyliukh was partially funded by the European Union’s Horizon 2020 research and\r\ninnovation program (2018-2020) under the Marie Sklodowska-Curie Grant (agreement no.\r\n665385). Taif University Researchers Supporting Project: TURSP-HC2022/02. and Austrian\r\nScience Fund (FWF): I 6123-B.We thank Prof. Eileen Lafer and Liping Wang for their suggestions regarding the optimisation of protein expression and purification. We thank Prof. Sebastian Y. Bednarek for the useful comments and constructive criticism of the project. We thank Maciek Adamowski for providing genetic material. This research was supported by the Scientific Service Units (SSU) of IST-Austria through resources provided by the Electron microscopy (EMF), Lab Support Facility (LSF) (particularly Dorota Jaworska) and the Bioimaging Facility (BIF)." article_number: jcs.261720 article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Nataliia full_name: Gnyliukh, Nataliia id: 390C1120-F248-11E8-B48F-1D18A9856A87 last_name: Gnyliukh orcid: 0000-0002-2198-0509 - first_name: Alexander J full_name: Johnson, Alexander J id: 46A62C3A-F248-11E8-B48F-1D18A9856A87 last_name: Johnson orcid: 0000-0002-2739-8843 - first_name: MK full_name: Nagel, MK last_name: Nagel - first_name: Aline full_name: Monzer, Aline id: 2DB5D88C-D7B3-11E9-B8FD-7907E6697425 last_name: Monzer - first_name: David full_name: Babic, David id: db566d23-f6e0-11ea-865d-e6f270e968e7 last_name: Babic - first_name: Annamaria full_name: Hlavata, Annamaria id: 36062FEC-F248-11E8-B48F-1D18A9856A87 last_name: Hlavata - first_name: SS full_name: Alotaibi, SS last_name: Alotaibi - first_name: E full_name: Isono, E last_name: Isono - first_name: Martin full_name: Loose, Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Gnyliukh N, Johnson AJ, Nagel M, et al. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in Arabidopsis thaliana. Journal of Cell Science. 2024;137(8). doi:10.1242/jcs.261720 apa: Gnyliukh, N., Johnson, A. J., Nagel, M., Monzer, A., Babic, D., Hlavata, A., … Friml, J. (2024). Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in Arabidopsis thaliana. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.261720 chicago: Gnyliukh, Nataliia, Alexander J Johnson, MK Nagel, Aline Monzer, David Babic, Annamaria Hlavata, SS Alotaibi, E Isono, Martin Loose, and Jiří Friml. “Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Arabidopsis Thaliana.” Journal of Cell Science. The Company of Biologists, 2024. https://doi.org/10.1242/jcs.261720. ieee: N. Gnyliukh et al., “Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in Arabidopsis thaliana,” Journal of Cell Science, vol. 137, no. 8. The Company of Biologists, 2024. ista: Gnyliukh N, Johnson AJ, Nagel M, Monzer A, Babic D, Hlavata A, Alotaibi S, Isono E, Loose M, Friml J. 2024. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in Arabidopsis thaliana. Journal of Cell Science. 137(8), jcs. 261720. mla: Gnyliukh, Nataliia, et al. “Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Arabidopsis Thaliana.” Journal of Cell Science, vol. 137, no. 8, jcs. 261720, The Company of Biologists, 2024, doi:10.1242/jcs.261720. short: N. Gnyliukh, A.J. Johnson, M. Nagel, A. Monzer, D. Babic, A. Hlavata, S. Alotaibi, E. Isono, M. Loose, J. Friml, Journal of Cell Science 137 (2024). corr_author: '1' das_tickbox: '0' date_created: 2024-04-19T09:54:59Z date_published: 2024-04-01T00:00:00Z date_updated: 2026-10-16T10:38:13Z day: '01' ddc: - '570' department: - _id: MaLo - _id: JiFr - _id: CaBe doi: 10.1242/jcs.261720 ec_funded: 1 external_id: isi: - '001266917100005' pmid: - '38506228' file: - access_level: open_access checksum: 6dc023f0cc7052ad3cf0a42589d2e30f content_type: application/pdf creator: dernst date_created: 2025-01-09T08:41:16Z date_updated: 2025-01-09T08:41:16Z file_id: '18792' file_name: 2024_JourCellScience_Gnyliukh.pdf file_size: 25845948 relation: main_file success: 1 file_date_updated: 2025-01-09T08:41:16Z fulldoi: https://doi.org/10.1242/jcs.261720 has_accepted_license: '1' intvolume: ' 137' isi: 1 issue: '8' language: - iso: eng month: '04' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: bd76d395-d553-11ed-ba76-f678c14f9033 grant_number: I06123 name: Peptide receptors for auxin canalization in Arabidopsis publication: Journal of Cell Science publication_identifier: eissn: - 1477-9137 issn: - 0021-9533 publication_status: published publisher: The Company of Biologists quality_controlled: '1' related_material: record: - id: '14591' relation: earlier_version status: public researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: yes title: Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in Arabidopsis thaliana tmp: image: /images/cc_by.png 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) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 137 year: '2024' ... --- _id: '15172' abstract: - lang: eng text: 'We propose a novel approach to concentration for non-independent random variables. The main idea is to “pretend” that the random variables are independent and pay a multiplicative price measuring how far they are from actually being independent. This price is encapsulated in the Hellinger integral between the joint and the product of the marginals, which is then upper bounded leveraging tensorisation properties. Our bounds represent a natural generalisation of concentration inequalities in the presence of dependence: we recover exactly the classical bounds (McDiarmid’s inequality) when the random variables are independent. Furthermore, in a “large deviations” regime, we obtain the same decay in the probability as for the independent case, even when the random variables display non-trivial dependencies. To show this, we consider a number of applications of interest. First, we provide a bound for Markov chains with finite state space. Then, we consider the Simple Symmetric Random Walk, which is a non-contracting Markov chain, and a non-Markovian setting in which the stochastic process depends on its entire past. To conclude, we propose an application to Markov Chain Monte Carlo methods, where our approach leads to an improved lower bound on the minimum burn-in period required to reach a certain accuracy. In all of these settings, we provide a regime of parameters in which our bound fares better than what the state of the art can provide.' