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Blanchette, J. C., Gheri, L., Popescu, A., & Traytel, D. (2019). Bindings as Bounded Natural Functors. Proceedings of the ACM on Programming Languages (Proc. POPL 2019), 3. doi:10.1145/3290335
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@article{Blanchette_POPL2019, TITLE = {Bindings as Bounded Natural Functors}, AUTHOR = {Blanchette, Jasmin Christian and Gheri, Lorenzo and Popescu, Andrei and Traytel, Dmitriy}, LANGUAGE = {eng}, ISSN = {2475-1421}, DOI = {10.1145/3290335}, PUBLISHER = {ACM}, ADDRESS = {New York, NY}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, JOURNAL = {Proceedings of the ACM on Programming Languages (Proc. POPL)}, VOLUME = {3}, EID = {22}, BOOKTITLE = {46th ACM SIGPLAN Symposium on Principles of Programming Languages (POPL 2019)}, }
Endnote
%0 Journal Article %A Blanchette, Jasmin Christian %A Gheri, Lorenzo %A Popescu, Andrei %A Traytel, Dmitriy %+ Automation of Logic, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations %T Bindings as Bounded Natural Functors : %G eng %U http://hdl.handle.net/21.11116/0000-0002-E59A-E %R 10.1145/3290335 %7 2019 %D 2019 %J Proceedings of the ACM on Programming Languages %O PACMPL %V 3 %Z sequence number: 22 %I ACM %C New York, NY %@ false %B 46th ACM SIGPLAN Symposium on Principles of Programming Languages %O POPL 2019 Sun 13 - Sat 19 January 2019 Cascais, Portugal
Blanchette, J. C. (2019). Formalizing the Metatheory of Logical Calculi and Automatic Provers in Isabelle/HOL (Invited Talk). In CPP’19, 8th ACM SIGPLAN International Conference onCertified Programs and Proofs. Cascais, Portugal: ACM. doi:10.1145/3293880.3294087
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@inproceedings{Blanchette_CPP2019, TITLE = {Formalizing the metatheory of logical calculi and automatic provers in {I}sabelle/{HOL} (invited talk)}, AUTHOR = {Blanchette, Jasmin Christian}, LANGUAGE = {eng}, ISBN = {978-1-4503-6222-1}, DOI = {10.1145/3293880.3294087}, PUBLISHER = {ACM}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, DATE = {2019}, BOOKTITLE = {CPP'19, 8th ACM SIGPLAN International Conference onCertified Programs and Proofs}, EDITOR = {Mahboubi, Assia and Myreen, Magnus O.}, PAGES = {1--13}, ADDRESS = {Cascais, Portugal}, }
Endnote
%0 Conference Proceedings %A Blanchette, Jasmin Christian %+ Automation of Logic, MPI for Informatics, Max Planck Society %T Formalizing the Metatheory of Logical Calculi and Automatic Provers in Isabelle/HOL (Invited Talk) : %G eng %U http://hdl.handle.net/21.11116/0000-0002-E5A0-6 %R 10.1145/3293880.3294087 %D 2019 %B 8th ACM SIGPLAN International Conference onCertified Programs and Proofs %Z date of event: 2019-01-14 - 2019-01-15 %C Cascais, Portugal %B CPP'19 %E Mahboubi, Assia; Myreen, Magnus O. %P 1 - 13 %I ACM %@ 978-1-4503-6222-1
Bradford, R., Davenport, J. H., England, M., Errami, H., Gerdt, V., Grigoriev, D., … Weber, A. (n.d.). Identifying the Parametric Occurrence of Multiple Steady States for some Biological Networks. Journal of Symbolic Computation.
