[{"issue":"7","_id":"20029","year":"2025","oa_version":"Published Version","title":"Arabidopsis phospholipase Dζ2 facilitates vacuolar acidification and autophagy under phosphorus starvation by interacting with VATD","article_processing_charge":"Yes (in subscription journal)","pmid":1,"month":"07","date_published":"2025-07-22T00:00:00Z","scopus_import":"1","abstract":[{"text":"Vacuolar acidification is crucial for the homeostasis of intracellular pH and the recycling of proteins and nutrients in cells, thereby playing important roles in various physiological processes related to vacuolar function. The key factors regulating vacuolar acidification and underlying mechanisms remain unclear. Here, we report that Arabidopsis phospholipase Dζ2 (PLDζ2) promotes the acidification of the vacuolar lumen to stimulate autophagic degradation under phosphorus deficiency. The pldζ2 mutant massively accumulates autophagic structures while exhibiting premature leaf senescence under nutrient starvation. Impaired autophagic flux, lytic vacuole morphology, and lytic degradation in pldζ2 indicate that PLDζ2 regulates autophagy by affecting the vacuolar function. PLDζ2 locates in both tonoplast and cytoplasm. Genetic, structural, and biochemical studies demonstrate that PLDζ2 directly interacts with vacuolar-type ATPase (V-ATPase) subunit D (VATD) to promote vacuolar acidification and autophagy under phosphorus starvation. These findings reveal the importance of V-ATPase and vacuolar pH in autophagic activity and provide clues in elucidating the regulatory mechanism of vacuolar acidification.","lang":"eng"}],"status":"public","OA_type":"hybrid","ddc":["580"],"acknowledgement":"The study was supported by National Natural Science Foundation of China (NSFC, 92354301, 32230011, 32200274, and 91954206). The computations were run on the Siyuan-1 cluster supported by the Center for High-Performance Computing at Shanghai Jiao Tong University.","publication_status":"published","article_type":"original","author":[{"id":"56aad729-cca2-11ed-a45a-9b4138991a48","full_name":"Guan, Bin","first_name":"Bin","last_name":"Guan"},{"last_name":"Xie","first_name":"Ke Xuan","full_name":"Xie, Ke Xuan"},{"full_name":"Du, Xin Qiao","first_name":"Xin Qiao","last_name":"Du"},{"last_name":"Bai","full_name":"Bai, Yu Xuan","first_name":"Yu Xuan"},{"last_name":"Hao","first_name":"Peng Chao","full_name":"Hao, Peng Chao"},{"full_name":"Lin, Wen Hui","first_name":"Wen Hui","last_name":"Lin"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"},{"full_name":"Xue, Hong Wei","first_name":"Hong Wei","last_name":"Xue"}],"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file":[{"checksum":"ee03deee47a084b0295251dc49470ad4","success":1,"date_updated":"2025-07-22T08:52:17Z","file_name":"2025_CellReports_Guan.pdf","access_level":"open_access","date_created":"2025-07-22T08:52:17Z","creator":"dernst","content_type":"application/pdf","relation":"main_file","file_size":37708120,"file_id":"20067"}],"oa":1,"citation":{"chicago":"Guan, Bin, Ke Xuan Xie, Xin Qiao Du, Yu Xuan Bai, Peng Chao Hao, Wen Hui Lin, Jiří Friml, and Hong Wei Xue. “Arabidopsis Phospholipase Dζ2 Facilitates Vacuolar Acidification and Autophagy under Phosphorus Starvation by Interacting with VATD.” Cell Reports. Elsevier, 2025. https://doi.org/10.1016/j.celrep.2025.116024.","ama":"Guan B, Xie KX, Du XQ, et al. Arabidopsis phospholipase Dζ2 facilitates vacuolar acidification and autophagy under phosphorus starvation by interacting with VATD. Cell Reports. 2025;44(7). doi:10.1016/j.celrep.2025.116024","apa":"Guan, B., Xie, K. X., Du, X. Q., Bai, Y. X., Hao, P. C., Lin, W. H., … Xue, H. W. (2025). Arabidopsis phospholipase Dζ2 facilitates vacuolar acidification and autophagy under phosphorus starvation by interacting with VATD. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2025.116024","ista":"Guan B, Xie KX, Du XQ, Bai YX, Hao PC, Lin WH, Friml J, Xue HW. 2025. Arabidopsis phospholipase Dζ2 facilitates vacuolar acidification and autophagy under phosphorus starvation by interacting with VATD. Cell Reports. 44(7), 116024.","mla":"Guan, Bin, et al. “Arabidopsis Phospholipase Dζ2 Facilitates Vacuolar Acidification and Autophagy under Phosphorus Starvation by Interacting with VATD.” Cell Reports, vol. 44, no. 7, 116024, Elsevier, 2025, doi:10.1016/j.celrep.2025.116024.","ieee":"B. Guan et al., “Arabidopsis phospholipase Dζ2 facilitates vacuolar acidification and autophagy under phosphorus starvation by interacting with VATD,” Cell Reports, vol. 44, no. 7. Elsevier, 2025.","short":"B. Guan, K.X. Xie, X.Q. Du, Y.X. Bai, P.C. Hao, W.H. Lin, J. Friml, H.W. Xue, Cell Reports 44 (2025)."},"volume":44,"doi":"10.1016/j.celrep.2025.116024","day":"22","publisher":"Elsevier","type":"journal_article","publication":"Cell Reports","quality_controlled":"1","language":[{"iso":"eng"}],"intvolume":" 44","publication_identifier":{"eissn":["2211-1247"],"issn":["2639-1856"]},"has_accepted_license":"1","OA_place":"publisher","date_updated":"2025-09-30T14:05:28Z","external_id":{"pmid":["40668679"],"isi":["001533244800001"]},"date_created":"2025-07-20T22:02:01Z","file_date_updated":"2025-07-22T08:52:17Z","department":[{"_id":"JiFr"}],"article_number":"116024","tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"}},{"OA_type":"gold","acknowledgement":"We thank the referee for the feedback and suggestions that greatly improved the quality of this manuscript. We would like to thank Carlos Contreras, Matías Díaz, Carla Fuentes, Mauricio Martínez, Alberto Pastén, Roger Leiton, Hugo Rivera, and Gabriel Prieto for their help and support during the Magellan/FIRE observations. We would also like to thank Rongmon Bordoloi for helpful discussions. R.A.M. acknowledges support from the Swiss National Science Foundation (SNSF) through project grant 200020_207349. This Letter includes data gathered with the 6.5 m Magellan Telescopes located at Las Campanas Observatory, Chile.\r\nBased on observations collected at the European Southern Observatory under ESO programs 106.215A and 096.A-0418.\r\n\r\nThe HST data presented in this Letter were obtained from the Mikulski Archive for Space Telescopes (MAST) at the Space Telescope Science Institute. The observations analyzed in this work can be accessed via doi:10.17909/gxmz-zd87.","arxiv":1,"ddc":["520"],"abstract":[{"text":"We report the discovery of a Lyα emitter (LAE) candidate in the immediate foreground of the quasar PSO J158-14 at zQSO = 6.0685 at a projected distance ∼29 pkpc that is associated with an extremely metal-poor absorption system. This system was found in archival observations of the quasar field with the Very Large Telescope (VLT)/Multi-Unit Spectroscopic Explorer (MUSE) and was previously missed in searches of absorption systems using quasar absorption line spectroscopy, as it imparts no detectable metal absorption lines on the background quasar spectrum. The detected Lyα emission line at a redshift of zLAE = 6.0323 is well aligned with the outer edge of the quasar’s proximity zone and can plausibly cause its observed damping wing if it is associated with a proximate subdamped Lyα absorption system with a column density of log Nhi/cm^-2 19.7. A >10 hr medium-resolution spectrum of the quasar observed with the Magellan/Folded-port InfraRed Echellette (FIRE) and VLT/X-Shooter spectrographs reveals a metallicity constraint of [Z/H] < −3. Such low metallicity makes this system an extremely metal-poor galaxy candidate and provides an exciting site to study possible signatures of Population III stars.","lang":"eng"}],"scopus_import":"1","date_published":"2025-07-10T00:00:00Z","status":"public","file":[{"file_id":"20066","relation":"main_file","file_size":6453728,"content_type":"application/pdf","date_created":"2025-07-22T08:38:14Z","creator":"dernst","access_level":"open_access","file_name":"2025_AstrophysicalJourLetters_Durovcikova.pdf","date_updated":"2025-07-22T08:38:14Z","success":1,"checksum":"75d0c08514209fc6e3078fdec8e815a2"}],"isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"article_type":"original","publication_status":"published","author":[{"last_name":"Ďurovčíková","full_name":"Ďurovčíková, Dominika","first_name":"Dominika"},{"first_name":"Anna Christina","full_name":"Eilers, Anna Christina","last_name":"Eilers"},{"full_name":"Simcoe, Robert A.","first_name":"Robert A.","last_name":"Simcoe"},{"last_name":"Welsh","first_name":"Louise","full_name":"Welsh, Louise"},{"first_name":"Romain A.","full_name":"Meyer, Romain A.","last_name":"Meyer"},{"orcid":"0000-0003-2871-127X","last_name":"Matthee","first_name":"Jorryt J","full_name":"Matthee, Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720"},{"first_name":"Emma V.","full_name":"Ryan-Weber, Emma V.","last_name":"Ryan-Weber"},{"full_name":"Yue, Minghao","first_name":"Minghao","last_name":"Yue"},{"full_name":"Katz, Harley","first_name":"Harley","last_name":"Katz"},{"last_name":"Satyavolu","first_name":"Sindhu","full_name":"Satyavolu, Sindhu"},{"full_name":"Becker, George","first_name":"George","last_name":"Becker"},{"first_name":"Frederick B.","full_name":"Davies, Frederick B.","last_name":"Davies"},{"last_name":"Farina","first_name":"Emanuele Paolo","full_name":"Farina, Emanuele Paolo"}],"title":"An extremely metal-poor Lyα emitter candidate at z = 6 revealed through absorption spectroscopy","year":"2025","issue":"2","_id":"20030","oa_version":"Published Version","month":"07","article_processing_charge":"Yes","date_updated":"2026-02-16T12:44:23Z","OA_place":"publisher","has_accepted_license":"1","external_id":{"arxiv":["2505.01499"],"isi":["001524847100001"]},"intvolume":" 987","language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"eissn":["2041-8213"],"issn":["2041-8205"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2025-07-20T22:02:01Z","file_date_updated":"2025-07-22T08:38:14Z","article_number":"L33","PlanS_conform":"1","department":[{"_id":"JoMa"}],"doi":"10.3847/2041-8213/ade71c","publisher":"IOP Publishing","day":"10","type":"journal_article","citation":{"ieee":"D. Ďurovčíková et al., “An extremely metal-poor Lyα emitter candidate at z = 6 revealed through absorption spectroscopy,” The Astrophysical Journal Letters, vol. 987, no. 2. IOP Publishing, 2025.","mla":"Ďurovčíková, Dominika, et al. “An Extremely Metal-Poor Lyα Emitter Candidate at z = 6 Revealed through Absorption Spectroscopy.” The Astrophysical Journal Letters, vol. 987, no. 2, L33, IOP Publishing, 2025, doi:10.3847/2041-8213/ade71c.","apa":"Ďurovčíková, D., Eilers, A. C., Simcoe, R. A., Welsh, L., Meyer, R. A., Matthee, J. J., … Farina, E. P. (2025). An extremely metal-poor Lyα emitter candidate at z = 6 revealed through absorption spectroscopy. The Astrophysical Journal Letters. IOP Publishing. https://doi.org/10.3847/2041-8213/ade71c","ista":"Ďurovčíková D, Eilers AC, Simcoe RA, Welsh L, Meyer RA, Matthee JJ, Ryan-Weber EV, Yue M, Katz H, Satyavolu S, Becker G, Davies FB, Farina EP. 2025. An extremely metal-poor Lyα emitter candidate at z = 6 revealed through absorption spectroscopy. The Astrophysical Journal Letters. 987(2), L33.","short":"D. Ďurovčíková, A.C. Eilers, R.A. Simcoe, L. Welsh, R.A. Meyer, J.J. Matthee, E.V. Ryan-Weber, M. Yue, H. Katz, S. Satyavolu, G. Becker, F.B. Davies, E.P. Farina, The Astrophysical Journal Letters 987 (2025).","chicago":"Ďurovčíková, Dominika, Anna Christina Eilers, Robert A. Simcoe, Louise Welsh, Romain A. Meyer, Jorryt J Matthee, Emma V. Ryan-Weber, et al. “An Extremely Metal-Poor Lyα Emitter Candidate at z = 6 Revealed through Absorption Spectroscopy.” The Astrophysical Journal Letters. IOP Publishing, 2025. https://doi.org/10.3847/2041-8213/ade71c.","ama":"Ďurovčíková D, Eilers AC, Simcoe RA, et al. An extremely metal-poor Lyα emitter candidate at z = 6 revealed through absorption spectroscopy. The Astrophysical Journal Letters. 2025;987(2). doi:10.3847/2041-8213/ade71c"},"DOAJ_listed":"1","volume":987,"publication":"The Astrophysical Journal Letters"},{"date_updated":"2025-09-30T14:04:16Z","external_id":{"pmid":["40056424"],"isi":["001482869200001"]},"intvolume":" 76","quality_controlled":"1","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1460-2431"],"issn":["0022-0957"]},"date_created":"2025-07-20T22:02:01Z","department":[{"_id":"JiFr"}],"page":"2700-2714","publisher":"Oxford University Press","day":"02","doi":"10.1093/jxb/eraf084","type":"journal_article","citation":{"ama":"Osorio-Navarro C, Neira-Valenzuela G, Sierra P, Adamowski M, Toledo J, Norambuena L. The configuration of the vacuole is driven by clathrin-mediated trafficking in root cells of Arabidopsis thaliana. Journal of Experimental Botany. 