645 papers
Injective and pseudo-injective polynomial equations: From permutations to dynamical systems
Finite discrete-time dynamical systems (FDDS) model phenomena that evolve deterministically in discrete time. It is possible to define sum and product operations on these systems (disjoint union and direct product, respectively), giving a commutative semiring. This algebraic structure led to several works employing polynomial equations to model hypotheses on phenomena modelled using FDDS. To solve these equations, algorithms for performing division and computing $k$-th roots are needed. In this paper, we propose two polynomial algorithms for these tasks, under the condition that the result is a connected FDDS. These algorithms exploit the notion of unroll of a FDDS, an alternative representation based on a forest of infinite trees constructed by computing the transition function of the system backwards. This ultimately leads to an efficient solution to equations of the type $AX^k=B$ for connected $X$ and some generalisations. These results are some of the important final steps for solving more general polynomial equations on FDDS.
2604.04065Apr 2026
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A Boolean encoding of the Most Permissive semantics for Boolean networks
Boolean networks are widely used to model biological regulatory networks and study their dynamics. Classical semantics, such as the asynchronous semantics, do not always accurately capture transient or asymptotic behaviors observed in quantitative models. To address this limitation, the Most Permissive semantics was introduced by Paulevé et al., extending Boolean dynamics with intermediate activity levels that allow components to transiently activate or inhibit their targets during transitions. In this work, we provide a Boolean encoding of the Most Permissive semantics: each component of the original network is represented by a triplet of Boolean variables, and we derive the extended logical function governing the resulting network. We prove that the asynchronous dynamics of the encoded network exactly reproduces the attainability properties of the original network under Most Permissive semantics. This encoding is implemented as a modifier within the bioLQM framework, making it directly compatible with existing tools such as GINsim. To address scalability limitations, we further extend the tool to support partial unfolding, restricted to a user-defined subset of components.
2604.03029Apr 2026
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2604.02949Sample compression schemes for balls in structurally sparse graphs
Sample compression schemes were defined by Littlestone and Warmuth (1986) as an abstraction of the structure underlying many learning algorithms. In a sample compression scheme, we are given a large sample of vertices of a fixed hypergraph with labels indicating the containment in some hyperedge. The task is to compress the sample in such a way that we can retrieve the labels of the original sample. The size of a sample compression scheme is the amount of information that is kept in the compression. Every hypergraph with a sample compression scheme of bounded size must have bounded VC-dimension. Conversely, Moran and Yehudayoff (J. ACM, 2016) showed that every hypergraph of bounded VC-dimension admits a sample compression scheme of bounded size. We study a specific class of hypergraphs emerging from balls in graphs. The schemes that we construct (contrary to the ones constructed by Moran and Yehudayoff) are \textit{proper}, meaning that we retrieve not only the labeling of the original sample but also a hyperedge (ball) consistent with the original labeling. First, we prove that for every graph $G$ of treewidth at most $t$, the hypergraph of balls in $G$ has a proper sample compression scheme of size $\mathcal{O}(t\log t)$; this is tight up to the logarithmic factor and improves the quadratic (improper) bound that follows from the result of Moran and Yehudayoff. Second, we prove an analogous result for graphs of cliquewidth at most $t$.
2604.02949Apr 2026
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Trapping and commutative Boolean networks
A Boolean network (BN) is a transformation of the set of Boolean configurations of a given length. A trapspace of a BN is a subcube invariant by the BN; a principal trapspace is the smallest trapspace containing a given configuration; a minimal trapspace is one that does not contain any smaller trapspace. In an unrelated development, commutative BNs have been introduced as those networks where all local updates commute. In this paper, we relate those two aspects of BN theory via five main contributions. First, we introduce the trapping graph and the trapping closure of a BN. We also define trapping networks as the networks with transitive general asynchronous graphs and we prove that those are exactly the trapping closures. Second, we show that two BNs have the same collection of (principal) trapspaces if and only if they have the same trapping closure. We then characterise the collections of (principal) trapspaces of BNs. We finally give analogous results for the collections of minimal trapspaces. Third, we prove that commutative networks are trapping, and we classify the collections of principal trapspaces of commutative networks. Fourth, we focus on bijective commutative networks, which we call Marseille networks. We provide several alternative definitions for Marseille networks, and we classify them as special commutative or trapping networks. Fifth, we focus on idempotent commutative networks, which we call Lille networks. We provide several alternative definitions for Lille networks, we classify them as special commutative or trapping networks, and we relate them to globally idempotent networks. Our investigations of Marseille and Lille networks also highlight relations amongst the asynchronous, general asynchronous, and trapping graphs of Boolean networks, as well as the structure of trapping networks in general.
