--- _id: '10022' abstract: - lang: eng text: We consider finite-volume approximations of Fokker-Planck equations on bounded convex domains in R^d and study the corresponding gradient flow structures. We reprove the convergence of the discrete to continuous Fokker-Planck equation via the method of Evolutionary Γ-convergence, i.e., we pass to the limit at the level of the gradient flow structures, generalising the one-dimensional result obtained by Disser and Liero. The proof is of variational nature and relies on a Mosco convergence result for functionals in the discrete-to-continuum limit that is of independent interest. Our results apply to arbitrary regular meshes, even though the associated discrete transport distances may fail to converge to the Wasserstein distance in this generality. acknowledgement: This work is supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 716117) and by the Austrian Science Fund (FWF), grants No F65 and W1245. article_number: '2008.10962' article_processing_charge: No author: - first_name: Dominik L full_name: Forkert, Dominik L id: 35C79D68-F248-11E8-B48F-1D18A9856A87 last_name: Forkert - first_name: Jan full_name: Maas, Jan id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 - first_name: Lorenzo full_name: Portinale, Lorenzo id: 30AD2CBC-F248-11E8-B48F-1D18A9856A87 last_name: Portinale citation: ama: Forkert DL, Maas J, Portinale L. Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions. arXiv. apa: Forkert, D. L., Maas, J., & Portinale, L. (n.d.). Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions. arXiv. chicago: Forkert, Dominik L, Jan Maas, and Lorenzo Portinale. “Evolutionary Γ-Convergence of Entropic Gradient Flow Structures for Fokker-Planck Equations in Multiple Dimensions.” ArXiv, n.d. ieee: D. L. Forkert, J. Maas, and L. Portinale, “Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions,” arXiv. . ista: Forkert DL, Maas J, Portinale L. Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions. arXiv, 2008.10962. mla: Forkert, Dominik L., et al. “Evolutionary Γ-Convergence of Entropic Gradient Flow Structures for Fokker-Planck Equations in Multiple Dimensions.” ArXiv, 2008.10962. short: D.L. Forkert, J. Maas, L. Portinale, ArXiv (n.d.). date_created: 2021-09-17T10:57:27Z date_published: 2020-08-25T00:00:00Z date_updated: 2023-09-07T13:31:05Z day: '25' department: - _id: JaMa ec_funded: 1 external_id: arxiv: - '2008.10962' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2008.10962 month: '08' oa: 1 oa_version: Preprint page: '33' project: - _id: 256E75B8-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '716117' name: Optimal Transport and Stochastic Dynamics - _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2 grant_number: F6504 name: Taming Complexity in Partial Differential Systems publication: arXiv publication_status: submitted related_material: record: - id: '11739' relation: later_version status: public - id: '10030' relation: dissertation_contains status: public status: public title: Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions type: preprint user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2020' ... --- _id: '8724' abstract: - lang: eng text: "We study the problem of learning from multiple untrusted data sources, a scenario of increasing practical relevance given the recent emergence of crowdsourcing and collaborative learning paradigms. Specifically, we analyze the situation in which a learning system obtains datasets from multiple sources, some of which might be biased or even adversarially perturbed. It is\r\nknown that in the single-source case, an adversary with the power to corrupt a fixed fraction of the training data can prevent PAC-learnability, that is, even in the limit of infinitely much training data, no learning system can approach the optimal test error. In this work we show that, surprisingly, the same is not true in the multi-source setting, where the adversary can arbitrarily\r\ncorrupt a fixed fraction of the data sources. Our main results are a generalization bound that provides finite-sample guarantees for this learning setting, as well as corresponding lower bounds. Besides establishing PAC-learnability our results also show that in a cooperative learning setting sharing data with other parties has provable benefits, even if some\r\nparticipants are malicious. " acknowledged_ssus: - _id: ScienComp acknowledgement: Dan Alistarh is supported in part by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML). This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp). article_processing_charge: No author: - first_name: Nikola H full_name: Konstantinov, Nikola H id: 4B9D76E4-F248-11E8-B48F-1D18A9856A87 last_name: Konstantinov - first_name: Elias full_name: Frantar, Elias id: 09a8f98d-ec99-11ea-ae11-c063a7b7fe5f last_name: Frantar - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Konstantinov NH, Frantar E, Alistarh D-A, Lampert C. On the sample complexity of adversarial multi-source PAC learning. In: Proceedings of the 37th International Conference on Machine Learning. Vol 119. ML Research Press; 2020:5416-5425.' apa: 'Konstantinov, N. H., Frantar, E., Alistarh, D.-A., & Lampert, C. (2020). On the sample complexity of adversarial multi-source PAC learning. In Proceedings of the 37th International Conference on Machine Learning (Vol. 119, pp. 5416–5425). Online: ML Research Press.' chicago: Konstantinov, Nikola H, Elias Frantar, Dan-Adrian Alistarh, and Christoph Lampert. “On the Sample Complexity of Adversarial Multi-Source PAC Learning.” In Proceedings of the 37th International Conference on Machine Learning, 119:5416–25. ML Research Press, 2020. ieee: N. H. Konstantinov, E. Frantar, D.-A. Alistarh, and C. Lampert, “On the sample complexity of adversarial multi-source PAC learning,” in Proceedings of the 37th International Conference on Machine Learning, Online, 2020, vol. 119, pp. 5416–5425. ista: 'Konstantinov NH, Frantar E, Alistarh D-A, Lampert C. 2020. On the sample complexity of adversarial multi-source PAC learning. Proceedings of the 37th International Conference on Machine Learning. ICML: International Conference on Machine Learning vol. 119, 5416–5425.' mla: Konstantinov, Nikola H., et al. “On the Sample Complexity of Adversarial Multi-Source PAC Learning.” Proceedings of the 37th International Conference on Machine Learning, vol. 119, ML Research Press, 2020, pp. 5416–25. short: N.H. Konstantinov, E. Frantar, D.-A. Alistarh, C. Lampert, in:, Proceedings of the 37th International Conference on Machine Learning, ML Research Press, 2020, pp. 5416–5425. conference: end_date: 2020-07-18 location: Online name: 'ICML: International Conference on Machine Learning' start_date: 2020-07-12 date_created: 2020-11-05T15:25:58Z date_published: 2020-07-12T00:00:00Z date_updated: 2023-09-07T13:42:08Z day: '12' ddc: - '000' department: - _id: DaAl - _id: ChLa ec_funded: 1 external_id: arxiv: - '2002.10384' file: - access_level: open_access checksum: cc755d0054bc4b2be778ea7aa7884d2f content_type: application/pdf creator: dernst date_created: 2021-02-15T09:00:01Z date_updated: 2021-02-15T09:00:01Z file_id: '9120' file_name: 2020_PMLR_Konstantinov.pdf file_size: 281286 relation: main_file success: 1 file_date_updated: 2021-02-15T09:00:01Z has_accepted_license: '1' intvolume: ' 119' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 5416-5425 project: - _id: 268A44D6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '805223' name: Elastic Coordination for Scalable Machine Learning publication: Proceedings of the 37th International Conference on Machine Learning publication_identifier: issn: - 2640-3498 publication_status: published publisher: ML Research Press quality_controlled: '1' related_material: link: - relation: supplementary_material url: http://proceedings.mlr.press/v119/konstantinov20a/konstantinov20a-supp.pdf record: - id: '10799' relation: dissertation_contains status: public scopus_import: '1' status: public title: On the sample complexity of adversarial multi-source PAC learning type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 119 year: '2020' ... --- _id: '8644' abstract: - lang: eng text: Determining the phase diagram of systems consisting of smaller subsystems 'connected' via a tunable coupling is a challenging task relevant for a variety of physical settings. A general question is whether new phases, not present in the uncoupled limit, may arise. We use machine learning and a suitable quasidistance between different points of the phase diagram to study layered spin models, in which the spin variables constituting each of the uncoupled systems (to which we refer as layers) are coupled to each other via an interlayer coupling. In such systems, in general, composite order parameters involving spins of different layers may emerge as a consequence of the interlayer coupling. We focus on the layered Ising and Ashkin–Teller models as a paradigmatic case study, determining their phase diagram via the application of a machine learning algorithm to the Monte Carlo data. Remarkably our technique is able to correctly characterize all the system phases also in the case of hidden order parameters, i.e. order parameters whose expression in terms of the microscopic configurations would require additional preprocessing of the data fed to the algorithm. We correctly retrieve the three known phases of the Ashkin–Teller model with ferromagnetic couplings, including the phase described by a composite order parameter. For the bilayer and trilayer Ising models the phases we find are only the ferromagnetic and the paramagnetic ones. Within the approach we introduce, owing to the construction of convolutional neural networks, naturally suitable for layered image-like data with arbitrary number of layers, no preprocessing of the Monte Carlo data is needed, also with regard to its spatial structure. The physical meaning of our results is discussed and compared with analytical data, where available. Yet, the method can be used without any a priori knowledge of the phases one seeks to find and can be applied to other models and structures. acknowledgement: We thank Gesualdo Delfino, Michele Fabrizio, Piero Ferrarese, Robert Konik, Christoph Lampert and Mikhail Lemeshko for stimulating discussions at various stages of this work. WR has received funding from the EU Horizon 2020 program under the Marie Skłodowska-Curie Grant Agreement No. 665385 and is a recipient of a DOC Fellowship of the Austrian Academy of Sciences. GB acknowledges support from the Austrian Science Fund (FWF), under project No. M2641-N27. ND acknowledges support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) via Collaborative Research Center SFB 1225 (ISOQUANT)--project-id 273811115--and under Germany's Excellence Strategy 'EXC-2181/1-390900948' (the Heidelberg STRUCTURES Excellence Cluster). article_number: '093026' article_processing_charge: No article_type: original author: - first_name: Wojciech full_name: Rzadkowski, Wojciech id: 48C55298-F248-11E8-B48F-1D18A9856A87 last_name: Rzadkowski orcid: 0000-0002-1106-4419 - first_name: N full_name: Defenu, N last_name: Defenu - first_name: S full_name: Chiacchiera, S last_name: Chiacchiera - first_name: A full_name: Trombettoni, A last_name: Trombettoni - first_name: Giacomo full_name: Bighin, Giacomo id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87 last_name: Bighin orcid: 0000-0001-8823-9777 citation: ama: Rzadkowski W, Defenu N, Chiacchiera S, Trombettoni A, Bighin G. Detecting composite orders in layered models via machine learning. New Journal of Physics. 