2025;76(10):2700-2714. doi:10.1093/jxb/eraf084","chicago":"Osorio-Navarro, Claudio, Gabriel Neira-Valenzuela, Paula Sierra, Maciek Adamowski, Jorge Toledo, and Lorena Norambuena. “The Configuration of the Vacuole Is Driven by Clathrin-Mediated Trafficking in Root Cells of Arabidopsis Thaliana.” Journal of Experimental Botany. Oxford University Press, 2025. https://doi.org/10.1093/jxb/eraf084.","short":"C. Osorio-Navarro, G. Neira-Valenzuela, P. Sierra, M. Adamowski, J. Toledo, L. Norambuena, Journal of Experimental Botany 76 (2025) 2700–2714.","apa":"Osorio-Navarro, C., Neira-Valenzuela, G., Sierra, P., Adamowski, M., Toledo, J., & Norambuena, L. (2025). The configuration of the vacuole is driven by clathrin-mediated trafficking in root cells of Arabidopsis thaliana. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/eraf084","ista":"Osorio-Navarro C, Neira-Valenzuela G, Sierra P, Adamowski M, Toledo J, Norambuena L. 2025. The configuration of the vacuole is driven by clathrin-mediated trafficking in root cells of Arabidopsis thaliana. Journal of Experimental Botany. 76(10), 2700–2714.","mla":"Osorio-Navarro, Claudio, et al. “The Configuration of the Vacuole Is Driven by Clathrin-Mediated Trafficking in Root Cells of Arabidopsis Thaliana.” Journal of Experimental Botany, vol. 76, no. 10, Oxford University Press, 2025, pp. 2700–14, doi:10.1093/jxb/eraf084.","ieee":"C. Osorio-Navarro, G. Neira-Valenzuela, P. Sierra, M. Adamowski, J. Toledo, and L. Norambuena, “The configuration of the vacuole is driven by clathrin-mediated trafficking in root cells of Arabidopsis thaliana,” Journal of Experimental Botany, vol. 76, no. 10. Oxford University Press, pp. 2700–2714, 2025."},"volume":76,"publication":"Journal of Experimental Botany","OA_type":"closed access","acknowledgement":"This research was supported by FONDECYT grants 1170950 and 1211311 and by ANID PhD fellowship 2020-21201663 to PhD student CO-N. The microscopes used in this work were funded by grants FONDEQUIP #EQM 140019 and #EQM12-0003 at the Advanced Microscopy Unit of the Biology Department, Faculty of Science, University of Chile.\r\nWe thank Jiri Friml for donating the XVE»AUXILIN-LIKE2 (AX2) line to support our research. We wish to acknowledge the active and helpful discussion of all the members of the LNM team and the Plant Molecular Biology Centre at Universidad de Chile.","scopus_import":"1","abstract":[{"lang":"eng","text":"The central vacuole is a multifunctional organelle with the most significant occupancy in a differentiated plant cell. Plants depend on the function of the vacuole for critical development, growth, and environmental responses. As the cell expands, the vacuole changes shape and size, increasing its membrane and luminal content. The set of these events is called the vacuolar configuration process, which has not been well described. Our research highlights the impact of plasma membrane internalization on vacuole morphology during the vacuolar configuration process. We observed a direct correlation between differential endocytosis rates and the enrichment of vacuolar membranous structures. Chemical and genetic interference with clathrin-mediated endocytosis (CME) revealed that it is required for the vacuolar configuration of growing root cells. The contribution of CME to the vacuole configuration process co-occurs with the induction of post-trans-Golgi network (TGN)/early endosome (EE) trafficking with the participation of the Rab GTPases ARA6 and ARA7. Our results show that the CME plays an active role during vacuole configuration, most probably carrying the material that allows the establishment of the vacuole in elongating cells. Since membrane trafficking through the EE/TGN is required to reach the vacuole, additional players must be defined."}],"date_published":"2025-07-02T00:00:00Z","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"publication_status":"published","article_type":"original","author":[{"first_name":"Claudio","full_name":"Osorio-Navarro, Claudio","last_name":"Osorio-Navarro"},{"full_name":"Neira-Valenzuela, Gabriel","first_name":"Gabriel","last_name":"Neira-Valenzuela"},{"first_name":"Paula","full_name":"Sierra, Paula","last_name":"Sierra"},{"orcid":"0000-0001-6463-5257","last_name":"Adamowski","first_name":"Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","full_name":"Adamowski, Maciek"},{"last_name":"Toledo","first_name":"Jorge","full_name":"Toledo, Jorge"},{"last_name":"Norambuena","first_name":"Lorena","full_name":"Norambuena, Lorena"}],"title":"The configuration of the vacuole is driven by clathrin-mediated trafficking in root cells of Arabidopsis thaliana","year":"2025","issue":"10","_id":"20031","oa_version":"None","pmid":1,"month":"07","article_processing_charge":"No"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"department":[{"_id":"DaAl"},{"_id":"FrLo"}],"date_created":"2025-07-20T22:02:01Z","file_date_updated":"2025-07-22T07:58:22Z","corr_author":"1","external_id":{"arxiv":["2410.06074"]},"has_accepted_license":"1","OA_place":"publisher","date_updated":"2025-08-04T08:03:11Z","publication_identifier":{"isbn":["9798331320850"]},"quality_controlled":"1","language":[{"iso":"eng"}],"publication":"13th International Conference on Learning Representations","type":"conference","related_material":{"link":[{"relation":"software","url":"https://github.com/IST-DASLab/ScalableMNN"}]},"publisher":"ICLR","day":"01","page":"63716-63737","citation":{"short":"J. Chen, D. Yao, A.A. Pervez, D.-A. Alistarh, F. Locatello, in:, 13th International Conference on Learning Representations, ICLR, 2025, pp. 63716–63737.","apa":"Chen, J., Yao, D., Pervez, A. A., Alistarh, D.-A., & Locatello, F. (2025). Scalable mechanistic neural networks. In 13th International Conference on Learning Representations (pp. 63716–63737). Singapore, Singapore: ICLR.","mla":"Chen, Jiale, et al. “Scalable Mechanistic Neural Networks.” 13th International Conference on Learning Representations, ICLR, 2025, pp. 63716–37.","ista":"Chen J, Yao D, Pervez AA, Alistarh D-A, Locatello F. 2025. Scalable mechanistic neural networks. 13th International Conference on Learning Representations. ICLR: International Conference on Learning Representations, 63716–63737.","ieee":"J. Chen, D. Yao, A. A. Pervez, D.-A. Alistarh, and F. Locatello, “Scalable mechanistic neural networks,” in 13th International Conference on Learning Representations, Singapore, Singapore, 2025, pp. 63716–63737.","ama":"Chen J, Yao D, Pervez AA, Alistarh D-A, Locatello F. Scalable mechanistic neural networks. In: 13th International Conference on Learning Representations. ICLR; 2025:63716-63737.","chicago":"Chen, Jiale, Dingling Yao, Adeel A Pervez, Dan-Adrian Alistarh, and Francesco Locatello. “Scalable Mechanistic Neural Networks.” In 13th International Conference on Learning Representations, 63716–37. ICLR, 2025."},"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"checksum":"64cfdb12ae3e4e8ba57b1403e1066776","success":1,"file_name":"2025_ICLR_Chen.pdf","date_updated":"2025-07-22T07:58:22Z","creator":"dernst","date_created":"2025-07-22T07:58:22Z","access_level":"open_access","content_type":"application/pdf","file_size":732745,"relation":"main_file","file_id":"20065"}],"author":[{"last_name":"Chen","orcid":"0000-0001-5337-5875","first_name":"Jiale","full_name":"Chen, Jiale","id":"4d0a9064-1ff6-11ee-9fa6-ec046c604785"},{"last_name":"Yao","full_name":"Yao, Dingling","id":"d3e02e50-48a8-11ee-8f62-c108061797fa","first_name":"Dingling"},{"full_name":"Pervez, Adeel A","id":"fca6d90c-d47f-11ee-bc87-93ff51604981","first_name":"Adeel A","last_name":"Pervez"},{"last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"},{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","full_name":"Locatello, Francesco","first_name":"Francesco","orcid":"0000-0002-4850-0683","last_name":"Locatello"}],"publication_status":"published","ddc":["000"],"arxiv":1,"conference":{"name":"ICLR: International Conference on Learning Representations","end_date":"2025-04-28","start_date":"2025-04-24","location":"Singapore, Singapore"},"OA_type":"diamond","status":"public","date_published":"2025-04-01T00:00:00Z","abstract":[{"lang":"eng","text":"We propose Scalable Mechanistic Neural Network (S-MNN), an enhanced neural network framework designed for scientific machine learning applications involving long temporal sequences. By reformulating the original Mechanistic Neural Network (MNN) (Pervez et al., 2024), we reduce the computational time and space complexities from cubic and quadratic with respect to the sequence length, respectively, to linear. This significant improvement enables efficient modeling of long-term dynamics without sacrificing accuracy or interpretability. Extensive experiments demonstrate that S-MNN matches the original MNN in precision while substantially reducing computational resources. Consequently, S-MNN can drop-in replace the original MNN in applications, providing a practical and efficient tool for integrating mechanistic bottlenecks into neural network models of complex dynamical systems. Source code is available at https://github.com/IST-DASLab/ScalableMNN."}],"scopus_import":"1","month":"04","article_processing_charge":"No","title":"Scalable mechanistic neural networks","oa_version":"Published Version","_id":"20032","year":"2025"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"checksum":"5a38b093ebb4ee4eb662ea142621a5ca","success":1,"file_name":"2025_ICLR_Ildiz.pdf","date_updated":"2025-08-04T08:32:38Z","creator":"dernst","date_created":"2025-08-04T08:32:38Z","access_level":"open_access","content_type":"application/pdf","file_size":528171,"relation":"main_file","file_id":"20112"}],"oa":1,"publication_status":"published","project":[{"grant_number":"101161364","_id":"911e6d1f-16d5-11f0-9cad-c5c68c6a1cdf","name":"Inference in High Dimensions: Light-speed Algorithms and Information Limits"}],"author":[{"first_name":"M.","full_name":"Emrullah Ildiz, M.","last_name":"Emrullah Ildiz"},{"first_name":"Halil Alperen","full_name":"Gozeten, Halil Alperen","last_name":"Gozeten"},{"first_name":"Ege Onur","full_name":"Taga, Ege Onur","last_name":"Taga"},{"id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco","first_name":"Marco","orcid":"0000-0002-3242-7020","last_name":"Mondelli"},{"first_name":"Samet","full_name":"Oymak, Samet","last_name":"Oymak"}],"OA_type":"diamond","arxiv":1,"ddc":["000"],"conference":{"name":"ICLR: International Conference on Learning Representations","end_date":"2025-04-28","start_date":"2025-04-24","location":"Singapore, Singapore"},"acknowledgement":"M.E.I., H.A.G., E.O.T., S.O. are supported by the NSF grants CCF-2046816, CCF-2403075, the Office of Naval Research grant N000142412289, an OpenAI Agentic AI Systems grant, and gifts by Open Philanthropy and Google Research. M. M. is funded by the European Union (ERC, INF2, project number 101161364). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council Executive Agency. Neither the European Union nor the granting authority can be held responsible for them.","scopus_import":"1","abstract":[{"text":"A growing number of machine learning scenarios rely on knowledge distillation where one uses the output of a surrogate model as labels to supervise the training of a target model. In this work, we provide a sharp characterization of this process for ridgeless, high-dimensional regression, under two settings: (i) model shift, where the surrogate model is arbitrary, and (ii) distribution shift, where the surrogate model is the solution of empirical risk minimization with out-of-distribution data. In both cases, we characterize the precise risk of the target model through non-asymptotic bounds in terms of sample size and data distribution under mild conditions. As a consequence, we identify the form of the optimal surrogate model, which reveals the benefits and limitations of discarding weak features in a data-dependent fashion. In the context of weak-to-strong (W2S) generalization, this has the interpretation that (i) W2S training, with the surrogate as the weak model, can provably outperform training with strong labels under the same data budget, but (ii) it is unable to improve the data scaling law. We validate our results on numerical experiments both on ridgeless regression and on neural network architectures.","lang":"eng"}],"date_published":"2025-04-01T00:00:00Z","status":"public","month":"04","article_processing_charge":"No","title":"High-dimensional analysis of knowledge distillation: Weak-to-Strong generalization and scaling laws","_id":"20033","year":"2025","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2025-07-20T22:02:02Z","file_date_updated":"2025-08-04T08:32:38Z","department":[{"_id":"MaMo"}],"has_accepted_license":"1","OA_place":"publisher","date_updated":"2025-08-04T08:33:58Z","external_id":{"arxiv":["2410.18837"]},"language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"isbn":["9798331320850"]},"publication":"13th International Conference on Learning Representations","day":"01","publisher":"ICLR","page":"2967-3006","type":"conference","citation":{"ama":"Emrullah Ildiz M, Gozeten HA, Taga EO, Mondelli M, Oymak S. High-dimensional analysis of knowledge distillation: Weak-to-Strong generalization and scaling laws. In: 13th International Conference on Learning Representations. ICLR; 2025:2967-3006.","chicago":"Emrullah Ildiz, M., Halil Alperen Gozeten, Ege Onur Taga, Marco Mondelli, and Samet Oymak. “High-Dimensional Analysis of Knowledge Distillation: Weak-to-Strong Generalization and Scaling Laws.” In 13th International Conference on Learning Representations, 2967–3006. ICLR, 2025.","short":"M. Emrullah Ildiz, H.A. Gozeten, E.O. Taga, M. Mondelli, S. Oymak, in:, 13th International Conference on Learning Representations, ICLR, 2025, pp. 2967–3006.","ista":"Emrullah Ildiz M, Gozeten HA, Taga EO, Mondelli M, Oymak S. 2025. High-dimensional analysis of knowledge distillation: Weak-to-Strong generalization and scaling laws. 13th International Conference on Learning Representations. ICLR: International Conference on Learning Representations, 2967–3006.","apa":"Emrullah Ildiz, M., Gozeten, H. A., Taga, E. O., Mondelli, M., & Oymak, S. (2025). High-dimensional analysis of knowledge distillation: Weak-to-Strong generalization and scaling laws. In 13th International Conference on Learning Representations (pp. 2967–3006). Singapore, Singapore: ICLR.","mla":"Emrullah Ildiz, M., et al. “High-Dimensional Analysis of Knowledge Distillation: Weak-to-Strong Generalization and Scaling Laws.” 13th International Conference on Learning Representations, ICLR, 2025, pp. 2967–3006.","ieee":"M. Emrullah Ildiz, H. A. Gozeten, E. O. Taga, M. Mondelli, and S. Oymak, “High-dimensional analysis of knowledge distillation: Weak-to-Strong generalization and scaling laws,” in 13th International Conference on Learning Representations, Singapore, Singapore, 2025, pp. 2967–3006."