[{"publication_status":"published","oa_version":"Published Version","acknowledged_ssus":[{"_id":"NanoFab"}],"article_number":"064026","volume":22,"fulldoi":"https://doi.org/10.1103/PhysRevApplied.22.064026","license":"https://creativecommons.org/licenses/by/4.0/","type":"journal_article","scopus_import":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"American Physical Society","abstract":[{"lang":"eng","text":"Charge sensing is a sensitive technique for probing quantum devices, of particular importance for spin-qubit readout. To achieve good readout sensitivities, the proximity of the charge sensor to the device to be measured is a necessity. However, this proximity also means that the operation of the device affects, in turn, the sensor tuning and ultimately the readout sensitivity. We present an approach for compensating for this crosstalk effect allowing for the gate voltages of the measured device to be swept in a 1-V × 1-V window while maintaining a sensor configuration chosen by a Bayesian optimizer. Our algorithm will hopefully be a major contribution to the suite of fully automated solutions required for the operation of large quantum device architectures."}],"article_type":"original","publication":"Physical Review Applied","researchdata_availability":"no","project":[{"grant_number":"I05060","name":"High impedance circuit quantum electrodynamics with hole spins","_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1"},{"_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452","grant_number":"101069515","name":"Integrated Germanium Quantum Technology"}],"article_processing_charge":"No","quality_controlled":"1","acknowledgement":"We thank Nicholas Sim for providing help with the experiment and Sebastian Orbell for helpful discussions. This work was supported by the Royal Society, the Engineering and Physical Sciences Research Council (EPSRC) National Quantum Technology Hub in Networked Quantum Information Technology (Grant No. EP/M013243/1), Quantum Technology Capital (Grant No. EP/N014995/1), the EPSRC Platform Grant (Grant No. EP/R029229/1), the European Research Council (Grant Agreement No. 948932), the Scientific Service Units of the Institute of Science and Technology Austria through resources provided by the nanofabrication facility and, the FWF-I 05060 and HORIZON-RIA 101069515 projects.","doi":"10.1103/PhysRevApplied.22.064026","file":[{"relation":"main_file","success":1,"file_id":"18662","file_size":3560132,"file_name":"2024_PhysicalReviewApplied_Hickie.pdf","creator":"dernst","checksum":"bc29a40819abc4969867b6cd6563f7ad","access_level":"open_access","content_type":"application/pdf","date_created":"2024-12-16T11:13:48Z","date_updated":"2024-12-16T11:13:48Z"}],"day":"01","issue":"6","isi":1,"language":[{"iso":"eng"}],"_id":"18653","title":"Automated long-range compensation of an rf quantum dot sensor","date_updated":"2026-10-02T11:04:04Z","date_published":"2024-12-01T00:00:00Z","ddc":["530"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file_date_updated":"2024-12-16T11:13:48Z","publication_identifier":{"eissn":["2331-7019"]},"supplementarymaterial":"yes","intvolume":"        22","das_tickbox":"0","OA_place":"publisher","author":[{"full_name":"Hickie, Joseph","first_name":"Joseph","last_name":"Hickie"},{"first_name":"Barnaby","last_name":"Van Straaten","full_name":"Van Straaten, Barnaby"},{"full_name":"Fedele, Federico","last_name":"Fedele","first_name":"Federico"},{"first_name":"Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","last_name":"Jirovec","orcid":"0000-0002-7197-4801","full_name":"Jirovec, Daniel"},{"first_name":"Andrea","last_name":"Ballabio","full_name":"Ballabio, Andrea"},{"full_name":"Chrastina, Daniel","first_name":"Daniel","last_name":"Chrastina"},{"first_name":"Giovanni","last_name":"Isella","full_name":"Isella, Giovanni"},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros","first_name":"Georgios","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X"},{"first_name":"Natalia","last_name":"Ares","full_name":"Ares, Natalia"}],"has_accepted_license":"1","oa":1,"month":"12","external_id":{"isi":["001379155900003"]},"department":[{"_id":"GeKa"}],"date_created":"2024-12-15T23:01:50Z","citation":{"ama":"Hickie J, Van Straaten B, Fedele F, et al. Automated long-range compensation of an rf quantum dot sensor. <i>Physical Review Applied</i>. 2024;22(6). doi:<a href=\"https://doi.org/10.1103/PhysRevApplied.22.064026\">10.1103/PhysRevApplied.22.064026</a>","apa":"Hickie, J., Van Straaten, B., Fedele, F., Jirovec, D., Ballabio, A., Chrastina, D., … Ares, N. (2024). Automated long-range compensation of an rf quantum dot sensor. <i>Physical Review Applied</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevApplied.22.064026\">https://doi.org/10.1103/PhysRevApplied.22.064026</a>","short":"J. Hickie, B. Van Straaten, F. Fedele, D. Jirovec, A. Ballabio, D. Chrastina, G. Isella, G. Katsaros, N. Ares, Physical Review Applied 22 (2024).","mla":"Hickie, Joseph, et al. “Automated Long-Range Compensation of an Rf Quantum Dot Sensor.” <i>Physical Review Applied</i>, vol. 22, no. 6, 064026, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/PhysRevApplied.22.064026\">10.1103/PhysRevApplied.22.064026</a>.","ista":"Hickie J, Van Straaten B, Fedele F, Jirovec D, Ballabio A, Chrastina D, Isella G, Katsaros G, Ares N. 2024. Automated long-range compensation of an rf quantum dot sensor. Physical Review Applied. 22(6), 064026.","chicago":"Hickie, Joseph, Barnaby Van Straaten, Federico Fedele, Daniel Jirovec, Andrea Ballabio, Daniel Chrastina, Giovanni Isella, Georgios Katsaros, and Natalia Ares. “Automated Long-Range Compensation of an Rf Quantum Dot Sensor.” <i>Physical Review Applied</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/PhysRevApplied.22.064026\">https://doi.org/10.1103/PhysRevApplied.22.064026</a>.","ieee":"J. Hickie <i>et al.</i>, “Automated long-range compensation of an rf quantum dot sensor,” <i>Physical Review Applied</i>, vol. 22, no. 6. American Physical Society, 2024."},"OA_type":"hybrid","year":"2024","status":"public"},{"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.13935166","open_access":"1"}],"OA_place":"repository","publisher":"Zenodo","fulldoi":"https://doi.org/10.5281/zenodo.13935166","type":"research_data_reference","date_updated":"2026-10-02T11:02:23Z","date_published":"2024-10-15T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["530"],"contributor":[{"last_name":"Oppliger","first_name":"Fabian","contributor_type":"project_member"}],"title":"Online data of \"Strong hole-photon coupling in planar Ge for probing charge degree and strongly correlated states\"","day":"15","oa_version":"None","_id":"23037","status":"public","department":[{"_id":"GeKa"}],"related_material":{"record":[{"id":"18602","status":"public","relation":"used_in_publication"}]},"doi":"10.5281/zenodo.13935166","date_created":"2026-10-02T11:02:18Z","citation":{"ieee":"F. De Palma <i>et al.</i>, “Online data of ‘Strong hole-photon coupling in planar Ge for probing charge degree and strongly correlated states.’” Zenodo, 2024.","ista":"De Palma F, Oppliger F, Jang W, Bosco S, Janík M, Calcaterra S, Katsaros G, Isella G, Loss D, Scarlino P. 2024. Online data of ‘Strong hole-photon coupling in planar Ge for probing charge degree and strongly correlated states’, Zenodo, <a href=\"https://doi.org/10.5281/zenodo.13935166\">10.5281/zenodo.13935166</a>.","chicago":"De Palma, Franco, Fabian Oppliger, Wonjin Jang, Stefano Bosco, Marián Janík, Stefano Calcaterra, Georgios Katsaros, Giovanni Isella, Daniel Loss, and Pasquale Scarlino. “Online Data of ‘Strong Hole-Photon Coupling in Planar Ge for Probing Charge Degree and Strongly Correlated States.’” Zenodo, 2024. <a href=\"https://doi.org/10.5281/zenodo.13935166\">https://doi.org/10.5281/zenodo.13935166</a>.","short":"F. De Palma, F. Oppliger, W. Jang, S. Bosco, M. Janík, S. Calcaterra, G. Katsaros, G. Isella, D. Loss, P. Scarlino, (2024).","apa":"De Palma, F., Oppliger, F., Jang, W., Bosco, S., Janík, M., Calcaterra, S., … Scarlino, P. (2024). Online data of “Strong hole-photon coupling in planar Ge for probing charge degree and strongly correlated states.” Zenodo. <a href=\"https://doi.org/10.5281/zenodo.13935166\">https://doi.org/10.5281/zenodo.13935166</a>","ama":"De Palma F, Oppliger F, Jang W, et al. Online data of “Strong hole-photon coupling in planar Ge for probing charge degree and strongly correlated states.” 2024. doi:<a href=\"https://doi.org/10.5281/zenodo.13935166\">10.5281/zenodo.13935166</a>","mla":"De Palma, Franco, et al. <i>Online Data of “Strong Hole-Photon Coupling in Planar Ge for Probing Charge Degree and Strongly Correlated States.”</i> Zenodo, 2024, doi:<a href=\"https://doi.org/10.5281/zenodo.13935166\">10.5281/zenodo.13935166</a>."},"OA_type":"green","year":"2024","month":"10","article_processing_charge":"No","abstract":[{"text":"The data for all figures in the main text can be found in csv files in ASCII format in the corresponing folders. For Figures 4-6, the panels are numbered from top to bottom.","lang":"eng"}],"author":[{"last_name":"De Palma","first_name":"Franco","full_name":"De Palma, Franco"},{"last_name":"Oppliger","first_name":"Fabian","full_name":"Oppliger, Fabian"},{"full_name":"Jang, Wonjin","first_name":"Wonjin","last_name":"Jang"},{"full_name":"Bosco, Stefano","first_name":"Stefano","last_name":"Bosco"},{"full_name":"Janík, Marián","last_name":"Janík","first_name":"Marián"},{"full_name":"Calcaterra, Stefano","first_name":"Stefano","last_name":"Calcaterra"},{"last_name":"Katsaros","first_name":"Georgios","full_name":"Katsaros, Georgios"},{"first_name":"Giovanni","last_name":"Isella","full_name":"Isella, Giovanni"},{"first_name":"Daniel","last_name":"Loss","full_name":"Loss, Daniel"},{"first_name":"Pasquale","last_name":"Scarlino","full_name":"Scarlino, Pasquale"}],"oa":1},{"article_processing_charge":"Yes (in subscription journal)","quality_controlled":"1","article_type":"original","abstract":[{"text":"The epitaxial growth of a strained Ge layer, which is a promising candidate for the channel material of a hole spin qubit, has been demonstrated on 300 mm Si wafers using commercially available Si0.3Ge0.7 strain relaxed buffer (SRB) layers. The assessment of the layer and the interface qualities for a buried strained Ge layer embedded in Si0.3Ge0.7 layers is reported. The XRD reciprocal space mapping confirmed that the reduction of the growth temperature enables the 2-dimensional growth of the Ge layer fully strained with respect to the Si0.3Ge0.7. Nevertheless, dislocations at the top and/or bottom interface of the Ge layer were observed by means of electron channeling contrast imaging, suggesting the importance of the careful dislocation assessment. The interface abruptness does not depend on the selection of the precursor gases, but it is strongly influenced by the growth temperature which affects the coverage of the surface H-passivation. The mobility of 2.7 × 105 cm2/Vs is promising, while the low percolation density of 3 × 1010 /cm2 measured with a Hall-bar device at 7 K illustrates the high quality of the heterostructure thanks to the high Si0.3Ge0.7 SRB quality.","lang":"eng"}],"publication":"Materials Science in Semiconductor Processing","researchdata_availability":"not applicable","project":[{"grant_number":"101069515","name":"Integrated Germanium Quantum Technology","_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452"}],"file":[{"file_id":"17312","success":1,"file_name":"2024_MaterialsScience_Shimura.pdf","checksum":"62e8e9ae960387a3dca32ec7f5e413ab","file_size":4220165,"creator":"dernst","relation":"main_file","date_updated":"2024-07-22T11:56:08Z","date_created":"2024-07-22T11:56:08Z","access_level":"open_access","content_type":"application/pdf"}],"acknowledgement":"The Ge project received funding from the European Union's Horizon Europe programme under the Grant Agreement 101069515 – IGNITE. Siltronic AG is acknowledged for providing the SRB wafers. This work was supported by Imec's Industrial Affiliation Program on Quantum Computing.","doi":"10.1016/j.mssp.2024.108231","volume":174,"article_number":"108231","oa_version":"Published Version","publication_status":"published","scopus_import":"1","publisher":"Elsevier","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"type":"journal_article","fulldoi":"https://doi.org/10.1016/j.mssp.2024.108231","dataavailabilitystatement":"No data was used for the research described in the article.","month":"05","external_id":{"isi":["001188520000001"]},"author":[{"full_name":"Shimura, Yosuke","first_name":"Yosuke","last_name":"Shimura"},{"last_name":"Godfrin","first_name":"Clement","full_name":"Godfrin, Clement"},{"full_name":"Hikavyy, Andriy","first_name":"Andriy","last_name":"Hikavyy"},{"full_name":"Li, Roy","first_name":"Roy","last_name":"Li"},{"first_name":"Juan L","id":"2A67C376-F248-11E8-B48F-1D18A9856A87","last_name":"Aguilera Servin","orcid":"0000-0002-2862-8372","full_name":"Aguilera Servin, Juan L"},{"full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios"},{"full_name":"Favia, Paola","first_name":"Paola","last_name":"Favia"},{"full_name":"Han, Han","last_name":"Han","first_name":"Han"},{"last_name":"Wan","first_name":"Danny","full_name":"Wan, Danny"},{"first_name":"Kristiaan","last_name":"de Greve","full_name":"de Greve, Kristiaan"},{"first_name":"Roger","last_name":"Loo","full_name":"Loo, Roger"}],"oa":1,"has_accepted_license":"1","status":"public","department":[{"_id":"GeKa"},{"_id":"NanoFab"}],"OA_type":"hybrid","year":"2024","date_created":"2024-02-22T14:10:40Z","citation":{"short":"Y. Shimura, C. Godfrin, A. Hikavyy, R. Li, J.L. Aguilera Servin, G. Katsaros, P. Favia, H. Han, D. Wan, K. de Greve, R. Loo, Materials Science in Semiconductor Processing 174 (2024).","apa":"Shimura, Y., Godfrin, C., Hikavyy, A., Li, R., Aguilera Servin, J. L., Katsaros, G., … Loo, R. (2024). Compressively strained epitaxial Ge layers for quantum computing applications. <i>Materials Science in Semiconductor Processing</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.mssp.2024.108231\">https://doi.org/10.1016/j.mssp.2024.108231</a>","ama":"Shimura Y, Godfrin C, Hikavyy A, et al. Compressively strained epitaxial Ge layers for quantum computing applications. <i>Materials Science in Semiconductor Processing</i>. 