2020;22(9). doi:10.1088/1367-2630/abae44 apa: Rzadkowski, W., Defenu, N., Chiacchiera, S., Trombettoni, A., & Bighin, G. (2020). Detecting composite orders in layered models via machine learning. New Journal of Physics. IOP Publishing. https://doi.org/10.1088/1367-2630/abae44 chicago: Rzadkowski, Wojciech, N Defenu, S Chiacchiera, A Trombettoni, and Giacomo Bighin. “Detecting Composite Orders in Layered Models via Machine Learning.” New Journal of Physics. IOP Publishing, 2020. https://doi.org/10.1088/1367-2630/abae44. ieee: W. Rzadkowski, N. Defenu, S. Chiacchiera, A. Trombettoni, and G. Bighin, “Detecting composite orders in layered models via machine learning,” New Journal of Physics, vol. 22, no. 9. IOP Publishing, 2020. ista: Rzadkowski W, Defenu N, Chiacchiera S, Trombettoni A, Bighin G. 2020. Detecting composite orders in layered models via machine learning. New Journal of Physics. 22(9), 093026. mla: Rzadkowski, Wojciech, et al. “Detecting Composite Orders in Layered Models via Machine Learning.” New Journal of Physics, vol. 22, no. 9, 093026, IOP Publishing, 2020, doi:10.1088/1367-2630/abae44. short: W. Rzadkowski, N. Defenu, S. Chiacchiera, A. Trombettoni, G. Bighin, New Journal of Physics 22 (2020). date_created: 2020-10-11T22:01:14Z date_published: 2020-09-01T00:00:00Z date_updated: 2023-09-07T13:44:16Z day: '01' ddc: - '530' department: - _id: MiLe doi: 10.1088/1367-2630/abae44 ec_funded: 1 external_id: isi: - '000573298000001' file: - access_level: open_access checksum: c9238fff422e7a957c3a0d559f756b3a content_type: application/pdf creator: dernst date_created: 2020-10-12T12:18:47Z date_updated: 2020-10-12T12:18:47Z file_id: '8650' file_name: 2020_NewJournalPhysics_Rzdkowski.pdf file_size: 2725143 relation: main_file success: 1 file_date_updated: 2020-10-12T12:18:47Z has_accepted_license: '1' intvolume: ' 22' isi: 1 issue: '9' language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 05A235A0-7A3F-11EA-A408-12923DDC885E grant_number: '25681' name: Analytic and machine learning approaches to composite quantum impurities - _id: 26986C82-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02641 name: A path-integral approach to composite impurities publication: New Journal of Physics publication_identifier: issn: - '13672630' publication_status: published publisher: IOP Publishing quality_controlled: '1' related_material: record: - id: '10759' relation: dissertation_contains status: public scopus_import: '1' status: public title: Detecting composite orders in layered models via machine learning tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 22 year: '2020' ... --- _id: '8705' abstract: - lang: eng text: We consider the quantum mechanical many-body problem of a single impurity particle immersed in a weakly interacting Bose gas. The impurity interacts with the bosons via a two-body potential. We study the Hamiltonian of this system in the mean-field limit and rigorously show that, at low energies, the problem is well described by the Fröhlich polaron model. acknowledgement: Financial support through the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme Grant agreement No. 694227 (R.S.) and the Maria Skłodowska-Curie Grant agreement No. 665386 (K.M.) is gratefully acknowledged. Funding Open access funding provided by Institute of Science and Technology (IST Austria) article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Krzysztof full_name: Mysliwy, Krzysztof id: 316457FC-F248-11E8-B48F-1D18A9856A87 last_name: Mysliwy - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Mysliwy K, Seiringer R. Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit. Annales Henri Poincare. 2020;21(12):4003-4025. doi:10.1007/s00023-020-00969-3 apa: Mysliwy, K., & Seiringer, R. (2020). Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-020-00969-3 chicago: Mysliwy, Krzysztof, and Robert Seiringer. “Microscopic Derivation of the Fröhlich Hamiltonian for the Bose Polaron in the Mean-Field Limit.” Annales Henri Poincare. Springer Nature, 2020. https://doi.org/10.1007/s00023-020-00969-3. ieee: K. Mysliwy and R. Seiringer, “Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit,” Annales Henri Poincare, vol. 21, no. 12. Springer Nature, pp. 4003–4025, 2020. ista: Mysliwy K, Seiringer R. 2020. Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit. Annales Henri Poincare. 21(12), 4003–4025. mla: Mysliwy, Krzysztof, and Robert Seiringer. “Microscopic Derivation of the Fröhlich Hamiltonian for the Bose Polaron in the Mean-Field Limit.” Annales Henri Poincare, vol. 21, no. 12, Springer Nature, 2020, pp. 4003–25, doi:10.1007/s00023-020-00969-3. short: K. Mysliwy, R. Seiringer, Annales Henri Poincare 21 (2020) 4003–4025. date_created: 2020-10-25T23:01:19Z date_published: 2020-12-01T00:00:00Z date_updated: 2023-09-07T13:43:51Z day: '01' ddc: - '530' department: - _id: RoSe doi: 10.1007/s00023-020-00969-3 ec_funded: 1 external_id: arxiv: - '2003.12371' isi: - '000578111800002' file: - access_level: open_access checksum: c12c9c1e6f08def245e42f3cb1d83827 content_type: application/pdf creator: cziletti date_created: 2020-10-27T12:49:04Z date_updated: 2020-10-27T12:49:04Z file_id: '8711' file_name: 2020_Annales_Mysliwy.pdf file_size: 469831 relation: main_file success: 1 file_date_updated: 2020-10-27T12:49:04Z has_accepted_license: '1' intvolume: ' 21' isi: 1 issue: '12' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 4003-4025 project: - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: Annales Henri Poincare publication_identifier: issn: - 1424-0637 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '11473' relation: dissertation_contains status: public scopus_import: '1' status: public title: Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 21 year: '2020' ... --- _id: '10861' abstract: - lang: eng text: We introduce in this paper AMT2.0, a tool for qualitative and quantitative analysis of hybrid continuous and Boolean signals that combine numerical values and discrete events. The evaluation of the signals is based on rich temporal specifications expressed in extended signal temporal logic, which integrates timed regular expressions within signal temporal logic. The tool features qualitative monitoring (property satisfaction checking), trace diagnostics for explaining and justifying property violations and specification-driven measurement of quantitative features of the signal. We demonstrate the tool functionality on several running examples and case studies, and evaluate its performance. article_processing_charge: No article_type: original author: - first_name: Dejan full_name: Nickovic, Dejan id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87 last_name: Nickovic - first_name: Olivier full_name: Lebeltel, Olivier last_name: Lebeltel - first_name: Oded full_name: Maler, Oded last_name: Maler - first_name: Thomas full_name: Ferrere, Thomas id: 40960E6E-F248-11E8-B48F-1D18A9856A87 last_name: Ferrere orcid: 0000-0001-5199-3143 - first_name: Dogan full_name: Ulus, Dogan last_name: Ulus citation: ama: 'Nickovic D, Lebeltel O, Maler O, Ferrere T, Ulus D. AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic. International Journal on Software Tools for Technology Transfer. 2020;22(6):741-758. doi:10.1007/s10009-020-00582-z' apa: 'Nickovic, D., Lebeltel, O., Maler, O., Ferrere, T., & Ulus, D. (2020). AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic. International Journal on Software Tools for Technology Transfer. Springer Nature. https://doi.org/10.1007/s10009-020-00582-z' chicago: 'Nickovic, Dejan, Olivier Lebeltel, Oded Maler, Thomas Ferrere, and Dogan Ulus. “AMT 2.0: Qualitative and Quantitative Trace Analysis with Extended Signal Temporal Logic.” International Journal on Software Tools for Technology Transfer. Springer Nature, 2020. https://doi.org/10.1007/s10009-020-00582-z.' ieee: 'D. Nickovic, O. Lebeltel, O. Maler, T. Ferrere, and D. Ulus, “AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic,” International Journal on Software Tools for Technology Transfer, vol. 22, no. 6. Springer Nature, pp. 741–758, 2020.' ista: 'Nickovic D, Lebeltel O, Maler O, Ferrere T, Ulus D. 2020. AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic. International Journal on Software Tools for Technology Transfer. 22(6), 741–758.' mla: 'Nickovic, Dejan, et al. “AMT 2.0: Qualitative and Quantitative Trace Analysis with Extended Signal Temporal Logic.” International Journal on Software Tools for Technology Transfer, vol. 22, no. 6, Springer Nature, 2020, pp. 741–58, doi:10.1007/s10009-020-00582-z.' short: D. Nickovic, O. Lebeltel, O. Maler, T. Ferrere, D. Ulus, International Journal on Software Tools for Technology Transfer 22 (2020) 741–758. date_created: 2022-03-18T10:10:53Z date_published: 2020-08-03T00:00:00Z date_updated: 2023-09-08T11:52:02Z day: '03' department: - _id: ToHe doi: 10.1007/s10009-020-00582-z external_id: isi: - '000555398600001' intvolume: ' 22' isi: 1 issue: '6' keyword: - Information Systems - Software language: - iso: eng month: '08' oa_version: None page: 741-758 publication: International Journal on Software Tools for Technology Transfer publication_identifier: eissn: - 1433-2787 issn: - 1433-2779 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '299' relation: earlier_version status: public scopus_import: '1' status: public title: 'AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic' type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 22 year: '2020' ... --- _id: '14125' abstract: - lang: eng text: "Motivation: Recent technological advances have led to an increase in the production and availability of single-cell data. The ability to integrate a set of multi-technology measurements would allow the identification of biologically or clinically meaningful observations through the unification of the perspectives afforded by each technology. In most cases, however, profiling technologies consume the used cells and thus pairwise correspondences between datasets are lost. Due to the sheer size single-cell datasets can acquire, scalable algorithms that are able to universally match single-cell measurements carried out in one cell to its corresponding sibling in another technology are needed.