Computational Modeling, Formal Analysis, and Tools for Systems Biology.

As the amount of biological data in the public domain grows, so does the range of modeling and analysis techniques employed in systems biology. In recent years, a number of theoretical computer science developments have enabled modeling methodology to keep pace. The growing interest in systems biology in executable models and their analysis has necessitated the borrowing of terms and methods from computer science, such as formal analysis, model checking, static analysis, and runtime verification. Here, we discuss the most important and exciting computational methods and tools currently available to systems biologists. We believe that a deeper understanding of the concepts and theory highlighted in this review will produce better software practice, improved investigation of complex biological processes, and even new ideas and better feedback into computer science

Computer Aided Verification

This open access two-volume set LNCS 11561 and 11562 constitutes the refereed proceedings of the 31st International Conference on Computer Aided Verification, CAV 2019, held in New York City, USA, in July 2019. The 52 full papers presented together with 13 tool papers and 2 case studies, were carefully reviewed and selected from 258 submissions. The papers were organized in the following topical sections: Part I: automata and timed systems; security and hyperproperties; synthesis; model checking; cyber-physical systems and machine learning; probabilistic systems, runtime techniques; dynamical, hybrid, and reactive systems; Part II: logics, decision procedures; and solvers; numerical programs; verification; distributed systems and networks; verification and invariants; and concurrency

Computer Aided Verification

This open access two-volume set LNCS 13371 and 13372 constitutes the refereed proceedings of the 34rd International Conference on Computer Aided Verification, CAV 2022, which was held in Haifa, Israel, in August 2022. The 40 full papers presented together with 9 tool papers and 2 case studies were carefully reviewed and selected from 209 submissions. The papers were organized in the following topical sections: Part I: Invited papers; formal methods for probabilistic programs; formal methods for neural networks; software Verification and model checking; hyperproperties and security; formal methods for hardware, cyber-physical, and hybrid systems. Part II: Probabilistic techniques; automata and logic; deductive verification and decision procedures; machine learning; synthesis and concurrency. This is an open access book

Méthodes logico-numériques pour la vérification des systèmes discrets et hybrides

Cette thèse étudie la vérification automatique de propriétés de sûreté de systèmes logico-numériques discrets ou hybrides. Ce sont des systèmes ayant des variables booléennes et numériques et des comportements discrets et continus. Notre approche est fondée sur l'analyse statique par interprétation abstraite. Nous adressons les problèmes suivants : les méthodes d'interprétation abstraite numériques exigent l'énumération des états booléens, et par conséquent, ils souffrent du probléme d'explosion d'espace d'états. En outre, il y a une perte de précision due à l'utilisation d'un opérateur d'élargissement afin de garantir la terminaison de l'analyse. Par ailleurs, nous voulons rendre les méthodes d'interprétation abstraite accessibles à des langages de simulation hybrides. Dans cette thèse, nous généralisons d'abord l'accélération abstraite, une méthode qui améliore la précision des invariants numériques inférés. Ensuite, nous montrons comment étendre l'accélération abstraite et l'itération de max-stratégies à des programmes logico-numériques, ce qui aide à améliorer le compromis entre l'efficacité et la précision. En ce qui concerne les systèmes hybrides, nous traduisons le langage de programmation synchrone et hybride Zelus vers les automates hybrides logico-numériques, et nous étendons les méthodes d'analyse logico-numérique aux systèmes hybrides. Enfin, nous avons mis en oeuvre les méthodes proposées dans un outil nommé ReaVer et nous fournissons des résultats expérimentaux. En conclusion, cette thèse propose une approche unifiée à la vérification de systèmes logico-numériques discrets et hybrides fondée sur l'interprétation abstraite qui est capable d'intégrer des méthodes d'interprétation abstraite numériques sophistiquées tout en améliorant le compromis entre l'efficacité et la précision.This thesis studies the automatic verification of safety properties of logico-numerical discrete and hybrid systems. These systems have Boolean and numerical variables and exhibit discrete and continuous behavior. Our approach is based on static analysis using abstract interpretation. We address the following issues: Numerical abstract interpretation methods require the enumeration of the Boolean states, and hence, they suffer from the state space explosion problem. Moreover, there is a precision loss due to widening operators used to guarantee termination of the analysis. Furthermore, we want to make abstract interpretation-based analysis methods accessible to simulation languages for hybrid systems. In this thesis, we first generalize abstract acceleration, a method that improves the precision of the inferred numerical invariants. Then, we show how to extend abstract acceleration and max-strategy iteration to logico-numerical programs while improving the trade-off between efficiency and precision. Concerning hybrid systems, we translate the Zelus hybrid synchronous programming language to logico-numerical hybrid automata and extend logico-numerical analysis methods to hybrid systems. Finally, we implemented the proposed methods in ReaVer, a REActive System VERification tool, and provide experimental results. Concluding, this thesis proposes a unified approach to the verification of discrete and hybrid logico-numerical systems based on abstract interpretation, which is capable of integrating sophisticated numerical abstract interpretation methods while successfully trading precision for efficiency.SAVOIE-SCD - Bib.électronique (730659901) / SudocGRENOBLE1/INP-Bib.électronique (384210012) / SudocGRENOBLE2/3-Bib.électronique (384219901) / SudocSudocFranceF