2024;174(5). doi:<a href=\"https://doi.org/10.1016/j.mssp.2024.108231\">10.1016/j.mssp.2024.108231</a>","mla":"Shimura, Yosuke, et al. “Compressively Strained Epitaxial Ge Layers for Quantum Computing Applications.” <i>Materials Science in Semiconductor Processing</i>, vol. 174, no. 5, 108231, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.mssp.2024.108231\">10.1016/j.mssp.2024.108231</a>.","ieee":"Y. Shimura <i>et al.</i>, “Compressively strained epitaxial Ge layers for quantum computing applications,” <i>Materials Science in Semiconductor Processing</i>, vol. 174, no. 5. Elsevier, 2024.","ista":"Shimura Y, Godfrin C, Hikavyy A, Li R, Aguilera Servin JL, Katsaros G, Favia P, Han H, Wan D, de Greve K, Loo R. 2024. Compressively strained epitaxial Ge layers for quantum computing applications. Materials Science in Semiconductor Processing. 174(5), 108231.","chicago":"Shimura, Yosuke, Clement Godfrin, Andriy Hikavyy, Roy Li, Juan L Aguilera Servin, Georgios Katsaros, Paola Favia, et al. “Compressively Strained Epitaxial Ge Layers for Quantum Computing Applications.” <i>Materials Science in Semiconductor Processing</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.mssp.2024.108231\">https://doi.org/10.1016/j.mssp.2024.108231</a>."},"keyword":["Mechanical Engineering","Mechanics of Materials","Condensed Matter Physics","General Materials Science"],"title":"Compressively strained epitaxial Ge layers for quantum computing applications","issue":"5","isi":1,"day":"20","language":[{"iso":"eng"}],"_id":"15018","supplementarymaterial":"no","publication_identifier":{"issn":["1369-8001"]},"intvolume":"       174","file_date_updated":"2024-07-22T11:56:08Z","das_tickbox":"1","OA_place":"publisher","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-10-02T11:06:21Z","ddc":["530"],"date_published":"2024-05-20T00:00:00Z"},{"publisher":"Institute of Science and Technology Austria","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"type":"research_data","fulldoi":"https://doi.org/10.15479/AT:ISTA:14705","contributor":[{"contributor_type":"researcher","first_name":"Vincent K","last_name":"Bett","id":"57854184-AAE0-11E9-8D04-98D6E5697425"},{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","last_name":"Macon","first_name":"Ariana","contributor_type":"project_member"},{"contributor_type":"supervisor","orcid":"0000-0002-4579-8306","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz"},{"first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi","contributor_type":"researcher","orcid":"0000-0002-5328-7231"}],"oa_version":"Published Version","corr_author":"1","file":[{"access_level":"open_access","content_type":"text/plain","date_updated":"2023-12-22T13:54:21Z","date_created":"2023-12-22T13:54:21Z","relation":"main_file","file_id":"14707","success":1,"file_name":"readme.txt.txt","creator":"melkrewi","checksum":"bdaf1392867786634ec5466d528c36ca","file_size":847},{"content_type":"application/x-zip-compressed","access_level":"open_access","date_created":"2023-12-22T14:14:06Z","date_updated":"2023-12-22T14:14:06Z","relation":"main_file","creator":"melkrewi","file_size":343632753,"file_name":"data_artemia_franciscana_genome.zip","checksum":"973e1cbdab923a71709782177980829f","file_id":"14708","success":1}],"related_material":{"record":[{"id":"15009","status":"public","relation":"used_in_publication"}]},"doi":"10.15479/AT:ISTA:14705","article_processing_charge":"No","abstract":[{"text":"Since the commercialization of brine shrimp (genus Artemia) in the 1950s, this lineage, and in particular the model species Artemia franciscana, has been the subject of extensive research. However, our understanding of the genetic mechanisms underlying various aspects of their reproductive biology, including sex determination, are still lacking. This is partly due to the scarcity of genomic resources for Artemia species and crustaceans in general. Here, we present a chromosome-level genome assembly of Artemia franciscana (Kellogg 1906), from the Great Salt Lake, USA. The genome is 1GB, and the majority of the genome (81%) is scaffolded into 21 linkage groups using a previously published high-density linkage map. We performed coverage and FST analyses using male and female genomic and transcriptomic reads to quantify the extent of differentiation between the Z and W chromosomes. Additionally, we quantified the expression levels in male and female heads and gonads and found further evidence for dosage compensation in this species.","lang":"eng"}],"project":[{"grant_number":"F8810","name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396"}],"file_date_updated":"2023-12-22T14:14:06Z","date_updated":"2026-10-02T11:13:43Z","ddc":["576"],"date_published":"2024-01-02T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","keyword":["sex chromosome evolution","genome assembly","dosage compensation"],"title":"Data from \"Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation\"","doi_confirm":"1","day":"02","_id":"14705","status":"public","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"year":"2024","citation":{"mla":"Elkrewi, Marwan N. <i>Data from “Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex-Chromosome Differentiation.”</i> Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14705\">10.15479/AT:ISTA:14705</a>.","ama":"Elkrewi MN. Data from “Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation.” 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14705\">10.15479/AT:ISTA:14705</a>","apa":"Elkrewi, M. N. (2024). Data from “Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:14705\">https://doi.org/10.15479/AT:ISTA:14705</a>","short":"M.N. Elkrewi, (2024).","ista":"Elkrewi MN. 2024. Data from ‘Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:14705\">10.15479/AT:ISTA:14705</a>.","chicago":"Elkrewi, Marwan N. “Data from ‘Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex-Chromosome Differentiation.’” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/AT:ISTA:14705\">https://doi.org/10.15479/AT:ISTA:14705</a>.","ieee":"M. N. Elkrewi, “Data from ‘Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation.’” Institute of Science and Technology Austria, 2024."},"date_created":"2023-12-22T13:40:48Z","month":"01","author":[{"first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi","full_name":"Elkrewi, Marwan N","orcid":"0000-0002-5328-7231"}],"has_accepted_license":"1","oa":1},{"file":[{"relation":"main_file","file_id":"17215","success":1,"file_name":"sig24_friction_authors.pdf","file_size":47309472,"checksum":"b8b203ed09e3995ba0d7e6a76288663a","creator":"yichen","access_level":"open_access","content_type":"application/pdf","date_updated":"2024-07-10T11:03:14Z","date_created":"2024-07-10T11:03:14Z"},{"date_created":"2024-07-10T11:03:12Z","date_updated":"2024-07-10T11:03:12Z","access_level":"open_access","content_type":"application/pdf","file_id":"17216","success":1,"creator":"yichen","checksum":"89d81b397b4b6469d828808a68b70820","file_size":10518286,"file_name":"sig24_friction_supplementary.pdf","relation":"main_file"},{"relation":"main_file","creator":"yichen","file_name":"friction_paper_extra_video_finished.mp4","checksum":"7123deed34a5456810e7b5336a31c657","file_size":71789192,"success":1,"file_id":"17217","content_type":"video/mp4","access_level":"open_access","date_updated":"2024-07-10T11:03:51Z","date_created":"2024-07-10T11:03:51Z"},{"date_updated":"2024-07-10T11:03:58Z","date_created":"2024-07-10T11:03:58Z","content_type":"video/mp4","access_level":"open_access","creator":"yichen","file_size":280610763,"checksum":"e606fc1ae8f2610ce3b4421566800b45","file_name":"friction_paper_video_finished.mp4","success":1,"file_id":"17218","relation":"main_file"}],"doi":"10.1145/3641519.3657485","acknowledgement":"We thank Vincent Acary for his help with Siconos, as well as the anonymous reviewers and the members of the Visual Computing Group at ISTA for their helpful comments. This research was funded in part by the European Union (ERC-2021-COG 101045083 CoDiNA).","quality_controlled":"1","article_processing_charge":"Yes (via OA deal)","publication":"Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers '24","researchdata_availability":"no","project":[{"name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","grant_number":"101045083","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088"}],"abstract":[{"lang":"eng","text":"Current numerical algorithms for simulating friction fall in one of two camps: smooth solvers sacrifice the stable treatment of static friction in exchange for fast convergence, and non-smooth solvers accurately compute friction at convergence rates that are often prohibitive for large graphics applications. We introduce a novel bridge between these two ideas that computes static and dynamic friction stably and efficiently. Our key idea is to convert the highly constrained non-smooth problem into an unconstrained smooth problem using logarithmic barriers that converges to the exact solution as accuracy increases. We phrase the problem as an interior point primal-dual problem that can be solved efficiently with Newton iteration. We observe quadratic convergence despite the non-smooth nature of the original problem, and our method is well-suited for large systems of tightly packed objects with many contact points. We demonstrate the efficacy of our method with stable piles of grains and stacks of objects, complex granular flows, and robust interlocking assemblies of rigid bodies."}],"publisher":"Association for Computing Machinery","scopus_import":"1","type":"conference","fulldoi":"https://doi.org/10.1145/3641519.3657485","corr_author":"1","oa_version":"Published Version","publication_status":"published","status":"public","year":"2024","citation":{"ama":"Chen Y-L, Ly M, Wojtan C. Primal-dual non-smooth friction for rigid body animation. In: <i>Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24</i>. Association for Computing Machinery; 2024. doi:<a href=\"https://doi.org/10.1145/3641519.3657485\">10.1145/3641519.3657485</a>","short":"Y.-L. Chen, M. Ly, C. Wojtan, in:, Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24, Association for Computing Machinery, 2024.","apa":"Chen, Y.-L., Ly, M., &#38; Wojtan, C. (2024). Primal-dual non-smooth friction for rigid body animation. In <i>Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24</i>. Denver, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3641519.3657485\">https://doi.org/10.1145/3641519.3657485</a>","mla":"Chen, Yi-Lu, et al. “Primal-Dual Non-Smooth Friction for Rigid Body Animation.” <i>Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24</i>, Association for Computing Machinery, 2024, doi:<a href=\"https://doi.org/10.1145/3641519.3657485\">10.1145/3641519.3657485</a>.","chicago":"Chen, Yi-Lu, Mickaël Ly, and Chris Wojtan. “Primal-Dual Non-Smooth Friction for Rigid Body Animation.” In <i>Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24</i>. Association for Computing Machinery, 2024. <a href=\"https://doi.org/10.1145/3641519.3657485\">https://doi.org/10.1145/3641519.3657485</a>.","ista":"Chen Y-L, Ly M, Wojtan C. 2024. Primal-dual non-smooth friction for rigid body animation. Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24. SIGGRAPH: Computer Graphics and Interactive Techniques Conference.","ieee":"Y.-L. Chen, M. Ly, and C. Wojtan, “Primal-dual non-smooth friction for rigid body animation,” in <i>Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24</i>, Denver, United States, 2024."},"date_created":"2024-07-10T11:06:20Z","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"external_id":{"isi":["001282218200091"]},"month":"07","oa":1,"has_accepted_license":"1","author":[{"id":"0b467602-dbcd-11ea-9d1d-ed480aa46b70","last_name":"Chen","first_name":"Yi-Lu","orcid":"0009-0005-0723-0655","full_name":"Chen, Yi-Lu"},{"first_name":"Mickaël","last_name":"Ly","id":"6340d7f0-b48d-11eb-b10d-b7487e71d9f1","full_name":"Ly, Mickaël"},{"last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546"}],"conference":{"location":"Denver, United States","end_date":"2024-08-01","name":"SIGGRAPH: Computer Graphics and Interactive Techniques Conference","start_date":"2024-07-28"},"das_tickbox":"0","supplementarymaterial":"yes","publication_identifier":{"isbn":["9798400705250"]},"file_date_updated":"2024-07-10T11:03:58Z","ddc":["621","531","006"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-07-01T00:00:00Z","date_updated":"2026-10-02T11:16:26Z","title":"Primal-dual non-smooth friction for rigid body animation","keyword":["physical simulation","frictional contact","rigid body mechanics","non-smooth dynamics"],"language":[{"iso":"eng"}],"_id":"17214","isi":1,"day":"01"},{"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2311.16833","open_access":"1"}],"publisher":"Computer Vision Foundation","fulldoi":"https://doi.org/10.1109/CVPR52733.2024.02320","type":"conference","page":"24574-24583","publication_status":"published","oa_version":"Preprint","corr_author":"1","acknowledgement":"This work was partially supported by project SERICS (PE00000014) under the MUR National Recovery and Resilience Plan funded by the European Union - NextGenerationEU.