[{"quality_controlled":"1","alternative_title":["ACM Transactions on Graphics"],"citation":{"chicago":"Miguel Villalba, Eder, Mathias Lepoutre, and Bernd Bickel. “Computational Design of Stable Planar-Rod Structures,” Vol. 35. ACM, 2016. <a href=\"https://doi.org/10.1145/2897824.2925978\">https://doi.org/10.1145/2897824.2925978</a>.","apa":"Miguel Villalba, E., Lepoutre, M., &#38; Bickel, B. (2016). Computational design of stable planar-rod structures (Vol. 35). Presented at the ACM SIGGRAPH, Anaheim, CA, USA: ACM. <a href=\"https://doi.org/10.1145/2897824.2925978\">https://doi.org/10.1145/2897824.2925978</a>","ama":"Miguel Villalba E, Lepoutre M, Bickel B. Computational design of stable planar-rod structures. In: Vol 35. ACM; 2016. doi:<a href=\"https://doi.org/10.1145/2897824.2925978\">10.1145/2897824.2925978</a>","mla":"Miguel Villalba, Eder, et al. <i>Computational Design of Stable Planar-Rod Structures</i>. Vol. 35, no. 4, 86, ACM, 2016, doi:<a href=\"https://doi.org/10.1145/2897824.2925978\">10.1145/2897824.2925978</a>.","short":"E. Miguel Villalba, M. Lepoutre, B. Bickel, in:, ACM, 2016.","ieee":"E. Miguel Villalba, M. Lepoutre, and B. Bickel, “Computational design of stable planar-rod structures,” presented at the ACM SIGGRAPH, Anaheim, CA, USA, 2016, vol. 35, no. 4.","ista":"Miguel Villalba E, Lepoutre M, Bickel B. 2016. Computational design of stable planar-rod structures. ACM SIGGRAPH, ACM Transactions on Graphics, vol. 35, 86."},"publication_status":"published","department":[{"_id":"BeBi"}],"language":[{"iso":"eng"}],"publist_id":"5878","abstract":[{"text":"We present a computational method for designing wire sculptures consisting of interlocking wires. Our method allows the computation of aesthetically pleasing structures that are structurally stable, efficiently fabricatable with a 2D wire bending machine, and assemblable without the need of additional connectors. Starting from a set of planar contours provided by the user, our method automatically tests for the feasibility of a design, determines a discrete ordering of wires at intersection points, and optimizes for the rest shape of the individual wires to maximize structural stability under frictional contact. In addition to their application to art, wire sculptures present an extremely efficient and fast alternative for low-fidelity rapid prototyping because manufacturing time and required material linearly scales with the physical size of objects. We demonstrate the effectiveness of our approach on a varied set of examples, all of which we fabricated.","lang":"eng"}],"file_date_updated":"2020-07-14T12:44:47Z","scopus_import":1,"file":[{"file_id":"4853","creator":"system","access_level":"open_access","checksum":"d00c2664a43d945df8876ea0193734e3","content_type":"application/pdf","file_name":"IST-2017-763-v1+1_wirebending.pdf","date_updated":"2020-07-14T12:44:47Z","file_size":44766392,"date_created":"2018-12-12T10:11:01Z","relation":"main_file"}],"publisher":"ACM","ddc":["006"],"type":"conference","month":"07","intvolume":"        35","pubrep_id":"763","article_number":"86","issue":"4","ec_funded":1,"author":[{"first_name":"Eder","full_name":"Miguel Villalba, Eder","last_name":"Miguel Villalba","id":"3FB91342-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lepoutre","first_name":"Mathias","full_name":"Lepoutre, Mathias"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385"}],"status":"public","oa_version":"Preprint","date_created":"2018-12-11T11:51:36Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":35,"doi":"10.1145/2897824.2925978","date_published":"2016-07-01T00:00:00Z","day":"01","title":"Computational design of stable planar-rod structures","conference":{"location":"Anaheim, CA, USA","name":"ACM SIGGRAPH","start_date":"2016-07-24","end_date":"2016-07-28"},"date_updated":"2021-01-12T06:50:10Z","_id":"1364","has_accepted_license":"1","acknowledgement":"This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 645599.","project":[{"call_identifier":"H2020","grant_number":"645599","_id":"25082902-B435-11E9-9278-68D0E5697425","name":"Soft-bodied intelligence for Manipulation"}],"year":"2016","oa":1},{"month":"08","intvolume":"      9815","year":"2016","oa":1,"page":"241 - 271","title":"Efficiently computing data-independent memory-hard functions","main_file_link":[{"url":"http://eprint.iacr.org/2016/115","open_access":"1"}],"conference":{"name":"CRYPTO: International Cryptology Conference","location":"Santa Barbara, CA, USA","start_date":"2016-08-14","end_date":"2016-08-18"},"_id":"1365","type":"conference","date_updated":"2021-01-12T06:50:11Z","publist_id":"5876","language":[{"iso":"eng"}],"department":[{"_id":"KrPi"}],"abstract":[{"lang":"eng","text":"A memory-hard function (MHF) f is equipped with a space cost σ and time cost τ parameter such that repeatedly computing fσ,τ on an application specific integrated circuit (ASIC) is not economically advantageous relative to a general purpose computer. Technically we would like that any (generalized) circuit for evaluating an iMHF fσ,τ has area × time (AT) complexity at Θ(σ2 ∗ τ). A data-independent MHF (iMHF) has the added property that it can be computed with almost optimal memory and time complexity by an algorithm which accesses memory in a pattern independent of the input value. Such functions can be specified by fixing a directed acyclic graph (DAG) G on n = Θ(σ ∗ τ) nodes representing its computation graph. In this work we develop new tools for analyzing iMHFs. First we define and motivate a new complexity measure capturing the amount of energy (i.e. electricity) required to compute a function. We argue that, in practice, this measure is at least as important as the more traditional AT-complexity. Next we describe an algorithm A for repeatedly evaluating an iMHF based on an arbitrary DAG G. We upperbound both its energy and AT complexities per instance evaluated in terms of a certain combinatorial property of G. Next we instantiate our attack for several general classes of DAGs which include those underlying many of the most important iMHF candidates in the literature. In particular, we obtain the following results which hold for all choices of parameters σ and τ (and thread-count) such that n = σ ∗ τ. -The Catena-Dragonfly function of [FLW13] has AT and energy complexities O(n1.67). -The Catena-Butterfly function of [FLW13] has complexities is O(n1.67). -The Double-Buffer and the Linear functions of [CGBS16] both have complexities in O(n1.67). -The Argon2i function of [BDK15] (winner of the Password Hashing Competition [PHC]) has complexities O(n7/4 log(n)). -The Single-Buffer function of [CGBS16] has complexities O(n7/4 log(n)). -Any iMHF can be computed by an algorithm with complexities O(n2/ log1 −ε(n)) for all ε &gt; 0. In particular when τ = 1 this shows that the goal of constructing an iMHF with AT-complexity Θ(σ2 ∗ τ ) is unachievable. Along the way we prove a lemma upper-bounding the depth-robustness of any DAG which may prove to be of independent interest."}],"scopus_import":1,"date_published":"2016-08-01T00:00:00Z","day":"01","publisher":"Springer","citation":{"apa":"Alwen, J. F., &#38; Blocki, J. (2016). Efficiently computing data-independent memory-hard functions (Vol. 9815, pp. 241–271). Presented at the CRYPTO: International Cryptology Conference, Santa Barbara, CA, USA: Springer. <a href=\"https://doi.org/10.1007/978-3-662-53008-5_9\">https://doi.org/10.1007/978-3-662-53008-5_9</a>","chicago":"Alwen, Joel F, and Jeremiah Blocki. “Efficiently Computing Data-Independent Memory-Hard Functions,” 9815:241–71. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-662-53008-5_9\">https://doi.org/10.1007/978-3-662-53008-5_9</a>.","ama":"Alwen JF, Blocki J. Efficiently computing data-independent memory-hard functions. In: Vol 9815. Springer; 2016:241-271. doi:<a href=\"https://doi.org/10.1007/978-3-662-53008-5_9\">10.1007/978-3-662-53008-5_9</a>","short":"J.F. Alwen, J. Blocki, in:, Springer, 2016, pp. 241–271.","mla":"Alwen, Joel F., and Jeremiah Blocki. <i>Efficiently Computing Data-Independent Memory-Hard Functions</i>. Vol. 9815, Springer, 2016, pp. 241–71, doi:<a href=\"https://doi.org/10.1007/978-3-662-53008-5_9\">10.1007/978-3-662-53008-5_9</a>.","ista":"Alwen JF, Blocki J. 2016. Efficiently computing data-independent memory-hard functions. CRYPTO: International Cryptology Conference, LNCS, vol. 9815, 241–271.","ieee":"J. F. Alwen and J. Blocki, “Efficiently computing data-independent memory-hard functions,” presented at the CRYPTO: International Cryptology Conference, Santa Barbara, CA, USA, 2016, vol. 9815, pp. 241–271."},"author":[{"first_name":"Joel F","full_name":"Alwen, Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","last_name":"Alwen"},{"first_name":"Jeremiah","full_name":"Blocki, Jeremiah","last_name":"Blocki"}],"status":"public","alternative_title":["LNCS"],"quality_controlled":"1","oa_version":"Preprint","volume":9815,"publication_status":"published","date_created":"2018-12-11T11:51:36Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/978-3-662-53008-5_9"},{"intvolume":"      9665","month":"05","page":"87 - 116","ec_funded":1,"main_file_link":[{"url":"https://eprint.iacr.org/2016/169/20160219:201940","open_access":"1"}],"type":"conference","abstract":[{"text":"We study the problem of devising provably secure PRNGs with input based on the sponge paradigm. Such constructions are very appealing, as efficient software/hardware implementations of SHA-3 can easily be translated into a PRNG in a nearly black-box way. The only existing sponge-based construction, proposed by Bertoni et al. (CHES 2010), fails to achieve the security notion of robustness recently considered by Dodis et al. (CCS 2013), for two reasons: (1) The construction is deterministic, and thus there are high-entropy input distributions on which the construction fails to extract random bits, and (2) The construction is not forward secure, and presented solutions aiming at restoring forward security have not been rigorously analyzed. We propose a seeded variant of Bertoni et al.’s PRNG with input which we prove secure in the sense of robustness, delivering in particular concrete security bounds. On the way, we make what we believe to be an important conceptual contribution, developing a variant of the security framework of Dodis et al. tailored at the ideal permutation model that captures PRNG security in settings where the weakly random inputs are provided from a large class of possible adversarial samplers which are also allowed to query the random permutation. As a further application of our techniques, we also present an efficient sponge-based key-derivation function (which can be instantiated from SHA-3 in a black-box fashion), which we also prove secure when fed with samples from permutation-dependent distributions.","lang":"eng"}],"publist_id":"5872","department":[{"_id":"KrPi"}],"language":[{"iso":"eng"}],"publisher":"Springer","scopus_import":1,"alternative_title":["LNCS"],"quality_controlled":"1","citation":{"ama":"Gazi P, Tessaro S. Provably robust sponge-based PRNGs and KDFs. In: Vol 9665. Springer; 2016:87-116. doi:<a href=\"https://doi.org/10.1007/978-3-662-49890-3_4\">10.1007/978-3-662-49890-3_4</a>","apa":"Gazi, P., &#38; Tessaro, S. (2016). Provably robust sponge-based PRNGs and KDFs (Vol. 9665, pp. 87–116). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Vienna, Austria: Springer. <a href=\"https://doi.org/10.1007/978-3-662-49890-3_4\">https://doi.org/10.1007/978-3-662-49890-3_4</a>","chicago":"Gazi, Peter, and Stefano Tessaro. “Provably Robust Sponge-Based PRNGs and KDFs,” 9665:87–116. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-662-49890-3_4\">https://doi.org/10.1007/978-3-662-49890-3_4</a>.","ieee":"P. Gazi and S. Tessaro, “Provably robust sponge-based PRNGs and KDFs,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Vienna, Austria, 2016, vol. 9665, pp. 87–116.","ista":"Gazi P, Tessaro S. 2016. Provably robust sponge-based PRNGs and KDFs. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 9665, 87–116.","short":"P. Gazi, S. Tessaro, in:, Springer, 2016, pp. 87–116.","mla":"Gazi, Peter, and Stefano Tessaro. <i>Provably Robust Sponge-Based PRNGs and KDFs</i>. Vol. 9665, Springer, 2016, pp. 87–116, doi:<a href=\"https://doi.org/10.1007/978-3-662-49890-3_4\">10.1007/978-3-662-49890-3_4</a>."},"publication_status":"published","year":"2016","project":[{"call_identifier":"FP7","grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425","name":"Provable Security for Physical Cryptography"}],"oa":1,"title":"Provably robust sponge-based PRNGs and KDFs","date_updated":"2021-01-12T06:50:11Z","_id":"1366","conference":{"name":"EUROCRYPT: Theory and Applications of Cryptographic Techniques","location":"Vienna, Austria","start_date":"2016-05-08","end_date":"2016-05-12"},"day":"01","date_published":"2016-05-01T00:00:00Z","oa_version":"Preprint","status":"public","author":[{"last_name":"Gazi","id":"3E0BFE38-F248-11E8-B48F-1D18A9856A87","full_name":"Gazi, Peter","first_name":"Peter"},{"full_name":"Tessaro, Stefano","first_name":"Stefano","last_name":"Tessaro"}],"doi":"10.1007/978-3-662-49890-3_4","date_created":"2018-12-11T11:51:36Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":9665},{"title":"Correlation driven d wave superconductivity in Anderson lattice model: Two gaps","date_updated":"2021-01-12T06:50:12Z","_id":"1368","project":[{"grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"year":"2016","acknowledgement":"The  work  has  been  supported  by  the  National Science  Center  (NCN)  under  the  Grant  MAESTRO,  No.\r\nDEC-2012/04/A/ST3/00342. ","oa":1,"oa_version":"Preprint","status":"public","author":[{"first_name":"Marcin","full_name":"Wysokiński, Marcin","last_name":"Wysokiński"},{"full_name":"Kaczmarczyk, Jan","first_name":"Jan","orcid":"0000-0002-1629-3675","id":"46C405DE-F248-11E8-B48F-1D18A9856A87","last_name":"Kaczmarczyk"},{"full_name":"Spałek, Jozef","first_name":"Jozef","last_name":"Spałek"}],"doi":"10.1103/PhysRevB.94.024517","date_created":"2018-12-11T11:51:37Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":94,"day":"01","date_published":"2016-07-01T00:00:00Z","main_file_link":[{"url":"https://arxiv.org/abs/1510.00224","open_access":"1"}],"type":"journal_article","intvolume":"        94","article_number":"024517","month":"07","ec_funded":1,"issue":"2","quality_controlled":"1","citation":{"mla":"Wysokiński, Marcin, et al. “Correlation Driven d Wave Superconductivity in Anderson Lattice Model: Two Gaps.” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 94, no. 2, 024517, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevB.94.024517\">10.1103/PhysRevB.94.024517</a>.","short":"M. Wysokiński, J. Kaczmarczyk, J. Spałek, Physical Review B - Condensed Matter and Materials Physics 94 (2016).","ista":"Wysokiński M, Kaczmarczyk J, Spałek J. 2016. Correlation driven d wave superconductivity in Anderson lattice model: Two gaps. Physical Review B - Condensed Matter and Materials Physics. 94(2), 024517.","ieee":"M. Wysokiński, J. Kaczmarczyk, and J. Spałek, “Correlation driven d wave superconductivity in Anderson lattice model: Two gaps,” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 94, no. 2. American Physical Society, 2016.","chicago":"Wysokiński, Marcin, Jan Kaczmarczyk, and Jozef Spałek. “Correlation Driven d Wave Superconductivity in Anderson Lattice Model: Two Gaps.” <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society, 2016. <a href=\"https://doi.org/10.1103/PhysRevB.94.024517\">https://doi.org/10.1103/PhysRevB.94.024517</a>.","apa":"Wysokiński, M., Kaczmarczyk, J., &#38; Spałek, J. (2016). Correlation driven d wave superconductivity in Anderson lattice model: Two gaps. <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.94.024517\">https://doi.org/10.1103/PhysRevB.94.024517</a>","ama":"Wysokiński M, Kaczmarczyk J, Spałek J. Correlation driven d wave superconductivity in Anderson lattice model: Two gaps. <i>Physical Review B - Condensed Matter and Materials Physics</i>. 2016;94(2). doi:<a href=\"https://doi.org/10.1103/PhysRevB.94.024517\">10.1103/PhysRevB.94.024517</a>"},"publication_status":"published","abstract":[{"text":"Superconductivity in heavy-fermion systems has an unconventional nature and is considered to originate from the universal features of the electronic structure. Here, the Anderson lattice model is studied by means of the full variational Gutzwiller wave function incorporating nonlocal effects of the on-site interaction. We show that the d-wave superconducting ground state can be driven solely by interelectronic correlations. The proposed microscopic mechanism leads to a multigap superconductivity with the dominant contribution due to f electrons and in the dx2−y2-wave channel. Our results rationalize several important observations for CeCoIn5.","lang":"eng"}],"publist_id":"5844","department":[{"_id":"MiLe"}],"language":[{"iso":"eng"}],"publisher":"American Physical Society","publication":"Physical Review B - Condensed Matter and Materials Physics","scopus_import":1},{"oa":1,"project":[{"call_identifier":"FP7","grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425","name":"Lifelong Learning of Visual Scene Understanding"}],"year":"2016","conference":{"start_date":"2016-10-11","end_date":"2016-10-14","location":"Amsterdam, The Netherlands","name":"ECCV: European Conference on Computer Vision"},"_id":"1369","date_updated":"2021-01-12T06:50:12Z","title":"Seed, expand and constrain: Three principles for weakly-supervised image segmentation","date_published":"2016-09-15T00:00:00Z","day":"15","volume":9908,"date_created":"2018-12-11T11:51:37Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/978-3-319-46493-0_42","status":"public","author":[{"full_name":"Kolesnikov, Alexander","first_name":"Alexander","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","last_name":"Kolesnikov"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","full_name":"Lampert, Christoph","first_name":"Christoph","orcid":"0000-0001-8622-7887"}],"oa_version":"Preprint","ec_funded":1,"page":"695 - 711","month":"09","intvolume":"      9908","type":"conference","main_file_link":[{"url":"https://arxiv.org/abs/1603.06098","open_access":"1"}],"scopus_import":1,"publisher":"Springer","language":[{"iso":"eng"}],"department":[{"_id":"ChLa"}],"publist_id":"5842","abstract":[{"lang":"eng","text":"We introduce a new loss function for the weakly-supervised training of semantic image segmentation models based on three guiding principles: to seed with weak localization cues, to expand objects based on the information about which classes can occur in an image, and to constrain the segmentations to coincide with object boundaries. We show experimentally that training a deep convolutional neural network using the proposed loss function leads to substantially better segmentations than previous state-of-the-art methods on the challenging PASCAL VOC 2012 dataset. We furthermore give insight into the working mechanism of our method by a detailed experimental study that illustrates how the segmentation quality is affected by each term of the proposed loss function as well as their combinations."}],"publication_status":"published","citation":{"ista":"Kolesnikov A, Lampert C. 2016. Seed, expand and constrain: Three principles for weakly-supervised image segmentation. ECCV: European Conference on Computer Vision, LNCS, vol. 9908, 695–711.","ieee":"A. Kolesnikov and C. Lampert, “Seed, expand and constrain: Three principles for weakly-supervised image segmentation,” presented at the ECCV: European Conference on Computer Vision, Amsterdam, The Netherlands, 2016, vol. 9908, pp. 695–711.","mla":"Kolesnikov, Alexander, and Christoph Lampert. <i>Seed, Expand and Constrain: Three Principles for Weakly-Supervised Image Segmentation</i>. Vol. 9908, Springer, 2016, pp. 695–711, doi:<a href=\"https://doi.org/10.1007/978-3-319-46493-0_42\">10.1007/978-3-319-46493-0_42</a>.","short":"A. Kolesnikov, C. Lampert, in:, Springer, 2016, pp. 695–711.","ama":"Kolesnikov A, Lampert C. Seed, expand and constrain: Three principles for weakly-supervised image segmentation. In: Vol 9908. Springer; 2016:695-711. doi:<a href=\"https://doi.org/10.1007/978-3-319-46493-0_42\">10.1007/978-3-319-46493-0_42</a>","apa":"Kolesnikov, A., &#38; Lampert, C. (2016). Seed, expand and constrain: Three principles for weakly-supervised image segmentation (Vol. 9908, pp. 695–711). Presented at the ECCV: European Conference on Computer Vision, Amsterdam, The Netherlands: Springer. <a href=\"https://doi.org/10.1007/978-3-319-46493-0_42\">https://doi.org/10.1007/978-3-319-46493-0_42</a>","chicago":"Kolesnikov, Alexander, and Christoph Lampert. “Seed, Expand and Constrain: Three Principles for Weakly-Supervised Image Segmentation,” 9908:695–711. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-319-46493-0_42\">https://doi.org/10.1007/978-3-319-46493-0_42</a>."},"quality_controlled":"1","alternative_title":["LNCS"]},{"issue":"3","intvolume":"        93","article_number":"033846","month":"03","type":"journal_article","main_file_link":[{"url":"http://arxiv.org/abs/1601.01818","open_access":"1"}],"publisher":"American Physical Society","scopus_import":1,"publication":"Physical Review A - Atomic, Molecular, and Optical Physics","abstract":[{"lang":"eng","text":"We study coherent phonon oscillations and tunneling between two coupled nonlinear nanomechanical resonators. We show that the coupling between two nanomechanical resonators creates an effective phonon Josephson junction, which exhibits two different dynamical behaviors: Josephson oscillation (phonon-Rabi oscillation) and macroscopic self-trapping (phonon blockade). Self-trapping originates from mechanical nonlinearities, meaning that when the nonlinearity exceeds its critical value, the energy exchange between the two resonators is suppressed, and phonon Josephson oscillations between them are completely blocked. An effective classical Hamiltonian for the phonon Josephson junction is derived and its mean-field dynamics is studied in phase space. Finally, we study the phonon-phonon coherence quantified by the mean fringe visibility, and show that the interaction between the two resonators may lead to the loss of coherence in the phononic junction."}],"department":[{"_id":"JoFi"}],"language":[{"iso":"eng"}],"publist_id":"5841","publication_status":"published","quality_controlled":"1","citation":{"ama":"Barzanjeh S, Vitali D. Phonon Josephson junction with nanomechanical resonators. <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. 2016;93(3). doi:<a href=\"https://doi.org/10.1103/PhysRevA.93.033846\">10.1103/PhysRevA.93.033846</a>","apa":"Barzanjeh, S., &#38; Vitali, D. (2016). Phonon Josephson junction with nanomechanical resonators. <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.93.033846\">https://doi.org/10.1103/PhysRevA.93.033846</a>","chicago":"Barzanjeh, Shabir, and David Vitali. “Phonon Josephson Junction with Nanomechanical Resonators.” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society, 2016. <a href=\"https://doi.org/10.1103/PhysRevA.93.033846\">https://doi.org/10.1103/PhysRevA.93.033846</a>.","ieee":"S. Barzanjeh and D. Vitali, “Phonon Josephson junction with nanomechanical resonators,” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 93, no. 3. American Physical Society, 2016.","ista":"Barzanjeh S, Vitali D. 2016. Phonon Josephson junction with nanomechanical resonators. Physical Review A - Atomic, Molecular, and Optical Physics. 93(3), 033846.","mla":"Barzanjeh, Shabir, and David Vitali. “Phonon Josephson Junction with Nanomechanical Resonators.” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 93, no. 3, 033846, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevA.93.033846\">10.1103/PhysRevA.93.033846</a>.","short":"S. Barzanjeh, D. Vitali, Physical Review A - Atomic, Molecular, and Optical Physics 93 (2016)."},"oa":1,"year":"2016","acknowledgement":"The work of S.B. has been supported by the European Commission (Belgium) via the SCALEQIT program and by the Alexander von Humboldt Foundation.  ","date_updated":"2023-02-21T10:36:32Z","_id":"1370","title":"Phonon Josephson junction with nanomechanical resonators","day":"28","date_published":"2016-03-28T00:00:00Z","doi":"10.1103/PhysRevA.93.033846","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:51:38Z","volume":93,"oa_version":"Preprint","author":[{"orcid":"0000-0003-0415-1423","first_name":"Shabir","full_name":"Barzanjeh, Shabir","last_name":"Barzanjeh","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Vitali","first_name":"David","full_name":"Vitali, David"}],"status":"public"},{"title":"Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function","type":"journal_article","_id":"1371","date_updated":"2021-01-12T06:50:13Z","project":[{"grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"intvolume":"        17","acknowledgement":"MZ has been supported by Polish National Science Centre Grant No. DEC-2012/07/N/NZ2/00107 and by Foundation of Polish Science award START. ","year":"2016","month":"07","ec_funded":1,"page":"124 - 158","oa_version":"None","citation":{"mla":"Martin, Olivier, et al. “Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function.” <i>Physics of Life Reviews</i>, vol. 17, Elsevier, 2016, pp. 124–58, doi:<a href=\"https://doi.org/10.1016/j.plrev.2016.06.002\">10.1016/j.plrev.2016.06.002</a>.","short":"O. Martin, A. Krzywicki, M.P. Zagórski, Physics of Life Reviews 17 (2016) 124–158.","ista":"Martin O, Krzywicki A, Zagórski MP. 2016. Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function. Physics of Life Reviews. 17, 124–158.","ieee":"O. Martin, A. Krzywicki, and M. P. Zagórski, “Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function,” <i>Physics of Life Reviews</i>, vol. 17. Elsevier, pp. 124–158, 2016.","chicago":"Martin, Olivier, André Krzywicki, and Marcin P Zagórski. “Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function.” <i>Physics of Life Reviews</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.plrev.2016.06.002\">https://doi.org/10.1016/j.plrev.2016.06.002</a>.","apa":"Martin, O., Krzywicki, A., &#38; Zagórski, M. P. (2016). Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function. <i>Physics of Life Reviews</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.plrev.2016.06.002\">https://doi.org/10.1016/j.plrev.2016.06.002</a>","ama":"Martin O, Krzywicki A, Zagórski MP. Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function. <i>Physics of Life Reviews</i>. 2016;17:124-158. doi:<a href=\"https://doi.org/10.1016/j.plrev.2016.06.002\">10.1016/j.plrev.2016.06.002</a>"},"status":"public","author":[{"first_name":"Olivier","full_name":"Martin, Olivier","last_name":"Martin"},{"first_name":"André","full_name":"Krzywicki, André","last_name":"Krzywicki"},{"last_name":"Zagórski","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7896-7762","first_name":"Marcin P","full_name":"Zagórski, Marcin P"}],"quality_controlled":"1","doi":"10.1016/j.plrev.2016.06.002","volume":17,"date_created":"2018-12-11T11:51:38Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_status":"published","abstract":[{"lang":"eng","text":"Living cells can maintain their internal states, react to changing environments, grow, differentiate, divide, etc. All these processes are tightly controlled by what can be called a regulatory program. The logic of the underlying control can sometimes be guessed at by examining the network of influences amongst genetic components. Some associated gene regulatory networks have been studied in prokaryotes and eukaryotes, unveiling various structural features ranging from broad distributions of out-degrees to recurrent &quot;motifs&quot;, that is small subgraphs having a specific pattern of interactions. To understand what factors may be driving such structuring, a number of groups have introduced frameworks to model the dynamics of gene regulatory networks. In that context, we review here such in silico approaches and show how selection for phenotypes, i.e., network function, can shape network structure."}],"publist_id":"5840","language":[{"iso":"eng"}],"department":[{"_id":"AnKi"}],"publisher":"Elsevier","day":"01","publication":"Physics of Life Reviews","scopus_import":1,"date_published":"2016-07-01T00:00:00Z"},{"oa_version":"Submitted Version","status":"public","author":[{"last_name":"Pernisová","full_name":"Pernisová, Markéta","first_name":"Markéta"},{"full_name":"Prat, Tomas","first_name":"Tomas","id":"3DA3BFEE-F248-11E8-B48F-1D18A9856A87","last_name":"Prat"},{"id":"399876EC-F248-11E8-B48F-1D18A9856A87","last_name":"Grones","first_name":"Peter","full_name":"Grones, Peter"},{"first_name":"Danka","full_name":"Haruštiaková, Danka","last_name":"Haruštiaková"},{"last_name":"Matonohova","first_name":"Martina","full_name":"Matonohova, Martina"},{"last_name":"Spíchal","full_name":"Spíchal, Lukáš","first_name":"Lukáš"},{"first_name":"Tomasz","full_name":"Nodzyński, Tomasz","last_name":"Nodzyński"},{"orcid":"0000-0002-8302-7596","first_name":"Jirí","full_name":"Friml, Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hejátko, Jan","first_name":"Jan","last_name":"Hejátko"}],"doi":"10.1111/nph.14049","volume":212,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:51:38Z","day":"01","date_published":"2016-10-01T00:00:00Z","title":"Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis","_id":"1372","date_updated":"2021-01-12T06:50:13Z","acknowledgement":"Funded by Ministry of Education, Youth and Sports Czech Republic. Grant Numbers: CEITEC 2020, LQ1601, LO1204, LH14104 and The European Research Council. Grant Number: ERC-2011-StG-20101109-PSDP and The Czech Science Foundation. Grant Numbers: GAP501/11/1150, GA13-40637S, GP14-30004P","year":"2016","has_accepted_license":"1","oa":1,"citation":{"ama":"Pernisová M, Prat T, Grones P, et al. Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis. <i>New Phytologist</i>. 2016;212(2):497-509. doi:<a href=\"https://doi.org/10.1111/nph.14049\">10.1111/nph.14049</a>","apa":"Pernisová, M., Prat, T., Grones, P., Haruštiaková, D., Matonohova, M., Spíchal, L., … Hejátko, J. (2016). Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis. <i>New Phytologist</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/nph.14049\">https://doi.org/10.1111/nph.14049</a>","chicago":"Pernisová, Markéta, Tomas Prat, Peter Grones, Danka Haruštiaková, Martina Matonohova, Lukáš Spíchal, Tomasz Nodzyński, Jiří Friml, and Jan Hejátko. “Cytokinins Influence Root Gravitropism via Differential Regulation of Auxin Transporter Expression and Localization in Arabidopsis.” <i>New Phytologist</i>. Wiley-Blackwell, 2016. <a href=\"https://doi.org/10.1111/nph.14049\">https://doi.org/10.1111/nph.14049</a>.","ieee":"M. Pernisová <i>et al.</i>, “Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis,” <i>New Phytologist</i>, vol. 212, no. 2. Wiley-Blackwell, pp. 497–509, 2016.","ista":"Pernisová M, Prat T, Grones P, Haruštiaková D, Matonohova M, Spíchal L, Nodzyński T, Friml J, Hejátko J. 2016. Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis. New Phytologist. 212(2), 497–509.","short":"M. Pernisová, T. Prat, P. Grones, D. Haruštiaková, M. Matonohova, L. Spíchal, T. Nodzyński, J. Friml, J. Hejátko, New Phytologist 212 (2016) 497–509.","mla":"Pernisová, Markéta, et al. “Cytokinins Influence Root Gravitropism via Differential Regulation of Auxin Transporter Expression and Localization in Arabidopsis.” <i>New Phytologist</i>, vol. 212, no. 2, Wiley-Blackwell, 2016, pp. 497–509, doi:<a href=\"https://doi.org/10.1111/nph.14049\">10.1111/nph.14049</a>."},"quality_controlled":"1","publication_status":"published","abstract":[{"text":"Redirection of intercellular auxin fluxes via relocalization of the PIN-FORMED 3 (PIN3) and PIN7 auxin efflux carriers has been suggested to be necessary for the root gravitropic response. Cytokinins have also been proposed to play a role in controlling root gravitropism, but conclusive evidence is lacking. We present a detailed study of the dynamics of root bending early after gravistimulation, which revealed a delayed gravitropic response in transgenic lines with depleted endogenous cytokinins (Pro35S:AtCKX) and cytokinin signaling mutants. Pro35S:AtCKX lines, as well as a cytokinin receptor mutant ahk3, showed aberrations in the auxin response distribution in columella cells consistent with defects in the auxin transport machinery. Using in vivo real-time imaging of PIN3-GFP and PIN7-GFP in AtCKX3 overexpression and ahk3 backgrounds, we observed wild-type-like relocalization of PIN proteins in the columella early after gravistimulation, with gravity-induced relocalization of PIN7 faster than that of PIN3. Nonetheless, the cellular distribution of PIN3 and PIN7 and expression of PIN7 and the auxin influx carrier AUX1 was affected in AtCKX overexpression lines. Based on the retained cytokinin sensitivity in pin3 pin4 pin7 mutant, we propose the AUX1-mediated auxin transport rather than columella-located PIN proteins as a target of endogenous cytokinins in the control of root gravitropism.","lang":"eng"}],"language":[{"iso":"eng"}],"publist_id":"5839","department":[{"_id":"JiFr"}],"publisher":"Wiley-Blackwell","file_date_updated":"2020-07-14T12:44:47Z","file":[{"file_size":972763,"date_created":"2018-12-12T10:14:53Z","date_updated":"2020-07-14T12:44:47Z","file_name":"IST-2018-1006-v1+1_Pernisova_NewPhytol_2016_peer_review.pdf","relation":"main_file","file_id":"5108","checksum":"27fd841ceaf0403559d7048ef51500f9","content_type":"application/pdf","access_level":"open_access","creator":"system"}],"scopus_import":1,"publication":"New Phytologist","type":"journal_article","ddc":["581"],"pubrep_id":"1006","intvolume":"       212","month":"10","page":"497 - 509","issue":"2"},{"doi":"10.1016/j.plrev.2016.06.006","volume":17,"publication_status":"published","date_created":"2018-12-11T11:51:39Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","citation":{"ama":"Martin O, Zagórski MP. Network architectures and operating principles. Reply to comments on &#38;quot;Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function&#38;quot; <i>Physics of Life Reviews</i>. 2016;17:168-171. doi:<a href=\"https://doi.org/10.1016/j.plrev.2016.06.006\">10.1016/j.plrev.2016.06.006</a>","chicago":"Martin, Olivier, and Marcin P Zagórski. “Network Architectures and Operating Principles. Reply to Comments on &#38;quot;Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function&#38;quot;” <i>Physics of Life Reviews</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.plrev.2016.06.006\">https://doi.org/10.1016/j.plrev.2016.06.006</a>.","apa":"Martin, O., &#38; Zagórski, M. P. (2016). Network architectures and operating principles. Reply to comments on &#38;quot;Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function&#38;quot; <i>Physics of Life Reviews</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.plrev.2016.06.006\">https://doi.org/10.1016/j.plrev.2016.06.006</a>","ista":"Martin O, Zagórski MP. 2016. Network architectures and operating principles. Reply to comments on &#38;quot;Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function&#38;quot; Physics of Life Reviews. 17, 168–171.","ieee":"O. Martin and M. P. Zagórski, “Network architectures and operating principles. Reply to comments on &#38;quot;Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function&#38;quot;,” <i>Physics of Life Reviews</i>, vol. 17. Elsevier, pp. 168–171, 2016.","short":"O. Martin, M.P. Zagórski, Physics of Life Reviews 17 (2016) 168–171.","mla":"Martin, Olivier, and Marcin P. Zagórski. “Network Architectures and Operating Principles. Reply to Comments on &#38;quot;Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function&#38;quot;” <i>Physics of Life Reviews</i>, vol. 17, Elsevier, 2016, pp. 168–71, doi:<a href=\"https://doi.org/10.1016/j.plrev.2016.06.006\">10.1016/j.plrev.2016.06.006</a>."},"author":[{"last_name":"Martin","first_name":"Olivier","full_name":"Martin, Olivier"},{"orcid":"0000-0001-7896-7762","full_name":"Zagórski, Marcin P","first_name":"Marcin P","last_name":"Zagórski","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87"}],"status":"public","quality_controlled":"1","day":"01","publisher":"Elsevier","scopus_import":"1","publication":"Physics of Life Reviews","date_published":"2016-07-01T00:00:00Z","department":[{"_id":"AnKi"}],"language":[{"iso":"eng"}],"publist_id":"5838","type":"journal_article","_id":"1373","date_updated":"2022-08-26T09:39:27Z","main_file_link":[{"open_access":"1","url":"https://hal.archives-ouvertes.fr/hal-01531698"}],"article_processing_charge":"No","title":"Network architectures and operating principles. Reply to comments on &quot;Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function&quot;","oa":1,"page":"168 - 171","year":"2016","intvolume":"        17","month":"07"},{"_id":"1377","date_updated":"2021-01-12T06:50:15Z","title":"Total variation on a tree","oa":1,"year":"2016","project":[{"name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","call_identifier":"FP7"}],"volume":9,"date_created":"2018-12-11T11:51:40Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","doi":"10.1137/15M1010257","author":[{"first_name":"Vladimir","full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pock","first_name":"Thomas","full_name":"Pock, Thomas"},{"last_name":"Rolinek","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","full_name":"Rolinek, Michal","first_name":"Michal"}],"status":"public","oa_version":"Preprint","date_published":"2016-05-03T00:00:00Z","day":"03","type":"journal_article","main_file_link":[{"url":"http://arxiv.org/abs/1502.07770","open_access":"1"}],"issue":"2","ec_funded":1,"page":"605 - 636","month":"05","intvolume":"         9","publication_status":"published","citation":{"apa":"Kolmogorov, V., Pock, T., &#38; Rolinek, M. (2016). Total variation on a tree. <i>SIAM Journal on Imaging Sciences</i>. Society for Industrial and Applied Mathematics . <a href=\"https://doi.org/10.1137/15M1010257\">https://doi.org/10.1137/15M1010257</a>","chicago":"Kolmogorov, Vladimir, Thomas Pock, and Michal Rolinek. “Total Variation on a Tree.” <i>SIAM Journal on Imaging Sciences</i>. Society for Industrial and Applied Mathematics , 2016. <a href=\"https://doi.org/10.1137/15M1010257\">https://doi.org/10.1137/15M1010257</a>.","ama":"Kolmogorov V, Pock T, Rolinek M. Total variation on a tree. <i>SIAM Journal on Imaging Sciences</i>. 2016;9(2):605-636. doi:<a href=\"https://doi.org/10.1137/15M1010257\">10.1137/15M1010257</a>","short":"V. Kolmogorov, T. Pock, M. Rolinek, SIAM Journal on Imaging Sciences 9 (2016) 605–636.","mla":"Kolmogorov, Vladimir, et al. “Total Variation on a Tree.” <i>SIAM Journal on Imaging Sciences</i>, vol. 9, no. 2, Society for Industrial and Applied Mathematics , 2016, pp. 605–36, doi:<a href=\"https://doi.org/10.1137/15M1010257\">10.1137/15M1010257</a>.","ista":"Kolmogorov V, Pock T, Rolinek M. 2016. Total variation on a tree. SIAM Journal on Imaging Sciences. 9(2), 605–636.","ieee":"V. Kolmogorov, T. Pock, and M. Rolinek, “Total variation on a tree,” <i>SIAM Journal on Imaging Sciences</i>, vol. 9, no. 2. Society for Industrial and Applied Mathematics , pp. 605–636, 2016."},"quality_controlled":"1","scopus_import":1,"publication":"SIAM Journal on Imaging Sciences","publisher":"Society for Industrial and Applied Mathematics ","publist_id":"5834","department":[{"_id":"VlKo"}],"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We consider the problem of minimizing the continuous valued total variation subject to different unary terms on trees and propose fast direct algorithms based on dynamic programming to solve these problems. We treat both the convex and the nonconvex case and derive worst-case complexities that are equal to or better than existing methods. We show applications to total variation based two dimensional image processing and computer vision problems based on a Lagrangian decomposition approach. The resulting algorithms are very effcient, offer a high degree of parallelism, and come along with memory requirements which are only in the order of the number of image pixels."