[{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"ToHe"}],"date_created":"2023-01-16T10:06:31Z","scopus_import":"1","date_published":"2022-08-06T00:00:00Z","external_id":{"isi":["000870310500006"],"arxiv":["2207.13549"]},"publisher":"Springer Nature","intvolume":"     13372","type":"conference","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1,"oa":1,"alternative_title":["LNCS"],"year":"2022","date_updated":"2023-09-05T15:13:36Z","publication":"Computer Aided Verification","page":"109-129","month":"08","ddc":["000"],"file_date_updated":"2023-01-30T12:51:02Z","citation":{"ama":"Doveri K, Ganty P, Mazzocchi NA. FORQ-based language inclusion formal testing. In: <i>Computer Aided Verification</i>. Vol 13372. Springer Nature; 2022:109-129. doi:<a href=\"https://doi.org/10.1007/978-3-031-13188-2_6\">10.1007/978-3-031-13188-2_6</a>","short":"K. Doveri, P. Ganty, N.A. Mazzocchi, in:, Computer Aided Verification, Springer Nature, 2022, pp. 109–129.","ista":"Doveri K, Ganty P, Mazzocchi NA. 2022. FORQ-based language inclusion formal testing. Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 13372, 109–129.","ieee":"K. Doveri, P. Ganty, and N. A. Mazzocchi, “FORQ-based language inclusion formal testing,” in <i>Computer Aided Verification</i>, Haifa, Israel, 2022, vol. 13372, pp. 109–129.","apa":"Doveri, K., Ganty, P., &#38; Mazzocchi, N. A. (2022). FORQ-based language inclusion formal testing. In <i>Computer Aided Verification</i> (Vol. 13372, pp. 109–129). Haifa, Israel: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-13188-2_6\">https://doi.org/10.1007/978-3-031-13188-2_6</a>","chicago":"Doveri, Kyveli, Pierre Ganty, and Nicolas Adrien Mazzocchi. “FORQ-Based Language Inclusion Formal Testing.” In <i>Computer Aided Verification</i>, 13372:109–29. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-031-13188-2_6\">https://doi.org/10.1007/978-3-031-13188-2_6</a>.","mla":"Doveri, Kyveli, et al. “FORQ-Based Language Inclusion Formal Testing.” <i>Computer Aided Verification</i>, vol. 13372, Springer Nature, 2022, pp. 109–29, doi:<a href=\"https://doi.org/10.1007/978-3-031-13188-2_6\">10.1007/978-3-031-13188-2_6</a>."},"day":"06","oa_version":"Published Version","conference":{"name":"CAV: Computer Aided Verification","end_date":"2022-08-10","start_date":"2022-08-07","location":"Haifa, Israel"},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_size":497682,"creator":"dernst","relation":"main_file","file_name":"2022_LNCS_Doveri.pdf","content_type":"application/pdf","checksum":"edc363b1be5447a09063e115c247918a","access_level":"open_access","date_updated":"2023-01-30T12:51:02Z","success":1,"date_created":"2023-01-30T12:51:02Z","file_id":"12465"}],"arxiv":1,"volume":13372,"article_processing_charge":"No","has_accepted_license":"1","_id":"12302","title":"FORQ-based language inclusion formal testing","author":[{"first_name":"Kyveli","full_name":"Doveri, Kyveli","last_name":"Doveri"},{"last_name":"Ganty","full_name":"Ganty, Pierre","first_name":"Pierre"},{"last_name":"Mazzocchi","full_name":"Mazzocchi, Nicolas Adrien","first_name":"Nicolas Adrien","id":"b26baa86-3308-11ec-87b0-8990f34baa85"}],"doi":"10.1007/978-3-031-13188-2_6","abstract":[{"text":"We propose a novel algorithm to decide the language inclusion between (nondeterministic) Büchi automata, a PSPACE-complete problem. Our approach, like others before, leverage a notion of quasiorder to prune the search for a counterexample by discarding candidates which are subsumed by others for the quasiorder. Discarded candidates are guaranteed to not compromise the completeness of the algorithm. The novelty of our work lies in the quasiorder used to discard candidates. We introduce FORQs (family of right quasiorders) that we obtain by adapting the notion of family of right congruences put forward by Maler and Staiger in 1993. We define a FORQ-based inclusion algorithm which we prove correct and instantiate it for a specific FORQ, called the structural FORQ, induced by the Büchi automaton to the right of the inclusion sign. The resulting implementation, called FORKLIFT, scales up better than the state-of-the-art on a variety of benchmarks including benchmarks from program verification and theorem proving for word combinatorics. Artifact: https://doi.org/10.5281/zenodo.6552870","lang":"eng"}],"project":[{"grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software"}],"publication_identifier":{"isbn":["9783031131875"],"eisbn":["9783031131882"],"issn":["0302-9743"],"eissn":["1611-3349"]},"ec_funded":1,"status":"public","publication_status":"published","acknowledgement":"This work was partially funded by the ESF Investing in your future, the Madrid regional project S2018/TCS-4339 BLOQUES, the Spanish project PGC2018-102210-B-I00 BOSCO, the Ramón y Cajal fellowship RYC-2016-20281, and the ERC grant PR1001ERC02."},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"TaHa"}],"date_created":"2023-01-16T10:06:41Z","scopus_import":"1","date_published":"2022-06-16T00:00:00Z","external_id":{"arxiv":["1810.10095"]},"publisher":"Springer Nature; Birkhäuser","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1810.10095"}],"series_title":"TM","language":[{"iso":"eng"}],"type":"book_chapter","quality_controlled":"1","oa":1,"alternative_title":["Trends in Mathematics"],"year":"2022","date_updated":"2023-01-27T07:07:31Z","publication":"Representation Theory and Algebraic Geometry","page":"347-392","month":"06","citation":{"chicago":"Mirković, Ivan, Yaping Yang, and Gufang Zhao. “Loop Grassmannians of Quivers and Affine Quantum Groups.” In <i>Representation Theory and Algebraic Geometry</i>, edited by Vladimir Baranovskky, Nicolas Guay, and Travis Schedler, 1st ed., 347–92. TM. Cham: Springer Nature; Birkhäuser, 2022. <a href=\"https://doi.org/10.1007/978-3-030-82007-7_8\">https://doi.org/10.1007/978-3-030-82007-7_8</a>.","mla":"Mirković, Ivan, et al. “Loop Grassmannians of Quivers and Affine Quantum Groups.” <i>Representation Theory and Algebraic Geometry</i>, edited by Vladimir Baranovskky et al., 1st ed., Springer Nature; Birkhäuser, 2022, pp. 347–92, doi:<a href=\"https://doi.org/10.1007/978-3-030-82007-7_8\">10.1007/978-3-030-82007-7_8</a>.","ieee":"I. Mirković, Y. Yang, and G. Zhao, “Loop Grassmannians of Quivers and Affine Quantum Groups,” in <i>Representation Theory and Algebraic Geometry</i>, 1st ed., V. Baranovskky, N. Guay, and T. Schedler, Eds. Cham: Springer Nature; Birkhäuser, 2022, pp. 347–392.","apa":"Mirković, I., Yang, Y., &#38; Zhao, G. (2022). Loop Grassmannians of Quivers and Affine Quantum Groups. In V. Baranovskky, N. Guay, &#38; T. Schedler (Eds.), <i>Representation Theory and Algebraic Geometry</i> (1st ed., pp. 347–392). Cham: Springer Nature; Birkhäuser. <a href=\"https://doi.org/10.1007/978-3-030-82007-7_8\">https://doi.org/10.1007/978-3-030-82007-7_8</a>","ama":"Mirković I, Yang Y, Zhao G. Loop Grassmannians of Quivers and Affine Quantum Groups. In: Baranovskky V, Guay N, Schedler T, eds. <i>Representation Theory and Algebraic Geometry</i>. 1st ed. TM. Cham: Springer Nature; Birkhäuser; 2022:347-392. doi:<a href=\"https://doi.org/10.1007/978-3-030-82007-7_8\">10.1007/978-3-030-82007-7_8</a>","ista":"Mirković I, Yang Y, Zhao G. 2022.Loop Grassmannians of Quivers and Affine Quantum Groups. In: Representation Theory and Algebraic Geometry. Trends in Mathematics, , 347–392.","short":"I. Mirković, Y. Yang, G. Zhao, in:, V. Baranovskky, N. Guay, T. Schedler (Eds.), Representation Theory and Algebraic Geometry, 1st ed., Springer Nature; Birkhäuser, Cham, 2022, pp. 347–392."},"day":"16","oa_version":"Preprint","arxiv":1,"article_processing_charge":"No","editor":[{"first_name":"Vladimir","last_name":"Baranovskky","full_name":"Baranovskky, Vladimir"},{"full_name":"Guay, Nicolas","last_name":"Guay","first_name":"Nicolas"},{"last_name":"Schedler","full_name":"Schedler, Travis","first_name":"Travis"}],"_id":"12303","title":"Loop Grassmannians of Quivers and Affine Quantum Groups","author":[{"full_name":"Mirković, Ivan","last_name":"Mirković","first_name":"Ivan"},{"first_name":"Yaping","full_name":"Yang, Yaping","last_name":"Yang"},{"id":"2BC2AC5E-F248-11E8-B48F-1D18A9856A87","first_name":"Gufang","full_name":"Zhao, Gufang","last_name":"Zhao"}],"doi":"10.1007/978-3-030-82007-7_8","abstract":[{"lang":"eng","text":"We construct for each choice of a quiver Q, a cohomology theory A, and a poset P a “loop Grassmannian” GP(Q,A). This generalizes loop Grassmannians of semisimple groups and the loop Grassmannians of based quadratic forms. The addition of a “dilation” torus D⊆G2m gives a quantization GPD(Q,A). This construction is motivated by the program of introducing an inner cohomology theory in algebraic geometry adequate for the Geometric Langlands program (Mirković, Some extensions of the notion of loop Grassmannians. Rad Hrvat. Akad. Znan. Umjet. Mat. Znan., the Mardešić issue. No. 532, 53–74, 2017) and on the construction of affine quantum groups from generalized cohomology theories (Yang and Zhao, Quiver varieties and elliptic quantum groups, preprint. arxiv1708.01418)."}],"project":[{"_id":"25E549F4-B435-11E9-9278-68D0E5697425","grant_number":"320593","name":"Arithmetic and physics of Higgs moduli spaces","call_identifier":"FP7"}],"edition":"1","publication_identifier":{"eisbn":["9783030820077"],"issn":["2297-0215"],"isbn":["9783030820060"],"eissn":["2297-024X"]},"place":"Cham","ec_funded":1,"status":"public","publication_status":"published","acknowledgement":"I.M. thanks Zhijie Dong for long-term discussions on the material that entered this work. We thank Misha Finkelberg for pointing out errors in earlier versions. His advice and his insistence have led to a much better paper. A part of the writing was done at the conference at IST (Vienna) attended by all coauthors. We therefore thank the organizers of the conference and the support of ERC Advanced Grant Arithmetic and Physics of Higgs moduli spaces No. 320593. The work of I.M. was partially supported by NSF grants. The work of Y.Y. was partially supported by the Australian Research Council (ARC) via the award DE190101231. The work of G.Z. was partially supported by ARC via the award DE190101222."},{"page":"1394-1434","article_type":"original","publication":"Communications in Partial Differential Equations","date_updated":"2023-08-04T10:34:31Z","year":"2022","keyword":["Applied Mathematics","Analysis"],"oa":1,"isi":1,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","publisher":"Taylor & Francis","intvolume":"        47","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.1907.05342","open_access":"1"}],"date_published":"2022-07-01T00:00:00Z","external_id":{"arxiv":["1907.05342"],"isi":["000805689800001"]},"date_created":"2023-01-16T10:06:50Z","scopus_import":"1","department":[{"_id":"JuFi"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","publication_status":"published","acknowledgement":"N. De Nitti acknowledges the kind hospitality of IST Austria within the framework of the ISTernship Summer Program 2018, during which most of the present article was written. N. DeNitti has received funding by The Austrian Agency for International Cooperation in Education &Research (OeAD-GmbH) via its financial support of the ISTernship Summer Program 2018. N.De Nitti would also like to thank Giuseppe Coclite, Giuseppe Devillanova, Giuseppe Florio, Sebastian Hensel, and Francesco Maddalena for several helpful conversations on topics related to this work.","publication_identifier":{"eissn":["1532-4133"],"issn":["0360-5302"]},"abstract":[{"lang":"eng","text":"We establish sharp criteria for the instantaneous propagation of free boundaries in solutions to the thin-film equation. The criteria are formulated in terms of the initial distribution of mass (as opposed to previous almost-optimal results), reflecting the fact that mass is a locally conserved quantity for the thin-film equation. In the regime of weak slippage, our criteria are at the same time necessary and sufficient. The proof of our upper bounds on free boundary propagation is based on a strategy of “propagation of degeneracy” down to arbitrarily small spatial scales: We combine estimates on the local mass and estimates on energies to show that “degeneracy” on a certain space-time cylinder entails “degeneracy” on a spatially smaller space-time cylinder with the same time horizon. The derivation of our lower bounds on free boundary propagation is based on a combination of a monotone quantity and almost optimal estimates established previously by the second author with a new estimate connecting motion of mass to entropy production."