2604.02303Apr 2026
View2604.01571Bipartite Exact Matching in P
The Exact Matching problem asks whether a bipartite graph with edges colored red and blue admits a perfect matching with exactly t red edges. Introduced by Papadimitriou and Yannakakis in 1982, the problem has resisted deterministic polynomial-time algorithms for over four decades, despite admitting a randomized solution via the Schwartz-Zippel lemma since 1987. We prove the Affine-Slice Nonvanishing Conjecture (ASNC) for all bipartite braces and give a deterministic O(n^6) algorithm for Exact Matching on all bipartite graphs. The algorithm follows via the tight-cut decomposition, which reduces the decision problem to brace blocks. The proof proceeds by structural induction on McCuaig's brace decomposition. We establish the McCuaig exceptional families, the replacement determinant algebra, and the narrow-extension cases (KA, J3 to D1). For the superfluous-edge step, we introduce two closure tools: a matching-induced Two-extra Hall theorem that resolves the rank-(m-2) branch via projective-collapse contradiction, and a distinguished-state q-circuit lemma that eliminates the rank-(m-1) branch entirely by showing that any minimal dependent set containing the superfluous state forces rank m-2. The entire proof has been formally verified in the Lean 4 proof assistant.
2604.01571Apr 2026
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Banach density of generated languages: Dichotomies in topology and dimension
The formalism of language generation in the limit studies generative models by requiring an algorithm, given strings from a hidden true language, to eventually generate new valid strings. A core issue is the tension between validity and breadth. Prior work quantified breadth via asymptotic density, where the priority is generating strings early in a natural countable ordering. Here, we study density when the strings are embedded in $d$ dimensions, a ubiquitous structure in current generative models. Our goal is for the generated strings to be dense throughout the embedding. This requires a different measure, the Banach density, which captures whether a set contains large sparse regions. Using Banach density uncovers a rich structure based on dimension and the topology of the language collection. We prove that in dimension one, when the underlying topological space has finite Cantor-Bendixson rank, an algorithm can always generate a subset of the true language with an optimal lower Banach density of 1/2. However, for collections with infinite Cantor-Bendixson rank, there are cases where no algorithm can achieve any positive lower Banach density; the generated set must contain arbitrarily large, sparse regions. This reveals a topological contrast unseen with asymptotic density, where 1/2 is always achievable. We also extend our results to a family of measures interpolating between Banach and asymptotic density. Finally, in dimension $d \geq 2$, our positive result for Banach density encounters a Ramsey-theoretic obstacle regarding two-colored point sets. Overcoming this requires a nondegeneracy condition: the embedding of the true language must be sufficiently represented throughout the full $d$-dimensional space.
2604.02385Apr 2026
View2604.00898Enumerating Two-Orbit Graphs
We present an approach to enumerate graphs whose automorphism group has exactly two orbits. Our method exploits the observation that we can enumerate all graphs whose automorphism group contains a given this permutation group. We obtain the relevant groups via Goursat's lemma. In order to scale the enumeration, we employ additional optimizations that prune irrelevant groups. In total, we enumerate, for the first time, all connected two-orbit graphs of up to 27 vertices, totaling 10,094,721 graphs, pushing the state of the art well beyond what direct enumeration methods can achieve.