}]},{"abstract":[{"lang":"eng","text":"We give a detailed and easily accessible proof of Gromov's Topological Overlap Theorem. Let X be a finite simplicial complex or, more generally, a finite polyhedral cell complex of dimension d. Informally, the theorem states that if X has sufficiently strong higher-dimensional expansion properties (which generalize edge expansion of graphs and are defined in terms of cellular cochains of X) then X has the following topological overlap property: for every continuous map X → ℝd there exists a point p ∈ ℝd whose preimage intersects a positive fraction μ &gt; 0 of the d-cells of X. More generally, the conclusion holds if ℝd is replaced by any d-dimensional piecewise-linear (PL) manifold M, with a constant μ that depends only on d and on the expansion properties of X, but not on M."}],"publist_id":"5833","language":[{"iso":"eng"}],"department":[{"_id":"UlWa"}],"publisher":"Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing","scopus_import":1,"file_date_updated":"2020-07-14T12:44:47Z","file":[{"relation":"main_file","file_name":"IST-2016-623-v1+1_LIPIcs-SoCG-2016-35.pdf","date_updated":"2020-07-14T12:44:47Z","file_size":536923,"date_created":"2018-12-12T10:08:38Z","creator":"system","access_level":"open_access","content_type":"application/pdf","checksum":"cee65b0e722d50f9d1cc70c90ec1d59b","file_id":"4699"}],"citation":{"short":"D. Dotterrer, T. Kaufman, U. Wagner, in:, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2016, p. 35.1-35.10.","mla":"Dotterrer, Dominic, et al. <i>On Expansion and Topological Overlap</i>. Vol. 51, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2016, p. 35.1-35.10, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2016.35\">10.4230/LIPIcs.SoCG.2016.35</a>.","ieee":"D. Dotterrer, T. Kaufman, and U. Wagner, “On expansion and topological overlap,” presented at the SoCG: Symposium on Computational Geometry, Medford, MA, USA, 2016, vol. 51, p. 35.1-35.10.","ista":"Dotterrer D, Kaufman T, Wagner U. 2016. On expansion and topological overlap. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 51, 35.1-35.10.","apa":"Dotterrer, D., Kaufman, T., &#38; Wagner, U. (2016). On expansion and topological overlap (Vol. 51, p. 35.1-35.10). Presented at the SoCG: Symposium on Computational Geometry, Medford, MA, USA: Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2016.35\">https://doi.org/10.4230/LIPIcs.SoCG.2016.35</a>","chicago":"Dotterrer, Dominic, Tali Kaufman, and Uli Wagner. “On Expansion and Topological Overlap,” 51:35.1-35.10. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2016. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2016.35\">https://doi.org/10.4230/LIPIcs.SoCG.2016.35</a>.","ama":"Dotterrer D, Kaufman T, Wagner U. On expansion and topological overlap. In: Vol 51. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing; 2016:35.1-35.10. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2016.35\">10.4230/LIPIcs.SoCG.2016.35</a>"},"quality_controlled":"1","alternative_title":["LIPIcs"],"license":"https://creativecommons.org/licenses/by/4.0/","publication_status":"published","pubrep_id":"623","intvolume":"        51","month":"06","page":"35.1 - 35.10","type":"conference","ddc":["510"],"day":"01","date_published":"2016-06-01T00:00:00Z","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"first_name":"Dominic","full_name":"Dotterrer, Dominic","last_name":"Dotterrer"},{"full_name":"Kaufman, Tali","first_name":"Tali","last_name":"Kaufman"},{"last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","first_name":"Uli"}],"status":"public","doi":"10.4230/LIPIcs.SoCG.2016.35","volume":51,"date_created":"2018-12-11T11:51:41Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2016","project":[{"grant_number":"PP00P2_138948","name":"Embeddings in Higher Dimensions: Algorithms and Combinatorics","_id":"25FA3206-B435-11E9-9278-68D0E5697425"}],"has_accepted_license":"1","oa":1,"title":"On expansion and topological overlap","_id":"1378","date_updated":"2023-09-27T12:29:56Z","related_material":{"record":[{"relation":"later_version","id":"742","status":"public"}]},"conference":{"location":"Medford, MA, USA","name":"SoCG: Symposium on Computational Geometry","start_date":"2016-06-14","end_date":"2016-06-17"}},{"publisher":"Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing","file_date_updated":"2020-07-14T12:44:47Z","file":[{"content_type":"application/pdf","checksum":"f04248a61c24297cfabd30c5f8e0deb9","access_level":"open_access","creator":"system","file_id":"4930","relation":"main_file","file_size":574770,"date_created":"2018-12-12T10:12:12Z","date_updated":"2020-07-14T12:44:47Z","file_name":"IST-2016-622-v1+1_LIPIcs-SoCG-2016-24.pdf"}],"scopus_import":1,"abstract":[{"lang":"eng","text":"We investigate the complexity of finding an embedded non-orientable surface of Euler genus g in a triangulated 3-manifold. This problem occurs both as a natural question in low-dimensional topology, and as a first non-trivial instance of embeddability of complexes into 3-manifolds. We prove that the problem is NP-hard, thus adding to the relatively few hardness results that are currently known in 3-manifold topology. In addition, we show that the problem lies in NP when the Euler genus g is odd, and we give an explicit algorithm in this case."}],"language":[{"iso":"eng"}],"publist_id":"5832","department":[{"_id":"UlWa"}],"publication_status":"published","citation":{"ama":"Burton B, de Mesmay AN, Wagner U. Finding non-orientable surfaces in 3-manifolds. In: Vol 51. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing; 2016:24.1-24.15. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2016.24\">10.4230/LIPIcs.SoCG.2016.24</a>","apa":"Burton, B., de Mesmay, A. N., &#38; Wagner, U. (2016). Finding non-orientable surfaces in 3-manifolds (Vol. 51, p. 24.1-24.15). Presented at the SoCG: Symposium on Computational Geometry, Medford, MA, USA: Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2016.24\">https://doi.org/10.4230/LIPIcs.SoCG.2016.24</a>","chicago":"Burton, Benjamin, Arnaud N de Mesmay, and Uli Wagner. “Finding Non-Orientable Surfaces in 3-Manifolds,” 51:24.1-24.15. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2016. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2016.24\">https://doi.org/10.4230/LIPIcs.SoCG.2016.24</a>.","ista":"Burton B, de Mesmay AN, Wagner U. 2016. Finding non-orientable surfaces in 3-manifolds. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 51, 24.1-24.15.","ieee":"B. Burton, A. N. de Mesmay, and U. Wagner, “Finding non-orientable surfaces in 3-manifolds,” presented at the SoCG: Symposium on Computational Geometry, Medford, MA, USA, 2016, vol. 51, p. 24.1-24.15.","mla":"Burton, Benjamin, et al. <i>Finding Non-Orientable Surfaces in 3-Manifolds</i>. Vol. 51, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2016, p. 24.1-24.15, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2016.24\">10.4230/LIPIcs.SoCG.2016.24</a>.","short":"B. Burton, A.N. de Mesmay, U. Wagner, in:, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2016, p. 24.1-24.15."},"alternative_title":["LIPIcs"],"quality_controlled":"1","page":"24.1 - 24.15","intvolume":"        51","pubrep_id":"622","month":"06","type":"conference","ddc":["510"],"day":"01","date_published":"2016-06-01T00:00:00Z","doi":"10.4230/LIPIcs.SoCG.2016.24","volume":51,"date_created":"2018-12-11T11:51:41Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"first_name":"Benjamin","full_name":"Burton, Benjamin","last_name":"Burton"},{"first_name":"Arnaud N","full_name":"De Mesmay, Arnaud N","id":"3DB2F25C-F248-11E8-B48F-1D18A9856A87","last_name":"De Mesmay"},{"orcid":"0000-0002-1494-0568","first_name":"Uli","full_name":"Wagner, Uli","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"year":"2016","has_accepted_license":"1","_id":"1379","date_updated":"2023-02-23T12:23:20Z","conference":{"end_date":"2016-06-17","start_date":"2016-06-14","name":"SoCG: Symposium on Computational Geometry","location":"Medford, MA, USA"},"related_material":{"record":[{"status":"public","id":"534","relation":"later_version"}]},"title":"Finding non-orientable surfaces in 3-manifolds"},{"citation":{"mla":"Chonev, Ventsislav K., et al. “On the Complexity of the Orbit Problem.” <i>Journal of the ACM</i>, vol. 63, no. 3, 23, ACM, 2016, doi:<a href=\"https://doi.org/10.1145/2857050\">10.1145/2857050</a>.","short":"V.K. Chonev, J. Ouaknine, J. Worrell, Journal of the ACM 63 (2016).","ista":"Chonev VK, Ouaknine J, Worrell J. 2016. On the complexity of the orbit problem. Journal of the ACM. 63(3), 23.","ieee":"V. K. Chonev, J. Ouaknine, and J. Worrell, “On the complexity of the orbit problem,” <i>Journal of the ACM</i>, vol. 63, no. 3. ACM, 2016.","chicago":"Chonev, Ventsislav K, Joël Ouaknine, and James Worrell. “On the Complexity of the Orbit Problem.” <i>Journal of the ACM</i>. ACM, 2016. <a href=\"https://doi.org/10.1145/2857050\">https://doi.org/10.1145/2857050</a>.","apa":"Chonev, V. K., Ouaknine, J., &#38; Worrell, J. (2016). On the complexity of the orbit problem. <i>Journal of the ACM</i>. ACM. <a href=\"https://doi.org/10.1145/2857050\">https://doi.org/10.1145/2857050</a>","ama":"Chonev VK, Ouaknine J, Worrell J. On the complexity of the orbit problem. <i>Journal of the ACM</i>. 2016;63(3). doi:<a href=\"https://doi.org/10.1145/2857050\">10.1145/2857050</a>"},"author":[{"id":"36CBE2E6-F248-11E8-B48F-1D18A9856A87","last_name":"Chonev","full_name":"Chonev, Ventsislav K","first_name":"Ventsislav K"},{"first_name":"Joël","full_name":"Ouaknine, Joël","last_name":"Ouaknine"},{"last_name":"Worrell","first_name":"James","full_name":"Worrell, James"}],"status":"public","quality_controlled":"1","oa_version":"Preprint","volume":63,"publication_status":"published","date_created":"2018-12-11T11:51:41Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","doi":"10.1145/2857050","publist_id":"5831","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We consider higher-dimensional versions of Kannan and Lipton's Orbit Problem - determining whether a target vector space V may be reached from a starting point x under repeated applications of a linear transformation A. Answering two questions posed by Kannan and Lipton in the 1980s, we show that when V has dimension one, this problem is solvable in polynomial time, and when V has dimension two or three, the problem is in NPRP."