[{"type":"journal_article","abstract":[{"text":"All attosecond time-resolved measurements have so far relied on the use of intense near-infrared laser pulses. In particular, attosecond streaking, laser-induced electron diffraction and high-harmonic generation all make use of non-perturbative light–matter interactions. Remarkably, the effect of the strong laser field on the studied sample has often been neglected in previous studies. Here we use high-harmonic spectroscopy to measure laser-induced modifications of the electronic structure of molecules. We study high-harmonic spectra of spatially oriented CH3F and CH3Br as generic examples of polar polyatomic molecules. We accurately measure intensity ratios of even and odd-harmonic orders, and of the emission from aligned and unaligned molecules. We show that these robust observables reveal a substantial modification of the molecular electronic structure by the external laser field. Our insights offer new challenges and opportunities for a range of emerging strong-field attosecond spectroscopies.","lang":"eng"}],"_id":"14016","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Observation of laser-induced electronic structure in oriented polyatomic molecules","status":"public","intvolume":" 6","oa_version":"Published Version","scopus_import":"1","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"day":"05","article_processing_charge":"No","publication":"Nature Communications","citation":{"ista":"Kraus PM, Tolstikhin OI, Baykusheva DR, Rupenyan A, Schneider J, Bisgaard CZ, Morishita T, Jensen F, Madsen LB, Wörner HJ. 2015. Observation of laser-induced electronic structure in oriented polyatomic molecules. Nature Communications. 6, 7039.","ieee":"P. M. Kraus et al., “Observation of laser-induced electronic structure in oriented polyatomic molecules,” Nature Communications, vol. 6. Springer Nature, 2015.","apa":"Kraus, P. M., Tolstikhin, O. I., Baykusheva, D. R., Rupenyan, A., Schneider, J., Bisgaard, C. Z., … Wörner, H. J. (2015). Observation of laser-induced electronic structure in oriented polyatomic molecules. Nature Communications. Springer Nature. https://doi.org/10.1038/ncomms8039","ama":"Kraus PM, Tolstikhin OI, Baykusheva DR, et al. Observation of laser-induced electronic structure in oriented polyatomic molecules. Nature Communications. 2015;6. doi:10.1038/ncomms8039","chicago":"Kraus, P. M., O. I. Tolstikhin, Denitsa Rangelova Baykusheva, A. Rupenyan, J. Schneider, C. Z. Bisgaard, T. Morishita, F. Jensen, L. B. Madsen, and H. J. Wörner. “Observation of Laser-Induced Electronic Structure in Oriented Polyatomic Molecules.” Nature Communications. Springer Nature, 2015. https://doi.org/10.1038/ncomms8039.","mla":"Kraus, P. M., et al. “Observation of Laser-Induced Electronic Structure in Oriented Polyatomic Molecules.” Nature Communications, vol. 6, 7039, Springer Nature, 2015, doi:10.1038/ncomms8039.","short":"P.M. Kraus, O.I. Tolstikhin, D.R. Baykusheva, A. Rupenyan, J. Schneider, C.Z. Bisgaard, T. Morishita, F. Jensen, L.B. Madsen, H.J. Wörner, Nature Communications 6 (2015)."},"article_type":"original","date_published":"2015-05-05T00:00:00Z","article_number":"7039","extern":"1","year":"2015","pmid":1,"publication_status":"published","publisher":"Springer Nature","author":[{"full_name":"Kraus, P. M.","last_name":"Kraus","first_name":"P. M."},{"full_name":"Tolstikhin, O. I.","first_name":"O. I.","last_name":"Tolstikhin"},{"full_name":"Baykusheva, Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","first_name":"Denitsa Rangelova","last_name":"Baykusheva"},{"last_name":"Rupenyan","first_name":"A.","full_name":"Rupenyan, A."},{"last_name":"Schneider","first_name":"J.","full_name":"Schneider, J."},{"full_name":"Bisgaard, C. Z.","last_name":"Bisgaard","first_name":"C. Z."},{"full_name":"Morishita, T.","first_name":"T.","last_name":"Morishita"},{"full_name":"Jensen, F.","first_name":"F.","last_name":"Jensen"},{"last_name":"Madsen","first_name":"L. B.","full_name":"Madsen, L. B."},{"last_name":"Wörner","first_name":"H. J.","full_name":"Wörner, H. J."}],"date_created":"2023-08-10T06:38:01Z","date_updated":"2023-08-22T08:52:56Z","volume":6,"month":"05","publication_identifier":{"eissn":["2041-1723"]},"external_id":{"pmid":["25940229"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/ncomms8039"}],"quality_controlled":"1","doi":"10.1038/ncomms8039","language":[{"iso":"eng"}]},{"scopus_import":"1","keyword":["Multidisciplinary"],"article_processing_charge":"No","day":"22","citation":{"ama":"Kraus PM, Mignolet B, Baykusheva DR, et al. Measurement and laser control of attosecond charge migration in ionized iodoacetylene. Science. 2015;350(6262):790-795. doi:10.1126/science.aab2160","ista":"Kraus PM, Mignolet B, Baykusheva DR, Rupenyan A, Horný L, Penka EF, Grassi G, Tolstikhin OI, Schneider J, Jensen F, Madsen LB, Bandrauk AD, Remacle F, Wörner HJ. 2015. Measurement and laser control of attosecond charge migration in ionized iodoacetylene. Science. 350(6262), 790–795.","ieee":"P. M. Kraus et al., “Measurement and laser control of attosecond charge migration in ionized iodoacetylene,” Science, vol. 350, no. 6262. American Association for the Advancement of Science, pp. 790–795, 2015.","apa":"Kraus, P. M., Mignolet, B., Baykusheva, D. R., Rupenyan, A., Horný, L., Penka, E. F., … Wörner, H. J. (2015). Measurement and laser control of attosecond charge migration in ionized iodoacetylene. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aab2160","mla":"Kraus, P. M., et al. “Measurement and Laser Control of Attosecond Charge Migration in Ionized Iodoacetylene.” Science, vol. 350, no. 6262, American Association for the Advancement of Science, 2015, pp. 790–95, doi:10.1126/science.aab2160.","short":"P.M. Kraus, B. Mignolet, D.R. Baykusheva, A. Rupenyan, L. Horný, E.F. Penka, G. Grassi, O.I. Tolstikhin, J. Schneider, F. Jensen, L.B. Madsen, A.D. Bandrauk, F. Remacle, H.J. Wörner, Science 350 (2015) 790–795.","chicago":"Kraus, P. M., B. Mignolet, Denitsa Rangelova Baykusheva, A. Rupenyan, L. Horný, E. F. Penka, G. Grassi, et al. “Measurement and Laser Control of Attosecond Charge Migration in Ionized Iodoacetylene.” Science. American Association for the Advancement of Science, 2015. https://doi.org/10.1126/science.aab2160."},"publication":"Science","page":"790-795","article_type":"original","date_published":"2015-10-22T00:00:00Z","type":"journal_article","issue":"6262","abstract":[{"text":"The ultrafast motion of electrons and holes after light-matter interaction is fundamental to a broad range of chemical and biophysical processes. We advanced high-harmonic spectroscopy to resolve spatially and temporally the migration of an electron hole immediately after ionization of iodoacetylene while simultaneously demonstrating extensive control over the process. A multidimensional approach, based on the measurement and accurate theoretical description of both even and odd harmonic orders, enabled us to reconstruct both quantum amplitudes and phases of the electronic states with a resolution of ~100 attoseconds. We separately reconstructed quasi-field-free and laser-controlled charge migration as a function of the spatial orientation of the molecule and determined the shape of the hole created by ionization. Our technique opens the prospect of laser control over electronic primary processes.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14013","intvolume":" 350","title":"Measurement and laser control of attosecond charge migration in ionized iodoacetylene","status":"public","oa_version":"None","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"month":"10","external_id":{"pmid":["26494175"]},"quality_controlled":"1","doi":"10.1126/science.aab2160","language":[{"iso":"eng"}],"extern":"1","pmid":1,"year":"2015","publisher":"American Association for the Advancement of Science","publication_status":"published","author":[{"first_name":"P. M.","last_name":"Kraus","full_name":"Kraus, P. M."},{"full_name":"Mignolet, B.","last_name":"Mignolet","first_name":"B."},{"id":"71b4d059-2a03-11ee-914d-dfa3beed6530","first_name":"Denitsa Rangelova","last_name":"Baykusheva","full_name":"Baykusheva, Denitsa Rangelova"},{"last_name":"Rupenyan","first_name":"A.","full_name":"Rupenyan, A."},{"full_name":"Horný, L.","first_name":"L.","last_name":"Horný"},{"last_name":"Penka","first_name":"E. F.","full_name":"Penka, E. F."},{"full_name":"Grassi, G.","first_name":"G.","last_name":"Grassi"},{"full_name":"Tolstikhin, O. I.","first_name":"O. I.","last_name":"Tolstikhin"},{"full_name":"Schneider, J.","last_name":"Schneider","first_name":"J."},{"first_name":"F.","last_name":"Jensen","full_name":"Jensen, F."},{"full_name":"Madsen, L. B.","first_name":"L. B.","last_name":"Madsen"},{"full_name":"Bandrauk, A. D.","last_name":"Bandrauk","first_name":"A. D."},{"first_name":"F.","last_name":"Remacle","full_name":"Remacle, F."},{"full_name":"Wörner, H. J.","first_name":"H. J.","last_name":"Wörner"}],"volume":350,"date_created":"2023-08-10T06:37:35Z","date_updated":"2023-08-22T08:47:39Z"},{"language":[{"iso":"eng"}],"doi":"10.1088/1742-6596/635/11/112136","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1088/1742-6596/635/11/112136"}],"month":"07","publication_identifier":{"eissn":["1742-6596"],"issn":["1742-6588"]},"date_updated":"2023-08-22T08:49:14Z","date_created":"2023-08-10T06:37:53Z","volume":635,"author":[{"last_name":"Kraus","first_name":"P M","full_name":"Kraus, P M"},{"full_name":"Mignolet, B","first_name":"B","last_name":"Mignolet"},{"full_name":"Baykusheva, Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","first_name":"Denitsa Rangelova","last_name":"Baykusheva"},{"full_name":"Rupenyan, A","first_name":"A","last_name":"Rupenyan"},{"last_name":"Horný","first_name":"L","full_name":"Horný, L"},{"full_name":"Penka, E F","last_name":"Penka","first_name":"E F"},{"full_name":"Tolstikhin, O I","first_name":"O I","last_name":"Tolstikhin"},{"full_name":"Schneider, J","first_name":"J","last_name":"Schneider"},{"full_name":"Jensen, F","last_name":"Jensen","first_name":"F"},{"last_name":"Madsen","first_name":"L B","full_name":"Madsen, L B"},{"full_name":"Bandrauk, A D","first_name":"A D","last_name":"Bandrauk"},{"first_name":"F","last_name":"Remacle","full_name":"Remacle, F"},{"full_name":"Wörner, H J","first_name":"H J","last_name":"Wörner"}],"publication_status":"published","publisher":"IOP Publishing","year":"2015","extern":"1","article_number":"112136","date_published":"2015-07-01T00:00:00Z","article_type":"original","publication":"Journal of Physics: Conference Series","citation":{"ista":"Kraus PM, Mignolet B, Baykusheva DR, Rupenyan A, Horný L, Penka EF, Tolstikhin OI, Schneider J, Jensen F, Madsen LB, Bandrauk AD, Remacle F, Wörner HJ. 2015. Attosecond charge migration and its laser control. Journal of Physics: Conference Series. 