2604.00898Apr 2026
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Generalized Resistance Geometry from Kron Reduction and Effective Resistance
We develop a generalized resistance geometry based on Kron reduction and effective resistance for directed graphs, paralleling classical undirected graph theory. For strongly connected directed graphs, we prove a Fiedler--Bapat identity that links the resistance matrix and the Laplacian through the symmetrized pseudoinverse. This identity provides a canonical definition of the resistance curvature and resistance radius in the strongly connected directed setting. In the strongly connected weight-balanced case, it also implies that the operation of associating an undirected Laplacian with a directed Laplacian via the pseudoinverse of the symmetrized pseudoinverse commutes with Kron reduction. We further introduce a class of signed undirected Laplacians for which effective resistance defines a distance between nodes. We call this distance the generalized resistance metric and prove that it coincides with the class of strict negative type metrics. Within this framework, we investigate analytical and geometric properties of resistance curvature and resistance radius, characterize the maximum graph-variance problem, and generalize resistive embeddings. These results place signed undirected resistance geometry on a footing parallel to the classical unsigned undirected theory and provide a unified perspective on model reduction, graph variance, and resistance-based embedding.
2603.29675Mar 2026
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Effective approach of the tridendriform Schroeder tree algebra
We introduce a primitive computation problem in the free tridendriform algebra generated by one element which is a Hopf algebra based on Schroeder trees. We know a complex way to generate all of them. To understand it clearer, we want to implement this method on a computer. However, we need to create some tools to implement Schroeder trees and the multiplications over this algebra to be able to compute the primitive elements. We also checked numerically that they are all primitive elements. In this paper, we detail how we made the problem mathematically understandable for a computer and how we implement it.
2603.29393Mar 2026
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On merge-models
Tree-ordered weakly sparse models have recently emerged as a robust framework for representing structures in an ``almost sparse'' way, while allowing the structure to be reconstructed through a simple first-order interpretation. A prominent example is given by twin-models, which are bounded twin-width tree-ordered weakly sparse representations of structures with bounded twin-width derived from contraction sequences. In this paper, we develop this perspective further. First, we show that twin-models can be chosen such that they preserve linear clique-width or clique-width up to a constant factor. Then, we introduce \emph{merge-models}, a natural analog of twin-models for merge-width. Merge-models represent binary relational structures by tree-ordered weakly sparse structures. The original structures can then be recovered by a fixed first-order interpretation. A merge-model can be constructed from a merge sequence. Then, its radius-$r$ merge-width will be, up to a constant factor, bounded by the radius-$r$ width of the merge sequence from which it is derived. Finally, we show that twin-models arise naturally as special cases of merge-models, and that binary structures with bounded twin-width are exactly those having a loopless merge-model with bounded radius-$r_0$ merge-width (for some sufficiently large constant $r_0$).
2603.26570Mar 2026
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Finding Minimal Clusters in st-DAGs
Directed Acylic Graphs with a single entry vertex and a single exit vertex (st-DAGs) have many applications. For instance, they are frequently used for modelling flow problems or precedence conditions among tasks, work packages, etc.. This paper presents an algorithm for finding special types of subgraphs in such st-DAGs, called clusters. Knowing the clusters of a given st-DAG is very useful during DAG analysis. Clusters are characterized by a kind of synchronizing behaviour at their entry border and at their exit border. In this context, we introduce the notion of syncpoint, a type of synchronisation point within a DAG, and for a given st-DAG we construct a second DAG, called MSP-DAG, whose edges are given by the precedence relation among maximum size syncpoints (MSPs). Our new cluster finding algorithm searches for clusters between potential pairs of enclosing MSPs. The efficiency of the algorithm stems from the fact that it works on the MSP-DAG, which is usually much smaller than the original st-DAG. The paper includes a thorough complexity analysis of the algorithm's runtime, which turns out to be quadratic in the number of DAG vertices and exponential in the number of MSP-DAG vertices. There is also a section reporting on experiments with randomly generated DAGs, which shows the practical applicability of the algorithm and confirm our theoretical findings.
2603.26538Mar 2026
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Computing fixed point free automorphisms of graphs
In 1981, Lubiw proved that the fixed point free automorphism problem (FPFAut) is NP-complete: given a graph G, determine whether there exists an automorphism that maps no vertex of G to itself. We revisit this problem and prove that FPFAut remains NP-complete when restricted to split, bipartite, k-subdivided, and H-free graphs, if H is not an induced subgraph of P_4. The class of P_4-free graphs receives the special name of cographs. We provide a polynomial time algorithm for three extensions of cographs: bounded modular-width graphs, tree-cographs and P_4-sparse graphs. Our approach uses the well known modular decomposition of graphs. As a consequence, we generalize a result of Abiad et. al. on the problem of computing 2-homogeneous equitable partitions.
