Abstract Chemical reaction networks (CRNs) are an established population model defined as a system of coupled nonlinear ordinary differential equations across many disciplines. In many applications, for example, in systems biology and epidemiology, CRN parameters such as the kinetic reaction rates can be used as control inputs to steer the system toward a given target. Unfortunately, the resulting optimal control problem is nonlinear, therefore, computationally very challenging. We address this issue by introducing an optimality-preserving reduction algorithm for CRNs. The algorithm partitions the original state variables into a reduced set of macro-variables for which one can define a reduced optimal control problem with provably identical optimal values. The reduction algorithm runs with polynomial time complexity in the size of the CRN. We use this result to reduce verification and control problems of large-scale vaccination models over real-world networks.

Network embedding is a fundamental technique to project a network into a lower-dimensional space while preserving similarities among nodes. Traditional network embeddings primarily capture node proximity, making them effective for community detection but insufficient for identifying roles, i.e., patterns of interaction beyond local neighborhoods. To address this limitation, we introduce a simple and efficient embedding technique based on approximate variants of equitable partitions. Our approach, called \varepsilon-BE, introduces a user-tunable tolerance parameter relaxing the otherwise strict condition for exact equitable partitions that can be hardly found in real-world networks. We exploit a relationship between equitable partitions and equivalence relations for Markov chains and ordinary differential equations to develop a partition refinement algorithm for computing an approximate equitable partition in polynomial time. We extend this framework to weighted and directed networks, ensuring applicability to a more general class of graphs and filling a gap in the literature where few approaches are present. We compare our method against state-of-the-art embedding techniques on synthetic and real-world networks. We report comparable—when not superior—performance for visualization, classification, clustering, and regression tasks with smaller running times, enabling the embedding of large-scale networks that could not be efficiently handled by most of the competing techniques. These results and the capability to handle weighted and directed networks make our approach a compelling alternative for structural network embedding.

Structural network embedding is a crucial step in enabling effective downstream tasks for complex systems that aim to project a network into a lower-dimensional space while preserving similarities among nodes. We introduce a simple and efficient embedding technique based on approximate variants of equitable partitions. The approximation consists in introducing a user-tunable tolerance parameter relaxing the otherwise strict condition for exact equitable partitions that can be hardly found in real-world networks. We exploit a relationship between equitable partitions and equivalence relations for Markov chains and ordinary differential equations to develop a partition refinement algorithm for computing an approximate equitable partition in polynomial time. We compare our method against state-of-the-art embedding techniques on benchmark networks. We report comparable-when not superior-performance for visualization, classification, and regression tasks at a cost between one and three orders of magnitude smaller using a prototype implementation, enabling the embedding of large-scale networks that could not be efficiently handled by most of the competing techniques.

Measuring stress level objectively is crucial for personalized health monitoring. While traditional methods require a clinical setting, wearables provide a valuable alternative. In this paper, we approach stress assessment as a regression task, focusing on stress exposure, and evaluate Functional Data Analysis (FDA) to extract richer information from physiological signals. We apply scalar-on-function regression and functional clustering to WESAD, a public dataset which contains signals from wearables and psychometric questionnaires that we use as a ground truth for stress. We compare the results obtained by applying FDA with those achieved by methods using features extracted from signals rather than the signals themselves. The comparison reveals that FDA excels in capturing signal variations and their association with stress, offering new insights into how this association changes with different stressful activities. While non-functional techniques suffice for some analyses, FDA is key to capture overtime patterns linked to stress levels.

This is a report on the reproducibility of the experiments in the paper “Efficient Non-Blocking Event Management for Speculative Parallel Discrete Event Simulation” presented at the 38th ACM SIGSIM conference on Principles of Advanced Discrete Simulation (PADS’24). The artifact got badges Artifacts Evaluated – Functional v1.1, Artifacts Available v1.1, and Results Reproduced v1.1. The Artifacts Evaluated Functional badge has been assigned since the artifact associated with the research is documented, consistent, complete, exercisable, and includes evidence of verification and validation. The Artifacts Available badge has been given since the authors made the artifact permanently available. Finally, the Result Replicated badge has been assigned because the results shown in the paper have been reproduced by persons other than the authors, using artifacts provided by the authors.