635(11), 112136.","apa":"Kraus, P. M., Mignolet, B., Baykusheva, D. R., Rupenyan, A., Horný, L., Penka, E. F., … Wörner, H. J. (2015). Attosecond charge migration and its laser control. Journal of Physics: Conference Series. IOP Publishing. https://doi.org/10.1088/1742-6596/635/11/112136","ieee":"P. M. Kraus et al., “Attosecond charge migration and its laser control,” Journal of Physics: Conference Series, vol. 635, no. 11. IOP Publishing, 2015.","ama":"Kraus PM, Mignolet B, Baykusheva DR, et al. Attosecond charge migration and its laser control. Journal of Physics: Conference Series. 2015;635(11). doi:10.1088/1742-6596/635/11/112136","chicago":"Kraus, P M, B Mignolet, Denitsa Rangelova Baykusheva, A Rupenyan, L Horný, E F Penka, O I Tolstikhin, et al. “Attosecond Charge Migration and Its Laser Control.” Journal of Physics: Conference Series. IOP Publishing, 2015. https://doi.org/10.1088/1742-6596/635/11/112136.","mla":"Kraus, P. M., et al. “Attosecond Charge Migration and Its Laser Control.” Journal of Physics: Conference Series, vol. 635, no. 11, 112136, IOP Publishing, 2015, doi:10.1088/1742-6596/635/11/112136.","short":"P.M. Kraus, B. Mignolet, D.R. Baykusheva, A. Rupenyan, L. Horný, E.F. Penka, O.I. Tolstikhin, J. Schneider, F. Jensen, L.B. Madsen, A.D. Bandrauk, F. Remacle, H.J. Wörner, Journal of Physics: Conference Series 635 (2015)."},"day":"01","article_processing_charge":"No","keyword":["General Physics and Astronomy"],"scopus_import":"1","oa_version":"Published Version","title":"Attosecond charge migration and its laser control","status":"public","intvolume":" 635","_id":"14015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We advance high-harmonic spectroscopy to resolve molecular charge migration in time and space and simultaneously demonstrate extensive control over the process. A multidimensional approach enables us to reconstruct both quantum amplitudes and phases with a resolution of better than 100 attoseconds and to separately reconstruct field-free and laser- driven charge migration. Our techniques make charge migration in molecules measurable on the attosecond time scale and open new avenues for laser control of electronic primary processes."}],"issue":"11","type":"journal_article"},{"article_type":"original","citation":{"apa":"Walt, S. G., Ram, N. B., von Conta, A., Baykusheva, D. R., Atala, M., & Wörner, H. J. (2015). Resolving the dynamics of valence-shell electrons and nuclei through laser-induced diffraction and holography. Journal of Physics: Conference Series. IOP Publishing. https://doi.org/10.1088/1742-6596/635/11/112135","ieee":"S. G. Walt, N. B. Ram, A. von Conta, D. R. Baykusheva, M. Atala, and H. J. Wörner, “Resolving the dynamics of valence-shell electrons and nuclei through laser-induced diffraction and holography,” Journal of Physics: Conference Series, vol. 635, no. 11. IOP Publishing, 2015.","ista":"Walt SG, Ram NB, von Conta A, Baykusheva DR, Atala M, Wörner HJ. 2015. Resolving the dynamics of valence-shell electrons and nuclei through laser-induced diffraction and holography. Journal of Physics: Conference Series. 635(11), 112135.","ama":"Walt SG, Ram NB, von Conta A, Baykusheva DR, Atala M, Wörner HJ. Resolving the dynamics of valence-shell electrons and nuclei through laser-induced diffraction and holography. Journal of Physics: Conference Series. 2015;635(11). doi:10.1088/1742-6596/635/11/112135","chicago":"Walt, Samuel G, N Bhargava Ram, Aaron von Conta, Denitsa Rangelova Baykusheva, Marcos Atala, and Hans Jakob Wörner. “Resolving the Dynamics of Valence-Shell Electrons and Nuclei through Laser-Induced Diffraction and Holography.” Journal of Physics: Conference Series. IOP Publishing, 2015. https://doi.org/10.1088/1742-6596/635/11/112135.","short":"S.G. Walt, N.B. Ram, A. von Conta, D.R. Baykusheva, M. Atala, H.J. Wörner, Journal of Physics: Conference Series 635 (2015).","mla":"Walt, Samuel G., et al. “Resolving the Dynamics of Valence-Shell Electrons and Nuclei through Laser-Induced Diffraction and Holography.” Journal of Physics: Conference Series, vol. 635, no. 11, 112135, IOP Publishing, 2015, doi:10.1088/1742-6596/635/11/112135."},"publication":"Journal of Physics: Conference Series","date_published":"2015-11-01T00:00:00Z","keyword":["General Physics and Astronomy"],"scopus_import":"1","article_processing_charge":"No","day":"01","intvolume":" 635","title":"Resolving the dynamics of valence-shell electrons and nuclei through laser-induced diffraction and holography","status":"public","_id":"14014","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","type":"journal_article","issue":"11","abstract":[{"lang":"eng","text":"We have studied a coupled electronic-nuclear wave packet in nitric oxide using time-resolved strong-field photoelectron holography and rescattering. We show that the electronic dynamics mainly appears in the holographic structures whereas nuclear motion strongly modulates the angular distribution of the rescattered photoelectrons."}],"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1088/1742-6596/635/11/112135"}],"language":[{"iso":"eng"}],"doi":"10.1088/1742-6596/635/11/112135","publication_identifier":{"eissn":["1742-6596"],"issn":["1742-6588"]},"month":"11","publisher":"IOP Publishing","publication_status":"published","year":"2015","volume":635,"date_updated":"2023-08-22T08:51:33Z","date_created":"2023-08-10T06:37:44Z","author":[{"full_name":"Walt, Samuel G","first_name":"Samuel G","last_name":"Walt"},{"last_name":"Ram","first_name":"N Bhargava","full_name":"Ram, N Bhargava"},{"first_name":"Aaron","last_name":"von Conta","full_name":"von Conta, Aaron"},{"full_name":"Baykusheva, Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","first_name":"Denitsa Rangelova","last_name":"Baykusheva"},{"first_name":"Marcos","last_name":"Atala","full_name":"Atala, Marcos"},{"full_name":"Wörner, Hans Jakob","first_name":"Hans Jakob","last_name":"Wörner"}],"article_number":"112135","extern":"1"},{"doi":"10.5061/dryad.cj910","date_published":"2015-12-21T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.cj910"}],"oa":1,"citation":{"short":"S. Wielgoss, T. Bergmiller, A.M. Bischofberger, A.R. Hall, (2015).","mla":"Wielgoss, Sébastien, et al. Data from: Adaptation to Parasites and Costs of Parasite Resistance in Mutator and Non-Mutator Bacteria. Dryad, 2015, doi:10.5061/dryad.cj910.","chicago":"Wielgoss, Sébastien, Tobias Bergmiller, Anna M. Bischofberger, and Alex R. Hall. “Data from: Adaptation to Parasites and Costs of Parasite Resistance in Mutator and Non-Mutator Bacteria.” Dryad, 2015. https://doi.org/10.5061/dryad.cj910.","ama":"Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. Data from: Adaptation to parasites and costs of parasite resistance in mutator and non-mutator bacteria. 2015. doi:10.5061/dryad.cj910","ieee":"S. Wielgoss, T. Bergmiller, A. M. Bischofberger, and A. R. Hall, “Data from: Adaptation to parasites and costs of parasite resistance in mutator and non-mutator bacteria.” Dryad, 2015.","apa":"Wielgoss, S., Bergmiller, T., Bischofberger, A. M., & Hall, A. R. (2015). 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However, the influence of these traits on host evolution when parasites are no longer present is unclear. We used experimental evolution and whole-genome sequencing of Escherichia coli to determine the effects of past and present exposure to parasitic viruses (phages) on the spread of mutator alleles, resistance, and bacterial competitive fitness. We found that mutator alleles spread rapidly during adaptation to any of four different phage species, and this pattern was even more pronounced with multiple phages present simultaneously. However, hypermutability did not detectably accelerate adaptation in the absence of phages and recovery of fitness costs associated with resistance. Several lineages evolved phage resistance through elevated mucoidy, and during subsequent evolution in phage-free conditions they rapidly reverted to nonmucoid, phage-susceptible phenotypes. Genome sequencing revealed that this phenotypic reversion was achieved by additional genetic changes rather than by genotypic reversion of the initial resistance mutations. Insertion sequence (IS) elements played a key role in both the acquisition of resistance and adaptation in the absence of parasites; unlike single nucleotide polymorphisms, IS insertions were not more frequent in mutator lineages. Our results provide a genetic explanation for rapid reversion of mucoidy, a phenotype observed in other bacterial species including human pathogens. Moreover, this demonstrates that the types of genetic change underlying adaptation to fitness costs, and consequently the impact of evolvability mechanisms such as increased point-mutation rates, depend critically on the mechanism of resistance."}],"type":"research_data_reference"},{"article_processing_charge":"No","has_accepted_license":"1","day":"01","page":"144","citation":{"short":"V. Sharmanska, Learning with Attributes for Object Recognition: Parametric and Non-Parametrics Views, Institute of Science and Technology Austria, 2015.","mla":"Sharmanska, Viktoriia. Learning with Attributes for Object Recognition: Parametric and Non-Parametrics Views. Institute of Science and Technology Austria, 2015, doi:10.15479/at:ista:1401.","chicago":"Sharmanska, Viktoriia. “Learning with Attributes for Object Recognition: Parametric and Non-Parametrics Views.” Institute of Science and Technology Austria, 2015. https://doi.org/10.15479/at:ista:1401.","ama":"Sharmanska V. Learning with attributes for object recognition: Parametric and non-parametrics views. 2015. doi:10.15479/at:ista:1401","apa":"Sharmanska, V. (2015). Learning with attributes for object recognition: Parametric and non-parametrics views. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:1401","ieee":"V. Sharmanska, “Learning with attributes for object recognition: Parametric and non-parametrics views,” Institute of Science and Technology Austria, 2015.","ista":"Sharmanska V. 2015. Learning with attributes for object recognition: Parametric and non-parametrics views. Institute of Science and Technology Austria."