}},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2025-07-20T22:02:02Z","file_date_updated":"2025-08-04T08:39:51Z","department":[{"_id":"DaAl"}],"date_updated":"2025-08-04T08:41:10Z","OA_place":"publisher","has_accepted_license":"1","external_id":{"arxiv":["2410.16103"]},"corr_author":"1","language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"isbn":["9798331320850"]},"publication":"13th International Conference on Learning Representations","page":"101877-101913","day":"01","publisher":"ICLR","related_material":{"link":[{"url":"https://github.com/IST-DASLab/LDAdam","relation":"software"}]},"type":"conference","citation":{"short":"T. Robert, M. Safaryan, I.-V. Modoranu, D.-A. Alistarh, in:, 13th International Conference on Learning Representations, ICLR, 2025, pp. 101877–101913.","ieee":"T. Robert, M. Safaryan, I.-V. Modoranu, and D.-A. Alistarh, “LDAdam: Adaptive optimization from low-dimensional gradient statistics,” in 13th International Conference on Learning Representations, Singapore, Singapore, 2025, pp. 101877–101913.","apa":"Robert, T., Safaryan, M., Modoranu, I.-V., & Alistarh, D.-A. (2025). LDAdam: Adaptive optimization from low-dimensional gradient statistics. In 13th International Conference on Learning Representations (pp. 101877–101913). Singapore, Singapore: ICLR.","mla":"Robert, Thomas, et al. “LDAdam: Adaptive Optimization from Low-Dimensional Gradient Statistics.” 13th International Conference on Learning Representations, ICLR, 2025, pp. 101877–913.","ista":"Robert T, Safaryan M, Modoranu I-V, Alistarh D-A. 2025. LDAdam: Adaptive optimization from low-dimensional gradient statistics. 13th International Conference on Learning Representations. ICLR: International Conference on Learning Representations, 101877–101913.","ama":"Robert T, Safaryan M, Modoranu I-V, Alistarh D-A. LDAdam: Adaptive optimization from low-dimensional gradient statistics. In: 13th International Conference on Learning Representations. ICLR; 2025:101877-101913.","chicago":"Robert, Thomas, Mher Safaryan, Ionut-Vlad Modoranu, and Dan-Adrian Alistarh. “LDAdam: Adaptive Optimization from Low-Dimensional Gradient Statistics.” In 13th International Conference on Learning Representations, 101877–913. ICLR, 2025."},"file":[{"success":1,"checksum":"9327d82569358d7bf1c3ec1a9952e721","date_updated":"2025-08-04T08:39:51Z","file_name":"2025_ICLR_Robert.pdf","content_type":"application/pdf","access_level":"open_access","date_created":"2025-08-04T08:39:51Z","creator":"dernst","file_id":"20113","file_size":1346111,"relation":"main_file"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publication_status":"published","author":[{"first_name":"Thomas","full_name":"Robert, Thomas","last_name":"Robert"},{"first_name":"Mher","full_name":"Safaryan, Mher","id":"dd546b39-0804-11ed-9c55-ef075c39778d","last_name":"Safaryan"},{"first_name":"Ionut-Vlad","full_name":"Modoranu, Ionut-Vlad","id":"449f7a18-f128-11eb-9611-9b430c0c6333","last_name":"Modoranu"},{"first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh"}],"OA_type":"diamond","conference":{"start_date":"2025-04-24","end_date":"2025-04-28","name":"ICLR: International Conference on Learning Representations","location":"Singapore, Singapore"},"arxiv":1,"ddc":["000"],"abstract":[{"text":"We introduce LDAdam, a memory-efficient optimizer for training large models, that performs adaptive optimization steps within lower dimensional subspaces, while consistently exploring the full parameter space during training. This strategy keeps the optimizer's memory footprint to a fraction of the model size. LDAdam relies on a new projection-aware update rule for the optimizer states that allows for transitioning between subspaces, i.e., estimation of the statistics of the projected gradients. To mitigate the errors due to low-rank projection, LDAdam integrates a new generalized error feedback mechanism, which explicitly accounts for both gradient and optimizer state compression. We prove the convergence of LDAdam under standard assumptions, and provide empirical evidence that LDAdam allows for efficient fine-tuning and pre-training of language models.","lang":"eng"}],"scopus_import":"1","date_published":"2025-04-01T00:00:00Z","status":"public","month":"04","article_processing_charge":"No","title":"LDAdam: Adaptive optimization from low-dimensional gradient statistics","year":"2025","_id":"20034","oa_version":"Published Version"},{"article_processing_charge":"No","month":"04","year":"2025","_id":"20035","oa_version":"Published Version","title":"Wide neural networks trained with weight decay provably exhibit neural collapse","project":[{"grant_number":"101161364","_id":"911e6d1f-16d5-11f0-9cad-c5c68c6a1cdf","name":"Inference in High Dimensions: Light-speed Algorithms and Information Limits"}],"publication_status":"published","author":[{"first_name":"Arthur","full_name":"Jacot, Arthur","last_name":"Jacot"},{"first_name":"Peter","full_name":"Súkeník, Peter","id":"d64d6a8d-eb8e-11eb-b029-96fd216dec3c","last_name":"Súkeník"},{"last_name":"Wang","first_name":"Zihan","full_name":"Wang, Zihan"},{"last_name":"Mondelli","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco"}],"file":[{"success":1,"checksum":"59c48c173887139647cc9839c0801136","date_updated":"2025-08-04T08:45:43Z","file_name":"2025_ICLR_Jacot.pdf","content_type":"application/pdf","access_level":"open_access","creator":"dernst","date_created":"2025-08-04T08:45:43Z","file_id":"20114","relation":"main_file","file_size":1337236}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"date_published":"2025-04-01T00:00:00Z","scopus_import":"1","abstract":[{"lang":"eng","text":"Deep neural networks (DNNs) at convergence consistently represent the training data in the last layer via a geometric structure referred to as neural collapse. This empirical evidence has spurred a line of theoretical research aimed at proving the emergence of neural collapse, mostly focusing on the unconstrained features model. Here, the features of the penultimate layer are free variables, which makes the model data-agnostic and puts into question its ability to capture DNN training. Our work addresses the issue, moving away from unconstrained features and\r\nstudying DNNs that end with at least two linear layers. We first prove generic guarantees on neural collapse that assume (i) low training error and balancedness of linear layers (for within-class variability collapse), and (ii) bounded conditioning of the features before the linear part (for orthogonality of class-means, and their alignment with weight matrices). The balancedness refers to the fact that W⊤ℓ+1Wℓ+1 ≈ WℓW⊤ℓfor any pair of consecutive weight matrices of the linear part, and the bounded conditioning requires a well-behaved ratio between largest and smallest non-zero singular values of the features. We then show that such assumptions hold for gradient descent training with weight decay: (i) for networks with a wide first layer, we prove low training error and balancedness, and (ii) for solutions that are either nearly optimal or stable under large learning rates, we additionally prove the bounded conditioning. Taken together, our results are the first to show neural collapse in the end-to-end training of DNNs."}],"status":"public","OA_type":"diamond","acknowledgement":"M. M. and P. S. are funded by the European Union (ERC, INF2, project number 101161364). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council Executive Agency. Neither the European Union nor the granting authority can be held responsible for them.","conference":{"end_date":"2025-04-28","name":"ICLR: International Conference on Learning Representations","start_date":"2025-04-24","location":"Singapore, Singapore"},"ddc":["000"],"arxiv":1,"publication":"13th International Conference on Learning Representations","citation":{"mla":"Jacot, Arthur, et al. “Wide Neural Networks Trained with Weight Decay Provably Exhibit Neural Collapse.” 13th International Conference on Learning Representations, ICLR, 2025, pp. 1905–31.","apa":"Jacot, A., Súkeník, P., Wang, Z., & Mondelli, M. (2025). Wide neural networks trained with weight decay provably exhibit neural collapse. In 13th International Conference on Learning Representations (pp. 1905–1931). Singapore, Singapore: ICLR.","ista":"Jacot A, Súkeník P, Wang Z, Mondelli M. 2025. Wide neural networks trained with weight decay provably exhibit neural collapse. 13th International Conference on Learning Representations. ICLR: International Conference on Learning Representations, 1905–1931.","ieee":"A. Jacot, P. Súkeník, Z. Wang, and M. Mondelli, “Wide neural networks trained with weight decay provably exhibit neural collapse,” in 13th International Conference on Learning Representations, Singapore, Singapore, 2025, pp. 1905–1931.","short":"A. Jacot, P. Súkeník, Z. Wang, M. Mondelli, in:, 13th International Conference on Learning Representations, ICLR, 2025, pp. 1905–1931.","chicago":"Jacot, Arthur, Peter Súkeník, Zihan Wang, and Marco Mondelli. “Wide Neural Networks Trained with Weight Decay Provably Exhibit Neural Collapse.” In 13th International Conference on Learning Representations, 1905–31. ICLR, 2025.","ama":"Jacot A, Súkeník P, Wang Z, Mondelli M. Wide neural networks trained with weight decay provably exhibit neural collapse. In: 13th International Conference on Learning Representations. ICLR; 2025:1905-1931."},"page":"1905-1931","day":"01","publisher":"ICLR","type":"conference","file_date_updated":"2025-08-04T08:45:43Z","date_created":"2025-07-20T22:02:02Z","department":[{"_id":"MaMo"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"quality_controlled":"1","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9798331320850"]},"date_updated":"2025-08-04T08:47:00Z","OA_place":"publisher","has_accepted_license":"1","external_id":{"arxiv":["2410.04887"]},"corr_author":"1"},{"title":"Near, far: Patch-ordering enhances vision foundation models' scene understanding","year":"2025","_id":"20036","oa_version":"Published Version","month":"04","article_processing_charge":"No","OA_type":"diamond","conference":{"location":"Singapore, Singapore","start_date":"2025-04-24","name":"ICLR: International Conference on Learning Representations","end_date":"2025-04-28"},"ddc":["000"],"arxiv":1,"abstract":[{"lang":"eng","text":"We introduce NeCo: Patch Neighbor Consistency, a novel self-supervised training loss that enforces patch-level nearest neighbor consistency across a student and teacher model. Compared to contrastive approaches that only yield binary learning signals, i.e. \"attract\" and \"repel\", this approach benefits from the more fine-grained learning signal of sorting spatially dense features relative to reference patches. Our method leverages differentiable sorting applied on top of pretrained representations, such as DINOv2-registers to bootstrap the learning signal and further improve upon them. This dense post-pretraining leads to superior performance across various models and datasets, despite requiring only 19 hours on a single GPU. This method generates high-quality dense feature encoders and establishes several new state-of-the-art results such as +2.3 % and +4.2% for non-parametric in-context semantic segmentation on ADE20k and Pascal VOC, +1.6% and +4.8% for linear segmentation evaluations on COCO-Things and -Stuff and improvements in the 3D understanding of multi-view consistency on SPair-71k, by more than 1.5%."