Under-approximating Cut Sets for Reachability in Large Scale Automata Networks

In the scope of discrete finite-state models of interacting components, we present a novel algorithm for identifying sets of local states of components whose activity is necessary for the reachability of a given local state. If all the local states from such a set are disabled in the model, the concerned reachability is impossible. Those sets are referred to as cut sets and are computed from a particular abstract causality structure, so-called Graph of Local Causality, inspired from previous work and generalised here to finite automata networks. The extracted sets of local states form an under-approximation of the complete minimal cut sets of the dynamics: there may exist smaller or additional cut sets for the given reachability. Applied to qualitative models of biological systems, such cut sets provide potential therapeutic targets that are proven to prevent molecules of interest to become active, up to the correctness of the model. Our new method makes tractable the formal analysis of very large scale networks, as illustrated by the computation of cut sets within a Boolean model of biological pathways interactions gathering more than 9000 components

Analyzing Large Network Dynamics with Process Hitting

In this chapter, we introduce the Process Hitting framework, which provides the methodology of constructing the most permissive dynamics and then using successive refinements to fine tune the model. We present static analysis methods designed to identify fixed points or answer successive reachability questions, and introduce the stochastic semantics of Process Hitting too

Goal-Driven Unfolding of Petri Nets

Unfoldings provide an efficient way to avoid the state-space explosion due to interleavings of concurrent transitions when exploring the runs of a Petri net. The theory of adequate orders allows one to define finite prefixes of unfoldings which contain all the reachable markings. In this paper we are interested in reachability of a single given marking, called the goal. We propose an algorithm for computing a finite prefix of the unfolding of a 1-safe Petri net that preserves all minimal configurations reaching this goal. Our algorithm combines the unfolding technique with on-the-fly model reduction by static analysis aiming at avoiding the exploration of branches which are not needed for reaching the goal. We present some experimental results

Systems Biology of Cancer: A Challenging Expedition for Clinical and Quantitative Biologists

A systems-biology approach to complex disease (such as cancer) is now complementing traditional experience-based approaches, which have typically been invasive and expensive. The rapid progress in biomedical knowledge is enabling the targeting of disease with therapies that are precise, proactive, preventive, and personalized. In this paper, we summarize and classify models of systems biology and model checking tools, which have been used to great success in computational biology and related fields. We demonstrate how these models and tools have been used to study some of the twelve biochemical pathways implicated in but not unique to pancreatic cancer, and conclude that the resulting mechanistic models will need to be further enhanced by various abstraction techniques to interpret phenomenological models of cancer progression

Tools and Algorithms for the Construction and Analysis of Systems

This open access book constitutes the proceedings of the 28th International Conference on Tools and Algorithms for the Construction and Analysis of Systems, TACAS 2022, which was held during April 2-7, 2022, in Munich, Germany, as part of the European Joint Conferences on Theory and Practice of Software, ETAPS 2022. The 46 full papers and 4 short papers presented in this volume were carefully reviewed and selected from 159 submissions. The proceedings also contain 16 tool papers of the affiliated competition SV-Comp and 1 paper consisting of the competition report. TACAS is a forum for researchers, developers, and users interested in rigorously based tools and algorithms for the construction and analysis of systems. The conference aims to bridge the gaps between different communities with this common interest and to support them in their quest to improve the utility, reliability, exibility, and efficiency of tools and algorithms for building computer-controlled systems

Recent Advances in Fully Dynamic Graph Algorithms

In recent years, significant advances have been made in the design and analysis of fully dynamic algorithms. However, these theoretical results have received very little attention from the practical perspective. Few of the algorithms are implemented and tested on real datasets, and their practical potential is far from understood. Here, we present a quick reference guide to recent engineering and theory results in the area of fully dynamic graph algorithms

A Novel Approach to Finding Near-Cliques: The Triangle-Densest Subgraph Problem

Many graph mining applications rely on detecting subgraphs which are near-cliques. There exists a dichotomy between the results in the existing work related to this problem: on the one hand the densest subgraph problem (DSP) which maximizes the average degree over all subgraphs is solvable in polynomial time but for many networks fails to find subgraphs which are near-cliques. On the other hand, formulations that are geared towards finding near-cliques are NP-hard and frequently inapproximable due to connections with the Maximum Clique problem. In this work, we propose a formulation which combines the best of both worlds: it is solvable in polynomial time and finds near-cliques when the DSP fails. Surprisingly, our formulation is a simple variation of the DSP. Specifically, we define the triangle densest subgraph problem (TDSP): given $G(V,E)$, find a subset of vertices $S^*$ such that $\tau(S^*)=\max_{S \subseteq V} \frac{t(S)}{|S|}$, where $t(S)$ is the number of triangles induced by the set $S$. We provide various exact and approximation algorithms which the solve the TDSP efficiently. Furthermore, we show how our algorithms adapt to the more general problem of maximizing the $k$-clique average density. Finally, we provide empirical evidence that the TDSP should be used whenever the output of the DSP fails to output a near-clique.Comment: 42 page

Goal-Driven Unfolding of Petri Nets

International audienceUnfoldings provide an efficient way to avoid the state-space explosion due to interleavings of concurrent transitions when exploring the runs of a Petri net. The theory of adequate orders allows one to define finite prefixes of unfoldings which contain all the reachable markings. In this paper we are interested in reachability of a single given marking, called the goal. We propose an algorithm for computing a finite prefix of the unfolding of a 1-safe Petri net that preserves all minimal configurations reaching this goal. Our algorithm combines the unfolding technique with on-the-fly model reduction by static analysis aiming at avoiding the exploration of branches which are not needed for reaching the goal. We present some experimental results

Goal-Driven Unfolding of Petri Nets

International audienceUnfoldings provide an efficient way to avoid the state-space explosion due to interleavings of concurrent transitions when exploring the runs of a Petri net. The theory of adequate orders allows one to define finite prefixes of unfoldings which contain all the reachable markings. In this paper we are interested in reachability of a single given marking, called the goal. We propose an algorithm for computing a finite prefix of the unfolding of a 1-safe Petri net that preserves all minimal configurations reaching this goal. Our algorithm combines the unfolding technique with on-the-fly model reduction by static analysis aiming at avoiding the exploration of branches which are not needed for reaching the goal. We present some experimental results