},"date_published":"2015-04-01T00:00:00Z","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"The human ability to recognize objects in complex scenes has driven research in the computer vision field over couple of decades. This thesis focuses on the object recognition task in images. That is, given the image, we want the computer system to be able to predict the class of the object that appears in the image. A recent successful attempt to bridge semantic understanding of the image perceived by humans and by computers uses attribute-based models. Attributes are semantic properties of the objects shared across different categories, which humans and computers can decide on. To explore the attribute-based models we take a statistical machine learning approach, and address two key learning challenges in view of object recognition task: learning augmented attributes as mid-level discriminative feature representation, and learning with attributes as privileged information. Our main contributions are parametric and non-parametric models and algorithms to solve these frameworks. In the parametric approach, we explore an autoencoder model combined with the large margin nearest neighbor principle for mid-level feature learning, and linear support vector machines for learning with privileged information. In the non-parametric approach, we propose a supervised Indian Buffet Process for automatic augmentation of semantic attributes, and explore the Gaussian Processes classification framework for learning with privileged information. A thorough experimental analysis shows the effectiveness of the proposed models in both parametric and non-parametric views.","lang":"eng"}],"status":"public","title":"Learning with attributes for object recognition: Parametric and non-parametrics views","ddc":["000"],"_id":"1401","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"date_updated":"2021-02-22T11:33:17Z","date_created":"2021-02-22T11:33:17Z","success":1,"checksum":"3605b402bb6934e09ae4cf672c84baf7","file_id":"9177","relation":"main_file","creator":"dernst","file_size":7964342,"content_type":"application/pdf","file_name":"2015_Thesis_Sharmanska.pdf","access_level":"open_access"},{"file_id":"10297","relation":"main_file","checksum":"e37593b3ee75bf3180629df2d6ca8f4e","date_created":"2021-11-16T14:40:45Z","date_updated":"2021-11-17T13:47:24Z","access_level":"closed","file_name":"2015_Thesis_Sharmanska_pdfa.pdf","creator":"cchlebak","file_size":7372241,"content_type":"application/pdf"}],"publication_identifier":{"issn":["2663-337X"]},"month":"04","main_file_link":[{"url":"http://users.sussex.ac.uk/~nq28/viktoriia/Thesis_Sharmanska.pdf"}],"oa":1,"language":[{"iso":"eng"}],"supervisor":[{"first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"}],"degree_awarded":"PhD","doi":"10.15479/at:ista:1401","publist_id":"5806","file_date_updated":"2021-11-17T13:47:24Z","department":[{"_id":"ChLa"},{"_id":"GradSch"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2015","acknowledgement":"I would like to thank my supervisor, Christoph Lampert, for guidance throughout my studies and for patience in transforming me into a scientist, and my thesis committee, Chris Wojtan and Horst Bischof, for their help and advice. \r\n\r\nI would like to thank Elisabeth Hacker who perfectly assisted all my administrative needs and was always nice and friendly to me, and the campus team for making the IST Austria campus my second home. \r\nI was honored to collaborate with brilliant researchers and to learn from their experience. Undoubtedly, I learned most of all from Novi Quadrianto: brainstorming our projects and getting exciting results was the most enjoyable part of my work – thank you! I am also grateful to David Knowles, Zoubin Ghahramani, Daniel Hernández-Lobato, Kristian Kersting and Anastasia Pentina for the fantastic projects we worked on together, and to Kristen Grauman and Adriana Kovashka for the exceptional experience working with user studies. I would like to thank my colleagues at IST Austria and my office mates who shared their happy moods, scientific breakthroughs and thought-provoking conversations with me: Chao, Filip, Rustem, Asya, Sameh, Alex, Vlad, Mayu, Neel, Csaba, Thomas, Vladimir, Cristina, Alex Z., Avro, Amelie and Emilie, Andreas H. and Andreas E., Chris, Lena, Michael, Ali and Ipek, Vera, Igor, Katia. Special thanks to Morten for the countless games of table soccer we played together and the tournaments we teamed up for: we will definitely win next time:) A very warm hug to Asya for always being so inspiring and supportive to me, and for helping me to increase the proportion of female computer scientists in our group. ","date_created":"2018-12-11T11:51:48Z","date_updated":"2023-09-07T11:40:11Z","author":[{"full_name":"Sharmanska, Viktoriia","id":"2EA6D09E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0192-9308","first_name":"Viktoriia","last_name":"Sharmanska"}]},{"publist_id":"5425","department":[{"_id":"KrCh"}],"publisher":"Royal Society","publication_status":"published","pmid":1,"year":"2015","acknowledgement":"This work was supported by grants from the John Templeton Foundation, ERC Start Grant (279307: Graph Games), FWF NFN Grant (No S11407N23 RiSE/SHiNE), FWF Grant (No P23499N23) and a Microsoft faculty fellows award.","volume":282,"date_updated":"2023-09-07T11:40:43Z","date_created":"2018-12-11T11:53:35Z","related_material":{"record":[{"id":"1400","relation":"dissertation_contains","status":"public"}]},"author":[{"full_name":"Reiter, Johannes","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0170-7353","first_name":"Johannes","last_name":"Reiter"},{"full_name":"Kanodia, Ayush","first_name":"Ayush","last_name":"Kanodia"},{"last_name":"Gupta","first_name":"Raghav","full_name":"Gupta, Raghav"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"}],"month":"07","project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4528522/"}],"external_id":{"pmid":["26180069"]},"language":[{"iso":"eng"}],"doi":"10.1098/rspb.2015.1041","type":"journal_article","issue":"1812","abstract":[{"text":"The competition for resources among cells, individuals or species is a fundamental characteristic of evolution. Biological all-pay auctions have been used to model situations where multiple individuals compete for a single resource. However, in many situations multiple resources with various values exist and single reward auctions are not applicable. We generalize the model to multiple rewards and study the evolution of strategies. In biological all-pay auctions the bid of an individual corresponds to its strategy and is equivalent to its payment in the auction. The decreasingly ordered rewards are distributed according to the decreasingly ordered bids of the participating individuals. The reproductive success of an individual is proportional to its fitness given by the sum of the rewards won minus its payments. Hence, successful bidding strategies spread in the population. We find that the results for the multiple reward case are very different from the single reward case. While the mixed strategy equilibrium in the single reward case with more than two players consists of mostly low-bidding individuals, we show that the equilibrium can convert to many high-bidding individuals and a few low-bidding individuals in the multiple reward case. Some reward values lead to a specialization among the individuals where one subpopulation competes for the rewards and the other subpopulation largely avoids costly competitions. Whether the mixed strategy equilibrium is an evolutionarily stable strategy (ESS) depends on the specific values of the rewards.","lang":"eng"}],"intvolume":" 282","title":"Biological auctions with multiple rewards","status":"public","_id":"1709","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","scopus_import":1,"article_processing_charge":"No","day":"15","article_type":"original","citation":{"ama":"Reiter J, Kanodia A, Gupta R, Nowak M, Chatterjee K. Biological auctions with multiple rewards. Proceedings of the Royal Society of London Series B Biological Sciences. 2015;282(1812). doi:10.1098/rspb.2015.1041","ieee":"J. Reiter, A. Kanodia, R. Gupta, M. Nowak, and K. Chatterjee, “Biological auctions with multiple rewards,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 282, no. 1812. Royal Society, 2015.","apa":"Reiter, J., Kanodia, A., Gupta, R., Nowak, M., & Chatterjee, K. (2015). Biological auctions with multiple rewards. Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society. https://doi.org/10.1098/rspb.2015.1041","ista":"Reiter J, Kanodia A, Gupta R, Nowak M, Chatterjee K. 2015. Biological auctions with multiple rewards. Proceedings of the Royal Society of London Series B Biological Sciences. 282(1812).","short":"J. Reiter, A. Kanodia, R. Gupta, M. Nowak, K. Chatterjee, Proceedings of the Royal Society of London Series B Biological Sciences 282 (2015).","mla":"Reiter, Johannes, et al. “Biological Auctions with Multiple Rewards.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 282, no. 1812, Royal Society, 2015, doi:10.1098/rspb.2015.1041.","chicago":"Reiter, Johannes, Ayush Kanodia, Raghav Gupta, Martin Nowak, and Krishnendu Chatterjee. “Biological Auctions with Multiple Rewards.” Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, 2015. https://doi.org/10.1098/rspb.2015.1041."