We propose a novel methodology to validate software product line (PL) models by integrating Statistical Model Checking (SMC) with Process Mining (PM). We consider the feature-oriented language QFLan from the PL engineering domain. QFLan allows to model PL equipped with rich cross-tree and quantitative constraints, as well as aspects of dynamic PLs such as the staged configurations. This richness allows us to easily obtain models with infinite state-space, calling for simulation-based analysis techniques, like SMC. For example, we use a running example with infinite state space. SMC is a family of analysis techniques based on the generation of samples of the dynamics of a system. SMC aims at estimating properties of a system like the probability of a given event (e.g., installing a feature), or the expected value of quantities in it (e.g., the average price of products from the studied family). Instead, PM is a family of data-driven techniques that uses logs collected on the execution of an information system to identify and reason about its underlying execution process. This often regards identifying and reasoning about process patterns, bottlenecks, and possibilities for improvement. In this paper, to the best of our knowledge, we propose, for the first time, the application of Process Mining (PM) techniques to the byproducts of Statistical Model Checking (SMC) simulations. This aims to enhance the utility of SMC analyses. Typically, if SMC gives unexpected results, the modeler has to discover whether these come from actual characteristics of the system, or from bugs in the model. This is done in a black-box manner, only based on the obtained numerical values. We improve on this by using PM to get a white-box perspective on the dynamics of the system observed by SMC. Roughly speaking, we feed the samples generated by SMC to PM tools, obtaining a compact graphical representation of the observed dynamics. This mined PM model is then transformed into a mined QFLan model, making it accessible to PL engineers. Using two well-known PL models, we show that our methodology is effective (helps in pinpointing issues in models, and in suggesting fixes), and that it scales to complex models. We also show that it is general, by applying it to the security domain.

Quantitative notions of bisimulation are well-known tools for the minimization of dynamical models such as Markov chains and ordinary differential equations (ODEs). In forward bisimulations, each state in the quotient model represents an equivalence class and the dynamical evolution gives the overall sum of its members in the original model. Here we introduce generalized forward bisimulation (GFB) for dynamical systems over commutative monoids and develop a partition refinement algorithm to compute the coarsest one. When the monoid is (ℝ,+), we recover probabilistic bisimulation for Markov chains and more recent forward bisimulations for nonlinear ODEs. Using (ℝ,•) we get nonlinear reductions for discrete-time dynamical systems and ODEs where each variable in the quotient model represents the product of original variables in the equivalence class. When the domain is a finite set such as the Booleans $\mathbb{B}$, we can apply GFB to Boolean networks (BN), a widely used dynamical model in computational biology. Using a prototype implementation of our minimization algorithm for GFB, we find disjunction- and conjunction-preserving reductions on 60 BN from two well-known repositories, and demonstrate the obtained analysis speed-ups. We also provide the biological interpretation of the reduction obtained for two selected BN, and we show how GFB enables the analysis of a large one that could not be analyzed otherwise. Using a randomized version of our algorithm we find product-preserving (therefore non-linear) reductions on 21 dynamical weighted networks from the literature that could not be handled by the exact algorithm.