(Accepted/in press)
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@article{BradfordDavenport:19a, TITLE = {Identifying the Parametric Occurrence of Multiple Steady States for some Biological Networks}, AUTHOR = {Bradford, Russell and Davenport, James H. and England, Matthew and Errami, Hassan and Gerdt, Vladimir and Grigoriev, Dima and Hoyt, Charles and Ko{\v s}ta, Marek and Radulescu, Ovidiu and Sturm, Thomas and Weber, Andreas}, LANGUAGE = {eng}, ISSN = {0747-7171}, PUBLISHER = {Academic Press}, ADDRESS = {London}, YEAR = {2019}, PUBLREMARK = {Accepted}, MARGINALMARK = {$\bullet$}, JOURNAL = {Journal of Symbolic Computation}, }
Endnote
%0 Journal Article %A Bradford, Russell %A Davenport, James H. %A England, Matthew %A Errami, Hassan %A Gerdt, Vladimir %A Grigoriev, Dima %A Hoyt, Charles %A Košta, Marek %A Radulescu, Ovidiu %A Sturm, Thomas %A Weber, Andreas %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Automation of Logic, MPI for Informatics, Max Planck Society External Organizations %T Identifying the Parametric Occurrence of Multiple Steady States for some Biological Networks : %G eng %U http://hdl.handle.net/21.11116/0000-0002-F04B-B %D 2019 %J Journal of Symbolic Computation %I Academic Press %C London %@ false
Bradford, R., Davenport, J. H., England, M., Errami, H., Gerdt, V., Grigoriev, D., … Weber, A. (2019). Identifying the Parametric Occurrence of Multiple Steady States for some Biological Networks. Retrieved from http://arxiv.org/abs/1902.04882
(arXiv: 1902.04882)
Abstract
We consider a problem from biological network analysis of determining regions in a parameter space over which there are multiple steady states for positive real values of variables and parameters. We describe multiple approaches to address the problem using tools from Symbolic Computation. We describe how progress was made to achieve semi-algebraic descriptions of the multistationarity regions of parameter space, and compare symbolic results to numerical methods. The biological networks studied are models of the mitogen-activated protein kinases (MAPK) network which has already consumed considerable effort using special insights into its structure of corresponding models. Our main example is a model with 11 equations in 11 variables and 19 parameters, 3 of which are of interest for symbolic treatment. The model also imposes positivity conditions on all variables and parameters. We apply combinations of symbolic computation methods designed for mixed equality/inequality systems, specifically virtual substitution, lazy real triangularization and cylindrical algebraic decomposition, as well as a simplification technique adapted from Gaussian elimination and graph theory. We are able to determine multistationarity of our main example over a 2-dimensional parameter space. We also study a second MAPK model and a symbolic grid sampling technique which can locate such regions in 3-dimensional parameter space.
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@online{Bradford_arXiv1902.04882, TITLE = {Identifying the Parametric Occurrence of Multiple Steady States for some Biological Networks}, AUTHOR = {Bradford, Russell and Davenport, James H. and England, Matthew and Errami, Hassan and Gerdt, Vladimir and Grigoriev, Dima and Hoyt, Charles and Ko{\v s}ta, Marek and Radulescu, Ovidiu and Sturm, Thomas and Weber, Andreas}, LANGUAGE = {eng}, URL = {http://arxiv.org/abs/1902.04882}, EPRINT = {1902.04882}, EPRINTTYPE = {arXiv}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, ABSTRACT = {We consider a problem from biological network analysis of determining regions in a parameter space over which there are multiple steady states for positive real values of variables and parameters. We describe multiple approaches to address the problem using tools from Symbolic Computation. We describe how progress was made to achieve semi-algebraic descriptions of the multistationarity regions of parameter space, and compare symbolic results to numerical methods. The biological networks studied are models of the mitogen-activated protein kinases (MAPK) network which has already consumed considerable effort using special insights into its structure of corresponding models. Our main example is a model with 11 equations in 11 variables and 19 parameters, 3 of which are of interest for symbolic treatment. The model also imposes positivity conditions on all variables and parameters. We apply combinations of symbolic computation methods designed for mixed equality/inequality systems, specifically virtual substitution, lazy real triangularization and cylindrical algebraic decomposition, as well as a simplification technique adapted from Gaussian elimination and graph theory. We are able to determine multistationarity of our main example over a 2-dimensional parameter space. We also study a second MAPK model and a symbolic grid sampling technique which can locate such regions in 3-dimensional parameter space.}, }
