[{"date_created":"2018-12-11T11:55:25Z","volume":7428,"oa_version":"Preprint","title":"Practical leakage-resilient symmetric cryptography","author":[{"first_name":"Sebastian","full_name":"Faust, Sebastian","last_name":"Faust"},{"orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z"},{"last_name":"Schipper","full_name":"Schipper, Joachim","id":"7BE863D4-E9CF-11E9-9EDB-90527418172C","first_name":"Joachim"}],"day":"01","scopus_import":1,"publication_status":"published","abstract":[{"text":"Leakage resilient cryptography attempts to incorporate side-channel leakage into the black-box security model and designs cryptographic schemes that are provably secure within it. Informally, a scheme is leakage-resilient if it remains secure even if an adversary learns a bounded amount of arbitrary information about the schemes internal state. Unfortunately, most leakage resilient schemes are unnecessarily complicated in order to achieve strong provable security guarantees. As advocated by Yu et al. [CCS’10], this mostly is an artefact of the security proof and in practice much simpler construction may already suffice to protect against realistic side-channel attacks. In this paper, we show that indeed for simpler constructions leakage-resilience can be obtained when we aim for relaxed security notions where the leakage-functions and/or the inputs to the primitive are chosen non-adaptively. For example, we show that a three round Feistel network instantiated with a leakage resilient PRF yields a leakage resilient PRP if the inputs are chosen non-adaptively (This complements the result of Dodis and Pietrzak [CRYPTO’10] who show that if a adaptive queries are allowed, a superlogarithmic number of rounds is necessary.) We also show that a minor variation of the classical GGM construction gives a leakage resilient PRF if both, the leakage-function and the inputs, are chosen non-adaptively.","lang":"eng"}],"intvolume":"      7428","department":[{"_id":"KrPi"}],"month":"09","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Faust S, Pietrzak KZ, Schipper J. Practical leakage-resilient symmetric cryptography. In: <i> Conference Proceedings CHES 2012</i>. Vol 7428. Springer; 2012:213-232. doi:<a href=\"https://doi.org/10.1007/978-3-642-33027-8_13\">10.1007/978-3-642-33027-8_13</a>","ieee":"S. Faust, K. Z. Pietrzak, and J. Schipper, “Practical leakage-resilient symmetric cryptography,” in <i> Conference proceedings CHES 2012</i>, Leuven, Belgium, 2012, vol. 7428, pp. 213–232.","short":"S. Faust, K.Z. Pietrzak, J. Schipper, in:,  Conference Proceedings CHES 2012, Springer, 2012, pp. 213–232.","ista":"Faust S, Pietrzak KZ, Schipper J. 2012. Practical leakage-resilient symmetric cryptography.  Conference proceedings CHES 2012. CHES: Cryptographic Hardware and Embedded Systems, LNCS, vol. 7428, 213–232.","chicago":"Faust, Sebastian, Krzysztof Z Pietrzak, and Joachim Schipper. “Practical Leakage-Resilient Symmetric Cryptography.” In <i> Conference Proceedings CHES 2012</i>, 7428:213–32. Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-33027-8_13\">https://doi.org/10.1007/978-3-642-33027-8_13</a>.","apa":"Faust, S., Pietrzak, K. Z., &#38; Schipper, J. (2012). Practical leakage-resilient symmetric cryptography. In <i> Conference proceedings CHES 2012</i> (Vol. 7428, pp. 213–232). Leuven, Belgium: Springer. <a href=\"https://doi.org/10.1007/978-3-642-33027-8_13\">https://doi.org/10.1007/978-3-642-33027-8_13</a>","mla":"Faust, Sebastian, et al. “Practical Leakage-Resilient Symmetric Cryptography.” <i> Conference Proceedings CHES 2012</i>, vol. 7428, Springer, 2012, pp. 213–32, doi:<a href=\"https://doi.org/10.1007/978-3-642-33027-8_13\">10.1007/978-3-642-33027-8_13</a>."},"language":[{"iso":"eng"}],"oa":1,"type":"conference","date_updated":"2021-01-12T06:54:58Z","_id":"2048","publisher":"Springer","doi":"10.1007/978-3-642-33027-8_13","alternative_title":["LNCS"],"quality_controlled":"1","main_file_link":[{"url":"http://www.iacr.org/archive/ches2012/74280211/74280211.pdf","open_access":"1"}],"page":"213 - 232","publist_id":"5003","year":"2012","conference":{"name":"CHES: Cryptographic Hardware and Embedded Systems","end_date":"2012-09-12","start_date":"2012-09-09","location":"Leuven, Belgium"},"date_published":"2012-09-01T00:00:00Z","acknowledgement":"Sebastian Faust acknowledges support from the Danish National Research Foundation and The National Science Foundation of China (under the grant 61061130540) for the Sino-Danish Center for the Theory of Interactive Computation, within part of this work was performed; and from the CFEM research center, supported by the Danish Strategic Research Council. \r\nSupported by the European Research Council/ERC Starting Grant 259668-PSPC.\r\n","ec_funded":1,"project":[{"call_identifier":"FP7","name":"Provable Security for Physical Cryptography","grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425"}],"status":"public","publication":" Conference proceedings CHES 2012"},{"date_created":"2018-12-11T11:55:25Z","volume":7549,"oa_version":"Preprint","title":"Lapin: An efficient authentication protocol based on ring-LPN","author":[{"first_name":"Stefan","full_name":"Heyse, Stefan","last_name":"Heyse"},{"full_name":"Kiltz, Eike","last_name":"Kiltz","first_name":"Eike"},{"first_name":"Vadim","full_name":"Lyubashevsky, Vadim","last_name":"Lyubashevsky"},{"full_name":"Paar, Christof","last_name":"Paar","first_name":"Christof"},{"first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak"}],"day":"01","scopus_import":1,"publication_status":"published","intvolume":"      7549","abstract":[{"lang":"eng","text":"We propose a new authentication protocol that is provably secure based on a ring variant of the learning parity with noise (LPN) problem. The protocol follows the design principle of the LPN-based protocol from Eurocrypt’11 (Kiltz et al.), and like it, is a two round protocol secure against active attacks. Moreover, our protocol has small communication complexity and a very small footprint which makes it applicable in scenarios that involve low-cost, resource-constrained devices.\r\n\r\nPerformance-wise, our protocol is more efficient than previous LPN-based schemes, such as the many variants of the Hopper-Blum (HB) protocol and the aforementioned protocol from Eurocrypt’11. Our implementation results show that it is even comparable to the standard challenge-and-response protocols based on the AES block-cipher. Our basic protocol is roughly 20 times slower than AES, but with the advantage of having 10 times smaller code size. Furthermore, if a few hundred bytes of non-volatile memory are available to allow the storage of some off-line pre-computations, then the online phase of our protocols is only twice as slow as AES.\r\n"}],"department":[{"_id":"KrPi"}],"month":"03","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Heyse S, Kiltz E, Lyubashevsky V, Paar C, Pietrzak KZ. 2012. Lapin: An efficient authentication protocol based on ring-LPN.  Conference proceedings FSE 2012. FSE: Fast Software Encryption, LNCS, vol. 7549, 346–365.","chicago":"Heyse, Stefan, Eike Kiltz, Vadim Lyubashevsky, Christof Paar, and Krzysztof Z Pietrzak. “Lapin: An Efficient Authentication Protocol Based on Ring-LPN.” In <i> Conference Proceedings FSE 2012</i>, 7549:346–65. Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-34047-5_20\">https://doi.org/10.1007/978-3-642-34047-5_20</a>.","mla":"Heyse, Stefan, et al. “Lapin: An Efficient Authentication Protocol Based on Ring-LPN.” <i> Conference Proceedings FSE 2012</i>, vol. 7549, Springer, 2012, pp. 346–65, doi:<a href=\"https://doi.org/10.1007/978-3-642-34047-5_20\">10.1007/978-3-642-34047-5_20</a>.","apa":"Heyse, S., Kiltz, E., Lyubashevsky, V., Paar, C., &#38; Pietrzak, K. Z. (2012). Lapin: An efficient authentication protocol based on ring-LPN. In <i> Conference proceedings FSE 2012</i> (Vol. 7549, pp. 346–365). Washington, DC, USA: Springer. <a href=\"https://doi.org/10.1007/978-3-642-34047-5_20\">https://doi.org/10.1007/978-3-642-34047-5_20</a>","ama":"Heyse S, Kiltz E, Lyubashevsky V, Paar C, Pietrzak KZ. Lapin: An efficient authentication protocol based on ring-LPN. In: <i> Conference Proceedings FSE 2012</i>. Vol 7549. Springer; 2012:346-365. doi:<a href=\"https://doi.org/10.1007/978-3-642-34047-5_20\">10.1007/978-3-642-34047-5_20</a>","short":"S. Heyse, E. Kiltz, V. Lyubashevsky, C. Paar, K.Z. Pietrzak, in:,  Conference Proceedings FSE 2012, Springer, 2012, pp. 346–365.","ieee":"S. Heyse, E. Kiltz, V. Lyubashevsky, C. Paar, and K. Z. Pietrzak, “Lapin: An efficient authentication protocol based on ring-LPN,” in <i> Conference proceedings FSE 2012</i>, Washington, DC, USA, 2012, vol. 7549, pp. 346–365."},"language":[{"iso":"eng"}],"oa":1,"type":"conference","date_updated":"2021-01-12T06:54:58Z","_id":"2049","publisher":"Springer","doi":"10.1007/978-3-642-34047-5_20","alternative_title":["LNCS"],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://www.iacr.org/archive/fse2012/75490350/75490350.pdf"}],"page":"346 - 365","publist_id":"5002","year":"2012","date_published":"2012-03-01T00:00:00Z","acknowledgement":"Supported by the European Research Council / ERC Starting Grant (259668- PSPC)\r\nWe would like to thank the anonymous referees of this confer- ence and those of the ECRYPT Workshop on Lightweight Cryptography for very useful comments, and in particular for the suggestion that the scheme is somewhat vulnerable to a man-in-the-middle attack whenever an adversary observes two reader challenges that are the same. We hope that the attack we described in Appendix A corresponds to what the reviewer had in mind. We also thank Tanja Lange for pointing us to the pa- per of [Kir11] and for discussions of some of her recent work. ","conference":{"start_date":"2012-03-19","end_date":"2012-03-21","name":"FSE: Fast Software Encryption","location":"Washington, DC, USA"},"ec_funded":1,"project":[{"name":"Provable Security for Physical Cryptography","grant_number":"259668","call_identifier":"FP7","_id":"258C570E-B435-11E9-9278-68D0E5697425"}],"status":"public","publication":" Conference proceedings FSE 2012"},{"year":"2012","publist_id":"4682","status":"public","publication":"Biology open","date_published":"2012-12-15T00:00:00Z","publisher":"The Company of Biologists","doi":"10.1242/bio.20122287","type":"journal_article","date_updated":"2021-01-12T06:56:23Z","_id":"2263","ddc":["576"],"page":"1200 - 1203","quality_controlled":"1","month":"12","file":[{"access_level":"open_access","content_type":"application/pdf","file_name":"IST-2015-387-v1+1_1200.full.pdf","checksum":"605a1800b81227848c361fd6ba7d22ba","relation":"main_file","creator":"system","date_updated":"2020-07-14T12:45:35Z","file_size":726695,"date_created":"2018-12-12T10:13:09Z","file_id":"4990"}],"department":[{"_id":"SiHi"}],"language":[{"iso":"eng"}],"pubrep_id":"387","oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","issue":"12","citation":{"ama":"Liang H, Hippenmeyer S, Ghashghaei H. A Nestin-cre transgenic mouse is insufficient for recombination in early embryonic neural progenitors. <i>Biology open</i>. 