2603.26006Mar 2026
View2603.22432On sampling diluted Spin-Glasses with unbounded interactions
Spin-glasses are natural Gibbs distributions that have been studied in Theoretical CS for many decades. Recently, they have been gaining attention from the community as they emerge naturally in neural computation and learning, network inference, optimisation and other areas. We study the problem of efficiently sampling from spin-glass distributions when the underlying graph is a typical instance of $G(n,d/n)$, i.e., the random graph on $n$ vertices such that each edge appears independently with probability $d/n$, and $d=Θ(1)$. Our focus is on the 2-spin model at inverse temperature $β$. We consider this distribution to be one of the most interesting case of spin-glasses, and one of the most challenging to analyse, since its Gaussian couplings give rise to unbounded interaction. We employ the well-known Glauber dynamics to sample from the aforementioned distribution. We show that for the typical instances of the 2-spin model on $G(n,d/n)$, the mixing time of Glauber dynamics is $O\left(n^{1+\frac{25}{\sqrt{\log d}}}\right)$, for any $β<\frac{1}{4\sqrt{d}}$. Our results can also be adapted for the case of spin-glass distributions with bounded interactions. In that respect, we obtain rapid mixing of Glauber dynamics for the Viana-Bray model on $G(n,d/n)$ when $β<\frac{1}{4\sqrt{d}}$. This improves on the current best bound which is $β<\frac{0.18}{\sqrt{d}}$. We utilise stochastic localisation, and in particular, we build and improve on the scheme introduced in [Liu, Mohanty, Rajaraman and Wu: FOCS 2024]. This is the first time that stochastic localisation is used for diluted spin-glasses, where both degrees and interactions can be unbounded.
2603.22432Mar 2026
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Non-trivial automata networks do exist that solve the global majority problem with the local majority rule
The global majority problem, often referred to as the Density Classification Task, is a classical benchmark in the context of probing the computational capabilities of automata networks. It poses the simple yet challenging problem of determining, by totally local means, whether an arbitrary initial configuration of binary states can evolve to a final, homogeneous global configuration that reflects the initial global majority. Although it is known that in the specific case of cellular automata with periodic boundaries no rule is able to solve the problem, in other formulations solutions are known and, in others, the problem is still open. Aligned with the latter, here we explore the possibility of solving the problem with automata networks, operating only with the local majority rule, with a focus on identifying non-trivial cases where it can be solved and explaining why they do so.
2603.19472Mar 2026
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On the Extension Theorem for Packing Steiner Forests
We consider the problem of packing edge-disjoint Steiner forests in a graph. The input consists of a multi-graph $G=(V,E)$ and a collection of $h$ vertex subsets $S = \{S_1,S_2,\ldots,S_h\}$. A Steiner forest for $S$, also called an $S$-forest, is a forest of $G$ in which each $S_i$ is connected. In the case where $h=1$, this is the Steiner Tree packing problem. Kriesell's conjecture postulates that $2k$-edge-connectivity of $S_1$ is sufficient to find $k$ edge-disjoint $S_1$-trees. Lau showed that $24k$-edge-connectivity suffices for the Steiner Tree packing problem, which was improved to $6.5k$ by West and Wu and $5k+4$ by Devos, McDonald and Pivotto. In his thesis, Lau asserts that for the Steiner Forest problem, if each $S_i$ is $30k$-edge-connected in $G$, then there exist $k$ edge-disjoint $S$-forests. However, Lau's proof relies on an intermediate theorem called the Extension Theorem, which in this paper we will demonstrate has a gap by providing a counterexample to Lau's Extension Theorem. Furthermore, we will resolve this gap by correcting Lau's proof to show that $36k$-edge-connectivity of each $S_i$ suffices to pack $k$ $S$-forests. More careful analysis yields that $35k$-edge-connectivity of each $S_i$ is sufficient when $k \geq 8$.
2603.16956Mar 2026
View2603.14922Closeness and Decision Making
In this article we consider networks, which for a given time period can have one link broken. Which new link should we build so the closeness of the resulting network satisfies some optimal criteria? We consider different criteria for optimization and different graphs: cycle, paths, lollipop graphs, and two complete graphs, connected by a link.
