arXiv subjects

Nikola Beneš

Publications and source records attributed to Nikola Beneš.

7 recordsLinked to original sources

arXiv2026

Inference of Qualitative Models from Steady-State Data via Weighted MaxSMT

Qualitative models provide crucial instruments for modelling complex biological systems. While advances in automated reasoning and symbolic encodings have enabled rigorous inference of these models from data, the process remains highly fragile. First, biological measurement errors inevitably propagate into formal model specifications. Second, when a specification becomes unsatisfiable, distinguishing between fundamental design flaws and minor technical errors is notoriously difficult. This uncertainty often leads to under-specification, as it is unclear which observations are still ``safe'' to incorporate. To overcome these challenges, we introduce a robust inference method based on weighted MaxSMT. By encoding uncertain biological observations as weighted soft constraints, our approach enables the solver to identify a model best reflecting the observations, even with some conflicting constraints. Our method allows for Boolean and multi-valued variable domains, alongside observations derived from discretisation (level constraints) and differential expression (ordering constraints). We show our approach can be used to successfully infer neural cell differentiation models from prior-knowledge networks with 200--1300 genes using ordering constraints on all included genes.

q-bio.MN↗

arXiv2022

BDD-Based Algorithm for SCC Decomposition of Edge-Coloured Graphs

Edge-coloured directed graphs provide an essential structure for modelling and analysis of complex systems arising in many scientific disciplines (e.g. feature-oriented systems, gene regulatory networks, etc.). One of the fundamental problems for edge-coloured graphs is the detection of strongly connected components, or SCCs. The size of edge-coloured graphs appearing in practice can be enormous both in the number of vertices and colours. The large number of vertices prevents us from analysing such graphs using explicit SCC detection algorithms, such as Tarjan's, which motivates the use of a symbolic approach. However, the large number of colours also renders existing symbolic SCC detection algorithms impractical. This paper proposes a novel algorithm that symbolically computes all the monochromatic strongly connected components of an edge-coloured graph. In the worst case, the algorithm performs $O(p \cdot n \cdot log~n)$ symbolic steps, where $p$ is the number of colours and $n$ is the number of vertices. We evaluate the algorithm using an experimental implementation based on binary decision diagrams (BDDs). Specifically, we use our implementation to explore the SCCs of a large collection of coloured graphs (up to $2^{48}$) obtained from Boolean networks -- a modelling framework commonly appearing in systems biology.

cs.DS↗

arXiv2016

LTL Parameter Synthesis of Parametric Timed Automata

The parameter synthesis problem for parametric timed automata is undecidable in general even for very simple reachability properties. In this paper we introduce restrictions on parameter valuations under which the parameter synthesis problem is decidable for LTL properties. The investigated bounded integer parameter synthesis problem could be solved using an explicit enumeration of all possible parameter valuations. We propose an alternative symbolic zone-based method for this problem which results in a faster computation. Our technique extends the ideas of the automata-based approach to LTL model checking of timed automata. To justify the usefulness of our approach, we provide experimental evaluation and compare our method with explicit enumeration technique.

cs.FL↗

arXiv2015

Analysing Sanity of Requirements for Avionics Systems (Preliminary Version)

In the last decade it became a common practice to formalise software requirements to improve the clarity of users' expectations. In this work we build on the fact that functional requirements can be expressed in temporal logic and we propose new sanity checking techniques that automatically detect flaws and suggest improvements of given requirements. Specifically, we describe and experimentally evaluate approaches to consistency and redundancy checking that identify all inconsistencies and pinpoint their exact source (the smallest inconsistent set). We further report on the experience obtained from employing the consistency and redundancy checking in an industrial environment. To complete the sanity checking we also describe a semi-automatic completeness evaluation that can assess the coverage of user requirements and suggest missing properties the user might have wanted to formulate. The usefulness of our completeness evaluation is demonstrated in a case study of an aeroplane control system.

cs.SE↗

arXiv2015

Language Emptiness of Continuous-Time Parametric Timed Automata

Parametric timed automata extend the standard timed automata with the possibility to use parameters in the clock guards. In general, if the parameters are real-valued, the problem of language emptiness of such automata is undecidable even for various restricted subclasses. We thus focus on the case where parameters are assumed to be integer-valued, while the time still remains continuous. On the one hand, we show that the problem remains undecidable for parametric timed automata with three clocks and one parameter. On the other hand, for the case with arbitrary many clocks where only one of these clocks is compared with (an arbitrary number of) parameters, we show that the parametric language emptiness is decidable. The undecidability result tightens the bounds of a previous result which assumed six parameters, while the decidability result extends the existing approaches that deal with discrete-time semantics only. To the best of our knowledge, this is the first positive result in the case of continuous-time and unbounded integer parameters, except for the rather simple case of single-clock automata.

cs.FL↗

arXiv2013

Hennessy-Milner Logic with Greatest Fixed Points as a Complete Behavioural Specification Theory

There are two fundamentally different approaches to specifying and verifying properties of systems. The logical approach makes use of specifications given as formulae of temporal or modal logics and relies on efficient model checking algorithms; the behavioural approach exploits various equivalence or refinement checking methods, provided the specifications are given in the same formalism as implementations. In this paper we provide translations between the logical formalism of Hennessy-Milner logic with greatest fixed points and the behavioural formalism of disjunctive modal transition systems. We also introduce a new operation of quotient for the above equivalent formalisms, which is adjoint to structural composition and allows synthesis of missing specifications from partial implementations. This is a substantial generalisation of the quotient for deterministic modal transition systems defined in earlier papers.

cs.LO↗

arXiv2011

CoInDiVinE: Parallel Distributed Model Checker for Component-Based Systems

CoInDiVinE is a tool for parallel distributed model checking of interactions among components in hierarchical component-based systems. The tool extends the DiVinE framework with a new input language (component-interaction automata) and a property specification logic (CI-LTL). As the language differs from the input language of DiVinE, our tool employs a new state space generation algorithm that also supports partial order reduction. Experiments indicate that the tool has good scaling properties when run in parallel setting.

cs.SE↗