\r\n","related_material":{"link":[{"relation":"software","url":"https://github.com/berndprach/1LipschitzLayersCompared"}],"record":[{"id":"19759","relation":"dissertation_contains","status":"public"}]},"doi":"10.1109/CVPR52733.2024.02320","article_processing_charge":"No","quality_controlled":"1","abstract":[{"lang":"eng","text":"The robustness of neural networks against input perturbations with bounded\r\nmagnitude represents a serious concern in the deployment of deep learning\r\nmodels in safety-critical systems. Recently, the scientific community has\r\nfocused on enhancing certifiable robustness guarantees by crafting 1-Lipschitz\r\nneural networks that leverage Lipschitz bounded dense and convolutional layers.\r\nAlthough different methods have been proposed in the literature to achieve this\r\ngoal, understanding the performance of such methods is not straightforward,\r\nsince different metrics can be relevant (e.g., training time, memory usage,\r\naccuracy, certifiable robustness) for different applications. For this reason,\r\nthis work provides a thorough theoretical and empirical comparison between\r\nmethods by evaluating them in terms of memory usage, speed, and certifiable\r\nrobust accuracy. The paper also provides some guidelines and recommendations to\r\nsupport the user in selecting the methods that work best depending on the\r\navailable resources. We provide code at\r\nhttps://github.com/berndprach/1LipschitzLayersCompared."}],"publication":"Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition","researchdata_availability":"no","supplementarymaterial":"no","OA_place":"repository","das_tickbox":"0","date_updated":"2026-10-02T11:16:04Z","date_published":"2024-06-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","arxiv":1,"title":"1-Lipschitz layers compared: Memory, speed, and certifiable robustness","day":"01","isi":1,"language":[{"iso":"eng"}],"_id":"17426","status":"public","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"citation":{"ama":"Prach B, Brau F, Buttazzo G, Lampert C. 1-Lipschitz layers compared: Memory, speed, and certifiable robustness. In: <i>Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>. Computer Vision Foundation; 2024:24574-24583. doi:<a href=\"https://doi.org/10.1109/CVPR52733.2024.02320\">10.1109/CVPR52733.2024.02320</a>","short":"B. Prach, F. Brau, G. Buttazzo, C. Lampert, in:, Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, Computer Vision Foundation, 2024, pp. 24574–24583.","apa":"Prach, B., Brau, F., Buttazzo, G., &#38; Lampert, C. (2024). 1-Lipschitz layers compared: Memory, speed, and certifiable robustness. In <i>Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition</i> (pp. 24574–24583). Seattle, WA, United States: Computer Vision Foundation. <a href=\"https://doi.org/10.1109/CVPR52733.2024.02320\">https://doi.org/10.1109/CVPR52733.2024.02320</a>","mla":"Prach, Bernd, et al. “1-Lipschitz Layers Compared: Memory, Speed, and Certifiable Robustness.” <i>Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, Computer Vision Foundation, 2024, pp. 24574–83, doi:<a href=\"https://doi.org/10.1109/CVPR52733.2024.02320\">10.1109/CVPR52733.2024.02320</a>.","chicago":"Prach, Bernd, Fabio Brau, Giorgio Buttazzo, and Christoph Lampert. “1-Lipschitz Layers Compared: Memory, Speed, and Certifiable Robustness.” In <i>Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, 24574–83. Computer Vision Foundation, 2024. <a href=\"https://doi.org/10.1109/CVPR52733.2024.02320\">https://doi.org/10.1109/CVPR52733.2024.02320</a>.","ista":"Prach B, Brau F, Buttazzo G, Lampert C. 2024. 1-Lipschitz layers compared: Memory, speed, and certifiable robustness. Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition, 24574–24583.","ieee":"B. Prach, F. Brau, G. Buttazzo, and C. Lampert, “1-Lipschitz layers compared: Memory, speed, and certifiable robustness,” in <i>Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, Seattle, WA, United States, 2024, pp. 24574–24583."},"date_created":"2024-08-14T08:42:32Z","year":"2024","OA_type":"green","month":"06","external_id":{"isi":["001344387500055"],"arxiv":["2311.16833"]},"conference":{"end_date":"2024-06-22","name":"CVPR: Conference on Computer Vision and Pattern Recognition","location":"Seattle, WA, United States","start_date":"2024-06-16"},"author":[{"first_name":"Bernd","last_name":"Prach","id":"2D561D42-C427-11E9-89B4-9C1AE6697425","full_name":"Prach, Bernd"},{"full_name":"Brau, Fabio","last_name":"Brau","first_name":"Fabio"},{"first_name":"Giorgio","last_name":"Buttazzo","full_name":"Buttazzo, Giorgio"},{"first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"}],"oa":1,"has_accepted_license":"1"},{"doi":"10.48550/arXiv.2412.04245","related_material":{"record":[{"relation":"later_version","status":"public","id":"20455"},{"relation":"dissertation_contains","status":"public","id":"19759"}]},"researchdata_availability":"no","publication":"arXiv","abstract":[{"text":"Despite extensive research since the community learned about adversarial\r\nexamples 10 years ago, we still do not know how to train high-accuracy\r\nclassifiers that are guaranteed to be robust to small perturbations of their\r\ninputs. Previous works often argued that this might be because no classifier\r\nexists that is robust and accurate at the same time. However, in computer\r\nvision this assumption does not match reality where humans are usually accurate\r\nand robust on most tasks of interest. We offer an alternative explanation and\r\nshow that in certain settings robust generalization is only possible with\r\nunrealistically large amounts of data. More precisely we find a setting where a\r\nrobust classifier exists, it is easy to learn an accurate classifier, yet it\r\nrequires an exponential amount of data to learn a robust classifier. Based on\r\nthis theoretical result, we explore how well robust classifiers generalize on\r\ndatasets such as CIFAR-10. We come to the conclusion that on this datasets, the\r\nlimitation of current robust models also lies in the generalization, and that\r\nthey require a lot of data to do well on the test set. We also show that the\r\nproblem is not in the expressiveness or generalization capabilities of current\r\narchitectures, and that there are low magnitude features in the data which are\r\nuseful for non-robust generalization but are not available for robust\r\nclassifiers.","lang":"eng"}],"article_processing_charge":"No","type":"preprint","fulldoi":"https://doi.org/10.48550/arXiv.2412.04245","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2412.04245"}],"corr_author":"1","oa_version":"Preprint","publication_status":"draft","article_number":"2412.04245","year":"2024","date_created":"2025-01-24T16:57:29Z","citation":{"mla":"Prach, Bernd, and Christoph Lampert. “Intriguing Properties of Robust Classification.” <i>ArXiv</i>, 2412.04245, doi:<a href=\"https://doi.org/10.48550/arXiv.2412.04245\">10.48550/arXiv.2412.04245</a>.","short":"B. Prach, C. Lampert, ArXiv (n.d.).","apa":"Prach, B., &#38; Lampert, C. (n.d.). Intriguing properties of robust classification. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2412.04245\">https://doi.org/10.48550/arXiv.2412.04245</a>","ama":"Prach B, Lampert C. Intriguing properties of robust classification. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2412.04245\">10.48550/arXiv.2412.04245</a>","ieee":"B. Prach and C. Lampert, “Intriguing properties of robust classification,” <i>arXiv</i>. .","chicago":"Prach, Bernd, and Christoph Lampert. “Intriguing Properties of Robust Classification.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2412.04245\">https://doi.org/10.48550/arXiv.2412.04245</a>.","ista":"Prach B, Lampert C. Intriguing properties of robust classification. arXiv, 2412.04245."},"department":[{"_id":"GradSch"},{"_id":"ChLa"}],"status":"public","oa":1,"author":[{"first_name":"Bernd","id":"2D561D42-C427-11E9-89B4-9C1AE6697425","last_name":"Prach","full_name":"Prach, Bernd"},{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph"}],"external_id":{"arxiv":["2412.04245"]},"month":"12","date_published":"2024-12-05T00:00:00Z","date_updated":"2026-10-02T11:15:43Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","das_tickbox":"0","OA_place":"repository","supplementarymaterial":"yes","_id":"18874","language":[{"iso":"eng"}],"day":"05","title":"Intriguing properties of robust classification","arxiv":1},{"citation":{"mla":"Bauer, Martin, et al. “Symplectic Structures on the Space of Space Curves.” <i>ArXiv</i>, doi:<a href=\"https://doi.org/10.48550/arXiv.2407.19908\">10.48550/arXiv.2407.19908</a>.","ama":"Bauer M, Ishida S, Michor PW. Symplectic structures on the space of space curves. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2407.19908\">10.48550/arXiv.2407.19908</a>","apa":"Bauer, M., Ishida, S., &#38; Michor, P. W. (n.d.). Symplectic structures on the space of space curves. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2407.19908\">https://doi.org/10.48550/arXiv.2407.19908</a>","short":"M. Bauer, S. Ishida, P.W. Michor, ArXiv (n.d.).","ista":"Bauer M, Ishida S, Michor PW. Symplectic structures on the space of space curves. arXiv, <a href=\"https://doi.org/10.48550/arXiv.2407.19908\">10.48550/arXiv.2407.19908</a>.","chicago":"Bauer, Martin, Sadashige Ishida, and Peter W. Michor. “Symplectic Structures on the Space of Space Curves.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2407.19908\">https://doi.org/10.48550/arXiv.2407.19908</a>.","ieee":"M. Bauer, S. Ishida, and P. W. Michor, “Symplectic structures on the space of space curves,” <i>arXiv</i>. ."},"date_created":"2024-08-01T06:34:08Z","year":"2024","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"status":"public","oa":1,"author":[{"full_name":"Bauer, Martin","first_name":"Martin","last_name":"Bauer"},{"first_name":"Sadashige","id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425","last_name":"Ishida","full_name":"Ishida, Sadashige","orcid":"0000-0002-3121-3100"},{"full_name":"Michor, Peter W.","first_name":"Peter W.","last_name":"Michor"}],"external_id":{"arxiv":["2407.19908"]},"month":"07","date_published":"2024-07-29T00:00:00Z","date_updated":"2026-10-02T11:16:46Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","das_tickbox":"0","OA_place":"repository","supplementarymaterial":"no","language":[{"iso":"eng"}],"_id":"17361","day":"29","title":"Symplectic structures on the space of space curves","arxiv":1,"keyword":["space of space curves","symplectic stuctures"],"doi":"10.48550/arXiv.2407.19908","acknowledgement":"The authors are grateful to Boris Khesin for valuable comments on the MW symplectic structure and S. Ishida thanks Albert Chern for insightful discussions on space curves and Chris Wojtan for his continuous support. M. Bauer was partially supported by NSF grant DMS-1953244 and by the Binational Science Foundation (BSF). S. Ishida was partially supported by ERC Consolidator Grant 101045083 “CoDiNA” funded by the European Research Council. Some figures were generated by the software Houdini and its education license was provided by SideFX.","related_material":{"record":[{"id":"20551","relation":"dissertation_contains","status":"public"},{"status":"public","relation":"later_version","id":"21743"}]},"project":[{"name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","grant_number":"101045083","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088"}],"researchdata_availability":"no","publication":"arXiv","abstract":[{"text":"We present symplectic structures on the shape space of unparameterized space curves that generalize the classical Marsden-Weinstein structure. Our method integrates the Liouville 1-form of the Marsden-Weinstein structure with Riemannian structures that have been introduced in mathematical shape analysis. We also derive Hamiltonian vector fields for several classical Hamiltonian functions with respect to these new symplectic structures.","lang":"eng"}],"article_processing_charge":"No","fulldoi":"https://doi.org/10.48550/arXiv.2407.19908","type":"preprint","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2407.19908"}],"publication_status":"draft","oa_version":"Preprint"},{"article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","article_type":"original","abstract":[{"text":"We introduce a multi-material non-manifold mesh-based surface tracking algorithm that converts self-intersections into topological changes. Our algorithm generalizes prior work on manifold surface tracking with topological changes: it preserves surface features like mesh-based methods, and it robustly handles topological changes like level set methods. Our method also offers improved efficiency and robustness over the state of the art. We demonstrate the effectiveness of the approach on a range of examples, including complex soap film simulations with thousands of interacting bubbles, and boolean unions of non-manifold meshes consisting of millions of triangles.","lang":"eng"}],"publication":"ACM Transactions on