\r\nResults: We propose Single-Cell data Integration via Matching (SCIM), a scalable approach to recover such correspondences in two or more technologies. SCIM assumes that cells share a common (low-dimensional) underlying structure and that the underlying cell distribution is approximately constant across technologies. It constructs a technology-invariant latent space using an autoencoder framework with an adversarial objective. Multi-modal datasets are integrated by pairing cells across technologies using a bipartite matching scheme that operates on the low-dimensional latent representations. We evaluate SCIM on a simulated cellular branching process and show that the cell-to-cell matches derived by SCIM reflect the same pseudotime on the simulated dataset. Moreover, we apply our method to two real-world scenarios, a melanoma tumor sample and a human bone marrow sample, where we pair cells from a scRNA dataset to their sibling cells in a CyTOF dataset achieving 90% and 78% cell-matching accuracy for each one of the samples, respectively." article_processing_charge: No article_type: original author: - first_name: Stefan G full_name: Stark, Stefan G last_name: Stark - first_name: Joanna full_name: Ficek, Joanna last_name: Ficek - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Ximena full_name: Bonilla, Ximena last_name: Bonilla - first_name: Stéphane full_name: Chevrier, Stéphane last_name: Chevrier - first_name: Franziska full_name: Singer, Franziska last_name: Singer - first_name: Rudolf full_name: Aebersold, Rudolf last_name: Aebersold - first_name: Faisal S full_name: Al-Quaddoomi, Faisal S last_name: Al-Quaddoomi - first_name: Jonas full_name: Albinus, Jonas last_name: Albinus - first_name: Ilaria full_name: Alborelli, Ilaria last_name: Alborelli - first_name: Sonali full_name: Andani, Sonali last_name: Andani - first_name: Per-Olof full_name: Attinger, Per-Olof last_name: Attinger - first_name: Marina full_name: Bacac, Marina last_name: Bacac - first_name: Daniel full_name: Baumhoer, Daniel last_name: Baumhoer - first_name: Beatrice full_name: Beck-Schimmer, Beatrice last_name: Beck-Schimmer - first_name: Niko full_name: Beerenwinkel, Niko last_name: Beerenwinkel - first_name: Christian full_name: Beisel, Christian last_name: Beisel - first_name: Lara full_name: Bernasconi, Lara last_name: Bernasconi - first_name: Anne full_name: Bertolini, Anne last_name: Bertolini - first_name: Bernd full_name: Bodenmiller, Bernd last_name: Bodenmiller - first_name: Ximena full_name: Bonilla, Ximena last_name: Bonilla - first_name: Ruben full_name: Casanova, Ruben last_name: Casanova - first_name: Stéphane full_name: Chevrier, Stéphane last_name: Chevrier - first_name: Natalia full_name: Chicherova, Natalia last_name: Chicherova - first_name: Maya full_name: D'Costa, Maya last_name: D'Costa - first_name: Esther full_name: Danenberg, Esther last_name: Danenberg - first_name: Natalie full_name: Davidson, Natalie last_name: Davidson - first_name: Monica-Andreea Dră full_name: gan, Monica-Andreea Dră last_name: gan - first_name: Reinhard full_name: Dummer, Reinhard last_name: Dummer - first_name: Stefanie full_name: Engler, Stefanie last_name: Engler - first_name: Martin full_name: Erkens, Martin last_name: Erkens - first_name: Katja full_name: Eschbach, Katja last_name: Eschbach - first_name: Cinzia full_name: Esposito, Cinzia last_name: Esposito - first_name: André full_name: Fedier, André last_name: Fedier - first_name: Pedro full_name: Ferreira, Pedro last_name: Ferreira - first_name: Joanna full_name: Ficek, Joanna last_name: Ficek - first_name: Anja L full_name: Frei, Anja L last_name: Frei - first_name: Bruno full_name: Frey, Bruno last_name: Frey - first_name: Sandra full_name: Goetze, Sandra last_name: Goetze - first_name: Linda full_name: Grob, Linda last_name: Grob - first_name: Gabriele full_name: Gut, Gabriele last_name: Gut - first_name: Detlef full_name: Günther, Detlef last_name: Günther - first_name: Martina full_name: Haberecker, Martina last_name: Haberecker - first_name: Pirmin full_name: Haeuptle, Pirmin last_name: Haeuptle - first_name: Viola full_name: Heinzelmann-Schwarz, Viola last_name: Heinzelmann-Schwarz - first_name: Sylvia full_name: Herter, Sylvia last_name: Herter - first_name: Rene full_name: Holtackers, Rene last_name: Holtackers - first_name: Tamara full_name: Huesser, Tamara last_name: Huesser - first_name: Anja full_name: Irmisch, Anja last_name: Irmisch - first_name: Francis full_name: Jacob, Francis last_name: Jacob - first_name: Andrea full_name: Jacobs, Andrea last_name: Jacobs - first_name: Tim M full_name: Jaeger, Tim M last_name: Jaeger - first_name: Katharina full_name: Jahn, Katharina last_name: Jahn - first_name: Alva R full_name: James, Alva R last_name: James - first_name: Philip M full_name: Jermann, Philip M last_name: Jermann - first_name: André full_name: Kahles, André last_name: Kahles - first_name: Abdullah full_name: Kahraman, Abdullah last_name: Kahraman - first_name: Viktor H full_name: Koelzer, Viktor H last_name: Koelzer - first_name: Werner full_name: Kuebler, Werner last_name: Kuebler - first_name: Jack full_name: Kuipers, Jack last_name: Kuipers - first_name: Christian P full_name: Kunze, Christian P last_name: Kunze - first_name: Christian full_name: Kurzeder, Christian last_name: Kurzeder - first_name: Kjong-Van full_name: Lehmann, Kjong-Van last_name: Lehmann - first_name: Mitchell full_name: Levesque, Mitchell last_name: Levesque - first_name: Sebastian full_name: Lugert, Sebastian last_name: Lugert - first_name: Gerd full_name: Maass, Gerd last_name: Maass - first_name: Markus full_name: Manz, Markus last_name: Manz - first_name: Philipp full_name: Markolin, Philipp last_name: Markolin - first_name: Julien full_name: Mena, Julien last_name: Mena - first_name: Ulrike full_name: Menzel, Ulrike last_name: Menzel - first_name: Julian M full_name: Metzler, Julian M last_name: Metzler - first_name: Nicola full_name: Miglino, Nicola last_name: Miglino - first_name: Emanuela S full_name: Milani, Emanuela S last_name: Milani - first_name: Holger full_name: Moch, Holger last_name: Moch - first_name: Simone full_name: Muenst, Simone last_name: Muenst - first_name: Riccardo full_name: Murri, Riccardo last_name: Murri - first_name: Charlotte KY full_name: Ng, Charlotte KY last_name: Ng - first_name: Stefan full_name: Nicolet, Stefan last_name: Nicolet - first_name: Marta full_name: Nowak, Marta last_name: Nowak - first_name: Patrick GA full_name: Pedrioli, Patrick GA last_name: Pedrioli - first_name: Lucas full_name: Pelkmans, Lucas last_name: Pelkmans - first_name: Salvatore full_name: Piscuoglio, Salvatore last_name: Piscuoglio - first_name: Michael full_name: Prummer, Michael last_name: Prummer - first_name: Mathilde full_name: Ritter, Mathilde last_name: Ritter - first_name: Christian full_name: Rommel, Christian last_name: Rommel - first_name: María L full_name: Rosano-González, María L last_name: Rosano-González - first_name: Gunnar full_name: Rätsch, Gunnar last_name: Rätsch - first_name: Natascha full_name: Santacroce, Natascha last_name: Santacroce - first_name: Jacobo Sarabia del full_name: Castillo, Jacobo Sarabia del last_name: Castillo - first_name: Ramona full_name: Schlenker, Ramona last_name: Schlenker - first_name: Petra C full_name: Schwalie, Petra C last_name: Schwalie - first_name: Severin full_name: Schwan, Severin last_name: Schwan - first_name: Tobias full_name: Schär, Tobias last_name: Schär - first_name: Gabriela full_name: Senti, Gabriela last_name: Senti - first_name: Franziska full_name: Singer, Franziska last_name: Singer - first_name: Sujana full_name: Sivapatham, Sujana last_name: Sivapatham - first_name: Berend full_name: Snijder, Berend last_name: Snijder - first_name: Bettina full_name: Sobottka, Bettina last_name: Sobottka - first_name: Vipin T full_name: Sreedharan, Vipin T last_name: Sreedharan - first_name: Stefan full_name: Stark, Stefan last_name: Stark - first_name: Daniel J full_name: Stekhoven, Daniel J last_name: Stekhoven - first_name: Alexandre PA full_name: Theocharides, Alexandre PA last_name: Theocharides - first_name: Tinu M full_name: Thomas, Tinu M last_name: Thomas - first_name: Markus full_name: Tolnay, Markus last_name: Tolnay - first_name: Vinko full_name: Tosevski, Vinko last_name: Tosevski - first_name: Nora C full_name: Toussaint, Nora C last_name: Toussaint - first_name: Mustafa A full_name: Tuncel, Mustafa A last_name: Tuncel - first_name: Marina full_name: Tusup, Marina last_name: Tusup - first_name: Audrey Van full_name: Drogen, Audrey Van last_name: Drogen - first_name: Marcus full_name: Vetter, Marcus last_name: Vetter - first_name: Tatjana full_name: Vlajnic, Tatjana last_name: Vlajnic - first_name: Sandra full_name: Weber, Sandra last_name: Weber - first_name: Walter P full_name: Weber, Walter P last_name: Weber - first_name: Rebekka full_name: Wegmann, Rebekka last_name: Wegmann - first_name: Michael full_name: Weller, Michael last_name: Weller - first_name: Fabian full_name: Wendt, Fabian last_name: Wendt - first_name: Norbert full_name: Wey, Norbert last_name: Wey - first_name: Andreas full_name: Wicki, Andreas last_name: Wicki - first_name: Bernd full_name: Wollscheid, Bernd last_name: Wollscheid - first_name: Shuqing full_name: Yu, Shuqing last_name: Yu - first_name: Johanna full_name: Ziegler, Johanna last_name: Ziegler - first_name: Marc full_name: Zimmermann, Marc last_name: Zimmermann - first_name: Martin full_name: Zoche, Martin last_name: Zoche - first_name: Gregor full_name: Zuend, Gregor last_name: Zuend - first_name: Gunnar full_name: Rätsch, Gunnar last_name: Rätsch - first_name: Kjong-Van full_name: Lehmann, Kjong-Van last_name: Lehmann citation: ama: 'Stark SG, Ficek J, Locatello F, et al. SCIM: Universal single-cell matching with unpaired feature sets. Bioinformatics. 2020;36(Supplement_2):i919-i927. doi:10.1093/bioinformatics/btaa843' apa: 'Stark, S. G., Ficek, J., Locatello, F., Bonilla, X., Chevrier, S., Singer, F., … Lehmann, K.-V. (2020). SCIM: Universal single-cell matching with unpaired feature sets. Bioinformatics. Oxford University Press. https://doi.org/10.1093/bioinformatics/btaa843' chicago: 'Stark, Stefan G, Joanna Ficek, Francesco Locatello, Ximena Bonilla, Stéphane Chevrier, Franziska Singer, Rudolf Aebersold, et al. “SCIM: Universal Single-Cell Matching with Unpaired Feature Sets.” Bioinformatics. Oxford University Press, 2020. https://doi.org/10.1093/bioinformatics/btaa843.' ieee: 'S. G. Stark et al., “SCIM: Universal single-cell matching with unpaired feature sets,” Bioinformatics, vol. 36, no. Supplement_2. Oxford University Press, pp. i919–i927, 2020.' ista: 'Stark SG et al. 2020. SCIM: Universal single-cell matching with unpaired feature sets. Bioinformatics. 36(Supplement_2), i919–i927.' mla: 'Stark, Stefan G., et al. “SCIM: Universal Single-Cell Matching with Unpaired Feature Sets.” Bioinformatics, vol. 36, no. Supplement_2, Oxford University Press, 2020, pp. i919–27, doi:10.1093/bioinformatics/btaa843.' short: S.G. Stark, J. Ficek, F. Locatello, X. Bonilla, S. Chevrier, F. Singer, R. Aebersold, F.S. Al-Quaddoomi, J. Albinus, I. Alborelli, S. Andani, P.-O. Attinger, M. Bacac, D. Baumhoer, B. Beck-Schimmer, N. Beerenwinkel, C. Beisel, L. Bernasconi, A. Bertolini, B. Bodenmiller, X. Bonilla, R. Casanova, S. Chevrier, N. Chicherova, M. D’Costa, E. Danenberg, N. Davidson, M.-A.D. gan, R. Dummer, S. Engler, M. Erkens, K. Eschbach, C. Esposito, A. Fedier, P. Ferreira, J. Ficek, A.L. Frei, B. Frey, S. Goetze, L. Grob, G. Gut, D. Günther, M. Haberecker, P. Haeuptle, V. Heinzelmann-Schwarz, S. Herter, R. Holtackers, T. Huesser, A. Irmisch, F. Jacob, A. Jacobs, T.M. Jaeger, K. Jahn, A.R. James, P.M. Jermann, A. Kahles, A. Kahraman, V.H. Koelzer, W. Kuebler, J. Kuipers, C.P. Kunze, C. Kurzeder, K.-V. Lehmann, M. Levesque, S. Lugert, G. Maass, M. Manz, P. Markolin, J. Mena, U. Menzel, J.M. Metzler, N. Miglino, E.S. Milani, H. Moch, S. Muenst, R. Murri, C.K. Ng, S. Nicolet, M. Nowak, P.G. Pedrioli, L. Pelkmans, S. Piscuoglio, M. Prummer, M. Ritter, C. Rommel, M.L. Rosano-González, G. Rätsch, N. Santacroce, J.S. del Castillo, R. Schlenker, P.C. Schwalie, S. Schwan, T. Schär, G. Senti, F. Singer, S. Sivapatham, B. Snijder, B. Sobottka, V.T. Sreedharan, S. Stark, D.J. Stekhoven, A.P. Theocharides, T.M. Thomas, M. Tolnay, V. Tosevski, N.C. Toussaint, M.A. Tuncel, M. Tusup, A.V. Drogen, M. Vetter, T. Vlajnic, S. Weber, W.P. Weber, R. Wegmann, M. Weller, F. Wendt, N. Wey, A. Wicki, B. Wollscheid, S. Yu, J. Ziegler, M. Zimmermann, M. Zoche, G. Zuend, G. Rätsch, K.