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Under-Approximating Cut Sets for Reachability in Large Scale Automata Networks [chapter]

Loïc Paulevé, Geoffroy Andrieux, Heinz Koeppl
2013 Lecture Notes in Computer Science  
The extracted sets of local states form an under-approximation of the complete minimal cut sets of the dynamics: there may exist smaller or additional cut sets for the given reachability.  ...  Our new method makes tractable the formal analysis of very large scale networks, as illustrated by the computation of cut sets within a Boolean model of biological pathways interactions gathering more  ...  LP and GA acknowledge the partial support of the French National Agency for Research (ANR-10-BLANC-0218 BioTempo project).  ... 
doi:10.1007/978-3-642-39799-8_4 fatcat:w43ha7cmlfhotf5vragcgnfxbi

Sufficient conditions for reachability in automata networks with priorities

Maxime Folschette, Loïc Paulevé, Morgan Magnin, Olivier Roux
2015 Theoretical Computer Science  
In this paper, we develop a framework for an efficient under-approximation of the dynamics of Asynchronous Automata Networks (AANs).  ...  Finally, we illustrate our method for the model checking of large-scale biological networks.  ...  Large-scale Applications In order to support the scalability and applicability of our under-approximation of reachability, we apply our new approach to the analysis of two large-scale models: a T-cell  ... 
doi:10.1016/j.tcs.2015.08.040 fatcat:4elqijzqcjgftbwymoup66whry

Identification of bifurcation transitions in biological regulatory networks using Answer-Set Programming

Louis Fippo Fitime, Olivier Roux, Carito Guziolowski, Loïc Paulevé
2017 Algorithms for Molecular Biology  
Our method combines Answer-Set Programming with static analysis of reachability properties to provide an under-approximation of all the existing bifurcations.  ...  Methods: In the context of non-deterministic automata networks, we propose a static identification of so-called bifurcations, i.e., transitions after which a given goal is no longer reachable.  ...  Availability of data and materials Models and scripts are provided in Additional file 2. Funding CG was supported by the CNRS chair of excellence funding.  ... 
doi:10.1186/s13015-017-0110-3 pmid:28736575 pmcid:PMC5520421 fatcat:bfhej6xuwjhltonh4a344cezei

Reduction of Qualitative Models of Biological Networks for Transient Dynamics Analysis

Loic Pauleve
2018 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
Applied to different large-scale biological networks from the litterature, we show that the reduction can lead to drastic improvement for the scalability of verification methods.  ...  In this paper, we describe a method to reduce a qualitative model for enhancing the tractability of analysis of transient reachability properties.  ...  cut set for the goal reachability.  ... 
doi:10.1109/tcbb.2017.2749225 pmid:28885158 fatcat:hrkd4jhc7be6xbw5w6gc2mlrqu

Some progress in the symbolic verification of timed automata [chapter]

Marius Bozga, Oded Maler, Amir Pnueli, Sergio Yovine
1997 Lecture Notes in Computer Science  
In this paper we discuss the practical di culty of analyzing the behavior of timed automata and report some results obtained using an experimental bdd-based extension of kronos.  ...  of timed automata veri cation tools.  ...  An array of such automata is an unavoidable component in any model for analyzing the behavior of circuits under all possible inputs.  ... 
doi:10.1007/3-540-63166-6_19 fatcat:26en2yzqyjg2hb5er6zkdocmwu

Analyzing Large Network Dynamics with Process Hitting [chapter]

Loïc Paulevé, Courtney Chancellor, Maxime Folschette, Morgan Magnin, Olivier Roux
2014 Logical Modeling of Biological Systems  
Regulation is a key aspect of biological systems, all the way from the molecular scale to the ecological one.  ...  The recent progress in molecular biology has made it possible to obtain a comprehensive map of the genomes of many living organisms.  ...  Finally, we briefly present benchmarks of PINT for the analysis of reachability and cut sets on large scale networks, up to 100 and approximatively 10,000 components.  ... 
doi:10.1002/9781119005223.ch4 fatcat:bnaoysvnrneqbb6mmnp4uhmcqi

Making the Right Cut in Model Checking Data-Intensive Timed Systems [chapter]

Rüdiger Ehlers, Michael Gerke, Hans-Jörg Peter
2010 Lecture Notes in Computer Science  
In this paper, we introduce a simple general framework for combining both data structures, enabling a joint symbolic representation of the timed state sets in the reachability fixed point construction.  ...  While difference bound matrices (DBMs) are effective for representing sets of clock values, binary decision diagrams (BDDs) can efficiently represent huge discrete state sets.  ...  Timed automata can be composed to networks, in which the automata run in parallel and synchronize on shared actions.  ... 
doi:10.1007/978-3-642-16901-4_37 fatcat:m64gkdflrfbetjjbi4ifdzfr4u

Computing reachable states for nonlinear biological models

Thao Dang, Colas Le Guernic, Oded Maler
2011 Theoretical Computer Science  
In this paper, we describe reachability computation for continuous and hybrid systems and its potential contribution to the process of building and debugging biological models.  ...  We summarize the state-of-the-art for linear systems and then develop a novel algorithm for computing reachable states for nonlinear systems.  ...  Girard for their contribution to the hybridization technique. E. Fanchon and Ph. Tracqui initiated our interest in angiogenesis. Special thanks to A. Donzé for preparing the angiogenesis model and R.  ... 
doi:10.1016/j.tcs.2011.01.014 fatcat:p2pyk4aulbcghlzerijychsmla