2012;1(12):1200-1203. doi:<a href=\"https://doi.org/10.1242/bio.20122287\">10.1242/bio.20122287</a>","ieee":"H. Liang, S. Hippenmeyer, and H. Ghashghaei, “A Nestin-cre transgenic mouse is insufficient for recombination in early embryonic neural progenitors,” <i>Biology open</i>, vol. 1, no. 12. The Company of Biologists, pp. 1200–1203, 2012.","short":"H. Liang, S. Hippenmeyer, H. Ghashghaei, Biology Open 1 (2012) 1200–1203.","chicago":"Liang, Huixuan, Simon Hippenmeyer, and H. Ghashghaei. “A Nestin-Cre Transgenic Mouse Is Insufficient for Recombination in Early Embryonic Neural Progenitors.” <i>Biology Open</i>. The Company of Biologists, 2012. <a href=\"https://doi.org/10.1242/bio.20122287\">https://doi.org/10.1242/bio.20122287</a>.","ista":"Liang H, Hippenmeyer S, Ghashghaei H. 2012. A Nestin-cre transgenic mouse is insufficient for recombination in early embryonic neural progenitors. Biology open. 1(12), 1200–1203.","apa":"Liang, H., Hippenmeyer, S., &#38; Ghashghaei, H. (2012). A Nestin-cre transgenic mouse is insufficient for recombination in early embryonic neural progenitors. <i>Biology Open</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/bio.20122287\">https://doi.org/10.1242/bio.20122287</a>","mla":"Liang, Huixuan, et al. “A Nestin-Cre Transgenic Mouse Is Insufficient for Recombination in Early Embryonic Neural Progenitors.” <i>Biology Open</i>, vol. 1, no. 12, The Company of Biologists, 2012, pp. 1200–03, doi:<a href=\"https://doi.org/10.1242/bio.20122287\">10.1242/bio.20122287</a>."},"oa_version":"Published Version","title":"A Nestin-cre transgenic mouse is insufficient for recombination in early embryonic neural progenitors","author":[{"last_name":"Liang","full_name":"Liang, Huixuan","first_name":"Huixuan"},{"last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon"},{"first_name":"H.","last_name":"Ghashghaei","full_name":"Ghashghaei, H."}],"day":"15","scopus_import":1,"date_created":"2018-12-11T11:56:38Z","volume":1,"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","tmp":{"image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"intvolume":"         1","abstract":[{"text":"Nestin-cre transgenic mice have been widely used to direct recombination to neural stem cells (NSCs) and intermediate neural progenitor cells (NPCs). Here we report that a readily utilized, and the only commercially available, Nestin-cre line is insufficient for directing recombination in early embryonic NSCs and NPCs. Analysis of recombination efficiency in multiple cre-dependent reporters and a genetic mosaic line revealed consistent temporal and spatial patterns of recombination in NSCs and NPCs. For comparison we utilized a knock-in Emx1cre line and found robust recombination in NSCs and NPCs in ventricular and subventricular zones of the cerebral cortices as early as embryonic day 12.5. In addition we found that the rate of Nestin-cre driven recombination only reaches sufficiently high levels in NSCs and NPCs during late embryonic and early postnatal periods. These findings are important when commercially available cre lines are considered for directing recombination to embryonic NSCs and NPCs.","lang":"eng"}],"has_accepted_license":"1","publication_status":"published","file_date_updated":"2020-07-14T12:45:35Z"},{"department":[{"_id":"ToHe"},{"_id":"CaGu"}],"month":"07","issue":"2","citation":{"ieee":"T. A. Henzinger and M. Mateescu, “The propagation approach for computing biochemical reaction networks,” <i>IEEE ACM Transactions on Computational Biology and Bioinformatics</i>, vol. 10, no. 2. IEEE, pp. 310–322, 2012.","short":"T.A. Henzinger, M. Mateescu, IEEE ACM Transactions on Computational Biology and Bioinformatics 10 (2012) 310–322.","ama":"Henzinger TA, Mateescu M. The propagation approach for computing biochemical reaction networks. <i>IEEE ACM Transactions on Computational Biology and Bioinformatics</i>. 2012;10(2):310-322. doi:<a href=\"https://doi.org/10.1109/TCBB.2012.91\">10.1109/TCBB.2012.91</a>","apa":"Henzinger, T. A., &#38; Mateescu, M. (2012). The propagation approach for computing biochemical reaction networks. <i>IEEE ACM Transactions on Computational Biology and Bioinformatics</i>. IEEE. <a href=\"https://doi.org/10.1109/TCBB.2012.91\">https://doi.org/10.1109/TCBB.2012.91</a>","mla":"Henzinger, Thomas A., and Maria Mateescu. “The Propagation Approach for Computing Biochemical Reaction Networks.” <i>IEEE ACM Transactions on Computational Biology and Bioinformatics</i>, vol. 10, no. 2, IEEE, 2012, pp. 310–22, doi:<a href=\"https://doi.org/10.1109/TCBB.2012.91\">10.1109/TCBB.2012.91</a>.","chicago":"Henzinger, Thomas A, and Maria Mateescu. “The Propagation Approach for Computing Biochemical Reaction Networks.” <i>IEEE ACM Transactions on Computational Biology and Bioinformatics</i>. IEEE, 2012. <a href=\"https://doi.org/10.1109/TCBB.2012.91\">https://doi.org/10.1109/TCBB.2012.91</a>.","ista":"Henzinger TA, Mateescu M. 2012. The propagation approach for computing biochemical reaction networks. IEEE ACM Transactions on Computational Biology and Bioinformatics. 10(2), 310–322."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"volume":10,"date_created":"2018-12-11T11:56:52Z","author":[{"first_name":"Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"first_name":"Maria","id":"3B43276C-F248-11E8-B48F-1D18A9856A87","full_name":"Mateescu, Maria","last_name":"Mateescu"}],"scopus_import":1,"day":"03","title":"The propagation approach for computing biochemical reaction networks","oa_version":"None","publication_status":"published","intvolume":"        10","abstract":[{"text":"We introduce propagation models (PMs), a formalism able to express several kinds of equations that describe the behavior of biochemical reaction networks. Furthermore, we introduce the propagation abstract data type (PADT), which separates concerns regarding different numerical algorithms for the transient analysis of biochemical reaction networks from concerns regarding their implementation, thus allowing for portable and efficient solutions. The state of a propagation abstract data type is given by a vector that assigns mass values to a set of nodes, and its (next) operator propagates mass values through this set of nodes. We propose an approximate implementation of the (next) operator, based on threshold abstraction, which propagates only &quot;significant&quot; mass values and thus achieves a compromise between efficiency and accuracy. Finally, we give three use cases for propagation models: the chemical master equation (CME), the reaction rate equation (RRE), and a hybrid method that combines these two equations. These three applications use propagation models in order to propagate probabilities and/or expected values and variances of the model's variables.","lang":"eng"}],"publist_id":"4625","year":"2012","external_id":{"pmid":["22778152"]},"pmid":1,"ec_funded":1,"date_published":"2012-07-03T00:00:00Z","project":[{"grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"}],"publication":"IEEE ACM Transactions on Computational Biology and Bioinformatics","status":"public","date_updated":"2021-01-12T06:56:38Z","_id":"2302","type":"journal_article","doi":"10.1109/TCBB.2012.91","publisher":"IEEE","quality_controlled":"1","page":"310 - 322"},{"publist_id":"4609","department":[{"_id":"RoSe"}],"month":"06","year":"2012","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","acknowledgement":"Partial financial support by NSERC ","date_published":"2012-06-24T00:00:00Z","citation":{"ista":"Seiringer R. 2012. Absence of bound states implies non-negativity of the scattering length. Journal of Spectral Theory. 2(3), 321–328.","chicago":"Seiringer, Robert. “Absence of Bound States Implies Non-Negativity of the Scattering Length.” <i>Journal of Spectral Theory</i>. European Mathematical Society, 2012. <a href=\"https://doi.org/10.4171/JST/31\">https://doi.org/10.4171/JST/31</a>.","mla":"Seiringer, Robert. “Absence of Bound States Implies Non-Negativity of the Scattering Length.” <i>Journal of Spectral Theory</i>, vol. 2, no. 3, European Mathematical Society, 2012, pp. 321–28, doi:<a href=\"https://doi.org/10.4171/JST/31\">10.4171/JST/31</a>.","apa":"Seiringer, R. (2012). Absence of bound states implies non-negativity of the scattering length. <i>Journal of Spectral Theory</i>. European Mathematical Society. <a href=\"https://doi.org/10.4171/JST/31\">https://doi.org/10.4171/JST/31</a>","ama":"Seiringer R. Absence of bound states implies non-negativity of the scattering length. <i>Journal of Spectral Theory</i>. 2012;2(3):321-328. doi:<a href=\"https://doi.org/10.4171/JST/31\">10.4171/JST/31</a>","short":"R. Seiringer, Journal of Spectral Theory 2 (2012) 321–328.","ieee":"R. Seiringer, “Absence of bound states implies non-negativity of the scattering length,” <i>Journal of Spectral Theory</i>, vol. 2, no. 3. European Mathematical Society, pp. 321–328, 2012."