Graphics","project":[{"grant_number":"101045083","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088"}],"researchdata_availability":"no","file":[{"creator":"dernst","file_size":48763368,"file_name":"2024_ACMToG_HeissSynak.pdf","checksum":"1917067d4b52d7729019b03560004e43","success":1,"file_id":"17317","relation":"main_file","date_updated":"2024-07-23T06:35:15Z","date_created":"2024-07-23T06:35:15Z","content_type":"application/pdf","access_level":"open_access"},{"access_level":"open_access","content_type":"video/mp4","date_updated":"2024-07-10T12:23:44Z","date_created":"2024-07-10T12:23:44Z","relation":"main_file","success":1,"file_id":"17221","file_size":48021463,"checksum":"a4f0e293184bfa034c0c585848806b17","creator":"akalinov","file_name":"sdtopofixer_final.mp4"},{"access_level":"open_access","content_type":"application/pdf","date_updated":"2025-11-11T09:50:52Z","date_created":"2025-11-11T09:50:52Z","title":"Authors' version of the text","relation":"preprint","file_id":"20633","checksum":"18fc310a78ec91651148c45a8b89fa44","creator":"akalinov","file_name":"SuperDuperTopoFixer.pdf","file_size":48639581}],"acknowledgement":"Peter Heiss-Synak helped conceive the project, helped formulate the algorithm structure, contributed ideas and code to Sections 6 & 8, the mesh data structure, algorithm robustness and benchmarks, helped write the paper, and provided supervision and conceptual solutions throughout the project. Aleksei Kalinov contributed ideas and code to Sections 7, 8.5, and 5, the sparse grid data structure, algorithm robustness and benchmarks, optimized the performance, produced all results, most figures, and the supplementary video, helped write the text, and provided conceptual solutions throughout the project. Malina Strugaru helped implement the mesh data structure and designed re-meshing operations for non-manifold triangle meshes. Arian Etemadi developed early prototypes for ideas in Sections 8.1 and 8.3 and helped write the paper. Huidong Yang developed early prototypes for isosurface extraction and visualization. Chris Wojtan helped conceive the project, helped write the paper, and provided supervision, prototype grid data structure code, and conceptual solutions throughout the project. We thank the anonymous reviewers for their helpful comments, the members of the Visual Computing Group at ISTA for their feedback, Christopher Batty for discussions about LosTopos, and SideFX for the Houdini Education software licenses.  This research was funded in part by the European Union (ERC-2021-COG 101045083 CoDiNA).","related_material":{"record":[{"id":"19630","relation":"dissertation_contains","status":"public"},{"relation":"dissertation_contains","status":"public","id":"18301"}]},"doi":"10.1145/3658223","volume":43,"article_number":"54","oa_version":"Published Version","publication_status":"published","corr_author":"1","scopus_import":"1","publisher":"Association for Computing Machinery","tmp":{"image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"type":"journal_article","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","fulldoi":"https://doi.org/10.1145/3658223","month":"07","external_id":{"isi":["001289270900021"]},"author":[{"full_name":"Synak, Peter","last_name":"Synak","id":"331776E2-F248-11E8-B48F-1D18A9856A87","first_name":"Peter"},{"orcid":"0000-0003-2189-3904","full_name":"Kalinov, Aleksei","id":"44b7120e-eb97-11eb-a6c2-e1557aa81d02","last_name":"Kalinov","first_name":"Aleksei"},{"full_name":"Strugaru, Irina-Malina","last_name":"Strugaru","id":"2afc607f-f128-11eb-9611-8f2a0dfcf074","first_name":"Irina-Malina"},{"full_name":"Etemadihaghighi, Arian","id":"36cea3aa-f38e-11ec-8ae0-c65ae6f6098f","last_name":"Etemadihaghighi","first_name":"Arian"},{"full_name":"Yang, Huidong","last_name":"Yang","first_name":"Huidong"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","first_name":"Christopher J","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546"}],"oa":1,"has_accepted_license":"1","status":"public","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"OA_type":"hybrid","year":"2024","date_created":"2024-07-10T12:24:00Z","citation":{"ama":"Synak P, Kalinov A, Strugaru I-M, Etemadi A, Yang H, Wojtan C. Multi-material mesh-based surface tracking with implicit topology changes. <i>ACM Transactions on Graphics</i>. 2024;43(4). doi:<a href=\"https://doi.org/10.1145/3658223\">10.1145/3658223</a>","short":"P. Synak, A. Kalinov, I.-M. Strugaru, A. Etemadi, H. Yang, C. Wojtan, ACM Transactions on Graphics 43 (2024).","apa":"Synak, P., Kalinov, A., Strugaru, I.-M., Etemadi, A., Yang, H., &#38; Wojtan, C. (2024). Multi-material mesh-based surface tracking with implicit topology changes. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3658223\">https://doi.org/10.1145/3658223</a>","mla":"Synak, Peter, et al. “Multi-Material Mesh-Based Surface Tracking with Implicit Topology Changes.” <i>ACM Transactions on Graphics</i>, vol. 43, no. 4, 54, Association for Computing Machinery, 2024, doi:<a href=\"https://doi.org/10.1145/3658223\">10.1145/3658223</a>.","chicago":"Synak, Peter, Aleksei Kalinov, Irina-Malina Strugaru, Arian Etemadi, Huidong Yang, and Chris Wojtan. “Multi-Material Mesh-Based Surface Tracking with Implicit Topology Changes.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2024. <a href=\"https://doi.org/10.1145/3658223\">https://doi.org/10.1145/3658223</a>.","ista":"Synak P, Kalinov A, Strugaru I-M, Etemadi A, Yang H, Wojtan C. 2024. Multi-material mesh-based surface tracking with implicit topology changes. ACM Transactions on Graphics. 43(4), 54.","ieee":"P. Synak, A. Kalinov, I.-M. Strugaru, A. Etemadi, H. Yang, and C. Wojtan, “Multi-material mesh-based surface tracking with implicit topology changes,” <i>ACM Transactions on Graphics</i>, vol. 43, no. 4. Association for Computing Machinery, 2024."},"keyword":["surface tracking","topology change","non- manifold meshes","multi-material flows","solid modeling"],"title":"Multi-material mesh-based surface tracking with implicit topology changes","issue":"4","isi":1,"day":"01","_id":"17219","language":[{"iso":"eng"}],"supplementarymaterial":"no","publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"intvolume":"        43","file_date_updated":"2025-11-11T09:50:52Z","das_tickbox":"0","OA_place":"publisher","date_updated":"2026-10-02T11:19:25Z","ddc":["004"],"date_published":"2024-07-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"status":"public","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"date_created":"2024-10-11T19:52:20Z","citation":{"chicago":"Etemadi, Arian. “Filling the Holes of Non-Manifold Self-Intersecting Meshes for Implicit Topology Changes in Surface Tracking.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18301\">https://doi.org/10.15479/at:ista:18301</a>.","ista":"Etemadi A. 2024. Filling the holes of non-manifold self-intersecting meshes for implicit topology changes in surface tracking. Institute of Science and Technology Austria.","ieee":"A. Etemadi, “Filling the holes of non-manifold self-intersecting meshes for implicit topology changes in surface tracking,” Institute of Science and Technology Austria, 2024.","ama":"Etemadi A. Filling the holes of non-manifold self-intersecting meshes for implicit topology changes in surface tracking. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18301\">10.15479/at:ista:18301</a>","apa":"Etemadi, A. (2024). <i>Filling the holes of non-manifold self-intersecting meshes for implicit topology changes in surface tracking</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18301\">https://doi.org/10.15479/at:ista:18301</a>","short":"A. Etemadi, Filling the Holes of Non-Manifold Self-Intersecting Meshes for Implicit Topology Changes in Surface Tracking, Institute of Science and Technology Austria, 2024.","mla":"Etemadi, Arian. <i>Filling the Holes of Non-Manifold Self-Intersecting Meshes for Implicit Topology Changes in Surface Tracking</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18301\">10.15479/at:ista:18301</a>."},"year":"2024","month":"10","author":[{"first_name":"Arian","id":"36cea3aa-f38e-11ec-8ae0-c65ae6f6098f","last_name":"Etemadihaghighi","full_name":"Etemadihaghighi, Arian"}],"has_accepted_license":"1","oa":1,"degree_awarded":"MS","file_date_updated":"2024-10-24T14:34:54Z","publication_identifier":{"issn":["2791-4585"]},"supplementarymaterial":"no","das_tickbox":"0","OA_place":"publisher","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["000"],"date_updated":"2026-10-02T11:19:26Z","date_published":"2024-10-15T00:00:00Z","keyword":["surface tracking","non-manifold","hole-filling","topology change","multi-material","solid-modeling"],"doi_confirm":"1","title":"Filling the holes of non-manifold self-intersecting meshes for implicit topology changes in surface tracking","day":"15","language":[{"iso":"eng"}],"_id":"18301","file":[{"access_level":"open_access","content_type":"application/pdf","date_created":"2024-10-24T14:34:42Z","date_updated":"2024-10-24T14:34:42Z","relation":"main_file","file_id":"18469","success":1,"file_size":8914218,"creator":"aetemadi","checksum":"80fb7923e229ad9d39253d7c8a8083d0","file_name":"thesis-arian-etemadi.pdf"},{"content_type":"application/x-zip-compressed","access_level":"closed","date_updated":"2024-10-24T14:34:54Z","date_created":"2024-10-24T14:34:54Z","relation":"source_file","checksum":"1c02586ed7d441d5ec441867650568d1","file_size":9802650,"creator":"aetemadi","file_name":"thesis-arian-etemadi-latex-source.zip","file_id":"18470"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"17219"}]},"supervisor":[{"first_name":"Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J"}],"doi":"10.15479/at:ista:18301","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Physics simulation in computer graphics can bring triangle meshes into topologically invalid states. The method in this thesis contributed to Heiss-Synak* and Kalinov* et al. [2024] who devised a non-manifold hybrid surface tracker—a surface tracker that repairs explicit non-manifold triangle meshes with the help of the implicit domain. Specifically, this thesis provides an algorithm for filling the holes that are left after removing problematic parts of the mesh."}],"researchdata_availability":"no","tmp":{"short":"CC BY-SA (4.0)","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode"},"publisher":"Institute of Science and Technology Austria","fulldoi":"https://doi.org/10.15479/at:ista:18301","license":"https://creativecommons.org/licenses/by-sa/4.0/","type":"dissertation","page":"39","alternative_title":["ISTA Master's Thesis"],"publication_status":"published","oa_version":"Published Version","corr_author":"1"},{"OA_place":"repository","das_tickbox":"0","intvolume":"         8","supplementarymaterial":"no","publication_identifier":{"eissn":["2470-6566"]},"date_published":"2024-09-23T00:00:00Z","date_updated":"2026-10-02T11:17:04Z","ddc":["516"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Area formula for spherical polygons via prequantization","arxiv":1,"language":[{"iso":"eng"}],"_id":"12846","isi":1,"issue":"3","day":"23","status":"public","year":"2024","OA_type":"green","citation":{"chicago":"Chern, Albert, and Sadashige Ishida. “Area Formula for Spherical Polygons via Prequantization.” <i>SIAM Journal on Applied Algebra and Geometry</i>. Society for Industrial and Applied Mathematics, 2024. <a href=\"https://doi.org/10.1137/23M1565255\">https://doi.org/10.1137/23M1565255</a>.","ista":"Chern A, Ishida S. 2024. Area formula for spherical polygons via prequantization. SIAM Journal on Applied Algebra and Geometry. 8(3), 782–796.","ieee":"A. Chern and S. Ishida, “Area formula for spherical polygons via prequantization,” <i>SIAM Journal on Applied Algebra and Geometry</i>, vol. 8, no. 3. Society for Industrial and Applied Mathematics, pp. 782–796, 2024.","ama":"Chern A, Ishida S. Area formula for spherical polygons via prequantization. <i>SIAM Journal on Applied Algebra and Geometry</i>. 2024;8(3):782-796. doi:<a href=\"https://doi.org/10.1137/23M1565255\">10.1137/23M1565255</a>","short":"A. Chern, S. Ishida, SIAM Journal on Applied Algebra and Geometry 8 (2024) 782–796.","apa":"Chern, A., &#38; Ishida, S. (2024). Area formula for spherical polygons via prequantization. <i>SIAM Journal on Applied Algebra and Geometry</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/23M1565255\">https://doi.org/10.1137/23M1565255</a>","mla":"Chern, Albert, and Sadashige Ishida. “Area Formula for Spherical Polygons via Prequantization.” <i>SIAM Journal on Applied Algebra and Geometry</i>, vol. 8, no. 3, Society for Industrial and Applied Mathematics, 2024, pp. 782–96, doi:<a href=\"https://doi.org/10.1137/23M1565255\">10.1137/23M1565255</a>."