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Amedeo Roberto full_name: Esposito, Amedeo Roberto id: 9583e921-e1ad-11ec-9862-cef099626dc9 last_name: Esposito - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 citation: ama: Esposito AR, Mondelli M. Concentration without independence via information measures. IEEE Transactions on Information Theory. 2024;70(6):3823-3839. doi:10.1109/TIT.2024.3367767 apa: Esposito, A. R., & Mondelli, M. (2024). Concentration without independence via information measures. IEEE Transactions on Information Theory. IEEE. https://doi.org/10.1109/TIT.2024.3367767 chicago: Esposito, Amedeo Roberto, and Marco Mondelli. “Concentration without Independence via Information Measures.” IEEE Transactions on Information Theory. IEEE, 2024. https://doi.org/10.1109/TIT.2024.3367767. ieee: A. R. Esposito and M. Mondelli, “Concentration without independence via information measures,” IEEE Transactions on Information Theory, vol. 70, no. 6. IEEE, pp. 3823–3839, 2024. ista: Esposito AR, Mondelli M. 2024. Concentration without independence via information measures. IEEE Transactions on Information Theory. 70(6), 3823–3839. mla: Esposito, Amedeo Roberto, and Marco Mondelli. “Concentration without Independence via Information Measures.” IEEE Transactions on Information Theory, vol. 70, no. 6, IEEE, 2024, pp. 3823–39, doi:10.1109/TIT.2024.3367767. short: A.R. Esposito, M. Mondelli, IEEE Transactions on Information Theory 70 (2024) 3823–3839. corr_author: '1' das_tickbox: '0' date_created: 2024-03-24T23:01:00Z date_published: 2024-06-01T00:00:00Z date_updated: 2026-10-16T10:39:43Z day: '01' department: - _id: MaMo doi: 10.1109/TIT.2024.3367767 external_id: arxiv: - '2303.07245' isi: - '001230181100001' fulldoi: https://doi.org/10.1109/TIT.2024.3367767 intvolume: ' 70' isi: 1 issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2303.07245 month: '06' oa: 1 oa_version: Preprint page: 3823-3839 project: - _id: 059876FA-7A3F-11EA-A408-12923DDC885E name: Prix Lopez-Loretta 2019 - Marco Mondelli publication: IEEE Transactions on Information Theory publication_identifier: eissn: - 1557-9654 issn: - 0018-9448 publication_status: published publisher: IEEE quality_controlled: '1' related_material: record: - id: '14922' relation: earlier_version status: public researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: yes title: Concentration without independence via information measures type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 70 year: '2024' ... --- _id: '17893' abstract: - lang: eng text: Strong data processing inequalities (SDPI) are an important object of study in Information Theory and have been well studied for f -divergences. Universal upper and lower bounds have been provided along with several applications, connecting them to impossibility (converse) results, concentration of measure, hypercontractivity, and so on. In this paper, we study Renyi divergence and the corresponding SDPI constant whose behavior seems to deviate from that of ordinary <1>-divergences. In particular, one can find examples showing that the universal upper bound relating its SDPI constant to the one of Total Variation does not hold in general. In this work, we prove, however, that the universal lower bound involving the SDPI constant of the Chi-square divergence does indeed hold. Furthermore, we also provide a characterization of the distribution that achieves the supremum when is equal to 2 and consequently compute the SDPI constant for Renyi divergence of the general binary channel. acknowledgement: "The work in this paper was supported in part by the Swiss National Science Foundation under Grant 200364.\r\n" article_processing_charge: No arxiv: 1 author: - first_name: Lifu full_name: Jin, Lifu last_name: Jin - first_name: Amedeo Roberto full_name: Esposito, Amedeo Roberto id: 9583e921-e1ad-11ec-9862-cef099626dc9 last_name: Esposito - first_name: Michael full_name: Gastpar, Michael last_name: Gastpar citation: ama: 'Jin L, Esposito AR, Gastpar M. Properties of the strong data processing constant for Rényi divergence. In: Proceedings of the 2024 IEEE International Symposium on Information Theory. IEEE; 2024:3178-3183. doi:10.1109/ISIT57864.2024.10619367' apa: 'Jin, L., Esposito, A. R., & Gastpar, M. (2024). Properties of the strong data processing constant for Rényi divergence. In Proceedings of the 2024 IEEE International Symposium on Information Theory (pp. 3178–3183). Athens, Greece: IEEE. https://doi.org/10.1109/ISIT57864.2024.10619367' chicago: Jin, Lifu, Amedeo Roberto Esposito, and Michael Gastpar. “Properties of the Strong Data Processing Constant for Rényi Divergence.” In Proceedings of the 2024 IEEE International Symposium on Information Theory, 3178–83. IEEE, 2024. https://doi.org/10.1109/ISIT57864.2024.10619367. ieee: L. Jin, A. R. Esposito, and M. Gastpar, “Properties of the strong data processing constant for Rényi divergence,” in Proceedings of the 2024 IEEE International Symposium on Information Theory, Athens, Greece, 2024, pp. 3178–3183. ista: 'Jin L, Esposito AR, Gastpar M. 2024. Properties of the strong data processing constant for Rényi divergence. Proceedings of the 2024 IEEE International Symposium on Information Theory. ISIT: International Symposium on Information Theory, 3178–3183.' mla: Jin, Lifu, et al. “Properties of the Strong Data Processing Constant for Rényi Divergence.” Proceedings of the 2024 IEEE International Symposium on Information Theory, IEEE, 2024, pp. 3178–83, doi:10.1109/ISIT57864.2024.10619367. short: L. Jin, A.R. Esposito, M. Gastpar, in:, Proceedings of the 2024 IEEE International Symposium on Information Theory, IEEE, 2024, pp. 3178–3183. conference: end_date: 2024-07-12 location: Athens, Greece name: 'ISIT: International Symposium on Information Theory' start_date: 2024-07-07 corr_author: '1' das_tickbox: '0' date_created: 2024-09-08T22:01:12Z date_published: 