},"issue":"3","status":"public","publication":"Journal of Spectral Theory","language":[{"iso":"eng"}],"oa":1,"date_created":"2018-12-11T11:56:58Z","type":"journal_article","_id":"2318","volume":2,"date_updated":"2021-01-12T06:56:44Z","publisher":"European Mathematical Society","oa_version":"Preprint","title":"Absence of bound states implies non-negativity of the scattering length","day":"24","doi":"10.4171/JST/31","author":[{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert","last_name":"Seiringer","orcid":"0000-0002-6781-0521","first_name":"Robert"}],"quality_controlled":"1","publication_status":"published","main_file_link":[{"url":"http://arxiv.org/abs/1204.0435","open_access":"1"}],"intvolume":"         2","abstract":[{"lang":"eng","text":"We show that bosons interacting via pair potentials with negative scattering length form bound states for a suitable number of particles. In other words, the absence of many-particle bound states of any kind implies the non-negativity of the scattering length of the interaction potential. "}],"page":"321-328"},{"has_accepted_license":"1","license":"https://creativecommons.org/licenses/by-nc/4.0/","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"abstract":[{"lang":"eng","text":"The kingdom of fungi provides model organisms for biotechnology, cell biology, genetics, and life sciences in general. Only when their phylogenetic relationships are stably resolved, can individual results from fungal research be integrated into a holistic picture of biology. However, and despite recent progress, many deep relationships within the fungi remain unclear. Here, we present the first phylogenomic study of an entire eukaryotic kingdom that uses a consistency criterion to strengthen phylogenetic conclusions. We reason that branches (splits) recovered with independent data and different tree reconstruction methods are likely to reflect true evolutionary relationships. Two complementary phylogenomic data sets based on 99 fungal genomes and 109 fungal expressed sequence tag (EST) sets analyzed with four different tree reconstruction methods shed light from different angles on the fungal tree of life. Eleven additional data sets address specifically the phylogenetic position of Blastocladiomycota, Ustilaginomycotina, and Dothideomycetes, respectively. The combined evidence from the resulting trees supports the deep-level stability of the fungal groups toward a comprehensive natural system of the fungi. In addition, our analysis reveals methodologically interesting aspects. Enrichment for EST encoded data-a common practice in phylogenomic analyses-introduces a strong bias toward slowly evolving and functionally correlated genes. Consequently, the generalization of phylogenomic data sets as collections of randomly selected genes cannot be taken for granted. A thorough characterization of the data to assess possible influences on the tree reconstruction should therefore become a standard in phylogenomic analyses."}],"intvolume":"        29","file_date_updated":"2020-07-14T12:45:40Z","publication_status":"published","scopus_import":1,"day":"01","author":[{"full_name":"Ebersberger, Ingo","last_name":"Ebersberger","first_name":"Ingo"},{"first_name":"Ricardo","full_name":"De Matos Simoes, Ricardo","last_name":"De Matos Simoes"},{"id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87","full_name":"Kupczok, Anne","last_name":"Kupczok","first_name":"Anne"},{"first_name":"Matthias","full_name":"Gube, Matthias","last_name":"Gube"},{"first_name":"Erika","full_name":"Kothe, Erika","last_name":"Kothe"},{"first_name":"Kerstin","full_name":"Voigt, Kerstin","last_name":"Voigt"},{"last_name":"Von Haeseler","full_name":"Von Haeseler, Arndt","first_name":"Arndt"}],"title":"A consistent phylogenetic backbone for the fungi","oa_version":"Published Version","volume":29,"date_created":"2018-12-11T11:57:30Z","oa":1,"pubrep_id":"384","language":[{"iso":"eng"}],"citation":{"mla":"Ebersberger, Ingo, et al. “A Consistent Phylogenetic Backbone for the Fungi.” <i>Molecular Biology and Evolution</i>, vol. 29, no. 5, Oxford University Press, 2012, pp. 1319–34, doi:<a href=\"https://doi.org/10.1093/molbev/msr285\">10.1093/molbev/msr285</a>.","apa":"Ebersberger, I., De Matos Simoes, R., Kupczok, A., Gube, M., Kothe, E., Voigt, K., &#38; Von Haeseler, A. (2012). A consistent phylogenetic backbone for the fungi. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msr285\">https://doi.org/10.1093/molbev/msr285</a>","ista":"Ebersberger I, De Matos Simoes R, Kupczok A, Gube M, Kothe E, Voigt K, Von Haeseler A. 2012. A consistent phylogenetic backbone for the fungi. Molecular Biology and Evolution. 29(5), 1319–1334.","chicago":"Ebersberger, Ingo, Ricardo De Matos Simoes, Anne Kupczok, Matthias Gube, Erika Kothe, Kerstin Voigt, and Arndt Von Haeseler. “A Consistent Phylogenetic Backbone for the Fungi.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2012. <a href=\"https://doi.org/10.1093/molbev/msr285\">https://doi.org/10.1093/molbev/msr285</a>.","short":"I. Ebersberger, R. De Matos Simoes, A. Kupczok, M. Gube, E. Kothe, K. Voigt, A. Von Haeseler, Molecular Biology and Evolution 29 (2012) 1319–1334.","ieee":"I. Ebersberger <i>et al.</i>, “A consistent phylogenetic backbone for the fungi,” <i>Molecular Biology and Evolution</i>, vol. 29, no. 5. Oxford University Press, pp. 1319–1334, 2012.","ama":"Ebersberger I, De Matos Simoes R, Kupczok A, et al. A consistent phylogenetic backbone for the fungi. <i>Molecular Biology and Evolution</i>. 2012;29(5):1319-1334. doi:<a href=\"https://doi.org/10.1093/molbev/msr285\">10.1093/molbev/msr285</a>"},"issue":"5","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"05","department":[{"_id":"JoBo"}],"file":[{"file_id":"5013","date_updated":"2020-07-14T12:45:40Z","creator":"system","date_created":"2018-12-12T10:13:30Z","file_size":754922,"checksum":"d565dcac27d1736c0c378ea6fcf22d69","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2015-384-v1+1_Mol_Biol_Evol-2012-Ebersberger-1319-34.pdf"}],"page":"1319 - 1334","ddc":["570","576"],"quality_controlled":"1","doi":"10.1093/molbev/msr285","publisher":"Oxford University Press","_id":"2411","date_updated":"2021-01-12T06:57:19Z","type":"journal_article","status":"public","publication":"Molecular Biology and Evolution","date_published":"2012-05-01T00:00:00Z","year":"2012","publist_id":"4515"},{"ddc":["004"],"quality_controlled":"1","doi":"10.3389/fnins.2012.00055","publisher":"Frontiers Research Foundation","_id":"493","date_updated":"2021-01-12T08:01:03Z","type":"journal_article","status":"public","publication":"Frontiers in Neuroscience","date_published":"2012-07-13T00:00:00Z","acknowledgement":"The studies were in part or completely supported by the Bundesministerium für Bildung und Forschung (BMBF), Fkz 01IB001A, 01GQ0850, by the German Science Foundation (DFG, contract MU 987/3-2), by the European ICT Programme Projects FP7-224631 and 216886, the World Class University Program through the National Research Foundation of Korea funded by the Ministry of Education, Science, and Technology (Grant R31-10008), the US Army Research Office [W911NF-08-1-0216 (Gerwin Schalk) and W911NF-07-1-0415 (Gerwin Schalk)] and the NIH [EB006356 (Gerwin Schalk) and EB000856 (Gerwin Schalk), the WIN-Kolleg of the Heidelberg Academy of Sciences and Humanities, German Federal Ministry of Education and Research grants 01GQ0420, 01GQ0761, 01GQ0762, and 01GQ0830, German Research Foundation grants 550/B5 and C6, and by a scholarship from the German National Academic Foundation. This paper only reflects the authors’ views and funding agencies are not liable for any use that may be made of the information contained herein.\r\n","year":"2012","publist_id":"7327","has_accepted_license":"1","abstract":[{"lang":"eng","text":"The BCI competition IV stands in the tradition of prior BCI competitions that aim to provide high quality neuroscientific data for open access to the scientific community. As experienced already in prior competitions not only scientists from the narrow field of BCI compete, but scholars with a broad variety of backgrounds and nationalities. They include high specialists as well as students.The goals of all BCI competitions have always been to challenge with respect to novel paradigms and complex data. We report on the following challenges: (1) asynchronous data, (2) synthetic, (3) multi-class continuous data, (4) sessionto-session transfer, (5) directionally modulated MEG, (6) finger movements recorded by ECoG. As after past competitions, our hope is that winning entries may enhance the analysis methods of future BCIs."