-V. Lehmann, Bioinformatics 36 (2020) i919–i927. date_created: 2023-08-21T12:28:20Z date_published: 2020-12-01T00:00:00Z date_updated: 2023-09-11T10:21:00Z day: '01' department: - _id: FrLo doi: 10.1093/bioinformatics/btaa843 extern: '1' external_id: pmid: - '33381818' intvolume: ' 36' issue: Supplement_2 keyword: - Computational Mathematics - Computational Theory and Mathematics - Computer Science Applications - Molecular Biology - Biochemistry - Statistics and Probability language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1093/bioinformatics/btaa843 month: '12' oa: 1 oa_version: Published Version page: i919-i927 pmid: 1 publication: Bioinformatics publication_identifier: eissn: - 1367-4811 publication_status: published publisher: Oxford University Press quality_controlled: '1' related_material: link: - relation: software url: https://github.com/ratschlab/scim scopus_import: '1' status: public title: 'SCIM: Universal single-cell matching with unpaired feature sets' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 36 year: '2020' ... --- _id: '14186' abstract: - lang: eng text: "The goal of the unsupervised learning of disentangled representations is to\r\nseparate the independent explanatory factors of variation in the data without\r\naccess to supervision. In this paper, we summarize the results of Locatello et\r\nal., 2019, and focus on their implications for practitioners. We discuss the\r\ntheoretical result showing that the unsupervised learning of disentangled\r\nrepresentations is fundamentally impossible without inductive biases and the\r\npractical challenges it entails. Finally, we comment on our experimental\r\nfindings, highlighting the limitations of state-of-the-art approaches and\r\ndirections for future research." article_processing_charge: No author: - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Stefan full_name: Bauer, Stefan last_name: Bauer - first_name: Mario full_name: Lucic, Mario last_name: Lucic - first_name: Gunnar full_name: Rätsch, Gunnar last_name: Rätsch - first_name: Sylvain full_name: Gelly, Sylvain last_name: Gelly - first_name: Bernhard full_name: Schölkopf, Bernhard last_name: Schölkopf - first_name: Olivier full_name: Bachem, Olivier last_name: Bachem citation: ama: 'Locatello F, Bauer S, Lucic M, et al. A commentary on the unsupervised learning of disentangled representations. In: The 34th AAAI Conference on Artificial Intelligence. Vol 34. Association for the Advancement of Artificial Intelligence; 2020:13681-13684. doi:10.1609/aaai.v34i09.7120' apa: 'Locatello, F., Bauer, S., Lucic, M., Rätsch, G., Gelly, S., Schölkopf, B., & Bachem, O. (2020). A commentary on the unsupervised learning of disentangled representations. In The 34th AAAI Conference on Artificial Intelligence (Vol. 34, pp. 13681–13684). New York, NY, United States: Association for the Advancement of Artificial Intelligence. https://doi.org/10.1609/aaai.v34i09.7120' chicago: Locatello, Francesco, Stefan Bauer, Mario Lucic, Gunnar Rätsch, Sylvain Gelly, Bernhard Schölkopf, and Olivier Bachem. “A Commentary on the Unsupervised Learning of Disentangled Representations.” In The 34th AAAI Conference on Artificial Intelligence, 34:13681–84. Association for the Advancement of Artificial Intelligence, 2020. https://doi.org/10.1609/aaai.v34i09.7120. ieee: F. Locatello et al., “A commentary on the unsupervised learning of disentangled representations,” in The 34th AAAI Conference on Artificial Intelligence, New York, NY, United States, 2020, vol. 34, no. 9, pp. 13681–13684. ista: 'Locatello F, Bauer S, Lucic M, Rätsch G, Gelly S, Schölkopf B, Bachem O. 2020. A commentary on the unsupervised learning of disentangled representations. The 34th AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence vol. 34, 13681–13684.' mla: Locatello, Francesco, et al. “A Commentary on the Unsupervised Learning of Disentangled Representations.” The 34th AAAI Conference on Artificial Intelligence, vol. 34, no. 9, Association for the Advancement of Artificial Intelligence, 2020, pp. 13681–84, doi:10.1609/aaai.v34i09.7120. short: F. Locatello, S. Bauer, M. Lucic, G. Rätsch, S. Gelly, B. Schölkopf, O. Bachem, in:, The 34th AAAI Conference on Artificial Intelligence, Association for the Advancement of Artificial Intelligence, 2020, pp. 13681–13684. conference: end_date: 2020-02-12 location: New York, NY, United States name: 'AAAI: Conference on Artificial Intelligence' start_date: 2020-02-07 date_created: 2023-08-22T14:07:26Z date_published: 2020-07-28T00:00:00Z date_updated: 2023-09-12T07:44:48Z day: '28' department: - _id: FrLo doi: 10.1609/aaai.v34i09.7120 extern: '1' external_id: arxiv: - '2007.14184' intvolume: ' 34' issue: '9' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2007.14184 month: '07' oa: 1 oa_version: Preprint page: 13681-13684 publication: The 34th AAAI Conference on Artificial Intelligence publication_identifier: eissn: - 2374-3468 isbn: - '9781577358350' publication_status: published publisher: Association for the Advancement of Artificial Intelligence quality_controlled: '1' scopus_import: '1' status: public title: A commentary on the unsupervised learning of disentangled representations type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 34 year: '2020' ... --- _id: '14188' abstract: - lang: eng text: "Intelligent agents should be able to learn useful representations by\r\nobserving changes in their environment. We model such observations as pairs of\r\nnon-i.i.d. images sharing at least one of the underlying factors of variation.\r\nFirst, we theoretically show that only knowing how many factors have changed,\r\nbut not which ones, is sufficient to learn disentangled representations.\r\nSecond, we provide practical algorithms that learn disentangled representations\r\nfrom pairs of images without requiring annotation of groups, individual\r\nfactors, or the number of factors that have changed. Third, we perform a\r\nlarge-scale empirical study and show that such pairs of observations are\r\nsufficient to reliably learn disentangled representations on several benchmark\r\ndata sets. Finally, we evaluate our learned representations and find that they\r\nare simultaneously useful on a diverse suite of tasks, including generalization\r\nunder covariate shifts, fairness, and abstract reasoning. Overall, our results\r\ndemonstrate that weak supervision enables learning of useful disentangled\r\nrepresentations in realistic scenarios." alternative_title: - PMLR article_processing_charge: No author: - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Ben full_name: Poole, Ben last_name: Poole - first_name: Gunnar full_name: Rätsch, Gunnar last_name: Rätsch - first_name: Bernhard full_name: Schölkopf, Bernhard last_name: Schölkopf - first_name: Olivier full_name: Bachem, Olivier last_name: Bachem - first_name: Michael full_name: Tschannen, Michael last_name: Tschannen citation: ama: 'Locatello F, Poole B, Rätsch G, Schölkopf B, Bachem O, Tschannen M. Weakly-supervised disentanglement without compromises. In: Proceedings of the 37th International Conference on Machine Learning. Vol 119. ; 2020:6348–6359.' apa: Locatello, F., Poole, B., Rätsch, G., Schölkopf, B., Bachem, O., & Tschannen, M. (2020). Weakly-supervised disentanglement without compromises. In Proceedings of the 37th International Conference on Machine Learning (Vol. 119, pp. 6348–6359). Virtual. chicago: Locatello, Francesco, Ben Poole, Gunnar Rätsch, Bernhard Schölkopf, Olivier Bachem, and Michael Tschannen. “Weakly-Supervised Disentanglement without Compromises.” In Proceedings of the 37th International Conference on Machine Learning, 119:6348–6359, 2020. ieee: F. Locatello, B. Poole, G. Rätsch, B. Schölkopf, O. Bachem, and M. Tschannen, “Weakly-supervised disentanglement without compromises,” in Proceedings of the 37th International Conference on Machine Learning, Virtual, 2020, vol. 119, pp. 6348–6359. ista: Locatello F, Poole B, Rätsch G, Schölkopf B, Bachem O, Tschannen M. 2020. Weakly-supervised disentanglement without compromises. Proceedings of the 37th International Conference on Machine Learning. International Conference on Machine Learning, PMLR, vol. 119, 6348–6359. mla: Locatello, Francesco, et al. “Weakly-Supervised Disentanglement without Compromises.” Proceedings of the 37th International Conference on Machine Learning, vol. 119, 2020, pp. 6348–6359. short: F. Locatello, B. Poole, G. Rätsch, B. Schölkopf, O. Bachem, M. Tschannen, in:, Proceedings of the 37th International Conference on Machine Learning, 2020, pp. 6348–6359. conference: end_date: 2020-07-18 location: Virtual name: International Conference on Machine Learning start_date: 2020-07-13 date_created: 2023-08-22T14:08:14Z date_published: 2020-07-07T00:00:00Z date_updated: 2023-09-12T07:59:29Z day: '07' department: - _id: FrLo extern: '1' external_id: arxiv: - '2002.02886' intvolume: ' 119' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2002.02886 month: '07' oa: 1 oa_version: Preprint page: 6348–6359 publication: Proceedings of the 37th International Conference on Machine Learning publication_status: published quality_controlled: '1' scopus_import: '1' status: public title: Weakly-supervised disentanglement without compromises type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 119 year: '2020' ... --- _id: '14187' abstract: - lang: eng text: "We propose a novel Stochastic Frank-Wolfe (a.k.a. conditional gradient)\r\nalgorithm for constrained smooth finite-sum minimization with a generalized\r\nlinear prediction/structure. This class of problems includes empirical risk\r\nminimization with sparse, low-rank, or other structured constraints. The\r\nproposed method is simple to implement, does not require step-size tuning, and\r\nhas a constant per-iteration cost that is independent of the dataset size.\r\nFurthermore, as a byproduct of the method we obtain a stochastic estimator of\r\nthe Frank-Wolfe gap that can be used as a stopping criterion. Depending on the\r\nsetting, the proposed method matches or improves on the best computational\r\nguarantees for Stochastic Frank-Wolfe algorithms. Benchmarks on several\r\ndatasets highlight different regimes in which the proposed method exhibits a\r\nfaster empirical convergence than related methods. Finally, we provide an\r\nimplementation of all considered methods in an open-source package." alternative_title: - PMLR article_processing_charge: No author: - first_name: Geoffrey full_name: Négiar, Geoffrey last_name: Négiar - first_name: Gideon full_name: Dresdner, Gideon last_name: Dresdner - first_name: Alicia full_name: Tsai, Alicia last_name: Tsai - first_name: Laurent El full_name: Ghaoui, Laurent El last_name: Ghaoui - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Robert M. full_name: Freund, Robert M. last_name: Freund - first_name: Fabian full_name: Pedregosa, Fabian last_name: Pedregosa citation: ama: 'Négiar G, Dresdner G, Tsai A, et al. Stochastic Frank-Wolfe for constrained finite-sum minimization. In: Proceedings of the 37th International Conference on Machine Learning. Vol 119. ; 2020:7253-7262.' apa: Négiar, G., Dresdner, G., Tsai, A., Ghaoui, L. E., Locatello, F., Freund, R. M., & Pedregosa, F. (2020). Stochastic Frank-Wolfe for constrained finite-sum minimization. In Proceedings of the 37th International Conference on Machine Learning (Vol. 119, pp. 7253–7262). Virtual. chicago: Négiar, Geoffrey, Gideon Dresdner, Alicia Tsai, Laurent El Ghaoui, Francesco Locatello, Robert M. Freund, and Fabian Pedregosa. “Stochastic Frank-Wolfe for Constrained Finite-Sum Minimization.” In Proceedings of the 37th International Conference on Machine Learning, 119:7253–62, 2020. ieee: G. Négiar et al., “Stochastic Frank-Wolfe for constrained finite-sum minimization,” in Proceedings of the 37th International Conference on Machine Learning, Virtual, 2020, vol. 119, pp. 7253–7262. ista: Négiar G, Dresdner G, Tsai A, Ghaoui LE, Locatello F, Freund RM, Pedregosa F. 2020. Stochastic Frank-Wolfe for constrained finite-sum minimization. Proceedings of the 37th International Conference on Machine Learning. International Conference on Machine Learning, PMLR, vol. 119, 7253–7262. mla: Négiar, Geoffrey, et al. “Stochastic Frank-Wolfe for Constrained Finite-Sum Minimization.” Proceedings of the 37th International Conference on Machine Learning, vol. 119, 2020, pp. 7253–62. short: G. Négiar, G. Dresdner, A. Tsai, L.E. Ghaoui, F. Locatello, R.M. Freund, F. Pedregosa, in:, Proceedings of the 37th International Conference on Machine Learning, 2020, pp. 7253–7262. conference: end_date: 2020-07-18 location: Virtual name: International Conference on