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Boolean automata networks (aka Boolean networks) are space-time discrete dynamical systems, studied as a model of computation and as a representative model of natural phenomena. A collection of simple entities (the automata) update their 0-1 states according to local rules. The dynamics of the network is highly sensitive to update modes, i.e., to the schedule according to which the automata apply their local rule. A new family of update modes appeared recently, called block-parallel, which is dual to the well studied block-sequential. Although basic, it embeds the rich feature of update repetitions among a temporal updating period, allowing for atypical asymptotic behaviors. In this paper, we prove that it is able to breed complex computations, squashing almost all decision problems on the dynamics to the traditionally highest (for reachability questions) class PSPACE. Despite obtaining these complexity bounds for a broad set of local and global properties, we also highlight a surprising gap: bijectivity is still coNP.

This systematic review focuses on analyzing the use of machine learning techniques for identifying and quantifying analytes in various electrochemical applications, presenting the available applications in the literature. Machine learning is a tool that can facilitate the analysis and enhance the understanding of processes involving various analytes. In electrochemical biosensors, it increases the precision of medical diagnostics, improving the identification of biomarkers and pathogens with high reliability. It can be effectively used for the classification of complex chemical products; in environmental monitoring, using low-cost sensors; in portable devices and wearable systems; among others. Currently, the analysis of some analytes is still performed manually, requiring the expertise of a specialist in the field and thus hindering the generalization of results. In light of the advancements in artificial intelligence today, this work proposes to carry out a systematic review of the literature on the applications of artificial intelligence techniques. A set of articles has been identified that address electrochemical problems using machine learning techniques, more specifically, supervised learning., Comment: in Portuguese language

Among the fundamental questions in computer science is that of the impact of synchronism/asynchronism on computations, which has been addressed in various fields of the discipline: in programming, in networking, in concurrence theory, in artificial learning, etc. In this paper, we tackle this question from a standpoint which mixes discrete dynamical system theory and computational complexity, by highlighting that the chosen way of making local computations can have a drastic influence on the performed global computation itself. To do so, we study how distinct update schedules may fundamentally change the asymptotic behaviors of finite dynamical systems, by analyzing in particular their limit cycle maximal period. For the message itself to be general and impacting enough, we choose to focus on a ``simple'' computational model which prevents underlying systems from having too many intrinsic degrees of freedom, namely elementary cellular automata. More precisely, for elementary cellular automata rules which are neither too simple nor too complex (the problem should be meaningless for both), we show that update schedule changes can lead to significant computational complexity jumps (from constant to superpolynomial ones) in terms of their temporal asymptotes.

In this paper, we explore the dynamic behavior of threshold networks on undirected signed graphs. Much attention has been dedicated to understand the convergence and long-term behavior of this model. Yet, an open question persists: How does the underlying graph structure impact network dynamics? Similar studies have been carried out for threshold networks and other types of networks, but these primarily focus on unsigned networks. Here, we address the question on signed threshold networks. We introduce the stability index of a graph, related to the concepts of frustration and balance in signed graphs, to establish a connection between the structure and the dynamics of such networks. We show that graphs which present a negative stability index exhibit stable dynamics, i.e., the dynamics converges to fixed points regardless of its threshold parameters. Conversely, if at least one subgraph has a positive stability index, oscillations in long term behavior may appear. Furthermore, we generalize the analysis to network dynamics under periodic update modes and explore the case of the existence of some subgraph with a positive stability index, for which we find that attractors of super-polynomial period in the size of the network may appear.

We state an algorithm that, given an automata network and a block-sequential update schedule, produces an automata network of the same size or smaller with the same limit dynamics under the parallel update schedule. Then, we focus on the family of automata cycles which share a unique path of automata, called tangential cycles, and show that a restriction of our algorithm allows to reduce any instance of these networks under a block-sequential update schedule into a smaller parallel network of the family and to characterize the number of reductions operated while conserving their limit dynamics. We also show that any tangential cycles reduced by our main algorithm are transformed into a network whose size is that of the largest cycle of the initial network. We end by showing that the restricted algorithm allows the direct characterization of block-sequential double cycles as parallel ones., Comment: Accepted at CIE 2023