},"publication":"Proceedings of the Royal Society of London Series B Biological Sciences","date_published":"2015-07-15T00:00:00Z"},{"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"1709"},{"status":"public","relation":"part_of_dissertation","id":"2000"},{"relation":"part_of_dissertation","status":"public","id":"2247"},{"status":"public","relation":"part_of_dissertation","id":"2816"},{"status":"public","relation":"part_of_dissertation","id":"2858"},{"id":"3157","relation":"part_of_dissertation","status":"public"},{"id":"3260","relation":"part_of_dissertation","status":"public"}]},"author":[{"last_name":"Reiter","first_name":"Johannes","orcid":"0000-0002-0170-7353","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","full_name":"Reiter, Johannes"}],"oa_version":"None","date_created":"2018-12-11T11:51:48Z","date_updated":"2023-09-07T11:40:44Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"1400","year":"2015","publisher":"Institute of Science and Technology Austria","department":[{"_id":"KrCh"}],"status":"public","title":"The subclonal evolution of cancer","publication_status":"published","publist_id":"5807","abstract":[{"lang":"eng","text":"Cancer results from an uncontrolled growth of abnormal cells. Sequentially accumulated genetic and epigenetic alterations decrease cell death and increase cell replication. We used mathematical models to quantify the effect of driver gene mutations. The recently developed targeted therapies can lead to dramatic regressions. However, in solid cancers, clinical responses are often short-lived because resistant cancer cells evolve. We estimated that approximately 50 different mutations can confer resistance to a typical targeted therapeutic agent. We find that resistant cells are likely to be present in expanded subclones before the start of the treatment. The dominant strategy to prevent the evolution of resistance is combination therapy. Our analytical results suggest that in most patients, dual therapy, but not monotherapy, can result in long-term disease control. However, long-term control can only occur if there are no possible mutations in the genome that can cause cross-resistance to both drugs. Furthermore, we showed that simultaneous therapy with two drugs is much more likely to result in long-term disease control than sequential therapy with the same drugs. To improve our understanding of the underlying subclonal evolution we reconstruct the evolutionary history of a patient's cancer from next-generation sequencing data of spatially-distinct DNA samples. Using a quantitative measure of genetic relatedness, we found that pancreatic cancers and their metastases demonstrated a higher level of relatedness than that expected for any two cells randomly taken from a normal tissue. This minimal amount of genetic divergence among advanced lesions indicates that genetic heterogeneity, when quantitatively defined, is not a fundamental feature of the natural history of untreated pancreatic cancers. Our newly developed, phylogenomic tool Treeomics finds evidence for seeding patterns of metastases and can directly be used to discover rules governing the evolution of solid malignancies to transform cancer into a more predictable disease."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2015-04-01T00:00:00Z","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"}],"citation":{"ama":"Reiter J. The subclonal evolution of cancer. 2015.","ista":"Reiter J. 2015. The subclonal evolution of cancer. Institute of Science and Technology Austria.","apa":"Reiter, J. (2015). The subclonal evolution of cancer. Institute of Science and Technology Austria.","ieee":"J. Reiter, “The subclonal evolution of cancer,” Institute of Science and Technology Austria, 2015.","mla":"Reiter, Johannes. The Subclonal Evolution of Cancer. Institute of Science and Technology Austria, 2015.","short":"J. Reiter, The Subclonal Evolution of Cancer, Institute of Science and Technology Austria, 2015.","chicago":"Reiter, Johannes. “The Subclonal Evolution of Cancer.” Institute of Science and Technology Austria, 2015."},"page":"183","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","month":"04","day":"01"},{"doi":"10.1016/j.jco.2015.06.002","date_published":"2015-12-01T00:00:00Z","language":[{"iso":"eng"}],"citation":{"ama":"Pausinger F, Svane A. A Koksma-Hlawka inequality for general discrepancy systems. Journal of Complexity. 2015;31(6):773-797. doi:10.1016/j.jco.2015.06.002","ista":"Pausinger F, Svane A. 2015. A Koksma-Hlawka inequality for general discrepancy systems. Journal of Complexity. 31(6), 773–797.","ieee":"F. Pausinger and A. Svane, “A Koksma-Hlawka inequality for general discrepancy systems,” Journal of Complexity, vol. 31, no. 6. Academic Press, pp. 773–797, 2015.","apa":"Pausinger, F., & Svane, A. (2015). A Koksma-Hlawka inequality for general discrepancy systems. Journal of Complexity. Academic Press. https://doi.org/10.1016/j.jco.2015.06.002","mla":"Pausinger, Florian, and Anne Svane. “A Koksma-Hlawka Inequality for General Discrepancy Systems.” Journal of Complexity, vol. 31, no. 6, Academic Press, 2015, pp. 773–97, doi:10.1016/j.jco.2015.06.002.","short":"F. Pausinger, A. Svane, Journal of Complexity 31 (2015) 773–797.","chicago":"Pausinger, Florian, and Anne Svane. “A Koksma-Hlawka Inequality for General Discrepancy Systems.” Journal of Complexity. Academic Press, 2015. https://doi.org/10.1016/j.jco.2015.06.002."},"publication":"Journal of Complexity","page":"773 - 797","quality_controlled":"1","month":"12","day":"01","scopus_import":1,"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"1399"}]},"author":[{"orcid":"0000-0002-8379-3768","id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","last_name":"Pausinger","first_name":"Florian","full_name":"Pausinger, Florian"},{"full_name":"Svane, Anne","last_name":"Svane","first_name":"Anne"}],"oa_version":"None","volume":31,"date_created":"2018-12-11T11:54:02Z","date_updated":"2023-09-07T11:41:25Z","_id":"1792","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"F.P. is supported by the Graduate School of IST Austria, A.M.S is supported by the Centre for Stochastic Geometry and Advanced Bioimaging funded by a grant from the Villum Foundation.","year":"2015","department":[{"_id":"HeEd"}],"intvolume":" 31","publisher":"Academic Press","title":"A Koksma-Hlawka inequality for general discrepancy systems","status":"public","publication_status":"published","publist_id":"5320","issue":"6","abstract":[{"text":"Motivated by recent ideas of Harman (Unif. Distrib. Theory, 2010) we develop a new concept of variation of multivariate functions on a compact Hausdorff space with respect to a collection D of subsets. We prove a general version of the Koksma-Hlawka theorem that holds for this notion of variation and discrepancy with respect to D. As special cases, we obtain Koksma-Hlawka inequalities for classical notions, such as extreme or isotropic discrepancy. For extreme discrepancy, our result coincides with the usual Koksma-Hlawka theorem. We show that the space of functions of bounded D-variation contains important discontinuous functions and is closed under natural algebraic operations. Finally, we illustrate the results on concrete integration problems from integral geometry and stereology.","lang":"eng"}],"type":"journal_article"},{"title":"On the approximation of intrinsic volumes","publication_status":"published","status":"public","department":[{"_id":"HeEd"}],"publisher":"Institute of Science and Technology Austria","year":"2015","_id":"1399","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:51:48Z","date_updated":"2023-09-07T11:41:25Z","oa_version":"None","author":[{"first_name":"Florian","last_name":"Pausinger","id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8379-3768","full_name":"Pausinger, Florian"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"1662"},{"status":"public","relation":"part_of_dissertation","id":"1792"},{"relation":"part_of_dissertation","status":"public","id":"2255"}]},"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"This thesis is concerned with the computation and approximation of intrinsic volumes. Given a smooth body M and a certain digital approximation of it, we develop algorithms to approximate various intrinsic volumes of M using only measurements taken from its digital approximations. The crucial idea behind our novel algorithms is to link the recent theory of persistent homology to the theory of intrinsic volumes via the Crofton formula from integral geometry and, in particular, via Euler characteristic computations. Our main contributions are a multigrid convergent digital algorithm to compute the first intrinsic volume of a solid body in R^n as well as an appropriate integration pipeline to approximate integral-geometric integrals defined over the Grassmannian manifold."}],"publist_id":"5808","page":"144","citation":{"chicago":"Pausinger, Florian. “On the Approximation of Intrinsic Volumes.” Institute of Science and Technology Austria, 2015.","mla":"Pausinger, Florian. On the Approximation of Intrinsic Volumes. Institute of Science and Technology Austria, 2015.","short":"F. Pausinger, On the Approximation of Intrinsic Volumes, Institute of Science and Technology Austria, 2015.","ista":"Pausinger F. 2015. On the approximation of intrinsic volumes. Institute of Science and Technology Austria.","apa":"Pausinger, F. (2015). On the approximation of intrinsic volumes. Institute of Science and Technology Austria.","ieee":"F. Pausinger, “On the approximation of intrinsic volumes,” Institute of Science and Technology Austria, 2015.","ama":"Pausinger F. On the approximation of intrinsic volumes. 2015."},"supervisor":[{"full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"date_published":"2015-06-01T00:00:00Z","day":"01","month":"06","article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]}},{"citation":{"ama":"Tugrul M, Paixao T, Barton NH, Tkačik G. Dynamics of transcription factor binding site evolution. PLoS Genetics. 2015;11(11). doi:10.1371/journal.pgen.1005639","ista":"Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Dynamics of transcription factor binding site evolution. PLoS Genetics. 11(11).","apa":"Tugrul, M., Paixao, T., Barton, N. H., & Tkačik, G. (2015). Dynamics of transcription factor binding site evolution. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1005639","ieee":"M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Dynamics of transcription factor binding site evolution,” PLoS Genetics, vol. 11, no. 11. Public Library of Science, 2015.","mla":"Tugrul, Murat, et al. “Dynamics of Transcription Factor Binding Site Evolution.” PLoS Genetics, vol. 11, no. 11, Public Library of Science, 2015, doi:10.1371/journal.pgen.1005639.","short":"M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, PLoS Genetics 11 (2015).","chicago":"Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Dynamics of Transcription Factor Binding Site Evolution.” PLoS Genetics. Public Library of Science, 2015. https://doi.org/10.1371/journal.pgen.1005639."