Machine Learning start_date: 2020-07-13 date_created: 2023-08-22T14:07:52Z date_published: 2020-07-27T00:00:00Z date_updated: 2023-09-12T08:03:40Z day: '27' department: - _id: FrLo extern: '1' external_id: arxiv: - '2002.11860' intvolume: ' 119' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2002.11860 month: '07' oa: 1 oa_version: Preprint page: 7253-7262 publication: Proceedings of the 37th International Conference on Machine Learning publication_status: published quality_controlled: '1' status: public title: Stochastic Frank-Wolfe for constrained finite-sum minimization type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 119 year: '2020' ... --- _id: '14195' abstract: - lang: eng text: "The idea behind the unsupervised learning of disentangled representations is that real-world data is generated by a few explanatory factors of variation which can be recovered by unsupervised learning algorithms. In this paper, we provide a sober look at recent progress in the field and challenge some common assumptions. We first theoretically show that the unsupervised learning of disentangled representations is fundamentally impossible without inductive biases on both the models and the data. Then, we train over 14000\r\n models covering most prominent methods and evaluation metrics in a reproducible large-scale experimental study on eight data sets. We observe that while the different methods successfully enforce properties “encouraged” by the corresponding losses, well-disentangled models seemingly cannot be identified without supervision. Furthermore, different evaluation metrics do not always agree on what should be considered “disentangled” and exhibit systematic differences in the estimation. Finally, increased disentanglement does not seem to necessarily lead to a decreased sample complexity of learning for downstream tasks. Our results suggest that future work on disentanglement learning should be explicit about the role of inductive biases and (implicit) supervision, investigate concrete benefits of enforcing disentanglement of the learned representations, and consider a reproducible experimental setup covering several data sets." article_number: '209' article_processing_charge: No article_type: original author: - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Stefan full_name: Bauer, Stefan last_name: Bauer - first_name: Mario full_name: Lucic, Mario last_name: Lucic - first_name: Gunnar full_name: Rätsch, Gunnar last_name: Rätsch - first_name: Sylvain full_name: Gelly, Sylvain last_name: Gelly - first_name: Bernhard full_name: Schölkopf, Bernhard last_name: Schölkopf - first_name: Olivier full_name: Bachem, Olivier last_name: Bachem citation: ama: Locatello F, Bauer S, Lucic M, et al. A sober look at the unsupervised learning of disentangled representations and their evaluation. Journal of Machine Learning Research. 2020;21. apa: Locatello, F., Bauer, S., Lucic, M., Rätsch, G., Gelly, S., Schölkopf, B., & Bachem, O. (2020). A sober look at the unsupervised learning of disentangled representations and their evaluation. Journal of Machine Learning Research. MIT Press. chicago: Locatello, Francesco, Stefan Bauer, Mario Lucic, Gunnar Rätsch, Sylvain Gelly, Bernhard Schölkopf, and Olivier Bachem. “A Sober Look at the Unsupervised Learning of Disentangled Representations and Their Evaluation.” Journal of Machine Learning Research. MIT Press, 2020. ieee: F. Locatello et al., “A sober look at the unsupervised learning of disentangled representations and their evaluation,” Journal of Machine Learning Research, vol. 21. MIT Press, 2020. ista: Locatello F, Bauer S, Lucic M, Rätsch G, Gelly S, Schölkopf B, Bachem O. 2020. A sober look at the unsupervised learning of disentangled representations and their evaluation. Journal of Machine Learning Research. 21, 209. mla: Locatello, Francesco, et al. “A Sober Look at the Unsupervised Learning of Disentangled Representations and Their Evaluation.” Journal of Machine Learning Research, vol. 21, 209, MIT Press, 2020. short: F. Locatello, S. Bauer, M. Lucic, G. Rätsch, S. Gelly, B. Schölkopf, O. Bachem, Journal of Machine Learning Research 21 (2020). date_created: 2023-08-22T14:10:34Z date_published: 2020-09-01T00:00:00Z date_updated: 2023-09-12T09:23:56Z day: '01' ddc: - '000' department: - _id: FrLo extern: '1' external_id: arxiv: - '2010.14766' has_accepted_license: '1' intvolume: ' 21' language: - iso: eng main_file_link: - open_access: '1' url: https://jmlr.csail.mit.edu/papers/v21/19-976.html month: '09' oa: 1 oa_version: Published Version publication: Journal of Machine Learning Research publication_status: published publisher: MIT Press quality_controlled: '1' scopus_import: '1' status: public title: A sober look at the unsupervised learning of disentangled representations and their evaluation tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 21 year: '2020' ... --- _id: '7569' abstract: - lang: eng text: 'Genes differ in the frequency at which they are expressed and in the form of regulation used to control their activity. In particular, positive or negative regulation can lead to activation of a gene in response to an external signal. Previous works proposed that the form of regulation of a gene correlates with its frequency of usage: positive regulation when the gene is frequently expressed and negative regulation when infrequently expressed. Such network design means that, in the absence of their regulators, the genes are found in their least required activity state, hence regulatory intervention is often necessary. Due to the multitude of genes and regulators, spurious binding and unbinding events, called “crosstalk”, could occur. To determine how the form of regulation affects the global crosstalk in the network, we used a mathematical model that includes multiple regulators and multiple target genes. We found that crosstalk depends non-monotonically on the availability of regulators. Our analysis showed that excess use of regulation entailed by the formerly suggested network design caused high crosstalk levels in a large part of the parameter space. We therefore considered the opposite ‘idle’ design, where the default unregulated state of genes is their frequently required activity state. We found, that ‘idle’ design minimized the use of regulation and thus minimized crosstalk. In addition, we estimated global crosstalk of S. cerevisiae using transcription factors binding data. We demonstrated that even partial network data could suffice to estimate its global crosstalk, suggesting its applicability to additional organisms. We found that S. cerevisiae estimated crosstalk is lower than that of a random network, suggesting that natural selection reduces crosstalk. In summary, our study highlights a new type of protein production cost which is typically overlooked: that of regulatory interference caused by the presence of excess regulators in the cell. It demonstrates the importance of whole-network descriptions, which could show effects missed by single-gene models.' article_number: e1007642 article_processing_charge: No article_type: original author: - first_name: Rok full_name: Grah, Rok id: 483E70DE-F248-11E8-B48F-1D18A9856A87 last_name: Grah orcid: 0000-0003-2539-3560 - first_name: Tamar full_name: Friedlander, Tamar last_name: Friedlander citation: ama: Grah R, Friedlander T. The relation between crosstalk and gene regulation form revisited. PLOS Computational Biology. 2020;16(2). doi:10.1371/journal.pcbi.1007642 apa: Grah, R., & Friedlander, T. (2020). The relation between crosstalk and gene regulation form revisited. PLOS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007642 chicago: Grah, Rok, and Tamar Friedlander. “The Relation between Crosstalk and Gene Regulation Form Revisited.” PLOS Computational Biology. Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642. ieee: R. Grah and T. Friedlander, “The relation between crosstalk and gene regulation form revisited,” PLOS Computational Biology, vol. 16, no. 2. Public Library of Science, 2020. ista: Grah R, Friedlander T. 2020. The relation between crosstalk and gene regulation form revisited. PLOS Computational Biology. 16(2), e1007642. mla: Grah, Rok, and Tamar Friedlander. “The Relation between Crosstalk and Gene Regulation Form Revisited.” PLOS Computational Biology, vol. 16, no. 2, e1007642, Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007642. short: R. Grah, T. Friedlander, PLOS Computational Biology 16 (2020). date_created: 2020-03-06T07:39:38Z date_published: 2020-02-25T00:00:00Z date_updated: 2023-09-12T11:02:24Z day: '25' ddc: - '000' - '570' department: - _id: CaGu - _id: GaTk doi: 10.1371/journal.pcbi.1007642 external_id: isi: - '000526725200019' file: - access_level: open_access checksum: 5239dd134dc6e1c71fe7b3ce2953da37 content_type: application/pdf creator: dernst date_created: 2020-03-09T15:12:21Z date_updated: 2020-07-14T12:48:00Z file_id: '7579' file_name: 2020_PlosCompBio_Grah.pdf file_size: 2209325 relation: main_file file_date_updated: 2020-07-14T12:48:00Z has_accepted_license: '1' intvolume: ' 16' isi: 1 issue: '2' language: - iso: eng month: '02' oa: 1 oa_version: Published Version publication: PLOS Computational Biology publication_identifier: issn: - 1553-7358 publication_status: published publisher: Public Library of Science quality_controlled: '1' related_material: record: - id: '9716' relation: research_data status: deleted - id: '9776' relation: research_data status: public - id: '9779' relation: used_in_publication status: public - id: '8155' relation: dissertation_contains status: public - id: '9777' relation: research_data status: public scopus_import: '1' status: public title: The relation between crosstalk and gene regulation form revisited tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 16 year: '2020' ... --- _id: '8813' abstract: - lang: eng text: 'In mammals, chromatin marks at imprinted genes are asymmetrically inherited to control parentally-biased gene expression. This control is thought predominantly to involve parent-specific differentially methylated regions (DMR) in genomic DNA. However, neither parent-of-origin-specific transcription nor DMRs have been comprehensively mapped. We here address this by integrating transcriptomic and epigenomic approaches in mouse preimplantation embryos (blastocysts). Transcriptome-analysis identified 71 genes expressed with previously unknown parent-of-origin-specific expression in blastocysts (nBiX: novel blastocyst-imprinted expression). Uniparental expression of nBiX genes disappeared soon after implantation. Micro-whole-genome bisulfite sequencing (μWGBS) of individual uniparental blastocysts detected 859 DMRs. Only 18% of nBiXs were associated with a DMR, whereas 60% were associated with parentally-biased H3K27me3. This suggests a major role for Polycomb-mediated imprinting in blastocysts. Five nBiX-clusters contained at least one known imprinted gene, and five novel clusters contained exclusively nBiX-genes. These data suggest a complex program of stage-specific imprinting involving different tiers of regulation.' article_processing_charge: No author: - first_name: Laura full_name: Santini, Laura last_name: Santini - first_name: Florian full_name: Halbritter, Florian last_name: Halbritter - first_name: Fabian full_name: Titz-Teixeira, Fabian last_name: Titz-Teixeira - first_name: Toru full_name: Suzuki, Toru last_name: Suzuki - first_name: Maki full_name: Asami, Maki last_name: Asami - first_name: Julia full_name: Ramesmayer, Julia last_name: Ramesmayer - first_name: Xiaoyan full_name: Ma, Xiaoyan last_name: Ma - first_name: Andreas full_name: Lackner, Andreas last_name: Lackner - first_name: Nick full_name: Warr, Nick last_name: Warr - first_name: Florian full_name: Pauler, Florian id: 48EA0138-F248-11E8-B48F-1D18A9856A87 last_name: Pauler orcid: 0000-0002-7462-0048 - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Ernest full_name: Laue, Ernest last_name: Laue - first_name: Matthias full_name: Farlik, Matthias last_name: Farlik - first_name: Christoph full_name: Bock, Christoph last_name: Bock - first_name: Andreas full_name: Beyer, Andreas last_name: Beyer - first_name: Anthony C. F. full_name: Perry, Anthony C. F. last_name: Perry - first_name: Martin full_name: Leeb, Martin last_name: Leeb citation: ama: Santini L, Halbritter F, Titz-Teixeira F, et al. Novel imprints in mouse blastocysts are predominantly DNA methylation independent. bioRxiv. doi:10.1101/2020.11.03.366948 apa: Santini, L., Halbritter, F., Titz-Teixeira, F., Suzuki, T., Asami, M., Ramesmayer, J., … Leeb, M. (n.d.). Novel imprints in mouse blastocysts are predominantly DNA methylation independent. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.11.03.366948 chicago: Santini, Laura, Florian Halbritter, Fabian Titz-Teixeira, Toru Suzuki, Maki Asami, Julia Ramesmayer, Xiaoyan Ma, et al. “Novel Imprints in Mouse Blastocysts Are Predominantly DNA Methylation Independent.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2020.11.03.366948. ieee: L. Santini et al., “Novel imprints in mouse blastocysts are predominantly DNA methylation independent,” bioRxiv. Cold Spring Harbor Laboratory. ista: Santini L, Halbritter F, Titz-Teixeira F, Suzuki T, Asami M, Ramesmayer J, Ma X, Lackner A, Warr N, Pauler F, Hippenmeyer S, Laue E, Farlik M, Bock C, Beyer A, Perry ACF, Leeb M. Novel imprints in mouse blastocysts are predominantly DNA methylation independent. bioRxiv, 10.1101/2020.11.03.366948. mla: Santini, Laura, et al. “Novel Imprints in Mouse Blastocysts Are Predominantly DNA Methylation Independent.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2020.11.03.366948. short: L. Santini, F. Halbritter, F. Titz-Teixeira, T. Suzuki, M. Asami, J. Ramesmayer, X. Ma, A. Lackner, N. Warr, F. Pauler, S. Hippenmeyer, E. Laue, M. Farlik, C. Bock, A. Beyer, A.C.F. Perry, M. Leeb, BioRxiv (n.d.). date_created: 2020-11-26T07:17:19Z date_published: 2020-11-05T00:00:00Z date_updated: 2023-09-12T11:05:28Z day: '05' department: - _id: SiHi doi: 10.1101/2020.11.03.366948 external_id: pmid: - 'PPR234457 ' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2020.11.03.366948 month: '11' oa: 1 oa_version: Preprint pmid: 1 publication: bioRxiv publication_status: submitted publisher: Cold Spring Harbor Laboratory status: public title: Novel imprints in mouse blastocysts are predominantly DNA methylation independent type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '9777' article_processing_charge: No author: - first_name: Rok full_name: Grah, Rok id: 483E70DE-F248-11E8-B48F-1D18A9856A87 last_name: Grah orcid: 0000-0003-2539-3560 - first_name: Tamar full_name: Friedlander, Tamar last_name: Friedlander citation: ama: Grah R, Friedlander T. Maximizing crosstalk. 2020. doi:10.1371/journal.pcbi.1007642.s002 apa: Grah, R., & Friedlander, T. (2020). Maximizing crosstalk. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007642.s002 chicago: Grah, Rok, and Tamar Friedlander. “Maximizing Crosstalk.” Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642.s002. ieee: R. Grah and T. Friedlander, “Maximizing crosstalk.” Public Library of Science, 2020. ista: Grah R, Friedlander T. 2020. Maximizing crosstalk, Public Library of Science, 10.1371/journal.pcbi.1007642.s002. mla: Grah, Rok, and Tamar Friedlander. Maximizing Crosstalk. Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007642.s002. short: R. Grah, T. Friedlander, (2020). date_created: 2021-08-06T07:21:51Z date_published: 2020-02-25T00:00:00Z date_updated: 2023-09-12T11:02:25Z day: '25' department: - _id: GaTk doi: 10.1371/journal.pcbi.1007642.s002 main_file_link: - open_access: '1' url: https://doi.org/10.1371/journal.pcbi.1007642.s002 month: '02' oa: 1 oa_version: None publisher: Public Library of Science related_material: record: - id: '7569' relation: used_in_publication status: public status: public title: Maximizing crosstalk type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '8332' abstract: - lang: eng text: "Designing and verifying concurrent programs is a notoriously challenging, time consuming, and error prone task, even for experts. This is due to the sheer number of possible interleavings of a concurrent program, all of which have to be tracked and accounted for in a formal proof. Inventing an inductive invariant that captures all interleavings of a low-level implementation is theoretically possible, but practically intractable. We develop a refinement-based verification framework that provides mechanisms to simplify proof construction by decomposing the verification task into smaller subtasks.\r\n\r\nIn a first line of work, we present a foundation for refinement reasoning over structured concurrent programs. We introduce layered concurrent programs as a compact notation to represent multi-layer refinement proofs. A layered concurrent program specifies a sequence of connected concurrent programs, from most concrete to most abstract, such that common parts of different programs are written exactly once. Each program in this sequence is expressed as structured concurrent program, i.e., a program over (potentially recursive) procedures, imperative control flow, gated atomic actions, structured parallelism, and asynchronous concurrency. This is in contrast to existing refinement-based verifiers, which represent concurrent systems as flat transition relations. We present a powerful refinement proof rule that decomposes refinement checking over structured programs into modular verification conditions. Refinement checking is supported by a new form of modular, parameterized invariants, called yield invariants, and a linear permission system to enhance local reasoning.\r\n\r\nIn a second line of work, we present two new reduction-based program transformations that target asynchronous programs. These transformations reduce the number of interleavings that need to be considered, thus reducing the complexity of invariants. Synchronization simplifies the verification of asynchronous programs by introducing the fiction, for proof purposes, that asynchronous operations complete synchronously. Synchronization summarizes an asynchronous computation as immediate atomic effect. Inductive sequentialization establishes sequential reductions that captures every behavior of the original program up to reordering of coarse-grained commutative actions. A sequential reduction of a concurrent program is easy to reason about since it corresponds to a simple execution of the program in an idealized synchronous environment, where processes act in a fixed order and at the same speed.\r\n\r\nOur approach is implemented the CIVL verifier, which has been successfully used for the verification of several complex concurrent programs. In our methodology, the overall correctness of a program is established piecemeal by focusing on the invariant required for each refinement step separately. While the programmer does the creative work of specifying the chain of programs and the inductive invariant justifying each link in the chain, the tool automatically constructs the verification conditions underlying each refinement step." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Bernhard full_name: Kragl, Bernhard id: 320FC952-F248-11E8-B48F-1D18A9856A87 last_name: Kragl orcid: 0000-0001-7745-9117 citation: ama: 'Kragl B. Verifying concurrent programs: Refinement, synchronization, sequentialization. 2020. doi:10.15479/AT:ISTA:8332' apa: 'Kragl, B. (2020). Verifying concurrent programs: Refinement, synchronization, sequentialization. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8332' chicago: 'Kragl, Bernhard. “Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8332.' ieee: 'B. Kragl, “Verifying concurrent programs: Refinement, synchronization, sequentialization,” Institute of Science and Technology Austria, 2020.' ista: 'Kragl B. 2020. Verifying concurrent programs: Refinement, synchronization, sequentialization. Institute of Science and Technology Austria.' mla: 'Kragl, Bernhard. Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8332.' short: 'B. Kragl, Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization, Institute of Science and Technology Austria, 2020.' date_created: 2020-09-04T12:24:12Z date_published: 2020-09-03T00:00:00Z date_updated: 2023-09-13T08:45:08Z day: '03' ddc: - '000' degree_awarded: PhD department: - _id: ToHe doi: 10.15479/AT:ISTA:8332 file: - access_level: open_access checksum: 26fe261550f691280bda4c454bf015c7 content_type: application/pdf creator: bkragl date_created: 2020-09-04T12:17:47Z date_updated: 2020-09-04T12:17:47Z file_id: '8333' file_name: kragl-thesis.pdf file_size: 1348815 relation: main_file - access_level: closed checksum: b9694ce092b7c55557122adba8337ebc content_type: application/zip creator: bkragl date_created: 2020-09-04T13:00:17Z date_updated: 2020-09-04T13:00:17Z file_id: '8335' file_name: kragl-thesis.zip file_size: 372312 relation: source_file file_date_updated: 2020-09-04T13:00:17Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '120' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '133' relation: part_of_dissertation status: public - id: '8012' relation: part_of_dissertation status: public - id: '8195' relation: part_of_dissertation status: public - id: '160' relation: part_of_dissertation status: public status: public supervisor: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 title: 'Verifying concurrent programs: Refinement, synchronization, sequentialization' type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2020' ... --- _id: '14326' abstract: - lang: eng text: "Learning object-centric representations of complex scenes is a promising step towards enabling efficient abstract reasoning from low-level perceptual features. Yet, most deep learning approaches learn distributed representations that do not capture the compositional properties of natural scenes. In this paper, we present the Slot Attention module, an architectural component that interfaces with perceptual representations such as the output of a convolutional neural network and produces a set of task-dependent abstract representations which we call slots. These slots are exchangeable and can bind to any object in the input by specializing through a competitive procedure over multiple rounds of attention. We empirically demonstrate that Slot Attention can extract object-centric representations that enable generalization to unseen compositions when trained on unsupervised object discovery and supervised property prediction tasks.\r\n\r\n" article_processing_charge: No author: - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Dirk full_name: Weissenborn, Dirk last_name: Weissenborn - first_name: Thomas full_name: Unterthiner, Thomas last_name: Unterthiner - first_name: Aravindh full_name: Mahendran, Aravindh last_name: Mahendran - first_name: Georg full_name: Heigold, Georg last_name: Heigold - first_name: Jakob full_name: Uszkoreit, Jakob last_name: Uszkoreit - first_name: Alexey full_name: Dosovitskiy, Alexey last_name: Dosovitskiy - first_name: Thomas full_name: Kipf, Thomas last_name: Kipf citation: ama: 'Locatello F, Weissenborn D, Unterthiner T, et al. Object-centric learning with slot attention. In: Advances in Neural Information Processing Systems. Vol 33. Curran Associates; 2020:11525-11538.' apa: 'Locatello, F., Weissenborn, D., Unterthiner, T., Mahendran, A., Heigold, G., Uszkoreit, J., … Kipf, T. (2020). Object-centric learning with slot attention. In Advances in Neural Information Processing Systems (Vol. 33, pp. 11525–11538). Virtual: Curran Associates.' chicago: Locatello, Francesco, Dirk Weissenborn, Thomas Unterthiner, Aravindh Mahendran, Georg Heigold, Jakob Uszkoreit, Alexey Dosovitskiy, and Thomas Kipf. “Object-Centric Learning with Slot Attention.” In Advances in Neural Information Processing Systems, 33:11525–38. Curran Associates, 2020. ieee: F. Locatello et al., “Object-centric learning with slot attention,” in Advances in Neural Information Processing Systems, Virtual, 2020, vol. 33, pp. 11525–11538. ista: 'Locatello F, Weissenborn D, Unterthiner T, Mahendran A, Heigold G, Uszkoreit J, Dosovitskiy A, Kipf T. 2020. Object-centric learning with slot attention. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 33, 11525–11538.' mla: Locatello, Francesco, et al. “Object-Centric Learning with Slot Attention.” Advances in Neural Information Processing Systems, vol. 33, Curran Associates, 2020, pp. 11525–38. short: F. Locatello, D. Weissenborn, T. Unterthiner, A. Mahendran, G. Heigold, J. Uszkoreit, A. Dosovitskiy, T. Kipf, in:, Advances in Neural Information Processing Systems, Curran Associates, 2020, pp. 11525–11538. conference: end_date: 2020-12-12 location: Virtual name: 'NeurIPS: Neural Information Processing Systems' start_date: 2020-12-06 date_created: 2023-09-13T12:03:46Z date_published: 2020-01-01T00:00:00Z date_updated: 2023-09-13T12:19:19Z department: - _id: FrLo extern: '1' external_id: arxiv: - '2006.15055' intvolume: ' 33' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2006.15055 oa: 1 oa_version: Preprint page: 11525-11538 publication: Advances in Neural Information Processing Systems publication_identifier: isbn: - '9781713829546' publication_status: published publisher: Curran Associates quality_controlled: '1' status: public title: Object-centric learning with slot attention type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 33 year: '2020' ... --- _id: '71' abstract: - lang: eng text: "We consider dynamical transport metrics for probability measures on discretisations of a bounded convex domain in ℝd. These metrics are natural discrete counterparts to the Kantorovich metric \U0001D54E2, defined using a Benamou-Brenier type formula. Under mild assumptions we prove an asymptotic upper bound for the discrete transport metric Wt in terms of \U0001D54E2, as the size of the mesh T tends to 0. However, we show that the corresponding lower bound may fail in general, even on certain one-dimensional and symmetric two-dimensional meshes. In addition, we show that the asymptotic lower bound holds under an isotropy assumption on the mesh, which turns out to be essentially necessary. This assumption is satisfied, e.g., for tilings by convex regular polygons, and it implies Gromov-Hausdorff convergence of the transport metric." article_processing_charge: No article_type: original author: - first_name: Peter full_name: Gladbach, Peter last_name: Gladbach - first_name: Eva full_name: Kopfer, Eva last_name: Kopfer - first_name: Jan full_name: Maas, Jan id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 citation: ama: Gladbach P, Kopfer E, Maas J. Scaling limits of discrete optimal transport. SIAM Journal on Mathematical Analysis. 2020;52(3):2759-2802. doi:10.1137/19M1243440 apa: Gladbach, P., Kopfer, E., & Maas, J. (2020). Scaling limits of discrete optimal transport. SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/19M1243440 chicago: Gladbach, Peter, Eva Kopfer, and Jan Maas. “Scaling Limits of Discrete Optimal Transport.” SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics, 2020. https://doi.org/10.1137/19M1243440. ieee: P. Gladbach, E. Kopfer, and J. Maas, “Scaling limits of discrete optimal transport,” SIAM Journal on Mathematical Analysis, vol. 52, no. 3. Society for Industrial and Applied Mathematics, pp. 2759–2802, 2020. ista: Gladbach P, Kopfer E, Maas J. 2020. Scaling limits of discrete optimal transport. SIAM Journal on Mathematical Analysis. 52(3), 2759–2802. mla: Gladbach, Peter, et al. “Scaling Limits of Discrete Optimal Transport.” SIAM Journal on Mathematical Analysis, vol. 52, no. 3, Society for Industrial and Applied Mathematics, 2020, pp. 2759–802, doi:10.1137/19M1243440. short: P. Gladbach, E. Kopfer, J. Maas, SIAM Journal on Mathematical Analysis 52 (2020) 2759–2802. date_created: 2018-12-11T11:44:28Z date_published: 2020-10-01T00:00:00Z date_updated: 2023-09-18T08:13:15Z day: '01' department: - _id: JaMa doi: 10.1137/19M1243440 external_id: arxiv: - '1809.01092' isi: - '000546975100017' intvolume: ' 52' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1809.01092 month: '10' oa: 1 oa_version: Preprint page: 2759-2802 publication: SIAM Journal on Mathematical Analysis publication_identifier: eissn: - '10957154' issn: - '00361410' publication_status: published publisher: Society for Industrial and Applied Mathematics publist_id: '7983' quality_controlled: '1' scopus_import: '1' status: public title: Scaling limits of discrete optimal transport type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 52 year: '2020' ... --- _id: '5681' abstract: - lang: eng text: 'We introduce dynamically warping grids for adaptive liquid simulation. Our primary contributions are a strategy for dynamically deforming regular grids over the course of a simulation and a method for efficiently utilizing these deforming grids for liquid simulation. Prior work has shown that unstructured grids are very effective for adaptive fluid simulations. However, unstructured grids often lead to complicated implementations and a poor cache hit rate due to inconsistent memory access. Regular grids, on the other hand, provide a fast, fixed memory access pattern and straightforward implementation. Our method combines the advantages of both: we leverage the simplicity of regular grids while still achieving practical and controllable spatial adaptivity. We demonstrate that our method enables adaptive simulations that are fast, flexible, and robust to null-space issues. At the same time, our method is simple to implement and takes advantage of existing highly-tuned algorithms.' acknowledged_ssus: - _id: ScienComp acknowledgement: This work was partially supported by JSPS Grant-in-Aid forYoung Scientists (Start-up) 16H07410, the ERC StartingGrantsrealFlow(StG-2015-637014) andBigSplash(StG-2014-638176). This research was supported by the Scientific Ser-vice Units (SSU) of IST Austria through resources providedby Scientific Computing. We would like to express my grati-tude to Nobuyuki Umetani and Tomas Skrivan for insight-ful discussion. article_processing_charge: No article_type: original author: - first_name: Ibayashi full_name: Hikaru, Ibayashi last_name: Hikaru - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 - first_name: Nils full_name: Thuerey, Nils last_name: Thuerey - first_name: Takeo full_name: Igarashi, Takeo last_name: Igarashi - first_name: Ryoichi full_name: Ando, Ryoichi last_name: Ando citation: ama: Hikaru I, Wojtan C, Thuerey N, Igarashi T, Ando R. Simulating liquids on dynamically warping grids. IEEE Transactions on Visualization and Computer Graphics. 2020;26(6):2288-2302. doi:10.1109/TVCG.2018.2883628 apa: Hikaru, I., Wojtan, C., Thuerey, N., Igarashi, T., & Ando, R. (2020). Simulating liquids on dynamically warping grids. IEEE Transactions on Visualization and Computer Graphics. IEEE. https://doi.org/10.1109/TVCG.2018.2883628 chicago: Hikaru, Ibayashi, Chris Wojtan, Nils Thuerey, Takeo Igarashi, and Ryoichi Ando. “Simulating Liquids on Dynamically Warping Grids.” IEEE Transactions on Visualization and Computer Graphics. IEEE, 2020. https://doi.org/10.1109/TVCG.2018.2883628. ieee: I. Hikaru, C. Wojtan, N. Thuerey, T. Igarashi, and R. Ando, “Simulating liquids on dynamically warping grids,” IEEE Transactions on Visualization and Computer Graphics, vol. 26, no. 6. IEEE, pp. 2288–2302, 2020. ista: Hikaru I, Wojtan C, Thuerey N, Igarashi T, Ando R. 2020. Simulating liquids on dynamically warping grids. IEEE Transactions on Visualization and Computer Graphics. 26(6), 2288–2302. mla: Hikaru, Ibayashi, et al. “Simulating Liquids on Dynamically Warping Grids.” IEEE Transactions on Visualization and Computer Graphics, vol. 26, no. 6, IEEE, 2020, pp. 2288–302, doi:10.1109/TVCG.2018.2883628. short: I. Hikaru, C. Wojtan, N. Thuerey, T. Igarashi, R. Ando, IEEE Transactions on Visualization and Computer Graphics 26 (2020) 2288–2302. date_created: 2018-12-16T22:59:21Z date_published: 2020-06-01T00:00:00Z date_updated: 2023-09-18T09:30:01Z day: '01' ddc: - '006' department: - _id: ChWo doi: 10.1109/TVCG.2018.2883628 external_id: isi: - '000532295600014' pmid: - '30507534' file: - access_level: open_access checksum: 8d4c55443a0ee335bb5bb652de503042 content_type: application/pdf creator: wojtan date_created: 2020-10-08T08:34:53Z date_updated: 2020-10-08T08:34:53Z file_id: '8626' file_name: preprint.pdf file_size: 21910098 relation: main_file success: 1 file_date_updated: 2020-10-08T08:34:53Z has_accepted_license: '1' intvolume: ' 26' isi: 1 issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Submitted Version page: 2288-2302 pmid: 1 publication: IEEE Transactions on Visualization and Computer Graphics publication_identifier: eissn: - '19410506' issn: - '10772626' publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: '1' status: public title: Simulating liquids on dynamically warping grids type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 26 year: '2020' ... --- _id: '8958' abstract: - lang: eng text: "The oft-quoted dictum by Arthur Schawlow: ``A diatomic molecule has one atom too many'' has been disavowed. Inspired by the possibility to experimentally manipulate and enhance chemical reactivity in helium nanodroplets, we investigate the rotation of coupled cold molecules in the presence of a many-body environment.\r\nIn this thesis, we introduce new variational approaches to quantum impurities and apply them to the Fröhlich polaron - a quasiparticle formed out of an electron (or other point-like impurity) in a polar medium, and to the angulon - a quasiparticle formed out of a rotating molecule in a bosonic bath.\r\nWith this theoretical toolbox, we reveal the self-localization transition for the angulon quasiparticle. We show that, unlike for polarons, self-localization of angulons occurs at finite impurity-bath coupling already at the mean-field level. The transition is accompanied by the spherical-symmetry breaking of the angulon ground state and a discontinuity in the first derivative of the ground-state energy. Moreover, the type of symmetry breaking is dictated by the symmetry of the microscopic impurity-bath interaction, which leads to a number of distinct self-localized states. \r\nFor the system containing multiple impurities, by analogy with the bipolaron, we introduce the biangulon quasiparticle describing two rotating molecules that align with respect to each other due to the effective attractive interaction mediated by the excitations of the bath. We study this system from the strong-coupling regime to the weak molecule-bath interaction regime. We show that the molecules tend to have a strong alignment in the ground state, the biangulon shows shifted angulon instabilities and an additional spectral instability, where resonant angular momentum transfer between the molecules and the bath takes place. Finally, we introduce a diagonalization scheme that allows us to describe the transition from two separated angulons to a biangulon as a function of the distance between the two molecules." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Xiang full_name: Li, Xiang id: 4B7E523C-F248-11E8-B48F-1D18A9856A87 last_name: Li citation: ama: Li X. Rotation of coupled cold molecules in the presence of a many-body environment. 