BACKGROUND: Boolean Networks (BNs) are a popular dynamical model in biology where the state of each component is represented by a variable taking binary values that express, for instance, activation/deactivation or high/low concentrations. Unfortunately, these models suffer from the state space explosion, i.e., there are exponentially many states in the number of BN variables, which hampers their analysis. RESULTS: We present Boolean Backward Equivalence (BBE), a novel reduction technique for BNs which collapses system variables that, if initialized with same value, maintain matching values in all states. A large-scale validation on 86 models from two online model repositories reveals that BBE is effective, since it is able to reduce more than 90% of the models. Furthermore, on such models we also show that BBE brings notable analysis speed-ups, both in terms of state space generation and steady-state analysis. In several cases, BBE allowed the analysis of models that were originally intractable due to the complexity. On two selected case studies, we show how one can tune the reduction power of BBE using model-specific information to preserve all dynamics of interest, and selectively exclude behavior that does not have biological relevance. CONCLUSIONS: BBE complements existing reduction methods, preserving properties that other reduction methods fail to reproduce, and vice versa. BBE drops all and only the dynamics, including attractors, originating from states where BBE-equivalent variables have been initialized with different activation values The remaining part of the dynamics is preserved exactly, including the length of the preserved attractors, and their reachability from given initial conditions, without adding any spurious behaviours. Given that BBE is a model-to-model reduction technique, it can be combined with further reduction methods for BNs.

It is well known that exact notions of model abstraction and reduction for dynamical systems may not be robust enough in practice because they are highly sensitive to the specific choice of parameters. In this paper we consider this problem for nonlinear ordinary differential equations (ODEs) with polynomial derivatives. We introduce a model reduction technique based on approximate differential equivalence, i.e., a partition of the set of ODE variables that performs an aggregation when the variables are governed by nearby derivatives. We develop algorithms to (i) compute the largest approximate differential equivalence; (ii) construct an approximately reduced model from the original one via an appropriate perturbation of the coefficients of the polynomials; and (iii) provide a formal certificate on the quality of the approximation as an error bound, computed as an over-approximation of the reachable set of the reduced model. Finally, we apply approximate differential equivalences to case studies on electric circuits, biological models, and polymerization reaction networks.

We introduce polynomial couplings, a generalization of probabilistic couplings, to develop an algorithm for the computation of equivalence relations which can be interpreted as a lifting of probabilistic bisimulation to polynomial differential equations, a ubiquitous model of dynamical systems across science and engineering. The algorithm enjoys polynomial time complexity and complements classical partition-refinement approaches because: (a) it implements a local exploration of the system, possibly yielding equivalences that do not necessarily involve the inspection of the whole system of differential equations; (b) it can be enhanced by up-to techniques; and (c) it allows the specification of pairs which ought not be included in the output. Using a prototype, these advantages are demonstrated on case studies from systems biology for applications to model reduction and comparison. Notably, we report four orders of magnitude smaller runtimes than partition-refinement approaches when disproving equivalences between Markov chains.

MOTIVATION: Stochastic reaction networks are a widespread model to describe biological systems where the presence of noise is relevant, such as in cell regulatory processes. Unfortunately, in all but simplest models the resulting discrete state-space representation hinders analytical tractability and makes numerical simulations expensive. Reduction methods can lower complexity by computing model projections that preserve dynamics of interest to the user. RESULTS: We present an exact lumping method for stochastic reaction networks with mass-action kinetics. It hinges on an equivalence relation between the species, resulting in a reduced network where the dynamics of each macro-species is stochastically equivalent to the sum of the original species in each equivalence class, for any choice of the initial state of the system. Furthermore, by an appropriate encoding of kinetic parameters as additional species, the method can establish equivalences that do not depend on specific values of the parameters. The method is supported by an efficient algorithm to compute the largest species equivalence, thus the maximal lumping. The effectiveness and scalability of our lumping technique, as well as the physical interpretability of resulting reductions, is demonstrated in several models of signaling pathways and epidemic processes on complex networks. AVAILABILITY AND IMPLEMENTATION: The algorithms for species equivalence have been implemented in the software tool ERODE, freely available for download from https://www.erode.eu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Domain-specific quantitative modeling and analysis approaches are fundamental in scenarios in which qualitative approaches are inappropriate or unfeasible. In this paper, we present a tool-supported approach to quantitative graph-based security risk modeling and analysis based on attack-defense trees. Our approach is based on QFLan, a successful domain-specific approach to support quantitative modeling and analysis of highly configurable systems, whose domain-specific components have been decoupled to facilitate the instantiation of the QFLan approach in the domain of graph-based security risk modeling and analysis. Our approach incorporates distinctive features from three popular kinds of attack trees, namely enhanced attack trees, capabilities-based attack trees and attack countermeasure trees, into the domain-specific modeling language. The result is a new framework, called RisQFLan, to support quantitative security risk modeling and analysis based on attack-defense diagrams. By offering either exact or statistical verification of probabilistic attack scenarios, RisQFLan constitutes a significant novel contribution to the existing toolsets in that domain. We validate our approach by highlighting the additional features offered by RisQFLan in three illustrative case studies from seminal approaches to graph-based security risk modeling analysis based on attack trees.