}],"issue":"7","doi":"10.1080/03605302.2022.2056702","title":"Sharp criteria for the waiting time phenomenon in solutions to the thin-film equation","author":[{"last_name":"De Nitti","full_name":"De Nitti, Nicola","first_name":"Nicola"},{"full_name":"Fischer, Julian L","last_name":"Fischer","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L","orcid":"0000-0002-0479-558X"}],"_id":"12304","article_processing_charge":"No","volume":47,"arxiv":1,"oa_version":"Preprint","citation":{"ista":"De Nitti N, Fischer JL. 2022. Sharp criteria for the waiting time phenomenon in solutions to the thin-film equation. Communications in Partial Differential Equations. 47(7), 1394–1434.","ama":"De Nitti N, Fischer JL. Sharp criteria for the waiting time phenomenon in solutions to the thin-film equation. <i>Communications in Partial Differential Equations</i>. 2022;47(7):1394-1434. doi:<a href=\"https://doi.org/10.1080/03605302.2022.2056702\">10.1080/03605302.2022.2056702</a>","short":"N. De Nitti, J.L. Fischer, Communications in Partial Differential Equations 47 (2022) 1394–1434.","ieee":"N. De Nitti and J. L. Fischer, “Sharp criteria for the waiting time phenomenon in solutions to the thin-film equation,” <i>Communications in Partial Differential Equations</i>, vol. 47, no. 7. Taylor &#38; Francis, pp. 1394–1434, 2022.","apa":"De Nitti, N., &#38; Fischer, J. L. (2022). Sharp criteria for the waiting time phenomenon in solutions to the thin-film equation. <i>Communications in Partial Differential Equations</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/03605302.2022.2056702\">https://doi.org/10.1080/03605302.2022.2056702</a>","mla":"De Nitti, Nicola, and Julian L. Fischer. “Sharp Criteria for the Waiting Time Phenomenon in Solutions to the Thin-Film Equation.” <i>Communications in Partial Differential Equations</i>, vol. 47, no. 7, Taylor &#38; Francis, 2022, pp. 1394–434, doi:<a href=\"https://doi.org/10.1080/03605302.2022.2056702\">10.1080/03605302.2022.2056702</a>.","chicago":"De Nitti, Nicola, and Julian L Fischer. “Sharp Criteria for the Waiting Time Phenomenon in Solutions to the Thin-Film Equation.” <i>Communications in Partial Differential Equations</i>. Taylor &#38; Francis, 2022. <a href=\"https://doi.org/10.1080/03605302.2022.2056702\">https://doi.org/10.1080/03605302.2022.2056702</a>."},"day":"01","month":"07"},{"year":"2022","keyword":["Applied Mathematics","Computational Mathematics","Analysis"],"oa":1,"article_type":"original","page":"114-172","publication":"SIAM Journal on Mathematical Analysis","date_updated":"2023-08-04T10:34:56Z","date_published":"2022-01-04T00:00:00Z","external_id":{"isi":["000762768000004"],"arxiv":["2105.08434"]},"scopus_import":"1","date_created":"2023-01-16T10:07:00Z","department":[{"_id":"JuFi"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2105.08434"}],"intvolume":"        54","publisher":"Society for Industrial and Applied Mathematics","issue":"1","abstract":[{"lang":"eng","text":"This paper is concerned with the sharp interface limit for the Allen--Cahn equation with a nonlinear Robin boundary condition in a bounded smooth domain Ω⊂\\R2. We assume that a diffuse interface already has developed and that it is in contact with the boundary ∂Ω. The boundary condition is designed in such a way that the limit problem is given by the mean curvature flow with constant α-contact angle. For α close to 90° we prove a local in time convergence result for well-prepared initial data for times when a smooth solution to the limit problem exists. Based on the latter we construct a suitable curvilinear coordinate system and carry out a rigorous asymptotic expansion for the Allen--Cahn equation with the nonlinear Robin boundary condition. Moreover, we show a spectral estimate for the corresponding linearized Allen--Cahn operator and with its aid we derive strong norm estimates for the difference of the exact and approximate solutions using a Gronwall-type argument."}],"doi":"10.1137/21m1424925","author":[{"last_name":"Abels","full_name":"Abels, Helmut","first_name":"Helmut"},{"full_name":"Moser, Maximilian","last_name":"Moser","id":"a60047a9-da77-11eb-85b4-c4dc385ebb8c","first_name":"Maximilian"}],"title":"Convergence of the Allen--Cahn equation with a nonlinear Robin boundary condition to mean curvature flow with contact angle close to 90°","_id":"12305","publication_status":"published","status":"public","publication_identifier":{"eissn":["1095-7154"],"issn":["0036-1410"]},"oa_version":"Preprint","day":"04","citation":{"apa":"Abels, H., &#38; Moser, M. (2022). Convergence of the Allen--Cahn equation with a nonlinear Robin boundary condition to mean curvature flow with contact angle close to 90°. <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/21m1424925\">https://doi.org/10.1137/21m1424925</a>","ieee":"H. Abels and M. Moser, “Convergence of the Allen--Cahn equation with a nonlinear Robin boundary condition to mean curvature flow with contact angle close to 90°,” <i>SIAM Journal on Mathematical Analysis</i>, vol. 54, no. 1. Society for Industrial and Applied Mathematics, pp. 114–172, 2022.","ama":"Abels H, Moser M. Convergence of the Allen--Cahn equation with a nonlinear Robin boundary condition to mean curvature flow with contact angle close to 90°. <i>SIAM Journal on Mathematical Analysis</i>. 2022;54(1):114-172. doi:<a href=\"https://doi.org/10.1137/21m1424925\">10.1137/21m1424925</a>","short":"H. Abels, M. Moser, SIAM Journal on Mathematical Analysis 54 (2022) 114–172.","ista":"Abels H, Moser M. 2022. Convergence of the Allen--Cahn equation with a nonlinear Robin boundary condition to mean curvature flow with contact angle close to 90°. SIAM Journal on Mathematical Analysis. 54(1), 114–172.","mla":"Abels, Helmut, and Maximilian Moser. “Convergence of the Allen--Cahn Equation with a Nonlinear Robin Boundary Condition to Mean Curvature Flow with Contact Angle Close to 90°.” <i>SIAM Journal on Mathematical Analysis</i>, vol. 54, no. 1, Society for Industrial and Applied Mathematics, 2022, pp. 114–72, doi:<a href=\"https://doi.org/10.1137/21m1424925\">10.1137/21m1424925</a>.","chicago":"Abels, Helmut, and Maximilian Moser. “Convergence of the Allen--Cahn Equation with a Nonlinear Robin Boundary Condition to Mean Curvature Flow with Contact Angle Close to 90°.” <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics, 2022. <a href=\"https://doi.org/10.1137/21m1424925\">https://doi.org/10.1137/21m1424925</a>."},"month":"01","article_processing_charge":"No","volume":54,"arxiv":1},{"oa_version":"None","day":"28","citation":{"mla":"Shipman, Barbara A., and Elizabeth R. Stephenson. “Tangible Topology through the Lens of Limits.” <i>PRIMUS</i>, vol. 32, no. 5, Taylor &#38; Francis, 2022, pp. 593–609, doi:<a href=\"https://doi.org/10.1080/10511970.2021.1872750\">10.1080/10511970.2021.1872750</a>.","chicago":"Shipman, Barbara A., and Elizabeth R Stephenson. “Tangible Topology through the Lens of Limits.” <i>PRIMUS</i>. Taylor &#38; Francis, 2022. <a href=\"https://doi.org/10.1080/10511970.2021.1872750\">https://doi.org/10.1080/10511970.2021.1872750</a>.","ieee":"B. A. Shipman and E. R. Stephenson, “Tangible topology through the lens of limits,” <i>PRIMUS</i>, vol. 32, no. 5. Taylor &#38; Francis, pp. 593–609, 2022.","apa":"Shipman, B. A., &#38; Stephenson, E. R. (2022). Tangible topology through the lens of limits. <i>PRIMUS</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/10511970.2021.1872750\">https://doi.org/10.1080/10511970.2021.1872750</a>","ama":"Shipman BA, Stephenson ER. Tangible topology through the lens of limits. <i>PRIMUS</i>. 2022;32(5):593-609. doi:<a href=\"https://doi.org/10.1080/10511970.2021.1872750\">10.1080/10511970.2021.1872750</a>","short":"B.A. Shipman, E.R. Stephenson, PRIMUS 32 (2022) 593–609.","ista":"Shipman BA, Stephenson ER. 2022. Tangible topology through the lens of limits. PRIMUS. 32(5), 593–609."},"month":"05","article_processing_charge":"No","volume":32,"issue":"5","abstract":[{"lang":"eng","text":"Point-set topology is among the most abstract branches of mathematics in that it lacks tangible notions of distance, length, magnitude, order, and size. There is no shape, no geometry, no algebra, and no direction. Everything we are used to visualizing is gone. In the teaching and learning of mathematics, this can present a conundrum. Yet, this very property makes point set topology perfect for teaching and learning abstract mathematical concepts. It clears our minds of preconceived intuitions and expectations and forces us to think in new and creative ways. In this paper, we present guided investigations into topology through questions and thinking strategies that open up fascinating problems. They are intended for faculty who already teach or are thinking about teaching a class in topology or abstract mathematical reasoning for undergraduates. They can be used to build simple to challenging projects in topology, proofs, honors programs, and research experiences."}],"doi":"10.1080/10511970.2021.1872750","author":[{"first_name":"Barbara A.","last_name":"Shipman","full_name":"Shipman, Barbara A."},{"orcid":"0000-0002-6862-208X","first_name":"Elizabeth R","id":"2D04F932-F248-11E8-B48F-1D18A9856A87","last_name":"Stephenson","full_name":"Stephenson, Elizabeth R"}],"title":"Tangible topology through the lens of limits","_id":"12307","status":"public","publication_status":"published","publication_identifier":{"eissn":["1935-4053"],"issn":["1051-1970"]},"date_published":"2022-05-28T00:00:00Z","scopus_import":"1","date_created":"2023-01-16T10:07:21Z","department":[{"_id":"HeEd"},{"_id":"GradSch"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":"        32","publisher":"Taylor & Francis","year":"2022","keyword":["Education","General Mathematics"],"article_type":"original","page":"593-609","publication":"PRIMUS","date_updated":"2023-01-30T13:02:30Z"},{"date_published":"2022-12-21T00:00:00Z","external_id":{"isi":["000925192000001"]},"date_created":"2023-01-22T23:00:55Z","scopus_import":"1","department":[{"_id":"GaTk"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","publisher":"Public Library of Science","intvolume":"        20","year":"2022","oa":1,"page":"e3001889","article_type":"original","publication":"PLoS Biology","date_updated":"2023-08-03T14:23:49Z","oa_version":"Published Version","citation":{"ama":"Mlynarski WF, Tkačik G. Efficient coding theory of dynamic attentional modulation. <i>PLoS Biology</i>. 2022;20(12):e3001889. doi:<a href=\"https://doi.org/10.1371/journal.pbio.3001889\">10.1371/journal.pbio.3001889</a>","short":"W.F. Mlynarski, G. Tkačik, PLoS Biology 20 (2022) e3001889.","ista":"Mlynarski WF, Tkačik G. 2022. Efficient coding theory of dynamic attentional modulation. PLoS Biology. 20(12), e3001889.","ieee":"W. F. Mlynarski and G. Tkačik, “Efficient coding theory of dynamic attentional modulation,” <i>PLoS Biology</i>, vol. 20, no. 12. Public Library of Science, p. e3001889, 2022.","apa":"Mlynarski, W. F., &#38; Tkačik, G. (2022). Efficient coding theory of dynamic attentional modulation. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.3001889\">https://doi.org/10.1371/journal.pbio.3001889</a>","mla":"Mlynarski, Wiktor F., and Gašper Tkačik. “Efficient Coding Theory of Dynamic Attentional Modulation.” <i>PLoS Biology</i>, vol. 20, no. 12, Public Library of Science, 2022, p. e3001889, doi:<a href=\"https://doi.org/10.1371/journal.pbio.3001889\">10.1371/journal.pbio.3001889</a>.","chicago":"Mlynarski, Wiktor F, and Gašper Tkačik. “Efficient Coding Theory of Dynamic Attentional Modulation.” <i>PLoS Biology</i>. Public Library of Science, 2022. <a href=\"https://doi.org/10.1371/journal.pbio.3001889\">https://doi.org/10.1371/journal.pbio.3001889</a>."