},"date_created":"2023-04-18T19:16:06Z","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"external_id":{"isi":["001342265800009"],"arxiv":["2303.14555"]},"month":"09","has_accepted_license":"1","oa":1,"author":[{"last_name":"Chern","first_name":"Albert","full_name":"Chern, Albert"},{"last_name":"Ishida","id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425","first_name":"Sadashige","orcid":"0000-0002-3121-3100","full_name":"Ishida, Sadashige"}],"publisher":"Society for Industrial and Applied Mathematics","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2303.14555"}],"type":"journal_article","fulldoi":"https://doi.org/10.1137/23M1565255","volume":8,"page":"782-796","corr_author":"1","oa_version":"Preprint","publication_status":"published","doi":"10.1137/23M1565255","acknowledgement":"This work was funded by European Research Council Consolidator grant 101045083 CoDiNA and National Science Foundation CAREER award 2239062. Some figures in the article were generated by the software Houdini and its education license was provided by SideFX. The authors acknowledge anonymous referees for their reviews and insightful suggestions, and Chris Wojtan for his continuous support through discussions. The second author thanks Anna Sisak for a fruitful discussion on prequantum bundles.","related_material":{"record":[{"id":"20551","relation":"dissertation_contains","status":"public"}]},"quality_controlled":"1","article_processing_charge":"No","publication":"SIAM Journal on Applied Algebra and Geometry","project":[{"_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","grant_number":"101045083"}],"researchdata_availability":"no","article_type":"original","abstract":[{"text":"We present a formula for the signed area of a spherical polygon via prequantization. In contrast to the traditional formula based on the Gauss-Bonnet theorem that requires measuring angles, the new formula mimics Green's theorem and is applicable to a wider range of degenerate spherical curves and polygons.","lang":"eng"}]},{"project":[{"call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning","grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"researchdata_availability":"no","abstract":[{"text":"Large language models (LLMs) have made tremendous progress in the past few years, from being able to generate coherent text to matching or surpassing humans in a wide variety of creative, knowledge or reasoning tasks. Much of this can be attributed to massively increased scale, both in the size of the model as well as the amount of training data, from 100s of millions to 100s of billions, or even trillions. This trend is expected to continue, which, although exciting, also raises major practical concerns. Already today's 100+ billion parameter LLMs require top-of-the-line hardware just to run. Hence, it is clear that sustaining these developments will require significant efficiency advances.\r\n\r\nHistorically, one of the most practical ways of improving model efficiency has been compression, especially in the form of sparsity or quantization. While this has been studied extensively in the past, existing accurate methods are all designed for models around 100 million parameters; scaling them up to ones literally 1000x larger is highly challenging. In this thesis, we introduce a new unified sparsification and quantization approach OBC, which through additional algorithmic enhancements leads to GPTQ and SparseGPT, the first techniques fast and accurate enough to compress 100+ billion parameter models to 4- or even 3-bit precision and 50% weight-sparsity, respectively. Additionally, we show how weight-only quantizion does not just bring space savings but also up to 4.5x faster generation speed, via custom GPU kernels.\r\n\r\nIn fact, we show for the first time that it is possible to develop an FP16 times INT4 mixed-precision matrix multiplication kernel, called Marlin, which comes close to simultaneously maximizing both memory and compute utilization, making weight-only quantization highly practical even for multi-user serving. Further, we demonstrate that GPTQ can be scaled to widely overparametrized trillion-parameter models, where extreme sub-1-bit compression rates can be achieved without any inference slow-down, by co-designing a bespoke entropy coding scheme together with an efficient kernel.\r\n\r\nFinally, we also study compression from the perspective of someone with access to massive amounts of compute resources for training large models completely from scratch. Here the key questions evolve around the joint scaling behavior between compression, model size, and amount of training data used. Based on extensive experimental results for both vision and text models, we introduce the first scaling law which accurately captures the relationship between weight-sparsity, number of non-zero weights and data. This further allows us to characterize the optimal sparsity, which we find to increase the longer a fixed cost model is being trained.\r\n\r\nOverall, this thesis presents contributions to three different angles of large model efficiency: affordable but accurate algorithms, highly efficient systems implementations, and fundamental scaling laws for compressed training.","lang":"eng"}],"article_processing_charge":"No","doi":"10.15479/at:ista:17485","supervisor":[{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"17378","status":"public","relation":"part_of_dissertation"},{"id":"17087","status":"public","relation":"part_of_dissertation"},{"id":"14458","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"18061"},{"id":"18062","status":"public","relation":"part_of_dissertation"}]},"file":[{"relation":"source_file","file_id":"17570","creator":"efrantar","file_name":"thesis-final.zip","file_size":1615167,"checksum":"5d785645805a78c5b4ce7cc3df557b09","access_level":"closed","content_type":"application/zip","date_updated":"2024-09-05T12:04:11Z","date_created":"2024-09-05T12:04:11Z"},{"date_created":"2024-09-06T16:24:59Z","date_updated":"2024-09-06T16:24:59Z","access_level":"open_access","content_type":"application/pdf","file_id":"17880","success":1,"file_name":"frantar_thesis_final.pdf","file_size":2376611,"checksum":"a9dd1c2d23734986924eb44ebb55fd8f","creator":"efrantar","relation":"main_file"}],"corr_author":"1","oa_version":"Published Version","publication_status":"published","alternative_title":["ISTA Thesis"],"page":"129","acknowledged_ssus":[{"_id":"ScienComp"}],"type":"dissertation","fulldoi":"https://doi.org/10.15479/at:ista:17485","ec_funded":1,"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","degree_awarded":"PhD","oa":1,"author":[{"first_name":"Elias","last_name":"Frantar","id":"09a8f98d-ec99-11ea-ae11-c063a7b7fe5f","full_name":"Frantar, Elias"}],"month":"09","year":"2024","citation":{"short":"E. Frantar, Compressing Large Neural Networks: Algorithms, Systems and Scaling Laws, Institute of Science and Technology Austria, 2024.","apa":"Frantar, E. (2024). <i>Compressing large neural networks: Algorithms, systems and scaling laws</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17485\">https://doi.org/10.15479/at:ista:17485</a>","ama":"Frantar E. Compressing large neural networks: Algorithms, systems and scaling laws. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17485\">10.15479/at:ista:17485</a>","mla":"Frantar, Elias. <i>Compressing Large Neural Networks: Algorithms, Systems and Scaling Laws</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17485\">10.15479/at:ista:17485</a>.","ieee":"E. Frantar, “Compressing large neural networks: Algorithms, systems and scaling laws,” Institute of Science and Technology Austria, 2024.","chicago":"Frantar, Elias. “Compressing Large Neural Networks: Algorithms, Systems and Scaling Laws.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17485\">https://doi.org/10.15479/at:ista:17485</a>.","ista":"Frantar E. 2024. Compressing large neural networks: Algorithms, systems and scaling laws. Institute of Science and Technology Austria."},"date_created":"2024-09-02T11:01:48Z","department":[{"_id":"GradSch"},{"_id":"DaAl"}],"status":"public","_id":"17485","language":[{"iso":"eng"}],"day":"05","title":"Compressing large neural networks: Algorithms, systems and scaling laws","doi_confirm":"1","ddc":["000"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-09-05T00:00:00Z","date_updated":"2026-10-02T11:19:46Z","das_tickbox":"0","OA_place":"publisher","supplementarymaterial":"no","publication_identifier":{"issn":["2663-337X"]},"file_date_updated":"2024-09-06T16:24:59Z"},{"title":"Scaling laws for sparsely-connected foundation models","arxiv":1,"_id":"18062","language":[{"iso":"eng"}],"day":"16","das_tickbox":"0","supplementarymaterial":"no","date_updated":"2026-10-02T11:19:46Z","ddc":["000"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-01-16T00:00:00Z","external_id":{"arxiv":["2309.08520"]},"month":"01","oa":1,"conference":{"start_date":"2024-05-07","location":"Vienna, Austria","end_date":"2024-05-07","name":"ICLR: International Conference on Learning Representations"},"author":[{"full_name":"Frantar, Elias","first_name":"Elias","last_name":"Frantar","id":"09a8f98d-ec99-11ea-ae11-c063a7b7fe5f"},{"last_name":"Ruiz","first_name":"Carlos Riquelme","full_name":"Ruiz, Carlos Riquelme"},{"full_name":"Houlsby, Neil","last_name":"Houlsby","first_name":"Neil"},{"orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian"},{"full_name":"Evci, Utku","last_name":"Evci","first_name":"Utku"}],"status":"public","date_created":"2024-09-13T10:31:08Z","citation":{"mla":"Frantar, Elias, et al. “Scaling Laws for Sparsely-Connected Foundation Models.” <i>The Twelfth International Conference on Learning Representations</i>, 2024.","ama":"Frantar E, Ruiz CR, Houlsby N, Alistarh D-A, Evci U. Scaling laws for sparsely-connected foundation models. In: <i>The Twelfth International Conference on Learning Representations</i>. ; 2024.","apa":"Frantar, E., Ruiz, C. R., Houlsby, N., Alistarh, D.-A., &#38; Evci, U. (2024). Scaling laws for sparsely-connected foundation models. In <i>The Twelfth International Conference on Learning Representations</i>. Vienna, Austria.","short":"E. Frantar, C.R. Ruiz, N. Houlsby, D.-A. Alistarh, U. Evci, in:, The Twelfth International Conference on Learning Representations, 2024.","ista":"Frantar E, Ruiz CR, Houlsby N, Alistarh D-A, Evci U. 2024. Scaling laws for sparsely-connected foundation models. The Twelfth International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","chicago":"Frantar, Elias, Carlos Riquelme Ruiz, Neil Houlsby, Dan-Adrian Alistarh, and Utku Evci. “Scaling Laws for Sparsely-Connected Foundation Models.” In <i>The Twelfth International Conference on Learning Representations</i>, 2024.","ieee":"E. Frantar, C. R. Ruiz, N. Houlsby, D.-A. Alistarh, and U. Evci, “Scaling laws for sparsely-connected foundation models,” in <i>The Twelfth International Conference on Learning Representations</i>, Vienna, Austria, 2024."},"year":"2024","department":[{"_id":"DaAl"}],"corr_author":"1","publication_status":"published","oa_version":"Published Version","main_file_link":[{"url":"https://openreview.net/forum?id=i9K2ZWkYIP","open_access":"1"}],"scopus_import":"1","type":"conference","quality_controlled":"1","article_processing_charge":"No","publication":"The Twelfth International Conference on Learning Representations","researchdata_availability":"no","abstract":[{"lang":"eng","text":"We explore the impact of parameter sparsity on the scaling behavior of Transformers trained on massive datasets (i.e., \"foundation models\"), in both vision and language domains. In this setting, we identify the first scaling law describing the relationship between weight sparsity, number of non-zero parameters, and amount of training data, which we validate empirically across model and data scales; on ViT/JFT-4B and T5/C4. These results allow us to characterize the \"optimal sparsity\", the sparsity level which yields the best performance for a given effective model size and training budget. For a fixed number of non-zero parameters, we identify that the optimal sparsity increases with the amount of data used for training. We also extend our study to different sparsity structures (such as the hardware-friendly n:m pattern) and strategies (such as starting from a pretrained dense model). Our findings shed light on the power and limitations of weight sparsity across various parameter and computational settings, offering both theoretical understanding and practical implications for leveraging sparsity towards computational efficiency improvements. We provide pruning and scaling law fitting code at: github.com/google-research/jaxpruner/tree/main/jaxpruner/projects/bigsparse."}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"17485"}]}},{"main_file_link":[{"url":"https://proceedings.mlsys.org/paper_files/paper/2024/hash/c74b624843218d9b6713fcf299d6d5e4-Abstract-Conference.html","open_access":"1"}],"type":"conference","volume":6,"corr_author":"1","oa_version":"Published Version","publication_status":"published","related_material":{"record":[{"id":"17485","relation":"dissertation_contains","status":"public"}]},"quality_controlled":"1","article_processing_charge":"No","publication":"Proceedings of Machine Learning and Systems","researchdata_availability":"yes","abstract":[{"lang":"eng","text":"Mixture-of-Experts (MoE) architectures offer a general solution to the high inference costs of large language models (LLMs) via sparse routing, bringing faster and more accurate models, at the cost of massive parameter counts. For example, the SwitchTransformer-c2048 model has 1.6 trillion parameters, requiring 3.2TB of accelerator memory to run efficiently, which makes practical deployment challenging and expensive. In this paper, we present a solution to this memory problem, in form of a new compression and execution framework called QMoE. Specifically, QMoE consists of a scalable algorithm which accurately compresses trillion-parameter MoEs to less than 1 bit per parameter, in a custom format co-designed with bespoke GPU decoding kernels to facilitate efficient end-to-end compressed inference, with minor runtime overheads relative to uncompressed execution. Concretely, QMoE can compress the 1.6 trillion parameter SwitchTransformer-c2048 model to less than 160GB (20x compression, 0.8 bits per parameter) at only minor accuracy loss, in less than a day on a single GPU. This enables, for the first time, the execution of a trillion-parameter model on affordable commodity hardware, like a single server with 4x NVIDIA A6000 or 8x NVIDIA 3090 GPUs, at less than 5% runtime overhead relative to ideal uncompressed inference. The anonymized code is available at: github.com/mlsys24-qmoe/qmoe."