2024-08-19T00:00:00Z date_updated: 2026-10-16T10:38:29Z day: '19' department: - _id: MaMo doi: 10.1109/ISIT57864.2024.10619367 external_id: arxiv: - '2403.10656' isi: - '001304426903055' fulldoi: https://doi.org/10.1109/ISIT57864.2024.10619367 isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: 'https://doi.org/10.48550/arXiv.2403.10656 ' month: '08' oa: 1 oa_version: Preprint page: 3178-3183 publication: Proceedings of the 2024 IEEE International Symposium on Information Theory publication_identifier: isbn: - '9798350382846' issn: - 2157-8095 publication_status: published publisher: IEEE quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: Properties of the strong data processing constant for Rényi divergence type: conference user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- _id: '14665' abstract: - lang: eng text: We derive lower bounds on the maximal rates for multiple packings in high-dimensional Euclidean spaces. For any N > 0 and L ∈ Z ≥2 , a multiple packing is a set C of points in R n such that any point in R n lies in the intersection of at most L - 1 balls of radius √ nN around points in C . This is a natural generalization of the sphere packing problem. We study the multiple packing problem for both bounded point sets whose points have norm at most √ nP for some constant P > 0, and unbounded point sets whose points are allowed to be anywhere in R n . Given a well-known connection with coding theory, multiple packings can be viewed as the Euclidean analog of list-decodable codes, which are well-studied over finite fields. We derive the best known lower bounds on the optimal multiple packing density. This is accomplished by establishing an inequality which relates the list-decoding error exponent for additive white Gaussian noise channels, a quantity of average-case nature, to the list-decoding radius, a quantity of worst-case nature. We also derive novel bounds on the list-decoding error exponent for infinite constellations and closed-form expressions for the list-decoding error exponents for the power-constrained AWGN channel, which may be of independent interest beyond multiple packing. acknowledgement: "The work of Yihan Zhang was supported by the European Union’s Horizon 2020 Research and Innovation Programme under Grant 682203-ERC-[Inf-Speed-Tradeoff]. The work of Shashank Vatedka was supported in part by the Core Research Grant from the Science and\r\nEngineering Research Board, India, under Grant CRG/2022/004464; and in\r\npart by the Department of Science and Technology (DST), India, under Grant\r\nDST/INT/RUS/RSF/P-41/2020 (TPN No. 65025)." article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Yihan full_name: Zhang, Yihan id: 2ce5da42-b2ea-11eb-bba5-9f264e9d002c last_name: Zhang orcid: 0000-0002-6465-6258 - first_name: Shashank full_name: Vatedka, Shashank last_name: Vatedka citation: ama: 'Zhang Y, Vatedka S. Multiple packing: Lower bounds via error exponents. IEEE Transactions on Information Theory. 2024;70(2):1008-1039. doi:10.1109/TIT.2023.3334032' apa: 'Zhang, Y., & Vatedka, S. (2024). Multiple packing: Lower bounds via error exponents. IEEE Transactions on Information Theory. IEEE. https://doi.org/10.1109/TIT.2023.3334032' chicago: 'Zhang, Yihan, and Shashank Vatedka. “Multiple Packing: Lower Bounds via Error Exponents.” IEEE Transactions on Information Theory. IEEE, 2024. https://doi.org/10.1109/TIT.2023.3334032.' ieee: 'Y. Zhang and S. Vatedka, “Multiple packing: Lower bounds via error exponents,” IEEE Transactions on Information Theory, vol. 70, no. 2. IEEE, pp. 1008–1039, 2024.' ista: 'Zhang Y, Vatedka S. 2024. Multiple packing: Lower bounds via error exponents. IEEE Transactions on Information Theory. 70(2), 1008–1039.' mla: 'Zhang, Yihan, and Shashank Vatedka. “Multiple Packing: Lower Bounds via Error Exponents.” IEEE Transactions on Information Theory, vol. 70, no. 2, IEEE, 2024, pp. 1008–39, doi:10.1109/TIT.2023.3334032.' short: Y. Zhang, S. Vatedka, IEEE Transactions on Information Theory 70 (2024) 1008–1039. corr_author: '1' das_tickbox: '0' date_created: 2023-12-10T23:01:00Z date_published: 2024-02-01T00:00:00Z date_updated: 2026-10-16T10:39:20Z day: '01' department: - _id: MaMo doi: 10.1109/TIT.2023.3334032 external_id: arxiv: - '2211.04408' isi: - '001166812100008' fulldoi: https://doi.org/10.1109/TIT.2023.3334032 intvolume: ' 70' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2211.04408 month: '02' oa: 1 oa_version: Preprint page: 1008-1039 publication: IEEE Transactions on Information Theory publication_identifier: eissn: - 1557-9654 issn: - 0018-9448 publication_status: published publisher: IEEE quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: yes title: 'Multiple packing: Lower bounds via error exponents' type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 70 year: '2024' ... --- _id: '17895' abstract: - lang: eng text: We propose a concatenated code construction for a class of discrete-alphabet oblivious arbitrarily varying channels (AVCs) with cost constraints. The code has time and space complexity polynomial in the blocklength n . It uses a Reed-Solomon outer code, logarithmic blocklength random inner codes, and stochastic encoding by permuting the codeword before transmission. When the channel satisfies a condition called strong DS-nonsymmetrizability (a modified version of nonsymmetrizability originally due to Dobrushin and Stambler), we show that the code achieves a rate that for a variety of oblivious AVCs (such as classically studied error/erasure channels) match the known capacities. acknowledgement: "The work of M. Langberg and A. D. Sarwate was supported in part by the US NSF under awards CCF-1909451 and CCF1909468. B. K. Dey was supported in part by the Bharti Centre\r\nfor Communication in IIT Bombay. " article_processing_charge: No author: - first_name: B. K. full_name: Dey, B. K. last_name: Dey - first_name: S. full_name: Jaggi, S. last_name: Jaggi - first_name: M. full_name: Langberg, M. last_name: Langberg - first_name: A. D. full_name: Sarwate, A. D. last_name: Sarwate - first_name: Yihan full_name: Zhang, Yihan id: 