2603.14922Mar 2026
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Universal cycle constructions for k-subsets and k-multisets
A universal cycle for a set S of combinatorial objects is a cyclic sequence of length |S|that contains a representation of each element in S exactly once as a substring. If S is the set of k-subsets of [n] = {1, 2, . . . , n}, it is well-known that universal cycles do not always exists when applying a simple string representation, where 12 or 21 could represent the subset {1, 2}. Similarly, if S is the set of k-multisets of [n], it is also known that universal cycles do not always exist using a similar representation, where 112, 121, or 211 could represent the multiset {1, 1, 2}. By mapping these sets to an appropriate family of labeled graphs, universal cycles are known to exist, but without a known efficient construction. In this paper we consider a new representation for k-subsets and k-multisets that leads to efficient universal cycle constructions for all n, k >=2. We provide successor-rule algorithms to construct such universal cycles in O(n) time per symbol using O(n) space and demonstrate that necklace concatenation algorithms allow the same sequences to be generated in O(1) amortized time per symbol. They are the first known efficient universal cycle constructions for k-multisets. The results are obtained by considering constructions for bounded-weight de Bruijn sequences. In particular, we demonstrate that a bounded-weight generalization of the Grandmama de Bruijn sequence can be constructed in O(1) amortized time per symbol.
2603.11954Mar 2026
View2603.11934Decoding universal cycles for t-subsets and t-multisets by decoding bounded-weight de Bruijn sequences
A universal cycle for a set S of combinatorial objects is a cyclic sequence of length |S| that contains a representative of each element in S exactly once as a substring. Despite the many universal cycle constructions known in the literature for various sets including k-ary strings of length n, permutations of order n, t-subsets of an n-set, and t-multisets of an n-set, remarkably few have efficient decoding (ranking/unranking) algorithms. In this paper we develop the first polynomial time/space decoding algorithms for bounded-weight de Bruijn sequences for strings of length nover an alphabet of size k. The results are then applied to decode universal cycles for t-subsets and t-multisets.
2603.11934Mar 2026
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Some polynomial classes for the acyclic orientation with parity constraint problem
We study the problem of finding an acyclic orientation of an undirected graph with constrained in-degree parities specified by a subset T of vertices. An orientation is called T -odd if a vertex v has odd in-degree if and only if v P T . While the unconstrained parity orientation problem is polynomial (Chevalier et al. (1983)), imposing acyclicity makes it more challenging, and its complexity remains an open question. Szegedy and Szegedy ( 2006) proposed a randomized polynomial-time algorithm for this problem, but it is not known whether it belongs to co-NP. Furthermore, Gravier et al. (2025) showed the problem becomes NP-complete on partially directed graphs, even when restricted to planar cubic graphs. We identify three necessary conditions for the existence of acyclic T -odd orientation: a global parity condition P, and two conditions S and S ensuring the existence of potential sources and sinks. Following the work of Frank and Kiraly (2002), we define graph classes containing the graphs for which a given subset of the necessary conditions P, S and S is also sufficient for the existence of an acyclic T -odd orientation. We establish the inclusion relationships between these classes. We complete the study of these classes by a characterization of the solvable instances for Cartesian products of paths and cycles. The proofs of these results are all constructive, so that acyclic T -odd orientations can be built in polynomial time whenever they exist. We use these families, along with cliques, to demonstrate the strictness of the class inclusions in our hierarchy.
2603.09475Mar 2026
View2603.08492WELLDOC property for words generated by morphisms
In this paper, we study an abelian-type property of infinite words called well distributed occurrences, or WELLDOC for short. An infinite word $w$ on a $d$-ary alphabet has the WELLDOC property if, for each factor $u$ of $w$, positive integer $m$, and vector $v\in \mathbb{N}^d$, there is an occurrence of $u$ such that the Parikh vector of the prefix of $w$ preceding such occurrence is congruent to $v$ modulo $m$. The Parikh vector of a finite word $v$ on an alphabet has its $i$-th component equal to the number of occurrences of the $i$-th letter in $v$. We provide a criterion of the WELLDOC property for words generated by morphisms.
2603.08492Mar 2026
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