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Compositional minimisation can be an effective technique to reduce the state space explosion problem. This technique considers a parallel composition of several processes. In its simplest form, each sequential process is replaced by an…
Functional graphs (FGs) model the graph structures used to analyse the behaviour of functions from a discrete set to itself. In turn, such functions are used to study real complex phenomena evolving in time. As the systems involved can be…
The large-scale properties of chemical reaction systems, such as the metabolism, can be studied with graph-based methods. To do this, one needs to reduce the information -- lists of chemical reactions -- available in databases. Even for the…
Constructing complex computation from simpler building blocks is a defining problem of computer science. In algebraic automata theory, we represent computing devices as semigroups. Accordingly, we use mathematical tools like products and…
Graph-based reaction systems were recently introduced as a generalization of the intensely studied set-based reaction systems. They deal with simple edge-labeled directed graphs, and dynamic semantics of graph-based reaction systems is…
Humans develop certain cognitive abilities to recognize objects and their transformations without explicit supervision, highlighting the importance of unsupervised representation learning. A fundamental challenge in unsupervised…
In this paper, we propose a graph classification approach for automatically determining whether to use a monolithic or a decomposition-based solution method. In this approach, an optimization problem is represented as a graph that captures…
It is an amazing fact that remarkably complex behaviors could emerge from a large collection of very rudimentary dynamical agents through very simple local interactions. However, it still remains elusive on how to design these local…
The shrinking core model describes the reaction of a spherical solid particle with a surrounding fluid. In this work, we revisit the SCM by deriving it from the underlying physical processes and performing a careful non-dimensionalisation,…
Analysis of signals defined on complex topologies modeled by graphs is a topic of increasing interest. Signal decomposition plays a crucial role in the representation and processing of such information, in particular, to process graph…
Counting problems, determining the number of possible states of a large system under certain constraints, play an important role in many areas of science. They naturally arise for complex disordered systems in physics and chemistry, in…
Presented in this paper is a derivation of a 2D catalytic reaction-based model to solve combinatorial optimization problems (COPs). The simulated catalytic reactions, a computational metaphor, occurs in an artificial chemical reactor that…
With the increase of graph size, it becomes difficult or even impossible to visualize graph structures clearly within the limited screen space. Consequently, it is crucial to design effective visual representations for large graphs. In this…
(Hyper)Graph decomposition is a family of problems that aim to break down large (hyper)graphs into smaller sub(hyper)graphs for easier analysis. The importance of this lies in its ability to enable efficient computation on large and complex…
The analysis of complex reaction networks is of great importance in several chemical and biochemical fields (interstellar chemistry, prebiotic chemistry, reaction mechanism, etc). In this article, we propose to simultaneously refine and…
We provide a category theoretical framework capturing two approaches to graph-based models of chemistry: formal reactions and disconnection rules. We model a translation from the latter to the former as a functor, which is faithful, and…
The reaction-coordinate mapping is a useful technique to study complex quantum dissipative dynamics into structured environments. In essence, it aims to mimic the original problem by means of an 'augmented system', which includes a suitably…
In the present paper a novel graph-based approach to the shape decomposition problem is addressed. The shape is appropriately transformed into a visibility graph enriched with local neighborhood information. A two-step diffusion process is…
Automata-based modeling languages, like Component Interaction Automata, offer an attractive means to capture and analyze the behavioral aspects of interacting components. At the center of these modeling languages we find finite state…
The bulk macroscopic response of a system of particles or inclusions with field-induced forces is studied. The susceptibilities and transport coefficients in such a system are expressed as averages of a multiple scattering expansion. A…