}],"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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"         6","file_date_updated":"2020-07-14T12:46:35Z","publication_status":"published","day":"13","scopus_import":1,"author":[{"full_name":"Tangermann, Michael","last_name":"Tangermann","first_name":"Michael"},{"last_name":"Müller","full_name":"Müller, Klaus","first_name":"Klaus"},{"last_name":"Aertsen","full_name":"Aertsen, Ad","first_name":"Ad"},{"full_name":"Birbaumer, Niels","last_name":"Birbaumer","first_name":"Niels"},{"full_name":"Braun, Christoph","last_name":"Braun","first_name":"Christoph"},{"first_name":"Clemens","full_name":"Brunner, Clemens","last_name":"Brunner"},{"first_name":"Robert","full_name":"Leeb, Robert","last_name":"Leeb"},{"first_name":"Carsten","full_name":"Mehring, Carsten","last_name":"Mehring"},{"last_name":"Miller","full_name":"Miller, Kai","first_name":"Kai"},{"full_name":"Müller Putz, Gernot","last_name":"Müller Putz","first_name":"Gernot"},{"last_name":"Nolte","full_name":"Nolte, Guido","first_name":"Guido"},{"first_name":"Gert","last_name":"Pfurtscheller","full_name":"Pfurtscheller, Gert"},{"last_name":"Preissl","full_name":"Preissl, Hubert","first_name":"Hubert"},{"last_name":"Schalk","full_name":"Schalk, Gerwin","first_name":"Gerwin"},{"last_name":"Schlögl","full_name":"Schlögl, Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100","first_name":"Alois"},{"full_name":"Vidaurre, Carmen","last_name":"Vidaurre","first_name":"Carmen"},{"first_name":"Stephan","last_name":"Waldert","full_name":"Waldert, Stephan"},{"first_name":"Benjamin","last_name":"Blankertz","full_name":"Blankertz, Benjamin"}],"oa_version":"Published Version","title":"Review of the BCI competition IV","volume":6,"date_created":"2018-12-11T11:46:46Z","oa":1,"pubrep_id":"945","language":[{"iso":"eng"}],"citation":{"mla":"Tangermann, Michael, et al. “Review of the BCI Competition IV.” <i>Frontiers in Neuroscience</i>, vol. 6, 55, Frontiers Research Foundation, 2012, doi:<a href=\"https://doi.org/10.3389/fnins.2012.00055\">10.3389/fnins.2012.00055</a>.","apa":"Tangermann, M., Müller, K., Aertsen, A., Birbaumer, N., Braun, C., Brunner, C., … Blankertz, B. (2012). Review of the BCI competition IV. <i>Frontiers in Neuroscience</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fnins.2012.00055\">https://doi.org/10.3389/fnins.2012.00055</a>","chicago":"Tangermann, Michael, Klaus Müller, Ad Aertsen, Niels Birbaumer, Christoph Braun, Clemens Brunner, Robert Leeb, et al. “Review of the BCI Competition IV.” <i>Frontiers in Neuroscience</i>. Frontiers Research Foundation, 2012. <a href=\"https://doi.org/10.3389/fnins.2012.00055\">https://doi.org/10.3389/fnins.2012.00055</a>.","ista":"Tangermann M, Müller K, Aertsen A, Birbaumer N, Braun C, Brunner C, Leeb R, Mehring C, Miller K, Müller Putz G, Nolte G, Pfurtscheller G, Preissl H, Schalk G, Schlögl A, Vidaurre C, Waldert S, Blankertz B. 2012. Review of the BCI competition IV. Frontiers in Neuroscience. 6, 55.","short":"M. Tangermann, K. Müller, A. Aertsen, N. Birbaumer, C. Braun, C. Brunner, R. Leeb, C. Mehring, K. Miller, G. Müller Putz, G. Nolte, G. Pfurtscheller, H. Preissl, G. Schalk, A. Schlögl, C. Vidaurre, S. Waldert, B. Blankertz, Frontiers in Neuroscience 6 (2012).","ieee":"M. Tangermann <i>et al.</i>, “Review of the BCI competition IV,” <i>Frontiers in Neuroscience</i>, vol. 6. Frontiers Research Foundation, 2012.","ama":"Tangermann M, Müller K, Aertsen A, et al. Review of the BCI competition IV. <i>Frontiers in Neuroscience</i>. 2012;6. doi:<a href=\"https://doi.org/10.3389/fnins.2012.00055\">10.3389/fnins.2012.00055</a>"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"07","department":[{"_id":"ScienComp"},{"_id":"PeJo"}],"file":[{"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2018-945-v1+1_2012_Schloegl_Review_of.pdf","checksum":"195238221c4b0b0f4035f6f6c16ea17c","relation":"main_file","creator":"system","date_updated":"2020-07-14T12:46:35Z","date_created":"2018-12-12T10:18:34Z","file_size":2693701,"file_id":"5356"}],"article_number":"55"},{"month":"10","year":"2012","article_number":"29","publist_id":"7326","department":[{"_id":"ToHe"}],"publication":"ACM Transactions on Computational Logic (TOCL)","language":[{"iso":"eng"}],"status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_published":"2012-10-01T00:00:00Z","citation":{"ista":"Boker U, Kupferman O. 2012. Translating to Co-Büchi made tight, unified, and useful. ACM Transactions on Computational Logic (TOCL). 13(4), 29.","chicago":"Boker, Udi, and Orna Kupferman. “Translating to Co-Büchi Made Tight, Unified, and Useful.” <i>ACM Transactions on Computational Logic (TOCL)</i>. ACM, 2012. <a href=\"https://doi.org/10.1145/2362355.2362357\">https://doi.org/10.1145/2362355.2362357</a>.","mla":"Boker, Udi, and Orna Kupferman. “Translating to Co-Büchi Made Tight, Unified, and Useful.” <i>ACM Transactions on Computational Logic (TOCL)</i>, vol. 13, no. 4, 29, ACM, 2012, doi:<a href=\"https://doi.org/10.1145/2362355.2362357\">10.1145/2362355.2362357</a>.","apa":"Boker, U., &#38; Kupferman, O. (2012). Translating to Co-Büchi made tight, unified, and useful. <i>ACM Transactions on Computational Logic (TOCL)</i>. ACM. <a href=\"https://doi.org/10.1145/2362355.2362357\">https://doi.org/10.1145/2362355.2362357</a>","ama":"Boker U, Kupferman O. Translating to Co-Büchi made tight, unified, and useful. <i>ACM Transactions on Computational Logic (TOCL)</i>. 2012;13(4). doi:<a href=\"https://doi.org/10.1145/2362355.2362357\">10.1145/2362355.2362357</a>","short":"U. Boker, O. Kupferman, ACM Transactions on Computational Logic (TOCL) 13 (2012).","ieee":"U. Boker and O. Kupferman, “Translating to Co-Büchi made tight, unified, and useful,” <i>ACM Transactions on Computational Logic (TOCL)</i>, vol. 13, no. 4. ACM, 2012."},"issue":"4","title":"Translating to Co-Büchi made tight, unified, and useful","publisher":"ACM","oa_version":"None","day":"01","scopus_import":1,"doi":"10.1145/2362355.2362357","author":[{"first_name":"Udi","full_name":"Boker, Udi","id":"31E297B6-F248-11E8-B48F-1D18A9856A87","last_name":"Boker"},{"first_name":"Orna","last_name":"Kupferman","full_name":"Kupferman, Orna"}],"date_created":"2018-12-11T11:46:47Z","type":"journal_article","volume":13,"_id":"494","date_updated":"2021-01-12T08:01:03Z","intvolume":"        13","abstract":[{"text":"We solve the longstanding open problems of the blow-up involved in the translations, when possible, of a nondeterministic Büchi word automaton (NBW) to a nondeterministic co-Büchi word automaton (NCW) and to a deterministic co-Büchi word automaton (DCW). For the NBW to NCW translation, the currently known upper bound is 2o(nlog n) and the lower bound is 1.5n. We improve the upper bound to n2n and describe a matching lower bound of 2ω(n). For the NBW to DCW translation, the currently known upper bound is 2o(nlog n). We improve it to 2 o(n), which is asymptotically tight. Both of our upper-bound constructions are based on a simple subset construction, do not involve intermediate automata with richer acceptance conditions, and can be implemented symbolically. We continue and solve the open problems of translating nondeterministic Streett, Rabin, Muller, and parity word automata to NCW and to DCW. Going via an intermediate NBW is not optimal and we describe direct, simple, and asymptotically tight constructions, involving a 2o(n) blow-up. The constructions are variants of the subset construction, providing a unified approach for translating all common classes of automata to NCW and DCW. Beyond the theoretical importance of the results, we point to numerous applications of the new constructions. In particular, they imply a simple subset-construction based translation, when possible, of LTL to deterministic Büchi word automata.","lang":"eng"}],"publication_status":"published","quality_controlled":"1"},{"alternative_title":["EPTCS"],"doi":"10.4204/EPTCS.96.18","publisher":"Open Publishing Association","_id":"495","date_updated":"2021-01-12T08:01:04Z","type":"conference","page":"238 - 246","ddc":["004"],"quality_controlled":"1","year":"2012","publist_id":"7325","status":"public","publication":"Proceedings GandALF 2012","project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"}],"ec_funded":1,"date_published":"2012-10-07T00:00:00Z","conference":{"location":"Napoli, Italy","end_date":"2012-09-08","start_date":"2012-09-06","name":"GandALF: Games, Automata, Logics and Formal Verification"},"scopus_import":1,"day":"07","author":[{"first_name":"Alex","full_name":"Kruckman, Alex","last_name":"Kruckman"},{"first_name":"Sasha","last_name":"Rubin","id":"2EC51194-F248-11E8-B48F-1D18A9856A87","full_name":"Rubin, Sasha"},{"last_name":"Sheridan","full_name":"Sheridan, John","first_name":"John"},{"full_name":"Zax, Ben","last_name":"Zax","first_name":"Ben"}],"title":"A Myhill Nerode theorem for automata with advice","oa_version":"Published Version","volume":96,"date_created":"2018-12-11T11:46:47Z","has_accepted_license":"1","intvolume":"        96","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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"An automaton with advice is a finite state automaton which has access to an additional fixed infinite string called an advice tape. We refine the Myhill-Nerode theorem to characterize the languages of finite strings that are accepted by automata with advice. We do the same for tree automata with advice."}],"file_date_updated":"2020-07-14T12:46:35Z","publication_status":"published","month":"10","department":[{"_id":"KrCh"}],"file":[{"file_name":"IST-2018-944-v1+1_2012_Rubin_A_Myhill.pdf","access_level":"open_access","content_type":"application/pdf","relation":"main_file","checksum":"56277f95edc9d531fa3bdc5f9579fda8","file_size":97736,"date_created":"2018-12-12T10:15:31Z","date_updated":"2020-07-14T12:46:35Z","creator":"system","file_id":"5152"}],"oa":1,"pubrep_id":"944","language":[{"iso":"eng"}],"citation":{"chicago":"Kruckman, Alex, Sasha Rubin, John Sheridan, and Ben Zax. “A Myhill Nerode Theorem for Automata with Advice.” In <i>Proceedings GandALF 2012</i>, 96:238–46. Open Publishing Association, 2012. <a href=\"https://doi.org/10.4204/EPTCS.96.18\">https://doi.org/10.4204/EPTCS.96.18</a>.","ista":"Kruckman A, Rubin S, Sheridan J, Zax B. 2012. A Myhill Nerode theorem for automata with advice. Proceedings GandALF 2012. GandALF: Games, Automata, Logics and Formal Verification, EPTCS, vol. 96, 238–246.","apa":"Kruckman, A., Rubin, S., Sheridan, J., &#38; Zax, B. (2012). A Myhill Nerode theorem for automata with advice. In <i>Proceedings GandALF 2012</i> (Vol. 96, pp. 238–246). Napoli, Italy: Open Publishing Association. <a href=\"https://doi.org/10.4204/EPTCS.96.18\">https://doi.org/10.4204/EPTCS.96.18</a>","mla":"Kruckman, Alex, et al. “A Myhill Nerode Theorem for Automata with Advice.” <i>Proceedings GandALF 2012</i>, vol. 96, Open Publishing Association, 2012, pp. 238–46, doi:<a href=\"https://doi.org/10.4204/EPTCS.96.18\">10.4204/EPTCS.96.18</a>.","ama":"Kruckman A, Rubin S, Sheridan J, Zax B. A Myhill Nerode theorem for automata with advice. In: <i>Proceedings GandALF 2012</i>. Vol 96. Open Publishing Association; 2012:238-246. doi:<a href=\"https://doi.org/10.4204/EPTCS.96.18\">10.4204/EPTCS.96.18</a>","ieee":"A. Kruckman, S. Rubin, J. Sheridan, and B. Zax, “A Myhill Nerode theorem for automata with advice,” in <i>Proceedings GandALF 2012</i>, Napoli, Italy, 2012, vol. 96, pp. 238–246.","short":"A. Kruckman, S. Rubin, J. Sheridan, B. Zax, in:, Proceedings GandALF 2012, Open Publishing Association, 2012, pp. 238–246."