2ce5da42-b2ea-11eb-bba5-9f264e9d002c last_name: Zhang orcid: 0000-0002-6465-6258 citation: ama: 'Dey BK, Jaggi S, Langberg M, Sarwate AD, Zhang Y. Computationally efficient codes for strongly Dobrushin-Stambler nonsymmetrizable oblivious AVCs. In: Proceedings of the 2024 IEEE International Symposium on Information Theory . IEEE; 2024:1586-1591. doi:10.1109/ISIT57864.2024.10619362' apa: 'Dey, B. K., Jaggi, S., Langberg, M., Sarwate, A. D., & Zhang, Y. (2024). Computationally efficient codes for strongly Dobrushin-Stambler nonsymmetrizable oblivious AVCs. In Proceedings of the 2024 IEEE International Symposium on Information Theory (pp. 1586–1591). Athens, Greece: IEEE. https://doi.org/10.1109/ISIT57864.2024.10619362' chicago: Dey, B. K., S. Jaggi, M. Langberg, A. D. Sarwate, and Yihan Zhang. “Computationally Efficient Codes for Strongly Dobrushin-Stambler Nonsymmetrizable Oblivious AVCs.” In Proceedings of the 2024 IEEE International Symposium on Information Theory , 1586–91. IEEE, 2024. https://doi.org/10.1109/ISIT57864.2024.10619362. ieee: B. K. Dey, S. Jaggi, M. Langberg, A. D. Sarwate, and Y. Zhang, “Computationally efficient codes for strongly Dobrushin-Stambler nonsymmetrizable oblivious AVCs,” in Proceedings of the 2024 IEEE International Symposium on Information Theory , Athens, Greece, 2024, pp. 1586–1591. ista: 'Dey BK, Jaggi S, Langberg M, Sarwate AD, Zhang Y. 2024. Computationally efficient codes for strongly Dobrushin-Stambler nonsymmetrizable oblivious AVCs. Proceedings of the 2024 IEEE International Symposium on Information Theory . ISIT: International Symposium on Information Theory, 1586–1591.' mla: Dey, B. K., et al. “Computationally Efficient Codes for Strongly Dobrushin-Stambler Nonsymmetrizable Oblivious AVCs.” Proceedings of the 2024 IEEE International Symposium on Information Theory , IEEE, 2024, pp. 1586–91, doi:10.1109/ISIT57864.2024.10619362. short: B.K. Dey, S. Jaggi, M. Langberg, A.D. Sarwate, Y. Zhang, in:, Proceedings of the 2024 IEEE International Symposium on Information Theory , IEEE, 2024, pp. 1586–1591. conference: end_date: 2024-07-12 location: Athens, Greece name: 'ISIT: International Symposium on Information Theory' start_date: 2024-07-07 das_tickbox: '0' date_created: 2024-09-08T22:01:12Z date_published: 2024-08-19T00:00:00Z date_updated: 2026-10-16T10:39:03Z day: '19' department: - _id: MaMo doi: 10.1109/ISIT57864.2024.10619362 external_id: isi: - '001304426901091' fulldoi: https://doi.org/10.1109/ISIT57864.2024.10619362 isi: 1 language: - iso: eng month: '08' oa_version: None page: 1586-1591 publication: 'Proceedings of the 2024 IEEE International Symposium on Information Theory ' publication_identifier: isbn: - '9798350382846' issn: - 2157-8095 publication_status: published publisher: IEEE quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: Computationally efficient codes for strongly Dobrushin-Stambler nonsymmetrizable oblivious AVCs type: conference user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- _id: '17894' abstract: - lang: eng text: 'Sibson''s α -mutual information has received renewed attention recently in several contexts: concentration of measure under dependence, statistical learning, hypothesis testing, and estimation theory. In this work, we introduce several variational representations of Sibson''s α -mutual information: 1) as a supremum over joint distributions of (a combination of) KL divergences; and 2) as a supremum over functions of opportune expected values. Leveraging them, we produce a variety of novel and known results, including a generalization of transportation-cost inequalities and Fano''s inequality.' acknowledgement: The work in this paper was supported in part by the Swiss National Science Foundation under Grant 200364. article_processing_charge: No author: - first_name: Amedeo Roberto full_name: Esposito, Amedeo Roberto id: 9583e921-e1ad-11ec-9862-cef099626dc9 last_name: Esposito - first_name: Michael full_name: Gastpar, Michael last_name: Gastpar - first_name: Ibrahim full_name: Issa, Ibrahim last_name: Issa citation: ama: 'Esposito AR, Gastpar M, Issa I. Variational characterizations of Sibson’s α-mutual information. In: Proceedings of the 2024 IEEE International Symposium on Information Theory . IEEE; 2024:2110-2115. doi:10.1109/ISIT57864.2024.10619378' apa: 'Esposito, A. R., Gastpar, M., & Issa, I. (2024). Variational characterizations of Sibson’s α-mutual information. In Proceedings of the 2024 IEEE International Symposium on Information Theory (pp. 2110–2115). Athens, Greece: IEEE. https://doi.org/10.1109/ISIT57864.2024.10619378' chicago: Esposito, Amedeo Roberto, Michael Gastpar, and Ibrahim Issa. “Variational Characterizations of Sibson’s α-Mutual Information.” In Proceedings of the 2024 IEEE International Symposium on Information Theory , 2110–15. IEEE, 2024. https://doi.org/10.1109/ISIT57864.2024.10619378. ieee: A. R. Esposito, M. Gastpar, and I. Issa, “Variational characterizations of Sibson’s α-mutual information,” in Proceedings of the 2024 IEEE International Symposium on Information Theory , Athens, Greece, 2024, pp. 2110–2115. ista: 'Esposito AR, Gastpar M, Issa I. 2024. Variational characterizations of Sibson’s α-mutual information. Proceedings of the 2024 IEEE International Symposium on Information Theory . ISIT: International Symposium on Information Theory, 2110–2115.' mla: Esposito, Amedeo Roberto, et al. “Variational Characterizations of Sibson’s α-Mutual Information.” Proceedings of the 2024 IEEE International Symposium on Information Theory , IEEE, 2024, pp. 2110–15, doi:10.1109/ISIT57864.2024.10619378. short: A.R. Esposito, M. Gastpar, I. Issa, in:, Proceedings of the 2024 IEEE International Symposium on Information Theory , IEEE, 2024, pp. 2110–2115. conference: end_date: 2024-07-12 location: Athens, Greece name: 'ISIT: International Symposium on Information Theory' start_date: 2024-07-07 corr_author: '1' das_tickbox: '0' date_created: 2024-09-08T22:01:12Z date_published: 2024-08-19T00:00:00Z date_updated: 2026-10-16T10:38:46Z day: '19' department: - _id: MaMo doi: 10.1109/ISIT57864.2024.10619378 external_id: isi: - '001304426902023' fulldoi: https://doi.org/10.1109/ISIT57864.2024.10619378 isi: 1 language: - iso: eng month: '08' oa_version: None page: 2110-2115 publication: 'Proceedings of the 2024 IEEE International Symposium on Information Theory ' publication_identifier: isbn: - '9798350382846' issn: - 2157-8095 publication_status: published publisher: IEEE quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: Variational characterizations of Sibson's α-mutual information type: conference user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- _id: '14932' abstract: - lang: eng text: The huge antlers of the extinct Irish elk have invited evolutionary speculation since Darwin. In the 1970s, Stephen Jay Gould presented the first extensive data on antler size in the Irish elk and combined these with comparative data from other deer to test the hypothesis that the gigantic antlers were the outcome of a positive allometry that constrained large-bodied deer to have proportionally even larger antlers. He concluded that the Irish elk had antlers as predicted for its size and interpreted this within his emerging framework of developmental constraints as an explanatory factor in evolution. Here we reanalyze antler allometry based on new morphometric data for 57 taxa of the family Cervidae. We also present a new phylogeny for the Cervidae, which we use for comparative analyses. In contrast to Gould, we find that the antlers of Irish elk were larger than predicted from the allometry within the true deer, Cervini, as analyzed by Gould, but follow the allometry across Cervidae as a whole. After dissecting the discrepancy, we reject the allometric-constraint hypothesis because, contrary to Gould, we find no similarity between static and evolutionary allometries, and because we document extensive non-allometric evolution of antler size across the Cervidae. acknowledgement: "Open access funding provided by University of Oslo (incl Oslo University Hospital).\r\nWe thank Adrian Lister, Louis Tomsett, Roberto Portela Miguez and Roula Pappa (NHMUK), Brian O'Toole and Eileen Westwig (AMNH), Daniela Kalthoff (NHRM), Alexander Bibl and Zachos Frank (NHMW), Darrin Lunde and John Ososky (NMNH), Matthew Parkes and Nigel Monaghan (NMI), Elizabetta Cioppi and Luca Bellucci (IGF), and Yoshihiro Tanaka and Hiroyuki Taruno (OMNH), who helped us in obtaining the museum data, and a special thanks to Jørgen Sikkeland (NTNU NHM) for assistance in obtaining the ontogenetic data for the red deer. We thank Olja Toljagic and Kjetil L. Voje for discussions, Ayumu Tsuboi for assistance with data collection, and Jean-Michel Gaillard and the anonymous reviewers for comments on the manuscript. We thank the Centre of Advanced Study (CAS) at the Norwegian Academy of Sciences and Letters for hosting us during the academic year of 2019/2020 when much of the analysis and writing were done. MT was funded by JSPS Research Fellowship for Young Scientists (201603238)." article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Masahito full_name: Tsuboi, Masahito last_name: Tsuboi - first_name: Bjørn Tore full_name: Kopperud, Bjørn Tore last_name: Kopperud - first_name: Michael full_name: Matschiner, Michael last_name: Matschiner - first_name: Mark full_name: Grabowski, Mark last_name: Grabowski - first_name: Chrsitine full_name: Syrowatka, Chrsitine id: 205ffb76-7fe7-11eb-aa17-958bd11b99ad last_name: Syrowatka - first_name: Christophe full_name: Pélabon, Christophe last_name: Pélabon - first_name: Thomas F. full_name: Hansen, Thomas F. last_name: Hansen citation: ama: Tsuboi M, Kopperud BT, Matschiner M, et al. Antler allometry, the Irish elk and Gould revisited. Evolutionary Biology. 2024;51:149-165. doi:10.1007/s11692-023-09624-1 apa: Tsuboi, M., Kopperud, B. T., Matschiner, M., Grabowski, M., Syrowatka, C., Pélabon, C., & Hansen, T. F. (2024). Antler allometry, the Irish elk and Gould revisited. Evolutionary Biology. Springer Nature. https://doi.org/10.1007/s11692-023-09624-1 chicago: Tsuboi, Masahito, Bjørn Tore Kopperud, Michael Matschiner, Mark Grabowski, Chrsitine Syrowatka, Christophe Pélabon, and Thomas F. Hansen. “Antler Allometry, the Irish Elk and Gould Revisited.” Evolutionary Biology. Springer Nature, 2024. https://doi.org/10.1007/s11692-023-09624-1. ieee: M. Tsuboi et al., “Antler allometry, the Irish elk and Gould revisited,” Evolutionary Biology, vol. 51. Springer Nature, pp. 149–165, 2024. ista: Tsuboi M, Kopperud BT, Matschiner M, Grabowski M, Syrowatka C, Pélabon C, Hansen TF. 2024. Antler allometry, the Irish elk and Gould revisited. Evolutionary Biology. 51, 149–165. mla: Tsuboi, Masahito, et al. “Antler Allometry, the Irish Elk and Gould Revisited.” Evolutionary Biology, vol. 51, Springer Nature, 2024, pp. 149–65, doi:10.1007/s11692-023-09624-1. short: M. Tsuboi, B.T. Kopperud, M. Matschiner, M. Grabowski, C. Syrowatka, C. Pélabon, T.F. Hansen, Evolutionary Biology 51 (2024) 149–165. das_tickbox: '1' dataavailabilitystatement: All data used in this paper are available from the authors on request. date_created: 2024-02-04T23:00:53Z date_published: 2024-03-01T00:00:00Z date_updated: 2026-10-16T10:43:26Z day: '01' ddc: - '570' department: - _id: MaRo doi: 10.1007/s11692-023-09624-1 external_id: isi: - '001151285200001' file: - access_level: open_access checksum: 416ab4dac751c443b9de51fb58278ff2 content_type: application/pdf creator: dernst date_created: 2024-07-22T11:53:43Z date_updated: 2024-07-22T11:53:43Z file_id: '17311' file_name: 2024_EvolutionaryBio_Tsuboi.pdf file_size: 1705974 relation: main_file success: 1 file_date_updated: 2024-07-22T11:53:43Z fulldoi: https://doi.org/10.1007/s11692-023-09624-1 has_accepted_license: '1' intvolume: ' 51' isi: 1 language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 149-165 publication: Evolutionary Biology publication_identifier: eissn: - 1934-2845 issn: - 0071-3260 publication_status: published publisher: Springer Nature quality_controlled: '1' researchdata_availability: upon request scopus_import: '1' status: public supplementarymaterial: yes title: Antler allometry, the Irish elk and Gould revisited tmp: image: /images/cc_by.png 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) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 51 year: '2024' ... --- OA_place: repository OA_type: green _id: '17147' abstract: - lang: eng text: Efficient utilization of large-scale biobank data is crucial for inferring the genetic basis of disease and predicting health outcomes from the DNA. Yet we lack efficient, accurate methods that scale to data where electronic health records are linked to whole genome sequence information. To address this issue, our paper develops a new algorithmic paradigm based on Approximate Message Passing (AMP), which is specifically tailored for genomic prediction and association testing. Our method yields comparable out-of-sample prediction accuracy to the state of the art on UK Biobank traits, whilst dramatically improving computational complexity, with a 8x-speed up in the run time. In addition, AMP theory provides a joint association testing framework, which outperforms the currently used REGENIE method, in roughly a third of the compute time. This first, truly large-scale application of the AMP framework lays the foundations for a far wider range of statistical analyses for hundreds of millions of variables measured on millions of people. acknowledged_ssus: - _id: ScienComp acknowledgement: "This work was supported by a Lopez-Loreta Prize to MM, an SNSF Eccellenza Grant to MRR (PCEGP3-181181), and core funding from ISTA. The authors thank Philip Schniter, Matthew Stephens and Pragya Sur for valuable suggestions on an early version of the work. The authors acknowledge the participants and investigators of the UK Biobank study. High-performance\r\ncomputing was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp)." article_processing_charge: No author: - first_name: Al full_name: Depope, Al id: 0b77531d-dbcd-11ea-9d1d-a8eee0bf3830 last_name: Depope - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 citation: ama: 'Depope A, Mondelli M, Robinson MR. Inference of genetic effects via approximate message passing. In: 2024 IEEE International Conference on Acoustics, Speech, and Signal Processing. IEEE; 2024:13151-13155. doi:10.1109/ICASSP48485.2024.10447198' apa: 'Depope, A., Mondelli, M., & Robinson, M. R. (2024). Inference of genetic effects via approximate message passing. In 2024 IEEE International Conference on Acoustics, Speech, and Signal Processing (pp. 13151–13155). Seoul, Korea: IEEE. https://doi.org/10.1109/ICASSP48485.2024.10447198' chicago: Depope, Al, Marco Mondelli, and Matthew Richard Robinson. “Inference of Genetic Effects via Approximate Message Passing.” In 2024 IEEE International Conference on Acoustics, Speech, and Signal Processing, 13151–55. IEEE, 2024. https://doi.org/10.1109/ICASSP48485.2024.10447198. ieee: A. Depope, M. Mondelli, and M. R. Robinson, “Inference of genetic effects via approximate message passing,” in 2024 IEEE International Conference on Acoustics, Speech, and Signal Processing, Seoul, Korea, 2024, pp. 13151–13155. ista: 'Depope A, Mondelli M, Robinson MR. 2024. Inference of genetic effects via approximate message passing. 2024 IEEE International Conference on Acoustics, Speech, and Signal Processing. ICASSP: International Conference on Acoustics, Speech and Signal Processing, 13151–13155.' mla: Depope, Al, et al. “Inference of Genetic Effects via Approximate Message Passing.” 2024 IEEE International Conference on Acoustics, Speech, and Signal Processing, IEEE, 2024, pp. 13151–55, doi:10.1109/ICASSP48485.2024.10447198. short: A. Depope, M. Mondelli, M.R. Robinson, in:, 2024 IEEE International Conference on Acoustics, Speech, and Signal Processing, IEEE, 2024, pp. 13151–13155. conference: end_date: 2024-04-19 location: Seoul, Korea name: 'ICASSP: International Conference on Acoustics, Speech and Signal Processing' start_date: 2024-04-14 corr_author: '1' das_tickbox: '0' date_created: 2024-06-16T22:01:07Z date_published: 2024-04-19T00:00:00Z date_updated: 2026-10-16T10:42:55Z day: '19' department: - _id: MaMo - _id: MaRo doi: 10.1109/ICASSP48485.2024.10447198 external_id: isi: - '001396233806078' fulldoi: https://doi.org/10.1109/ICASSP48485.2024.10447198 isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://openreview.net/forum?id=aQYCDxfZV0 month: '04' oa: 1 oa_version: Submitted Version page: 13151-13155 project: - _id: 059876FA-7A3F-11EA-A408-12923DDC885E name: Prix Lopez-Loretta 2019 - Marco Mondelli - _id: 9B8D11D6-BA93-11EA-9121-9846C619BF3A grant_number: PCEGP3_181181 name: Improving estimation and prediction of common complex disease risk publication: 2024 IEEE International Conference on Acoustics, Speech, and Signal Processing publication_identifier: isbn: - '9798350344851' issn: - 1520-6149 publication_status: published publisher: IEEE quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: Inference of genetic effects via approximate message passing type: conference user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- OA_place: repository OA_type: green _id: '18973' abstract: - lang: eng text: 'Understanding the reasons behind the exceptional success of transformers requires a better analysis of why attention layers are suitable for NLP tasks. In particular, such tasks require predictive models to capture contextual meaning which often depends on one or few words, even if the sentence is long. Our work studies this key property, dubbed word sensitivity (WS), in the prototypical setting of random features. We show that attention layers enjoy high WS, namely, there exists a vector in the space of embeddings that largely perturbs the random attention features map. The argument critically exploits the role of the softmax in the attention layer, highlighting its benefit compared to other activations (e.g., ReLU). In contrast, the WS of standard random features is of order 1/n−−√, n being the number of words in the textual sample, and thus it decays with the length of the context. We then translate these results on the word sensitivity into generalization bounds: due to their low WS, random features provably cannot learn to distinguish between two sentences that