Related papers: Fixing monotone Boolean networks asynchronously
This paper (parts I and II) provides an expository introduction to monotone and near-monotone dynamical systems associated to biochemical networks, those whose graphs are consistent or near-consistent. Many conclusions can be drawn from…
Given two functions $\mathbf{a}\!:\! [n] \rightarrow [n]$ and $\mathbf{b}\!:\! [n] \rightarrow [n]$ chosen uniformly at random, any word $w=w_1w_2\dots w_k\in \{a,b\}^k$ induces a random function $\mathbf{w}\!:\! [n] \rightarrow [n]$ by…
Given an infinite word ${\bf w}$ on a finite alphabet, an immediate question arises:~can we understand the frequency of letters in ${\bf w}$\,? For words that are the fixed points of substitutions, the answer to this question is often `yes'…
The \v{C}ern\'y's conjecture states that for every synchronizing automaton with n states there exists a reset word of length not exceeding (n-11)^2. We prove this conjecture for a class of automata preserving certain properties of intervals…
A deterministic finite automaton in which every non-empty set of states occurs as the image of the whole state set under the action of a suitable input word is called completely reachable. It was conjectured that in each completely…
Unambiguous non-deterministic finite automata have intermediate expressive power and succinctness between deterministic and non-deterministic automata. It has been conjectured that every unambiguous non-deterministic one-way finite…
Finite automata (FA) are a fundamental computational abstraction that is widely used in practice for various tasks in computer science, linguistics, biology, electrical engineering, and artificial intelligence. Given an input word, an FA…
Boolean networks model finite discrete dynamical systems with complex behaviours. The state of each component is determined by a Boolean function of the state of (a subset of) the components of the network. This paper addresses the…
In threshold-linear networks (TLNs), a fixed point is called minimal if no proper subset of its support is also a fixed point. Curto et al (Advances in Applied Mathematics, 2024) conjectured that every stable fixed point of any TLN must be…
Traditionally, finite automata theory has been used as a framework for the representation of possibly infinite sets of strings. In this work, we introduce the notion of second-order finite automata, a formalism that combines finite automata…
Morphic words are letter-to-letter images of fixed points $x$ of morphisms on finite alphabets. There are situations where these letter-to-letter maps do not occur naturally, but have to be replaced by a morphism. We call this a decoration…
To each Boolean function F from {0,1}^n to itself and each point x in {0,1}^n, we associate the signed directed graph G_F(x) of order n that contains a positive (resp. negative) arc from j to i if the partial derivative of f_i with respect…
We show that for any two distinct words $ s_1, s_2 $ over an arbitrary alphabets, there exists a deterministic finite automaton with $ O(\log^2 n) $ states that accepts $ s_1 $ and rejects $ s_2 $. This improves the previous upper bound of…
Let $w$ be an infinite word on an alphabet $A$. We denote by $(n_i)_{i \geq 1}$ the increasing sequence (assumed to be infinite) of all lengths of palindrome prefixes of $w$. In this text, we give an explicit construction of all words $w$…
This paper (parts I and II) provides an expository introduction to monotone and near-monotone dynamical systems associated to biochemical networks, those whose graphs are consistent or near-consistent. Many conclusions can be drawn from…
A zero-one matrix is a matrix with entries from $\{0, 1\}$. We study monoids containing only such matrices. A finite set of zero-one matrices generating such a monoid can be seen as the matrix representation of an unambiguous finite…
Fixed points are fundamental states in any dynamical system. In the case of gene regulatory networks (GRNs) they correspond to stable genes profiles associated to the various cell types. We use Kauffman's approach to model GRNs with random…
The states of a deterministic finite automaton A can be identified with collections of words in Pf(L(A)) -- the set of prefixes of words belonging to the regular language accepted by A. But words can be ordered and among the many possible…
We investigated the properties of Boolean networks that follow a given reliable trajectory in state space. A reliable trajectory is defined as a sequence of states which is independent of the order in which the nodes are updated. We…
We study the problem of computing a minimal subset of nodes of a given asynchronous Boolean network that need to be controlled to drive its dynamics from an initial steady state (or attractor) to a target steady state. Due to the phenomenon…