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_published":"2012-01-01T00:00:00Z","conference":{"location":"Dubrovnik, Croatia","start_date":"2012-06-25","end_date":"2012-06-28","name":"LICS: Symposium on Logic in Computer Science"},"ec_funded":1,"citation":{"ama":"Rabinovich A, Rubin S. Interpretations in trees with countably many branches. In: IEEE; 2012. doi:<a href=\"https://doi.org/10.1109/LICS.2012.65\">10.1109/LICS.2012.65</a>","short":"A. Rabinovich, S. Rubin, in:, IEEE, 2012.","ieee":"A. Rabinovich and S. Rubin, “Interpretations in trees with countably many branches,” presented at the LICS: Symposium on Logic in Computer Science, Dubrovnik, Croatia, 2012.","chicago":"Rabinovich, Alexander, and Sasha Rubin. “Interpretations in Trees with Countably Many Branches.” IEEE, 2012. <a href=\"https://doi.org/10.1109/LICS.2012.65\">https://doi.org/10.1109/LICS.2012.65</a>.","ista":"Rabinovich A, Rubin S. 2012. Interpretations in trees with countably many branches. LICS: Symposium on Logic in Computer Science, LICS, , 6280474.","mla":"Rabinovich, Alexander, and Sasha Rubin. <i>Interpretations in Trees with Countably Many Branches</i>. 6280474, IEEE, 2012, doi:<a href=\"https://doi.org/10.1109/LICS.2012.65\">10.1109/LICS.2012.65</a>.","apa":"Rabinovich, A., &#38; Rubin, S. (2012). Interpretations in trees with countably many branches. Presented at the LICS: Symposium on Logic in Computer Science, Dubrovnik, Croatia: IEEE. <a href=\"https://doi.org/10.1109/LICS.2012.65\">https://doi.org/10.1109/LICS.2012.65</a>"},"status":"public","language":[{"iso":"eng"}],"project":[{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"oa":1,"article_number":"6280474","publist_id":"7324","department":[{"_id":"KrCh"}],"month":"01","year":"2012","quality_controlled":"1","publication_status":"published","main_file_link":[{"url":"https://arise.or.at/pubpdf/Interpretations_in_Trees_with_Countably_Many_Branches.pdf","open_access":"1"}],"abstract":[{"lang":"eng","text":"We study the expressive power of logical interpretations on the class of scattered trees, namely those with countably many infinite branches. Scattered trees can be thought of as the tree analogue of scattered linear orders. Every scattered tree has an ordinal rank that reflects the structure of its infinite branches. We prove, roughly, that trees and orders of large rank cannot be interpreted in scattered trees of small rank. We consider a quite general notion of interpretation: each element of the interpreted structure is represented by a set of tuples of subsets of the interpreting tree. Our trees are countable, not necessarily finitely branching, and may have finitely many unary predicates as labellings. We also show how to replace injective set-interpretations in (not necessarily scattered) trees by 'finitary' set-interpretations."}],"date_created":"2018-12-11T11:46:47Z","type":"conference","_id":"496","date_updated":"2021-01-12T08:01:05Z","oa_version":"Preprint","publisher":"IEEE","title":"Interpretations in trees with countably many branches","scopus_import":1,"alternative_title":["LICS"],"day":"01","author":[{"last_name":"Rabinovich","full_name":"Rabinovich, Alexander","first_name":"Alexander"},{"last_name":"Rubin","full_name":"Rubin, Sasha","id":"2EC51194-F248-11E8-B48F-1D18A9856A87","first_name":"Sasha"}],"doi":"10.1109/LICS.2012.65"},{"month":"09","file":[{"file_id":"4712","date_updated":"2020-07-14T12:46:35Z","creator":"system","date_created":"2018-12-12T10:08:50Z","file_size":471236,"checksum":"f1b0dd99240800db2d7dbf9b5131fe5e","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2018-943-v1+1_2012_Chatterjee_Faster_Algorithms.pdf"}],"department":[{"_id":"KrCh"}],"pubrep_id":"943","language":[{"iso":"eng"}],"oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"short":"K. Chatterjee, S. Chaubal, P. Kamath, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2012, pp. 167–182.","ieee":"K. Chatterjee, S. Chaubal, and P. Kamath, “Faster algorithms for alternating refinement relations,” presented at the EACSL: European Association for Computer Science Logic, Fontainebleau, France, 2012, vol. 16, pp. 167–182.","ama":"Chatterjee K, Chaubal S, Kamath P. Faster algorithms for alternating refinement relations. In: Vol 16. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2012:167-182. doi:<a href=\"https://doi.org/10.4230/LIPIcs.CSL.2012.167\">10.4230/LIPIcs.CSL.2012.167</a>","mla":"Chatterjee, Krishnendu, et al. <i>Faster Algorithms for Alternating Refinement Relations</i>. Vol. 16, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2012, pp. 167–82, doi:<a href=\"https://doi.org/10.4230/LIPIcs.CSL.2012.167\">10.4230/LIPIcs.CSL.2012.167</a>.","apa":"Chatterjee, K., Chaubal, S., &#38; Kamath, P. (2012). Faster algorithms for alternating refinement relations (Vol. 16, pp. 167–182). Presented at the EACSL: European Association for Computer Science Logic, Fontainebleau, France: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.CSL.2012.167\">https://doi.org/10.4230/LIPIcs.CSL.2012.167</a>","ista":"Chatterjee K, Chaubal S, Kamath P. 2012. Faster algorithms for alternating refinement relations. EACSL: European Association for Computer Science Logic, LIPIcs, vol. 16, 167–182.","chicago":"Chatterjee, Krishnendu, Siddhesh Chaubal, and Pritish Kamath. “Faster Algorithms for Alternating Refinement Relations,” 16:167–82. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2012. <a href=\"https://doi.org/10.4230/LIPIcs.CSL.2012.167\">https://doi.org/10.4230/LIPIcs.CSL.2012.167</a>."},"title":"Faster algorithms for alternating refinement relations","oa_version":"Published Version","author":[{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"last_name":"Chaubal","full_name":"Chaubal, Siddhesh","first_name":"Siddhesh"},{"first_name":"Pritish","full_name":"Kamath, Pritish","last_name":"Kamath"}],"scopus_import":1,"day":"01","date_created":"2018-12-11T11:46:48Z","volume":16,"intvolume":"        16","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"abstract":[{"text":"One central issue in the formal design and analysis of reactive systems is the notion of refinement that asks whether all behaviors of the implementation is allowed by the specification. The local interpretation of behavior leads to the notion of simulation. Alternating transition systems (ATSs) provide a general model for composite reactive systems, and the simulation relation for ATSs is known as alternating simulation. The simulation relation for fair transition systems is called fair simulation. In this work our main contributions are as follows: (1) We present an improved algorithm for fair simulation with Büchi fairness constraints; our algorithm requires O(n 3·m) time as compared to the previous known O(n 6)-time algorithm, where n is the number of states and m is the number of transitions. (2) We present a game based algorithm for alternating simulation that requires O(m2)-time as compared to the previous known O((n·m)2)-time algorithm, where n is the number of states and m is the size of transition relation. (3) We present an iterative algorithm for alternating simulation that matches the time complexity of the game based algorithm, but is more space efficient than the game based algorithm. © Krishnendu Chatterjee, Siddhesh Chaubal, and Pritish Kamath.","lang":"eng"}],"has_accepted_license":"1","publication_status":"published","file_date_updated":"2020-07-14T12:46:35Z","related_material":{"record":[{"id":"5378","relation":"earlier_version","status":"public"}]},"year":"2012","publist_id":"7323","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"status":"public","conference":{"location":"Fontainebleau, France","end_date":"2012-09-06","start_date":"2012-09-03","name":"EACSL: European Association for Computer Science Logic"},"date_published":"2012-09-01T00:00:00Z","ec_funded":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","doi":"10.4230/LIPIcs.CSL.2012.167","alternative_title":["LIPIcs"],"type":"conference","date_updated":"2023-02-23T12:23:32Z","_id":"497","ddc":["004"],"page":"167 - 182","quality_controlled":"1"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","issue":"8","citation":{"apa":"Pickup, M., Field, D., Rowell, D., &#38; Young, A. (2012). Predicting local adaptation in fragmented plant populations: Implications for restoration genetics. <i>Evolutionary Applications</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1752-4571.2012.00284.x\">https://doi.org/10.1111/j.1752-4571.2012.00284.x</a>","mla":"Pickup, Melinda, et al. “Predicting Local Adaptation in Fragmented Plant Populations: Implications for Restoration Genetics.” <i>Evolutionary Applications</i>, vol. 5, no. 8, Wiley-Blackwell, 2012, pp. 913–24, doi:<a href=\"https://doi.org/10.1111/j.1752-4571.2012.00284.x\">10.1111/j.1752-4571.2012.00284.x</a>.","chicago":"Pickup, Melinda, David Field, David Rowell, and Andrew Young. “Predicting Local Adaptation in Fragmented Plant Populations: Implications for Restoration Genetics.” <i>Evolutionary Applications</i>. Wiley-Blackwell, 2012. <a href=\"https://doi.org/10.1111/j.1752-4571.2012.00284.x\">https://doi.org/10.1111/j.1752-4571.2012.00284.x</a>.","ista":"Pickup M, Field D, Rowell D, Young A. 2012. Predicting local adaptation in fragmented plant populations: Implications for restoration genetics. Evolutionary Applications. 5(8), 913–924.","ieee":"M. Pickup, D. Field, D. Rowell, and A. Young, “Predicting local adaptation in fragmented plant populations: Implications for restoration genetics,” <i>Evolutionary Applications</i>, vol. 5, no. 8. Wiley-Blackwell, pp. 913–924, 2012.","short":"M. Pickup, D. Field, D. Rowell, A. Young, Evolutionary Applications 5 (2012) 913–924.","ama":"Pickup M, Field D, Rowell D, Young A. Predicting local adaptation in fragmented plant populations: Implications for restoration genetics. <i>Evolutionary Applications</i>. 