}],"das_tickbox":"0","supplementarymaterial":"no","intvolume":"         6","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["000"],"date_updated":"2026-10-02T11:19:46Z","date_published":"2024-05-01T00:00:00Z","title":"QMoE: Sub-1-bit compression of trillion parameter models","_id":"18061","language":[{"iso":"eng"}],"day":"01","status":"public","year":"2024","date_created":"2024-09-13T10:01:38Z","citation":{"ieee":"E. Frantar and D.-A. Alistarh, “QMoE: Sub-1-bit compression of trillion parameter models,” in <i>Proceedings of Machine Learning and Systems</i>, Santa Clara, CA, United States, 2024, vol. 6.","chicago":"Frantar, Elias, and Dan-Adrian Alistarh. “QMoE: Sub-1-Bit Compression of Trillion Parameter Models.” In <i>Proceedings of Machine Learning and Systems</i>, Vol. 6, 2024.","ista":"Frantar E, Alistarh D-A. 2024. QMoE: Sub-1-bit compression of trillion parameter models. Proceedings of Machine Learning and Systems. MLSys: Machine Learning and Systems vol. 6.","short":"E. Frantar, D.-A. Alistarh, in:, Proceedings of Machine Learning and Systems, 2024.","apa":"Frantar, E., &#38; Alistarh, D.-A. (2024). QMoE: Sub-1-bit compression of trillion parameter models. In <i>Proceedings of Machine Learning and Systems</i> (Vol. 6). Santa Clara, CA, United States.","ama":"Frantar E, Alistarh D-A. QMoE: Sub-1-bit compression of trillion parameter models. In: <i>Proceedings of Machine Learning and Systems</i>. Vol 6. ; 2024.","mla":"Frantar, Elias, and Dan-Adrian Alistarh. “QMoE: Sub-1-Bit Compression of Trillion Parameter Models.” <i>Proceedings of Machine Learning and Systems</i>, vol. 6, 2024."},"department":[{"_id":"DaAl"}],"month":"05","oa":1,"author":[{"full_name":"Frantar, Elias","id":"09a8f98d-ec99-11ea-ae11-c063a7b7fe5f","last_name":"Frantar","first_name":"Elias"},{"orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"}],"conference":{"start_date":"2024-05-13","end_date":"2024-05-16","name":"MLSys: Machine Learning and Systems","location":"Santa Clara, CA, United States"}},{"article_processing_charge":"No","abstract":[{"text":"Deep learning is essential in numerous applications nowadays, with many recent advancements made possible by training very large models. Despite their broad applicability, training neural networks is often time-intensive, and it is usually impractical to manage large models and datasets on a single machine. To address these issues, distributed deep learning training has become increasingly important. However, distributed training requires synchronization among nodes, and the mini-batch stochastic gradient descent algorithm places a significant load on network connections. A possible solution to tackle the synchronization bottleneck is to reduce a message size by lossy compression.\r\n\r\nIn this thesis, we investigate systems and algorithmic approaches to communication compression during training. From the systems perspective, we demonstrate that a common approach of expensive hardware overprovisioning can be replaced through a thorough system design. We introduce a framework that introduces efficient software support for compressed communication in machine learning applications, applicable to both multi-GPU single-node training and larger-scale multi-node training. Our framework integrates with popular ML frameworks, providing up to 3x speedups for multi-GPU nodes based on commodity hardware and order-of-magnitude improvements in the multi-node setting, with negligible impact on accuracy.\r\n\r\nAlso, we consider an application of our framework to different communication schemes, such as Fully Sharded Data Parallel. We provide strong convergence guarantees for the compression in such a setup. Empirical validation shows that our method preserves model accuracy for GPT-family models with up to 1.3 billion parameters, while completely removing the communication bottlenecks of non-compressed alternatives, providing up to 2.2x speedups end-to-end.\r\n\r\nFrom the algorithmic side, we propose a general framework that dynamically adjusts the degree of compression across a model's layers during training. This approach enhances overall compression and results in significant speedups without compromising accuracy. Our algorithm utilizes an adaptive algorithm that automatically selects the optimal compression parameters for model layers, ensuring the best compression ratio while adhering to an error constraint. Our method is effective across all existing families of compression methods. It achieves up to 2.5x faster training and up to a 5x improvement in compression compared to efficient implementations of current approaches. Additionally, LGreCo can complement existing adaptive algorithms.\r\n","lang":"eng"}],"project":[{"call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425","name":"Elastic Coordination for Scalable Machine Learning","grant_number":"805223"}],"researchdata_availability":"no","file":[{"creator":"imarkov","file_name":"Thesis.zip","file_size":43327753,"checksum":"77609f4835d2730e46fa0d42d9134ed9","file_id":"17491","relation":"source_file","date_created":"2024-09-04T08:35:35Z","date_updated":"2024-09-04T08:35:35Z","content_type":"application/x-zip-compressed","access_level":"closed"},{"date_created":"2024-09-04T08:36:06Z","date_updated":"2024-09-04T08:36:06Z","content_type":"application/pdf","access_level":"open_access","file_name":"Thesis_final_version_pdfa2.pdf","creator":"imarkov","file_size":2756082,"checksum":"9e68f7217570f756ceb8f70b980938cd","success":1,"file_id":"17492","relation":"main_file"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"14461"},{"status":"public","relation":"part_of_dissertation","id":"12780"},{"id":"17456","status":"public","relation":"part_of_dissertation"}]},"supervisor":[{"first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"}],"doi":"10.15479/at:ista:17490","acknowledged_ssus":[{"_id":"ScienComp"}],"alternative_title":["ISTA Thesis"],"page":"102","oa_version":"Published Version","publication_status":"published","corr_author":"1","publisher":"Institute of Science and Technology Austria","tmp":{"image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"type":"dissertation","ec_funded":1,"fulldoi":"https://doi.org/10.15479/at:ista:17490","month":"09","author":[{"last_name":"Markov","id":"D0CF4148-C985-11E9-8066-0BDEE5697425","first_name":"Ilia","full_name":"Markov, Ilia"}],"degree_awarded":"PhD","has_accepted_license":"1","oa":1,"status":"public","department":[{"_id":"GradSch"},{"_id":"DaAl"}],"year":"2024","date_created":"2024-09-04T08:51:11Z","citation":{"mla":"Markov, Ilia. <i>Communication-Efficient Distributed Training of Deep Neural Networks : An Algorithms and Systems Perspective</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17490\">10.15479/at:ista:17490</a>.","short":"I. Markov, Communication-Efficient Distributed Training of Deep Neural Networks : An Algorithms and Systems Perspective, Institute of Science and Technology Austria, 2024.","apa":"Markov, I. (2024). <i>Communication-efficient distributed training of deep neural networks : An algorithms and systems perspective</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17490\">https://doi.org/10.15479/at:ista:17490</a>","ama":"Markov I. Communication-efficient distributed training of deep neural networks : An algorithms and systems perspective. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17490\">10.15479/at:ista:17490</a>","ieee":"I. Markov, “Communication-efficient distributed training of deep neural networks : An algorithms and systems perspective,” Institute of Science and Technology Austria, 2024.","ista":"Markov I. 2024. Communication-efficient distributed training of deep neural networks : An algorithms and systems perspective. Institute of Science and Technology Austria.","chicago":"Markov, Ilia. “Communication-Efficient Distributed Training of Deep Neural Networks : An Algorithms and Systems Perspective.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17490\">https://doi.org/10.15479/at:ista:17490</a>."},"title":"Communication-efficient distributed training of deep neural networks : An algorithms and systems perspective","doi_confirm":"1","day":"04","language":[{"iso":"eng"}],"_id":"17490","supplementarymaterial":"no","publication_identifier":{"issn":["2663-337X"]},"file_date_updated":"2024-09-04T08:36:06Z","das_tickbox":"0","OA_place":"publisher","date_updated":"2026-10-02T11:20:06Z","date_published":"2024-09-04T00:00:00Z","ddc":["000"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"editor":[{"full_name":"Gibbons, P.","first_name":"P.","last_name":"Gibbons"},{"last_name":"Pekhimenko","first_name":"G.","full_name":"Pekhimenko, G."},{"full_name":"De Sa, C.","last_name":"De Sa","first_name":"C."}],"related_material":{"record":[{"id":"17490","relation":"dissertation_contains","status":"public"}]},"article_processing_charge":"No","quality_controlled":"1","abstract":[{"text":"Data-parallel distributed training of deep neural networks (DNN) has gained very widespread adoption, but can still experience communication bottlenecks. To address this issue, entire families of compression mechanisms have been developed, including quantization, sparsification, and low-rank approximation, some of which are seeing significant practical adoption. Despite this progress, almost all known compression schemes apply compression uniformly across DNN layers, although layers are heterogeneous in terms of parameter count and their impact on model accuracy.In this work, we provide a general framework for adapting the degree of compression across the model's layers dynamically during training, improving the overall compression, while leading to substantial speedups, without sacrificing accuracy. Our framework, called L-GreCo, is based on an adaptive algorithm, which automatically picks the optimal compression parameters for model layers guaranteeing the best compression ratio while satisfying an error constraint. Extensive experiments over image classification and language modeling tasks shows that L-GreCo is effective across all existing families of compression methods, and achieves up to 2.5\r\n×\r\n training speedup and up to 5\r\n×\r\n compression improvement over efficient implementations of existing approaches, while recovering full accuracy. Moreover, L-GreCo is complementary to existing adaptive algorithms, improving their compression ratio by 50\\% and practical throughput by 66\\%. An anonymized implementation is available at https://github.com/LGrCo/L-GreCo.","lang":"eng"}],"researchdata_availability":"no","publication":"Proceedings of Machine Learning and Systems ","main_file_link":[{"open_access":"1","url":"https://proceedings.mlsys.org/paper_files/paper/2024/hash/9069a8976ff06f6443e7f4172990a580-Abstract-Conference.html"}],"publisher":"Association for Computing Machinery","type":"conference","volume":6,"oa_version":"Published Version","publication_status":"published","corr_author":"1","status":"public","department":[{"_id":"DaAl"}],"year":"2024","date_created":"2024-08-22T08:29:25Z","citation":{"apa":"Markov, I., Alimohammadi, K., Frantar, E., &#38; Alistarh, D.-A. (2024). L-GreCo: Layerwise-adaptive gradient compression for efficient data-parallel deep learning. In P. Gibbons, G. Pekhimenko, &#38; C. De Sa (Eds.), <i>Proceedings of Machine Learning and Systems </i> (Vol. 6). Athens, Greece: Association for Computing Machinery.","short":"I. Markov, K. Alimohammadi, E. Frantar, D.-A. Alistarh, in:, P. Gibbons, G. Pekhimenko, C. De Sa (Eds.), Proceedings of Machine Learning and Systems , Association for Computing Machinery, 2024.","ama":"Markov I, Alimohammadi K, Frantar E, Alistarh D-A. L-GreCo: Layerwise-adaptive gradient compression for efficient data-parallel deep learning. In: Gibbons P, Pekhimenko G, De Sa C, eds. <i>Proceedings of Machine Learning and Systems </i>. Vol 6. Association for Computing Machinery; 2024.","mla":"Markov, Ilia, et al. “L-GreCo: Layerwise-Adaptive Gradient Compression for Efficient Data-Parallel Deep Learning.” <i>Proceedings of Machine Learning and Systems </i>, edited by P. Gibbons et al., vol. 6, Association for Computing Machinery, 2024.","ieee":"I. Markov, K. Alimohammadi, E. Frantar, and D.-A. Alistarh, “L-GreCo: Layerwise-adaptive gradient compression for efficient data-parallel deep learning,” in <i>Proceedings of Machine Learning and Systems </i>, Athens, Greece, 2024, vol. 6.","ista":"Markov I, Alimohammadi K, Frantar E, Alistarh D-A. 2024. L-GreCo: Layerwise-adaptive gradient compression for efficient data-parallel deep learning. Proceedings of Machine Learning and Systems . MLSys: Machine Learning and Systems vol. 6.","chicago":"Markov, Ilia, Kaveh Alimohammadi, Elias Frantar, and Dan-Adrian Alistarh. “L-GreCo: Layerwise-Adaptive Gradient Compression for Efficient Data-Parallel Deep Learning.” In <i>Proceedings of Machine Learning and Systems </i>, edited by P. Gibbons, G. Pekhimenko, and C. De Sa, Vol. 6. Association for Computing Machinery, 2024."