}],"date_published":"2025-04-01T00:00:00Z","scopus_import":"1","status":"public","file":[{"access_level":"open_access","date_created":"2025-08-04T08:09:43Z","creator":"dernst","content_type":"application/pdf","file_size":37788223,"relation":"main_file","file_id":"20109","checksum":"ddbe981f3ad3f6cb6daf12c954822eb8","success":1,"date_updated":"2025-08-04T08:09:43Z","file_name":"2025_ICLR_Pariza.pdf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publication_status":"published","author":[{"first_name":"Valentinos","full_name":"Pariza, Valentinos","last_name":"Pariza"},{"full_name":"Salehi, Mohammadreza","first_name":"Mohammadreza","last_name":"Salehi"},{"first_name":"Gertjan","full_name":"Burghouts, Gertjan","last_name":"Burghouts"},{"last_name":"Locatello","orcid":"0000-0002-4850-0683","first_name":"Francesco","full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"first_name":"Yuki M.","full_name":"Asano, Yuki M.","last_name":"Asano"}],"page":"72303-72330","publisher":"ICLR","day":"01","type":"conference","citation":{"ieee":"V. Pariza, M. Salehi, G. Burghouts, F. Locatello, and Y. M. Asano, “Near, far: Patch-ordering enhances vision foundation models’ scene understanding,” in 13th International Conference on Learning Representations, Singapore, Singapore, 2025, pp. 72303–72330.","mla":"Pariza, Valentinos, et al. “Near, Far: Patch-Ordering Enhances Vision Foundation Models’ Scene Understanding.” 13th International Conference on Learning Representations, ICLR, 2025, pp. 72303–30.","apa":"Pariza, V., Salehi, M., Burghouts, G., Locatello, F., & Asano, Y. M. (2025). Near, far: Patch-ordering enhances vision foundation models’ scene understanding. In 13th International Conference on Learning Representations (pp. 72303–72330). Singapore, Singapore: ICLR.","ista":"Pariza V, Salehi M, Burghouts G, Locatello F, Asano YM. 2025. Near, far: Patch-ordering enhances vision foundation models’ scene understanding. 13th International Conference on Learning Representations. ICLR: International Conference on Learning Representations, 72303–72330.","short":"V. Pariza, M. Salehi, G. Burghouts, F. Locatello, Y.M. Asano, in:, 13th International Conference on Learning Representations, ICLR, 2025, pp. 72303–72330.","chicago":"Pariza, Valentinos, Mohammadreza Salehi, Gertjan Burghouts, Francesco Locatello, and Yuki M. Asano. “Near, Far: Patch-Ordering Enhances Vision Foundation Models’ Scene Understanding.” In 13th International Conference on Learning Representations, 72303–30. ICLR, 2025.","ama":"Pariza V, Salehi M, Burghouts G, Locatello F, Asano YM. Near, far: Patch-ordering enhances vision foundation models’ scene understanding. In: 13th International Conference on Learning Representations. ICLR; 2025:72303-72330."},"publication":"13th International Conference on Learning Representations","date_updated":"2025-08-04T08:10:55Z","OA_place":"publisher","has_accepted_license":"1","external_id":{"arxiv":["2408.11054"]},"language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"isbn":["9798331320850"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2025-07-20T22:02:03Z","file_date_updated":"2025-08-04T08:09:43Z","department":[{"_id":"FrLo"}]},{"oa_version":"Published Version","_id":"20037","year":"2025","title":"Wasserstein distances, neuronal entanglement, and sparsity","article_processing_charge":"No","month":"04","status":"public","scopus_import":"1","date_published":"2025-04-01T00:00:00Z","abstract":[{"lang":"eng","text":"Disentangling polysemantic neurons is at the core of many current approaches to interpretability of large language models. Here we attempt to study how disentanglement can be used to understand performance, particularly under weight sparsity, a leading post-training optimization technique. We suggest a novel measure for estimating neuronal entanglement: the Wasserstein distance of a neuron's output distribution to a Gaussian. Moreover, we show the existence of a small number of highly entangled \"Wasserstein Neurons\" in each linear layer of an LLM, characterized by their highly non-Gaussian output distributions, their role in mapping similar inputs to dissimilar outputs, and their significant impact on model accuracy. To study these phenomena, we propose a new experimental framework for disentangling polysemantic neurons. Our framework separates each layer's inputs to create a mixture of experts where each neuron's output is computed by a mixture of neurons of lower Wasserstein distance, each better at maintaining accuracy when sparsified without retraining. We provide strong evidence that this is because the mixture of sparse experts is effectively disentangling the input-output relationship of individual neurons, in particular the difficult Wasserstein neurons."}],"arxiv":1,"ddc":["000"],"acknowledgement":"The authors would like to extend their gratitude to Lori Leu for her insightful comments on the\r\napplication of the Wasserstein distance metric. We also wish to thank Elias Frantar for his help in\r\nworking with the SparseGPT implementation and his advice for the project. Additionally, we would like to thank Tony Tong Wang and Thomas Athey for their valuable feedback and constructive discussions.\r\nThis work was supported by an NIH Brains CONNECTS U01 grant and AMD’s AI & HPC Fund.","conference":{"location":"Singapore, Singapore","start_date":"2025-04-24","end_date":"2025-04-28","name":"ICLR: International Conference on Learning Representations"},"OA_type":"diamond","author":[{"full_name":"Sawmya, Shashata","first_name":"Shashata","last_name":"Sawmya"},{"last_name":"Kong","full_name":"Kong, Linghao","first_name":"Linghao"},{"last_name":"Markov","id":"D0CF4148-C985-11E9-8066-0BDEE5697425","full_name":"Markov, Ilia","first_name":"Ilia"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","last_name":"Alistarh","orcid":"0000-0003-3650-940X"},{"full_name":"Shavit, Nir","first_name":"Nir","last_name":"Shavit"}],"publication_status":"published","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"access_level":"open_access","date_created":"2025-08-04T08:14:09Z","creator":"dernst","content_type":"application/pdf","file_size":5447177,"relation":"main_file","file_id":"20110","checksum":"39a8fa7dbdd7029859e156f53f20f6bc","success":1,"date_updated":"2025-08-04T08:14:09Z","file_name":"2025_ICLR_Sawmya.pdf"}],"citation":{"ieee":"S. Sawmya, L. Kong, I. Markov, D.-A. Alistarh, and N. Shavit, “Wasserstein distances, neuronal entanglement, and sparsity,” in 13th International Conference on Learning Representations, Singapore, Singapore, 2025, pp. 26244–26274.","ista":"Sawmya S, Kong L, Markov I, Alistarh D-A, Shavit N. 2025. Wasserstein distances, neuronal entanglement, and sparsity. 13th International Conference on Learning Representations. ICLR: International Conference on Learning Representations, 26244–26274.","mla":"Sawmya, Shashata, et al. “Wasserstein Distances, Neuronal Entanglement, and Sparsity.” 13th International Conference on Learning Representations, ICLR, 2025, pp. 26244–74.","apa":"Sawmya, S., Kong, L., Markov, I., Alistarh, D.-A., & Shavit, N. (2025). Wasserstein distances, neuronal entanglement, and sparsity. In 13th International Conference on Learning Representations (pp. 26244–26274). Singapore, Singapore: ICLR.","short":"S. Sawmya, L. Kong, I. Markov, D.-A. Alistarh, N. Shavit, in:, 13th International Conference on Learning Representations, ICLR, 2025, pp. 26244–26274.","chicago":"Sawmya, Shashata, Linghao Kong, Ilia Markov, Dan-Adrian Alistarh, and Nir Shavit. “Wasserstein Distances, Neuronal Entanglement, and Sparsity.” In 13th International Conference on Learning Representations, 26244–74. ICLR, 2025.","ama":"Sawmya S, Kong L, Markov I, Alistarh D-A, Shavit N. Wasserstein distances, neuronal entanglement, and sparsity. In: 13th International Conference on Learning Representations. ICLR; 2025:26244-26274."},"type":"conference","related_material":{"link":[{"relation":"software","url":"https://github.com/Shavit-Lab/Sparse-Expansion"}]},"publisher":"ICLR","day":"01","page":"26244-26274","publication":"13th International Conference on Learning Representations","publication_identifier":{"isbn":["9798331320850"]},"language":[{"iso":"eng"}],"quality_controlled":"1","corr_author":"1","external_id":{"arxiv":["2405.15756"]},"OA_place":"publisher","has_accepted_license":"1","date_updated":"2025-08-04T08:16:43Z","department":[{"_id":"DaAl"}],"file_date_updated":"2025-08-04T08:14:09Z","date_created":"2025-07-20T22:02:03Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}},{"oa_version":"Published Version","year":"2025","_id":"20038","title":"The journey matters: Average parameter count over pre-training unifies sparse and dense scaling laws","article_processing_charge":"No","month":"04","status":"public","scopus_import":"1","date_published":"2025-04-01T00:00:00Z","abstract":[{"text":"Pruning eliminates unnecessary parameters in neural networks; it offers a promising solution to the growing computational demands of large language models (LLMs). While many focus on post-training pruning, sparse pre-training--which combines pruning and pre-training into a single phase--provides a simpler alternative. In this work, we present the first systematic exploration of optimal sparse pre-training configurations for LLMs through an examination of 80 unique pruning schedules across different sparsity levels and training durations. We find that initiating pruning at 25% of total training compute and concluding at 75% achieves near-optimal final evaluation loss. These findings provide valuable insights for efficient and effective sparse pre-training of LLMs. Furthermore, we propose a new scaling law that modifies the Chinchilla scaling law to use the average parameter count over pre-training. Through empirical and theoretical validation, we demonstrate that this modified scaling law accurately models evaluation loss for both sparsely and densely pre-trained LLMs, unifying scaling laws across pre-training paradigms. Our findings indicate that while sparse pre-training achieves the same final model quality as dense pre-training for equivalent compute budgets, it provides substantial benefits through reduced model size, enabling significant potential computational savings during inference.","lang":"eng"}],"acknowledgement":"We are deeply grateful to Elias Frantar, Naveen Kumar, Sanjiv Kumar, Daniel\r\nM. Roy, and Clemens Schaefer for their valuable feedback and thoughtful review of this paper.\r\nWe also acknowledge the critical support provided by the Google CoreML Performance Team, and Google Research during this project. We further recognize the extended team at Google DeepMind, who enabled and supported this research direction.\r\nThis work was in part supported by the Sloan Foundation, the MIT-IBM Watson AI Lab, Apple, and SRC JUMP 2.0 (CoCoSys).","conference":{"location":"Singapore, Singapore","start_date":"2025-04-24","end_date":"2025-04-28","name":"ICLR: International Conference on Learning Representations"},"ddc":["000"],"arxiv":1,"OA_type":"diamond","author":[{"full_name":"Jin, Tian","first_name":"Tian","last_name":"Jin"},{"first_name":"Ahmed Imtiaz","full_name":"Humayun, Ahmed Imtiaz","last_name":"Humayun"},{"full_name":"Evci, Utku","first_name":"Utku","last_name":"Evci"},{"last_name":"Subramanian","full_name":"Subramanian, Suvinay","first_name":"Suvinay"},{"last_name":"Yazdanbakhsh","full_name":"Yazdanbakhsh, Amir","first_name":"Amir"},{"first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","last_name":"Alistarh"},{"last_name":"Dziugaite","full_name":"Dziugaite, Gintare Karolina","first_name":"Gintare Karolina"}],"publication_status":"published","oa":1,"file":[{"date_created":"2025-08-04T08:23:47Z","creator":"dernst","access_level":"open_access","content_type":"application/pdf","file_size":704989,"relation":"main_file","file_id":"20111","checksum":"dbc27120e9aba67dffbd9e5d513a6803","success":1,"file_name":"2025_ICLR_Jin.pdf","date_updated":"2025-08-04T08:23:47Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Jin T, Humayun AI, Evci U, et al. The journey matters: Average parameter count over pre-training unifies sparse and dense scaling laws. In: 13th International Conference on Learning Representations. ICLR; 2025:85165-85181.","chicago":"Jin, Tian, Ahmed Imtiaz Humayun, Utku Evci, Suvinay Subramanian, Amir Yazdanbakhsh, Dan-Adrian Alistarh, and Gintare Karolina Dziugaite. “The Journey Matters: Average Parameter Count over Pre-Training Unifies Sparse and Dense Scaling Laws.” In 13th International Conference on Learning Representations, 85165–81. ICLR, 2025.","short":"T. Jin, A.I. Humayun, U. Evci, S. Subramanian, A. Yazdanbakhsh, D.