Enhanced Distributed Behavioral Cartography of Parametric Timed Automata

André, Étienne; Coti, Camille; Nguyen, Hoang Gia

doi:10.1007/978-3-319-25423-4_21

Cited by 6 publications

(4 citation statements)

References 18 publications

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“…This problem can therefore be connected to the MCS problem, in which the computation time to find a common subgraph and how the domain can be decomposed cannot be known before the common subgraph has been found. Heuristics and dynamic algorithms have been designed and evaluated in [1, 2]. Their conclusion is that for small parameter spaces, a random distribution of points works well, and for larger parameter spaces, a dynamic domain decomposition with work stealing works better.…”

Section: Related Workmentioning

confidence: 99%

Parallel maximal common subgraphs with labels for molecular biology

Agbeto,

Coti,

Reinharz

2024

Preprint

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Advances in graph algorithmics have allowed in-depth study of many natural objects from molecular biology or chemistry to social networks. Particularly in molecular biology and cheminformatics, understanding complex structures by identifying conserved sub-structures is a key milestone towards the artificial design of novel components with specific functions. Given a dataset of structures, we are interested in identifying all maximum common connected partial subgraphs between each pair of graphs, a task notoriously NP-Hard. In this work, we present 3 parallel algorithms over shared and distributed memory to enumerate all maximal connected common sub-graphs between pairs of arbitrary multi-directed graphs with labels on their edges. We offer an implementation of these methods and evaluate their performance on the non-redundant dataset of all known RNA 3D structures. We show that we can compute the exact results in a reasonable time for each pairwise comparison while taking into account a much more diverse set of interactions---resulting in much denser graphs---resulting in an order of magnitude more conserved modules. All code is available at https://gitlab.info.uqam.ca/cbe/pasigraph and results in the branch results.

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Section: Related Workmentioning

confidence: 99%

Parallel maximal common subgraphs with labels for molecular biology

Agbeto,

Coti,

Reinharz

2024

Preprint

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“…IMITATOR features a number of additional algorithms, including i) non-Zeno infinite run synthesis [27], ii) behavioral cartography [16] that partitions the parameter space into tiles where the discrete behavior is uniform, or iii) parametric reachability preservation, that takes as input a discrete state and a reference valuation, and synthesizes valuations for which this discrete state is reachable iff it is reachable for the reference valuation [25]. The two latter algorithms can be distributed over a cluster, showing interesting results, and can be used to perform reachability synthesis while being faster than the normal reachability synthesis algorithm for some benchmarks [14,15]. Finally, compositional verification for a subclass of IPTAs (a parametric extension of event-recording automata [4]) was proposed in [24].…”

Section: # Synth Deadlockfreementioning

confidence: 99%

IMITATOR 3: Synthesis of Timing Parameters Beyond Decidability

André

2021

Computer Aided Verification

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Real-time systems are notoriously hard to verify due to nondeterminism, concurrency and timing constraints. When timing constants are uncertain (in early the design phase, or due to slight variations of the timing bounds), timed model checking techniques may not be satisfactory. In contrast, parametric timed model checking synthesizes timing values ensuring correctness. takes as input an extension of parametric timed automata (PTAs), a powerful formalism to formally verify critical real-time systems. extends PTAs with multi-rate clocks, global rational-valued variables and a set of additional useful features. We describe here the new features and algorithms offered by 3, that moved along the years from a simple prototype dedicated to robustness analysis to a standalone parametric model checker for timed systems.

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“…robustness: synthesize parameter valuations preserving the discrete behavior (untimed language) w.r.t. to a given valuation (see e. g., [ACEF09,San15]).…”

Section: Propertiesmentioning

confidence: 99%

A Benchmark Library for Parametric Timed Model Checking

André

2019

Communications in Computer and Information Science

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Verification of real-time systems involving hard timing constraints and concurrency is of utmost importance. Parametric timed model checking allows for formal verification in the presence of unknown timing constants or uncertainty (e. g., imprecision for periods). With the recent development of several techniques and tools to improve the efficiency of parametric timed model checking, there is a growing need for proper benchmarks to test and compare fairly these tools. We present here a benchmark library for parametric timed model checking made of benchmarks accumulated over the years. Our benchmarks include academic benchmarks, industrial case studies and examples unsolvable using existing techniques.

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Enhanced Distributed Behavioral Cartography of Parametric Timed Automata

Cited by 6 publications

References 18 publications

Parallel maximal common subgraphs with labels for molecular biology

Parallel maximal common subgraphs with labels for molecular biology

IMITATOR 3: Synthesis of Timing Parameters Beyond Decidability

A Benchmark Library for Parametric Timed Model Checking

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