2020. doi:10.15479/AT:ISTA:8958 apa: Li, X. (2020). Rotation of coupled cold molecules in the presence of a many-body environment. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8958 chicago: Li, Xiang. “Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8958. ieee: X. Li, “Rotation of coupled cold molecules in the presence of a many-body environment,” Institute of Science and Technology Austria, 2020. ista: Li X. 2020. Rotation of coupled cold molecules in the presence of a many-body environment. Institute of Science and Technology Austria. mla: Li, Xiang. Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8958. short: X. Li, Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment, Institute of Science and Technology Austria, 2020. date_created: 2020-12-21T09:44:30Z date_published: 2020-12-21T00:00:00Z date_updated: 2023-09-20T11:30:58Z day: '21' ddc: - '539' degree_awarded: PhD department: - _id: MiLe doi: 10.15479/AT:ISTA:8958 ec_funded: 1 file: - access_level: open_access checksum: 3994c54a1241451d561db1d4f43bad30 content_type: application/pdf creator: xli date_created: 2020-12-22T10:55:56Z date_updated: 2020-12-22T10:55:56Z file_id: '8967' file_name: THESIS_Xiang_Li.pdf file_size: 3622305 relation: main_file success: 1 - access_level: closed checksum: 0954ecfc5554c05615c14de803341f00 content_type: application/x-zip-compressed creator: xli date_created: 2020-12-22T10:56:03Z date_updated: 2020-12-30T07:18:03Z file_id: '8968' file_name: THESIS_Xiang_Li.zip file_size: 4018859 relation: source_file file_date_updated: 2020-12-30T07:18:03Z has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: '125' project: - _id: 26031614-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29902 name: Quantum rotations in the presence of a many-body environment - _id: 2688CF98-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '801770' name: 'Angulon: physics and applications of a new quasiparticle' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '5886' relation: part_of_dissertation status: public - id: '8587' relation: part_of_dissertation status: public - id: '1120' relation: part_of_dissertation status: public status: public supervisor: - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 title: Rotation of coupled cold molecules in the presence of a many-body environment type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2020' ... --- _id: '8386' abstract: - lang: eng text: "Form versus function is a long-standing debate in various design-related fields, such as architecture as well as graphic and industrial design. A good design that balances form and function often requires considerable human effort and collaboration among experts from different professional fields. Computational design tools provide a new paradigm for designing functional objects. In computational design, form and function are represented as mathematical\r\nquantities, with the help of numerical and combinatorial algorithms, they can assist even novice users in designing versatile models that exhibit their desired functionality. This thesis presents three disparate research studies on the computational design of functional objects: The appearance of 3d print—we optimize the volumetric material distribution for faithfully replicating colored surface texture in 3d printing; the dynamic motion of mechanical structures—\r\nour design system helps the novice user to retarget various mechanical templates with different functionality to complex 3d shapes; and a more abstract functionality, multistability—our algorithm automatically generates models that exhibit multiple stable target poses. For each of these cases, our computational design tools not only ensure the functionality of the results but also permit the user aesthetic freedom over the form. Moreover, fabrication constraints\r\nwere taken into account, which allow for the immediate creation of physical realization via 3D printing or laser cutting." acknowledged_ssus: - _id: SSU acknowledgement: The research in this thesis has received funding from the European Union’s Horizon 2020 research and innovation programme, under the Marie Skłodowska-Curie grant agreement No 642841 (DISTRO) and the European Research Council grant agreement No 715767 (MATERIALIZABLE). All the research projects in this thesis were also supported by Scientific Service Units (SSUs) at IST Austria. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Ran full_name: Zhang, Ran id: 4DDBCEB0-F248-11E8-B48F-1D18A9856A87 last_name: Zhang orcid: 0000-0002-3808-281X citation: ama: Zhang R. Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability. 2020. doi:10.15479/AT:ISTA:8386 apa: Zhang, R. (2020). Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8386 chicago: Zhang, Ran. “Structure-Aware Computational Design and Its Application to 3D Printable Volume Scattering, Mechanism, and Multistability.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8386. ieee: R. Zhang, “Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability,” Institute of Science and Technology Austria, 2020. ista: Zhang R. 2020. Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability. Institute of Science and Technology Austria. mla: Zhang, Ran. Structure-Aware Computational Design and Its Application to 3D Printable Volume Scattering, Mechanism, and Multistability. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8386. short: R. Zhang, Structure-Aware Computational Design and Its Application to 3D Printable Volume Scattering, Mechanism, and Multistability, Institute of Science and Technology Austria, 2020. date_created: 2020-09-14T01:04:53Z date_published: 2020-09-14T00:00:00Z date_updated: 2023-09-22T09:49:31Z day: '14' ddc: - '003' degree_awarded: PhD department: - _id: BeBi doi: 10.15479/AT:ISTA:8386 ec_funded: 1 file: - access_level: closed checksum: edcf578b6e1c9b0dd81ff72d319b66ba content_type: application/x-zip-compressed creator: rzhang date_created: 2020-09-14T01:02:59Z date_updated: 2020-09-14T12:18:43Z file_id: '8388' file_name: Thesis_Ran.zip file_size: 1245800191 relation: source_file - access_level: open_access checksum: 817e20c33be9247f906925517c56a40d content_type: application/pdf creator: rzhang date_created: 2020-09-15T12:51:53Z date_updated: 2020-09-15T12:51:53Z file_id: '8396' file_name: PhD_thesis_Ran Zhang_20200915.pdf file_size: 161385316 relation: main_file success: 1 file_date_updated: 2020-09-15T12:51:53Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '148' project: - _id: 2508E324-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '642841' name: Distributed 3D Object Design - _id: 24F9549A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715767' name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '486' relation: part_of_dissertation status: public - id: '1002' relation: part_of_dissertation status: public status: public supervisor: - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 title: Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2020' ... --- _id: '7996' abstract: - lang: eng text: "Quantum computation enables the execution of algorithms that have exponential complexity. This might open the path towards the synthesis of new materials or medical drugs, optimization of transport or financial strategies etc., intractable on even the fastest classical computers. A quantum computer consists of interconnected two level quantum systems, called qubits, that satisfy DiVincezo’s criteria. Worldwide, there are ongoing efforts to find the qubit architecture which will unite quantum error correction compatible single and two qubit fidelities, long distance qubit to qubit coupling and \r\n calability. Superconducting qubits have gone the furthest in this race, demonstrating an algorithm running on 53 coupled qubits, but still the fidelities are not even close to those required for realizing a single logical qubit. emiconductor qubits offer extremely good characteristics, but they are currently investigated across different platforms. Uniting those good characteristics into a single platform might be a big step towards the quantum computer realization.\r\nHere we describe the implementation of a hole spin qubit hosted in a Ge hut wire double quantum dot. The high and tunable spin-orbit coupling together with a heavy hole state character is expected to allow fast spin manipulation and long coherence times. Furthermore large lever arms, for hut wire devices, should allow good coupling to superconducting resonators enabling efficient long distance spin to spin coupling and a sensitive gate reflectometry spin readout. The developed cryogenic setup (printed circuit board sample holders, filtering, high-frequency wiring) enabled us to perform low temperature spin dynamics experiments. Indeed, we measured the fastest single spin qubit Rabi frequencies reported so far, reaching 140 MHz, while the dephasing times of 130 ns oppose the long decoherence predictions. In order to further investigate this, a double quantum dot gate was connected directly to a lumped element\r\nresonator which enabled gate reflectometry readout. The vanishing inter-dot transition signal, for increasing external magnetic field, revealed the spin nature of the measured quantity." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Josip full_name: Kukucka, Josip id: 3F5D8856-F248-11E8-B48F-1D18A9856A87 last_name: Kukucka citation: ama: Kukucka J. Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing. 2020. doi:10.15479/AT:ISTA:7996 apa: Kukucka, J. (2020). Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7996 chicago: Kukucka, Josip. “Implementation of a Hole Spin Qubit in Ge Hut Wires and Dispersive Spin Sensing.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7996. ieee: J. Kukucka, “Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing,” Institute of Science and Technology Austria, 2020. ista: Kukucka J. 2020. Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing. Institute of Science and Technology Austria. mla: Kukucka, Josip. Implementation of a Hole Spin Qubit in Ge Hut Wires and Dispersive Spin Sensing. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7996. short: J. Kukucka, Implementation of a Hole Spin Qubit in Ge Hut Wires and Dispersive Spin Sensing, Institute of Science and Technology Austria, 2020. date_created: 2020-06-22T09:22:23Z date_published: 2020-06-22T00:00:00Z date_updated: 2023-09-26T15:50:22Z day: '22' ddc: - '530' degree_awarded: PhD department: - _id: GeKa doi: 10.15479/AT:ISTA:7996 file: - access_level: closed checksum: 467e52feb3e361ce8cf5fe8d5c254ece content_type: application/x-zip-compressed creator: dernst date_created: 2020-06-22T09:22:04Z date_updated: 2020-07-14T12:48:07Z file_id: '7997' file_name: JK_thesis_latex_source_files.zip file_size: 392794743 relation: main_file - access_level: open_access checksum: 1de716bf110dbd77d383e479232bf496 content_type: application/pdf creator: dernst date_created: 2020-06-22T09:21:29Z date_updated: 2020-07-14T12:48:07Z file_id: '7998' file_name: PhD_thesis_JK_pdfa.pdf file_size: 28453247 relation: main_file file_date_updated: 2020-07-14T12:48:07Z has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: '178' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '1328' relation: part_of_dissertation status: public - id: '7541' relation: part_of_dissertation status: public - id: '77' relation: part_of_dissertation status: public - id: '23' relation: part_of_dissertation status: public - id: '840' relation: part_of_dissertation status: public status: public supervisor: - first_name: Georgios full_name: Katsaros, Georgios id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros orcid: 0000-0001-8342-202X title: Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2020' ...