Forward Analysis for WSTS, Part III: Karp-Miller Trees

This paper is a sequel of "Forward Analysis for WSTS, Part I: Completions" [STACS 2009, LZI Intl. Proc. in Informatics 3, 433-444] and "Forward Analysis for WSTS, Part II: Complete WSTS" [Logical Methods in Computer Science 8(3), 2012]. In these two papers, we provided a framework to conduct forward reachability analyses of WSTS, using finite representations of downward-closed sets. We further develop this framework to obtain a generic Karp-Miller algorithm for the new class of very-WSTS. This allows us to show that coverability sets of very-WSTS can be computed as their finite ideal decompositions. Under natural effectiveness assumptions, we also show that LTL model checking for very-WSTS is decidable. The termination of our procedure rests on a new notion of acceleration levels, which we study. We characterize those domains that allow for only finitely many accelerations, based on ordinal ranks

Simulation-based model checking approach to cell fate specification during Caenorhabditis elegans vulval development by hybrid functional Petri net with extension

<p>Abstract</p> <p>Background</p> <p>Model checking approaches were applied to biological pathway validations around 2003. Recently, Fisher <it>et al</it>. have proved the importance of model checking approach by inferring new regulation of signaling crosstalk in <it>C. elegans </it>and confirming the regulation with biological experiments. They took a discrete and state-based approach to explore all possible states of the system underlying vulval precursor cell (VPC) fate specification for desired properties. However, since both discrete and continuous features appear to be an indispensable part of biological processes, it is more appropriate to use quantitative models to capture the dynamics of biological systems. Our key motivation of this paper is to establish a quantitative methodology to model and analyze <it>in silico </it>models incorporating the use of model checking approach.</p> <p>Results</p> <p>A novel method of modeling and simulating biological systems with the use of model checking approach is proposed based on hybrid functional Petri net with extension (HFPNe) as the framework dealing with both discrete and continuous events. Firstly, we construct a quantitative VPC fate model with 1761 components by using HFPNe. Secondly, we employ two major biological fate determination rules – Rule I and Rule II – to VPC fate model. We then conduct 10,000 simulations for each of 48 sets of different genotypes, investigate variations of cell fate patterns under each genotype, and validate the two rules by comparing three simulation targets consisting of fate patterns obtained from <it>in silico </it>and <it>in vivo </it>experiments. In particular, an evaluation was successfully done by using our VPC fate model to investigate one target derived from biological experiments involving hybrid lineage observations. However, the understandings of hybrid lineages are hard to make on a discrete model because the hybrid lineage occurs when the system comes close to certain thresholds as discussed by Sternberg and Horvitz in 1986. Our simulation results suggest that: Rule I that cannot be applied with qualitative based model checking, is more reasonable than Rule II owing to the high coverage of predicted fate patterns (except for the genotype of <it>lin-15ko; lin-12ko </it>double mutants). More insights are also suggested.</p> <p>Conclusion</p> <p>The quantitative simulation-based model checking approach is a useful means to provide us valuable biological insights and better understandings of biological systems and observation data that may be hard to capture with the qualitative one.</p

Computer Aided Verification

The 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 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

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

Criteria to Evaluate Voting Indicators and a Recipe for a New One

This paper is made up of two interrelated parts. Part I contains a critical evaluation of the so called StemWijzer 2002, an internet application that helped and advised voters which political party to choose at the Dutch, German and Suisse parliamentary elections. Applying some validity tests and checking the discriminatory power, it is argued that the StemWijzer 2002 is seriously flawed. Part II is devoted to designing an interactive voting indicator, where the propositions to be evaluated by the voter depends on his responses to other propositions at an earlier stage. The viability of such an indicator hinges on the possibility to determine the partisanship leaning (leftist or rightist) of voters by means of a limited number of questions. For this purpose a rather minimalist voting indicator (the VoteFork) was developed. The empirical results show that it is indeed possible to ascertain for the majority of voters whether they belong to left-wing or right-wing parties. In this part I also present a simple model which can be used as a benchmark to assess the quality of voting indicators, where quality is simply defined as the fraction of correct voting advises. This paper is pioneering in the sense that yet no serious attention is paid to voting indicators in general, to the criteria they should ideally meet and to the possibility to make them interactive. Comments are welcome.voting indicator

The Difference Prevention Makes: Regulating Preventive Justice

Since the terrorist attacks of September 11, 2001, the United States and many other countries have adopted a ‘‘paradigm of prevention,’’ employing a range of measures in an attempt to prevent future terrorist attacks. This includes the use of pre textual charges for preventive detention, the expansion of criminal liability to prohibit conduct that precedes terrorism, and expansion of surveillance at home and abroad. Politicians and government officials often speak of prevention as if it is an unqualified good. Everyone wants to prevent the next terrorist attack, after all. And many preventive initiatives, especially where they are not coercive and do not intrude on liberty, are welcome. But the move to a ‘‘preventive justice’’ model also creates potential for significant abuse. These risks suggest that we should be cautious about adopting preventive approaches, especially where they involve coercion. In part I of this essay, I articulate why preventive coercion is a problem. I respond, in particular, to a recent essay by Fred Schauer, ‘‘The Ubiquity of Prevention,’’ which argued that ‘‘it is a mistake to assume that preventive justice is a problem in itself [because] preventive justice is all around us, and it is hard to imagine a functioning society that could avoid it.’’ In part II, I outline the formal constitutional and other constraints that are implicated by preventive measures in the United States, and I demonstrate that these constraints play a relatively small role in the actual operation of preventive measures. In part III, I maintain that informal constraints may actually play a more significant operational role in checking the abuses of prevention