}],"publication":"Journal of the ACM","scopus_import":1,"date_published":"2016-06-01T00:00:00Z","publisher":"ACM","day":"01","title":"On the complexity of the orbit problem","main_file_link":[{"url":"http://arxiv.org/abs/1303.2981","open_access":"1"}],"_id":"1380","type":"journal_article","date_updated":"2021-01-12T06:50:17Z","month":"06","article_number":"23","intvolume":"        63","year":"2016","issue":"3","oa":1},{"ddc":["510"],"type":"conference","month":"06","intvolume":"        51","pubrep_id":"621","page":"51.1 - 51.12","alternative_title":["LIPIcs"],"quality_controlled":"1","citation":{"ama":"Mabillard I, Wagner U. Eliminating higher-multiplicity intersections, II. The deleted product criterion in the r-metastable range. In: Vol 51. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH; 2016:51.1-51.12. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2016.51\">10.4230/LIPIcs.SoCG.2016.51</a>","chicago":"Mabillard, Isaac, and Uli Wagner. “Eliminating Higher-Multiplicity Intersections, II. The Deleted Product Criterion in the r-Metastable Range,” 51:51.1-51.12. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, 2016. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2016.51\">https://doi.org/10.4230/LIPIcs.SoCG.2016.51</a>.","apa":"Mabillard, I., &#38; Wagner, U. (2016). Eliminating higher-multiplicity intersections, II. The deleted product criterion in the r-metastable range (Vol. 51, p. 51.1-51.12). Presented at the SoCG: Symposium on Computational Geometry, Medford, MA, USA: Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2016.51\">https://doi.org/10.4230/LIPIcs.SoCG.2016.51</a>","ista":"Mabillard I, Wagner U. 2016. Eliminating higher-multiplicity intersections, II. The deleted product criterion in the r-metastable range. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 51, 51.1-51.12.","ieee":"I. Mabillard and U. Wagner, “Eliminating higher-multiplicity intersections, II. The deleted product criterion in the r-metastable range,” presented at the SoCG: Symposium on Computational Geometry, Medford, MA, USA, 2016, vol. 51, p. 51.1-51.12.","short":"I. Mabillard, U. Wagner, in:, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, 2016, p. 51.1-51.12.","mla":"Mabillard, Isaac, and Uli Wagner. <i>Eliminating Higher-Multiplicity Intersections, II. The Deleted Product Criterion in the r-Metastable Range</i>. Vol. 51, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, 2016, p. 51.1-51.12, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2016.51\">10.4230/LIPIcs.SoCG.2016.51</a>."},"publication_status":"published","department":[{"_id":"UlWa"}],"publist_id":"5830","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Motivated by Tverberg-type problems in topological combinatorics and by classical results about embeddings (maps without double points), we study the question whether a finite simplicial complex K can be mapped into double-struck Rd without higher-multiplicity intersections. We focus on conditions for the existence of almost r-embeddings, i.e., maps f : K → double-struck Rd such that f(σ1) ∩ ⋯ ∩ f(σr) = ∅ whenever σ1, ..., σr are pairwise disjoint simplices of K. Generalizing the classical Haefliger-Weber embeddability criterion, we show that a well-known necessary deleted product condition for the existence of almost r-embeddings is sufficient in a suitable r-metastable range of dimensions: If rd ≥ (r + 1) dim K + 3, then there exists an almost r-embedding K → double-struck Rd if and only if there exists an equivariant map (K)Δ r → Sr Sd(r-1)-1, where (K)Δ r is the deleted r-fold product of K, the target Sd(r-1)-1 is the sphere of dimension d(r - 1) - 1, and Sr is the symmetric group. This significantly extends one of the main results of our previous paper (which treated the special case where d = rk and dim K = (r - 1)k for some k ≥ 3), and settles an open question raised there."}],"scopus_import":1,"file":[{"file_id":"4791","creator":"system","access_level":"open_access","content_type":"application/pdf","checksum":"92c0c3735fe908f8ded6e484005cb3b1","file_name":"IST-2016-621-v1+1_LIPIcs-SoCG-2016-51.pdf","date_updated":"2020-07-14T12:44:47Z","date_created":"2018-12-12T10:10:06Z","file_size":622969,"relation":"main_file"}],"file_date_updated":"2020-07-14T12:44:47Z","publisher":"Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH","title":"Eliminating higher-multiplicity intersections, II. The deleted product criterion in the r-metastable range","conference":{"start_date":"2016-06-14","end_date":"2016-06-17","name":"SoCG: Symposium on Computational Geometry","location":"Medford, MA, USA"},"date_updated":"2021-01-12T06:50:17Z","_id":"1381","has_accepted_license":"1","year":"2016","project":[{"grant_number":"PP00P2_138948","_id":"25FA3206-B435-11E9-9278-68D0E5697425","name":"Embeddings in Higher Dimensions: Algorithms and Combinatorics"}],"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","author":[{"full_name":"Mabillard, Isaac","first_name":"Isaac","id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87","last_name":"Mabillard"},{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","full_name":"Wagner, Uli","first_name":"Uli","orcid":"0000-0002-1494-0568"}],"oa_version":"Published Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:51:41Z","volume":51,"doi":"10.4230/LIPIcs.SoCG.2016.51","date_published":"2016-06-01T00:00:00Z","day":"01"},{"year":"2016","intvolume":"       117","acknowledgement":"We thank Melinda Pickup, Spencer Barrett, Nick Barton and four anonymous reviewers for helpful discussions on previous versions  of  this  manuscript.  We  also  thank  Jana  Porsche  for her efforts in tracking down the more obscure references.","month":"06","page":"1133 - 1140","issue":"7","title":"Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae","date_updated":"2024-02-21T13:49:53Z","_id":"1382","type":"journal_article","related_material":{"record":[{"relation":"popular_science","id":"5550","status":"public"}]},"abstract":[{"text":"Background and aims Angiosperms display remarkable diversity in flower colour, implying that transitions between pigmentation phenotypes must have been common. Despite progress in understanding transitions between anthocyanin (blue, purple, pink or red) and unpigmented (white) flowers, little is known about the evolutionary patterns of flower-colour transitions in lineages with both yellow and anthocyanin-pigmented flowers. This study investigates the relative rates of evolutionary transitions between different combinations of yellow- and anthocyanin-pigmentation phenotypes in the tribe Antirrhineae. Methods We surveyed taxonomic literature for data on anthocyanin and yellow floral pigmentation for 369 species across the tribe. We then reconstructed the phylogeny of 169 taxa and used phylogenetic comparative methods to estimate transition rates among pigmentation phenotypes across the phylogeny. Key Results In contrast to previous studies we found a bias towards transitions involving a gain in pigmentation, although transitions to phenotypes with both anthocyanin and yellow taxa are nevertheless extremely rare. Despite the dominance of yellow and anthocyanin-pigmented taxa, transitions between these phenotypes are constrained to move through a white intermediate stage, whereas transitions to double-pigmentation are very rare. The most abundant transitions are between anthocyanin-pigmented and unpigmented flowers, and similarly the most abundant polymorphic taxa were those with anthocyanin-pigmented and unpigmented flowers. Conclusions Our findings show that pigment evolution is limited by the presence of other floral pigments. This interaction between anthocyanin and yellow pigments constrains the breadth of potential floral diversity observed in nature. In particular, they suggest that selection has repeatedly acted to promote the spread of single-pigmented phenotypes across the Antirrhineae phylogeny. Furthermore, the correlation between transition rates and polymorphism suggests that the forces causing and maintaining variance in the short term reflect evolutionary processes on longer time scales.","lang":"eng"}],"language":[{"iso":"eng"}],"publist_id":"5828","department":[{"_id":"NiBa"}],"publisher":"Oxford University Press","day":"1","date_published":"2016-06-01T00:00:00Z","scopus_import":1,"publication":"Annals of Botany","oa_version":"None","status":"public","quality_controlled":"1","author":[{"id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","last_name":"Ellis","full_name":"Ellis, Thomas","first_name":"Thomas","orcid":"0000-0002-8511-0254"},{"full_name":"Field, David","first_name":"David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field"}],"citation":{"chicago":"Ellis, Thomas, and David Field. “Repeated Gains in Yellow and Anthocyanin Pigmentation in Flower Colour Transitions in the Antirrhineae.” <i>Annals of Botany</i>. Oxford University Press, 2016. <a href=\"https://doi.org/10.1093/aob/mcw043\">https://doi.org/10.1093/aob/mcw043</a>.","apa":"Ellis, T., &#38; Field, D. (2016). Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae. <i>Annals of Botany</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/aob/mcw043\">https://doi.org/10.1093/aob/mcw043</a>","ama":"Ellis T, Field D. Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae. <i>Annals of Botany</i>. 2016;117(7):1133-1140. doi:<a href=\"https://doi.org/10.1093/aob/mcw043\">10.1093/aob/mcw043</a>","short":"T. Ellis, D. Field, Annals of Botany 117 (2016) 1133–1140.","mla":"Ellis, Thomas, and David Field. “Repeated Gains in Yellow and Anthocyanin Pigmentation in Flower Colour Transitions in the Antirrhineae.” <i>Annals of Botany</i>, vol. 117, no. 7, Oxford University Press, 2016, pp. 1133–40, doi:<a href=\"https://doi.org/10.1093/aob/mcw043\">10.1093/aob/mcw043</a>.","ista":"Ellis T, Field D. 2016. Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae. Annals of Botany. 117(7), 1133–1140.","ieee":"T. Ellis and D. Field, “Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae,” <i>Annals of Botany</i>, vol. 117, no. 7. Oxford University Press, pp. 1133–1140, 2016."},"doi":"10.1093/aob/mcw043","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:51:42Z","publication_status":"published","volume":117},{"author":[{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","last_name":"Fu","first_name":"Hongfei","full_name":"Fu, Hongfei"},{"orcid":"0000-0003-1702-6584","first_name":"Amir","full_name":"Goharshady, Amir","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87"}],"status":"public","oa_version":"Preprint","volume":9779,"date_created":"2018-12-11T11:51:43Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/978-3-319-41528-4_1","date_published":"2016-07-01T00:00:00Z","day":"01","title":"Termination analysis of probabilistic programs through Positivstellensatz's","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8934"}]},"conference":{"start_date":"2016-07-17","end_date":"2016-07-23","name":"CAV: Computer Aided Verification","location":"Toronto, Canada"},"_id":"1386","date_updated":"2024-03-25T23:30:18Z","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"},{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","call_identifier":"FP7","grant_number":"267989"}],"year":"2016","oa":1,"citation":{"ama":"Chatterjee K, Fu H, Goharshady AK. Termination analysis of probabilistic programs through Positivstellensatz’s. In: Vol 9779. Springer; 2016:3-22. doi:<a href=\"https://doi.org/10.1007/978-3-319-41528-4_1\">10.1007/978-3-319-41528-4_1</a>","apa":"Chatterjee, K., Fu, H., &#38; Goharshady, A. K. (2016). Termination analysis of probabilistic programs through Positivstellensatz’s (Vol. 9779, pp. 3–22). Presented at the CAV: Computer Aided Verification, Toronto, Canada: Springer. <a href=\"https://doi.org/10.1007/978-3-319-41528-4_1\">https://doi.org/10.1007/978-3-319-41528-4_1</a>","chicago":"Chatterjee, Krishnendu, Hongfei Fu, and Amir Kafshdar Goharshady. “Termination Analysis of Probabilistic Programs through Positivstellensatz’s,” 9779:3–22. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-319-41528-4_1\">https://doi.org/10.1007/978-3-319-41528-4_1</a>.","ista":"Chatterjee K, Fu H, Goharshady AK. 2016. Termination analysis of probabilistic programs through Positivstellensatz’s. CAV: Computer Aided Verification, LNCS, vol. 9779, 3–22.","ieee":"K. Chatterjee, H. Fu, and A. K. Goharshady, “Termination analysis of probabilistic programs through Positivstellensatz’s,” presented at the CAV: Computer Aided Verification, Toronto, Canada, 2016, vol. 9779, pp. 3–22.","mla":"Chatterjee, Krishnendu, et al. <i>Termination Analysis of Probabilistic Programs through Positivstellensatz’s</i>. Vol. 9779, Springer, 2016, pp. 3–22, doi:<a href=\"https://doi.org/10.1007/978-3-319-41528-4_1\">10.1007/978-3-319-41528-4_1</a>.","short":"K. Chatterjee, H. Fu, A.K. Goharshady, in:, Springer, 2016, pp. 3–22."},"alternative_title":["LNCS"],"quality_controlled":"1","publication_status":"published","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"publist_id":"5824","abstract":[{"text":"We consider nondeterministic probabilistic programs with the most basic liveness property of termination. We present efficient methods for termination analysis of nondeterministic probabilistic programs with polynomial guards and assignments. Our approach is through synthesis of polynomial ranking supermartingales, that on one hand significantly generalizes linear ranking supermartingales and on the other hand is a counterpart of polynomial ranking-functions for proving termination of nonprobabilistic programs. The approach synthesizes polynomial ranking-supermartingales through Positivstellensatz's, yielding an efficient method which is not only sound, but also semi-complete over a large subclass of programs. We show experimental results to demonstrate that our approach can handle several classical programs with complex polynomial guards and assignments, and can synthesize efficient quadratic ranking-supermartingales when a linear one does not exist even for simple affine programs.","lang":"eng"}],"scopus_import":1,"publisher":"Springer","main_file_link":[{"url":"http://arxiv.org/abs/1604.07169","open_access":"1"}],"type":"conference","month":"07","intvolume":"      9779","ec_funded":1,"page":"3 - 22"},{"title":"On recurrent reachability for continuous linear dynamical systems","main_file_link":[{"url":"https://arxiv.org/abs/1507.03632","open_access":"1"}],"conference":{"end_date":"2018-07-08","start_date":"2018-07-05","location":"New York, NY, USA","name":"LICS: Logic in Computer Science"},"type":"conference","_id":"1389","date_updated":"2021-01-12T06:50:20Z","month":"07","year":"2016","project":[{"grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"},{"call_identifier":"FP7","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling"}],"ec_funded":1,"oa":1,"page":"515 - 524","citation":{"short":"V.K. Chonev, J. Ouaknine, J. Worrell, in:, LICS ’16, IEEE, 2016, pp. 515–524.","mla":"Chonev, Ventsislav K., et al. “On Recurrent Reachability for Continuous Linear Dynamical Systems.” <i>LICS ’16</i>, IEEE, 2016, pp. 515–24, doi:<a href=\"https://doi.org/10.1145/2933575.2934548\">10.1145/2933575.2934548</a>.","ieee":"V. K. Chonev, J. Ouaknine, and J. Worrell, “On recurrent reachability for continuous linear dynamical systems,” in <i>LICS ’16</i>, New York, NY, USA, 2016, pp. 515–524.","ista":"Chonev VK, Ouaknine J, Worrell J. 2016. On recurrent reachability for continuous linear dynamical systems. LICS ’16. LICS: Logic in Computer Science, 515–524.","apa":"Chonev, V. K., Ouaknine, J., &#38; Worrell, J. (2016). On recurrent reachability for continuous linear dynamical systems. In <i>LICS ’16</i> (pp. 515–524). New York, NY, USA: IEEE. <a href=\"https://doi.org/10.1145/2933575.2934548\">https://doi.org/10.1145/2933575.2934548</a>","chicago":"Chonev, Ventsislav K, Joël Ouaknine, and James Worrell. “On Recurrent Reachability for Continuous Linear Dynamical Systems.” In <i>LICS ’16</i>, 515–24. IEEE, 2016. <a href=\"https://doi.org/10.1145/2933575.2934548\">https://doi.org/10.1145/2933575.2934548</a>.","ama":"Chonev VK, Ouaknine J, Worrell J. On recurrent reachability for continuous linear dynamical systems. In: <i>LICS ’16</i>. IEEE; 2016:515-524. doi:<a href=\"https://doi.org/10.1145/2933575.2934548\">10.1145/2933575.2934548</a>"},"author":[{"id":"36CBE2E6-F248-11E8-B48F-1D18A9856A87","last_name":"Chonev","first_name":"Ventsislav K","full_name":"Chonev, Ventsislav K"},{"last_name":"Ouaknine","full_name":"Ouaknine, Joël","first_name":"Joël"},{"full_name":"Worrell, James","first_name":"James","last_name":"Worrell"}],"quality_controlled":"1","status":"public","oa_version":"Preprint","publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:51:44Z","doi":"10.1145/2933575.2934548","language":[{"iso":"eng"}],"publist_id":"5820","department":[{"_id":"KrCh"}],"abstract":[{"lang":"eng","text":"The continuous evolution of a wide variety of systems, including continous-time Markov chains and linear hybrid automata, can be\r\ndescribed in terms of linear differential equations. In this paper we study the decision problem of whether the solution x(t) of a system of linear differential equations dx/dt = Ax reaches a target halfspace infinitely often. This recurrent reachability problem can\r\nequivalently be formulated as the following Infinite Zeros Problem: does a real-valued function f:R≥0 --&gt; R satisfying a given linear\r\ndifferential equation have infinitely many zeros? Our main decidability result is that if the differential equation has order at most 7, then the Infinite Zeros Problem is decidable. On the other hand, we show that a decision procedure for the Infinite Zeros Problem at order 9 (and above) would entail a major breakthrough in Diophantine Approximation, specifically an algorithm for computing the Lagrange constants of arbitrary real algebraic numbers to arbitrary precision."}],"publication":"LICS '16","scopus_import":1,"date_published":"2016-07-05T00:00:00Z","day":"05","publisher":"IEEE"},{"intvolume":"      9780","year":"2016","project":[{"call_identifier":"FP7","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211"}],"month":"07","ec_funded":1,"page":"383 - 401","title":"QLOSE: Program repair with quantitative objectives","_id":"1390","type":"conference","date_updated":"2021-01-12T06:50:21Z","conference":{"end_date":"2016-07-23","start_date":"2016-07-17","location":"Toronto, Canada","name":"CAV: Computer Aided Verification"},"abstract":[{"lang":"eng","text":"The goal of automatic program repair is to identify a set of syntactic changes that can turn a program that is incorrect with respect\r\nto a given specification into a correct one. Existing program repair techniques typically aim to find any program that meets the given specification. Such “best-effort” strategies can end up generating a program that is quite different from the original one. Novel techniques have been proposed to compute syntactically minimal program fixes, but the smallest syntactic fix to a program can still significantly alter the original program’s behaviour. We propose a new approach to program repair based on program distances, which can quantify changes not only to the program syntax but also to the program semantics. We call this the quantitative program repair problem where the “optimal” repair is derived using multiple distances. We implement a solution to the quantitative repair\r\nproblem in a prototype tool called Qlose\r\n(Quantitatively close), using the program synthesizer Sketch. We evaluate the effectiveness of different distances in obtaining desirable repairs by evaluating\r\nQlose on programs taken from educational tools such as CodeHunt and edX."