},"publication":"PLoS Genetics","date_published":"2015-11-06T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"06","intvolume":" 11","title":"Dynamics of transcription factor binding site evolution","ddc":["576"],"status":"public","_id":"1666","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"file_name":"IST-2016-463-v1+1_journal.pgen.1005639.pdf","access_level":"open_access","file_size":2580778,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"4657","date_updated":"2020-07-14T12:45:10Z","date_created":"2018-12-12T10:07:58Z","checksum":"a4e72fca5ccf40ddacf4d08c8e46b554"}],"pubrep_id":"463","type":"journal_article","issue":"11","abstract":[{"text":"Evolution of gene regulation is crucial for our understanding of the phenotypic differences between species, populations and individuals. Sequence-specific binding of transcription factors to the regulatory regions on the DNA is a key regulatory mechanism that determines gene expression and hence heritable phenotypic variation. We use a biophysical model for directional selection on gene expression to estimate the rates of gain and loss of transcription factor binding sites (TFBS) in finite populations under both point and insertion/deletion mutations. Our results show that these rates are typically slow for a single TFBS in an isolated DNA region, unless the selection is extremely strong. These rates decrease drastically with increasing TFBS length or increasingly specific protein-DNA interactions, making the evolution of sites longer than ∼ 10 bp unlikely on typical eukaryotic speciation timescales. Similarly, evolution converges to the stationary distribution of binding sequences very slowly, making the equilibrium assumption questionable. The availability of longer regulatory sequences in which multiple binding sites can evolve simultaneously, the presence of “pre-sites” or partially decayed old sites in the initial sequence, and biophysical cooperativity between transcription factors, can all facilitate gain of TFBS and reconcile theoretical calculations with timescales inferred from comparative genomics.","lang":"eng"}],"project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.1371/journal.pgen.1005639","month":"11","department":[{"_id":"NiBa"},{"_id":"CaGu"},{"_id":"GaTk"}],"publisher":"Public Library of Science","publication_status":"published","year":"2015","volume":11,"date_updated":"2023-09-07T11:53:49Z","date_created":"2018-12-11T11:53:21Z","related_material":{"record":[{"id":"9712","status":"public","relation":"research_data"},{"id":"1131","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Tugrul, Murat","first_name":"Murat","last_name":"Tugrul","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8523-0758"},{"full_name":"Paixao, Tiago","first_name":"Tiago","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gasper","last_name":"Tkacik","full_name":"Tkacik, Gasper"}],"publist_id":"5483","ec_funded":1,"file_date_updated":"2020-07-14T12:45:10Z"},{"date_created":"2018-12-11T11:52:24Z","date_updated":"2023-09-07T11:58:33Z","author":[{"last_name":"Beneš","first_name":"Nikola","full_name":"Beneš, Nikola"},{"full_name":"Daca, Przemyslaw","last_name":"Daca","first_name":"Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"last_name":"Kretinsky","first_name":"Jan","orcid":"0000-0002-8122-2881","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","full_name":"Kretinsky, Jan"},{"full_name":"Nickovic, Dejan","last_name":"Nickovic","first_name":"Dejan"}],"related_material":{"record":[{"id":"1155","relation":"dissertation_contains","status":"public"}]},"publication_status":"published","publisher":"ACM","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"year":"2015","acknowledgement":"This research was funded in part by the European Research Council (ERC) under grant agreement 267989 (QUAREM), by the Austrian Science Fund (FWF) projects S11402-N23(RiSE) and Z211-N23 (Wittgestein Award), by People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement 291734, and by the ARTEMIS JU under grant agreement 295373 (nSafeCer). Jan Křetínský has been partially supported by the Czech Science Foundation, grant No. P202/12/G061. Nikola Beneš has been supported by the\r\nMEYS project No. CZ.1.07/2.3.00/30.0009 Employment of Newly Graduated Doctors of Science for Scientific Excellence.","file_date_updated":"2020-07-14T12:44:59Z","ec_funded":1,"publist_id":"5676","language":[{"iso":"eng"}],"conference":{"name":"CBSE: Component-Based Software Engineering ","location":"Montreal, QC, Canada","start_date":"2015-05-04","end_date":"2015-05-08"},"doi":"10.1145/2737166.2737175","quality_controlled":"1","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"oa":1,"month":"05","publication_identifier":{"isbn":["978-1-4503-3471-6"]},"oa_version":"Submitted Version","file":[{"file_name":"IST-2016-625-v1+1_conf-cbse-BenesDHKN15.pdf","access_level":"open_access","creator":"system","file_size":467561,"content_type":"application/pdf","file_id":"5303","relation":"main_file","date_created":"2018-12-12T10:17:46Z","date_updated":"2020-07-14T12:44:59Z","checksum":"c6ce681035c163a158751f240cb7d389"}],"pubrep_id":"625","title":"Complete composition operators for IOCO-testing theory","ddc":["000"],"status":"public","_id":"1502","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We extend the theory of input-output conformance with operators for merge and quotient. The former is useful when testing against multiple requirements or views. The latter can be used to generate tests for patches of an already tested system. Both operators can combine systems with different action alphabets, which is usually the case when constructing complex systems and specifications from parts, for instance different views as well as newly defined functionality of a~previous version of the system."}],"alternative_title":["Proceedings of the 18th International ACM SIGSOFT Symposium on Component-Based Software Engineering "],"type":"conference","date_published":"2015-05-01T00:00:00Z","page":"101 - 110","citation":{"ama":"Beneš N, Daca P, Henzinger TA, Kretinsky J, Nickovic D. Complete composition operators for IOCO-testing theory. In: ACM; 2015:101-110. doi:10.1145/2737166.2737175","ista":"Beneš N, Daca P, Henzinger TA, Kretinsky J, Nickovic D. 2015. Complete composition operators for IOCO-testing theory. CBSE: Component-Based Software Engineering , Proceedings of the 18th International ACM SIGSOFT Symposium on Component-Based Software Engineering , , 101–110.","apa":"Beneš, N., Daca, P., Henzinger, T. A., Kretinsky, J., & Nickovic, D. (2015). Complete composition operators for IOCO-testing theory (pp. 101–110). Presented at the CBSE: Component-Based Software Engineering , Montreal, QC, Canada: ACM. https://doi.org/10.1145/2737166.2737175","ieee":"N. Beneš, P. Daca, T. A. Henzinger, J. Kretinsky, and D. Nickovic, “Complete composition operators for IOCO-testing theory,” presented at the CBSE: Component-Based Software Engineering , Montreal, QC, Canada, 2015, pp. 101–110.","mla":"Beneš, Nikola, et al. Complete Composition Operators for IOCO-Testing Theory. ACM, 2015, pp. 101–10, doi:10.1145/2737166.2737175.","short":"N. Beneš, P. Daca, T.A. Henzinger, J. Kretinsky, D. Nickovic, in:, ACM, 2015, pp. 101–110.","chicago":"Beneš, Nikola, Przemyslaw Daca, Thomas A Henzinger, Jan Kretinsky, and Dejan Nickovic. “Complete Composition Operators for IOCO-Testing Theory,” 101–10. ACM, 2015. https://doi.org/10.1145/2737166.2737175."},"day":"01","has_accepted_license":"1","scopus_import":1},{"day":"01","scopus_import":1,"date_published":"2015-10-01T00:00:00Z","page":"230 - 264","citation":{"chicago":"Chatterjee, Krishnendu, Martin Chmelik, and Przemyslaw Daca. “CEGAR for Compositional Analysis of Qualitative Properties in Markov Decision Processes.” Formal Methods in System Design. Springer, 2015. https://doi.org/10.1007/s10703-015-0235-2.","short":"K. Chatterjee, M. Chmelik, P. Daca, Formal Methods in System Design 47 (2015) 230–264.","mla":"Chatterjee, Krishnendu, et al. “CEGAR for Compositional Analysis of Qualitative Properties in Markov Decision Processes.” Formal Methods in System Design, vol. 47, no. 2, Springer, 2015, pp. 230–64, doi:10.1007/s10703-015-0235-2.","apa":"Chatterjee, K., Chmelik, M., & Daca, P. (2015). CEGAR for compositional analysis of qualitative properties in Markov decision processes. Formal Methods in System Design. Springer. https://doi.org/10.1007/s10703-015-0235-2","ieee":"K. Chatterjee, M. Chmelik, and P. Daca, “CEGAR for compositional analysis of qualitative properties in Markov decision processes,” Formal Methods in System Design, vol. 47, no. 2. Springer, pp. 230–264, 2015.","ista":"Chatterjee K, Chmelik M, Daca P. 2015. CEGAR for compositional analysis of qualitative properties in Markov decision processes. Formal Methods in System Design. 47(2), 230–264.","ama":"Chatterjee K, Chmelik M, Daca P. CEGAR for compositional analysis of qualitative properties in Markov decision processes. Formal Methods in System Design. 2015;47(2):230-264. doi:10.1007/s10703-015-0235-2"},"publication":"Formal Methods in System Design","issue":"2","abstract":[{"text":"We consider Markov decision processes (MDPs) which are a standard model for probabilistic systems. We focus on qualitative properties for MDPs that can express that desired behaviors of the system arise almost-surely (with probability 1) or with positive probability. We introduce a new simulation relation to capture the refinement relation of MDPs with respect to qualitative properties, and present discrete graph algorithms with quadratic complexity to compute the simulation relation. We present an automated technique for assume-guarantee style reasoning for compositional analysis of two-player games by giving a counterexample guided abstraction-refinement approach to compute our new simulation relation. We show a tight link between two-player games and MDPs, and as a consequence the results for games are lifted to MDPs with qualitative properties. We have implemented our algorithms and show that the compositional analysis leads to significant improvements. ","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","intvolume":" 47","status":"public","title":"CEGAR for compositional analysis of qualitative properties in Markov decision processes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1501","month":"10","language":[{"iso":"eng"}],"doi":"10.1007/s10703-015-0235-2","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling"}],"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1405.0835","open_access":"1"}],"ec_funded":1,"publist_id":"5677","volume":47,"date_created":"2018-12-11T11:52:23Z","date_updated":"2023-09-07T11:58:33Z","related_material":{"record":[{"id":"1155","relation":"dissertation_contains","status":"public"}]},"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"last_name":"Chmelik","first_name":"Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","full_name":"Chmelik, Martin"},{"full_name":"Daca, Przemyslaw","last_name":"Daca","first_name":"Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"Springer","publication_status":"published","year":"2015","acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No. P23499- N23, FWF NFN Grant No. S11407-N23, FWF Grant S11403-N23 (RiSE), and FWF Grant Z211-N23 (Wittgenstein Award), ERC Start Grant (279307: Graph Games), Microsoft faculty fellows award, the ERC Advanced Grant QUAREM (Quantitative Reactive Modeling)."