Endnote
%0 Report %A Bradford, Russell %A Davenport, James H. %A England, Matthew %A Errami, Hassan %A Gerdt, Vladimir %A Grigoriev, Dima %A Hoyt, Charles %A Košta, Marek %A Radulescu, Ovidiu %A Sturm, Thomas %A Weber, Andreas %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Automation of Logic, MPI for Informatics, Max Planck Society External Organizations %T Identifying the Parametric Occurrence of Multiple Steady States for some Biological Networks : %G eng %U http://hdl.handle.net/21.11116/0000-0002-FF3C-D %U http://arxiv.org/abs/1902.04882 %D 2019 %X We consider a problem from biological network analysis of determining regions in a parameter space over which there are multiple steady states for positive real values of variables and parameters. We describe multiple approaches to address the problem using tools from Symbolic Computation. We describe how progress was made to achieve semi-algebraic descriptions of the multistationarity regions of parameter space, and compare symbolic results to numerical methods. The biological networks studied are models of the mitogen-activated protein kinases (MAPK) network which has already consumed considerable effort using special insights into its structure of corresponding models. Our main example is a model with 11 equations in 11 variables and 19 parameters, 3 of which are of interest for symbolic treatment. The model also imposes positivity conditions on all variables and parameters. We apply combinations of symbolic computation methods designed for mixed equality/inequality systems, specifically virtual substitution, lazy real triangularization and cylindrical algebraic decomposition, as well as a simplification technique adapted from Gaussian elimination and graph theory. We are able to determine multistationarity of our main example over a 2-dimensional parameter space. We also study a second MAPK model and a symbolic grid sampling technique which can locate such regions in 3-dimensional parameter space. %K Computer Science, Symbolic Computation, cs.SC
Schlichtkrull, A., Blanchette, J. C., & Traytel, D. (2019). A Verified Prover Based on Ordered Resolution. In CPP’19, 8th ACM SIGPLAN International Conference onCertified Programs and Proofs. Cascais, Portugal: ACM. doi:10.1145/3293880.3294100
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@inproceedings{Schlichtkrull_CPP2019, TITLE = {A Verified Prover Based on Ordered Resolution}, AUTHOR = {Schlichtkrull, Anders and Blanchette, Jasmin Christian and Traytel, Dmitriy}, LANGUAGE = {eng}, ISBN = {978-1-4503-6222-1}, DOI = {10.1145/3293880.3294100}, PUBLISHER = {ACM}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, DATE = {2019}, BOOKTITLE = {CPP'19, 8th ACM SIGPLAN International Conference onCertified Programs and Proofs}, EDITOR = {Mahboubi, Assia and Myreen, Magnus O.}, PAGES = {152--165}, ADDRESS = {Cascais, Portugal}, }
Endnote
%0 Conference Proceedings %A Schlichtkrull, Anders %A Blanchette, Jasmin Christian %A Traytel, Dmitriy %+ External Organizations Automation of Logic, MPI for Informatics, Max Planck Society External Organizations %T A Verified Prover Based on Ordered Resolution : %G eng %U http://hdl.handle.net/21.11116/0000-0002-E59E-A %R 10.1145/3293880.3294100 %D 2019 %B 8th ACM SIGPLAN International Conference onCertified Programs and Proofs %Z date of event: 2019-01-14 - 2019-01-15 %C Cascais, Portugal %B CPP'19 %E Mahboubi, Assia; Myreen, Magnus O. %P 152 - 165 %I ACM %@ 978-1-4503-6222-1
Tourret, S., & Cropper, A. (n.d.). SLD-Resolution Reduction of Second-Order Horn Fragments. In 16th edition of the European Conference on Logics in Artificial Intelligence (JELIA 2019). Rende, Italy: Springer.
(Accepted/in press)
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@inproceedings{Tourret_JELIA2019, TITLE = {{SLD}-Resolution Reduction of Second-Order {H}orn Fragments}, AUTHOR = {Tourret, Sophie and Cropper, Andrew}, LANGUAGE = {eng}, PUBLISHER = {Springer}, YEAR = {2019}, PUBLREMARK = {Accepted}, MARGINALMARK = {$\bullet$}, BOOKTITLE = {16th edition of the European Conference on Logics in Artificial Intelligence (JELIA 2019)}, SERIES = {Lecture Notes in Computer Science}, ADDRESS = {Rende, Italy}, }
Endnote
%0 Conference Proceedings %A Tourret, Sophie %A Cropper, Andrew %+ Automation of Logic, MPI for Informatics, Max Planck Society External Organizations %T SLD-Resolution Reduction of Second-Order Horn Fragments : %G eng %U http://hdl.handle.net/21.11116/0000-0002-D2B3-6 %D 2019 %B 16th European Conference on Logics in Artificial Intelligence %Z date of event: 2019-05-08 - 2019-05-10 %C Rende, Italy %B 16th edition of the European Conference on Logics in Artificial Intelligence %I Springer %B Lecture Notes in Computer Science