},"day":"21","ddc":["570"],"month":"12","file_date_updated":"2023-01-23T08:46:40Z","has_accepted_license":"1","article_processing_charge":"No","volume":20,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_name":"2022_PloSBiology_Mlynarski.pdf","creator":"dernst","relation":"main_file","file_size":4248838,"success":1,"date_updated":"2023-01-23T08:46:40Z","access_level":"open_access","checksum":"5d7f1111a87e5f2c1bf92f8886738894","content_type":"application/pdf","file_id":"12337","date_created":"2023-01-23T08:46:40Z"}],"abstract":[{"lang":"eng","text":"Activity of sensory neurons is driven not only by external stimuli but also by feedback signals from higher brain areas. Attention is one particularly important internal signal whose presumed role is to modulate sensory representations such that they only encode information currently relevant to the organism at minimal cost. This hypothesis has, however, not yet been expressed in a normative computational framework. Here, by building on normative principles of probabilistic inference and efficient coding, we developed a model of dynamic population coding in the visual cortex. By continuously adapting the sensory code to changing demands of the perceptual observer, an attention-like modulation emerges. This modulation can dramatically reduce the amount of neural activity without deteriorating the accuracy of task-specific inferences. Our results suggest that a range of seemingly disparate cortical phenomena such as intrinsic gain modulation, attention-related tuning modulation, and response variability could be manifestations of the same underlying principles, which combine efficient sensory coding with optimal probabilistic inference in dynamic environments."}],"issue":"12","doi":"10.1371/journal.pbio.3001889","title":"Efficient coding theory of dynamic attentional modulation","author":[{"full_name":"Mlynarski, Wiktor F","last_name":"Mlynarski","id":"358A453A-F248-11E8-B48F-1D18A9856A87","first_name":"Wiktor F"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","full_name":"Tkačik, Gašper","last_name":"Tkačik","orcid":"1"}],"_id":"12332","acknowledgement":"We thank Robbe Goris for generously providing figures from his work and Ann M. Hermundstad for helpful discussions.\r\nGT & WM were supported by the Austrian Science Fund Standalone Grant P 34015 \"Efficient Coding with Biophysical Realism\" (https://pf.fwf.ac.at/) WM was additionally supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (https://ec.europa.eu/research/mariecurieactions/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","status":"public","publication_status":"published","ec_funded":1,"publication_identifier":{"eissn":["1545-7885"]},"project":[{"name":"Efficient coding with biophysical realism","grant_number":"P34015","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}]},{"date_created":"2023-01-22T23:00:55Z","scopus_import":"1","external_id":{"isi":["000912674700001"]},"date_published":"2022-12-22T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"CaGu"}],"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","isi":1,"publisher":"eLife Sciences Publications","intvolume":"        11","year":"2022","oa":1,"article_number":"e82240","article_type":"original","related_material":{"link":[{"relation":"software","url":"https://doi.org/10.5281/zenodo.6974122"}],"record":[{"status":"public","relation":"research_data","id":"12339"}]},"date_updated":"2023-08-03T14:23:07Z","publication":"eLife","oa_version":"Published Version","month":"12","ddc":["570"],"file_date_updated":"2023-01-23T08:56:21Z","citation":{"ista":"Tomanek I, Guet CC. 2022. Adaptation dynamics between copynumber and point mutations. eLife. 11, e82240.","short":"I. Tomanek, C.C. Guet, ELife 11 (2022).","ama":"Tomanek I, Guet CC. Adaptation dynamics between copynumber and point mutations. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/ELIFE.82240\">10.7554/ELIFE.82240</a>","ieee":"I. Tomanek and C. C. Guet, “Adaptation dynamics between copynumber and point mutations,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022.","apa":"Tomanek, I., &#38; Guet, C. C. (2022). Adaptation dynamics between copynumber and point mutations. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/ELIFE.82240\">https://doi.org/10.7554/ELIFE.82240</a>","chicago":"Tomanek, Isabella, and Calin C Guet. “Adaptation Dynamics between Copynumber and Point Mutations.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/ELIFE.82240\">https://doi.org/10.7554/ELIFE.82240</a>.","mla":"Tomanek, Isabella, and Calin C. Guet. “Adaptation Dynamics between Copynumber and Point Mutations.” <i>ELife</i>, vol. 11, e82240, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/ELIFE.82240\">10.7554/ELIFE.82240</a>."},"day":"22","volume":11,"article_processing_charge":"No","has_accepted_license":"1","file":[{"date_created":"2023-01-23T08:56:21Z","file_id":"12338","file_size":8835954,"creator":"dernst","relation":"main_file","file_name":"2022_eLife_Tomanek.pdf","content_type":"application/pdf","checksum":"9321fd5f06ff59d5e2d33daee84b3da1","access_level":"open_access","date_updated":"2023-01-23T08:56:21Z","success":1}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.7554/ELIFE.82240","abstract":[{"text":"Together, copy-number and point mutations form the basis for most evolutionary novelty, through the process of gene duplication and divergence. While a plethora of genomic data reveals the long-term fate of diverging coding sequences and their cis-regulatory elements, little is known about the early dynamics around the duplication event itself. In microorganisms, selection for increased gene expression often drives the expansion of gene copy-number mutations, which serves as a crude adaptation, prior to divergence through refining point mutations. Using a simple synthetic genetic reporter system that can distinguish between copy-number and point mutations, we study their early and transient adaptive dynamics in real time in Escherichia coli. We find two qualitatively different routes of adaptation, depending on the level of functional improvement needed. In conditions of high gene expression demand, the two mutation types occur as a combination. However, under low gene expression demand, copy-number and point mutations are mutually exclusive; here, owing to their higher frequency, adaptation is dominated by copy-number mutations, in a process we term amplification hindrance. Ultimately, due to high reversal rates and pleiotropic cost, copy-number mutations may not only serve as a crude and transient adaptation, but also constrain sequence divergence over evolutionary time scales.","lang":"eng"}],"_id":"12333","title":"Adaptation dynamics between copynumber and point mutations","author":[{"id":"3981F020-F248-11E8-B48F-1D18A9856A87","first_name":"Isabella","full_name":"Tomanek, Isabella","last_name":"Tomanek","orcid":"0000-0001-6197-363X"},{"orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C"}],"publication_status":"published","acknowledgement":"We are grateful to N Barton, F Kondrashov, M Lagator, M Pleska, R Roemhild, D Siekhaus, and G\r\nTkacik for input on the manuscript and to K Tomasek for help with flow cytometry.","status":"public","publication_identifier":{"eissn":["2050-084X"]}},{"oa_version":"Published Version","date_created":"2023-01-23T09:00:37Z","date_published":"2022-12-23T00:00:00Z","ddc":["570"],"month":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Tomanek, I., &#38; Guet, C. C. (2022). Flow cytometry YFP and CFP data and deep sequencing data of populations evolving in galactose. Dryad. <a href=\"https://doi.org/10.5061/dryad.rfj6q57ds\">https://doi.org/10.5061/dryad.rfj6q57ds</a>","ieee":"I. Tomanek and C. C. Guet, “Flow cytometry YFP and CFP data and deep sequencing data of populations evolving in galactose.” Dryad, 2022.","short":"I. Tomanek, C.C. Guet, (2022).","ama":"Tomanek I, Guet CC. Flow cytometry YFP and CFP data and deep sequencing data of populations evolving in galactose. 2022. doi:<a href=\"https://doi.org/10.5061/dryad.rfj6q57ds\">10.5061/dryad.rfj6q57ds</a>","ista":"Tomanek I, Guet CC. 2022. Flow cytometry YFP and CFP data and deep sequencing data of populations evolving in galactose, Dryad, <a href=\"https://doi.org/10.5061/dryad.rfj6q57ds\">10.5061/dryad.rfj6q57ds</a>.","chicago":"Tomanek, Isabella, and Calin C Guet. “Flow Cytometry YFP and CFP Data and Deep Sequencing Data of Populations Evolving in Galactose.” Dryad, 2022. <a href=\"https://doi.org/10.5061/dryad.rfj6q57ds\">https://doi.org/10.5061/dryad.rfj6q57ds</a>.","mla":"Tomanek, Isabella, and Calin C. Guet. <i>Flow Cytometry YFP and CFP Data and Deep Sequencing Data of Populations Evolving in Galactose</i>. Dryad, 2022, doi:<a href=\"https://doi.org/10.5061/dryad.rfj6q57ds\">10.5061/dryad.rfj6q57ds</a>."},"department":[{"_id":"CaGu"}],"day":"23","article_processing_charge":"No","type":"research_data_reference","publisher":"Dryad","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.rfj6q57ds"}],"doi":"10.5061/dryad.rfj6q57ds","abstract":[{"lang":"eng","text":"Copy-number and point mutations form the basis for most evolutionary novelty through the process of gene duplication and divergence. While a plethora of genomic sequence data reveals the long-term fate of diverging coding sequences and their cis-regulatory elements, little is known about the early dynamics around the duplication event itself. In microorganisms, selection for increased gene expression often drives the expansion of gene copy-number mutations, which serves as a crude adaptation, prior to divergence through refining point mutations. Using a simple synthetic genetic system that allows us to distinguish copy-number and point mutations, we study their early and transient adaptive dynamics in real-time in Escherichia coli. We find two qualitatively different routes of adaptation depending on the level of functional improvement selected for: In conditions of high gene expression demand, the two types of mutations occur as a combination. Under low gene expression demand, negative epistasis between the two types of mutations renders them mutually exclusive. Thus, owing to their higher frequency, adaptation is dominated by copy-number mutations. Ultimately, due to high rates of reversal and pleiotropic cost, copy-number mutations may not only serve as a crude and transient adaptation but also constrain sequence divergence over evolutionary time scales."}],"year":"2022","_id":"12339","title":"Flow cytometry YFP and CFP data and deep sequencing data of populations evolving in galactose","oa":1,"author":[{"orcid":"0000-0001-6197-363X","full_name":"Tomanek, Isabella","last_name":"Tomanek","id":"3981F020-F248-11E8-B48F-1D18A9856A87","first_name":"Isabella"},{"orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"12333"}]},"status":"public","date_updated":"2023-08-03T14:23:06Z"},{"date_published":"2022-09-22T00:00:00Z","date_created":"2023-01-24T10:49:46Z","acknowledged_ssus":[{"_id":"SSU"}],"department":[{"_id":"GradSch"},{"_id":"ChWo"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","language":[{"iso":"eng"}],"type":"dissertation","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"year":"2022","oa":1,"related_material":{"record":[{"id":"11736","relation":"part_of_dissertation","status":"public"},{"id":"9818","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"8385"}]},"page":"138","date_updated":"2024-02-28T12:57:46Z","oa_version":"Published Version","citation":{"apa":"Sperl, G. (2022). <i>Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12103\">https://doi.org/10.15479/at:ista:12103</a>","ieee":"G. Sperl, “Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting,” Institute of Science and Technology Austria, 2022.","short":"G. Sperl, Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting, Institute of Science and Technology Austria, 2022.","ama":"Sperl G. Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:12103\">10.15479/at:ista:12103</a>","ista":"Sperl G. 2022. Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting. Institute of Science and Technology Austria.","chicago":"Sperl, Georg. “Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:12103\">https://doi.org/10.15479/at:ista:12103</a>.","mla":"Sperl, Georg. <i>Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:12103\">10.15479/at:ista:12103</a>."