-A. Alistarh, G.K. Dziugaite, in:, 13th International Conference on Learning Representations, ICLR, 2025, pp. 85165–85181.","mla":"Jin, Tian, et al. “The Journey Matters: Average Parameter Count over Pre-Training Unifies Sparse and Dense Scaling Laws.” 13th International Conference on Learning Representations, ICLR, 2025, pp. 85165–81.","apa":"Jin, T., Humayun, A. I., Evci, U., Subramanian, S., Yazdanbakhsh, A., Alistarh, D.-A., & Dziugaite, G. K. (2025). The journey matters: Average parameter count over pre-training unifies sparse and dense scaling laws. In 13th International Conference on Learning Representations (pp. 85165–85181). Singapore, Singapore: ICLR.","ista":"Jin T, Humayun AI, Evci U, Subramanian S, Yazdanbakhsh A, Alistarh D-A, Dziugaite GK. 2025. The journey matters: Average parameter count over pre-training unifies sparse and dense scaling laws. 13th International Conference on Learning Representations. ICLR: International Conference on Learning Representations, 85165–85181.","ieee":"T. Jin et al., “The journey matters: Average parameter count over pre-training unifies sparse and dense scaling laws,” in 13th International Conference on Learning Representations, Singapore, Singapore, 2025, pp. 85165–85181."},"type":"conference","page":"85165-85181","publisher":"ICLR","day":"01","publication":"13th International Conference on Learning Representations","publication_identifier":{"isbn":["9798331320850"]},"quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"arxiv":["2501.12486 "]},"date_updated":"2025-08-04T08:24:59Z","has_accepted_license":"1","OA_place":"publisher","department":[{"_id":"DaAl"}],"file_date_updated":"2025-08-04T08:23:47Z","date_created":"2025-07-20T22:02:03Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"oa":1,"article_type":"original","publication_status":"published","project":[{"grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425","name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020"},{"name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504"}],"author":[{"first_name":"Francesco","id":"d3ac8ac6-dc8d-11ea-abe3-e2a9628c4c3c","full_name":"Pedrotti, Francesco","last_name":"Pedrotti"}],"OA_type":"green","arxiv":1,"acknowledgement":"The author warmly thanks Jan Maas for suggesting the project and for his guidance, and Melchior Wirth and Haonan Zhang for useful discussions. The author is also grateful to an anonymous reviewer for carefully reading the manuscript and providing many valuable suggestions. The author gratefully acknowledges support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme\r\n(grant agreement No. 716117) and by the Austrian Science Fund (FWF), Project SFB F65.","scopus_import":"1","date_published":"2025-02-01T00:00:00Z","abstract":[{"text":"Contractive coupling rates have been recently introduced by Conforti as a tool to establish convex Sobolev inequalities (including modified log-Sobolev and Poincaré inequality) for some classes of Markov chains. In this work, for most of the examples discussed by Conforti, we use contractive coupling rates to prove stronger inequalities, in the form of curvature lower bounds (in entropic and discrete Bakry–Émery sense) and geodesic convexity of some entropic functionals. In addition, we recall and give straightforward generalizations of some notions of coarse Ricci curvature, and we discuss some of their properties and relations with the concepts of couplings and coupling rates: as an application, we show exponential contraction of the p-Wasserstein distance for the heat flow in the aforementioned examples.","lang":"eng"}],"status":"public","month":"02","article_processing_charge":"No","title":"Contractive coupling rates and curvature lower bounds for Markov chains","issue":"1","_id":"20040","year":"2025","oa_version":"Preprint","date_created":"2025-07-21T07:49:15Z","department":[{"_id":"JaMa"}],"OA_place":"repository","date_updated":"2025-11-05T13:50:07Z","corr_author":"1","external_id":{"isi":["001434322900006"],"arxiv":["2308.00516"]},"quality_controlled":"1","language":[{"iso":"eng"}],"intvolume":" 35","publication_identifier":{"issn":["1050-5164"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2308.00516","open_access":"1"}],"publication":"The Annals of Applied Probability","publisher":"Institute of Mathematical Statistics","day":"01","doi":"10.1214/24-aap2113","page":"196 - 250","ec_funded":1,"type":"journal_article","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"17351"}]},"citation":{"short":"F. Pedrotti, The Annals of Applied Probability 35 (2025) 196–250.","apa":"Pedrotti, F. (2025). Contractive coupling rates and curvature lower bounds for Markov chains. The Annals of Applied Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/24-aap2113","mla":"Pedrotti, Francesco. “Contractive Coupling Rates and Curvature Lower Bounds for Markov Chains.” The Annals of Applied Probability, vol. 35, no. 1, Institute of Mathematical Statistics, 2025, pp. 196–250, doi:10.1214/24-aap2113.","ista":"Pedrotti F. 2025. Contractive coupling rates and curvature lower bounds for Markov chains. The Annals of Applied Probability. 35(1), 196–250.","ieee":"F. Pedrotti, “Contractive coupling rates and curvature lower bounds for Markov chains,” The Annals of Applied Probability, vol. 35, no. 1. Institute of Mathematical Statistics, pp. 196–250, 2025.","ama":"Pedrotti F. Contractive coupling rates and curvature lower bounds for Markov chains. The Annals of Applied Probability. 2025;35(1):196-250. doi:10.1214/24-aap2113","chicago":"Pedrotti, Francesco. “Contractive Coupling Rates and Curvature Lower Bounds for Markov Chains.” The Annals of Applied Probability. Institute of Mathematical Statistics, 2025. https://doi.org/10.1214/24-aap2113."},"volume":35},{"month":"03","article_processing_charge":"Yes","title":"Complex K-theory of moduli spaces of Higgs bundles","oa_version":"Published Version","_id":"20043","year":"2025","oa":1,"isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Groechenig","full_name":"Groechenig, Michael","first_name":"Michael"},{"id":"544cccd3-9005-11ec-87bc-94aef1c5b814","full_name":"Shen, Shiyu","first_name":"Shiyu","last_name":"Shen","orcid":"0000-0002-4444-8718"}],"article_type":"original","publication_status":"epub_ahead","project":[{"grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program"}],"arxiv":1,"acknowledgement":"It is a pleasure to thank Tom Baird for sharing his insights about vanishing of torsion for H.M{1\r\n2/. Furthermore, we would like to thank him for bringing [25] to our attention. We also thank Alexander Kupers for enlightening conversations about the Atiyah–Hirzebruch spectral sequence and for pointing out a reference. We are grateful to Victoria Hoskins and Simon Pepin-Lehalleur for sharing a preprint of their recent paper on a motivic version of topological mirror symmetry and for useful remarks on Section 6. Anne Larsen pointed out that our previous proof Lemma 4.5 was incomplete, we thank her for bringing this to our attention. We are grateful to the anonymous referee for many valuable comments that have improved the paper tremendously. The report we received was one of the most detailed referee report either of us has ever seen. We thank them for their hard work and the resulting contribution to this paper. Michael Groechenig was supported by an NSERC discovery grant and an Alfred P. Sloan\r\nfellowship. Shiyu Shen has received funding from the European Union’s Horizon 2020 research\r\nand innovation program under the Marie Skłodowska-Curie grant agreement No. 101034413.","OA_type":"gold","status":"public","date_published":"2025-03-20T00:00:00Z","abstract":[{"lang":"eng","text":"We establish an isomorphism of complex K-theory of the moduli space M of “SL n ”-Higgs bundles of degree d and rank n (in the sense of Hausel–Thaddeus) and twisted complex K-theory of the orbifold M of PGL n -Higgs bundles of degree e, where (n,d)=(n,e)=1. Along the way, we prove the vanishing of torsion for H ∗ ( M ) and certain twisted complex K-theory groups of M . We also extend Arinkin’s autoduality of compactified Jacobian to a derived equivalence between SL n - and PGL n -Hitchin systems over the elliptic locus. In the appendix, we develop a formalism of G-sheaves of spectra, generalising equivariant homotopy theory to a relative setting."}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.4171/JEMS/1601"}],"publication":"Journal of the European Mathematical Society","ec_funded":1,"type":"journal_article","doi":"10.4171/jems/1601","day":"20","publisher":"EMS Press","DOAJ_listed":"1","citation":{"chicago":"Groechenig, Michael, and Shiyu Shen. “Complex K-Theory of Moduli Spaces of Higgs Bundles.” Journal of the European Mathematical Society. EMS Press, 2025. https://doi.org/10.4171/jems/1601.","ama":"Groechenig M, Shen S. Complex K-theory of moduli spaces of Higgs bundles. Journal of the European Mathematical Society. 2025. doi:10.4171/jems/1601","ista":"Groechenig M, Shen S. 2025. Complex K-theory of moduli spaces of Higgs bundles. Journal of the European Mathematical Society.","apa":"Groechenig, M., & Shen, S. (2025). Complex K-theory of moduli spaces of Higgs bundles. Journal of the European Mathematical Society. EMS Press. https://doi.org/10.4171/jems/1601","mla":"Groechenig, Michael, and Shiyu Shen. “Complex K-Theory of Moduli Spaces of Higgs Bundles.” Journal of the European Mathematical Society, EMS Press, 2025, doi:10.4171/jems/1601.","ieee":"M. Groechenig and S. Shen, “Complex K-theory of moduli spaces of Higgs bundles,” Journal of the European Mathematical Society. EMS Press, 2025.","short":"M. Groechenig, S. Shen, Journal of the European Mathematical Society (2025)."},"department":[{"_id":"TaHa"}],"date_created":"2025-07-21T07:54:50Z","corr_author":"1","external_id":{"arxiv":["2212.10695"],"isi":["001608254800001"]},"OA_place":"publisher","date_updated":"2026-02-19T09:24:54Z","publication_identifier":{"issn":["1435-9855"],"eissn":["1435-9863"]},"language":[{"iso":"eng"}],"quality_controlled":"1"},{"file":[{"file_id":"20068","relation":"main_file","file_size":8150623,"content_type":"application/pdf","date_created":"2025-07-22T10:04:57Z","creator":"dernst","access_level":"open_access","file_name":"2025_Evolution_Connallon.pdf","date_updated":"2025-07-22T10:04:57Z","success":1,"checksum":"68c4c996d0e8c9ee3d4fb61bca75b31a"}],"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program"}],"publication_status":"published","article_type":"original","author":[{"full_name":"Connallon, Tim","first_name":"Tim","last_name":"Connallon"},{"first_name":"Peter","full_name":"Czuppon, Peter","last_name":"Czuppon"},{"full_name":"Olito, Colin","first_name":"Colin","last_name":"Olito"},{"first_name":"Debora","full_name":"Goedert, Debora","last_name":"Goedert"},{"full_name":"Kokko, Hanna","first_name":"Hanna","last_name":"Kokko"},{"full_name":"Nava-Bolaños, Angela","first_name":"Angela","last_name":"Nava-Bolaños"},{"last_name":"Nilén","full_name":"Nilén, Sofie","first_name":"Sofie"},{"full_name":"Svensson, Erik I","first_name":"Erik I","last_name":"Svensson"},{"first_name":"Martyna","full_name":"Zwoinska, Martyna","last_name":"Zwoinska"},{"first_name":"Ludovic","full_name":"Dutoit, Ludovic","last_name":"Dutoit"},{"last_name":"Ruzicka","first_name":"Filip","full_name":"Ruzicka, Filip","id":"347955dd-57b0-11ee-9095-c28bdd368f4b"}],"OA_type":"hybrid","acknowledgement":"Support for this research came from the European Society of Evolutionary Biology (ESEB) through a “Special Topics Network” grant. Further financial support came from the European Research Council (ERC-2023-STG916 #101117517, to C.O.), the Swedish Research Council (#2022-03603, to C.O.; #2020‑03123, to E.I.S.), the Research Council of Norway (Norges forskningsråd #302619, to D.G.), the Alexander von Humboldt Foundation and the GenEvo graduate school (to H.K.), the Foundation for Zoological Research and the Birgitta Sintring Foundation (#S2024-0007, to M.K.Z.), a postdoctoral fellowship from the Consejo Nacional de Humanidades, Ciencias y Tecnología (to A.N.B.), and a H2020 Marie Skłodowska-Curie COFUND Action fellowship (#101034413, to F.R.). We wish to express our deepest gratitude to Lotte de Vries for extensive discussion of the project, rederiving some of our results, and providing comments on an earlier version of the manuscript, and to the European Society of Evolutionary Biology (ESEB) for a “Special Topics Network” grant that supported workshops that initiated this collaboration and facilitated many new ideas and friendships. We also thank two anonymous reviewers for their thoughtful comments and suggestions that helped us to substantially improve upon the original version of the article.","ddc":["570"],"abstract":[{"text":"Genetic trade-offs—which occur when variants that are beneficial in some