[{"year":"2018","acknowledgement":" FöFoLe project 947 (F.G.), the Friedrich-Baur-Stiftung project 41/16 (F.G.)","publication_status":"published","publisher":"Bio-Protocol","department":[{"_id":"MiSi"}],"author":[{"last_name":"Fan","first_name":"Shuxia","full_name":"Fan, Shuxia"},{"full_name":"Lorenz, Michael","first_name":"Michael","last_name":"Lorenz"},{"full_name":"Massberg, Steffen","first_name":"Steffen","last_name":"Massberg"},{"full_name":"Gärtner, Florian R","first_name":"Florian R","last_name":"Gärtner","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6120-3723"}],"date_created":"2019-04-29T09:40:33Z","date_updated":"2021-01-12T08:07:12Z","volume":8,"article_number":"e3018","file_date_updated":"2020-07-14T12:47:28Z","ec_funded":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","grant_number":"747687","_id":"260AA4E2-B435-11E9-9278-68D0E5697425"}],"doi":"10.21769/bioprotoc.3018","language":[{"iso":"eng"}],"month":"09","publication_identifier":{"issn":["2331-8325"]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"6354","status":"public","ddc":["570"],"title":"Platelet migration and bacterial trapping assay under flow","intvolume":" 8","file":[{"file_size":2928337,"content_type":"application/pdf","creator":"dernst","file_name":"2018_BioProtocol_Fan.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:28Z","date_created":"2019-04-30T08:04:33Z","checksum":"d4588377e789da7f360b553ae02c5119","relation":"main_file","file_id":"6360"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Blood platelets are critical for hemostasis and thrombosis, but also play diverse roles during immune responses. We have recently reported that platelets migrate at sites of infection in vitro and in vivo. Importantly, platelets use their ability to migrate to collect and bundle fibrin (ogen)-bound bacteria accomplishing efficient intravascular bacterial trapping. Here, we describe a method that allows analyzing platelet migration in vitro, focusing on their ability to collect bacteria and trap bacteria under flow.","lang":"eng"}],"issue":"18","publication":"Bio-Protocol","citation":{"short":"S. Fan, M. Lorenz, S. Massberg, F.R. Gärtner, Bio-Protocol 8 (2018).","mla":"Fan, Shuxia, et al. “Platelet Migration and Bacterial Trapping Assay under Flow.” Bio-Protocol, vol. 8, no. 18, e3018, Bio-Protocol, 2018, doi:10.21769/bioprotoc.3018.","chicago":"Fan, Shuxia, Michael Lorenz, Steffen Massberg, and Florian R Gärtner. “Platelet Migration and Bacterial Trapping Assay under Flow.” Bio-Protocol. Bio-Protocol, 2018. https://doi.org/10.21769/bioprotoc.3018.","ama":"Fan S, Lorenz M, Massberg S, Gärtner FR. Platelet migration and bacterial trapping assay under flow. Bio-Protocol. 2018;8(18). doi:10.21769/bioprotoc.3018","apa":"Fan, S., Lorenz, M., Massberg, S., & Gärtner, F. R. (2018). Platelet migration and bacterial trapping assay under flow. Bio-Protocol. Bio-Protocol. https://doi.org/10.21769/bioprotoc.3018","ieee":"S. Fan, M. Lorenz, S. Massberg, and F. R. Gärtner, “Platelet migration and bacterial trapping assay under flow,” Bio-Protocol, vol. 8, no. 18. Bio-Protocol, 2018.","ista":"Fan S, Lorenz M, Massberg S, Gärtner FR. 2018. Platelet migration and bacterial trapping assay under flow. Bio-Protocol. 8(18), e3018."},"date_published":"2018-09-20T00:00:00Z","keyword":["Platelets","Cell migration","Bacteria","Shear flow","Fibrinogen","E. coli"],"day":"20","has_accepted_license":"1"},{"keyword":["Open Access","Publication Analysis"],"month":"09","day":"24","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"mla":"Petritsch, Barbara. Open Access at IST Austria 2009-2017. IST Austria, 2018, doi:10.5281/zenodo.1410279.","short":"B. Petritsch, Open Access at IST Austria 2009-2017, IST Austria, 2018.","chicago":"Petritsch, Barbara. Open Access at IST Austria 2009-2017. IST Austria, 2018. https://doi.org/10.5281/zenodo.1410279.","ama":"Petritsch B. Open Access at IST Austria 2009-2017. IST Austria; 2018. doi:10.5281/zenodo.1410279","ista":"Petritsch B. 2018. Open Access at IST Austria 2009-2017, IST Austria,p.","apa":"Petritsch, B. (2018). Open Access at IST Austria 2009-2017. Presented at the Open-Access-Tage, Graz, Austria: IST Austria. https://doi.org/10.5281/zenodo.1410279","ieee":"B. Petritsch, Open Access at IST Austria 2009-2017. IST Austria, 2018."},"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"Open-Access-Tage","location":"Graz, Austria","start_date":"2018-09-24","end_date":"2018-09-26"},"date_published":"2018-09-24T00:00:00Z","doi":"10.5281/zenodo.1410279","type":"conference_poster","file_date_updated":"2020-07-14T12:47:30Z","ddc":["020"],"title":"Open Access at IST Austria 2009-2017","publication_status":"published","status":"public","department":[{"_id":"E-Lib"}],"publisher":"IST Austria","_id":"6459","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2018","date_created":"2019-05-16T07:27:14Z","date_updated":"2020-07-14T23:06:21Z","oa_version":"Published Version","file":[{"file_size":1967778,"content_type":"application/pdf","creator":"dernst","file_name":"Poster_Beitrag_125_Petritsch.pdf","access_level":"open_access","date_created":"2019-05-16T07:26:25Z","date_updated":"2020-07-14T12:47:30Z","checksum":"9063ab4d10ea93353c3a03bbf53fbcf1","relation":"main_file","file_id":"6460"}],"author":[{"first_name":"Barbara","last_name":"Petritsch","id":"406048EC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2724-4614","full_name":"Petritsch, Barbara"}]},{"month":"06","external_id":{"arxiv":["1605.08767"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1605.08767"}],"oa":1,"project":[{"name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","doi":"10.1007/s00440-017-0787-8","language":[{"iso":"eng"}],"article_number":"543-616","publist_id":"7017","ec_funded":1,"year":"2018","department":[{"_id":"LaEr"}],"publisher":"Springer","publication_status":"published","author":[{"last_name":"Lee","first_name":"Jii","full_name":"Lee, Jii"},{"full_name":"Schnelli, Kevin","first_name":"Kevin","last_name":"Schnelli","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0954-3231"}],"volume":171,"date_created":"2018-12-11T11:47:56Z","date_updated":"2021-01-12T08:09:33Z","scopus_import":1,"day":"14","citation":{"chicago":"Lee, Jii, and Kevin Schnelli. “Local Law and Tracy–Widom Limit for Sparse Random Matrices.” Probability Theory and Related Fields. Springer, 2018. https://doi.org/10.1007/s00440-017-0787-8.","short":"J. Lee, K. Schnelli, Probability Theory and Related Fields 171 (2018).","mla":"Lee, Jii, and Kevin Schnelli. “Local Law and Tracy–Widom Limit for Sparse Random Matrices.” Probability Theory and Related Fields, vol. 171, no. 1–2, 543–616, Springer, 2018, doi:10.1007/s00440-017-0787-8.","ieee":"J. Lee and K. Schnelli, “Local law and Tracy–Widom limit for sparse random matrices,” Probability Theory and Related Fields, vol. 171, no. 1–2. Springer, 2018.","apa":"Lee, J., & Schnelli, K. (2018). Local law and Tracy–Widom limit for sparse random matrices. Probability Theory and Related Fields. Springer. https://doi.org/10.1007/s00440-017-0787-8","ista":"Lee J, Schnelli K. 2018. Local law and Tracy–Widom limit for sparse random matrices. Probability Theory and Related Fields. 171(1–2), 543–616.","ama":"Lee J, Schnelli K. Local law and Tracy–Widom limit for sparse random matrices. Probability Theory and Related Fields. 2018;171(1-2). doi:10.1007/s00440-017-0787-8"},"publication":"Probability Theory and Related Fields","date_published":"2018-06-14T00:00:00Z","type":"journal_article","issue":"1-2","abstract":[{"lang":"eng","text":"We consider spectral properties and the edge universality of sparse random matrices, the class of random matrices that includes the adjacency matrices of the Erdős–Rényi graph model G(N, p). We prove a local law for the eigenvalue density up to the spectral edges. Under a suitable condition on the sparsity, we also prove that the rescaled extremal eigenvalues exhibit GOE Tracy–Widom fluctuations if a deterministic shift of the spectral edge due to the sparsity is included. For the adjacency matrix of the Erdős–Rényi graph this establishes the Tracy–Widom fluctuations of the second largest eigenvalue when p is much larger than N−2/3 with a deterministic shift of order (Np)−1."}],"_id":"690","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 171","title":"Local law and Tracy–Widom limit for sparse random matrices","status":"public","oa_version":"Preprint"},{"scopus_import":1,"day":"01","page":"1668-1682","publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","citation":{"mla":"Shekhovtsov, Alexander, et al. “Maximum Persistency via Iterative Relaxed Inference with Graphical Models.” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 40, no. 7, IEEE, 2018, pp. 1668–82, doi:10.1109/TPAMI.2017.2730884.","short":"A. Shekhovtsov, P. Swoboda, B. Savchynskyy, IEEE Transactions on Pattern Analysis and Machine Intelligence 40 (2018) 1668–1682.","chicago":"Shekhovtsov, Alexander, Paul Swoboda, and Bogdan Savchynskyy. “Maximum Persistency via Iterative Relaxed Inference with Graphical Models.” IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE, 2018. https://doi.org/10.1109/TPAMI.2017.2730884.","ama":"Shekhovtsov A, Swoboda P, Savchynskyy B. Maximum persistency via iterative relaxed inference with graphical models. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2018;40(7):1668-1682. doi:10.1109/TPAMI.2017.2730884","ista":"Shekhovtsov A, Swoboda P, Savchynskyy B. 2018. Maximum persistency via iterative relaxed inference with graphical models. IEEE Transactions on Pattern Analysis and Machine Intelligence. 