},"day":"22","file_date_updated":"2023-02-02T09:39:25Z","ddc":["000","620"],"month":"09","has_accepted_license":"1","article_processing_charge":"No","degree_awarded":"PhD","file":[{"access_level":"open_access","description":"This is the main PDF file of the thesis. File size: 105 MB","content_type":"application/pdf","checksum":"083722acbb8115e52e3b0fdec6226769","date_updated":"2023-02-02T09:29:57Z","file_name":"thesis_gsperl.pdf","relation":"main_file","creator":"cchlebak","file_size":104497530,"title":"Thesis","file_id":"12371","date_created":"2023-01-25T12:04:41Z"},{"file_id":"12483","date_created":"2023-02-02T09:33:37Z","title":"Thesis (compressed 23MB)","file_name":"thesis_gsperl_compressed.pdf","file_size":23183710,"relation":"main_file","creator":"cchlebak","date_updated":"2023-02-02T09:33:37Z","description":"This version of the thesis uses stronger image compression for a smaller file size of 23MB.","access_level":"open_access","checksum":"511f82025e5fcb70bff4731d6896ca07","content_type":"application/pdf"},{"file_size":98382247,"relation":"source_file","creator":"cchlebak","file_name":"thesis-source.zip","date_updated":"2023-02-02T09:39:25Z","content_type":"application/x-zip-compressed","checksum":"ed4cb85225eedff761c25bddfc37a2ed","access_level":"open_access","date_created":"2023-02-02T09:39:25Z","file_id":"12484"}],"abstract":[{"lang":"eng","text":"The complex yarn structure of knitted and woven fabrics gives rise to both a mechanical and\r\nvisual complexity. The small-scale interactions of yarns colliding with and pulling on each\r\nother result in drastically different large-scale stretching and bending behavior, introducing\r\nanisotropy, curling, and more. While simulating cloth as individual yarns can reproduce this\r\ncomplexity and match the quality of real fabric, it may be too computationally expensive for\r\nlarge fabrics. On the other hand, continuum-based approaches do not need to discretize the\r\ncloth at a stitch-level, but it is non-trivial to find a material model that would replicate the\r\nlarge-scale behavior of yarn fabrics, and they discard the intricate visual detail. In this thesis,\r\nwe discuss three methods to try and bridge the gap between small-scale and large-scale yarn\r\nmechanics using numerical homogenization: fitting a continuum model to periodic yarn simulations, adding mechanics-aware yarn detail onto thin-shell simulations, and quantitatively\r\nfitting yarn parameters to physical measurements of real fabric.\r\nTo start, we present a method for animating yarn-level cloth effects using a thin-shell solver.\r\nWe first use a large number of periodic yarn-level simulations to build a model of the potential\r\nenergy density of the cloth, and then use it to compute forces in a thin-shell simulator. The\r\nresulting simulations faithfully reproduce expected effects like the stiffening of woven fabrics\r\nand the highly deformable nature and anisotropy of knitted fabrics at a fraction of the cost of\r\nfull yarn-level simulation.\r\nWhile our thin-shell simulations are able to capture large-scale yarn mechanics, they lack\r\nthe rich visual detail of yarn-level simulations. Therefore, we propose a method to animate\r\nyarn-level cloth geometry on top of an underlying deforming mesh in a mechanics-aware\r\nfashion in real time. Using triangle strains to interpolate precomputed yarn geometry, we are\r\nable to reproduce effects such as knit loops tightening under stretching at negligible cost.\r\nFinally, we introduce a methodology for inverse-modeling of yarn-level mechanics of cloth,\r\nbased on the mechanical response of fabrics in the real world. We compile a database from\r\nphysical tests of several knitted fabrics used in the textile industry spanning diverse physical\r\nproperties like stiffness, nonlinearity, and anisotropy. We then develop a system for approximating these mechanical responses with yarn-level cloth simulation, using homogenized\r\nshell models to speed up computation and adding some small-but-necessary extensions to\r\nyarn-level models used in computer graphics.\r\n"}],"doi":"10.15479/at:ista:12103","supervisor":[{"orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J"}],"title":"Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting","author":[{"last_name":"Sperl","full_name":"Sperl, Georg","first_name":"Georg","id":"4DD40360-F248-11E8-B48F-1D18A9856A87"}],"_id":"12358","publication_status":"published","status":"public","ec_funded":1,"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-020-6"]},"project":[{"call_identifier":"H2020","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176"}]},{"has_accepted_license":"1","article_processing_charge":"No","degree_awarded":"PhD","file":[{"file_id":"12365","date_created":"2023-01-24T13:15:45Z","date_updated":"2023-09-20T22:30:03Z","access_level":"open_access","checksum":"896f4cac9adb6d3f26a6605772f4e1a3","content_type":"application/pdf","embargo":"2023-09-19","file_name":"220923_Thesis_CDotter_Final.pdf","file_size":20457465,"creator":"cchlebak","relation":"main_file"},{"date_created":"2023-02-02T09:15:35Z","file_id":"12482","embargo_to":"open_access","date_updated":"2023-09-20T22:30:03Z","content_type":"application/x-zip-compressed","checksum":"ad01bb20da163be6893b7af832e58419","access_level":"closed","relation":"source_file","file_size":22433512,"creator":"cchlebak","file_name":"latex_source_CDotter_Thesis_2022.zip"}],"oa_version":"Published Version","citation":{"mla":"Dotter, Christoph. <i>Transcriptional Consequences of Mutations in Genes Associated with Autism Spectrum Disorder</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:12094\">10.15479/at:ista:12094</a>.","chicago":"Dotter, Christoph. “Transcriptional Consequences of Mutations in Genes Associated with Autism Spectrum Disorder.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:12094\">https://doi.org/10.15479/at:ista:12094</a>.","ama":"Dotter C. Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:12094\">10.15479/at:ista:12094</a>","ista":"Dotter C. 2022. Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder. Institute of Science and Technology Austria.","short":"C. Dotter, Transcriptional Consequences of Mutations in Genes Associated with Autism Spectrum Disorder, Institute of Science and Technology Austria, 2022.","apa":"Dotter, C. (2022). <i>Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12094\">https://doi.org/10.15479/at:ista:12094</a>","ieee":"C. Dotter, “Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder,” Institute of Science and Technology Austria, 2022."},"day":"19","ddc":["570"],"file_date_updated":"2023-09-20T22:30:03Z","month":"09","status":"public","publication_status":"published","ec_funded":1,"publication_identifier":{"issn":["2663-337X"]},"project":[{"grant_number":"401299","_id":"254BA948-B435-11E9-9278-68D0E5697425","name":"Probing development and reversibility of autism spectrum disorders"},{"grant_number":"707964","_id":"9B91375C-BA93-11EA-9121-9846C619BF3A","name":"Critical windows and reversibility of ASD associated with mutations in chromatin remodelers"},{"name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","call_identifier":"H2020","_id":"25444568-B435-11E9-9278-68D0E5697425","grant_number":"715508"},{"grant_number":"I04205","_id":"2690FEAC-B435-11E9-9278-68D0E5697425","name":"Identification of converging Molecular Pathways Across Chromatinopathies as Targets for Therapy","call_identifier":"FWF"}],"abstract":[{"lang":"eng","text":"Autism spectrum disorders (ASDs) are a group of neurodevelopmental disorders character\u0002ized by behavioral symptoms such as problems in social communication and interaction, as\r\nwell as repetitive, restricted behaviors and interests. These disorders show a high degree\r\nof heritability and hundreds of risk genes have been identifed using high throughput\r\nsequencing technologies. This genetic heterogeneity has hampered eforts in understanding\r\nthe pathogenesis of ASD but at the same time given rise to the concept of convergent\r\nmechanisms. Previous studies have identifed that risk genes for ASD broadly converge\r\nonto specifc functional categories with transcriptional regulation being one of the biggest\r\ngroups. In this thesis, I focus on this subgroup of genes and investigate the gene regulatory\r\nconsequences of some of them in the context of neurodevelopment.\r\nFirst, we showed that mutations in the ASD and intellectual disability risk gene Setd5 lead\r\nto perturbations of gene regulatory programs in early cell fate specifcation. In addition,\r\nadult animals display abnormal learning behavior which is mirrored at the transcriptional\r\nlevel by altered activity dependent regulation of postsynaptic gene expression. Lastly,\r\nwe link the regulatory function of Setd5 to its interaction with the Paf1 and the NCoR\r\ncomplex.\r\nSecond, by modeling the heterozygous loss of the top ASD gene CHD8 in human cerebral\r\norganoids we demonstrate profound changes in the developmental trajectories of both\r\ninhibitory and excitatory neurons using single cell RNA-sequencing. While the former\r\nwere generated earlier in CHD8+/- organoids, the generation of the latter was shifted to\r\nlater times in favor of a prolonged progenitor expansion phase and ultimately increased\r\norganoid size.\r\nFinally, by modeling heterozygous mutations for four ASD associated chromatin modifers,\r\nASH1L, KDM6B, KMT5B, and SETD5 in human cortical spheroids we show evidence of\r\nregulatory convergence across three of those genes. We observe a shift from dorsal cortical\r\nexcitatory neuron fates towards partially ventralized cell types resembling cells from the\r\nlateral ganglionic eminence. As this project is still ongoing at the time of writing, future\r\nexperiments will aim at elucidating the regulatory mechanisms underlying this shift with\r\nthe aim of linking these three ASD risk genes through biological convergence."}],"doi":"10.15479/at:ista:12094","supervisor":[{"full_name":"Novarino, Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","orcid":"0000-0002-7673-7178"}],"title":"Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder","author":[{"full_name":"Dotter, Christoph","last_name":"Dotter","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","orcid":"0000-0002-9033-9096"}],"_id":"12364","type":"dissertation","language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","date_published":"2022-09-19T00:00:00Z","date_created":"2023-01-24T13:09:57Z","department":[{"_id":"GradSch"},{"_id":"GaNo"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","related_material":{"record":[{"id":"3","relation":"part_of_dissertation","status":"public"},{"id":"11160","relation":"part_of_dissertation","status":"public"}]},"page":"152","date_updated":"2023-11-16T13:10:22Z","alternative_title":["ISTA Thesis"],"year":"2022","oa":1},{"status":"public","publication_status":"published","ec_funded":1,"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-024-4"]},"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"},{"_id":"26336814-B435-11E9-9278-68D0E5697425","grant_number":"758053","name":"A Fiber Optic Transceiver for Superconducting Qubits","call_identifier":"H2020"},{"call_identifier":"H2020","name":"Quantum readout techniques and technologies","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","grant_number":"862644"}],"abstract":[{"lang":"eng","text":"Recent substantial advances in the feld of superconducting circuits have shown its\r\npotential as a leading platform for future quantum computing. In contrast to classical\r\ncomputers based on bits that are represented by a single binary value, 0 or 1, quantum\r\nbits (or qubits) can be in a superposition of both. Thus, quantum computers can store\r\nand handle more information at the same time and a quantum advantage has already\r\nbeen demonstrated for two types of computational tasks. Rapid progress in academic\r\nand industry labs accelerates the development of superconducting processors which may\r\nsoon fnd applications in complex computations, chemical simulations, cryptography, and\r\noptimization. Now that these machines are scaled up to tackle such problems the questions\r\nof qubit interconnects and networks becomes very relevant. How to route signals on-chip\r\nbetween diferent processor components? What is the most efcient way to entangle\r\nqubits? And how to then send and process entangled signals between distant cryostats\r\nhosting superconducting processors?\r\nIn this thesis, we are looking for solutions to these problems by studying the collective\r\nbehavior of superconducting qubit ensembles. We frst demonstrate on-demand tunable\r\ndirectional scattering of microwave photons from a pair of qubits in a waveguide. Such a\r\ndevice can route microwave photons on-chip with a high diode efciency. Then we focus\r\non studying ultra-strong coupling regimes between light (microwave photons) and matter\r\n(superconducting qubits), a regime that could be promising for extremely fast multi-qubit\r\nentanglement generation. Finally, we show coherent pulse storage and periodic revivals\r\nin a fve qubit ensemble strongly coupled to a resonator. Such a reconfgurable storage\r\ndevice could be used as part of a quantum repeater that is needed for longer-distance\r\nquantum communication.