}],"language":[{"iso":"eng"}],"publist_id":"5819","department":[{"_id":"ToHe"}],"publisher":"Springer","day":"13","scopus_import":1,"date_published":"2016-07-13T00:00:00Z","oa_version":"None","citation":{"ama":"D’Antoni L, Samanta R, Singh R. QLOSE: Program repair with quantitative objectives. In: Vol 9780. Springer; 2016:383-401. doi:<a href=\"https://doi.org/10.1007/978-3-319-41540-6_21\">10.1007/978-3-319-41540-6_21</a>","chicago":"D’Antoni, Loris, Roopsha Samanta, and Rishabh Singh. “QLOSE: Program Repair with Quantitative Objectives,” 9780:383–401. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-319-41540-6_21\">https://doi.org/10.1007/978-3-319-41540-6_21</a>.","apa":"D’Antoni, L., Samanta, R., &#38; Singh, R. (2016). QLOSE: Program repair with quantitative objectives (Vol. 9780, pp. 383–401). Presented at the CAV: Computer Aided Verification, Toronto, Canada: Springer. <a href=\"https://doi.org/10.1007/978-3-319-41540-6_21\">https://doi.org/10.1007/978-3-319-41540-6_21</a>","ieee":"L. D’Antoni, R. Samanta, and R. Singh, “QLOSE: Program repair with quantitative objectives,” presented at the CAV: Computer Aided Verification, Toronto, Canada, 2016, vol. 9780, pp. 383–401.","ista":"D’Antoni L, Samanta R, Singh R. 2016. QLOSE: Program repair with quantitative objectives. CAV: Computer Aided Verification, LNCS, vol. 9780, 383–401.","mla":"D’Antoni, Loris, et al. <i>QLOSE: Program Repair with Quantitative Objectives</i>. Vol. 9780, Springer, 2016, pp. 383–401, doi:<a href=\"https://doi.org/10.1007/978-3-319-41540-6_21\">10.1007/978-3-319-41540-6_21</a>.","short":"L. D’Antoni, R. Samanta, R. Singh, in:, Springer, 2016, pp. 383–401."},"quality_controlled":"1","author":[{"last_name":"D'Antoni","first_name":"Loris","full_name":"D'Antoni, Loris"},{"first_name":"Roopsha","full_name":"Samanta, Roopsha","last_name":"Samanta","id":"3D2AAC08-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Singh, Rishabh","first_name":"Rishabh","last_name":"Singh"}],"alternative_title":["LNCS"],"status":"public","doi":"10.1007/978-3-319-41540-6_21","volume":9780,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_status":"published","date_created":"2018-12-11T11:51:45Z"},{"abstract":[{"text":"We present an extension to the quantifier-free theory of integer arrays which allows us to express counting. The properties expressible in Array Folds Logic (AFL) include statements such as &quot;the first array cell contains the array length,&quot; and &quot;the array contains equally many minimal and maximal elements.&quot; These properties cannot be expressed in quantified fragments of the theory of arrays, nor in the theory of concatenation. Using reduction to counter machines, we show that the satisfiability problem of AFL is PSPACE-complete, and with a natural restriction the complexity decreases to NP. We also show that adding either universal quantifiers or concatenation leads to undecidability.\r\nAFL contains terms that fold a function over an array. We demonstrate that folding, a well-known concept from functional languages, allows us to concisely summarize loops that count over arrays, which occurs frequently in real-life programs. We provide a tool that can discharge proof obligations in AFL, and we demonstrate on practical examples that our decision procedure can solve a broad range of problems in symbolic testing and program verification.","lang":"eng"}],"publist_id":"5818","department":[{"_id":"ToHe"}],"language":[{"iso":"eng"}],"publisher":"Springer","scopus_import":1,"quality_controlled":"1","alternative_title":["LNCS"],"citation":{"chicago":"Daca, Przemyslaw, Thomas A Henzinger, and Andrey Kupriyanov. “Array Folds Logic,” 9780:230–48. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-319-41540-6_13\">https://doi.org/10.1007/978-3-319-41540-6_13</a>.","apa":"Daca, P., Henzinger, T. A., &#38; Kupriyanov, A. (2016). Array folds logic (Vol. 9780, pp. 230–248). Presented at the CAV: Computer Aided Verification, Toronto, Canada: Springer. <a href=\"https://doi.org/10.1007/978-3-319-41540-6_13\">https://doi.org/10.1007/978-3-319-41540-6_13</a>","ama":"Daca P, Henzinger TA, Kupriyanov A. Array folds logic. In: Vol 9780. Springer; 2016:230-248. doi:<a href=\"https://doi.org/10.1007/978-3-319-41540-6_13\">10.1007/978-3-319-41540-6_13</a>","short":"P. Daca, T.A. Henzinger, A. Kupriyanov, in:, Springer, 2016, pp. 230–248.","mla":"Daca, Przemyslaw, et al. <i>Array Folds Logic</i>. Vol. 9780, Springer, 2016, pp. 230–48, doi:<a href=\"https://doi.org/10.1007/978-3-319-41540-6_13\">10.1007/978-3-319-41540-6_13</a>.","ieee":"P. Daca, T. A. Henzinger, and A. Kupriyanov, “Array folds logic,” presented at the CAV: Computer Aided Verification, Toronto, Canada, 2016, vol. 9780, pp. 230–248.","ista":"Daca P, Henzinger TA, Kupriyanov A. 2016. Array folds logic. CAV: Computer Aided Verification, LNCS, vol. 9780, 230–248."},"publication_status":"published","intvolume":"      9780","month":"07","page":"230 - 248","ec_funded":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1603.06850"}],"type":"conference","day":"13","date_published":"2016-07-13T00:00:00Z","oa_version":"Preprint","status":"public","author":[{"first_name":"Przemyslaw","full_name":"Daca, Przemyslaw","last_name":"Daca","id":"49351290-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"last_name":"Kupriyanov","id":"2C311BF8-F248-11E8-B48F-1D18A9856A87","first_name":"Andrey","full_name":"Kupriyanov, Andrey"}],"doi":"10.1007/978-3-319-41540-6_13","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:51:45Z","volume":9780,"year":"2016","project":[{"call_identifier":"FP7","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling"},{"call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize"}],"oa":1,"title":"Array folds logic","date_updated":"2023-09-07T11:58:33Z","_id":"1391","related_material":{"record":[{"status":"public","id":"1155","relation":"dissertation_contains"}]},"conference":{"start_date":"2016-07-17","end_date":"2016-07-23","location":"Toronto, Canada","name":"CAV: Computer Aided Verification"}},{"title":"Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli","date_updated":"2021-01-12T06:50:23Z","_id":"1394","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"}],"acknowledgement":"The research leading to these results has received funding from the from the Marie\r\nCurie Action ITN NETADIS, grant agreement no. 290038.","year":"2016","oa":1,"status":"public","author":[{"orcid":"0000-0002-5214-4706","full_name":"De Martino, Daniele","first_name":"Daniele","last_name":"De Martino","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Capuani","full_name":"Capuani, Fabrizio","first_name":"Fabrizio"},{"full_name":"De Martino, Andrea","first_name":"Andrea","last_name":"De Martino"}],"oa_version":"Preprint","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:51:46Z","volume":13,"doi":"10.1088/1478-3975/13/3/036005","date_published":"2016-05-27T00:00:00Z","day":"27","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1601.03243"}],"type":"journal_article","month":"05","intvolume":"        13","article_number":"036005","issue":"3","ec_funded":1,"quality_controlled":"1","citation":{"apa":"De Martino, D., Capuani, F., &#38; De Martino, A. (2016). Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli. <i>Physical Biology</i>. IOP Publishing Ltd. <a href=\"https://doi.org/10.1088/1478-3975/13/3/036005\">https://doi.org/10.1088/1478-3975/13/3/036005</a>","chicago":"De Martino, Daniele, Fabrizio Capuani, and Andrea De Martino. “Growth against Entropy in Bacterial Metabolism: The Phenotypic Trade-off behind Empirical Growth Rate Distributions in E. Coli.” <i>Physical Biology</i>. IOP Publishing Ltd., 2016. <a href=\"https://doi.org/10.1088/1478-3975/13/3/036005\">https://doi.org/10.1088/1478-3975/13/3/036005</a>.","ama":"De Martino D, Capuani F, De Martino A. Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli. <i>Physical Biology</i>. 2016;13(3). doi:<a href=\"https://doi.org/10.1088/1478-3975/13/3/036005\">10.1088/1478-3975/13/3/036005</a>","short":"D. De Martino, F. Capuani, A. De Martino, Physical Biology 13 (2016).","mla":"De Martino, Daniele, et al. “Growth against Entropy in Bacterial Metabolism: The Phenotypic Trade-off behind Empirical Growth Rate Distributions in E. Coli.” <i>Physical Biology</i>, vol. 13, no. 3, 036005, IOP Publishing Ltd., 2016, doi:<a href=\"https://doi.org/10.1088/1478-3975/13/3/036005\">10.1088/1478-3975/13/3/036005</a>.","ieee":"D. De Martino, F. Capuani, and A. De Martino, “Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli,” <i>Physical Biology</i>, vol. 13, no. 3. IOP Publishing Ltd., 2016.","ista":"De Martino D, Capuani F, De Martino A. 2016. Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli. Physical Biology. 13(3), 036005."},"publication_status":"published","language":[{"iso":"eng"}],"publist_id":"5815","department":[{"_id":"GaTk"}],"abstract":[{"text":"The solution space of genome-scale models of cellular metabolism provides a map between physically\r\nviable flux configurations and cellular metabolic phenotypes described, at the most basic level, by the\r\ncorresponding growth rates. By sampling the solution space of E. coliʼs metabolic network, we show\r\nthat empirical growth rate distributions recently obtained in experiments at single-cell resolution can\r\nbe explained in terms of a trade-off between the higher fitness of fast-growing phenotypes and the\r\nhigher entropy of slow-growing ones. Based on this, we propose a minimal model for the evolution of\r\na large bacterial population that captures this trade-off. The scaling relationships observed in\r\nexperiments encode, in such frameworks, for the same distance from the maximum achievable growth\r\nrate, the same degree of growth rate maximization, and/or the same rate of phenotypic change. Being\r\ngrounded on genome-scale metabolic network reconstructions, these results allow for multiple\r\nimplications and extensions in spite of the underlying conceptual simplicity.","lang":"eng"}],"scopus_import":1,"publication":"Physical Biology","publisher":"IOP Publishing Ltd."}]