This paper presents our approach to the quantitative modeling and analysis of highly (re)configurable systems, such as software product lines. Different combinations of the optional features of such a system give rise to combinatorially many individual system variants. We use a formal modeling language that allows us to model systems with probabilistic behavior, possibly subject to quantitative feature constraints, and able to dynamically install, remove or replace features. More precisely, our models are defined in the probabilistic feature-oriented language QFLan, a rich domain specific language (DSL) for systems with variability defined in terms of features. QFLan specifications are automatically encoded in terms of a process algebra whose operational behavior interacts with a store of constraints, and hence allows to separate system configuration from system behavior. The resulting probabilistic configurations and behavior converge seamlessly in a semantics based on discrete-time Markov chains, thus enabling quantitative analysis. Our analysis is based on statistical model checking techniques, which allow us to scale to larger models with respect to precise probabilistic analysis techniques. The analyses we can conduct range from the likelihood of specific behavior to the expected average cost, in terms of feature attributes, of specific system variants. Our approach is supported by a novel Eclipse-based tool which includes state-of-the-art DSL utilities for QFLan based on the Xtext framework as well as analysis plug-ins to seamlessly run statistical model checking analyses. We provide a number of case studies that have driven and validated the development of our framework.

Discovering relations between chemical reaction networks (CRNs) is a relevant problem in computational systems biology for model reduction, to explain if a given system can be seen as an abstraction of another one; and for model comparison, useful to establish an evolutionary path from simpler networks to more complex ones. This is also related to foundational issues in computer science regarding program equivalence, in light of the established interpretation of a CRN as a kernel programming language for concurrency. Criteria for deciding if two CRNs can be formally related have been recently developed, but these require that a candidate mapping be provided. Automatically finding candidate mappings is very hard in general since the search space essentially consists of all possible partitions of a set. In this paper we tackle this problem by developing a genetic algorithm for a class of CRNs called influence networks, which can be used to model a variety of biological systems including cell-cycle switches and gene networks. An extensive numerical evaluation shows that our approach can successfully establish relations between influence networks from the literature which cannot be found by exact algorithms due to their large computational requirements.

Business Process Modelling has acquired increasing relevance in software development. Available notations, such as BPMN, permit to describe activities of complex organisations. On the one hand, this shortens the communication gap between domain experts and IT specialists. On the other hand, this permits to clarify the characteristics of software systems introduced to provide automatic support for such activities. Nevertheless, the lack of formal semantics hinders the automatic verification of relevant properties. This paper presents a novel verification framework for BPMN 2.0, called BProVe. It is based on an operational semantics, implemented using MAUDE, devised to make the verification general and effective. A complete tool chain, based on the Eclipse modelling environment, allows for rigorous modelling and analysis of Business Processes. The approach has been validated using more than one thousand models available on a publicly accessible repository. Besides showing the performance of BProVe, this validation demonstrates its practical benefits in identifying correctness issues in real models.