\r\nThe achieved high degree of control over multi-qubit ensembles highlights not only the\r\nbeautiful physics of circuit quantum electrodynamics, it also represents the frst step\r\ntoward new quantum simulation and communication methods, and certain techniques\r\nmay also fnd applications in future superconducting quantum computing hardware.\r\n"}],"doi":"10.15479/at:ista:12132","author":[{"full_name":"Redchenko, Elena","last_name":"Redchenko","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","first_name":"Elena"}],"title":"Controllable states of superconducting Qubit ensembles","supervisor":[{"orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M"}],"_id":"12366","has_accepted_license":"1","article_processing_charge":"No","degree_awarded":"PhD","file":[{"file_id":"12367","date_created":"2023-01-25T09:41:49Z","file_name":"Final_Thesis_ES_Redchenko.pdf","relation":"main_file","creator":"cchlebak","file_size":56076868,"embargo":"2022-12-28","access_level":"open_access","checksum":"39eabb1e006b41335f17f3b29af09648","content_type":"application/pdf","date_updated":"2023-01-26T23:30:44Z"}],"oa_version":"Published Version","day":"26","citation":{"ieee":"E. Redchenko, “Controllable states of superconducting Qubit ensembles,” Institute of Science and Technology Austria, 2022.","apa":"Redchenko, E. (2022). <i>Controllable states of superconducting Qubit ensembles</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12132\">https://doi.org/10.15479/at:ista:12132</a>","ama":"Redchenko E. Controllable states of superconducting Qubit ensembles. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:12132\">10.15479/at:ista:12132</a>","ista":"Redchenko E. 2022. Controllable states of superconducting Qubit ensembles. Institute of Science and Technology Austria.","short":"E. Redchenko, Controllable States of Superconducting Qubit Ensembles, Institute of Science and Technology Austria, 2022.","chicago":"Redchenko, Elena. “Controllable States of Superconducting Qubit Ensembles.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:12132\">https://doi.org/10.15479/at:ista:12132</a>.","mla":"Redchenko, Elena. <i>Controllable States of Superconducting Qubit Ensembles</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:12132\">10.15479/at:ista:12132</a>."},"month":"09","ddc":["530"],"file_date_updated":"2023-01-26T23:30:44Z","page":"168","date_updated":"2024-08-07T07:11:56Z","alternative_title":["ISTA Thesis"],"year":"2022","oa":1,"language":[{"iso":"eng"}],"type":"dissertation","publisher":"Institute of Science and Technology Austria","date_published":"2022-09-26T00:00:00Z","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"},{"_id":"EM-Fac"}],"date_created":"2023-01-25T09:17:02Z","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"status":"public","publication_status":"published","ec_funded":1,"publication_identifier":{"issn":["2663-337X"],"isbn":[" 978-3-99078-025-1 "]},"project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"}],"abstract":[{"lang":"eng","text":"Metazoan development relies on the formation and remodeling of cell-cell contacts. The \r\nbinding of adhesion receptors and remodeling of the actomyosin cell cortex at cell-cell \r\ninteraction sites have been implicated in cell-cell contact formation. Yet, how these two \r\nprocesses functionally interact to drive cell-cell contact expansion and strengthening \r\nremains unclear. Here, we study how primary germ layer progenitor cells from zebrafish \r\nbind to supported lipid bilayers (SLB) functionalized with E-cadherin ectodomains as an \r\nassay system for monitoring cell-cell contact formation at high spatiotemporal resolution. \r\nWe show that cell-cell contact formation represents a two-tiered process: E-cadherin\u0002mediated downregulation of the small GTPase RhoA at the forming contact leads to both \r\ndepletion of Myosin-2 and decrease of F-actin. This is followed by centrifugal actin \r\nnetwork flows at the contact triggered by a sharp gradient of Myosin-2 at the rim of the \r\ncontact zone, with Myosin-2 displaying higher cortical localization outside than inside of \r\nthe contact. These centrifugal cortical actin flows, in turn, not only further dilute the actin \r\nnetwork at the contact disc, but also lead to an accumulation of both F-actin and E\u0002cadherin at the contact rim. Eventually, this combination of actomyosin downregulation \r\nand flows at the contact contribute to the characteristic molecular organization implicated \r\nin contact formation and maintenance: depletion of cortical actomyosin at the contact disc, \r\ndriving contact expansion by lowering interfacial tension at the contact, and accumulation \r\nof both E-cadherin and F-actin at the contact rim, mechanically linking the contractile \r\ncortices of the adhering cells. Thus, using a biomimetic assay, we exemplify how \r\nadhesion signaling and cell mechanics function together to modulate the spatial \r\norganization of cell-cell contacts."}],"doi":"10.15479/at:ista:12153","title":"Remodeling of E-cadherin-mediated contacts via cortical  flows","supervisor":[{"orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"}],"author":[{"id":"49DA7910-F248-11E8-B48F-1D18A9856A87","first_name":"Feyza N","full_name":"Arslan, Feyza N","last_name":"Arslan","orcid":"0000-0001-5809-9566"}],"_id":"12368","has_accepted_license":"1","article_processing_charge":"No","degree_awarded":"PhD","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_id":"12369","date_created":"2023-01-25T10:52:46Z","access_level":"open_access","content_type":"application/pdf","checksum":"e54a3e69b83ebf166544164afd25608e","success":1,"date_updated":"2023-01-25T10:52:46Z","file_name":"THESIS_FINAL_FArslan_pdfa.pdf","relation":"main_file","file_size":14581024,"creator":"cchlebak"}],"oa_version":"Published Version","citation":{"mla":"Arslan, Feyza N. <i>Remodeling of E-Cadherin-Mediated Contacts via Cortical  Flows</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:12153\">10.15479/at:ista:12153</a>.","chicago":"Arslan, Feyza N. “Remodeling of E-Cadherin-Mediated Contacts via Cortical  Flows.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:12153\">https://doi.org/10.15479/at:ista:12153</a>.","ama":"Arslan FN. Remodeling of E-cadherin-mediated contacts via cortical  flows. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:12153\">10.15479/at:ista:12153</a>","ista":"Arslan FN. 2022. Remodeling of E-cadherin-mediated contacts via cortical  flows. Institute of Science and Technology Austria.","short":"F.N. Arslan, Remodeling of E-Cadherin-Mediated Contacts via Cortical  Flows, Institute of Science and Technology Austria, 2022.","apa":"Arslan, F. N. (2022). <i>Remodeling of E-cadherin-mediated contacts via cortical  flows</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12153\">https://doi.org/10.15479/at:ista:12153</a>","ieee":"F. N. Arslan, “Remodeling of E-cadherin-mediated contacts via cortical  flows,” Institute of Science and Technology Austria, 2022."},"day":"29","month":"09","file_date_updated":"2023-01-25T10:52:46Z","ddc":["570"],"related_material":{"record":[{"id":"9350","relation":"part_of_dissertation","status":"public"}]},"page":"113","date_updated":"2023-08-08T13:14:10Z","year":"2022","alternative_title":["ISTA Thesis"],"oa":1,"type":"dissertation","language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","date_published":"2022-09-29T00:00:00Z","date_created":"2023-01-25T10:43:24Z","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"NanoFab"}],"department":[{"_id":"GradSch"},{"_id":"CaHe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"abstract":[{"lang":"eng","text":"Environmental cues influence the highly dynamic morphology of microglia. Strategies to \r\ncharacterize these changes usually involve user-selected morphometric features, which \r\npreclude the identification of a spectrum of context-dependent morphological phenotypes. \r\nHere, we develop MorphOMICs, a topological data analysis approach, which enables semi\u0002automatic mapping of microglial morphology into an atlas of cue-dependent phenotypes,\r\novercomes feature-selection bias and minimizes biological variability. \r\nFirst, with MorphOMICs we derive the morphological spectrum of microglia across seven \r\nbrain regions during postnatal development and in two distinct Alzheimer’s disease \r\ndegeneration mouse models. We uncover region-specific and sexually dimorphic\r\nmorphological trajectories, with females showing an earlier morphological shift than males in \r\nthe degenerating brain. Overall, we demonstrate that both long primary- and short terminal \r\nprocesses provide distinct insights to morphological phenotypes. Moreover, using machine \r\nlearning to map novel condition on the spectrum, we observe that microglia morphologies \r\nreflect a dose-dependent adaptation upon ketamine anesthesia and do not recover to control \r\nmorphologies.\r\nNext, we took advantage of MorphOMICs to build a high-resolution and layer-specific map of \r\nmicroglial morphological spectrum in the retina, covering postnatal development and rd10 \r\ndegeneration. Here, following photoreceptor death, microglia assume an early development\u0002like morphology. Finally, we map microglial morphology following optic nerve crush on the \r\nretinal spectrum and observe a layer- and sex-dependent response. \r\nOverall, MorphOMICs opens a new perspective to analyze microglial morphology across \r\nmultiple conditions, and provides a novel tool to characterize microglial morphology beyond \r\nthe traditionally dichotomized view of microglia."}],"doi":"10.15479/at:ista:12378","author":[{"orcid":"0000-0001-9434-8902","full_name":"Colombo, Gloria","last_name":"Colombo","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","first_name":"Gloria"}],"title":"MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes","supervisor":[{"full_name":"Siegert, Sandra","last_name":"Siegert","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","first_name":"Sandra","orcid":"0000-0001-8635-0877"}],"_id":"12378","status":"public","publication_status":"published","ec_funded":1,"publication_identifier":{"issn":["2663-337X"]},"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"}],"oa_version":"Published Version","day":"11","citation":{"chicago":"Colombo, Gloria. “MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:12378\">https://doi.org/10.15479/at:ista:12378</a>.","mla":"Colombo, Gloria. <i>MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:12378\">10.15479/at:ista:12378</a>.","ieee":"G. Colombo, “MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes,” Institute of Science and Technology Austria, 2022.","apa":"Colombo, G. (2022). <i>MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12378\">https://doi.org/10.15479/at:ista:12378</a>","ista":"Colombo G. 2022. MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes. Institute of Science and Technology Austria.","short":"G. Colombo, MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes, Institute of Science and Technology Austria, 2022.","ama":"Colombo G. MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:12378\">10.15479/at:ista:12378</a>"},"month":"11","ddc":["570"],"file_date_updated":"2023-04-12T22:30:03Z","has_accepted_license":"1","article_processing_charge":"No","degree_awarded":"PhD","file":[{"embargo_to":"open_access","date_created":"2023-01-25T14:31:32Z","file_id":"12379","checksum":"8cd3ddfe9b53381dcf086023d8d8893a","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","date_updated":"2023-04-12T22:30:03Z","creator":"cchlebak","file_size":23890382,"relation":"source_file","file_name":"Gloria_Colombo_Thesis.docx"},{"file_id":"12380","date_created":"2023-01-25T14:31:36Z","file_name":"Gloria_Colombo_Thesis.pdf","relation":"main_file","creator":"cchlebak","file_size":13802421,"embargo":"2023-04-11","access_level":"open_access","content_type":"application/pdf","checksum":"8af4319c18b516e8758e9a6cb02b103b","date_updated":"2023-04-12T22:30:03Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"alternative_title":["ISTA