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Natural language generation provides designers with methods for automatically generating text, e.g. for creating summaries, chatbots and game content. In practise, text generators are often either learned and hard to interpret, or created…
This paper investigates the use of graph rewriting systems as a modelling tool, and advocates the embedding of such systems in an interactive environment. One important application domain is the modelling of biochemical systems, where…
Discovering the underlying structures present in large real world graphs is a fundamental scientific problem. In this paper we show that a graph's clique tree can be used to extract a hyperedge replacement grammar. If we store an ordering…
Engelfriet and Vereijken have shown that linear graph grammars based on hyperedge replacement generate graph languages that can be considered as interpretations of regular string languages over typed symbols. In this paper we show that…
Our work is concerned with the generation and targeted design of RNA, a type of genetic macromolecule that can adopt complex structures which influence their cellular activities and functions. The design of large scale and complex…
Graph-based representations of images have recently acquired an important role for classification purposes within the context of machine learning approaches. The underlying idea is to consider that relevant information of an image is…
This paper studies infinite graphs produced from a natural unfolding operation applied to finite graphs. Graphs produced via such operations are of finite degree and automatic over the unary alphabet (that is, they can be described by…
Spontaneous self-replication in cellular automata has long been considered rare, with most known examples requiring careful design or artificial initialization. In this paper, we present formal, causal evidence that such replication can…
In this work, we introduce a filtration on temporal graphs based on $\delta$-temporal motifs (recurrent subgraphs), yielding a multi-scale representation of temporal structure. Our temporal filtration allows tools developed for filtered…
Many scientific datasets are of high dimension, and the analysis usually requires visual manipulation by retaining the most important structures of data. Principal curve is a widely used approach for this purpose. However, many existing…
Research on the similarity of a graph to being a tree - called the treewidth of the graph - has seen an enormous rise within the last decade, but a practically fast algorithm for this task has been discovered only recently by Tamaki (ESA…
Gene assembly is an intricate biological process that has been studied formally and modeled through string and graph rewriting systems. Recently, a restriction of the general (intramolecular) model, called simple gene assembly, has been…
We present an intuitive formalism for implementing cellular automata on arbitrary topologies. By that means, we identify a symmetry operation in the class of elementary cellular automata. Moreover, we determine the subset of topologically…
Temporal graphs represent the dynamic relationships among entities and occur in many real life application like social networks, e commerce, communication, road networks, biological systems, and many more. They necessitate research beyond…
Directed acyclic graphs (DAGs) are a class of graphs commonly used in practice, with examples that include electronic circuits, Bayesian networks, and neural architectures. While many effective encoders exist for DAGs, it remains…
Graphs are widespread data structures used to model a wide variety of problems. The sheer amount of data to be processed has prompted the creation of a myriad of systems that help us cope with massive scale graphs. The pressure to deliver…
Unmeasured causal forces influence diverse experimental time series, such as the transcription factors that regulate genes, or the descending neurons that steer motor circuits. Combining the theory of skew-product dynamical systems with…
Cyclic cellular automata (CCA) are models of excitable media. Started from random initial conditions, they produce several different kinds of spatial structure, depending on their control parameters. We introduce new tools from information…
The several algebraic approaches to graph transformation proposed in the literature all ensure that if an item is preserved by a rule, so are its connections with the context graph where it is embedded. But there are applications in which…
We investigate subshifts with a general algebraic structure and cellular automata on them, with an emphasis on (order-theoretic) lattices. Our main results concern the characterization of Boolean algebraic subshifts, conditions for…