Computer Aided Verification

This open access two-volume set LNCS 10980 and 10981 constitutes the refereed proceedings of the 30th International Conference on Computer Aided Verification, CAV 2018, held in Oxford, UK, in July 2018. The 52 full and 13 tool papers presented together with 3 invited papers and 2 tutorials were carefully reviewed and selected from 215 submissions. The papers cover a wide range of topics and techniques, from algorithmic and logical foundations of verification to practical applications in distributed, networked, cyber-physical, and autonomous systems. They are organized in topical sections on model checking, program analysis using polyhedra, synthesis, learning, runtime verification, hybrid and timed systems, tools, probabilistic systems, static analysis, theory and security, SAT, SMT and decisions procedures, concurrency, and CPS, hardware, industrial applications

Computer Aided Verification

This open access two-volume set LNCS 11561 and 11562 constitutes the refereed proceedings of the 31st International Conference on Computer Aided Verification, CAV 2019, held in New York City, USA, in July 2019. The 52 full papers presented together with 13 tool papers and 2 case studies, were carefully reviewed and selected from 258 submissions. The papers were organized in the following topical sections: Part I: automata and timed systems; security and hyperproperties; synthesis; model checking; cyber-physical systems and machine learning; probabilistic systems, runtime techniques; dynamical, hybrid, and reactive systems; Part II: logics, decision procedures; and solvers; numerical programs; verification; distributed systems and networks; verification and invariants; and concurrency

Computer Aided Verification

This open access two-volume set LNCS 10980 and 10981 constitutes the refereed proceedings of the 30th International Conference on Computer Aided Verification, CAV 2018, held in Oxford, UK, in July 2018. The 52 full and 13 tool papers presented together with 3 invited papers and 2 tutorials were carefully reviewed and selected from 215 submissions. The papers cover a wide range of topics and techniques, from algorithmic and logical foundations of verification to practical applications in distributed, networked, cyber-physical, and autonomous systems. They are organized in topical sections on model checking, program analysis using polyhedra, synthesis, learning, runtime verification, hybrid and timed systems, tools, probabilistic systems, static analysis, theory and security, SAT, SMT and decisions procedures, concurrency, and CPS, hardware, industrial applications

Tools and Algorithms for the Construction and Analysis of Systems

This book is Open Access under a CC BY licence. The LNCS 11427 and 11428 proceedings set constitutes the proceedings of the 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems, TACAS 2019, which took place in Prague, Czech Republic, in April 2019, held as part of the European Joint Conferences on Theory and Practice of Software, ETAPS 2019. The total of 42 full and 8 short tool demo papers presented in these volumes was carefully reviewed and selected from 164 submissions. The papers are organized in topical sections as follows: Part I: SAT and SMT, SAT solving and theorem proving; verification and analysis; model checking; tool demo; and machine learning. Part II: concurrent and distributed systems; monitoring and runtime verification; hybrid and stochastic systems; synthesis; symbolic verification; and safety and fault-tolerant systems