Thesis"],"year":"2022","oa":1,"related_material":{"record":[{"id":"12244","relation":"part_of_dissertation","status":"public"}]},"page":"142","date_updated":"2023-08-04T09:40:37Z","date_published":"2022-11-11T00:00:00Z","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"ScienComp"}],"date_created":"2023-01-25T14:27:43Z","department":[{"_id":"GradSch"},{"_id":"SaSi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"type":"dissertation","publisher":"Institute of Science and Technology Austria"},{"year":"2022","alternative_title":["ISTA Thesis"],"oa":1,"page":"196","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"9005"}]},"date_updated":"2023-08-07T13:32:09Z","date_created":"2023-01-26T10:00:42Z","date_published":"2022-12-15T00:00:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"language":[{"iso":"eng"}],"type":"dissertation","publisher":"Institute of Science and Technology Austria","doi":"10.15479/at:ista:12390","abstract":[{"text":"The scope of this thesis is to study quantum systems exhibiting a continuous symmetry that\r\nis broken on the level of the corresponding effective theory. In particular we are going to\r\ninvestigate translation-invariant Bose gases in the mean field limit, effectively described by\r\nthe Hartree functional, and the Fröhlich Polaron in the regime of strong coupling, effectively\r\ndescribed by the Pekar functional. The latter is a model describing the interaction between a\r\ncharged particle and the optical modes of a polar crystal. Regarding the former, we assume in\r\naddition that the particles in the gas are unconfined, and typically we will consider particles\r\nthat are subject to an attractive interaction. In both cases the ground state energy of the\r\nHamiltonian is not a proper eigenvalue due to the underlying translation-invariance, while on\r\nthe contrary there exists a whole invariant orbit of minimizers for the corresponding effective\r\nfunctionals. Both, the absence of proper eigenstates and the broken symmetry of the effective\r\ntheory, make the study significantly more involved and it is the content of this thesis to\r\ndevelop a frameworks which allows for a systematic way to circumvent these issues.\r\nIt is a well-established result that the ground state energy of Bose gases in the mean field limit,\r\nas well as the ground state energy of the Fröhlich Polaron in the regime of strong coupling, is\r\nto leading order given by the minimal energy of the corresponding effective theory. As part\r\nof this thesis we identify the sub-leading term in the expansion of the ground state energy,\r\nwhich can be interpreted as the quantum correction to the classical energy, since the effective\r\ntheories under consideration can be seen as classical counterparts.\r\nWe are further going to establish an asymptotic expression for the energy-momentum relation\r\nof the Fröhlich Polaron in the strong coupling limit. In the regime of suitably small momenta,\r\nthis asymptotic expression agrees with the energy-momentum relation of a free particle having\r\nan effectively increased mass, and we find that this effectively increased mass agrees with the\r\nconjectured value in the physics literature.\r\nIn addition we will discuss two unrelated papers written by the author during his stay at ISTA\r\nin the appendix. The first one concerns the realization of anyons, which are quasi-particles\r\nacquiring a non-trivial phase under the exchange of two particles, as molecular impurities.\r\nThe second one provides a classification of those vector fields defined on a given manifold\r\nthat can be written as the gradient of a given functional with respect to a suitable metric,\r\nprovided that some mild smoothness assumptions hold. This classification is subsequently\r\nused to identify those quantum Markov semigroups that can be written as a gradient flow of\r\nthe relative entropy.\r\n","lang":"eng"}],"_id":"12390","author":[{"last_name":"Brooks","full_name":"Brooks, Morris","first_name":"Morris","id":"B7ECF9FC-AA38-11E9-AC9A-0930E6697425","orcid":"0000-0002-6249-0928"}],"title":"Translation-invariant quantum systems with effectively broken symmetry","supervisor":[{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Seiringer, Robert","last_name":"Seiringer","orcid":"0000-0002-6781-0521"}],"ec_funded":1,"publication_status":"published","status":"public","project":[{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"issn":["2663-337X"]},"oa_version":"Published Version","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","file_date_updated":"2023-01-26T10:02:42Z","ddc":["500"],"month":"12","day":"15","citation":{"mla":"Brooks, Morris. <i>Translation-Invariant Quantum Systems with Effectively Broken Symmetry</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:12390\">10.15479/at:ista:12390</a>.","chicago":"Brooks, Morris. “Translation-Invariant Quantum Systems with Effectively Broken Symmetry.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:12390\">https://doi.org/10.15479/at:ista:12390</a>.","short":"M. Brooks, Translation-Invariant Quantum Systems with Effectively Broken Symmetry, Institute of Science and Technology Austria, 2022.","ista":"Brooks M. 2022. Translation-invariant quantum systems with effectively broken symmetry. Institute of Science and Technology Austria.","ama":"Brooks M. Translation-invariant quantum systems with effectively broken symmetry. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:12390\">10.15479/at:ista:12390</a>","apa":"Brooks, M. (2022). <i>Translation-invariant quantum systems with effectively broken symmetry</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12390\">https://doi.org/10.15479/at:ista:12390</a>","ieee":"M. Brooks, “Translation-invariant quantum systems with effectively broken symmetry,” Institute of Science and Technology Austria, 2022."},"article_processing_charge":"No","has_accepted_license":"1","file":[{"date_created":"2023-01-26T10:02:34Z","file_id":"12391","file_size":3095225,"relation":"main_file","creator":"cchlebak","file_name":"Brooks_Thesis.pdf","content_type":"application/pdf","checksum":"b31460e937f33b557abb40ebef02b567","access_level":"open_access","date_updated":"2023-01-26T10:02:34Z","success":1},{"file_name":"Brooks_Thesis.tex","creator":"cchlebak","relation":"source_file","file_size":809842,"access_level":"closed","content_type":"application/octet-stream","checksum":"9751869fa5e7981588ad4228f4fd4bd6","date_updated":"2023-01-26T10:02:42Z","file_id":"12392","date_created":"2023-01-26T10:02:42Z"}],"tmp":{"image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"degree_awarded":"PhD"},{"date_published":"2022-12-22T00:00:00Z","date_created":"2023-01-26T11:55:16Z","department":[{"_id":"GradSch"},{"_id":"MiSi"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"dissertation","language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"year":"2022","oa":1,"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"679"},{"status":"public","relation":"part_of_dissertation","id":"10703"},{"status":"public","relation":"part_of_dissertation","id":"7885"},{"relation":"part_of_dissertation","status":"public","id":"9429"}]},"page":"105","date_updated":"2024-09-10T12:04:26Z","oa_version":"Published Version","citation":{"mla":"Tasciyan, Saren. <i>Role of Microenvironment Heterogeneity in Cancer Cell Invasion</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:12401\">10.15479/at:ista:12401</a>.","chicago":"Tasciyan, Saren. “Role of Microenvironment Heterogeneity in Cancer Cell Invasion.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:12401\">https://doi.org/10.15479/at:ista:12401</a>.","ieee":"S. Tasciyan, “Role of microenvironment heterogeneity in cancer cell invasion,” Institute of Science and Technology Austria, 2022.","apa":"Tasciyan, S. (2022). <i>Role of microenvironment heterogeneity in cancer cell invasion</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12401\">https://doi.org/10.15479/at:ista:12401</a>","ista":"Tasciyan S. 2022. Role of microenvironment heterogeneity in cancer cell invasion. Institute of Science and Technology Austria.","ama":"Tasciyan S. Role of microenvironment heterogeneity in cancer cell invasion. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:12401\">10.15479/at:ista:12401</a>","short":"S. Tasciyan, Role of Microenvironment Heterogeneity in Cancer Cell Invasion, Institute of Science and Technology Austria, 2022."},"day":"22","month":"12","ddc":["610"],"file_date_updated":"2023-12-21T23:30:03Z","has_accepted_license":"1","article_processing_charge":"No","degree_awarded":"PhD","file":[{"file_id":"12402","date_created":"2023-01-26T11:58:14Z","embargo":"2023-12-20","file_name":"PhD-Thesis_Saren Tasciyan_formatted_aftercrash_fixed_600dpi_95pc_final_PDFA3b.pdf","file_size":42059787,"relation":"main_file","creator":"cchlebak","date_updated":"2023-12-21T23:30:03Z","access_level":"open_access","content_type":"application/pdf","checksum":"cc4a2b4a7e3c4ee8ef7f2dbf909b12bd"},{"file_name":"Source Files - Saren Tasciyan - PhD Thesis.zip","creator":"cchlebak","file_size":261256696,"relation":"source_file","access_level":"closed","checksum":"f1b4ca98b8ab0cb043b1830971e9bd9c","content_type":"application/x-zip-compressed","date_updated":"2023-12-21T23:30:03Z","embargo_to":"open_access","file_id":"12403","date_created":"2023-01-26T12:00:10Z"}],"abstract":[{"text":"Detachment of the cancer cells from the bulk of the tumor is the first step of metastasis, which\r\nis the primary cause of cancer related deaths. It is unclear, which factors contribute to this step.\r\nRecent studies indicate a crucial role of the tumor microenvironment in malignant\r\ntransformation and metastasis. Studying cancer cell invasion and detachments quantitatively in\r\nthe context of its physiological microenvironment is technically challenging. Especially, precise\r\ncontrol of microenvironmental properties in vivo is currently not possible. Here, I studied the\r\nrole of microenvironment geometry in the invasion and detachment of cancer cells from the\r\nbulk with a simplistic and reductionist approach. In this approach, I engineered microfluidic\r\ndevices to mimic a pseudo 3D extracellular matrix environment, where I was able to\r\nquantitatively tune the geometrical configuration of the microenvironment and follow tumor\r\ncells with fluorescence live imaging. To aid quantitative analysis I developed a widely applicable\r\nsoftware application to automatically analyze and visualize particle tracking data.\r\nQuantitative analysis of tumor cell invasion in isotropic and anisotropic microenvironments\r\nshowed that heterogeneity in the microenvironment promotes faster invasion and more\r\nfrequent detachment of cells. These observations correlated with overall higher speed of cells at\r\nthe edge of the bulk of the cells. In heterogeneous microenvironments cells preferentially\r\npassed through larger pores, thus invading areas of least resistance and generating finger-like\r\ninvasive structures. The detachments occurred mostly at the tips of these structures.