40(7), 1668–1682.","apa":"Shekhovtsov, A., Swoboda, P., & Savchynskyy, B. (2018). Maximum persistency via iterative relaxed inference with graphical models. IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2017.2730884","ieee":"A. Shekhovtsov, P. Swoboda, and B. Savchynskyy, “Maximum persistency via iterative relaxed inference with graphical models,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 40, no. 7. IEEE, pp. 1668–1682, 2018."},"date_published":"2018-07-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"We consider the NP-hard problem of MAP-inference for undirected discrete graphical models. We propose a polynomial time and practically efficient algorithm for finding a part of its optimal solution. Specifically, our algorithm marks some labels of the considered graphical model either as (i) optimal, meaning that they belong to all optimal solutions of the inference problem; (ii) non-optimal if they provably do not belong to any solution. With access to an exact solver of a linear programming relaxation to the MAP-inference problem, our algorithm marks the maximal possible (in a specified sense) number of labels. We also present a version of the algorithm, which has access to a suboptimal dual solver only and still can ensure the (non-)optimality for the marked labels, although the overall number of the marked labels may decrease. We propose an efficient implementation, which runs in time comparable to a single run of a suboptimal dual solver. Our method is well-scalable and shows state-of-the-art results on computational benchmarks from machine learning and computer vision."}],"issue":"7","status":"public","title":"Maximum persistency via iterative relaxed inference with graphical models","intvolume":" 40","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"703","oa_version":"Preprint","month":"07","publication_identifier":{"issn":["01628828"]},"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1508.07902"}],"external_id":{"arxiv":["1508.07902"]},"language":[{"iso":"eng"}],"doi":"10.1109/TPAMI.2017.2730884","publist_id":"6992","publication_status":"published","publisher":"IEEE","department":[{"_id":"VlKo"}],"year":"2018","date_created":"2018-12-11T11:48:01Z","date_updated":"2021-01-12T08:11:32Z","volume":40,"author":[{"full_name":"Shekhovtsov, Alexander","last_name":"Shekhovtsov","first_name":"Alexander"},{"last_name":"Swoboda","first_name":"Paul","id":"446560C6-F248-11E8-B48F-1D18A9856A87","full_name":"Swoboda, Paul"},{"first_name":"Bogdan","last_name":"Savchynskyy","full_name":"Savchynskyy, Bogdan"}]},{"article_processing_charge":"No","has_accepted_license":"1","day":"26","scopus_import":1,"date_published":"2018-03-26T00:00:00Z","page":"145-156","citation":{"ama":"Grubic D, Tam L, Alistarh D-A, Zhang C. Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study. In: Proceedings of the 21st International Conference on Extending Database Technology. OpenProceedings; 2018:145-156. doi:10.5441/002/EDBT.2018.14","apa":"Grubic, D., Tam, L., Alistarh, D.-A., & Zhang, C. (2018). Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study. In Proceedings of the 21st International Conference on Extending Database Technology (pp. 145–156). Vienna, Austria: OpenProceedings. https://doi.org/10.5441/002/EDBT.2018.14","ieee":"D. Grubic, L. Tam, D.-A. Alistarh, and C. Zhang, “Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study,” in Proceedings of the 21st International Conference on Extending Database Technology, Vienna, Austria, 2018, pp. 145–156.","ista":"Grubic D, Tam L, Alistarh D-A, Zhang C. 2018. Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study. Proceedings of the 21st International Conference on Extending Database Technology. EDBT: Conference on Extending Database Technology, 145–156.","short":"D. Grubic, L. Tam, D.-A. Alistarh, C. Zhang, in:, Proceedings of the 21st International Conference on Extending Database Technology, OpenProceedings, 2018, pp. 145–156.","mla":"Grubic, Demjan, et al. “Synchronous Multi-GPU Training for Deep Learning with Low-Precision Communications: An Empirical Study.” Proceedings of the 21st International Conference on Extending Database Technology, OpenProceedings, 2018, pp. 145–56, doi:10.5441/002/EDBT.2018.14.","chicago":"Grubic, Demjan, Leo Tam, Dan-Adrian Alistarh, and Ce Zhang. “Synchronous Multi-GPU Training for Deep Learning with Low-Precision Communications: An Empirical Study.” In Proceedings of the 21st International Conference on Extending Database Technology, 145–56. OpenProceedings, 2018. https://doi.org/10.5441/002/EDBT.2018.14."},"publication":"Proceedings of the 21st International Conference on Extending Database Technology","abstract":[{"lang":"eng","text":"Training deep learning models has received tremendous research interest recently. In particular, there has been intensive research on reducing the communication cost of training when using multiple computational devices, through reducing the precision of the underlying data representation. Naturally, such methods induce system trade-offs—lowering communication precision could de-crease communication overheads and improve scalability; but, on the other hand, it can also reduce the accuracy of training. In this paper, we study this trade-off space, and ask:Can low-precision communication consistently improve the end-to-end performance of training modern neural networks, with no accuracy loss?From the performance point of view, the answer to this question may appear deceptively easy: compressing communication through low precision should help when the ratio between communication and computation is high. However, this answer is less straightforward when we try to generalize this principle across various neural network architectures (e.g., AlexNet vs. ResNet),number of GPUs (e.g., 2 vs. 8 GPUs), machine configurations(e.g., EC2 instances vs. NVIDIA DGX-1), communication primitives (e.g., MPI vs. NCCL), and even different GPU architectures(e.g., Kepler vs. Pascal). Currently, it is not clear how a realistic realization of all these factors maps to the speed up provided by low-precision communication. In this paper, we conduct an empirical study to answer this question and report the insights."}],"type":"conference","file":[{"file_name":"2018_OpenProceedings_Grubic.pdf","access_level":"open_access","creator":"dernst","file_size":1603204,"content_type":"application/pdf","file_id":"7118","relation":"main_file","date_updated":"2020-07-14T12:47:49Z","date_created":"2019-11-26T14:23:04Z","checksum":"ec979b56abc71016d6e6adfdadbb4afe"}],"oa_version":"Published Version","title":"Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study","ddc":["000"],"status":"public","_id":"7116","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2367-2005"],"isbn":["9783893180783"]},"month":"03","language":[{"iso":"eng"}],"doi":"10.5441/002/EDBT.2018.14","conference":{"name":"EDBT: Conference on Extending Database Technology","location":"Vienna, Austria","start_date":"2018-03-26","end_date":"2018-03-29"},"quality_controlled":"1","tmp":{"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)","image":"/images/cc_by_nc_nd.png"},"oa":1,"file_date_updated":"2020-07-14T12:47:49Z","date_updated":"2023-02-23T12:59:17Z","date_created":"2019-11-26T14:19:11Z","author":[{"full_name":"Grubic, Demjan","last_name":"Grubic","first_name":"Demjan"},{"last_name":"Tam","first_name":"Leo","full_name":"Tam, Leo"},{"last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian"},{"last_name":"Zhang","first_name":"Ce","full_name":"Zhang, Ce"}],"department":[{"_id":"DaAl"}],"publisher":"OpenProceedings","publication_status":"published","year":"2018"},{"scopus_import":1,"has_accepted_license":"1","article_processing_charge":"No","day":"31","page":"59:1-59:25","citation":{"chicago":"Pietrzak, Krzysztof Z. “Proofs of Catalytic Space.” In 10th Innovations in Theoretical Computer Science Conference (ITCS 2019), 124:59:1-59:25. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPICS.ITCS.2019.59.","short":"K.Z. Pietrzak, in:, 10th Innovations in Theoretical Computer Science Conference (ITCS 2019), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 59:1-59:25.","mla":"Pietrzak, Krzysztof Z. “Proofs of Catalytic Space.” 10th Innovations in Theoretical Computer Science Conference (ITCS 2019), vol. 124, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 59:1-59:25, doi:10.4230/LIPICS.ITCS.2019.59.","ieee":"K. Z. Pietrzak, “Proofs of catalytic space,” in 10th Innovations in Theoretical Computer Science Conference (ITCS 2019), San Diego, CA, United States, 2018, vol. 124, p. 59:1-59:25.","apa":"Pietrzak, K. Z. (2018). Proofs of catalytic space. In 10th Innovations in Theoretical Computer Science Conference (ITCS 2019) (Vol. 124, p. 59:1-59:25). San Diego, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ITCS.2019.59","ista":"Pietrzak KZ. 2018. Proofs of catalytic space. 10th Innovations in Theoretical Computer Science Conference (ITCS 2019). ITCS: Innovations in theoretical Computer Science Conference, LIPIcs, vol. 124, 59:1-59:25.","ama":"Pietrzak KZ. Proofs of catalytic space. In: 10th Innovations in Theoretical Computer Science Conference (ITCS 2019). Vol 124. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:59:1-59:25. doi:10.4230/LIPICS.ITCS.2019.59"},"publication":"10th Innovations in Theoretical Computer Science Conference (ITCS 2019)","date_published":"2018-12-31T00:00:00Z","alternative_title":["LIPIcs"],"type":"conference","abstract":[{"text":"Proofs of space (PoS) [Dziembowski et al., CRYPTO'15] are proof systems where a prover can convince a verifier that he \"wastes\" disk space. PoS were introduced as a more ecological and economical replacement for proofs of work which are currently used to secure blockchains like Bitcoin. In this work we investigate extensions of PoS which allow the prover to embed useful data into the dedicated space, which later can be recovered. Our first contribution is a security proof for the original PoS from CRYPTO'15 in the random oracle model (the original proof only applied to a restricted class of adversaries which can store a subset of the data an honest prover would store). When this PoS is instantiated with recent constructions of maximally depth robust graphs, our proof implies basically optimal security. As a second contribution we show three different extensions of this PoS where useful data can be embedded into the space required by the prover. Our security proof for the PoS extends (non-trivially) to these constructions. We discuss how some of these variants can be used as proofs of catalytic space (PoCS), a notion we put forward in this work, and which basically is a PoS where most of the space required by the prover can be used to backup useful data. Finally we discuss how one of the extensions is a candidate construction for a proof of replication (PoR), a proof system recently suggested in the Filecoin whitepaper. ","lang":"eng"}],"intvolume":" 124","title":"Proofs of catalytic space","status":"public","ddc":["000"],"_id":"7407","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"checksum":"5cebb7f7849a3beda898f697d755dd96","date_created":"2020-02-04T08:17:52Z","date_updated":"2020-07-14T12:47:57Z","file_id":"7443","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":822884,"access_level":"open_access","file_name":"2018_LIPIcs_Pietrzak.pdf"}],"publication_identifier":{"isbn":["978-3-95977-095-8"],"issn":["1868-8969"]},"month":"12","project":[{"grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"url":"https://eprint.iacr.org/2018/194","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.4230/LIPICS.ITCS.2019.59","conference":{"name":"ITCS: Innovations in theoretical Computer Science Conference","end_date":"2019-01-12","location":"San Diego, CA, United States","start_date":"2019-01-10"},"ec_funded":1,"file_date_updated":"2020-07-14T12:47:57Z","department":[{"_id":"KrPi"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","year":"2018","volume":124,"date_updated":"2021-01-12T08:13:26Z","date_created":"2020-01-30T09:16:05Z","author":[{"last_name":"Pietrzak","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z"}]},{"oa":1,"citation":{"ista":"Polino A, Pascanu R, Alistarh D-A. 2018. Model compression via distillation and quantization. 6th International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","apa":"Polino, A., Pascanu, R., & Alistarh, D.-A. (2018). Model compression via distillation and quantization. In 6th International Conference on Learning Representations. Vancouver, Canada.","ieee":"A. Polino, R. Pascanu, and D.-A. Alistarh, “Model compression via distillation and quantization,” in 6th International Conference on Learning Representations, Vancouver, Canada, 2018.","ama":"Polino A, Pascanu R, Alistarh D-A. Model compression via distillation and quantization. In: 6th International Conference on Learning Representations. ; 2018.","chicago":"Polino, Antonio, Razvan Pascanu, and Dan-Adrian Alistarh. “Model Compression via Distillation and Quantization.” In 6th International Conference on Learning Representations, 2018.","mla":"Polino, Antonio, et al. “Model Compression via Distillation and Quantization.” 6th International Conference on Learning Representations, 2018.","short":"A. Polino, R. Pascanu, D.-A. Alistarh, in:, 6th International Conference on Learning Representations, 2018."},"external_id":{"arxiv":["1802.05668"]},"publication":"6th International Conference on Learning Representations","quality_controlled":"1","date_published":"2018-05-01T00:00:00Z","conference":{"name":"ICLR: International Conference on Learning Representations","location":"Vancouver, Canada","start_date":"2018-04-30","end_date":"2018-05-03"},"language":[{"iso":"eng"}],"scopus_import":1,"article_processing_charge":"No","has_accepted_license":"1","day":"01","month":"05","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7812","year":"2018","department":[{"_id":"DaAl"}],"status":"public","publication_status":"published","title":"Model compression via distillation and quantization","ddc":["000"],"author":[{"full_name":"Polino, Antonio","first_name":"Antonio","last_name":"Polino"},{"first_name":"Razvan","last_name":"Pascanu","full_name":"Pascanu, Razvan"},{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian"}],"file":[{"date_created":"2020-05-26T13:02:00Z","date_updated":"2020-07-14T12:48:03Z","checksum":"a4336c167978e81891970e4e4517a8c3","file_id":"7894","relation":"main_file","creator":"dernst","file_size":308339,"content_type":"application/pdf","file_name":"2018_ICLR_Polino.pdf","access_level":"open_access"}],"oa_version":"Published Version","date_created":"2020-05-10T22:00:51Z","date_updated":"2023-02-23T13:18:41Z","type":"conference","file_date_updated":"2020-07-14T12:48:03Z","abstract":[{"text":"Deep neural networks (DNNs) continue to make significant advances, solving tasks from image classification to translation or reinforcement learning. One aspect of the field receiving considerable attention is efficiently executing deep models in resource-constrained environments, such as mobile or embedded devices. This paper focuses on this problem, and proposes two new compression methods, which jointly leverage weight quantization and distillation of larger teacher networks into smaller student networks. The first method we propose is called quantized distillation and leverages distillation during the training process, by incorporating distillation loss, expressed with respect to the teacher, into the training of a student network whose weights are quantized to a limited set of levels. The second method, differentiable quantization, optimizes the location of quantization points through stochastic gradient descent, to better fit the behavior of the teacher model. We validate both methods through experiments on convolutional and recurrent architectures. We show that quantized shallow students can reach similar accuracy levels to full-precision teacher models, while providing order of magnitude compression, and inference speedup that is linear in the depth reduction. In sum, our results enable DNNs for resource-constrained environments to leverage architecture and accuracy advances developed on more powerful devices.","lang":"eng"}]},{"project":[{"call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425"},{"grant_number":"M02416","_id":"264E56E2-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex","call_identifier":"FWF"}],"publication":"bioRxiv","citation":{"mla":"Llorca, Alfredo, et al. “Heterogeneous Progenitor Cell Behaviors Underlie the Assembly of Neocortical Cytoarchitecture.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/494088.","short":"A. Llorca, G. Ciceri, R.J. Beattie, F.K. Wong, G. Diana, E. Serafeimidou, M. Fernández-Otero, C. Streicher, S.J. Arnold, M. Meyer, S. Hippenmeyer, M. Maravall, O. Marín, BioRxiv (n.d.).","chicago":"Llorca, Alfredo, Gabriele Ciceri, Robert J Beattie, Fong K. Wong, Giovanni Diana, Eleni Serafeimidou, Marian Fernández-Otero, et al. “Heterogeneous Progenitor Cell Behaviors Underlie the Assembly of Neocortical Cytoarchitecture.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/494088.","ama":"Llorca A, Ciceri G, Beattie RJ, et al. Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. bioRxiv. doi:10.1101/494088","ista":"Llorca A, Ciceri G, Beattie RJ, Wong FK, Diana G, Serafeimidou E, Fernández-Otero M, Streicher C, Arnold SJ, Meyer M, Hippenmeyer S, Maravall M, Marín O. Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. bioRxiv, 10.1101/494088.","apa":"Llorca, A., Ciceri, G., Beattie, R. J., Wong, F. K., Diana, G., Serafeimidou, E., … Marín, O. (n.d.). Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/494088","ieee":"A. Llorca et al., “Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture,” bioRxiv. Cold Spring Harbor Laboratory."},"main_file_link":[{"url":"https://doi.org/10.1101/494088","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1101/494088","date_published":"2018-12-13T00:00:00Z","month":"12","day":"13","article_processing_charge":"No","status":"public","title":"Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture","publication_status":"submitted","department":[{"_id":"SiHi"}],"publisher":"Cold Spring Harbor Laboratory","year":"2018","_id":"8547","acknowledgement":"We thank I. Andrew and S.E. Bae for excellent technical assistance, F. Gage for plasmids, and K. Nave (Nex-Cre) for mouse colonies. We thank members of the Marín and Rico laboratories for stimulating discussions and ideas. Our research on this topic is supported by grants from the European Research Council (ERC-2017-AdG 787355 to O.M and ERC2016-CoG 725780 to S.H.) and Wellcome Trust (103714MA) to O.M. L.L. was the recipient of an EMBO long-term postdoctoral fellowship, R.B. received support from FWF Lise-Meitner program (M 2416) and F.K.W. was supported by an EMBO postdoctoral fellowship and is currently a Marie Skłodowska-Curie Fellow from the European Commission under the H2020 Programme.