differ only in a single word; in contrast, due to their high WS, random attention features have higher generalization capabilities. We validate our theoretical results with experimental evidence over the BERT-Base word embeddings of the imdb review dataset.' acknowledgement: The authors were partially supported by the 2019 LopezLoreta prize, and they would like to thank Mohammad Hossein Amani, Lorenzo Beretta, and Clement Rebuffel for helpful discussions. alternative_title: - PMLR article_processing_charge: No arxiv: 1 author: - first_name: Simone full_name: Bombari, Simone id: ca726dda-de17-11ea-bc14-f9da834f63aa last_name: Bombari - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 citation: ama: 'Bombari S, Mondelli M. Towards understanding the word sensitivity of attention layers: A study via random features. In: 41st International Conference on Machine Learning. Vol 235. ML Research Press; 2024:4300-4328.' apa: 'Bombari, S., & Mondelli, M. (2024). Towards understanding the word sensitivity of attention layers: A study via random features. In 41st International Conference on Machine Learning (Vol. 235, pp. 4300–4328). Vienna, Austria: ML Research Press.' chicago: 'Bombari, Simone, and Marco Mondelli. “Towards Understanding the Word Sensitivity of Attention Layers: A Study via Random Features.” In 41st International Conference on Machine Learning, 235:4300–4328. ML Research Press, 2024.' ieee: 'S. Bombari and M. Mondelli, “Towards understanding the word sensitivity of attention layers: A study via random features,” in 41st International Conference on Machine Learning, Vienna, Austria, 2024, vol. 235, pp. 4300–4328.' ista: 'Bombari S, Mondelli M. 2024. Towards understanding the word sensitivity of attention layers: A study via random features. 41st International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 235, 4300–4328.' mla: 'Bombari, Simone, and Marco Mondelli. “Towards Understanding the Word Sensitivity of Attention Layers: A Study via Random Features.” 41st International Conference on Machine Learning, vol. 235, ML Research Press, 2024, pp. 4300–28.' short: S. Bombari, M. Mondelli, in:, 41st International Conference on Machine Learning, ML Research Press, 2024, pp. 4300–4328. conference: end_date: 2024-07-27 location: Vienna, Austria name: 'ICML: International Conference on Machine Learning' start_date: 2024-07-21 corr_author: '1' das_tickbox: '0' date_created: 2025-01-30T07:35:49Z date_published: 2024-07-30T00:00:00Z date_updated: 2026-10-16T10:42:17Z day: '30' department: - _id: MaMo external_id: arxiv: - '2402.02969' intvolume: ' 235' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2402.02969 month: '07' oa: 1 oa_version: Preprint page: 4300-4328 project: - _id: 059876FA-7A3F-11EA-A408-12923DDC885E name: Prix Lopez-Loretta 2019 - Marco Mondelli publication: 41st International Conference on Machine Learning publication_identifier: eissn: - 2640-3498 publication_status: published publisher: ML Research Press quality_controlled: '1' related_material: record: - id: '22857' relation: dissertation_contains status: public researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: 'Towards understanding the word sensitivity of attention layers: A study via random features' type: conference user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 235 year: '2024' ... --- OA_place: repository OA_type: green _id: '18972' abstract: - lang: eng text: 'Deep learning models are known to overfit and memorize spurious features in the training dataset. While numerous empirical studies have aimed at understanding this phenomenon, a rigorous theoretical framework to quantify it is still missing. In this paper, we consider spurious features that are uncorrelated with the learning task, and we provide a precise characterization of how they are memorized via two separate terms: (i) the stability of the model with respect to individual training samples, and (ii) the feature alignment between the spurious pattern and the full sample. While the first term is well established in learning theory and it is connected to the generalization error in classical work, the second one is, to the best of our knowledge, novel. Our key technical result gives a precise characterization of the feature alignment for the two prototypical settings of random features (RF) and neural tangent kernel (NTK) regression. We prove that the memorization of spurious features weakens as the generalization capability increases and, through the analysis of the feature alignment, we unveil the role of the model and of its activation function. Numerical experiments show the predictive power of our theory on standard datasets (MNIST, CIFAR-10).' acknowledgement: "The authors were partially supported by the 2019 LopezLoreta prize, and they would like to thank (in alphabetical order) Grigorios Chrysos, Simone Maria Giancola, Mahyar\r\nJafari Nodeh, Christoph Lampert, Marco Miani, GuanWen Qiu, and Peter Sukenık for helpful discussions." alternative_title: - PMLR article_processing_charge: No arxiv: 1 author: - first_name: Simone full_name: Bombari, Simone id: ca726dda-de17-11ea-bc14-f9da834f63aa last_name: Bombari - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 citation: ama: 'Bombari S, Mondelli M. How spurious features are memorized: Precise analysis for random and NTK features. In: 41st International Conference on Machine Learning. Vol 235. ML Research Press; 2024:4267-4299.' apa: 'Bombari, S., & Mondelli, M. (2024). How spurious features are memorized: Precise analysis for random and NTK features. In 41st International Conference on Machine Learning (Vol. 235, pp. 4267–4299). Vienna, Austria: ML Research Press.' chicago: 'Bombari, Simone, and Marco Mondelli. “How Spurious Features Are Memorized: Precise Analysis for Random and NTK Features.” In 41st International Conference on Machine Learning, 235:4267–99. ML Research Press, 2024.' ieee: 'S. Bombari and M. Mondelli, “How spurious features are memorized: Precise analysis for random and NTK features,” in 41st International Conference on Machine Learning, Vienna, Austria, 2024, vol. 235, pp. 4267–4299.' ista: 'Bombari S, Mondelli M. 2024. How spurious features are memorized: Precise analysis for random and NTK features. 