\r\nTo investigate the potential mechanism, we established a two dimensional model to simulate\r\nactive Brownian particles representing the cell nuclei dynamics. These simulations backed our in\r\nvitro observations without the need of precise fitting the simulation parameters. Our model\r\nsuggests the importance of the pore heterogeneity in the direction perpendicular to the\r\norientation of bias field (lateral heterogeneity), which causes the interface roughening.","lang":"eng"}],"doi":"10.15479/at:ista:12401","supervisor":[{"full_name":"Sixt, Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","orcid":"0000-0002-6620-9179"}],"title":"Role of microenvironment heterogeneity in cancer cell invasion","author":[{"full_name":"Tasciyan, Saren","last_name":"Tasciyan","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","first_name":"Saren","orcid":"0000-0003-1671-393X"}],"_id":"12401","publication_status":"published","status":"public","publication_identifier":{"issn":["2663-337X"]}},{"article_number":"241","article_type":"original","date_updated":"2023-08-04T09:37:23Z","publication":"ACM Transactions on Graphics","year":"2022","oa":1,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","isi":1,"publisher":"Association for Computing Machinery","intvolume":"        41","date_created":"2023-01-29T23:00:59Z","scopus_import":"1","date_published":"2022-12-01T00:00:00Z","external_id":{"isi":["000891651900061"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"ChWo"}],"publication_status":"published","status":"public","acknowledgement":"We thank the visual computing group at IST Austria for their valuable discussions and feedback. Houdini Education licenses were provided by SideFX software. This project was funded in part by the European Research Council (ERC Consolidator Grant 101045083 CoDiNA).","project":[{"name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","grant_number":"101045083","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088"}],"publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"doi":"10.1145/3550454.3555459","abstract":[{"lang":"eng","text":"This paper presents a new representation of curve dynamics, with applications to vortex filaments in fluid dynamics. Instead of representing these filaments with explicit curve geometry and Lagrangian equations of motion, we represent curves implicitly with a new co-dimensional 2 level set description. Our implicit representation admits several redundant mathematical degrees of freedom in both the configuration and the dynamics of the curves, which can be tailored specifically to improve numerical robustness, in contrast to naive approaches for implicit curve dynamics that suffer from overwhelming numerical stability problems. Furthermore, we note how these hidden degrees of freedom perfectly map to a Clebsch representation in fluid dynamics. Motivated by these observations, we introduce untwisted level set functions and non-swirling dynamics which successfully regularize sources of numerical instability, particularly in the twisting modes around curve filaments. A consequence is a novel simulation method which produces stable dynamics for large numbers of interacting vortex filaments and effortlessly handles topological changes and re-connection events."}],"issue":"6","_id":"12431","title":"Hidden degrees of freedom in implicit vortex filaments","author":[{"full_name":"Ishida, Sadashige","last_name":"Ishida","id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425","first_name":"Sadashige"},{"full_name":"Wojtan, Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","orcid":"0000-0001-6646-5546"},{"first_name":"Albert","last_name":"Chern","full_name":"Chern, Albert"}],"article_processing_charge":"No","volume":41,"has_accepted_license":"1","file":[{"date_created":"2023-01-30T07:15:48Z","file_id":"12433","date_updated":"2023-01-30T07:15:48Z","success":1,"checksum":"a2fba257fdefe0e747182be6c0f7c70c","content_type":"application/pdf","access_level":"open_access","file_size":15551202,"creator":"dernst","relation":"main_file","file_name":"2022_ACM_Ishida.pdf"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","month":"12","ddc":["000"],"file_date_updated":"2023-01-30T07:15:48Z","citation":{"apa":"Ishida, S., Wojtan, C., &#38; Chern, A. (2022). Hidden degrees of freedom in implicit vortex filaments. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3550454.3555459\">https://doi.org/10.1145/3550454.3555459</a>","ieee":"S. Ishida, C. Wojtan, and A. Chern, “Hidden degrees of freedom in implicit vortex filaments,” <i>ACM Transactions on Graphics</i>, vol. 41, no. 6. Association for Computing Machinery, 2022.","ista":"Ishida S, Wojtan C, Chern A. 2022. Hidden degrees of freedom in implicit vortex filaments. ACM Transactions on Graphics. 41(6), 241.","ama":"Ishida S, Wojtan C, Chern A. Hidden degrees of freedom in implicit vortex filaments. <i>ACM Transactions on Graphics</i>. 2022;41(6). doi:<a href=\"https://doi.org/10.1145/3550454.3555459\">10.1145/3550454.3555459</a>","short":"S. Ishida, C. Wojtan, A. Chern, ACM Transactions on Graphics 41 (2022).","chicago":"Ishida, Sadashige, Chris Wojtan, and Albert Chern. “Hidden Degrees of Freedom in Implicit Vortex Filaments.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3550454.3555459\">https://doi.org/10.1145/3550454.3555459</a>.","mla":"Ishida, Sadashige, et al. “Hidden Degrees of Freedom in Implicit Vortex Filaments.” <i>ACM Transactions on Graphics</i>, vol. 41, no. 6, 241, Association for Computing Machinery, 2022, doi:<a href=\"https://doi.org/10.1145/3550454.3555459\">10.1145/3550454.3555459</a>."},"day":"01"},{"_id":"12432","title":"Solving the Hamilton cycle problem fast on average","author":[{"last_name":"Anastos","full_name":"Anastos, Michael","first_name":"Michael","id":"0b2a4358-bb35-11ec-b7b9-e3279b593dbb"}],"doi":"10.1109/FOCS54457.2022.00091","abstract":[{"lang":"eng","text":"We present CertifyHAM, a deterministic algorithm that takes a graph G as input and either finds a Hamilton cycle of G or outputs that such a cycle does not exist. If G ∼ G(n, p) and p ≥\r\n100 log n/n then the expected running time of CertifyHAM is O(n/p) which is best possible. This improves upon previous results due to Gurevich and Shelah, Thomason and Alon, and\r\nKrivelevich, who proved analogous results for p being constant, p ≥ 12n −1/3 and p ≥ 70n\r\n−1/2 respectively."}],"project":[{"call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"publication_identifier":{"issn":["0272-5428"],"isbn":["9781665455190"]},"ec_funded":1,"publication_status":"published","status":"public","acknowledgement":"This project has received funding from the European Union’s Horizon 2020\r\nresearch and innovation programme under the Marie Skłodowska-Curie grant\r\nagreement No 101034413","month":"12","citation":{"ieee":"M. Anastos, “Solving the Hamilton cycle problem fast on average,” in <i>63rd Annual IEEE Symposium on Foundations of Computer Science</i>, Denver, CO, United States, 2022, vol. 2022–October, pp. 919–930.","apa":"Anastos, M. (2022). Solving the Hamilton cycle problem fast on average. In <i>63rd Annual IEEE Symposium on Foundations of Computer Science</i> (Vol. 2022–October, pp. 919–930). Denver, CO, United States: Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/FOCS54457.2022.00091\">https://doi.org/10.1109/FOCS54457.2022.00091</a>","ama":"Anastos M. Solving the Hamilton cycle problem fast on average. In: <i>63rd Annual IEEE Symposium on Foundations of Computer Science</i>. Vol 2022-October. Institute of Electrical and Electronics Engineers; 2022:919-930. doi:<a href=\"https://doi.org/10.1109/FOCS54457.2022.00091\">10.1109/FOCS54457.2022.00091</a>","ista":"Anastos M. 2022. Solving the Hamilton cycle problem fast on average. 63rd Annual IEEE Symposium on Foundations of Computer Science. FOCS: Symposium on Foundations of Computer Science vol. 2022–October, 919–930.","short":"M. Anastos, in:, 63rd Annual IEEE Symposium on Foundations of Computer Science, Institute of Electrical and Electronics Engineers, 2022, pp. 919–930.","chicago":"Anastos, Michael. “Solving the Hamilton Cycle Problem Fast on Average.” In <i>63rd Annual IEEE Symposium on Foundations of Computer Science</i>, 2022–October:919–30. Institute of Electrical and Electronics Engineers, 2022. <a href=\"https://doi.org/10.1109/FOCS54457.2022.00091\">https://doi.org/10.1109/FOCS54457.2022.00091</a>.","mla":"Anastos, Michael. “Solving the Hamilton Cycle Problem Fast on Average.” <i>63rd Annual IEEE Symposium on Foundations of Computer Science</i>, vol. 2022–October, Institute of Electrical and Electronics Engineers, 2022, pp. 919–30, doi:<a href=\"https://doi.org/10.1109/FOCS54457.2022.00091\">10.1109/FOCS54457.2022.00091</a>."},"day":"01","oa_version":"None","conference":{"end_date":"2022-11-03","location":"Denver, CO, United States","start_date":"2022-10-31","name":"FOCS: Symposium on Foundations of Computer Science"},"volume":"2022-October","article_processing_charge":"No","year":"2022","date_updated":"2023-08-04T09:37:56Z","publication":"63rd Annual IEEE Symposium on Foundations of Computer Science","page":"919-930","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"MaKw"}],"date_created":"2023-01-29T23:00:59Z","scopus_import":"1","external_id":{"isi":["000909382900084"]},"date_published":"2022-12-01T00:00:00Z","publisher":"Institute of Electrical and Electronics Engineers","language":[{"iso":"eng"}],"quality_controlled":"1","type":"conference","isi":1},{"article_processing_charge":"No","has_accepted_license":"1","file":[{"creator":"bbickel","file_size":5202710,"relation":"main_file","file_name":"vorf_main.pdf","checksum":"b60b70bb48700aee709c85a69231821d","content_type":"application/pdf","access_level":"open_access","date_updated":"2023-01-30T10:48:18Z","date_created":"2023-01-30T10:48:18Z","file_id":"12453","title":"VoRF: Volumetric Relightable Faces"},{"date_created":"2023-01-30T10:48:29Z","file_id":"12454","title":"VoRF: Volumetric Relightable Faces – SUPPLEMENTAL MATERIAL –","relation":"supplementary_material","file_size":37953188,"creator":"bbickel","file_name":"vorf_supp.pdf","date_updated":"2023-01-30T10:48:29Z","checksum":"ce5f4ce66eaaa1590ee5df989fca6f61","content_type":"application/pdf","access_level":"open_access"},{"date_updated":"2023-01-30T10:48:37Z","content_type":"video/mp4","checksum":"08aecca434b08fee75ee1efe87943718","access_level":"open_access","file_size":57855492,"relation":"supplementary_material","creator":"bbickel","file_name":"video.mp4","date_created":"2023-01-30T10:48:37Z","file_id":"12455"}],"conference":{"start_date":"2022-11-21","location":"London, United Kingdom","end_date":"2022-11-24","name":"BMVC: British Machine Vision Conference"},"oa_version":"Published Version","month":"12","ddc":["000"],"file_date_updated":"2023-01-30T10:48:37Z","day":"01","citation":{"ieee":"P. Rao <i>et al.</i>, “VoRF: Volumetric Relightable Faces,” in <i>33rd British Machine Vision Conference</i>, London, United Kingdom, 2022.","apa":"Rao, P., B R, M., Fox, G., Weyrich, T., Bickel, B., Seidel, H.-P., … Elgharib, M. (2022). VoRF: Volumetric Relightable Faces. In <i>33rd British Machine Vision Conference</i>. London, United Kingdom: British Machine Vision Association and Society for Pattern Recognition.","ista":"Rao P, B R M, Fox G, Weyrich T, Bickel B, Seidel H-P, Pfister H, Matusik W, Tewari A, Theobalt C, Elgharib M. 2022. VoRF: Volumetric Relightable Faces. 33rd British Machine Vision Conference. BMVC: British Machine Vision Conference, 708.","ama":"Rao P, B R M, Fox G, et al. VoRF: Volumetric Relightable Faces. In: <i>33rd British Machine Vision Conference</i>. British Machine Vision Association and Society for Pattern Recognition; 2022.","short":"P. Rao, M. B R, G. Fox, T. Weyrich, B. Bickel, H.-P. Seidel, H. Pfister, W. Matusik, A. Tewari, C. Theobalt, M. Elgharib, in:, 33rd British Machine Vision Conference, British Machine Vision Association and Society for Pattern Recognition, 2022.","chicago":"Rao, Pramod, Mallikarjun B R, Gereon Fox, Tim Weyrich, Bernd Bickel, Hans-Peter Seidel, Hanspeter Pfister, et al. “VoRF: Volumetric Relightable Faces.” In <i>33rd British Machine Vision Conference</i>. British Machine Vision Association and Society for Pattern Recognition, 2022.","mla":"Rao, Pramod, et al. “VoRF: Volumetric Relightable Faces.” <i>33rd British Machine Vision Conference</i>, 708, British Machine Vision Association and Society for Pattern Recognition, 2022."},"status":"public","publication_status":"published","acknowledgement":"This work was supported by the ERC Consolidator Grant 4DReply (770784).","abstract":[{"lang":"eng","text":"Portrait viewpoint and illumination editing is an important problem with several applications in VR/AR, movies, and photography. Comprehensive knowledge of geometry and illumination is critical for obtaining photorealistic results. Current methods are unable to explicitly model in 3D while handing both viewpoint and illumination editing from a single image. In this paper, we propose VoRF, a novel approach that can take even a single portrait image as input and relight human heads under novel illuminations that can be viewed from arbitrary viewpoints. VoRF represents a human head as a continuous volumetric field and learns a prior model of human heads using a coordinate-based MLP with separate latent spaces for identity and illumination. The prior model is learnt in an auto-decoder manner over a diverse class of head shapes and appearances, allowing VoRF to generalize to novel test identities from a single input image. Additionally, VoRF has a reflectance MLP that uses the intermediate features of the prior model for rendering One-Light-at-A-Time (OLAT) images under novel views. We synthesize novel illuminations by combining these OLAT images with target environment maps. Qualitative and quantitative evaluations demonstrate the effectiveness of VoRF for relighting and novel view synthesis even when applied to unseen subjects under uncontrolled illuminations."