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-09-21T12:01:50Z","date_updated":"2021-01-12T08:20:00Z","oa_version":"Preprint","author":[{"full_name":"Llorca, Alfredo","first_name":"Alfredo","last_name":"Llorca"},{"last_name":"Ciceri","first_name":"Gabriele","full_name":"Ciceri, Gabriele"},{"orcid":"0000-0002-8483-8753","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","last_name":"Beattie","first_name":"Robert J","full_name":"Beattie, Robert J"},{"full_name":"Wong, Fong K.","first_name":"Fong K.","last_name":"Wong"},{"last_name":"Diana","first_name":"Giovanni","full_name":"Diana, Giovanni"},{"full_name":"Serafeimidou, Eleni","first_name":"Eleni","last_name":"Serafeimidou"},{"last_name":"Fernández-Otero","first_name":"Marian","full_name":"Fernández-Otero, Marian"},{"full_name":"Streicher, Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen","last_name":"Streicher"},{"full_name":"Arnold, Sebastian J.","last_name":"Arnold","first_name":"Sebastian J."},{"last_name":"Meyer","first_name":"Martin","full_name":"Meyer, Martin"},{"full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer"},{"full_name":"Maravall, Miguel","first_name":"Miguel","last_name":"Maravall"},{"full_name":"Marín, Oscar","last_name":"Marín","first_name":"Oscar"}],"type":"preprint","abstract":[{"lang":"eng","text":"The cerebral cortex contains multiple hierarchically organized areas with distinctive cytoarchitectonical patterns, but the cellular mechanisms underlying the emergence of this diversity remain unclear. Here, we have quantitatively investigated the neuronal output of individual progenitor cells in the ventricular zone of the developing mouse neocortex using a combination of methods that together circumvent the biases and limitations of individual approaches. We found that individual cortical progenitor cells show a high degree of stochasticity and generate pyramidal cell lineages that adopt a wide range of laminar configurations. Mathematical modelling these lineage data suggests that a small number of progenitor cell populations, each generating pyramidal cells following different stochastic developmental programs, suffice to generate the heterogenous complement of pyramidal cell lineages that collectively build the complex cytoarchitecture of the neocortex."}],"ec_funded":1},{"doi":"10.1007/978-3-319-95246-8_9","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory","call_identifier":"FWF"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"}],"month":"07","author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A"},{"full_name":"Otop, Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Otop"}],"date_updated":"2021-01-12T08:20:14Z","date_created":"2018-12-11T11:44:33Z","volume":10760,"year":"2018","acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23, S11407-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), ERC Start grant (279307: Graph Games), Vienna Science and Technology Fund (WWTF) through project ICT15-003 and by the National Science Centre (NCN), Poland under grant 2014/15/D/ST6/04543.","publication_status":"published","publisher":"Springer","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"editor":[{"full_name":"Lohstroh, Marten","last_name":"Lohstroh","first_name":"Marten"},{"full_name":"Derler, Patricia","first_name":"Patricia","last_name":"Derler"},{"first_name":"Marjan","last_name":"Sirjani","full_name":"Sirjani, Marjan"}],"file_date_updated":"2020-07-14T12:48:14Z","publist_id":"7968","ec_funded":1,"date_published":"2018-07-20T00:00:00Z","publication":"Principles of Modeling","citation":{"ista":"Chatterjee K, Henzinger TA, Otop J. 2018.Computing average response time. In: Principles of Modeling. LNCS, vol. 10760, 143–161.","apa":"Chatterjee, K., Henzinger, T. A., & Otop, J. (2018). Computing average response time. In M. Lohstroh, P. Derler, & M. Sirjani (Eds.), Principles of Modeling (Vol. 10760, pp. 143–161). Springer. https://doi.org/10.1007/978-3-319-95246-8_9","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Computing average response time,” in Principles of Modeling, vol. 10760, M. Lohstroh, P. Derler, and M. Sirjani, Eds. Springer, 2018, pp. 143–161.","ama":"Chatterjee K, Henzinger TA, Otop J. Computing average response time. In: Lohstroh M, Derler P, Sirjani M, eds. Principles of Modeling. Vol 10760. Springer; 2018:143-161. doi:10.1007/978-3-319-95246-8_9","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Computing Average Response Time.” In Principles of Modeling, edited by Marten Lohstroh, Patricia Derler, and Marjan Sirjani, 10760:143–61. Springer, 2018. https://doi.org/10.1007/978-3-319-95246-8_9.","mla":"Chatterjee, Krishnendu, et al. “Computing Average Response Time.” Principles of Modeling, edited by Marten Lohstroh et al., vol. 10760, Springer, 2018, pp. 143–61, doi:10.1007/978-3-319-95246-8_9.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, M. Lohstroh, P. Derler, M. Sirjani (Eds.), Principles of Modeling, Springer, 2018, pp. 143–161."},"page":"143 - 161","day":"20","has_accepted_license":"1","scopus_import":1,"file":[{"checksum":"9995c6ce6957333baf616fc4f20be597","date_created":"2019-11-19T08:22:18Z","date_updated":"2020-07-14T12:48:14Z","relation":"main_file","file_id":"7053","file_size":516307,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2018_PrinciplesModeling_Chatterjee.pdf"}],"oa_version":"Submitted Version","_id":"86","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","ddc":["000"],"title":"Computing average response time","intvolume":" 10760","abstract":[{"text":"Responsiveness—the requirement that every request to a system be eventually handled—is one of the fundamental liveness properties of a reactive system. Average response time is a quantitative measure for the responsiveness requirement used commonly in performance evaluation. We show how average response time can be computed on state-transition graphs, on Markov chains, and on game graphs. In all three cases, we give polynomial-time algorithms.","lang":"eng"}],"type":"book_chapter","alternative_title":["LNCS"]},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"9229","title":"Diffraction-unlimited optical imaging for synaptic physiology","status":"public","intvolume":" 4","oa_version":"Published Version","type":"journal_article","alternative_title":["Molecular and cellular neuroscience"],"issue":"S1","publication":"Opera Medica et Physiologica","citation":{"chicago":"Danzl, Johann G. “Diffraction-Unlimited Optical Imaging for Synaptic Physiology.” Opera Medica et Physiologica. Lobachevsky State University of Nizhny Novgorod, 2018. https://doi.org/10.20388/omp2018.00s1.001.","short":"J.G. Danzl, Opera Medica et Physiologica 4 (2018) 11.","mla":"Danzl, Johann G. “Diffraction-Unlimited Optical Imaging for Synaptic Physiology.” Opera Medica et Physiologica, vol. 4, no. S1, Lobachevsky State University of Nizhny Novgorod, 2018, p. 11, doi:10.20388/omp2018.00s1.001.","apa":"Danzl, J. G. (2018). Diffraction-unlimited optical imaging for synaptic physiology. Opera Medica et Physiologica. Lobachevsky State University of Nizhny Novgorod. https://doi.org/10.20388/omp2018.00s1.001","ieee":"J. G. Danzl, “Diffraction-unlimited optical imaging for synaptic physiology,” Opera Medica et Physiologica, vol. 4, no. S1. Lobachevsky State University of Nizhny Novgorod, p. 11, 2018.","ista":"Danzl JG. 2018. Diffraction-unlimited optical imaging for synaptic physiology. Opera Medica et Physiologica. 4(S1), 11.","ama":"Danzl JG. Diffraction-unlimited optical imaging for synaptic physiology. Opera Medica et Physiologica. 2018;4(S1):11. doi:10.20388/omp2018.00s1.001"},"article_type":"letter_note","page":"11","date_published":"2018-06-30T00:00:00Z","scopus_import":"1","day":"30","article_processing_charge":"No","year":"2018","publication_status":"published","publisher":"Lobachevsky State University of Nizhny Novgorod","department":[{"_id":"JoDa"}],"author":[{"full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","first_name":"Johann G","last_name":"Danzl"}],"date_created":"2021-03-07T23:01:25Z","date_updated":"2021-12-03T07:31:05Z","volume":4,"oa":1,"main_file_link":[{"open_access":"1","url":"http://operamedphys.org/content/molecular-and-cellular-neuroscience"}],"quality_controlled":"1","doi":"10.20388/omp2018.00s1.001","language":[{"iso":"eng"}],"month":"06","publication_identifier":{"eissn":["2500-2295"],"issn":["2500-2287"]}},{"date_published":"2018-08-01T00:00:00Z","citation":{"chicago":"Avni, Guy, Shibashis Guha, and Orna Kupferman. “Timed Network Games with Clocks,” Vol. 117. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPICS.MFCS.2018.23.","short":"G. Avni, S. Guha, O. Kupferman, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","mla":"Avni, Guy, et al. Timed Network Games with Clocks. Vol. 117, 23, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPICS.MFCS.2018.23.","ieee":"G. Avni, S. Guha, and O. Kupferman, “Timed network games with clocks,” presented at the MFCS: Mathematical Foundations of Computer Science, Liverpool, United Kingdom, 2018, vol. 117.","apa":"Avni, G., Guha, S., & Kupferman, O. (2018). Timed network games with clocks (Vol. 117). Presented at the MFCS: Mathematical Foundations of Computer Science, Liverpool, United Kingdom: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.MFCS.2018.23","ista":"Avni G, Guha S, Kupferman O. 2018. Timed network games with clocks. MFCS: Mathematical Foundations of Computer Science, LIPIcs, vol. 117, 23.","ama":"Avni G, Guha S, Kupferman O. Timed network games with clocks. In: Vol 117. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPICS.MFCS.2018.23"},"day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","oa_version":"Published Version","file":[{"creator":"dernst","file_size":542889,"content_type":"application/pdf","file_name":"2018_LIPIcs_Avni.pdf","access_level":"open_access","date_created":"2019-02-14T14:22:04Z","date_updated":"2020-07-14T12:47:15Z","checksum":"41ab2ae9b63f5eb49fa995250c0ba128","file_id":"6007","relation":"main_file"}],"ddc":["000"],"title":"Timed network games with clocks","status":"public","intvolume":" 117","_id":"6005","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Network games are widely used as a model for selfish resource-allocation problems. In the classicalmodel, each player selects a path connecting her source and target vertices. The cost of traversingan edge depends on theload; namely, number of players that traverse it. Thus, it abstracts the factthat different users may use a resource at different times and for different durations, which playsan important role in determining the costs of the users in reality. For example, when transmittingpackets in a communication network, routing traffic in a road network, or processing a task in aproduction system, actual sharing and congestion of resources crucially depends on time.In [13], we introducedtimed network games, which add a time component to network games.Each vertexvin the network is associated with a cost function, mapping the load onvto theprice that a player pays for staying invfor one time unit with this load. Each edge in thenetwork is guarded by the time intervals in which it can be traversed, which forces the players tospend time in the vertices. In this work we significantly extend the way time can be referred toin timed network games. In the model we study, the network is equipped withclocks, and, as intimed automata, edges are guarded by constraints on the values of the clocks, and their traversalmay involve a reset of some clocks. We argue that the stronger model captures many realisticnetworks. The addition of clocks breaks the techniques we developed in [13] and we developnew techniques in order to show that positive results on classic network games carry over to thestronger timed setting."}],"alternative_title":["LIPIcs"],"type":"conference","language":[{"iso":"eng"}],"conference":{"name":"MFCS: Mathematical Foundations of Computer Science","start_date":"2018-08-27","location":"Liverpool, United Kingdom","end_date":"2018-08-31"},"doi":"10.4230/LIPICS.MFCS.2018.23","quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"name":"Formal Methods meets Algorithmic Game Theory","call_identifier":"FWF","_id":"264B3912-B435-11E9-9278-68D0E5697425","grant_number":"M02369"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"08","publication_identifier":{"issn":["1868-8969"]},"date_created":"2019-02-14T14:12:09Z","date_updated":"2023-02-23T14:02:58Z","volume":117,"author":[{"full_name":"Avni, Guy","first_name":"Guy","last_name":"Avni","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5588-8287"},{"first_name":"Shibashis","last_name":"Guha","full_name":"Guha, Shibashis"},{"full_name":"Kupferman, Orna","first_name":"Orna","last_name":"Kupferman"}],"related_material":{"record":[{"id":"963","status":"public","relation":"earlier_version"}]},"publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","year":"2018","file_date_updated":"2020-07-14T12:47:15Z","article_number":"23"},{"scopus_import":1,"has_accepted_license":"1","day":"15","citation":{"ista":"Polechova J. 2018. Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. 16(6), e2005372.","ieee":"J. Polechova, “Is the sky the limit? On the expansion threshold of a species’ range,” PLoS Biology, vol. 16, no. 6. Public Library of Science, 2018.","apa":"Polechova, J. (2018). Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005372","ama":"Polechova J. Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. 2018;16(6). doi:10.1371/journal.pbio.2005372","chicago":"Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” PLoS Biology. Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005372.","mla":"Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” PLoS Biology, vol. 16, no. 6, e2005372, Public Library of Science, 2018, doi:10.1371/journal.pbio.2005372.","short":"J. Polechova, PLoS Biology 16 (2018)."},"publication":"PLoS Biology","date_published":"2018-06-15T00:00:00Z","type":"journal_article","issue":"6","abstract":[{"text":"More than 100 years after Grigg’s influential analysis of species’ borders, the causes of limits to species’ ranges still represent a puzzle that has never been understood with clarity. The topic has become especially important recently as many scientists have become interested in the potential for species’ ranges to shift in response to climate change—and yet nearly all of those studies fail to recognise or incorporate evolutionary genetics in a way that relates to theoretical developments. I show that range margins can be understood based on just two measurable parameters: (i) the fitness cost of dispersal—a measure of environmental heterogeneity—and (ii) the strength of genetic drift, which reduces genetic diversity. Together, these two parameters define an ‘expansion threshold’: adaptation fails when genetic drift reduces genetic diversity below that required for adaptation to a heterogeneous environment. When the key parameters drop below this expansion threshold locally, a sharp range margin forms. When they drop below this threshold throughout the species’ range, adaptation collapses everywhere, resulting in either extinction or formation of a fragmented metapopulation. Because the effects of dispersal differ fundamentally with dimension, the second parameter—the strength of genetic drift—is qualitatively different compared to a linear habitat. In two-dimensional habitats, genetic drift becomes effectively independent of selection. It decreases with ‘neighbourhood size’—the number of individuals accessible by dispersal within one generation. Moreover, in contrast to earlier predictions, which neglected evolution of genetic variance and/or stochasticity in two dimensions, dispersal into small marginal populations aids adaptation. This is because the reduction of both genetic and demographic stochasticity has a stronger effect than the cost of dispersal through increased maladaptation. The expansion threshold thus provides a novel, theoretically justified, and testable prediction for formation of the range margin and collapse of the species’ range.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"315","intvolume":" 16","status":"public","title":"Is the sky the limit? On the expansion threshold of a species’ range","ddc":["576"],"file":[{"date_updated":"2020-07-14T12:46:01Z","date_created":"2019-01-22T08:30:03Z","checksum":"908c52751bba30c55ed36789e5e4c84d","relation":"main_file","file_id":"5870","content_type":"application/pdf","file_size":6968201,"creator":"dernst","file_name":"2017_PLOS_Polechova.pdf","access_level":"open_access"}],"oa_version":"Published Version","publication_identifier":{"issn":["15449173"]},"month":"06","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","doi":"10.1371/journal.pbio.2005372","language":[{"iso":"eng"}],"article_number":"e2005372","publist_id":"7550","file_date_updated":"2020-07-14T12:46:01Z","year":"2018","publisher":"Public Library of Science","department":[{"_id":"NiBa"}],"publication_status":"published","related_material":{"record":[{"id":"9839","status":"public","relation":"research_data"}]},"author":[{"full_name":"Polechova, Jitka","orcid":"0000-0003-0951-3112","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","last_name":"Polechova","first_name":"Jitka"}],"volume":16,"date_created":"2018-12-11T11:45:46Z","date_updated":"2023-02-23T14:10:16Z"},{"month":"06","doi":"10.4230/LIPIcs.SoCG.2018.40","conference":{"end_date":"2018-06-14","start_date":"2018-06-11","location":"Budapest, Hungary","name":"SoCG: Symposium on Computational Geometry"},"language":[{"iso":"eng"}],"external_id":{"arxiv":["1803.05085"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.05085"}],"oa":1,"project":[{"name":"Eliminating intersections in drawings of graphs","call_identifier":"FWF","_id":"261FA626-B435-11E9-9278-68D0E5697425","grant_number":"M02281"}],"quality_controlled":"1","publist_id":"7734","related_material":{"record":[{"id":"11593","relation":"later_version","status":"public"}]},"author":[{"full_name":"Fulek, Radoslav","orcid":"0000-0001-8485-1774","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","last_name":"Fulek","first_name":"Radoslav"},{"first_name":"Jan","last_name":"Kynčl","full_name":"Kynčl, Jan"}],"volume":99,"date_updated":"2023-08-14T12:43:51Z","date_created":"2018-12-11T11:45:05Z","year":"2018","department":[{"_id":"UlWa"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","article_processing_charge":"No","day":"11","scopus_import":"1","date_published":"2018-06-11T00:00:00Z","citation":{"ista":"Fulek R, Kynčl J. 2018. The ℤ2-Genus of Kuratowski minors. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 99, 40.1-40.14.","apa":"Fulek, R., & Kynčl, J. (2018). The ℤ2-Genus of Kuratowski minors (Vol. 99, p. 40.1-40.14). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.40","ieee":"R. Fulek and J. Kynčl, “The ℤ2-Genus of Kuratowski minors,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99, p. 40.1-40.14.","ama":"Fulek R, Kynčl J. The ℤ2-Genus of Kuratowski minors. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:40.1-40.14. doi:10.4230/LIPIcs.SoCG.2018.40","chicago":"Fulek, Radoslav, and Jan Kynčl. “The ℤ2-Genus of Kuratowski Minors,” 99:40.1-40.14. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.40.","mla":"Fulek, Radoslav, and Jan Kynčl. The ℤ2-Genus of Kuratowski Minors. Vol. 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 40.1-40.14, doi:10.4230/LIPIcs.SoCG.2018.40.","short":"R. Fulek, J. Kynčl, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 40.1-40.14."},"page":"40.1 - 40.14","abstract":[{"text":"A drawing of a graph on a surface is independently even if every pair of nonadjacent edges in the drawing crosses an even number of times. The ℤ2-genus of a graph G is the minimum g such that G has an independently even drawing on the orientable surface of genus g. An unpublished result by Robertson and Seymour implies that for every t, every graph of sufficiently large genus contains as a minor a projective t × t grid or one of the following so-called t-Kuratowski graphs: K3, t, or t copies of K5 or K3,3 sharing at most 2 common vertices. We show that the ℤ2-genus of graphs in these families is unbounded in t; in fact, equal to their genus. Together, this implies that the genus of a graph is bounded from above by a function of its ℤ2-genus, solving a problem posed by Schaefer and Štefankovič, and giving an approximate version of the Hanani-Tutte theorem on orientable surfaces.","lang":"eng"}],"type":"conference","alternative_title":["LIPIcs"],"oa_version":"Submitted Version","_id":"186","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 99","status":"public","title":"The ℤ2-Genus of Kuratowski minors"},{"oa_version":"Submitted Version","_id":"433","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Thrackles: An improved upper bound","status":"public","intvolume":" 10692","abstract":[{"lang":"eng","text":"A thrackle is a graph drawn in the plane so that every pair of its edges meet exactly once: either at a common end vertex or in a proper crossing. We prove that any thrackle of n vertices has at most 1.3984n edges. Quasi-thrackles are defined similarly, except that every pair of edges that do not share a vertex are allowed to cross an odd number of times. It is also shown that the maximum number of edges of a quasi-thrackle on n vertices is 3/2(n-1), and that this bound is best possible for infinitely many values of n."}],"type":"conference","alternative_title":["LNCS"],"date_published":"2018-01-21T00:00:00Z","citation":{"chicago":"Fulek, Radoslav, and János Pach. “Thrackles: An Improved Upper Bound,” 10692:160–66. Springer, 2018. https://doi.org/10.1007/978-3-319-73915-1_14.","short":"R. Fulek, J. Pach, in:, Springer, 2018, pp. 160–166.","mla":"Fulek, Radoslav, and János Pach. Thrackles: An Improved Upper Bound. Vol. 10692, Springer, 2018, pp. 160–66, doi:10.1007/978-3-319-73915-1_14.","apa":"Fulek, R., & Pach, J. (2018). Thrackles: An improved upper bound (Vol. 10692, pp. 160–166). Presented at the GD 2017: Graph Drawing and Network Visualization, Boston, MA, United States: Springer. https://doi.org/10.1007/978-3-319-73915-1_14","ieee":"R. Fulek and J. Pach, “Thrackles: An improved upper bound,” presented at the GD 2017: Graph Drawing and Network Visualization, Boston, MA, United States, 2018, vol. 10692, pp. 160–166.","ista":"Fulek R, Pach J. 2018. Thrackles: An improved upper bound. GD 2017: Graph Drawing and Network Visualization, LNCS, vol. 10692, 160–166.","ama":"Fulek R, Pach J. Thrackles: An improved upper bound. In: Vol 10692. Springer; 2018:160-166. doi:10.1007/978-3-319-73915-1_14"},"page":"160 - 166","day":"21","scopus_import":1,"author":[{"full_name":"Fulek, Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8485-1774","first_name":"Radoslav","last_name":"Fulek"},{"last_name":"Pach","first_name":"János","full_name":"Pach, János"}],"related_material":{"record":[{"id":"5857","status":"public","relation":"later_version"}]},"date_updated":"2023-08-24T14:39:32Z","date_created":"2018-12-11T11:46:27Z","volume":10692,"year":"2018","publication_status":"published","publisher":"Springer","department":[{"_id":"UlWa"}],"publist_id":"7390","conference":{"name":"GD 2017: Graph Drawing and Network Visualization","end_date":"2017-09-27","location":"Boston, MA, United States","start_date":"201-09-25"},"doi":"10.1007/978-3-319-73915-1_14","language":[{"iso":"eng"}],"external_id":{"arxiv":["1708.08037"]},"main_file_link":[{"url":"https://arxiv.org/abs/1708.08037","open_access":"1"}],"oa":1,"quality_controlled":"1","month":"01"},{"title":"Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes","status":"public","department":[{"_id":"NiBa"}],"publisher":"Dryad","year":"2018","_id":"9837","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-08-24T14:50:26Z","date_created":"2021-08-09T12:46:39Z","oa_version":"Published Version","author":[{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"last_name":"Chaube","first_name":"Pragya","full_name":"Chaube, Pragya"},{"first_name":"Hernán E.","last_name":"Morales","full_name":"Morales, Hernán E."},{"last_name":"Larsson","first_name":"Tomas","full_name":"Larsson, Tomas"},{"last_name":"Lemmon","first_name":"Alan R.","full_name":"Lemmon, Alan R."},{"first_name":"Emily M.","last_name":"Lemmon","full_name":"Lemmon, Emily M."},{"full_name":"Rafajlović, Marina","first_name":"Marina","last_name":"Rafajlović"},{"first_name":"Marina","last_name":"Panova","full_name":"Panova, Marina"},{"full_name":"Ravinet, Mark","first_name":"Mark","last_name":"Ravinet"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","first_name":"Anja M","last_name":"Westram","full_name":"Westram, Anja M"},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"6095"}]},"type":"research_data_reference","abstract":[{"text":"Both classical and recent studies suggest that chromosomal inversion polymorphisms are important in adaptation and speciation. However, biases in discovery and reporting of inversions make it difficult to assess their prevalence and biological importance. Here, we use an approach based on linkage disequilibrium among markers genotyped for samples collected across a transect between contrasting habitats to detect chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in a single locality for the coastal marine snail, Littorina saxatilis. Patterns of diversity in the field and of recombination in controlled crosses provide strong evidence that at least the majority of these rearrangements are inversions. Most show clinal changes in frequency between habitats, suggestive of divergent selection, but only one appears to be fixed for different arrangements in the two habitats. Consistent with widespread evidence for balancing selection on inversion polymorphisms, we argue that a combination of heterosis and divergent selection can explain the observed patterns and should be considered in other systems spanning environmental gradients.","lang":"eng"}],"citation":{"ama":"Faria R, Chaube P, Morales HE, et al. Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. 2018. doi:10.5061/dryad.72cg113","ista":"Faria R, Chaube P, Morales HE, Larsson T, Lemmon AR, Lemmon EM, Rafajlović M, Panova M, Ravinet M, Johannesson K, Westram AM, Butlin RK. 2018. Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes, Dryad, 10.5061/dryad.72cg113.","ieee":"R. Faria et al., “Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes.” Dryad, 2018.","apa":"Faria, R., Chaube, P., Morales, H. E., Larsson, T., Lemmon, A. R., Lemmon, E. M., … Butlin, R. K. (2018). Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Dryad. https://doi.org/10.5061/dryad.72cg113","mla":"Faria, Rui, et al. Data from: Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes. Dryad, 2018, doi:10.5061/dryad.72cg113.","short":"R. Faria, P. Chaube, H.E. Morales, T. Larsson, A.R. Lemmon, E.M. Lemmon, M. Rafajlović, M. Panova, M. Ravinet, K. Johannesson, A.M. Westram, R.K. Butlin, (2018).","chicago":"Faria, Rui, Pragya Chaube, Hernán E. Morales, Tomas Larsson, Alan R. Lemmon, Emily M. Lemmon, Marina Rafajlović, et al. “Data from: Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes.” Dryad, 2018. https://doi.org/10.5061/dryad.72cg113."},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.72cg113","open_access":"1"}],"oa":1,"date_published":"2018-10-09T00:00:00Z","doi":"10.5061/dryad.72cg113","month":"10","day":"09","article_processing_charge":"No"},{"type":"technical_report","alternative_title":["IST Austria Technical Report"],"file_date_updated":"2020-07-14T12:47:00Z","abstract":[{"lang":"eng","text":"We consider the problem of expected cost analysis over nondeterministic probabilistic programs, which aims at automated methods for analyzing the resource-usage of such programs. Previous approaches for this problem could only handle nonnegative bounded costs. However, in many scenarios, such as queuing networks or analysis of cryptocurrency protocols, both positive and negative costs are necessary and the costs are unbounded as well.