41st International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 235, 4267–4299.' mla: 'Bombari, Simone, and Marco Mondelli. “How Spurious Features Are Memorized: Precise Analysis for Random and NTK Features.” 41st International Conference on Machine Learning, vol. 235, ML Research Press, 2024, pp. 4267–99.' short: S. Bombari, M. Mondelli, in:, 41st International Conference on Machine Learning, ML Research Press, 2024, pp. 4267–4299. conference: end_date: 2024-07-27 location: Vienna, Austria name: 'ICML: International Conference on Machine Learning' start_date: 2024-07-21 corr_author: '1' das_tickbox: '0' date_created: 2025-01-30T07:29:47Z date_published: 2024-07-30T00:00:00Z date_updated: 2026-10-16T10:42:37Z day: '30' department: - _id: MaMo external_id: arxiv: - '2305.12100' intvolume: ' 235' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2305.12100 month: '07' oa: 1 oa_version: Preprint page: 4267-4299 project: - _id: 059876FA-7A3F-11EA-A408-12923DDC885E name: Prix Lopez-Loretta 2019 - Marco Mondelli publication: 41st International Conference on Machine Learning publication_identifier: eissn: - 2640-3498 publication_status: published publisher: ML Research Press quality_controlled: '1' related_material: record: - id: '22857' relation: dissertation_contains status: public researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: yes title: 'How spurious features are memorized: Precise analysis for random and NTK features' type: conference user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 235 year: '2024' ... --- OA_place: repository OA_type: green _id: '17330' abstract: - lang: eng text: In this work we consider the list-decodability and list-recoverability of arbitrary q -ary codes, for all integer values of q ⩾ 2. A code is called ( p , L ) q -list-decodable if every radius pn Hamming ball contains less than L codewords; ( p , ℓ, L ) q -recoverability is a generalization where we place radius pn Hamming balls on every point of a combinatorial rectangle with side length ℓ and again stipulate that there be less than L codewords. Our main contribution is to precisely calculate the maximum value of p for which there exist infinite families of positive rate ( p , ℓ, L ) q -list-recoverable codes, the quantity we call the zero-rate threshold . Denoting this value by p *, we in fact show that codes correcting a p * + ε fraction of errors must have size O ε (1), i.e., independent of n . Such a result is typically referred to as a “Plotkin bound.” To complement this, a standard random code with expurgation construction shows that there exist positive rate codes correcting a p * − ε fraction of errors. We also follow a classical proof template (typically attributed to Elias and Bassalygo) to derive from the zero-rate threshold other tradeoffs between rate and decoding radius for list-decoding and list-recovery. Technically, proving the Plotkin bound boils down to demon-strating the Schur convexity of a certain function defined on the q -simplex as well as the convexity of a univariate function derived from it. We remark that an earlier argument claimed similar results for q -ary list-decoding; however, we point out that this earlier proof is flawed. acknowledgement: Part of this work was done while Nicolas Resch was affiliated with the Centrum Wiskunde & Informatica and supported in part by ERC H2020 grant No.74079 (ALGSTRONGCRYPTO). Chen Yuan is supported in part by the National Key Research and Development Projects under Grant 2022YFA1004900 and Grant 2021YFE0109900, the National Natural Science Foundation of China under Grant 12101403 and Grant 12031011. article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Nicolas full_name: Resch, Nicolas last_name: Resch - first_name: Chen full_name: Yuan, Chen last_name: Yuan - first_name: Yihan full_name: Zhang, Yihan id: 2ce5da42-b2ea-11eb-bba5-9f264e9d002c last_name: Zhang orcid: 0000-0002-6465-6258 citation: ama: Resch N, Yuan C, Zhang Y. Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery. IEEE Transactions on Information Theory. 2024;70(9):6211-6238. doi:10.1109/TIT.2024.3430842 apa: Resch, N., Yuan, C., & Zhang, Y. (2024). Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery. IEEE Transactions on Information Theory. IEEE. https://doi.org/10.1109/TIT.2024.3430842 chicago: Resch, Nicolas, Chen Yuan, and Yihan Zhang. “Zero-Rate Thresholds and New Capacity Bounds for List-Decoding and List-Recovery.” IEEE Transactions on Information Theory. IEEE, 2024. https://doi.org/10.1109/TIT.2024.3430842. ieee: N. Resch, C. Yuan, and Y. Zhang, “Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery,” IEEE Transactions on Information Theory, vol. 70, no. 9. IEEE, pp. 6211–6238, 2024. ista: Resch N, Yuan C, Zhang Y. 2024. Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery. IEEE Transactions on Information Theory. 70(9), 6211–6238. mla: Resch, Nicolas, et al. “Zero-Rate Thresholds and New Capacity Bounds for List-Decoding and List-Recovery.” IEEE Transactions on Information Theory, vol. 70, no. 9, IEEE, 2024, pp. 6211–38, doi:10.1109/TIT.2024.3430842. short: N. Resch, C. Yuan, Y. Zhang, IEEE Transactions on Information Theory 70 (2024) 6211–6238. corr_author: '1' das_tickbox: '0' date_created: 2024-07-28T22:01:10Z date_published: 2024-09-01T00:00:00Z date_updated: 2026-10-16T10:41:59Z day: '01' department: - _id: MaMo doi: 10.1109/TIT.2024.3430842 external_id: arxiv: - '2210.07754' isi: - '001299623600019' fulldoi: https://doi.org/10.1109/TIT.2024.3430842 intvolume: ' 70' isi: 1 issue: '9' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2210.07754 month: '09' oa: 1 oa_version: Preprint page: 6211-6238 publication: IEEE Transactions on Information Theory publication_identifier: eissn: - 1557-9654 issn: - 0018-9448 publication_status: published publisher: IEEE quality_controlled: '1' related_material: record: - id: '14083' relation: earlier_version status: public researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 70 year: '2024' ...