Computing Reachable States for Nonlinear Biological Models [chapter]

Thao Dang, Colas Le Guernic, Oded Maler
2009 Lecture Notes in Computer Science  
In this paper, we describe reachability computation for continuous and hybrid systems and its potential contribution to the process of building and debugging biological models.  ...  We summarize the state-of-the-art for linear systems and then develop a novel algorithm for computing reachable states for nonlinear systems.  ...  Girard for their contribution to the hybridization technique. E. Fanchon and Ph. Tracqui initiated our interest in angiogenesis. Special thanks to A. Donzé for preparing the angiogenesis model and R.  ... 
doi:10.1007/978-3-642-03845-7_9 fatcat:ac54vmltbncjdgwuymzeb4l6zm

AMYTISS: Parallelized Automated Controller Synthesis for Large-Scale Stochastic Systems [chapter]

Abolfazl Lavaei, Mahmoud Khaled, Sadegh Soudjani, Majid Zamani
2020 Lecture Notes in Computer Science  
In this paper, we propose a software tool, called AMYTISS, implemented in C++/OpenCL, for designing correct-by-construction controllers for large-scale discrete-time stochastic systems.  ...  is always present in analyzing large-scale stochastic systems.  ...  The authors would like to thank Thomas Gabler for his help in implementing traditional serial algorithms for the purpose of analysis and then comparing with the parallel ones.  ... 
doi:10.1007/978-3-030-53291-8_24 fatcat:jsbksoaoczgrnmufodo3uplvtq

Characterizing and Mining the Citation Graph of the Computer Science Literature

Yuan An, Jeannette Janssen, Evangelos E. Milios
2004 Knowledge and Information Systems  
Finally, minimum cuts between authority papers of different areas did not result in a balanced partitioning of the graph into areas, pointing to the need for more sophisticated algorithms for clustering  ...  We discovered the existence of a single large weakly-connected and a single large biconnected component, and confirmed the expected lack of a large strongly-connected component.  ...  As to structural analysis of large scale networks, Broder et al.  ... 
doi:10.1007/s10115-003-0128-3 fatcat:5zhhqvnwinf3pa4ydx4unpbugy

Transformations for Compositional Verification of Assumption-Commitment Properties [chapter]

Ahmed Mahdi, Bernd Westphal, Martin Fränzle
2014 Lecture Notes in Computer Science  
and finite automata.  ...  Our approach applies to all computational models where an automaton syntax with locations and edges induces a transition system semantics in a consistent way which is the case for hybrid, timed, Büchi,  ...  Further work consists of an investigation of further uses of the notion of supporting edges, for example to indicate cut-points in a model where automata which over-approximate certain features of a multi-feature  ... 
doi:10.1007/978-3-319-11439-2_17 fatcat:qq4nb7yirzhdjhpz7kjdy5z2sm

Computational Analysis of Large-Scale Multi-affine ODE Models

Lubos Brim, Jiri Barnat, Ivana Cerna, Sven Drazan, Jana Fabrikova, David Safranek
2009 2009 International Workshop on High Performance Computational Systems Biology  
Complexity of these networks is inherently enormous, even for simple (e.g., procaryotic) organisms.  ...  Effects of different settings of the heuristics is firstly compared on a set of experiments performed on small models. Subsequently, experiments on large models are provided as well.  ...  In higher organisms, these modules form large and complex interaction networks.  ... 
doi:10.1109/hibi.2009.14 fatcat:opqtc34plzbzfnkgmlctk7ywva

Estimating node connectedness in spatial network under stochastic link disconnection based on efficient sampling

Takayasu Fushimi, Kazumi Saito, Tetsuo Ikeda, Kazuhiro Kazama
2019 Applied Network Science  
In a large-scale network, however, since the number of combinations of possible graphs is enormous, it is difficult to strictly calculate the expected value.  ...  set reachable from more nodes even in a situation that many links are deleted; and 3) computes much more efficient, compared to existing centrality measures and community extraction methods.  ...  Seiya Okubo of the University of Shizuoka, Shizuoka, Japan, for supporting computation environments.  ... 
doi:10.1007/s41109-019-0187-3 fatcat:kp6vsssavjewbpbzh5bzack6na

Computational Issues in Intelligent Control: Discrete-Event and Hybrid Systems [chapter]

XENOFON D. KOUTSOUKOS, PANOS J. ANTSAKLIS
2000 Soft Computing and Intelligent Systems  
In view of hybrid systems, we also review basic computational issues for hybrid automata.  ...  In this paper, we identify and discuss several computational issues that are central in intelligent control.  ...  Nikos Chrisochoides of the Computer Science and Engineering Department at the University of Notre Dame for his valuable assistance concerning the parallel computing architecture.  ... 
doi:10.1016/b978-012646490-0/50006-8 fatcat:tpqu57oywrhwtfcrvohzhr3trq
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