},{"month":"01","quality_controlled":"1","project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"main_file_link":[{"url":"https://arxiv.org/abs/1410.7724","open_access":"1"}],"external_id":{"arxiv":["1410.7724"]},"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"SIGPLAN: Symposium on Principles of Programming Languages","location":"Mumbai, India","start_date":"2015-01-15","end_date":"2015-01-17"},"doi":"10.1145/2676726.2676979","publist_id":"5565","ec_funded":1,"publication_status":"published","publisher":"ACM","department":[{"_id":"KrCh"}],"acknowledgement":"We thank anonymous reviewers for helpful comments to improve the presentation of the paper.","year":"2015","date_created":"2018-12-11T11:52:58Z","date_updated":"2023-09-07T12:01:58Z","volume":50,"author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"first_name":"Rasmus","last_name":"Ibsen-Jensen","id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus"},{"id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","first_name":"Andreas","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas"},{"full_name":"Goyal, Prateesh","last_name":"Goyal","first_name":"Prateesh"}],"related_material":{"record":[{"id":"821","relation":"dissertation_contains","status":"public"}]},"scopus_import":1,"day":"01","page":"97 - 109","publication":"ACM SIGPLAN Notices","citation":{"chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, Andreas Pavlogiannis, and Prateesh Goyal. “Faster Algorithms for Algebraic Path Properties in Recursive State Machines with Constant Treewidth.” ACM SIGPLAN Notices. ACM, 2015. https://doi.org/10.1145/2676726.2676979.","mla":"Chatterjee, Krishnendu, et al. “Faster Algorithms for Algebraic Path Properties in Recursive State Machines with Constant Treewidth.” ACM SIGPLAN Notices, vol. 50, no. 1, ACM, 2015, pp. 97–109, doi:10.1145/2676726.2676979.","short":"K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, P. Goyal, ACM SIGPLAN Notices 50 (2015) 97–109.","ista":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A, Goyal P. 2015. Faster algorithms for algebraic path properties in recursive state machines with constant treewidth. ACM SIGPLAN Notices. 50(1), 97–109.","apa":"Chatterjee, K., Ibsen-Jensen, R., Pavlogiannis, A., & Goyal, P. (2015). Faster algorithms for algebraic path properties in recursive state machines with constant treewidth. ACM SIGPLAN Notices. Mumbai, India: ACM. https://doi.org/10.1145/2676726.2676979","ieee":"K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, and P. Goyal, “Faster algorithms for algebraic path properties in recursive state machines with constant treewidth,” ACM SIGPLAN Notices, vol. 50, no. 1. ACM, pp. 97–109, 2015.","ama":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A, Goyal P. Faster algorithms for algebraic path properties in recursive state machines with constant treewidth. ACM SIGPLAN Notices. 2015;50(1):97-109. doi:10.1145/2676726.2676979"},"date_published":"2015-01-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Interprocedural analysis is at the heart of numerous applications in programming languages, such as alias analysis, constant propagation, etc. Recursive state machines (RSMs) are standard models for interprocedural analysis. We consider a general framework with RSMs where the transitions are labeled from a semiring, and path properties are algebraic with semiring operations. RSMs with algebraic path properties can model interprocedural dataflow analysis problems, the shortest path problem, the most probable path problem, etc. The traditional algorithms for interprocedural analysis focus on path properties where the starting point is fixed as the entry point of a specific method. In this work, we consider possible multiple queries as required in many applications such as in alias analysis. The study of multiple queries allows us to bring in a very important algorithmic distinction between the resource usage of the one-time preprocessing vs for each individual query. The second aspect that we consider is that the control flow graphs for most programs have constant treewidth. Our main contributions are simple and implementable algorithms that supportmultiple queries for algebraic path properties for RSMs that have constant treewidth. Our theoretical results show that our algorithms have small additional one-time preprocessing, but can answer subsequent queries significantly faster as compared to the current best-known solutions for several important problems, such as interprocedural reachability and shortest path. We provide a prototype implementation for interprocedural reachability and intraprocedural shortest path that gives a significant speed-up on several benchmarks."}],"issue":"1","title":"Faster algorithms for algebraic path properties in recursive state machines with constant treewidth","status":"public","intvolume":" 50","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1602","oa_version":"Preprint"},{"author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","first_name":"Andreas","full_name":"Pavlogiannis, Andreas"},{"last_name":"Velner","first_name":"Yaron","full_name":"Velner, Yaron"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"5445"},{"status":"public","relation":"dissertation_contains","id":"821"}]},"date_created":"2018-12-11T11:52:59Z","date_updated":"2023-09-07T12:01:59Z","volume":50,"year":"2015","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"ACM","ec_funded":1,"publist_id":"5563","conference":{"name":"SIGPLAN: Symposium on Principles of Programming Languages","location":"Mumbai, India","start_date":"2015-01-15","end_date":"2015-01-17"},"doi":"10.1145/2676726.2676968","language":[{"iso":"eng"}],"quality_controlled":"1","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"month":"01","publication_identifier":{"isbn":["978-1-4503-3300-9"]},"pubrep_id":"523","oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1604","status":"public","title":"Quantitative interprocedural analysis","intvolume":" 50","abstract":[{"lang":"eng","text":"We consider the quantitative analysis problem for interprocedural control-flow graphs (ICFGs). The input consists of an ICFG, a positive weight function that assigns every transition a positive integer-valued number, and a labelling of the transitions (events) as good, bad, and neutral events. The weight function assigns to each transition a numerical value that represents ameasure of how good or bad an event is. The quantitative analysis problem asks whether there is a run of the ICFG where the ratio of the sum of the numerical weights of good events versus the sum of weights of bad events in the long-run is at least a given threshold (or equivalently, to compute the maximal ratio among all valid paths in the ICFG). The quantitative analysis problem for ICFGs can be solved in polynomial time, and we present an efficient and practical algorithm for the problem. We show that several problems relevant for static program analysis, such as estimating the worst-case execution time of a program or the average energy consumption of a mobile application, can be modeled in our framework. We have implemented our algorithm as a tool in the Java Soot framework. We demonstrate the effectiveness of our approach with two case studies. First, we show that our framework provides a sound approach (no false positives) for the analysis of inefficiently-used containers. Second, we show that our approach can also be used for static profiling of programs which reasons about methods that are frequently invoked. Our experimental results show that our tool scales to relatively large benchmarks, and discovers relevant and useful information that can be used to optimize performance of the programs."}],"issue":"1","type":"journal_article","date_published":"2015-01-01T00:00:00Z","publication":"Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT ","citation":{"chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, and Yaron Velner. “Quantitative Interprocedural Analysis.” Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT . ACM, 2015. https://doi.org/10.1145/2676726.2676968.","short":"K. Chatterjee, A. Pavlogiannis, Y. Velner, Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT 50 (2015) 539–551.","mla":"Chatterjee, Krishnendu, et al. “Quantitative Interprocedural Analysis.” Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT , vol. 50, no. 1, ACM, 2015, pp. 539–51, doi:10.1145/2676726.2676968.","apa":"Chatterjee, K., Pavlogiannis, A., & Velner, Y. (2015). Quantitative interprocedural analysis. Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT . Mumbai, India: ACM. https://doi.org/10.1145/2676726.2676968","ieee":"K. Chatterjee, A. Pavlogiannis, and Y. Velner, “Quantitative interprocedural analysis,” Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT , vol. 50, no. 1. ACM, pp. 539–551, 2015.","ista":"Chatterjee K, Pavlogiannis A, Velner Y. 2015. Quantitative interprocedural analysis. Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT . 50(1), 539–551.","ama":"Chatterjee K, Pavlogiannis A, Velner Y. Quantitative interprocedural analysis. Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT . 2015;50(1):539-551. doi:10.1145/2676726.2676968"},"page":"539 - 551","day":"01","scopus_import":1},{"ec_funded":1,"publist_id":"5560","year":"2015","acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499- N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Springer","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389","first_name":"Rasmus","last_name":"Ibsen-Jensen","full_name":"Ibsen-Jensen, Rasmus"},{"id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","first_name":"Andreas","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"5430"},{"id":"5437","status":"public","relation":"earlier_version"},{"id":"821","status":"public","relation":"dissertation_contains"}]},"date_created":"2018-12-11T11:52:59Z","date_updated":"2023-09-07T12:01:59Z","volume":9206,"month":"07","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1504.07384","open_access":"1"}],"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"conference":{"name":"CAV: Computer Aided Verification","end_date":"2015-07-24","start_date":"2015-07-18","location":"San Francisco, CA, USA"},"doi":"10.1007/978-3-319-21690-4_9","language":[{"iso":"eng"}],"type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"We consider the core algorithmic problems related to verification of systems with respect to three classical quantitative properties, namely, the mean-payoff property, the ratio property, and the minimum initial credit for energy property. The algorithmic problem given a graph and a quantitative property asks to compute the optimal value (the infimum value over all traces) from every node of the graph. We consider graphs with constant treewidth, and it is well-known that the control-flow graphs of most programs have constant treewidth. Let n denote the number of nodes of a graph, m the number of edges (for constant treewidth graphs m=O(n)) and W the largest absolute value of the weights. Our main theoretical results are as follows. First, for constant treewidth graphs we present an algorithm that approximates the mean-payoff value within a multiplicative factor of ϵ in time O(n⋅log(n/ϵ)) and linear space, as compared to the classical algorithms that require quadratic time. Second, for the ratio property we present an algorithm that for constant treewidth graphs works in time O(n⋅log(|a⋅b|))=O(n⋅log(n⋅W)), when the output is ab, as compared to the previously best known algorithm with running time O(n2⋅log(n⋅W)). Third, for the minimum initial credit problem we show that (i) for general graphs the problem can be solved in O(n2⋅m) time and the associated decision problem can be solved in O(n⋅m) time, improving the previous known O(n3⋅m⋅log(n⋅W)) and O(n2⋅m) bounds, respectively; and (ii) for constant treewidth graphs we present an algorithm that requires O(n⋅logn) time, improving the previous known O(n4⋅log(n⋅W)) bound. We have implemented some of our algorithms and show that they present a significant speedup on standard benchmarks."}],"_id":"1607","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Faster algorithms for quantitative verification in constant treewidth graphs","status":"public","intvolume":" 9206","oa_version":"Preprint","scopus_import":1,"day":"16","citation":{"short":"K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, in:, Springer, 2015, pp. 140–157.","mla":"Chatterjee, Krishnendu, et al. Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs. Vol. 9206, Springer, 2015, pp. 140–57, doi:10.1007/978-3-319-21690-4_9.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs,” 9206:140–57. Springer, 2015. https://doi.org/10.1007/978-3-319-21690-4_9.","ama":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. Faster algorithms for quantitative verification in constant treewidth graphs. In: Vol 9206. Springer; 2015:140-157. doi:10.1007/978-3-319-21690-4_9","apa":"Chatterjee, K., Ibsen-Jensen, R., & Pavlogiannis, A. (2015). Faster algorithms for quantitative verification in constant treewidth graphs (Vol. 9206, pp. 140–157). Presented at the CAV: Computer Aided Verification, San Francisco, CA, USA: Springer. https://doi.org/10.1007/978-3-319-21690-4_9","ieee":"K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, “Faster algorithms for quantitative verification in constant treewidth graphs,” presented at the CAV: Computer Aided Verification, San Francisco, CA, USA, 2015, vol. 9206, pp. 140–157.","ista":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2015. Faster algorithms for quantitative verification in constant treewidth graphs. CAV: Computer Aided Verification, LNCS, vol. 9206, 140–157."},"page":"140 - 157","date_published":"2015-07-16T00:00:00Z"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1714","intvolume":" 2015","status":"public","title":"A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks","oa_version":"None","type":"conference","issue":"January","abstract":[{"text":"We present a flexible framework for the automated competitive analysis of on-line scheduling algorithms for firm-deadline real-time tasks based on multi-objective graphs: Given a task set and an on-line scheduling algorithm specified as a labeled transition system, along with some optional safety, liveness, and/or limit-average constraints for the adversary, we automatically compute the competitive ratio of the algorithm w.r.t. A clairvoyant scheduler. We demonstrate the flexibility and power of our approach by comparing the competitive ratio of several on-line algorithms, including Dover, that have been proposed in the past, for various task sets. Our experimental results reveal that none of these algorithms is universally optimal, in the sense that there are task sets where other schedulers provide better performance. Our framework is hence a very useful design tool for selecting optimal algorithms for a given application.","lang":"eng"}],"citation":{"ista":"Chatterjee K, Pavlogiannis A, Kößler A, Schmid U. 2015. A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks. Real-Time Systems Symposium. RTSS: Real-Time Systems Symposium vol. 2015, 118–127.","apa":"Chatterjee, K., Pavlogiannis, A., Kößler, A., & Schmid, U. (2015). A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks. In Real-Time Systems Symposium (Vol. 2015, pp. 118–127). Rome, Italy: IEEE. https://doi.org/10.1109/RTSS.2014.9","ieee":"K. Chatterjee, A. Pavlogiannis, A. Kößler, and U. Schmid, “A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks,” in Real-Time Systems Symposium, Rome, Italy, 2015, vol. 2015, no. January, pp. 118–127.","ama":"Chatterjee K, Pavlogiannis A, Kößler A, Schmid U. A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks. In: Real-Time Systems Symposium. Vol 2015. IEEE; 2015:118-127. doi:10.1109/RTSS.2014.9","chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, Alexander Kößler, and Ulrich Schmid. “A Framework for Automated Competitive Analysis of On-Line Scheduling of Firm-Deadline Tasks.” In Real-Time Systems Symposium, 2015:118–27. IEEE, 2015. https://doi.org/10.1109/RTSS.2014.9.","mla":"Chatterjee, Krishnendu, et al. “A Framework for Automated Competitive Analysis of On-Line Scheduling of Firm-Deadline Tasks.” Real-Time Systems Symposium, vol. 2015, no. January, IEEE, 2015, pp. 118–27, doi:10.1109/RTSS.2014.9.","short":"K. Chatterjee, A. Pavlogiannis, A. Kößler, U. Schmid, in:, Real-Time Systems Symposium, IEEE, 2015, pp. 118–127."},"publication":"Real-Time Systems Symposium","page":"118 - 127","date_published":"2015-01-15T00:00:00Z","scopus_import":1,"article_processing_charge":"No","day":"15","year":"2015","department":[{"_id":"KrCh"}],"publisher":"IEEE","publication_status":"published","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"5423"},{"status":"public","relation":"dissertation_contains","id":"821"}]},"author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","first_name":"Andreas","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas"},{"full_name":"Kößler, Alexander","last_name":"Kößler","first_name":"Alexander"},{"full_name":"Schmid, Ulrich","first_name":"Ulrich","last_name":"Schmid"}],"volume":2015,"date_updated":"2023-09-07T12:01:59Z","date_created":"2018-12-11T11:53:37Z","publist_id":"5417","quality_controlled":"1","doi":"10.1109/RTSS.2014.9","conference":{"end_date":"2014-12-05","location":"Rome, Italy","start_date":"2014-12-02","name":"RTSS: Real-Time Systems Symposium"},"language":[{"iso":"eng"}],"month":"01"},{"abstract":[{"text":"We present a method for simulating brittle fracture under the assumptions of quasi-static linear elastic fracture mechanics (LEFM). Using the boundary element method (BEM) and Lagrangian crack-fronts, we produce highly detailed fracture surfaces. The computational cost of the BEM is alleviated by using a low-resolution mesh and interpolating the resulting stress intensity factors when propagating the high-resolution crack-front.\r\n\r\nOur system produces physics-based fracture surfaces with high spatial and temporal resolution, taking spatial variation of material toughness and/or strength into account. It also allows for crack initiation to be handled separately from crack propagation, which is not only more reasonable from a physics perspective, but can also be used to control the simulation.\r\n\r\nSeparating the resolution of the crack-front from the resolution of the computational mesh increases the efficiency and therefore the amount of visual detail on the resulting fracture surfaces. The BEM also allows us to re-use previously computed blocks of the system matrix.","lang":"eng"}],"issue":"4","type":"conference","oa_version":"Submitted Version","file":[{"date_updated":"2020-07-14T12:45:07Z","date_created":"2018-12-12T10:15:13Z","checksum":"955aee971983f6b6152bcc1c9b4a7c20","file_id":"5131","relation":"main_file","creator":"system","file_size":20154270,"content_type":"application/pdf","file_name":"IST-2016-609-v1+1_FractureBEM.pdf","access_level":"open_access"}],"pubrep_id":"609","status":"public","ddc":["000"],"title":"High-resolution brittle fracture simulation with boundary elements","intvolume":" 34","_id":"1633","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"27","has_accepted_license":"1","scopus_import":1,"date_published":"2015-07-27T00:00:00Z","citation":{"ieee":"D. Hahn and C. Wojtan, “High-resolution brittle fracture simulation with boundary elements,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States, 2015, vol. 34, no. 4.","apa":"Hahn, D., & Wojtan, C. (2015). High-resolution brittle fracture simulation with boundary elements (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States: ACM. https://doi.org/10.1145/2766896","ista":"Hahn D, Wojtan C. 2015. High-resolution brittle fracture simulation with boundary elements. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques vol. 34, 151.","ama":"Hahn D, Wojtan C. High-resolution brittle fracture simulation with boundary elements. In: Vol 34. ACM; 2015. doi:10.1145/2766896","chicago":"Hahn, David, and Chris Wojtan. “High-Resolution Brittle Fracture Simulation with Boundary Elements,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2766896.","short":"D. Hahn, C. Wojtan, in:, ACM, 2015.","mla":"Hahn, David, and Chris Wojtan. High-Resolution Brittle Fracture Simulation with Boundary Elements. Vol. 34, no. 4, 151, ACM, 2015, doi:10.1145/2766896."},"file_date_updated":"2020-07-14T12:45:07Z","ec_funded":1,"publist_id":"5522","article_number":"151","date_created":"2018-12-11T11:53:09Z","date_updated":"2023-09-07T12:02:56Z","volume":34,"author":[{"last_name":"Hahn","first_name":"David","id":"357A6A66-F248-11E8-B48F-1D18A9856A87","full_name":"Hahn, David"},{"full_name":"Wojtan, Christopher J","last_name":"Wojtan","first_name":"Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"839","status":"public","relation":"dissertation_contains"}]},"publication_status":"published","department":[{"_id":"ChWo"}],"publisher":"ACM","year":"2015","month":"07","language":[{"iso":"eng"}],"conference":{"name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques","end_date":"2015-08-13","start_date":"2015-08-09","location":"Los Angeles, CA, United States"},"doi":"10.1145/2766896","quality_controlled":"1","project":[{"name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020","_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176"}],"oa":1},{"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"961"}]},"author":[{"full_name":"Ruprecht, Verena","first_name":"Verena","last_name":"Ruprecht","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4088-8633"},{"full_name":"Wieser, Stefan","first_name":"Stefan","last_name":"Wieser","id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2670-2217"},{"full_name":"Callan Jones, Andrew","last_name":"Callan Jones","first_name":"Andrew"},{"last_name":"Smutny","first_name":"Michael","orcid":"0000-0002-5920-9090","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","full_name":"Smutny, Michael"},{"id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87","first_name":"Hitoshi","last_name":"Morita","full_name":"Morita, Hitoshi"},{"full_name":"Sako, Keisuke","orcid":"0000-0002-6453-8075","id":"3BED66BE-F248-11E8-B48F-1D18A9856A87","last_name":"Sako","first_name":"Keisuke"},{"full_name":"Barone, Vanessa","first_name":"Vanessa","last_name":"Barone","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2676-3367"},{"first_name":"Monika","last_name":"Ritsch Marte","full_name":"Ritsch Marte, Monika"},{"full_name":"Sixt, Michael K","first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"},{"first_name":"Raphaël","last_name":"Voituriez","full_name":"Voituriez, Raphaël"},{"last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"volume":160,"date_updated":"2023-09-07T12:05:08Z","date_created":"2018-12-11T11:52:35Z","acknowledgement":"We would like to thank R. Hausschild and E. Papusheva for technical assistance and the service facilities at the IST Austria for continuous support. The caRhoA plasmid was a kind gift of T. Kudoh and A. Takesono. We thank M. Piel and E. Paluch for exchanging unpublished data. ","year":"2015","publisher":"Cell Press","department":[{"_id":"CaHe"},{"_id":"MiSi"}],"publication_status":"published","publist_id":"5634","file_date_updated":"2020-07-14T12:45:01Z","doi":"10.1016/j.cell.2015.01.008","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"SSU"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"_id":"2529486C-B435-11E9-9278-68D0E5697425","grant_number":"T 560-B17","call_identifier":"FWF","name":"Cell- and Tissue Mechanics in Zebrafish Germ Layer Formation"},{"name":"Cell Cortex and Germ Layer Formation in Zebrafish Gastrulation","call_identifier":"FWF","grant_number":"I 812-B12","_id":"2527D5CC-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","month":"02","pubrep_id":"484","file":[{"checksum":"228d3edf40627d897b3875088a0ac51f","date_created":"2018-12-12T10:13:21Z","date_updated":"2020-07-14T12:45:01Z","file_id":"5003","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":4362653,"access_level":"open_access","file_name":"IST-2016-484-v1+1_1-s2.0-S0092867415000094-main.pdf"}],"oa_version":"Published Version","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"1537","intvolume":" 160","status":"public","ddc":["570"],"title":"Cortical contractility triggers a stochastic switch to fast amoeboid cell motility","issue":"4","abstract":[{"lang":"eng","text":"3D amoeboid cell migration is central to many developmental and disease-related processes such as cancer metastasis. Here, we identify a unique prototypic amoeboid cell migration mode in early zebrafish embryos, termed stable-bleb migration. Stable-bleb cells display an invariant polarized balloon-like shape with exceptional migration speed and persistence. Progenitor cells can be reversibly transformed into stable-bleb cells irrespective of their primary fate and motile characteristics by increasing myosin II activity through biochemical or mechanical stimuli. Using a combination of theory and experiments, we show that, in stable-bleb cells, cortical contractility fluctuations trigger a stochastic switch into amoeboid motility, and a positive feedback between cortical flows and gradients in contractility maintains stable-bleb cell polarization. We further show that rearward cortical flows drive stable-bleb cell migration in various adhesive and non-adhesive environments, unraveling a highly versatile amoeboid migration phenotype."}],"type":"journal_article","date_published":"2015-02-12T00:00:00Z","citation":{"short":"V. Ruprecht, S. Wieser, A. Callan Jones, M. Smutny, H. Morita, K. Sako, V. Barone, M. Ritsch Marte, M.K. Sixt, R. Voituriez, C.-P.J. Heisenberg, Cell 160 (2015) 673–685.","mla":"Ruprecht, Verena, et al. “Cortical Contractility Triggers a Stochastic Switch to Fast Amoeboid Cell Motility.” Cell, vol. 160, no. 4, Cell Press, 2015, pp. 673–85, doi:10.1016/j.cell.2015.01.008.","chicago":"Ruprecht, Verena, Stefan Wieser, Andrew Callan Jones, Michael Smutny, Hitoshi Morita, Keisuke Sako, Vanessa Barone, et al. “Cortical Contractility Triggers a Stochastic Switch to Fast Amoeboid Cell Motility.” Cell. Cell Press, 2015. https://doi.org/10.1016/j.cell.2015.01.008.","ama":"Ruprecht V, Wieser S, Callan Jones A, et al. Cortical contractility triggers a stochastic switch to fast amoeboid cell motility. Cell. 2015;160(4):673-685. doi:10.1016/j.cell.2015.01.008","ieee":"V. Ruprecht et al., “Cortical contractility triggers a stochastic switch to fast amoeboid cell motility,” Cell, vol. 160, no. 4. Cell Press, pp. 673–685, 2015.","apa":"Ruprecht, V., Wieser, S., Callan Jones, A., Smutny, M., Morita, H., Sako, K., … Heisenberg, C.-P. J. (2015). Cortical contractility triggers a stochastic switch to fast amoeboid cell motility. Cell. Cell Press. https://doi.org/10.1016/j.cell.2015.01.008","ista":"Ruprecht V, Wieser S, Callan Jones A, Smutny M, Morita H, Sako K, Barone V, Ritsch Marte M, Sixt MK, Voituriez R, Heisenberg C-PJ. 2015. Cortical contractility triggers a stochastic switch to fast amoeboid cell motility. Cell. 160(4), 673–685."},"publication":"Cell","page":"673 - 685","has_accepted_license":"1","day":"12","scopus_import":1},{"publist_id":"5580","year":"2015","pmid":1,"publication_status":"published","publisher":"American Society of Plant Biologists","department":[{"_id":"JiFr"}],"author":[{"full_name":"Adamowski, Maciek","first_name":"Maciek","last_name":"Adamowski","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6463-5257"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"938"}]},"date_updated":"2023-09-07T12:06:09Z","date_created":"2018-12-11T11:52:54Z","volume":27,"month":"01","oa":1,"external_id":{"pmid":["25604445"]},"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4330589/"}],"quality_controlled":"1","doi":"10.1105/tpc.114.134874","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"Auxin participates in a multitude of developmental processes, as well as responses to environmental cues. Compared with other plant hormones, auxin exhibits a unique property, as it undergoes directional, cell-to-cell transport facilitated by plasma membrane-localized transport proteins. Among them, a prominent role has been ascribed to the PIN family of auxin efflux facilitators. PIN proteins direct polar auxin transport on account of their asymmetric subcellular localizations. In this review, we provide an overview of the multiple developmental roles of PIN proteins, including the atypical endoplasmic reticulum-localized members of the family, and look at the family from an evolutionary perspective. Next, we cover the cell biological and molecular aspects of PIN function, in particular the establishment of their polar subcellular localization. Hormonal and environmental inputs into the regulation of PIN action are summarized as well.","lang":"eng"}],"issue":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1591","title":"PIN-dependent auxin transport: Action, regulation, and evolution","status":"public","intvolume":" 27","oa_version":"Submitted Version","scopus_import":1,"day":"20","publication":"Plant Cell","citation":{"ieee":"M. Adamowski and J. Friml, “PIN-dependent auxin transport: Action, regulation, and evolution,” Plant Cell, vol. 27, no. 1. American Society of Plant Biologists, pp. 20–32, 2015.","apa":"Adamowski, M., & Friml, J. (2015). PIN-dependent auxin transport: Action, regulation, and evolution. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.114.134874","ista":"Adamowski M, Friml J. 2015. PIN-dependent auxin transport: Action, regulation, and evolution. Plant Cell. 27(1), 20–32.","ama":"Adamowski M, Friml J. PIN-dependent auxin transport: Action, regulation, and evolution. Plant Cell. 2015;27(1):20-32. doi:10.1105/tpc.114.134874","chicago":"Adamowski, Maciek, and Jiří Friml. “PIN-Dependent Auxin Transport: Action, Regulation, and Evolution.” Plant Cell. American Society of Plant Biologists, 2015. https://doi.org/10.1105/tpc.114.134874.","short":"M. Adamowski, J. Friml, Plant Cell 27 (2015) 20–32.","mla":"Adamowski, Maciek, and Jiří Friml. “PIN-Dependent Auxin Transport: Action, Regulation, and Evolution.” Plant Cell, vol. 27, no. 1, American Society of Plant Biologists, 2015, pp. 20–32, doi:10.1105/tpc.114.134874."},"page":"20 - 32","date_published":"2015-01-20T00:00:00Z"}]