contexts of natural selection are harmful in others—can influence a wide range of evolutionary phenomena, from the maintenance of genetic variation to the evolution of aging and sex differences. An extensive body of evolutionary theory has focused on the consequences of such trade-offs, and recent analyses of Fisher’s geometric model have further quantified the expected proportion of new mutations that exhibit trade-offs. However, the theory remains silent regarding the prevalence of trade-offs among the variants that contribute to adaptation. Here, we extend Fisher’s geometric model to predict the prevalence of trade-offs among the adaptive mutations that become established or fixed in a population. We consider trade-offs between sexes, habitats, fitness components, and temporally fluctuating environments. In all 4 scenarios, trade-off alleles are consistently under-represented among established relative to new beneficial mutations—an effect that arises from the greater susceptibility of trade-off alleles to genetic drift. Adaptation during a population size decline exacerbates this deficit of trade-offs among established mutations, whereas population expansions dampen it. Consequently, threatened populations should primarily adapt using unconditionally beneficial alleles, while invasive populations are more prone to adaptation using variants that exhibit trade-offs.","lang":"eng"}],"date_published":"2025-07-01T00:00:00Z","status":"public","month":"07","article_processing_charge":"Yes (in subscription journal)","title":"Predicting the prevalence of genetic trade-offs among adaptive substitutions","year":"2025","_id":"20044","issue":"7","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2025-07-21T07:57:28Z","file_date_updated":"2025-07-22T10:04:57Z","PlanS_conform":"1","department":[{"_id":"BeVi"}],"date_updated":"2025-09-30T14:06:38Z","has_accepted_license":"1","OA_place":"publisher","external_id":{"isi":["001477180800001"]},"intvolume":" 79","language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"publication":"Evolution","page":"1243-1255","publisher":"Oxford University Press","day":"01","doi":"10.1093/evolut/qpaf061","type":"journal_article","ec_funded":1,"citation":{"ama":"Connallon T, Czuppon P, Olito C, et al. Predicting the prevalence of genetic trade-offs among adaptive substitutions. Evolution. 2025;79(7):1243-1255. doi:10.1093/evolut/qpaf061","chicago":"Connallon, Tim, Peter Czuppon, Colin Olito, Debora Goedert, Hanna Kokko, Angela Nava-Bolaños, Sofie Nilén, et al. “Predicting the Prevalence of Genetic Trade-Offs among Adaptive Substitutions.” Evolution. Oxford University Press, 2025. https://doi.org/10.1093/evolut/qpaf061.","short":"T. Connallon, P. Czuppon, C. Olito, D. Goedert, H. Kokko, A. Nava-Bolaños, S. Nilén, E.I. Svensson, M. Zwoinska, L. Dutoit, F. Ruzicka, Evolution 79 (2025) 1243–1255.","ieee":"T. Connallon et al., “Predicting the prevalence of genetic trade-offs among adaptive substitutions,” Evolution, vol. 79, no. 7. Oxford University Press, pp. 1243–1255, 2025.","ista":"Connallon T, Czuppon P, Olito C, Goedert D, Kokko H, Nava-Bolaños A, Nilén S, Svensson EI, Zwoinska M, Dutoit L, Ruzicka F. 2025. Predicting the prevalence of genetic trade-offs among adaptive substitutions. Evolution. 79(7), 1243–1255.","apa":"Connallon, T., Czuppon, P., Olito, C., Goedert, D., Kokko, H., Nava-Bolaños, A., … Ruzicka, F. (2025). Predicting the prevalence of genetic trade-offs among adaptive substitutions. Evolution. Oxford University Press. https://doi.org/10.1093/evolut/qpaf061","mla":"Connallon, Tim, et al. “Predicting the Prevalence of Genetic Trade-Offs among Adaptive Substitutions.” Evolution, vol. 79, no. 7, Oxford University Press, 2025, pp. 1243–55, doi:10.1093/evolut/qpaf061."},"volume":79},{"OA_type":"green","arxiv":1,"abstract":[{"lang":"eng","text":"We consider the time evolution of the renormalized Nelson model, which describes N bosons linearly coupled to a quantized scalar field, in the mean-field limit of many particles N≫1 with coupling constant proportional to N^−1/2. First, we show that initial states exhibiting Bose–Einstein condensation for the particles and approximating a coherent state for the quantum field retain their structure under the many-body time evolution. Concretely, the dynamics of the reduced densities are approximated by solutions of two coupled PDEs, the Schrödinger–Klein–Gordon equations. Second, we construct a renormalized Bogoliubov evolution that describes the quantum fluctuations around the Schrödinger–Klein–Gordon equations. This evolution is used to extend the approximation of the evolved many-body state to the full norm topology. In summary, we provide a comprehensive analysis of the Nelson model that reveals the role of renormalization in the mean-field Bogoliubov theory."}],"date_published":"2025-05-06T00:00:00Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"article_type":"original","publication_status":"epub_ahead","author":[{"last_name":"Falconi","full_name":"Falconi, Marco","first_name":"Marco"},{"full_name":"Lampart, Jonas","first_name":"Jonas","last_name":"Lampart"},{"first_name":"Nikolai","full_name":"Leopold, Nikolai","last_name":"Leopold"},{"last_name":"Mitrouskas","full_name":"Mitrouskas, David Johannes","id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d","first_name":"David Johannes"}],"title":"Renormalized Bogoliubov theory for the Nelson model","year":"2025","_id":"20045","oa_version":"Preprint","month":"05","article_processing_charge":"No","date_updated":"2025-12-30T07:31:09Z","OA_place":"repository","external_id":{"arxiv":["2305.06722"]},"quality_controlled":"1","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1873-1430"],"issn":["0294-1449"]},"date_created":"2025-07-21T07:59:16Z","department":[{"_id":"RoSe"}],"doi":"10.4171/aihpc/154","day":"06","publisher":"EMS Press","type":"journal_article","DOAJ_listed":"1","citation":{"short":"M. Falconi, J. Lampart, N. Leopold, D.J. Mitrouskas, Annales de l’Institut Henri Poincaré C (2025).","apa":"Falconi, M., Lampart, J., Leopold, N., & Mitrouskas, D. J. (2025). Renormalized Bogoliubov theory for the Nelson model. Annales de l’Institut Henri Poincaré C. EMS Press. https://doi.org/10.4171/aihpc/154","ista":"Falconi M, Lampart J, Leopold N, Mitrouskas DJ. 2025. Renormalized Bogoliubov theory for the Nelson model. Annales de l’Institut Henri Poincaré C.","mla":"Falconi, Marco, et al. “Renormalized Bogoliubov Theory for the Nelson Model.” Annales de l’Institut Henri Poincaré C, EMS Press, 2025, doi:10.4171/aihpc/154.","ieee":"M. Falconi, J. Lampart, N. Leopold, and D. J. Mitrouskas, “Renormalized Bogoliubov theory for the Nelson model,” Annales de l’Institut Henri Poincaré C. EMS Press, 2025.","ama":"Falconi M, Lampart J, Leopold N, Mitrouskas DJ. Renormalized Bogoliubov theory for the Nelson model. Annales de l’Institut Henri Poincaré C. 2025. doi:10.4171/aihpc/154","chicago":"Falconi, Marco, Jonas Lampart, Nikolai Leopold, and David Johannes Mitrouskas. “Renormalized Bogoliubov Theory for the Nelson Model.” Annales de l’Institut Henri Poincaré C. EMS Press, 2025. https://doi.org/10.4171/aihpc/154."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2305.06722"}],"publication":"Annales de l'Institut Henri Poincaré C"},{"date_created":"2025-07-21T08:06:18Z","file_date_updated":"2025-07-23T08:35:53Z","department":[{"_id":"LaEr"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":" 30","publication_identifier":{"eissn":["1083-6489"]},"OA_place":"publisher","has_accepted_license":"1","date_updated":"2025-09-30T14:07:19Z","corr_author":"1","external_id":{"isi":["001540927000024"],"arxiv":["2211.17175"]},"publication":"Electronic Journal of Probability","citation":{"chicago":"Campbell, Andrew J, Kyle Luh, Sean O’Rourke, Santiago Arenas-Velilla, and Victor Perez-Abreu. “Extreme Eigenvalues of Laplacian Random Matrices with Gaussian Entries.” Electronic Journal of Probability. Institute of Mathematical Statistics, 2025. https://doi.org/10.1214/25-ejp1366.","ama":"Campbell AJ, Luh K, O’Rourke S, Arenas-Velilla S, Perez-Abreu V. Extreme eigenvalues of Laplacian random matrices with Gaussian entries. Electronic Journal of Probability. 2025;30:1-52. doi:10.1214/25-ejp1366","ieee":"A. J. Campbell, K. Luh, S. O’Rourke, S. Arenas-Velilla, and V. Perez-Abreu, “Extreme eigenvalues of Laplacian random matrices with Gaussian entries,” Electronic Journal of Probability, vol. 30. Institute of Mathematical Statistics, pp. 1–52, 2025.","apa":"Campbell, A. J., Luh, K., O’Rourke, S., Arenas-Velilla, S., & Perez-Abreu, V. (2025). Extreme eigenvalues of Laplacian random matrices with Gaussian entries. Electronic Journal of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/25-ejp1366","ista":"Campbell AJ, Luh K, O’Rourke S, Arenas-Velilla S, Perez-Abreu V. 2025. Extreme eigenvalues of Laplacian random matrices with Gaussian entries. Electronic Journal of Probability. 30, 1–52.","mla":"Campbell, Andrew J., et al. “Extreme Eigenvalues of Laplacian Random Matrices with Gaussian Entries.” Electronic Journal of Probability, vol. 30, Institute of Mathematical Statistics, 2025, pp. 1–52, doi:10.1214/25-ejp1366.","short":"A.J. Campbell, K. Luh, S. O’Rourke, S. Arenas-Velilla, V. Perez-Abreu, Electronic Journal of Probability 30 (2025) 1–52."},"DOAJ_listed":"1","volume":30,"publisher":"Institute of Mathematical Statistics","doi":"10.1214/25-ejp1366","day":"27","page":"1-52","type":"journal_article","ec_funded":1,"article_type":"original","publication_status":"published","project":[{"call_identifier":"H2020","name":"Random matrices beyond Wigner-Dyson-Mehta","_id":"62796744-2b32-11ec-9570-940b20777f1d","grant_number":"101020331"}],"author":[{"first_name":"Andrew J","full_name":"Campbell, Andrew J","id":"582b06a9-1f1c-11ee-b076-82ffce00dde4","last_name":"Campbell"},{"full_name":"Luh, Kyle","first_name":"Kyle","last_name":"Luh"},{"last_name":"O’Rourke","first_name":"Sean","full_name":"O’Rourke, Sean"},{"last_name":"Arenas-Velilla","first_name":"Santiago","full_name":"Arenas-Velilla, Santiago"},{"first_name":"Victor","full_name":"Perez-Abreu, Victor","last_name":"Perez-Abreu"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"file":[{"content_type":"application/pdf","access_level":"open_access","creator":"dernst","date_created":"2025-07-23T08:35:53Z","file_id":"20069","file_size":580591,"relation":"main_file","success":1,"checksum":"a7a9f2bb7a6295786c16d4c7bd612621","date_updated":"2025-07-23T08:35:53Z","file_name":"2025_ElectronJourProbab_Campbell.pdf"}],"oa":1,"date_published":"2025-06-27T00:00:00Z","abstract":[{"text":"A Laplacian matrix is a real symmetric matrix whose row and column sums are zero. We investigate the limiting distribution of the largest eigenvalues of a Laplacian random matrix with Gaussian entries. Unlike many classical matrix ensembles, this random matrix model contains dependent entries. Our main results show that the extreme eigenvalues of this model exhibit Poisson statistics. In particular, after properly shifting and scaling, we show that the largest eigenvalue converges to the Gumbel distribution as the dimension of the matrix tends to infinity. While the largest diagonal entry is also shown to have Gumbel fluctuations, there is a rather surprising difference between its deterministic centering term and the centering term required for the largest eigenvalues.","lang":"eng"}],"status":"public","OA_type":"gold","ddc":["510"],"arxiv":1,"acknowledgement":"The authors thank Santiago Arenas-Velilla and Victor Pérez-Abreu for comments on an earlier draft of this manuscript and for contributing Appendix A. The authors also thank Yan Fyodorov for providing useful references.\r\nA. Campbell was partially supported by the European Research Council Grant No. 101020331. K. Luh was supported in part by the Ralph E. Powe Junior Faculty Enhancement Award and Simons Foundation Grant MP-TSM-00001988. S. O’Rourke has been supported in part by NSF CAREER grant DMS-2143142. ","article_processing_charge":"Yes","month":"06","_id":"20046","year":"2025","oa_version":"Published Version","title":"Extreme eigenvalues of Laplacian random matrices with Gaussian entries"},{"article_number":"dev204261","department":[{"_id":"CaHe"}],"PlanS_conform":"1","date_created":"2025-07-21T08:10:32Z","file_date_updated":"2025-07-23T08:43:01Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"intvolume":" 152","language":[{"iso":"eng"}],"quality_controlled":"1","external_id":{"pmid":["40576478"],"isi":["001525252300001"]},"corr_author":"1","date_updated":"2025-09-30T14:07:51Z","OA_place":"publisher","has_accepted_license":"1","publication":"Development","volume":152,"citation":{"chicago":"Moriyama, Yuuta, Toshiyuki Mitsui, and Carl-Philipp J Heisenberg. “Hoxb Genes Determine the Timing of Cell Ingression by Regulating Cell Surface Fluctuations during Zebrafish Gastrulation.” Development. The Company of Biologists, 2025. https://doi.org/10.1242/dev.204261.","ama":"Moriyama Y, Mitsui T, Heisenberg C-PJ. Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation. Development. 2025;152(12). doi:10.1242/dev.204261","ieee":"Y. Moriyama, T. Mitsui, and C.-P. J. Heisenberg, “Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation,” Development, vol. 152, no. 12. The Company of Biologists, 2025.","apa":"Moriyama, Y., Mitsui, T., & Heisenberg, C.-P. J. (2025). Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation. Development. The Company of Biologists. https://doi.org/10.1242/dev.204261","mla":"Moriyama, Yuuta, et al. “Hoxb Genes Determine the Timing of Cell Ingression by Regulating Cell Surface Fluctuations during Zebrafish Gastrulation.” Development, vol. 152, no. 12, dev204261, The Company of Biologists, 2025, doi:10.1242/dev.204261.","ista":"Moriyama Y, Mitsui T, Heisenberg C-PJ. 2025. Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation. Development. 152(12), dev204261.","short":"Y. Moriyama, T. Mitsui, C.-P.J. Heisenberg, Development 152 (2025)."},"type":"journal_article","doi":"10.1242/dev.204261","publisher":"The Company of Biologists","day":"27","author":[{"full_name":"Moriyama, Yuuta","id":"addc9b8c-67a0-11f0-b374-a2e094825470","first_name":"Yuuta","last_name":"Moriyama","orcid":"0000-0002-2853-8051"},{"first_name":"Toshiyuki","full_name":"Mitsui, Toshiyuki","last_name":"Mitsui"},{"orcid":"0000-0002-0912-4566","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"publication_status":"published","article_type":"original","oa":1,"file":[{"checksum":"808d8aa28df79d23fb661838d1fdc1be","success":1,"file_name":"2025_Development_Moriyama.pdf","date_updated":"2025-07-23T08:43:01Z","creator":"dernst","date_created":"2025-07-23T08:43:01Z","access_level":"open_access","content_type":"application/pdf","file_size":25935563,"relation":"main_file","file_id":"20070"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"status":"public","abstract":[{"lang":"eng","text":"During embryonic development, cell behaviors need to be tightly regulated in time and space. Yet how the temporal and spatial regulations of cell behaviors are interconnected during embryonic development remains elusive. To address this, we turned to zebrafish gastrulation, the process whereby dynamic cell behaviors generate the three principal germ layers of the early embryo. Here, we show that Hoxb cluster genes are expressed in a temporally collinear manner at the blastoderm margin, where mesodermal and endodermal (mesendoderm) progenitor cells are specified and ingress to form mesendoderm/hypoblast. Functional analysis shows that these Hoxb genes regulate the timing of cell ingression: under- or overexpression of Hoxb genes perturb the timing of mesendoderm cell ingression and, consequently, the positioning of these cells along the forming anterior-posterior body axis after gastrulation. Finally, we found that Hoxb genes control the timing of mesendoderm ingression by regulating cellular bleb formation and cell surface fluctuations in the ingressing cells. Collectively, our findings suggest that Hoxb genes interconnect the temporal and spatial pattern of cell behaviors during zebrafish gastrulation by controlling cell surface fluctuations."}],"date_published":"2025-06-27T00:00:00Z","scopus_import":"1","acknowledgement":"We thank all the Heisenberg lab members for discussions and comments on the manuscript, and the Bioimaging and Life Science facilities of ISTA for support with microscopy and fish maintenance, respectively. This study was funded by a Japan Society for the Promotion of Science (JSPS) Overseas Research Fellowship and a Japan Science and Technology Agency PRESTO grant (JPMJPR214B) to Y.M. Open Access funding provided by the Japan Science and Technology Agency. Deposited in PMC for immediate release.","ddc":["570"],"OA_type":"hybrid","article_processing_charge":"Yes (via OA deal)","month":"06","pmid":1,"oa_version":"Published Version","year":"2025","issue":"12","_id":"20048","title":"Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation"},{"external_id":{"arxiv":["2402.04151"],"isi":["001523520000012"]},"corr_author":"1","date_updated":"2025-09-30T14:12:48Z","OA_place":"repository","publication_identifier":{"issn":["1050-5164"]},"intvolume":" 35","quality_controlled":"1","language":[{"iso":"eng"}],"department":[{"_id":"JaMa"}],"date_created":"2025-07-21T08:13:54Z","related_material":{"record":[{"status":"public","id":"17352","relation":"earlier_version"}]},"type":"journal_article","page":"1913-1940","day":"01","publisher":"Institute of Mathematical Statistics","doi":"10.1214/25-aap2162","volume":35,"citation":{"ama":"Khudiakova K, Maas J, Pedrotti F. L∞-optimal transport of anisotropic log-concave measures and exponential convergence in Fisher’s infinitesimal model. The Annals of Applied Probability. 2025;35(3):1913-1940. doi:10.1214/25-aap2162","chicago":"Khudiakova, Kseniia, Jan Maas, and Francesco Pedrotti. “L∞-Optimal Transport of Anisotropic Log-Concave Measures and Exponential Convergence in Fisher’s Infinitesimal Model.” The Annals of Applied Probability. Institute of Mathematical Statistics, 2025. https://doi.org/10.1214/25-aap2162.","short":"K. Khudiakova, J. Maas, F. Pedrotti, The Annals of Applied Probability 35 (2025) 1913–1940.","ista":"Khudiakova K, Maas J, Pedrotti F. 2025. L∞-optimal transport of anisotropic log-concave measures and exponential convergence in Fisher’s infinitesimal model. The Annals of Applied Probability. 35(3), 1913–1940.","apa":"Khudiakova, K., Maas, J., & Pedrotti, F. (2025). L∞-optimal transport of anisotropic log-concave measures and exponential convergence in Fisher’s infinitesimal model. The Annals of Applied Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/25-aap2162","mla":"Khudiakova, Kseniia, et al. “L∞-Optimal Transport of Anisotropic Log-Concave Measures and Exponential Convergence in Fisher’s Infinitesimal Model.” The Annals of Applied Probability, vol. 35, no. 3, Institute of Mathematical Statistics, 2025, pp. 1913–40, doi:10.1214/25-aap2162.","ieee":"K. Khudiakova, J. Maas, and F. Pedrotti, “L∞-optimal transport of anisotropic log-concave measures and exponential convergence in Fisher’s infinitesimal model,” The Annals of Applied Probability, vol. 35, no. 3. Institute of Mathematical Statistics, pp. 1913–1940, 2025."},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2402.04151","open_access":"1"}],"publication":"The Annals of Applied Probability","acknowledgement":"This research was funded in part by the Austrian Science Fund (FWF) project 10.55776/F65 and the Austrian Academy of Science, DOC fellowship nr. 26293.","arxiv":1,"OA_type":"green","status":"public","abstract":[{"lang":"eng","text":"We prove upper bounds on the L∞-Wasserstein distance from optimal transport between strongly log-concave probability densities and log-Lipschitz perturbations. In the simplest setting, such a bound amounts to a transport-information inequality involving the L∞-Wasserstein metric and the relative L∞-Fisher information. We show that this inequality can be sharpened significantly in situations where the involved densities are anisotropic. Our proof is based on probabilistic techniques using Langevin dynamics. As an application of these results, we obtain sharp exponential rates of convergence in Fisher’s infinitesimal model from quantitative genetics, generalising recent results by Calvez, Poyato, and Santambrogio in dimension 1 to arbitrary dimensions."}],"date_published":"2025-06-01T00:00:00Z","scopus_import":"1","oa":1,"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"last_name":"Khudiakova","orcid":"0000-0002-6246-1465","full_name":"Khudiakova, Kseniia","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","first_name":"Kseniia"},{"last_name":"Maas","orcid":"0000-0002-0845-1338","first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","full_name":"Maas, Jan"},{"full_name":"Pedrotti, Francesco","id":"d3ac8ac6-dc8d-11ea-abe3-e2a9628c4c3c","first_name":"Francesco","last_name":"Pedrotti"}],"project":[{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems"},{"name":"The impact of deleterious mutations on small populations","_id":"34d33d68-11ca-11ed-8bc3-ec13763c0ca8","grant_number":"26293"}],"publication_status":"published","article_type":"original","title":"L∞-optimal transport of anisotropic log-concave measures and exponential convergence in Fisher’s infinitesimal model","oa_version":"Preprint","year":"2025","_id":"20050","issue":"3","month":"06","article_processing_charge":"No"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"department":[{"_id":"MoHe"}],"date_created":"2025-07-21T08:16:15Z","file_date_updated":"2025-08-04T09:10:55Z","external_id":{"isi":["001525534800066"],"arxiv":["2505.02765"]},"corr_author":"1","date_updated":"2025-10-16T13:08:45Z","OA_place":"publisher","has_accepted_license":"1","publication_identifier":{"isbn":[" 9798400718854"]},"quality_controlled":"1","language":[{"iso":"eng"}],"publication":"Proceedings of the ACM Symposium on Principles of Distributed Computing","ec_funded":1,"type":"conference","day":"13","publisher":"Association for Computing Machinery","doi":"10.1145/3732772.3733505","citation":{"chicago":"El-Hayek, Antoine, Robert Elsässer, and Stefan Schmid. “An Almost Tight Lower Bound for Plurality Consensus with Undecided State Dynamics in the Population Protocol Model.” In Proceedings of the ACM Symposium on Principles of Distributed Computing. Association for Computing Machinery, 2025. https://doi.org/10.1145/3732772.3733505.","ama":"El-Hayek A, Elsässer R, Schmid S. An almost tight lower bound for plurality consensus with undecided state dynamics in the population protocol model. In: Proceedings of the ACM Symposium on Principles of Distributed Computing. Association for Computing Machinery; 2025. doi:10.1145/3732772.3733505","apa":"El-Hayek, A., Elsässer, R., & Schmid, S. (2025). An almost tight lower bound for plurality consensus with undecided state dynamics in the population protocol model. In Proceedings of the ACM Symposium on Principles of Distributed Computing. Huatulco, Mexico: Association for Computing Machinery. https://doi.org/10.1145/3732772.3733505","mla":"El-Hayek, Antoine, et al. “An Almost Tight Lower Bound for Plurality Consensus with Undecided State Dynamics in the Population Protocol Model.” Proceedings of the ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2025, doi:10.1145/3732772.3733505.","ista":"El-Hayek A, Elsässer R, Schmid S. 2025. An almost tight lower bound for plurality consensus with undecided state dynamics in the population protocol model. Proceedings of the ACM Symposium on Principles of Distributed Computing. PODC: Symposium on Principles of Distributed Computing.","ieee":"A. El-Hayek, R. Elsässer, and S. Schmid, “An almost tight lower bound for plurality consensus with undecided state dynamics in the population protocol model,” in Proceedings of the ACM Symposium on Principles of Distributed Computing, Huatulco, Mexico, 2025.","short":"A. El-Hayek, R. Elsässer, S. Schmid, in:, Proceedings of the ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2025."},"oa":1,"file":[{"file_name":"2025_PODC_ElHayek.pdf","date_updated":"2025-08-04T09:10:55Z","success":1,"checksum":"52976d226f3f691aa519d71c1c718fa5","file_id":"20115","relation":"main_file","file_size":2200347,"content_type":"application/pdf","creator":"dernst","date_created":"2025-08-04T09:10:55Z","access_level":"open_access"}],"isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Antoine","id":"888a098e-fcac-11ee-aff7-d347be57b725","full_name":"El-Hayek, Antoine","last_name":"El-Hayek","orcid":"0000-0003-4268-7368"},{"last_name":"Elsässer","full_name":"Elsässer, Robert","first_name":"Robert"},{"last_name":"Schmid","full_name":"Schmid, Stefan","first_name":"Stefan"}],"project":[{"_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","grant_number":"101019564","call_identifier":"H2020","name":"The design and evaluation of modern fully dynamic data structures"},{"name":"Static and Dynamic Hierarchical Graph Decompositions","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103","grant_number":"I05982"},{"_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","grant_number":"P33775","name":"Fast Algorithms for a Reactive Network Layer"}],"publication_status":"published","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (MoDynStruct, No. 101019564) and the Austrian Science Fund (FWF) grant DOI 10.55776/I5862,grant DOI 10.55776/I5982, and grant DOI 10.55776/P33775 with\r\nadditional funding from the netidee SCIENCE Stiftung, 2020–2024\r\nand the German Research Foundation (DFG), grant 470029389\r\n(FlexNets).","conference":{"location":"Huatulco, Mexico","start_date":"2025-06-16","end_date":"2025-06-20","name":"PODC: Symposium on Principles of Distributed Computing"},"arxiv":1,"ddc":["000"],"OA_type":"hybrid","status":"public","abstract":[{"text":"We revisit the majority problem in the population protocol communication model, as first studied by Angluin et al. (Distributed Computing 2008). We consider a more general version of this problem known as plurality consensus, which has already been studied intensively in the literature. In this problem, each node in a system of n nodes, has initially one of k different opinions, and they need to agree on the (relative) majority opinion. In particular, we consider the important and intensively studied model of Undecided State Dynamics.