2012;5(8):913-924. doi:<a href=\"https://doi.org/10.1111/j.1752-4571.2012.00284.x\">10.1111/j.1752-4571.2012.00284.x</a>"},"language":[{"iso":"eng"}],"pubrep_id":"942","oa":1,"file":[{"creator":"system","date_updated":"2020-07-14T12:46:35Z","file_size":396136,"date_created":"2018-12-12T10:10:33Z","file_id":"4821","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2018-942-v1+1_Pickup_et_al-2012-Evolutionary_Applications.pdf","checksum":"233007138606aca5a2f75f7ae1742f43","relation":"main_file"}],"department":[{"_id":"NiBa"}],"month":"12","publication_status":"published","file_date_updated":"2020-07-14T12:46:35Z","abstract":[{"text":"Understanding patterns and correlates of local adaptation in heterogeneous landscapes can provide important information in the selection of appropriate seed sources for restoration. We assessed the extent of local adaptation of fitness components in 12 population pairs of the perennial herb Rutidosis leptorrhynchoides (Asteraceae) and examined whether spatial scale (0.7-600 km), environmental distance, quantitative (QST) and neutral (FST) genetic differentiation, and size of the local and foreign populations could predict patterns of adaptive differentiation. Local adaptation varied among populations and fitness components. Including all population pairs, local adaptation was observed for seedling survival, but not for biomass, while foreign genotype advantage was observed for reproduction (number of inflorescences). Among population pairs, local adaptation increased with QST and local population size for biomass. QST was associated with environmental distance, suggesting ecological selection for phenotypic divergence. However, low FST and variation in population structure in small populations demonstrates the interaction of gene flow and drift in constraining local adaptation in R. leptorrhynchoides. Our study indicates that for species in heterogeneous landscapes, collecting seed from large populations from similar environments to candidate sites is likely to provide the most appropriate seed sources for restoration.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"intvolume":"         5","has_accepted_license":"1","date_created":"2018-12-11T11:46:48Z","volume":5,"title":"Predicting local adaptation in fragmented plant populations: Implications for restoration genetics","oa_version":"Published Version","author":[{"first_name":"Melinda","orcid":"0000-0001-6118-0541","last_name":"Pickup","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","full_name":"Pickup, Melinda"},{"first_name":"David","orcid":"0000-0002-4014-8478","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","full_name":"Field, David"},{"first_name":"David","full_name":"Rowell, David","last_name":"Rowell"},{"full_name":"Young, Andrew","last_name":"Young","first_name":"Andrew"}],"day":"01","date_published":"2012-12-01T00:00:00Z","acknowledgement":"We thank Graham Pickup, David Steer, Linda Broadhurst, Lan Li and Carole Elliott for technical assistance. The New\r\nSouth Wales Department of Environment and Climate Change, ACT Parks, Conservation and Lands and the\r\nDepartment of Sustainability and Environment in Victoria provided permits for seed and soil collection. We thank\r\nSpencer C. H. Barrett for comments that improved the quality of the manuscript.\r\n","status":"public","publication":"Evolutionary Applications","publist_id":"7322","year":"2012","quality_controlled":"1","ddc":["576"],"page":"913 - 924","type":"journal_article","date_updated":"2021-01-12T08:01:06Z","_id":"498","publisher":"Wiley-Blackwell","doi":"10.1111/j.1752-4571.2012.00284.x"},{"file_date_updated":"2020-07-14T12:46:36Z","publication_status":"published","intvolume":"       197","tmp":{"image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"has_accepted_license":"1","date_created":"2018-12-11T11:46:51Z","article_type":"original","volume":197,"title":"Cell migration: Fibroblasts find a new way to get ahead","oa_version":"Published Version","scopus_import":1,"day":"30","author":[{"orcid":"0000-0002-6620-9179","first_name":"Michael K","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Sixt, Michael K. “Cell Migration: Fibroblasts Find a New Way to Get Ahead.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2012. <a href=\"https://doi.org/10.1083/jcb.201204039\">https://doi.org/10.1083/jcb.201204039</a>.","ista":"Sixt MK. 2012. Cell migration: Fibroblasts find a new way to get ahead. Journal of Cell Biology. 197(3), 347–349.","apa":"Sixt, M. K. (2012). Cell migration: Fibroblasts find a new way to get ahead. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.201204039\">https://doi.org/10.1083/jcb.201204039</a>","mla":"Sixt, Michael K. “Cell Migration: Fibroblasts Find a New Way to Get Ahead.” <i>Journal of Cell Biology</i>, vol. 197, no. 3, Rockefeller University Press, 2012, pp. 347–49, doi:<a href=\"https://doi.org/10.1083/jcb.201204039\">10.1083/jcb.201204039</a>.","ama":"Sixt MK. Cell migration: Fibroblasts find a new way to get ahead. <i>Journal of Cell Biology</i>. 2012;197(3):347-349. doi:<a href=\"https://doi.org/10.1083/jcb.201204039\">10.1083/jcb.201204039</a>","ieee":"M. K. Sixt, “Cell migration: Fibroblasts find a new way to get ahead,” <i>Journal of Cell Biology</i>, vol. 197, no. 3. Rockefeller University Press, pp. 347–349, 2012.","short":"M.K. Sixt, Journal of Cell Biology 197 (2012) 347–349."},"issue":"3","language":[{"iso":"eng"}],"oa":1,"file":[{"file_name":"2012_CellBiology_Sixt.pdf","access_level":"open_access","content_type":"application/pdf","relation":"main_file","checksum":"45c02be33ebd99fc3077d60b9c90bdfa","file_size":986566,"date_created":"2019-02-12T09:03:09Z","date_updated":"2020-07-14T12:46:36Z","creator":"kschuh","file_id":"5957"}],"department":[{"_id":"MiSi"}],"month":"04","quality_controlled":"1","ddc":["570"],"page":"347 - 349","type":"journal_article","_id":"506","date_updated":"2021-01-12T08:01:11Z","publisher":"Rockefeller University Press","article_processing_charge":"No","doi":"10.1083/jcb.201204039","date_published":"2012-04-30T00:00:00Z","status":"public","publication":"Journal of Cell Biology","publist_id":"7314","year":"2012"},{"department":[{"_id":"KrCh"}],"file":[{"file_id":"5522","date_created":"2018-12-12T11:54:00Z","file_size":592098,"date_updated":"2020-07-14T12:46:38Z","creator":"system","relation":"main_file","checksum":"a03c08c1589dbb0c96183a8bcf3ab240","file_name":"IST-2012-002_IST-2012-0002.pdf","access_level":"open_access","content_type":"application/pdf"}],"year":"2012","related_material":{"record":[{"id":"2956","status":"public","relation":"later_version"}]},"month":"07","citation":{"mla":"Chatterjee, Krishnendu, and Yaron Velner. <i>Mean-Payoff Pushdown Games</i>. IST Austria, 2012, doi:<a href=\"https://doi.org/10.15479/AT:IST-2012-0002\">10.15479/AT:IST-2012-0002</a>.","apa":"Chatterjee, K., &#38; Velner, Y. (2012). <i>Mean-payoff pushdown games</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2012-0002\">https://doi.org/10.15479/AT:IST-2012-0002</a>","ista":"Chatterjee K, Velner Y. 2012. Mean-payoff pushdown games, IST Austria, 33p.","chicago":"Chatterjee, Krishnendu, and Yaron Velner. <i>Mean-Payoff Pushdown Games</i>. IST Austria, 2012. <a href=\"https://doi.org/10.15479/AT:IST-2012-0002\">https://doi.org/10.15479/AT:IST-2012-0002</a>.","short":"K. Chatterjee, Y. Velner, Mean-Payoff Pushdown Games, IST Austria, 2012.","ieee":"K. Chatterjee and Y. Velner, <i>Mean-payoff pushdown games</i>. IST Austria, 2012.","ama":"Chatterjee K, Velner Y. <i>Mean-Payoff Pushdown Games</i>. IST Austria; 2012. doi:<a href=\"https://doi.org/10.15479/AT:IST-2012-0002\">10.15479/AT:IST-2012-0002</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2012-07-02T00:00:00Z","oa":1,"language":[{"iso":"eng"}],"status":"public","pubrep_id":"10","_id":"5377","date_updated":"2023-02-23T11:05:50Z","date_created":"2018-12-12T11:38:59Z","type":"technical_report","day":"02","alternative_title":["IST Austria Technical Report"],"author":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Velner, Yaron","last_name":"Velner","first_name":"Yaron"}],"doi":"10.15479/AT:IST-2012-0002","publisher":"IST Austria","oa_version":"Published Version","title":"Mean-payoff pushdown games","file_date_updated":"2020-07-14T12:46:38Z","publication_status":"published","publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1","page":"33","ddc":["000","005"],"abstract":[{"text":"Two-player games on graphs are central in many problems in formal verification and program analysis such as synthesis and verification of open systems. In this work we consider solving recursive game graphs (or pushdown game graphs) that can model the control flow of sequential programs with recursion. While pushdown games have been studied before with qualitative objectives, such as reachability and ω-regular objectives, in this work we study for the first time such games with the most well-studied quantitative objective, namely, mean-payoff objectives. In pushdown games two types of strategies are relevant: (1) global strategies, that depend on the entire global history; and (2) modular strategies, that have only local memory and thus do not depend on the context of invocation, but only on the history of the current invocation of the module. Our main results are as follows: (1) One-player pushdown games with mean-payoff objectives under global strategies are decidable in polynomial time. (2) Two- player pushdown games with mean-payoff objectives under global strategies are undecidable. (3) One-player pushdown games with mean-payoff objectives under modular strategies are NP- hard. (4) Two-player pushdown games with mean-payoff objectives under modular strategies can be solved in NP (i.e., both one-player and two-player pushdown games with mean-payoff objectives under modular strategies are NP-complete). We also establish the optimal strategy complexity showing that global strategies for mean-payoff objectives require infinite memory even in one-player pushdown