\r\n\r\nIn this work, we present a sound and efficient approach to obtain polynomial bounds on the expected accumulated cost of nondeterministic probabilistic programs. Our approach can handle (a) general positive and negative costs with bounded updates in variables; and (b) nonnegative costs with general updates to variables. We show that several natural examples which could not be handled by previous approaches are captured in our framework.\r\n\r\nMoreover, our approach leads to an efficient polynomial-time algorithm, while no previous approach for cost analysis of probabilistic programs could guarantee polynomial runtime. Finally, we show the effectiveness of our approach by presenting experimental results on a variety of programs, motivated by real-world applications, for which we efficiently synthesize tight resource-usage bounds."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5457","year":"2018","publication_status":"published","ddc":["000"],"title":"Cost analysis of nondeterministic probabilistic programs","status":"public","publisher":"IST Austria","author":[{"full_name":"Anonymous, 1","first_name":"1","last_name":"Anonymous"},{"last_name":"Anonymous","first_name":"2","full_name":"Anonymous, 2"},{"last_name":"Anonymous","first_name":"3","full_name":"Anonymous, 3"},{"full_name":"Anonymous, 4","first_name":"4","last_name":"Anonymous"},{"first_name":"5","last_name":"Anonymous","full_name":"Anonymous, 5"},{"first_name":"6","last_name":"Anonymous","full_name":"Anonymous, 6"}],"pubrep_id":"1066","related_material":{"record":[{"status":"public","relation":"later_version","id":"6175"}]},"date_created":"2018-12-12T11:39:26Z","date_updated":"2023-08-25T08:07:48Z","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2018-1066-v1+1_techreport.pdf","file_size":4202966,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"5493","checksum":"ba3adafd36fe200385ccda583063b9eb","date_created":"2018-12-12T11:53:32Z","date_updated":"2020-07-14T12:47:00Z"},{"file_size":322,"content_type":"text/plain","creator":"dernst","access_level":"closed","file_name":"authors-names.txt","checksum":"6cf3a19164bb8e5048a9c8c84dfd9fa3","date_created":"2019-05-10T13:22:12Z","date_updated":"2020-07-14T12:47:00Z","relation":"main_file","file_id":"6402"}],"scopus_import":1,"day":"11","month":"11","publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1","citation":{"mla":"Anonymous, 1, et al. Cost Analysis of Nondeterministic Probabilistic Programs. IST Austria, 2018.","short":"1 Anonymous, 2 Anonymous, 3 Anonymous, 4 Anonymous, 5 Anonymous, 6 Anonymous, Cost Analysis of Nondeterministic Probabilistic Programs, IST Austria, 2018.","chicago":"Anonymous, 1, 2 Anonymous, 3 Anonymous, 4 Anonymous, 5 Anonymous, and 6 Anonymous. Cost Analysis of Nondeterministic Probabilistic Programs. IST Austria, 2018.","ama":"Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4, Anonymous 5, Anonymous 6. Cost Analysis of Nondeterministic Probabilistic Programs. IST Austria; 2018.","ista":"Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4, Anonymous 5, Anonymous 6. 2018. Cost analysis of nondeterministic probabilistic programs, IST Austria, 27p.","apa":"Anonymous, 1, Anonymous, 2, Anonymous, 3, Anonymous, 4, Anonymous, 5, & Anonymous, 6. (2018). Cost analysis of nondeterministic probabilistic programs. IST Austria.","ieee":"1 Anonymous, 2 Anonymous, 3 Anonymous, 4 Anonymous, 5 Anonymous, and 6 Anonymous, Cost analysis of nondeterministic probabilistic programs. IST Austria, 2018."},"oa":1,"page":"27","date_published":"2018-11-11T00:00:00Z","language":[{"iso":"eng"}]},{"abstract":[{"lang":"eng","text":"We prove that every congruence distributive variety has directed Jónsson terms, and every congruence modular variety has directed Gumm terms. The directed terms we construct witness every case of absorption witnessed by the original Jónsson or Gumm terms. This result is equivalent to a pair of claims about absorption for admissible preorders in congruence distributive and congruence modular varieties, respectively. For finite algebras, these absorption theorems have already seen significant applications, but until now, it was not clear if the theorems hold for general algebras as well. Our method also yields a novel proof of a result by P. Lipparini about the existence of a chain of terms (which we call Pixley terms) in varieties that are at the same time congruence distributive and k-permutable for some k."}],"type":"book_chapter","oa_version":"Preprint","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10864","intvolume":" 16","title":"Absorption and directed Jónsson terms","status":"public","article_processing_charge":"No","day":"21","scopus_import":"1","series_title":"OCTR","date_published":"2018-03-21T00:00:00Z","citation":{"ama":"Kazda A, Kozik M, McKenzie R, Moore M. Absorption and directed Jónsson terms. In: Czelakowski J, ed. Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science. Vol 16. OCTR. Cham: Springer Nature; 2018:203-220. doi:10.1007/978-3-319-74772-9_7","apa":"Kazda, A., Kozik, M., McKenzie, R., & Moore, M. (2018). Absorption and directed Jónsson terms. In J. Czelakowski (Ed.), Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science (Vol. 16, pp. 203–220). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-74772-9_7","ieee":"A. Kazda, M. Kozik, R. McKenzie, and M. Moore, “Absorption and directed Jónsson terms,” in Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science, vol. 16, J. Czelakowski, Ed. Cham: Springer Nature, 2018, pp. 203–220.","ista":"Kazda A, Kozik M, McKenzie R, Moore M. 2018.Absorption and directed Jónsson terms. In: Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science. vol. 16, 203–220.","short":"A. Kazda, M. Kozik, R. McKenzie, M. Moore, in:, J. Czelakowski (Ed.), Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science, Springer Nature, Cham, 2018, pp. 203–220.","mla":"Kazda, Alexandr, et al. “Absorption and Directed Jónsson Terms.” Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science, edited by J Czelakowski, vol. 16, Springer Nature, 2018, pp. 203–20, doi:10.1007/978-3-319-74772-9_7.","chicago":"Kazda, Alexandr, Marcin Kozik, Ralph McKenzie, and Matthew Moore. “Absorption and Directed Jónsson Terms.” In Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science, edited by J Czelakowski, 16:203–20. OCTR. Cham: Springer Nature, 2018. https://doi.org/10.1007/978-3-319-74772-9_7."},"publication":"Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science","page":"203-220","place":"Cham","author":[{"first_name":"Alexandr","last_name":"Kazda","id":"3B32BAA8-F248-11E8-B48F-1D18A9856A87","full_name":"Kazda, Alexandr"},{"first_name":"Marcin","last_name":"Kozik","full_name":"Kozik, Marcin"},{"first_name":"Ralph","last_name":"McKenzie","full_name":"McKenzie, Ralph"},{"full_name":"Moore, Matthew","last_name":"Moore","first_name":"Matthew"}],"volume":16,"date_updated":"2023-09-05T15:37:18Z","date_created":"2022-03-18T10:30:32Z","year":"2018","acknowledgement":"The second author was supported by National Science Center grant DEC-2011-/01/B/ST6/01006.","editor":[{"first_name":"J","last_name":"Czelakowski","full_name":"Czelakowski, J"}],"department":[{"_id":"VlKo"}],"publisher":"Springer Nature","publication_status":"published","publication_identifier":{"eisbn":["9783319747729"],"issn":["2211-2758"],"isbn":["9783319747712"],"eissn":["2211-2766"]},"month":"03","doi":"10.1007/978-3-319-74772-9_7","language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["1502.01072"]},"main_file_link":[{"url":"https://arxiv.org/abs/1502.01072","open_access":"1"}],"quality_controlled":"1"},{"file_date_updated":"2020-07-14T12:45:18Z","publist_id":"7736","date_created":"2018-12-11T11:45:04Z","date_updated":"2023-09-06T11:10:57Z","volume":99,"author":[{"full_name":"Goaoc, Xavier","last_name":"Goaoc","first_name":"Xavier"},{"full_name":"Paták, Pavel","first_name":"Pavel","last_name":"Paták"},{"full_name":"Patakova, Zuzana","orcid":"0000-0002-3975-1683","id":"48B57058-F248-11E8-B48F-1D18A9856A87","last_name":"Patakova","first_name":"Zuzana"},{"full_name":"Tancer, Martin","last_name":"Tancer","first_name":"Martin","orcid":"0000-0002-1191-6714","id":"38AC689C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","first_name":"Uli"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"7108"}]},"publication_status":"published","department":[{"_id":"UlWa"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","acknowledgement":"Partially supported by the project EMBEDS II (CZ: 7AMB17FR029, FR: 38087RM) of Czech-French collaboration.","year":"2018","month":"06","language":[{"iso":"eng"}],"conference":{"end_date":"2018-06-14","location":"Budapest, Hungary","start_date":"2018-06-11","name":"SoCG: Symposium on Computational Geometry"},"doi":"10.4230/LIPIcs.SoCG.2018.41","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"abstract":[{"text":"We prove that for every d ≥ 2, deciding if a pure, d-dimensional, simplicial complex is shellable is NP-hard, hence NP-complete. This resolves a question raised, e.g., by Danaraj and Klee in 1978. Our reduction also yields that for every d ≥ 2 and k ≥ 0, deciding if a pure, d-dimensional, simplicial complex is k-decomposable is NP-hard. For d ≥ 3, both problems remain NP-hard when restricted to contractible pure d-dimensional complexes.","lang":"eng"}],"alternative_title":["Leibniz International Proceedings in Information, LIPIcs"],"type":"conference","file":[{"relation":"main_file","file_id":"5725","date_updated":"2020-07-14T12:45:18Z","date_created":"2018-12-17T16:35:02Z","checksum":"d12bdd60f04a57307867704b5f930afd","file_name":"2018_LIPIcs_Goaoc.pdf","access_level":"open_access","content_type":"application/pdf","file_size":718414,"creator":"dernst"}],"oa_version":"Published Version","title":"Shellability is NP-complete","status":"public","ddc":["516","000"],"intvolume":" 99","_id":"184","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"11","has_accepted_license":"1","scopus_import":1,"date_published":"2018-06-11T00:00:00Z","page":"41:1 - 41:16","citation":{"ista":"Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. 