This demo introduces BProVe, a tool supporting automated verification of Business Process models. BProVe analysis is based on a formal operational semantics defined for the BPMN 2.0 modelling language, and is provided as a freely accessible service that uses open standard formats as input data. Furthermore a plug-in for the Eclipse platform has been developed making available a tool chain supporting users in modelling and visualising, in a friendly manner, the results of the verification. Finally we have conducted a validation through more than one thousand models, showing the effectiveness of our verification tool in practice. (Demo video: https://youtu.be/iF5OM7vKtDA).

We study chemical reaction networks (CRNs) as a kernel language for concurrency models with semantics based on ordinary differential equations. We investigate the problem of comparing two CRNs, i.e., to decide whether the trajectories of a source CRN can be matched by a target CRN under an appropriate choice of initial conditions. Using a categorical framework, we extend and relate model-comparison approaches based on structural (syntactic) and on dynamical (semantic) properties of a CRN, proving their equivalence. Then, we provide an algorithm to compare CRNs, running linearly in time with respect to the cardinality of all possible comparisons. Finally, we apply our results to biological models from the literature.

Ordinary differential equations (ODEs) are widespread in many natural sciences including chemistry, ecology, and systems biology, and in disciplines such as control theory and electrical engineering. Building on the celebrated molecules-as-processes paradigm, they have become increasingly popular in computer science, with high-level languages and formal methods such as Petri nets, process algebra, and rule-based systems that are interpreted as ODEs. We consider the problem of comparing and minimizing ODEs automatically. Influenced by traditional approaches in the theory of programming, we propose differential equivalence relations. We study them for a basic intermediate language, for which we have decidability results, that can be targeted by a class of high-level specifications. An ODE implicitly represents an uncountable state space, hence reasoning techniques cannot be borrowed from established domains such as probabilistic programs with finite-state Markov chain semantics. We provide novel symbolic procedures to check an equivalence and compute the largest one via partition refinement algorithms that use satisfiability modulo theories. We illustrate the generality of our framework by showing that differential equivalences include (i) well-known notions for the minimization of continuous-time Markov chains (lumpability), (ii)~bisimulations for chemical reaction networks recently proposed by Cardelli et al., and (iii) behavioral relations for process algebra with ODE semantics. With a prototype implementation we are able to detect equivalences in biochemical models from the literature that cannot be reduced using competing automatic techniques.

We present two quantitative behavioral equivalences over species of a chemical reaction network (CRN) with semantics based on ordinary differential equations. Forward CRN bisimulation identifies a partition where each equivalence class represents the exact sum of the concentrations of the species belonging to that class. Backward CRN bisimulation relates species that have identical solutions at all time points when starting from the same initial conditions. Both notions can be checked using only CRN syntactical information, i.e., by inspection of the set of reactions. We provide a unified algorithm that computes the coarsest refinement up to our bisimulations in polynomial time. Further, we give algorithms to compute quotient CRNs induced by a bisimulation. As an application, we find significant reductions in a number of models of biological processes from the literature. In two cases we allow the analysis of benchmark models which would be otherwise intractable due to their memory requirements.

We investigate the suitability of statistical model checking for the analysis of probabilistic models of software product lines with complex quantitative constraints and advanced feature installation options. Such models are specified in the feature-oriented language QFLan, a rich process algebra whose operational behaviour interacts with a store of constraints, neatly separating product configuration from product behaviour. The resulting probabilistic configurations and behaviour converge seamlessly in a semantics based on DTMCs, thus enabling quantitative analyses ranging from the likelihood of certain behaviour to the expected average cost of products. This is supported by a Maude implementation of QFLan, integrated with the SMT solver Z3 and the distributed statistical model checker MultiVeStA. Our approach is illustrated with a bikes product line case study.

Quantified μ-calculi combine the fix-point and modal operators of temporal logics with (existential and universal) quantifiers, and they allow for reasoning about the possible behaviour of individual components within a software system. In this paper