games; and memoryless modular strategies are sufficient in two- player pushdown games. Finally we also show that all the problems have the same complexity if the stack boundedness condition is added, where along with the mean-payoff objective the player must also ensure that the stack height is bounded.","lang":"eng"}]},{"author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"last_name":"Chaubal","full_name":"Chaubal, Siddhesh","first_name":"Siddhesh"},{"first_name":"Pritish","full_name":"Kamath, Pritish","last_name":"Kamath"}],"doi":"10.15479/AT:IST-2012-0001","day":"04","alternative_title":["IST Austria Technical Report"],"title":"Faster algorithms for alternating refinement relations","oa_version":"Published Version","publisher":"IST Austria","date_updated":"2023-02-23T12:21:38Z","_id":"5378","type":"technical_report","date_created":"2018-12-12T11:38:59Z","page":"21","has_accepted_license":"1","abstract":[{"lang":"eng","text":"One central issue in the formal design and analysis of reactive systems is the notion of refinement that asks whether all behaviors of the implementation is allowed by the specification. The local interpretation of behavior leads to the notion of simulation. Alternating transition systems (ATSs) provide a general model for composite reactive systems, and the simulation relation for ATSs is known as alternating simulation. The simulation relation for fair transition systems is called fair simulation. In this work our main contributions are as follows: (1) We present an improved algorithm for fair simulation with Büchi fairness constraints; our algorithm requires O(n3 · m) time as compared to the previous known O(n6)-time algorithm, where n is the number of states and m is the number of transitions. (2) We present a game based algorithm for alternating simulation that requires O(m2)-time as compared to the previous known O((n · m)2)-time algorithm, where n is the number of states and m is the size of transition relation. (3) We present an iterative algorithm for alternating simulation that matches the time complexity of the game based algorithm, but is more space efficient than the game based algorithm."}],"ddc":["000","005"],"publication_identifier":{"issn":["2664-1690"]},"publication_status":"published","file_date_updated":"2020-07-14T12:46:39Z","year":"2012","month":"07","related_material":{"record":[{"id":"497","status":"public","relation":"later_version"}]},"department":[{"_id":"KrCh"}],"file":[{"file_size":394256,"date_created":"2018-12-12T11:53:28Z","creator":"system","date_updated":"2020-07-14T12:46:39Z","file_id":"5489","file_name":"IST-2012-0001_IST-2012-0001.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"ec8d1857cc7095d3de5107a0162ced37"}],"oa":1,"status":"public","pubrep_id":"14","language":[{"iso":"eng"}],"citation":{"chicago":"Chatterjee, Krishnendu, Siddhesh Chaubal, and Pritish Kamath. <i>Faster Algorithms for Alternating Refinement Relations</i>. IST Austria, 2012. <a href=\"https://doi.org/10.15479/AT:IST-2012-0001\">https://doi.org/10.15479/AT:IST-2012-0001</a>.","ista":"Chatterjee K, Chaubal S, Kamath P. 2012. Faster algorithms for alternating refinement relations, IST Austria, 21p.","apa":"Chatterjee, K., Chaubal, S., &#38; Kamath, P. (2012). <i>Faster algorithms for alternating refinement relations</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2012-0001\">https://doi.org/10.15479/AT:IST-2012-0001</a>","mla":"Chatterjee, Krishnendu, et al. <i>Faster Algorithms for Alternating Refinement Relations</i>. IST Austria, 2012, doi:<a href=\"https://doi.org/10.15479/AT:IST-2012-0001\">10.15479/AT:IST-2012-0001</a>.","ama":"Chatterjee K, Chaubal S, Kamath P. <i>Faster Algorithms for Alternating Refinement Relations</i>. IST Austria; 2012. doi:<a href=\"https://doi.org/10.15479/AT:IST-2012-0001\">10.15479/AT:IST-2012-0001</a>","ieee":"K. Chatterjee, S. Chaubal, and P. Kamath, <i>Faster algorithms for alternating refinement relations</i>. IST Austria, 2012.","short":"K. Chatterjee, S. Chaubal, P. Kamath, Faster Algorithms for Alternating Refinement Relations, IST Austria, 2012."},"date_published":"2012-07-04T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"publication_status":"published","publication_identifier":{"issn":["2664-1690"]},"file_date_updated":"2020-07-14T12:46:44Z","page":"13","has_accepted_license":"1","abstract":[{"text":"We consider the problem of inference in agraphical model with binary variables. While in theory it is arguably preferable to compute marginal probabilities, in practice researchers often use MAP inference due to the availability of efficient discrete optimization algorithms. We bridge the gap between the two approaches by introducing the Discrete  Marginals technique in which approximate marginals are obtained by minimizing an objective function with unary and pair-wise terms over a discretized domain. This allows the use of techniques originally devel-oped for MAP-MRF inference and learning. We explore two ways to set up the objective function - by discretizing the Bethe free energy and by learning it  from training data. Experimental results show that for certain types of graphs a learned function can out-perform the  Bethe approximation. We also establish a link between the Bethe free energy and submodular functions.","lang":"eng"}],"ddc":["000"],"date_updated":"2023-02-23T11:13:22Z","_id":"5396","type":"technical_report","date_created":"2018-12-12T11:39:06Z","doi":"10.15479/AT:IST-2012-0003","author":[{"first_name":"Filip","last_name":"Korc","full_name":"Korc, Filip","id":"476A2FD6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir"},{"orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph"}],"alternative_title":["IST Austria Technical Report"],"day":"23","title":"Approximating marginals using discrete energy minimization","oa_version":"Published Version","publisher":"IST Austria","citation":{"apa":"Korc, F., Kolmogorov, V., &#38; Lampert, C. (2012). <i>Approximating marginals using discrete energy minimization</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2012-0003\">https://doi.org/10.15479/AT:IST-2012-0003</a>","mla":"Korc, Filip, et al. <i>Approximating Marginals Using Discrete Energy Minimization</i>. IST Austria, 2012, doi:<a href=\"https://doi.org/10.15479/AT:IST-2012-0003\">10.15479/AT:IST-2012-0003</a>.","chicago":"Korc, Filip, Vladimir Kolmogorov, and Christoph Lampert. <i>Approximating Marginals Using Discrete Energy Minimization</i>. IST Austria, 2012. <a href=\"https://doi.org/10.15479/AT:IST-2012-0003\">https://doi.org/10.15479/AT:IST-2012-0003</a>.","ista":"Korc F, Kolmogorov V, Lampert C. 2012. Approximating marginals using discrete energy minimization, IST Austria, 13p.","ieee":"F. Korc, V. Kolmogorov, and C. Lampert, <i>Approximating marginals using discrete energy minimization</i>. IST Austria, 2012.","short":"F. Korc, V. Kolmogorov, C. Lampert, Approximating Marginals Using Discrete Energy Minimization, IST Austria, 2012.","ama":"Korc F, Kolmogorov V, Lampert C. <i>Approximating Marginals Using Discrete Energy Minimization</i>. IST Austria; 2012. doi:<a href=\"https://doi.org/10.15479/AT:IST-2012-0003\">10.15479/AT:IST-2012-0003</a>"},"date_published":"2012-07-23T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}],"status":"public","pubrep_id":"36","department":[{"_id":"VlKo"},{"_id":"ChLa"}],"file":[{"file_id":"5490","date_updated":"2020-07-14T12:46:44Z","creator":"system","date_created":"2018-12-12T11:53:29Z","file_size":618744,"checksum":"7e0ba85ad123b13223aaf6cdde2d288c","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"IST-2012-0003_IST-2012-0003.pdf"}],"year":"2012","month":"07","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"3124"}]}},{"file_date_updated":"2020-07-14T12:46:44Z","publication_status":"published","ddc":["020"],"abstract":[{"text":"This document is created as a part of the project “Repository for Research Data on IST Austria”. It summarises the actual state of research data at IST Austria, based on survey results. It supports the choice of appropriate software, which would best fit the requirements of their users, the researchers.","lang":"eng"}],"has_accepted_license":"1","date_created":"2018-12-12T11:39:06Z","type":"report","_id":"5398","date_updated":"2020-07-14T23:04:49Z","oa_version":"Published Version","title":"Actual state of research data @ ISTAustria","publisher":"IST Austria","day":"12","author":[{"first_name":"Jana","last_name":"Porsche","id":"3252EDC2-F248-11E8-B48F-1D18A9856A87","full_name":"Porsche, Jana"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2012-11-12T00:00:00Z","citation":{"short":"J. Porsche, Actual State of Research Data @ ISTAustria, IST Austria, 2012.","ieee":"J. Porsche, <i>Actual state of research data @ ISTAustria</i>. IST Austria, 2012.","ama":"Porsche J. <i>Actual State of Research Data @ ISTAustria</i>. IST Austria; 2012.","mla":"Porsche, Jana. <i>Actual State of Research Data @ ISTAustria</i>. IST Austria, 2012.","apa":"Porsche, J. (2012). <i>Actual state of research data @ ISTAustria</i>. IST Austria.","chicago":"Porsche, Jana. <i>Actual State of Research Data @ ISTAustria</i>. IST Austria, 2012.","ista":"Porsche J. 2012. Actual state of research data @ ISTAustria, IST Austria,p."