2018. Shellability is NP-complete. SoCG: Symposium on Computational Geometry, Leibniz International Proceedings in Information, LIPIcs, vol. 99, 41:1-41:16.","ieee":"X. Goaoc, P. Paták, Z. Patakova, M. Tancer, and U. Wagner, “Shellability is NP-complete,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99, p. 41:1-41:16.","apa":"Goaoc, X., Paták, P., Patakova, Z., Tancer, M., & Wagner, U. (2018). Shellability is NP-complete (Vol. 99, p. 41:1-41:16). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.41","ama":"Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. Shellability is NP-complete. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:41:1-41:16. doi:10.4230/LIPIcs.SoCG.2018.41","chicago":"Goaoc, Xavier, Pavel Paták, Zuzana Patakova, Martin Tancer, and Uli Wagner. “Shellability Is NP-Complete,” 99:41:1-41:16. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.41.","mla":"Goaoc, Xavier, et al. Shellability Is NP-Complete. Vol. 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 41:1-41:16, doi:10.4230/LIPIcs.SoCG.2018.41.","short":"X. Goaoc, P. Paták, Z. Patakova, M. Tancer, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 41:1-41:16."}},{"citation":{"ama":"Huszár K, Spreer J, Wagner U. On the treewidth of triangulated 3-manifolds. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPIcs.SoCG.2018.46","ista":"Huszár K, Spreer J, Wagner U. 2018. On the treewidth of triangulated 3-manifolds. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 99, 46.","ieee":"K. Huszár, J. Spreer, and U. Wagner, “On the treewidth of triangulated 3-manifolds,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99.","apa":"Huszár, K., Spreer, J., & Wagner, U. (2018). On the treewidth of triangulated 3-manifolds (Vol. 99). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.46","mla":"Huszár, Kristóf, et al. On the Treewidth of Triangulated 3-Manifolds. Vol. 99, 46, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPIcs.SoCG.2018.46.","short":"K. Huszár, J. Spreer, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","chicago":"Huszár, Kristóf, Jonathan Spreer, and Uli Wagner. “On the Treewidth of Triangulated 3-Manifolds,” Vol. 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.46."},"date_published":"2018-06-01T00:00:00Z","scopus_import":1,"has_accepted_license":"1","article_processing_charge":"No","day":"01","intvolume":" 99","status":"public","ddc":["516","000"],"title":"On the treewidth of triangulated 3-manifolds","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"285","file":[{"relation":"main_file","file_id":"5713","checksum":"530d084116778135d5bffaa317479cac","date_updated":"2020-07-14T12:45:51Z","date_created":"2018-12-17T15:32:38Z","access_level":"open_access","file_name":"2018_LIPIcs_Huszar.pdf","content_type":"application/pdf","file_size":642522,"creator":"dernst"}],"oa_version":"Submitted Version","alternative_title":["LIPIcs"],"type":"conference","abstract":[{"lang":"eng","text":"In graph theory, as well as in 3-manifold topology, there exist several width-type parameters to describe how "simple" or "thin" a given graph or 3-manifold is. These parameters, such as pathwidth or treewidth for graphs, or the concept of thin position for 3-manifolds, play an important role when studying algorithmic problems; in particular, there is a variety of problems in computational 3-manifold topology - some of them known to be computationally hard in general - that become solvable in polynomial time as soon as the dual graph of the input triangulation has bounded treewidth. In view of these algorithmic results, it is natural to ask whether every 3-manifold admits a triangulation of bounded treewidth. We show that this is not the case, i.e., that there exists an infinite family of closed 3-manifolds not admitting triangulations of bounded pathwidth or treewidth (the latter implies the former, but we present two separate proofs). We derive these results from work of Agol and of Scharlemann and Thompson, by exhibiting explicit connections between the topology of a 3-manifold M on the one hand and width-type parameters of the dual graphs of triangulations of M on the other hand, answering a question that had been raised repeatedly by researchers in computational 3-manifold topology. In particular, we show that if a closed, orientable, irreducible, non-Haken 3-manifold M has a triangulation of treewidth (resp. pathwidth) k then the Heegaard genus of M is at most 48(k+1) (resp. 4(3k+1))."}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["1712.00434"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.SoCG.2018.46","conference":{"start_date":"2018-06-11","location":"Budapest, Hungary","end_date":"2018-06-14","name":"SoCG: Symposium on Computational Geometry"},"publication_identifier":{"issn":["18688969"]},"month":"06","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"UlWa"}],"publication_status":"published","year":"2018","acknowledgement":"Research of the second author was supported by the Einstein Foundation (project “Einstein Visiting Fellow Santos”) and by the Simons Foundation (“Simons Visiting Professors” program).","volume":99,"date_created":"2018-12-11T11:45:37Z","date_updated":"2023-09-06T11:13:41Z","related_material":{"record":[{"id":"7093","status":"public","relation":"later_version"}]},"author":[{"first_name":"Kristóf","last_name":"Huszár","id":"33C26278-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5445-5057","full_name":"Huszár, Kristóf"},{"full_name":"Spreer, Jonathan","first_name":"Jonathan","last_name":"Spreer"},{"full_name":"Wagner, Uli","last_name":"Wagner","first_name":"Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"}],"article_number":"46","publist_id":"7614","file_date_updated":"2020-07-14T12:45:51Z"},{"_id":"13059","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"title":"Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method","status":"public","publisher":"Zenodo","department":[{"_id":"FyKo"}],"author":[{"full_name":"Garriga, Edgar","last_name":"Garriga","first_name":"Edgar"},{"full_name":"di Tommaso, Paolo","first_name":"Paolo","last_name":"di Tommaso"},{"full_name":"Magis, Cedrik","last_name":"Magis","first_name":"Cedrik"},{"full_name":"Erb, Ionas","first_name":"Ionas","last_name":"Erb"},{"last_name":"Mansouri","first_name":"Leila","full_name":"Mansouri, Leila"},{"full_name":"Baltzis, Athanasios","last_name":"Baltzis","first_name":"Athanasios"},{"full_name":"Laayouni, Hafid","first_name":"Hafid","last_name":"Laayouni"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor"},{"last_name":"Floden","first_name":"Evan","full_name":"Floden, Evan"},{"last_name":"Notredame","first_name":"Cedric","full_name":"Notredame, Cedric"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"7181"}]},"date_updated":"2023-09-06T14:32:51Z","date_created":"2023-05-23T16:08:20Z","oa_version":"Published Version","type":"research_data_reference","abstract":[{"text":"This dataset contains a GitHub repository containing all the data, analysis, Nextflow workflows and Jupyter notebooks to replicate the manuscript titled \"Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method\".\r\nIt also contains the Multiple Sequence Alignments (MSAs) generated and well as the main figures and tables from the manuscript.\r\nThe repository is also available at GitHub (https://github.com/cbcrg/dpa-analysis) release `v1.2`.\r\nFor details on how to use the regressive alignment algorithm, see the T-Coffee software suite (https://github.com/cbcrg/tcoffee).","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.3271452","open_access":"1"}],"citation":{"ista":"Garriga E, di Tommaso P, Magis C, Erb I, Mansouri L, Baltzis A, Laayouni H, Kondrashov F, Floden E, Notredame C. 2018. Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method, Zenodo, 10.5281/ZENODO.2025846.","apa":"Garriga, E., di Tommaso, P., Magis, C., Erb, I., Mansouri, L., Baltzis, A., … Notredame, C. (2018). Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method. Zenodo. https://doi.org/10.5281/ZENODO.2025846","ieee":"E. Garriga et al., “Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method.” Zenodo, 2018.","ama":"Garriga E, di Tommaso P, Magis C, et al. Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method. 2018. doi:10.5281/ZENODO.2025846","chicago":"Garriga, Edgar, Paolo di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri, Athanasios Baltzis, Hafid Laayouni, Fyodor Kondrashov, Evan Floden, and Cedric Notredame. “Fast and Accurate Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” Zenodo, 2018. https://doi.org/10.5281/ZENODO.2025846.","mla":"Garriga, Edgar, et al. Fast and Accurate Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method. Zenodo, 2018, doi:10.5281/ZENODO.2025846.","short":"E. Garriga, P. di Tommaso, C. Magis, I. Erb, L. Mansouri, A. Baltzis, H. Laayouni, F. Kondrashov, E. Floden, C. Notredame, (2018)."},"oa":1,"date_published":"2018-12-07T00:00:00Z","doi":"10.5281/ZENODO.2025846","month":"12","day":"07","article_processing_charge":"No"}]