When we focus on finite dynamical systems from both the computability/complexity and the modelling standpoints, automata networks seem to be a particularly appropriate mathematical model on which theory shall be developed. In this paper, automata networks are finite collections of entities (the automata), each automaton having its own set of possible states, which interact with each other over discrete time, interactions being defined as local functions allowing the automata to change their state according to the states of their neighbourhoods. The studies on this model of computation have underlined the very importance of the way (i.e. the schedule) according to which the automata update their states, namely the update modes which can be deterministic, periodic, fair, or not. Indeed, a given network may admit numerous underlying dynamics, these latter depending highly on the update modes under which we let the former evolve. In this paper, we pay attention to a new kind of deterministic, periodic and fair update mode family introduced recently in a modelling framework, called the block-parallel update modes by duality with the well-known and studied block-sequential update modes. More precisely, in the general context of automata networks, this work aims at presenting what distinguish block-parallel update modes from block-sequential ones, and at counting and enumerating them: in absolute terms, by keeping only representatives leading to distinct dynamics, and by keeping only representatives giving rise to distinct isomorphic limit dynamics. Put together, this paper constitutes a first theoretical analysis of these update modes and their impact on automata networks dynamics.

In automata networks, it is well known that the way entities update their states over time has a major impact on their dynamics. In particular, depending on the chosen update schedule, the underlying dynamical systems may exhibit more or less asymptotic dynamical behaviours such as fixed points or limit cycles. Since such mathematical models have been used in the framework of biological networks modelling, the question of choosing appropriate update schedules has arised soon. In this note, focusing on Boolean networks, our aim is to emphasise that the adequate way of thinking regulations and genetic expression over time is certainly not to consider a wall segregating synchronicity from asynchronicity because they actually complement rather well. In particular, we highlight that specific update schedules, namely block-parallel update schedules, whose intrinsic features are still not known from a theoretical point of view, admit realistic and pertinent properties in the context of biological modelling and deserve certainly more attention from the community.

In this paper we study the dynamical behavior of Boolean networks with firing memory, namely Boolean networks whose vertices are updated synchronously depending on their proper Boolean local transition functions so that each vertex remains at its firing state a finite number of steps. We prove in particular that these networks have the same computational power than the classical ones, ie any Boolean network with firing memory composed of $m$ vertices can be simulated by a Boolean network by adding vertices. We also prove general results on specific classes of networks. For instance, we show that the existence of at least one delay greater than 1 in disjunctive networks makes such networks have only fixed points as attractors. Moreover, for arbitrary networks composed of two vertices, we characterize the delay phase space, \ie the delay values such that networks admits limit cycles or fixed points. Finally, we analyze two classical biological models by introducing delays: the model of the immune control of the $\lambda$-phage and that of the genetic control of the floral morphogenesis of the plant \emph{Arabidopsis thaliana}.

Our daily social and political life is more and more impacted by social networks. The functioning of our living bodies is deeply dependent on biological regulation networks such as neural, genetic, and protein networks. And the physical world in which we evolve, is also structured by systems of interacting particles. Interaction networks can be seen in all spheres of existence that concern us, and yet, our understanding of interaction networks remains severely limited by our present lack of both theoretical and applied insight into their clockworks. In the past, efforts at understanding interaction networks have mostly been directed towards applications. This has happened at the expense of developing understanding of the generic and fundamental aspects of interaction networks. Intrinsic properties of interaction networks (eg the ways in which they transmit information along entities, their ability to produce this or that kind of global dynamical behaviour depending on local interactions) are thus still not well understood. Lack of fundamental knowledge tends to limit the innovating power of applications. Without more theoretical fundamental knowledge, applications cannot evolve deeply and become more impacting. Hence, it is necessary to better apprehend and comprehend the intrinsic properties of interaction networks, notably the relations between their architecture and their dynamics and how they are affected by and set in time. In this chapter, we use the elementary mathematical model of Boolean automata networks as a formal archetype of interaction networks. We survey results concerning the role of feedback cycles and the role of intersections between feedback cycles, in shaping the asymptotic dynamical behaviours of interaction networks.