},"language":[{"iso":"eng"}],"pubrep_id":"103","status":"public","oa":1,"file":[{"creator":"system","date_updated":"2020-07-14T12:46:44Z","date_created":"2018-12-12T11:53:11Z","file_size":238544,"file_id":"5472","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2012-103-v1+1_Actual_state_of_research_data_@_IST_Austria.pdf","checksum":"e0a7c041eea1ca4b70ab6f9ec5177f4e","relation":"main_file"}],"department":[{"_id":"E-Lib"}],"month":"11","year":"2012"},{"date_created":"2018-12-18T13:01:46Z","volume":7561,"oa_version":"None","title":"Improved Single Pass Algorithms for Resolution Proof Reduction","author":[{"first_name":"Ashutosh","last_name":"Gupta","full_name":"Gupta, Ashutosh"}],"file_date_updated":"2020-07-14T12:47:10Z","publication_status":"published","publication_identifier":{"isbn":["9783642333859","9783642333866"],"issn":["0302-9743"],"eissn":["1611-3349"]},"intvolume":"      7561","has_accepted_license":"1","file":[{"file_id":"5746","date_created":"2018-12-18T13:07:35Z","file_size":465502,"date_updated":"2020-07-14T12:47:10Z","creator":"dernst","relation":"main_file","checksum":"68415837a315de3cc4d120f6019d752c","file_name":"2012_ATVA_Gupta.pdf","access_level":"open_access","content_type":"application/pdf"}],"department":[{"_id":"ToHe"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","place":"Berlin, Heidelberg","citation":{"ieee":"A. Gupta, “Improved Single Pass Algorithms for Resolution Proof Reduction,” in <i>Automated Technology for Verification and Analysis</i>, vol. 7561, Berlin, Heidelberg: Springer Berlin Heidelberg, 2012, pp. 107–121.","short":"A. Gupta, in:, Automated Technology for Verification and Analysis, Springer Berlin Heidelberg, Berlin, Heidelberg, 2012, pp. 107–121.","ama":"Gupta A. Improved Single Pass Algorithms for Resolution Proof Reduction. In: <i>Automated Technology for Verification and Analysis</i>. Vol 7561. LNCS. Berlin, Heidelberg: Springer Berlin Heidelberg; 2012:107-121. doi:<a href=\"https://doi.org/10.1007/978-3-642-33386-6_10\">10.1007/978-3-642-33386-6_10</a>","apa":"Gupta, A. (2012). Improved Single Pass Algorithms for Resolution Proof Reduction. In <i>Automated Technology for Verification and Analysis</i> (Vol. 7561, pp. 107–121). Berlin, Heidelberg: Springer Berlin Heidelberg. <a href=\"https://doi.org/10.1007/978-3-642-33386-6_10\">https://doi.org/10.1007/978-3-642-33386-6_10</a>","mla":"Gupta, Ashutosh. “Improved Single Pass Algorithms for Resolution Proof Reduction.” <i>Automated Technology for Verification and Analysis</i>, vol. 7561, Springer Berlin Heidelberg, 2012, pp. 107–21, doi:<a href=\"https://doi.org/10.1007/978-3-642-33386-6_10\">10.1007/978-3-642-33386-6_10</a>.","ista":"Gupta A. 2012.Improved Single Pass Algorithms for Resolution Proof Reduction. In: Automated Technology for Verification and Analysis. vol. 7561, 107–121.","chicago":"Gupta, Ashutosh. “Improved Single Pass Algorithms for Resolution Proof Reduction.” In <i>Automated Technology for Verification and Analysis</i>, 7561:107–21. LNCS. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012. <a href=\"https://doi.org/10.1007/978-3-642-33386-6_10\">https://doi.org/10.1007/978-3-642-33386-6_10</a>."},"language":[{"iso":"eng"}],"pubrep_id":"180","oa":1,"series_title":"LNCS","type":"book_chapter","_id":"5745","date_updated":"2023-09-05T14:15:29Z","publisher":"Springer Berlin Heidelberg","article_processing_charge":"No","doi":"10.1007/978-3-642-33386-6_10","quality_controlled":"1","ddc":["005"],"page":"107-121","year":"2012","date_published":"2012-01-01T00:00:00Z","conference":{"location":"Thiruvananthapuram, Kerala, India","end_date":"2012-10-06","start_date":"2012-10-03","name":"ATVA 2012"},"ec_funded":1,"status":"public","publication":"Automated Technology for Verification and Analysis","project":[{"name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"}]},{"page":"63-78","main_file_link":[{"url":"http://mi.mathnet.ru/eng/jmag525","open_access":"1"}],"quality_controlled":"1","article_processing_charge":"No","publisher":"B. Verkin Institute for Low Temperature Physics and Engineering","_id":"6588","date_updated":"2023-10-16T09:41:31Z","type":"journal_article","publication":"Journal of Mathematical Physics, Analysis, Geometry","status":"public","acknowledgement":"This work is supported by the Austrian Science Fund (FWF), Project P22025-N18.\r\n","date_published":"2012-01-01T00:00:00Z","year":"2012","isi":1,"external_id":{"isi":["000301173600004"]},"abstract":[{"text":"First we note that the best polynomial approximation to vertical bar x vertical bar on the set, which consists of an interval on the positive half-axis and a point on the negative half-axis, can be given by means of the classical Chebyshev polynomials. Then we explore the cases when a solution of the related problem on two intervals can be given in elementary functions.","lang":"eng"}],"intvolume":"         8","publication_identifier":{"issn":["1812-9471"]},"publication_status":"published","scopus_import":"1","day":"01","author":[{"last_name":"Pausinger","id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","full_name":"Pausinger, Florian","first_name":"Florian","orcid":"0000-0002-8379-3768"}],"oa_version":"Published Version","title":"Elementary solutions of the Bernstein problem on two intervals","volume":8,"date_created":"2019-06-27T08:16:56Z","article_type":"original","oa":1,"language":[{"iso":"eng"}],"citation":{"ama":"Pausinger F. Elementary solutions of the Bernstein problem on two intervals. <i>Journal of Mathematical Physics, Analysis, Geometry</i>. 2012;8(1):63-78.","ieee":"F. Pausinger, “Elementary solutions of the Bernstein problem on two intervals,” <i>Journal of Mathematical Physics, Analysis, Geometry</i>, vol. 8, no. 1. B. Verkin Institute for Low Temperature Physics and Engineering, pp. 63–78, 2012.","short":"F. Pausinger, Journal of Mathematical Physics, Analysis, Geometry 8 (2012) 63–78.","chicago":"Pausinger, Florian. “Elementary Solutions of the Bernstein Problem on Two Intervals.” <i>Journal of Mathematical Physics, Analysis, Geometry</i>. B. Verkin Institute for Low Temperature Physics and Engineering, 2012.","ista":"Pausinger F. 2012. Elementary solutions of the Bernstein problem on two intervals. Journal of Mathematical Physics, Analysis, Geometry. 8(1), 63–78.","apa":"Pausinger, F. (2012). Elementary solutions of the Bernstein problem on two intervals. <i>Journal of Mathematical Physics, Analysis, Geometry</i>. B. Verkin Institute for Low Temperature Physics and Engineering.","mla":"Pausinger, Florian. “Elementary Solutions of the Bernstein Problem on Two Intervals.” <i>Journal of Mathematical Physics, Analysis, Geometry</i>, vol. 8, no. 1, B. Verkin Institute for Low Temperature Physics and Engineering, 2012, pp. 63–78."},"issue":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","department":[{"_id":"HeEd"}]},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.0g0fs"}],"ddc":["570"],"tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","short":"CC0 (1.0)"},"license":"https://creativecommons.org/publicdomain/zero/1.0/","abstract":[{"lang":"eng","text":"Little is known about the stability of trophic relationships in complex natural communities over evolutionary timescales. Here, we use sequence data from 18 nuclear loci to reconstruct and compare the intraspecific histories of major Pleistocene refugial populations in the Middle East, the Balkans and Iberia in a guild of four Chalcid parasitoids (Cecidostiba fungosa, C. semifascia, Hobbya stenonota and Mesopolobus amaenus) all attacking Cynipid oak galls. We develop a likelihood method to numerically estimate models of divergence between three populations from multilocus data. We investigate the power of this framework on simulated data, and - using triplet alignments of intronic loci - quantify the support for all possible divergence relationships between refugial populations in the four parasitoids. Although an East to West order of population divergence has highest support in all but one species, we cannot rule out alternative population tree topologies. Comparing the estimated times of population splits between species, we find that one species, M. amaenus, has a significantly older history than the rest of the guild and must have arrived in central Europe at least one glacial cycle prior to other guild members. This suggests that although all four species may share a common origin in the East, they expanded westwards into Europe at different times."}],"date_created":"2023-05-23T17:01:02Z","type":"research_data_reference","_id":"13075","date_updated":"2025-05-28T11:56:58Z","title":"Data from: A likelihood-based comparison of population histories in a parasitoid guild","publisher":"Dryad","oa_version":"Published Version","day":"08","article_processing_charge":"No","doi":"10.5061/DRYAD.0G0FS","author":[{"first_name":"Konrad","last_name":"Lohse","full_name":"Lohse, Konrad"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240","first_name":"Nicholas H"},{"full_name":"Stone, Graham","last_name":"Stone","first_name":"Graham"},{"full_name":"Melika, George","last_name":"Melika","first_name":"George"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2012-06-08T00:00:00Z","citation":{"ama":"Lohse K, Barton NH, Stone G, Melika G. Data from: A likelihood-based comparison of population histories in a parasitoid guild. 2012. doi:<a href=\"https://doi.org/10.5061/DRYAD.0G0FS\">10.5061/DRYAD.0G0FS</a>","ieee":"K. Lohse, N. H. Barton, G. Stone, and G. Melika, “Data from: A likelihood-based comparison of population histories in a parasitoid guild.” Dryad, 2012.","short":"K. Lohse, N.H. Barton, G. Stone, G. Melika, (2012).","chicago":"Lohse, Konrad, Nicholas H Barton, Graham Stone, and George Melika. “Data from: A Likelihood-Based Comparison of Population Histories in a Parasitoid Guild.” Dryad, 2012. <a href=\"https://doi.org/10.5061/DRYAD.0G0FS\">https://doi.org/10.5061/DRYAD.0G0FS</a>.","ista":"Lohse K, Barton NH, Stone G, Melika G. 2012. Data from: A likelihood-based comparison of population histories in a parasitoid guild, Dryad, <a href=\"https://doi.org/10.5061/DRYAD.0G0FS\">10.5061/DRYAD.0G0FS</a>.","apa":"Lohse, K., Barton, N. H., Stone, G., &#38; Melika, G. (2012). Data from: A likelihood-based comparison of population histories in a parasitoid guild. Dryad. <a href=\"https://doi.org/10.5061/DRYAD.0G0FS\">https://doi.org/10.5061/DRYAD.0G0FS</a>","mla":"Lohse, Konrad, et al. <i>Data from: A Likelihood-Based Comparison of Population Histories in a Parasitoid Guild</i>. Dryad, 2012, doi:<a href=\"https://doi.org/10.5061/DRYAD.0G0FS\">10.5061/DRYAD.0G0FS</a>."},"status":"public","oa":1,"department":[{"_id":"NiBa"}],"related_material":{"record":[{"id":"2968","status":"public","relation":"used_in_publication"}]},"month":"06","year":"2012"}]