\r\nOur main contribution is an almost tight lower bound on the stabilization time: we prove that there exists an initial configuration, even with bias \\Delta = \\omega(\\sqrt{n\\log n}), where stabilization requires \\Omega(kn\\log \\frac {\\sqrt n} {k \\log n}) interactions, or equivalently, \\Omega(k\\log \\frac {\\sqrt n} {k \\log n}) parallel time for any k = o\\left(\\frac {\\sqrt n}{\\log n}\\right). This bound is tight for any k \\le n^{\\frac 1 2 - \\epsilon}, where \\epsilon >0 can be any small constant, as Amir et al.~(PODC'23) gave a O(k\\log n) parallel time upper bound for k = O\\left(\\frac {\\sqrt n} {\\log ^2 n}\\right).","lang":"eng"}],"date_published":"2025-06-13T00:00:00Z","month":"06","article_processing_charge":"Yes (via OA deal)","title":"An almost tight lower bound for plurality consensus with undecided state dynamics in the population protocol model","oa_version":"Published Version","year":"2025","_id":"20051"},{"corr_author":"1","external_id":{"isi":["001525534800069"]},"OA_place":"publisher","has_accepted_license":"1","date_updated":"2026-02-16T11:46:37Z","publication_identifier":{"isbn":["9798400718854"]},"quality_controlled":"1","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"department":[{"_id":"MoHe"}],"file_date_updated":"2025-08-05T07:32:01Z","date_created":"2025-07-21T08:17:04Z","type":"conference","ec_funded":1,"day":"13","publisher":"Association for Computing Machinery","doi":"10.1145/3732772.3733512","page":"549-552","citation":{"mla":"Breitkopf, Tom-Lukas, et al. “Brief Announcement: Minimizing Energy Solves Relative Majority with a Cubic Number of States in Population Protocols.” Proceedings of the ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2025, pp. 549–52, doi:10.1145/3732772.3733512.","ista":"Breitkopf T-L, Dallot J, El-Hayek A, Schmid S. 2025. Brief announcement: Minimizing energy solves relative majority with a cubic number of states in population protocols. Proceedings of the ACM Symposium on Principles of Distributed Computing. PODC: Symposium on Principles of Distributed Computing, 549–552.","apa":"Breitkopf, T.-L., Dallot, J., El-Hayek, A., & Schmid, S. (2025). Brief announcement: Minimizing energy solves relative majority with a cubic number of states in population protocols. In Proceedings of the ACM Symposium on Principles of Distributed Computing (pp. 549–552). Huatulco, Mexico: Association for Computing Machinery. https://doi.org/10.1145/3732772.3733512","ieee":"T.-L. Breitkopf, J. Dallot, A. El-Hayek, and S. Schmid, “Brief announcement: Minimizing energy solves relative majority with a cubic number of states in population protocols,” in Proceedings of the ACM Symposium on Principles of Distributed Computing, Huatulco, Mexico, 2025, pp. 549–552.","short":"T.-L. Breitkopf, J. Dallot, A. El-Hayek, S. Schmid, in:, Proceedings of the ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2025, pp. 549–552.","chicago":"Breitkopf, Tom-Lukas, Julien Dallot, Antoine El-Hayek, and Stefan Schmid. “Brief Announcement: Minimizing Energy Solves Relative Majority with a Cubic Number of States in Population Protocols.” In Proceedings of the ACM Symposium on Principles of Distributed Computing, 549–52. Association for Computing Machinery, 2025. https://doi.org/10.1145/3732772.3733512.","ama":"Breitkopf T-L, Dallot J, El-Hayek A, Schmid S. Brief announcement: Minimizing energy solves relative majority with a cubic number of states in population protocols. In: Proceedings of the ACM Symposium on Principles of Distributed Computing. Association for Computing Machinery; 2025:549-552. doi:10.1145/3732772.3733512"},"publication":"Proceedings of the ACM Symposium on Principles of Distributed Computing","ddc":["000"],"conference":{"start_date":"2025-06-16","end_date":"2025-06-20","name":"PODC: Symposium on Principles of Distributed Computing","location":"Huatulco, Mexico"},"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (MoDynStruct, No. 101019564) and the Austrian Science Fund (FWF) grant DOI 10.55776/I5982, and grant DOI 10.55776/P33775 with additional funding from the netidee SCIENCE Stiftung, 2020–2024 and the German Research Foundation (DFG), grant 470029389 (FlexNets). ","OA_type":"hybrid","status":"public","abstract":[{"text":"This paper revisits a fundamental distributed computing problem in the population protocol model. Provided n agents each starting with an input color in [k], the relative majority problem asks to find the predominant color. In the population protocol model, at each time step, a scheduler selects two agents that first learn each other's states and then update their states based on what they learned.\r\nWe present the Circles protocol that solves the relative majority problem with k3 states. It is always-correct under weakly fair scheduling. Not only does it improve upon the best known upper bound of O(k7), but it also shows a strikingly simpler design inspired by energy minimization in chemical settings.","lang":"eng"}],"date_published":"2025-06-13T00:00:00Z","oa":1,"isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_name":"2025_PODC_Breitkopf.pdf","date_updated":"2025-08-05T07:32:01Z","checksum":"e99679ffb28877b7cea4d54860302790","success":1,"file_size":549706,"relation":"main_file","file_id":"20123","date_created":"2025-08-05T07:32:01Z","creator":"dernst","access_level":"open_access","content_type":"application/pdf"}],"author":[{"full_name":"Breitkopf, Tom-Lukas","first_name":"Tom-Lukas","last_name":"Breitkopf"},{"full_name":"Dallot, Julien","first_name":"Julien","last_name":"Dallot"},{"last_name":"El-Hayek","orcid":"0000-0003-4268-7368","first_name":"Antoine","full_name":"El-Hayek, Antoine","id":"888a098e-fcac-11ee-aff7-d347be57b725"},{"first_name":"Stefan","full_name":"Schmid, Stefan","last_name":"Schmid"}],"publication_status":"published","project":[{"grant_number":"101019564","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","call_identifier":"H2020","name":"The design and evaluation of modern fully dynamic data structures"},{"_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103","grant_number":"I05982","name":"Static and Dynamic Hierarchical Graph Decompositions"},{"name":"Fast Algorithms for a Reactive Network Layer","grant_number":"P33775","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe"}],"title":"Brief announcement: Minimizing energy solves relative majority with a cubic number of states in population protocols","oa_version":"Published Version","_id":"20052","year":"2025","month":"06","article_processing_charge":"No"},{"department":[{"_id":"KrCh"},{"_id":"KrPi"}],"file_date_updated":"2025-08-05T07:15:31Z","date_created":"2025-07-21T08:18:26Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publication_identifier":{"isbn":["9798400718854"]},"quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"isi":["001525534800030"]},"corr_author":"1","date_updated":"2026-02-16T11:46:51Z","OA_place":"publisher","has_accepted_license":"1","publication":"Proceedings of the ACM Symposium on Principles of Distributed Computing","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2025/745"}],"citation":{"short":"K. Chatterjee, S. Gilbert, S. Schmid, J. Svoboda, M.X. Yeo, in:, Proceedings of the ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2025, pp. 241–251.","mla":"Chatterjee, Krishnendu, et al. “When Is Liquid Democracy Possible?: On the Manipulation of Variance.” Proceedings of the ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2025, pp. 241–51, doi:10.1145/3732772.3733544.","apa":"Chatterjee, K., Gilbert, S., Schmid, S., Svoboda, J., & Yeo, M. X. (2025). When is liquid democracy possible?: On the manipulation of variance. In Proceedings of the ACM Symposium on Principles of Distributed Computing (pp. 241–251). Huatulco, Mexico: Association for Computing Machinery. https://doi.org/10.1145/3732772.3733544","ista":"Chatterjee K, Gilbert S, Schmid S, Svoboda J, Yeo MX. 2025. When is liquid democracy possible?: On the manipulation of variance. Proceedings of the ACM Symposium on Principles of Distributed Computing. PODC: Symposium on Principles of Distributed Computing, 241–251.","ieee":"K. Chatterjee, S. Gilbert, S. Schmid, J. Svoboda, and M. X. Yeo, “When is liquid democracy possible?: On the manipulation of variance,” in Proceedings of the ACM Symposium on Principles of Distributed Computing, Huatulco, Mexico, 2025, pp. 241–251.","ama":"Chatterjee K, Gilbert S, Schmid S, Svoboda J, Yeo MX. When is liquid democracy possible?: On the manipulation of variance. In: Proceedings of the ACM Symposium on Principles of Distributed Computing. Association for Computing Machinery; 2025:241-251. doi:10.1145/3732772.3733544","chicago":"Chatterjee, Krishnendu, Seth Gilbert, Stefan Schmid, Jakub Svoboda, and Michelle X Yeo. “When Is Liquid Democracy Possible?: On the Manipulation of Variance.” In Proceedings of the ACM Symposium on Principles of Distributed Computing, 241–51. Association for Computing Machinery, 2025. https://doi.org/10.1145/3732772.3733544."},"type":"conference","ec_funded":1,"page":"241-251","publisher":"Association for Computing Machinery","day":"13","doi":"10.1145/3732772.3733544","author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Seth","full_name":"Gilbert, Seth","last_name":"Gilbert"},{"first_name":"Stefan","full_name":"Schmid, Stefan","last_name":"Schmid"},{"first_name":"Jakub","full_name":"Svoboda, Jakub","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","last_name":"Svoboda","orcid":"0000-0002-1419-3267"},{"last_name":"Yeo","orcid":"0009-0001-3676-4809","full_name":"Yeo, Michelle X","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle X"}],"project":[{"grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020"}],"publication_status":"published","oa":1,"file":[{"checksum":"cd628fe54d96e9fc6cc789bb8145422b","success":1,"file_name":"2025_PODC_Chatterjee.pdf","date_updated":"2025-08-05T07:15:31Z","creator":"dernst","date_created":"2025-08-05T07:15:31Z","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_size":783297,"file_id":"20122"}],"isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_published":"2025-06-13T00:00:00Z","abstract":[{"lang":"eng","text":"Liquid democracy is a transitive vote delegation mechanism over voting graphs. It enables each voter to delegate their vote(s) to another better-informed voter, with the goal of collectively making a better decision. The question of whether liquid democracy outperforms direct voting has been previously studied in the context of local delegation mechanisms (where voters can only delegate to someone in their neighbourhood) and binary decision problems. It has previously been shown that it is impossible for local delegation mechanisms to outperform direct voting in general graphs. This raises the question: for which classes of graphs do local delegation mechanisms yield good results?\r\nIn this work, we analyse (1) properties of specific graphs and (2) properties of local delegation mechanisms on these graphs, determining where local delegation actually outperforms direct voting. We show that a critical graph property enabling liquid democracy is that the voting outcome of local delegation mechanisms preserves a sufficient amount of variance, thereby avoiding situations where delegation falls behind direct voting1. These insights allow us to prove our main results, namely that there exist local delegation mechanisms that perform no worse and in fact quantitatively better than direct voting in natural graph topologies like complete, random d-regular, and bounded degree graphs, lending a more nuanced perspective to previous impossibility results."}],"acknowledgement":"This work was partially supported by MOE-T2EP20122-0014 (DataDriven Distributed Algorithms), German Research Foundation (DFG) project ReNO (SPP 2378) from 2023-2027, ERC CoG 863818 (ForMSMArt) and Austrian Science Fund (FWF) 10.55776/COE12.","conference":{"location":"Huatulco, Mexico","name":"PODC: Symposium on Principles of Distributed Computing","end_date":"2025-06-20","start_date":"2025-06-16"},"ddc":["000"],"OA_type":"hybrid","article_processing_charge":"No","month":"06","oa_version":"Published Version","year":"2025","_id":"20053","title":"When is liquid democracy possible?: On the manipulation of variance"}]