}],"_id":"12452","author":[{"last_name":"Rao","full_name":"Rao, Pramod","first_name":"Pramod"},{"first_name":"Mallikarjun","full_name":"B R, Mallikarjun","last_name":"B R"},{"first_name":"Gereon","last_name":"Fox","full_name":"Fox, Gereon"},{"full_name":"Weyrich, Tim","last_name":"Weyrich","first_name":"Tim"},{"last_name":"Bickel","full_name":"Bickel, Bernd","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385"},{"full_name":"Seidel, Hans-Peter","last_name":"Seidel","first_name":"Hans-Peter"},{"first_name":"Hanspeter","full_name":"Pfister, Hanspeter","last_name":"Pfister"},{"full_name":"Matusik, Wojciech","last_name":"Matusik","first_name":"Wojciech"},{"last_name":"Tewari","full_name":"Tewari, Ayush","first_name":"Ayush"},{"last_name":"Theobalt","full_name":"Theobalt, Christian","first_name":"Christian"},{"first_name":"Mohamed","last_name":"Elgharib","full_name":"Elgharib, Mohamed"}],"title":"VoRF: Volumetric Relightable Faces","quality_controlled":"1","type":"conference","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://bmvc2022.mpi-inf.mpg.de/708/","open_access":"1"}],"publisher":"British Machine Vision Association and Society for Pattern Recognition","scopus_import":"1","date_created":"2023-01-30T10:47:06Z","date_published":"2022-12-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"BeBi"}],"article_number":"708","date_updated":"2023-10-31T08:40:55Z","publication":"33rd British Machine Vision Conference","year":"2022","oa":1},{"year":"2022","keyword":["Statistics","Probability and Uncertainty","Statistics and Probability","Statistical and Nonlinear Physics"],"oa":1,"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"10598"}]},"article_number":"114003","article_type":"original","publication":"Journal of Statistical Mechanics: Theory and Experiment","date_updated":"2024-03-07T10:36:52Z","external_id":{"isi":["000889589900001"]},"date_published":"2022-11-24T00:00:00Z","date_created":"2023-02-02T08:31:57Z","scopus_import":"1","department":[{"_id":"MaMo"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","publisher":"IOP Publishing","intvolume":"      2022","abstract":[{"lang":"eng","text":"We consider the problem of estimating a signal from measurements obtained via a generalized linear model. We focus on estimators based on approximate message passing (AMP), a family of iterative algorithms with many appealing features: the performance of AMP in the high-dimensional limit can be succinctly characterized under suitable model assumptions; AMP can also be tailored to the empirical distribution of the signal entries, and for a wide class of estimation problems, AMP is conjectured to be optimal among all polynomial-time algorithms. However, a major issue of AMP is that in many models (such as phase retrieval), it requires an initialization correlated with the ground-truth signal and independent from the measurement matrix. Assuming that such an initialization is available is typically not realistic. In this paper, we solve this problem by proposing an AMP algorithm initialized with a spectral estimator. With such an initialization, the standard AMP analysis fails since the spectral estimator depends in a complicated way on the design matrix. Our main contribution is a rigorous characterization of the performance of AMP with spectral initialization in the high-dimensional limit. The key technical idea is to define and analyze a two-phase artificial AMP algorithm that first produces the spectral estimator, and then closely approximates the iterates of the true AMP. We also provide numerical results that demonstrate the validity of the proposed approach."}],"issue":"11","doi":"10.1088/1742-5468/ac9828","title":"Approximate message passing with spectral initialization for generalized linear models","author":[{"orcid":"0000-0002-3242-7020","last_name":"Mondelli","full_name":"Mondelli, Marco","first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425"},{"first_name":"Ramji","last_name":"Venkataramanan","full_name":"Venkataramanan, Ramji"}],"_id":"12480","status":"public","publication_status":"published","acknowledgement":"The authors would like to thank Andrea Montanari for helpful discussions.\r\nM Mondelli was partially supported by the 2019 Lopez-Loreta Prize. R Venkataramanan was partially supported by the Alan Turing Institute under the EPSRC Grant\r\nEP/N510129/1.","publication_identifier":{"issn":["1742-5468"]},"project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"oa_version":"Published Version","citation":{"apa":"Mondelli, M., &#38; Venkataramanan, R. (2022). Approximate message passing with spectral initialization for generalized linear models. <i>Journal of Statistical Mechanics: Theory and Experiment</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1742-5468/ac9828\">https://doi.org/10.1088/1742-5468/ac9828</a>","ieee":"M. Mondelli and R. Venkataramanan, “Approximate message passing with spectral initialization for generalized linear models,” <i>Journal of Statistical Mechanics: Theory and Experiment</i>, vol. 2022, no. 11. IOP Publishing, 2022.","ista":"Mondelli M, Venkataramanan R. 2022. Approximate message passing with spectral initialization for generalized linear models. Journal of Statistical Mechanics: Theory and Experiment. 2022(11), 114003.","ama":"Mondelli M, Venkataramanan R. Approximate message passing with spectral initialization for generalized linear models. <i>Journal of Statistical Mechanics: Theory and Experiment</i>. 2022;2022(11). doi:<a href=\"https://doi.org/10.1088/1742-5468/ac9828\">10.1088/1742-5468/ac9828</a>","short":"M. Mondelli, R. Venkataramanan, Journal of Statistical Mechanics: Theory and Experiment 2022 (2022).","mla":"Mondelli, Marco, and Ramji Venkataramanan. “Approximate Message Passing with Spectral Initialization for Generalized Linear Models.” <i>Journal of Statistical Mechanics: Theory and Experiment</i>, vol. 2022, no. 11, 114003, IOP Publishing, 2022, doi:<a href=\"https://doi.org/10.1088/1742-5468/ac9828\">10.1088/1742-5468/ac9828</a>.","chicago":"Mondelli, Marco, and Ramji Venkataramanan. “Approximate Message Passing with Spectral Initialization for Generalized Linear Models.” <i>Journal of Statistical Mechanics: Theory and Experiment</i>. IOP Publishing, 2022. <a href=\"https://doi.org/10.1088/1742-5468/ac9828\">https://doi.org/10.1088/1742-5468/ac9828</a>."},"day":"24","ddc":["510","530"],"file_date_updated":"2023-02-02T08:35:52Z","month":"11","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","volume":2022,"file":[{"creator":"dernst","relation":"main_file","file_size":1729997,"file_name":"2022_JourStatisticalMechanics_Mondelli.pdf","content_type":"application/pdf","checksum":"01411ffa76d3e380a0446baeb89b1ef7","access_level":"open_access","date_updated":"2023-02-02T08:35:52Z","success":1,"date_created":"2023-02-02T08:35:52Z","file_id":"12481"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"status":"public","publication_status":"published","acknowledgement":"The authors would like to thank Bernd Prach, Elias Frantar, Alexandra Peste, Mahdi Nikdan, and Peter Súkeník for their helpful feedback. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp). This publication was made possible by an ETH AI Center postdoctoral fellowship granted to Nikola Konstantinov. Eugenia Iofinova was supported in part by the FWF DK VGSCO, grant agreement number W1260-N35. ","publication_identifier":{"issn":["2835-8856"]},"project":[{"_id":"9B9290DE-BA93-11EA-9121-9846C619BF3A","grant_number":" W1260-N35","name":"Vienna Graduate School on Computational Optimization"}],"abstract":[{"lang":"eng","text":"Fairness-aware learning aims at constructing classifiers that not only make accurate predictions, but also do not discriminate against specific groups. It is a fast-growing area of\r\nmachine learning with far-reaching societal impact. However, existing fair learning methods\r\nare vulnerable to accidental or malicious artifacts in the training data, which can cause\r\nthem to unknowingly produce unfair classifiers. In this work we address the problem of\r\nfair learning from unreliable training data in the robust multisource setting, where the\r\navailable training data comes from multiple sources, a fraction of which might not be representative of the true data distribution. We introduce FLEA, a filtering-based algorithm\r\nthat identifies and suppresses those data sources that would have a negative impact on\r\nfairness or accuracy if they were used for training. As such, FLEA is not a replacement of\r\nprior fairness-aware learning methods but rather an augmentation that makes any of them\r\nrobust against unreliable training data. We show the effectiveness of our approach by a\r\ndiverse range of experiments on multiple datasets. Additionally, we prove formally that\r\n–given enough data– FLEA protects the learner against corruptions as long as the fraction of\r\naffected data sources is less than half. Our source code and documentation are available at\r\nhttps://github.com/ISTAustria-CVML/FLEA."}],"title":"FLEA: Provably robust fair multisource learning from unreliable training data","author":[{"last_name":"Iofinova","full_name":"Iofinova, Eugenia B","first_name":"Eugenia B","id":"f9a17499-f6e0-11ea-865d-fdf9a3f77117","orcid":"0000-0002-7778-3221"},{"full_name":"Konstantinov, Nikola H","last_name":"Konstantinov","id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87","first_name":"Nikola H"},{"orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","full_name":"Lampert, Christoph","last_name":"Lampert"}],"_id":"12495","has_accepted_license":"1","article_processing_charge":"No","arxiv":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"date_created":"2023-02-23T10:30:04Z","file_id":"12673","creator":"dernst","file_size":1948063,"relation":"main_file","file_name":"2022_TMLR_Iofinova.pdf","checksum":"97c8a8470759cab597abb973ca137a3b","content_type":"application/pdf","access_level":"open_access","date_updated":"2023-02-23T10:30:04Z","success":1}],"oa_version":"Published Version","citation":{"chicago":"Iofinova, Eugenia B, Nikola H Konstantinov, and Christoph Lampert. “FLEA: Provably Robust Fair Multisource Learning from Unreliable Training Data.” <i>Transactions on Machine Learning Research</i>. ML Research Press, 2022.","mla":"Iofinova, Eugenia B., et al. “FLEA: Provably Robust Fair Multisource Learning from Unreliable Training Data.” <i>Transactions on Machine Learning Research</i>, ML Research Press, 2022.","apa":"Iofinova, E. B., Konstantinov, N. H., &#38; Lampert, C. (2022). FLEA: Provably robust fair multisource learning from unreliable training data. <i>Transactions on Machine Learning Research</i>. ML Research Press.","ieee":"E. B. Iofinova, N. H. Konstantinov, and C. Lampert, “FLEA: Provably robust fair multisource learning from unreliable training data,” <i>Transactions on Machine Learning Research</i>. ML Research Press, 2022.","ama":"Iofinova EB, Konstantinov NH, Lampert C. FLEA: Provably robust fair multisource learning from unreliable training data. <i>Transactions on Machine Learning Research</i>. 2022.","ista":"Iofinova EB, Konstantinov NH, Lampert C. 2022. FLEA: Provably robust fair multisource learning from unreliable training data. Transactions on Machine Learning Research.","short":"E.B. Iofinova, N.H. Konstantinov, C. Lampert, Transactions on Machine Learning Research (2022)."},"day":"22","month":"12","file_date_updated":"2023-02-23T10:30:04Z","ddc":["000"],"related_material":{"link":[{"relation":"software","url":"https://github.com/ISTAustria-CVML/FLEA","description":"source code"}]},"article_type":"original","publication":"Transactions on Machine Learning Research","date_updated":"2023-02-23T10:30:54Z","year":"2022","oa":1,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","publisher":"ML Research Press","main_file_link":[{"open_access":"1","url":"https://openreview.net/forum?id=XsPopigZXV"}],"date_published":"2022-12-22T00:00:00Z","external_id":{"arxiv":["2106.11732"]},"date_created":"2023-02-02T20:29:57Z","acknowledged_ssus":[{"_id":"ScienComp"}],"department":[{"_id":"ChLa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"}]