},"month":"04","external_id":{"arxiv":["2210.17357"]},"author":[{"first_name":"Ilia","last_name":"Markov","id":"D0CF4148-C985-11E9-8066-0BDEE5697425","full_name":"Markov, Ilia"},{"full_name":"Alimohammadi, Kaveh","last_name":"Alimohammadi","first_name":"Kaveh"},{"full_name":"Frantar, Elias","last_name":"Frantar","id":"09a8f98d-ec99-11ea-ae11-c063a7b7fe5f","first_name":"Elias"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X"}],"conference":{"location":"Athens, Greece","end_date":"2024-04-22","name":"MLSys: Machine Learning and Systems","start_date":"2024-04-22"},"oa":1,"supplementarymaterial":"no","intvolume":"         6","das_tickbox":"0","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["000"],"date_updated":"2026-10-02T11:20:05Z","date_published":"2024-04-01T00:00:00Z","arxiv":1,"title":"L-GreCo: Layerwise-adaptive gradient compression for efficient data-parallel deep learning","day":"01","language":[{"iso":"eng"}],"_id":"17456"},{"page":"106","alternative_title":["ISTA thesis"],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"corr_author":"1","publication_status":"published","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"publisher":"Institute of Science and Technology Austria","fulldoi":"https://doi.org/10.15479/at:ista:18766","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","type":"dissertation","article_processing_charge":"No","researchdata_availability":"yes","project":[{"call_identifier":"FWF","_id":"26736D6A-B435-11E9-9278-68D0E5697425","grant_number":"P31445","name":"Structural conservation and diversity in retroviral capsid"}],"abstract":[{"text":"Poxviruses are large pleomorphic double-stranded DNA viruses that include well known members such as variola virus, the causative agent of smallpox, Mpox virus, as well as Vaccinia virus (VACV), which serves as a vaccination strain for formerly mentioned viruses. VACV is a valuable model for studying large pleomorphic DNA viruses in general and poxviruses specifically, as many features, such as core morphology and structural proteins, are well conserved within this family. Despite decades of research, our understanding of the structural components and proteins that comprise the poxvirus core in mature virions remains limited. Although major core proteins were identified via indirect experimental evidence, the core's complexity, with its large size, structure and number of involved proteins, has hindered efforts to achieve high-resolution insights and to define the roles of the individual proteins. The specific protein composition of the core's individual layers, including the palisade layer and the inner core wall, has remained unclear. In this study, we have merged multiple approaches, including single particle cryo electron microscopy of purified virus cores, cryo-electron tomography and subtomogram averaging of mature virions and molecular modeling to elucidate the structural determinants of the VACV core. Due to the lack of experimentally derived structures, either in situ or reconstituted in vitro, we used Alphafold to predict models of the putative major core protein candidates, A10, 23k, A3, A4, and L4. Our results show that the VACV core is composed of several layers with varying local symmetries, forming more intricate interactions than observed previously. This allowed us to identify several molecular building blocks forming the viral core lattice. In particular, we identified trimers of protein A10 as a major core structure that forms the palisade layer of the viral core. Additionally, we revealed that six petals of a flower shaped core pore within the core wall are composed of A10 trimers. Furthermore, we obtained a cryo-EM density for the inner core wall that could potentially accommodate an A3 dimer. Integrating descriptions of protein interactions from previous studies enabled us to provide a detailed structural model of the poxvirus core wall, and our findings indicate that the interactions within A10 trimers are likely consistent across orthopox- and parapoxviruses. This combined application of cryo-SPA and cryo-ET can help overcome obstacles in studying complex virus structures in the future, including their key assembly proteins, interactions, and the formation into a core lattice. Our work provides important fundamental new insights into poxvirus core architecture, also considering the recent re-emergence of poxviruses.","lang":"eng"}],"file":[{"date_created":"2025-01-07T12:15:11Z","date_updated":"2025-01-07T12:15:11Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_size":38814932,"checksum":"3e51cab327c754045c3d29c1a50cc9a9","file_name":"PhD_thesis_Julia_Datler.docx","creator":"jstanger","file_id":"18769","relation":"source_file"},{"relation":"main_file","checksum":"22fabe5b97950bf852212f6edb555173","file_size":12044865,"creator":"jstanger","file_name":"PhD_thesis_Julia_Datler.pdf","success":1,"file_id":"18770","content_type":"application/pdf","access_level":"open_access","date_created":"2025-01-07T12:15:14Z","date_updated":"2025-01-07T12:15:14Z"}],"supervisor":[{"full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur"}],"doi":"10.15479/at:ista:18766","related_material":{"record":[{"id":"12334","status":"public","relation":"part_of_dissertation"},{"id":"14979","relation":"part_of_dissertation","status":"public"}]},"acknowledgement":"This work was funded by the Austrian Science Fund (FWF) grant P31445 and ISTA. I\r\nwould like to express my gratitude to the Scientific Service Units, particularly the Lab\r\nSupport Facility, the Scientific Computing Facility and the Electron Microscopy Facility\r\nfor their tremendous support. I want to especially thank Alois for assisting me with the\r\ninstallation of countless new software and for troubleshooting cluster issues. A special\r\nthanks goes to Valentin for his outstanding support in cryo-EM data acquisition and\r\nhis ongoing help in improving the process to ensure that I obtained the best possible\r\ndata from my sample.","doi_confirm":"1","title":"Elucidating the structural determinants of the poxvirus core using multi-modal cryo-EM","keyword":["cryo-EM","cryo-ET","cryo-SPA","Structural Virology","Poxvirus","Vaccinia Virus","Structural Biology"],"_id":"18766","language":[{"iso":"eng"}],"day":"30","das_tickbox":"1","OA_place":"publisher","file_date_updated":"2025-01-07T12:15:14Z","supplementarymaterial":"no","publication_identifier":{"isbn":["978-3-99078-049-7"],"issn":["2663-337X"]},"date_updated":"2026-10-02T11:21:19Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["570"],"date_published":"2024-12-30T00:00:00Z","month":"12","oa":1,"has_accepted_license":"1","degree_awarded":"PhD","author":[{"orcid":"0000-0002-3616-8580","full_name":"Datler, Julia","first_name":"Julia","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","last_name":"Datler"}],"status":"public","date_created":"2025-01-07T10:23:12Z","citation":{"ieee":"J. Datler, “Elucidating the structural determinants of the poxvirus core using multi-modal cryo-EM,” Institute of Science and Technology Austria, 2024.","ista":"Datler J. 2024. Elucidating the structural determinants of the poxvirus core using multi-modal cryo-EM. Institute of Science and Technology Austria.","chicago":"Datler, Julia. “Elucidating the Structural Determinants of the Poxvirus Core Using Multi-Modal Cryo-EM.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18766\">https://doi.org/10.15479/at:ista:18766</a>.","mla":"Datler, Julia. <i>Elucidating the Structural Determinants of the Poxvirus Core Using Multi-Modal Cryo-EM</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18766\">10.15479/at:ista:18766</a>.","apa":"Datler, J. (2024). <i>Elucidating the structural determinants of the poxvirus core using multi-modal cryo-EM</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18766\">https://doi.org/10.15479/at:ista:18766</a>","short":"J. Datler, Elucidating the Structural Determinants of the Poxvirus Core Using Multi-Modal Cryo-EM, Institute of Science and Technology Austria, 2024.","ama":"Datler J. Elucidating the structural determinants of the poxvirus core using multi-modal cryo-EM. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18766\">10.15479/at:ista:18766</a>"},"year":"2024","department":[{"_id":"GradSch"},{"_id":"FlSc"}]},{"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"18766"}],"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/down-to-the-core-of-poxviruses/","description":"News on ISTA Website"}]},"acknowledgement":"We thank A. Bergthaler (Research Center for Molecular Medicine of the Austrian Academy of Sciences) for providing VACV WR. We thank A. Nicholas and his team at the ISTA proteomics facility, and S. Elefante at the ISTA Scientific Computing facility for their support. We also thank F. Fäßler, D. Porley, T. Muthspiel and other members of the Schur group for support and helpful discussions. We also thank D. Castaño-Díez for support with Dynamo. We thank D. Farrell for his help optimizing the Rosetta protocol to refine the atomic model into the cryo-EM map with symmetry.\r\n\r\nF.K.M.S. acknowledges support from ISTA and EMBO. F.K.M.S. also received support from the Austrian Science Fund (FWF) grant P31445. This publication has been made possible in part by CZI grant DAF2021-234754 and grant https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (funder https://doi.org/10.13039/100014989) awarded to F.K.M.S.\r\n\r\nThis research was also supported by the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF). We also acknowledge the use of COSMIC45 and Colabfold46.","doi":"10.1038/s41594-023-01201-6","file":[{"relation":"main_file","file_size":17485494,"file_name":"2024_NatureStrucBio_Datler.pdf","creator":"dernst","checksum":"bda7bf65d81455480efaed8ca293b0db","file_id":"17307","success":1,"content_type":"application/pdf","access_level":"open_access","date_updated":"2024-07-22T11:27:22Z","date_created":"2024-07-22T11:27:22Z"}],"abstract":[{"lang":"eng","text":"Poxviruses are among the largest double-stranded DNA viruses, with members such as variola virus, monkeypox virus and the vaccination strain vaccinia virus (VACV). Knowledge about the structural proteins that form the viral core has remained sparse. While major core proteins have been annotated via indirect experimental evidence, their structures have remained elusive and they could not be assigned to individual core features. Hence, which proteins constitute which layers of the core, such as the palisade layer and the inner core wall, has remained enigmatic. Here we show, using a multi-modal cryo-electron microscopy (cryo-EM) approach in combination with AlphaFold molecular modeling, that trimers formed by the cleavage product of VACV protein A10 are the key component of the palisade layer. This allows us to place previously obtained descriptions of protein interactions within the core wall into perspective and to provide a detailed model of poxvirus core architecture. Importantly, we show that interactions within A10 trimers are likely generalizable over members of orthopox- and parapoxviruses."}],"article_type":"original","project":[{"name":"Structural conservation and diversity in retroviral capsid","grant_number":"P31445","_id":"26736D6A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"publication":"Nature Structural & Molecular Biology","researchdata_availability":"yes","article_processing_charge":"Yes (in subscription journal)","quality_controlled":"1","type":"journal_article","fulldoi":"https://doi.org/10.1038/s41594-023-01201-6","dataavailabilitystatement":"The electron microscopy density maps of the A10 trimer and the hexameric flower-shaped pore, the subtomogram average of the palisade layer and representative tomograms for complete viruses as well as isolated cores have been deposited in the Electron Microscopy Data Bank under accession codes: EMD-17410, EMD-17411, EMD-17412, EMD-17413, EMD-17414 and EMD-18452.\r\n\r\nThe refined model of the A10 trimer has been deposited in the Protein Data Bank accession code: PDB 8P4K.\r\n\r\nThe UniProt codes of VACV core proteins used for structure prediction are: A10 (P16715), A3 (P06440), A4 (P29191) and L4 (P03295).\r\n\r\nGenBank Protein IDs of variola virus A10 (ABF23487.1), monkeypox virus A10 (YP_010377118.1), rabbitpox virus A10 (AAS49831.1), cowpox virus A10 (ADZ29251.1), ectromelia virus A10 (NP_671631.1), orf virus P4a (AY386264.1), Amsacta moorei entomopoxvirus AMV139 (NP_064921.1) and Melanoplus sanguinipes entomopoxvirus putative core protein P4a homolog (AF063866.1) were used for protein sequence alignment. Source data for MS experiments are provided as Supplementary Information accompanying this manuscript.","scopus_import":"1","publisher":"Springer Nature","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","publication_status":"published","corr_author":"1","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"volume":31,"page":"1114-1123","department":[{"_id":"FlSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"year":"2024","OA_type":"hybrid","citation":{"mla":"Datler, Julia, et al. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” <i>Nature Structural &#38; Molecular Biology</i>, vol. 31, Springer Nature, 2024, pp. 1114–23, doi:<a href=\"https://doi.org/10.1038/s41594-023-01201-6\">10.1038/s41594-023-01201-6</a>.","short":"J. Datler, J. Hansen, A. Thader, A. Schlögl, L.W. Bauer, V.-V. Hodirnau, F.K. Schur, Nature Structural &#38; Molecular Biology 31 (2024) 1114–1123.","apa":"Datler, J., Hansen, J., Thader, A., Schlögl, A., Bauer, L. W., Hodirnau, V.-V., &#38; Schur, F. K. (2024). Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41594-023-01201-6\">https://doi.org/10.1038/s41594-023-01201-6</a>","ama":"Datler J, Hansen J, Thader A, et al. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. <i>Nature Structural &#38; Molecular Biology</i>. 2024;31:1114-1123. doi:<a href=\"https://doi.org/10.1038/s41594-023-01201-6\">10.1038/s41594-023-01201-6</a>","ieee":"J. Datler <i>et al.</i>, “Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores,” <i>Nature Structural &#38; Molecular Biology</i>, vol. 31. Springer Nature, pp. 1114–1123, 2024.","ista":"Datler J, Hansen J, Thader A, Schlögl A, Bauer LW, Hodirnau V-V, Schur FK. 2024. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural &#38; Molecular Biology. 31, 1114–1123.","chicago":"Datler, Julia, Jesse Hansen, Andreas Thader, Alois Schlögl, Lukas W Bauer, Victor-Valentin Hodirnau, and Florian KM Schur. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41594-023-01201-6\">https://doi.org/10.1038/s41594-023-01201-6</a>."},"date_created":"2024-02-12T09:59:45Z","APC_amount":"11700 EUR","status":"public","author":[{"id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","last_name":"Datler","first_name":"Julia","orcid":"0000-0002-3616-8580","full_name":"Datler, Julia"},{"last_name":"Hansen","id":"1063c618-6f9b-11ec-9123-f912fccded63","first_name":"Jesse","full_name":"Hansen, Jesse","orcid":"0000-0001-7967-2085"},{"first_name":"Andreas","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87","last_name":"Thader","full_name":"Thader, Andreas"},{"orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois","last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois"},{"full_name":"Bauer, Lukas W","first_name":"Lukas W","last_name":"Bauer","id":"0c894dcf-897b-11ed-a09c-8186353224b0"},{"full_name":"Hodirnau, Victor-Valentin","orcid":"0000-0003-3904-947X","first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","last_name":"Hodirnau"},{"orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","first_name":"Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","oa":1,"month":"07","external_id":{"pmid":["38316877"],"isi":["001158144600002"]},"date_published":"2024-07-01T00:00:00Z","ddc":["570"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-10-02T11:21:19Z","publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]},"intvolume":"        31","supplementarymaterial":"yes","file_date_updated":"2024-07-22T11:27:22Z","das_tickbox":"1","OA_place":"publisher","pmid":1,"isi":1,"day":"01","language":[{"iso":"eng"}],"_id":"14979","keyword":["Molecular Biology","Structural Biology"],"title":"Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores"},{"language":[{"iso":"eng"}],"_id":"17850","day":"06","doi_confirm":"1","title":"Fitness landscapes of orthologous green fluorescent proteins","date_updated":"2026-10-02T11:21:41Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-09-06T00:00:00Z","ddc":["570"],"das_tickbox":"0","OA_place":"publisher","file_date_updated":"2024-09-27T10:34:34Z","supplementarymaterial":"no","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","oa":1,"has_accepted_license":"1","author":[{"last_name":"Gonzalez Somermeyer","id":"4720D23C-F248-11E8-B48F-1D18A9856A87","first_name":"Louisa","full_name":"Gonzalez Somermeyer, Louisa","orcid":"0000-0001-9139-5383"}],"month":"09","date_created":"2024-09-06T12:57:44Z","citation":{"chicago":"Gonzalez Somermeyer, Louisa. “Fitness Landscapes of Orthologous Green Fluorescent Proteins.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17850\">https://doi.org/10.15479/at:ista:17850</a>.","ista":"Gonzalez Somermeyer L. 2024. Fitness landscapes of orthologous green fluorescent proteins. Institute of Science and Technology Austria.","ieee":"L. Gonzalez Somermeyer, “Fitness landscapes of orthologous green fluorescent proteins,” Institute of Science and Technology Austria, 2024.","mla":"Gonzalez Somermeyer, Louisa. <i>Fitness Landscapes of Orthologous Green Fluorescent Proteins</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17850\">10.15479/at:ista:17850</a>.","ama":"Gonzalez Somermeyer L. Fitness landscapes of orthologous green fluorescent proteins. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17850\">10.15479/at:ista:17850</a>","short":"L. Gonzalez Somermeyer, Fitness Landscapes of Orthologous Green Fluorescent Proteins, Institute of Science and Technology Austria, 2024.","apa":"Gonzalez Somermeyer, L. (2024). <i>Fitness landscapes of orthologous green fluorescent proteins</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17850\">https://doi.org/10.15479/at:ista:17850</a>"},"year":"2024","department":[{"_id":"GradSch"},{"_id":"FyKo"}],"status":"public","corr_author":"1","publication_status":"published","oa_version":"Published Version","page":"89","alternative_title":["ISTA Thesis"],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"fulldoi":"https://doi.org/10.15479/at:ista:17850","ec_funded":1,"type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"publisher":"Institute of Science and Technology Austria","project":[{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"H2020","_id":"26580278-B435-11E9-9278-68D0E5697425","name":"Characterizing the fitness landscape on population and global scales","grant_number":"771209"}],"researchdata_availability":"no","abstract":[{"text":"Understanding the relationship between a given phenotype and its underlying genotype or genotypes is one of the most pressing challenges of biology, as it lies at the heart of not only basic understanding of evolutionary theory, but also of practical applications in medicine and bioengineering. Understanding this relationship is complicated by the ubiquitous phenomenon of epistasis, wherein mutation effects are dependent on their genetic context. Fitness landscapes — representations of phenotype as a function of genotype — are being increasingly used as a tool to study the effects and interactions of thousands of mutations, but are experimentally limited to exploring a small fraction of a protein’s theoretical sequence space. Furthermore, not all regions of said sequence space are necessarily equally informative. Thus, gene selection for landscape surveys should be carefully considered in order to maximize the usable output of necessarily limited data.\r\n\r\nIn this work, we analyzed the fitness landscapes of orthologous green fluorescent proteins from four different species, by systematically measuring the phenotype, fluorescence, of tens of thousands of mutant genotypes from each protein. These landscapes were highly heterogeneous, with some genes being mutationally robust and displaying epistasis only rarely, and others being highly epistatic and mutationally fragile. We used this data to train machine learning models to predict fluorescence from genotype. Although the training data contained almost exclusively genotypes with less than 3% sequence divergence from the original wild-type sequences, we were able to create novel, functional genotypes with up to 20% sequence divergence. Counterintuitively however, genes with high mutational robustness and rare epistasis were more difficult to introduce large numbers of mutations into, not less. This represents the first study of large-scale fitness landscapes of a protein family, and provides insights into how to approach future landscape surveys and their applications in novel protein design.","lang":"eng"}],"article_processing_charge":"No","supervisor":[{"first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694"}],"doi":"10.15479/at:ista:17850","related_material":{"link":[{"url":"https://github.com/aequorea238/Orthologous_GFP_Fitness_Peaks","relation":"software"}],"record":[{"id":"11448","relation":"part_of_dissertation","status":"public"}]},"file":[{"date_updated":"2024-09-27T10:32:33Z","date_created":"2024-09-27T10:32:33Z","content_type":"application/pdf","access_level":"open_access","checksum":"d3303724e8d3c91321d71bbad4062048","file_size":11219837,"creator":"lgonzale","file_name":"louisa_thesis_draft__240904b.pdf","file_id":"18151","relation":"main_file"},{"relation":"source_file","file_id":"18152","file_name":"louisa_thesis_draft__240904b.docx","checksum":"22e63f7f9014dffde2af7a47e7d1d014","creator":"lgonzale","file_size":43338677,"access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2024-09-27T10:34:34Z","date_updated":"2024-09-27T10:34:34Z"}]},{"supplementarymaterial":"yes","intvolume":"        18","publication_identifier":{"issn":["1875-0281"]},"file_date_updated":"2024-02-05T10:06:35Z","das_tickbox":"0","date_published":"2024-01-11T00:00:00Z","ddc":["550"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-10-02T11:22:03Z","keyword":["Sociology and Political Science"],"title":"Tipping points of space debris in low earth orbit","issue":"1","day":"11","_id":"14901","language":[{"iso":"eng"}],"status":"public","department":[{"_id":"GradSch"},{"_id":"GaTk"}],"year":"2024","citation":{"ieee":"K. Nomura <i>et al.</i>, “Tipping points of space debris in low earth orbit,” <i>International Journal of the Commons</i>, vol. 18, no. 1. Ubiquity Press, 2024.","chicago":"Nomura, Keiko, Simon Rella, Haily Merritt, Mathieu Baltussen, Darcy Bird, Annika Tjuka, and Dan Falk. “Tipping Points of Space Debris in Low Earth Orbit.” <i>International Journal of the Commons</i>. Ubiquity Press, 2024. <a href=\"https://doi.org/10.5334/ijc.1275\">https://doi.org/10.5334/ijc.1275</a>.","ista":"Nomura K, Rella S, Merritt H, Baltussen M, Bird D, Tjuka A, Falk D. 2024. Tipping points of space debris in low earth orbit. International Journal of the Commons. 18(1).","apa":"Nomura, K., Rella, S., Merritt, H., Baltussen, M., Bird, D., Tjuka, A., &#38; Falk, D. (2024). Tipping points of space debris in low earth orbit. <i>International Journal of the Commons</i>. Ubiquity Press. <a href=\"https://doi.org/10.5334/ijc.1275\">https://doi.org/10.5334/ijc.1275</a>","short":"K. Nomura, S. Rella, H. Merritt, M. Baltussen, D. Bird, A. Tjuka, D. Falk, International Journal of the Commons 18 (2024).","ama":"Nomura K, Rella S, Merritt H, et al. Tipping points of space debris in low earth orbit. <i>International Journal of the Commons</i>. 2024;18(1). doi:<a href=\"https://doi.org/10.5334/ijc.1275\">10.5334/ijc.1275</a>","mla":"Nomura, Keiko, et al. “Tipping Points of Space Debris in Low Earth Orbit.” <i>International Journal of the Commons</i>, vol. 18, no. 1, Ubiquity Press, 2024, doi:<a href=\"https://doi.org/10.5334/ijc.1275\">10.5334/ijc.1275</a>."},"date_created":"2024-01-30T11:58:02Z","month":"01","author":[{"first_name":"Keiko","last_name":"Nomura","full_name":"Nomura, Keiko"},{"id":"B4765ACA-AA38-11E9-AC9A-0930E6697425","last_name":"Rella","first_name":"Simon","full_name":"Rella, Simon"},{"last_name":"Merritt","first_name":"Haily","full_name":"Merritt, Haily"},{"full_name":"Baltussen, Mathieu","first_name":"Mathieu","last_name":"Baltussen"},{"first_name":"Darcy","last_name":"Bird","full_name":"Bird, Darcy"},{"last_name":"Tjuka","first_name":"Annika","full_name":"Tjuka, Annika"},{"first_name":"Dan","last_name":"Falk","full_name":"Falk, Dan"}],"has_accepted_license":"1","oa":1,"scopus_import":"1","publisher":"Ubiquity Press","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"type":"journal_article","fulldoi":"https://doi.org/10.5334/ijc.1275","volume":18,"oa_version":"Published Version","publication_status":"published","file":[{"relation":"main_file","file_size":1305786,"checksum":"b80ebc889033c365d8f8c05a0c655382","creator":"dernst","file_name":"2023_IntJourCommons_Nomura.pdf","file_id":"14939","success":1,"content_type":"application/pdf","access_level":"open_access","date_created":"2024-02-05T10:06:35Z","date_updated":"2024-02-05T10:06:35Z"}],"acknowledgement":"The authors would like to thank the special issue co-editors, Marco Janssen and Xiao-Shan Yap, and the anonymous reviewers for their comments that helped improve the manuscript. The paper also benefited from suggestions by other author participants in this special issue. We would also like to thank the 2022 Santa Fe Institute Complex Systems Summer School for providing space to initiate this study.","doi":"10.5334/ijc.1275","article_processing_charge":"Yes","quality_controlled":"1","article_type":"original","abstract":[{"lang":"eng","text":"Global services like navigation, communication, and Earth observation have increased dramatically in the 21st century due to advances in outer space industries. But as orbits become increasingly crowded with both satellites and inevitable space debris pollution, continued operations become endangered by the heightened risks of debris collisions in orbit. Kessler Syndrome is the term for when a critical threshold of orbiting debris triggers a runaway positive feedback loop of debris collisions, creating debris congestion that can render orbits unusable. As this potential tipping point becomes more widely recognized, there have been renewed calls for debris mitigation and removal. Here, we combine complex systems and social-ecological systems approaches to study how these efforts may affect space debris accumulation and the likelihood of reaching Kessler Syndrome. Specifically, we model how debris levels are affected by future launch rates, cleanup activities, and collisions between extant debris. We contextualize and interpret our dynamic model within a discussion of existing space debris governance and other social, economic, and geopolitical factors that may influence effective collective management of the orbital commons. In line with previous studies, our model finds that debris congestion may be reached in less than 200 years, though a holistic management strategy combining removal and mitigation actions can avoid such outcomes while continuing space activities. Moreover, although active debris removal may be particularly effective, the current lack of market and governance support may impede its implementation. Research into these critical dynamics and the multi-faceted variables that influence debris outcomes can support policymakers in curating impactful governance strategies and realistic transition pathways to sustaining debris-free orbits. Overall, our study is useful for communicating about space debris sustainability in policy and education settings by providing an exploration of policy portfolio options supported by a simple and clear social-ecological modeling approach."}],"publication":"International Journal of the Commons","researchdata_availability":"no"}]