Related papers: Artificial chemistry experiments with chemlambda, …
The stabilization algorithm of Weisfeiler and Leman has as an input any square matrix A of order n and returns the minimal cellular (coherent) algebra W(A) which includes A. In case when A=A(G) is the adjacency matrix of a graph G the…
The analysis of the structure of chemical reaction networks is crucial for a better understanding of chemical processes. Such networks are well described as hypergraphs. However, due to the available methods, analyses regarding network…
Chemistry is an example of a discipline where the advancements of technology have led to multi-level and often tangled and tricky processes ongoing in the lab. The repeatedly complex workflows are combined with information from chemical…
Graphs are central to the chemical sciences, providing a natural language to describe molecules, proteins, reactions, and industrial processes. They capture interactions and structures that underpin materials, biology, and medicine. This…
Graph neural networks are widely used to learn global representations of graphs, which are then used for regression or classification tasks. Typically, the graphs in such data sets are connected, i.e. each training sample consists of a…
Chemists now routinely use software as part of their work. For example, virtual chemistry allows chemical reactions to be simulated. In particular, a selection of software is available for the visualisation of complex 3-dimensional…
Computational chemistry tools are widely used to study the behaviour of chemical phenomena. Yet, the complexity of these tools can make them inaccessible to non-specialists and challenging even for experts. In this work, we introduce El…
We consider graph classes $\mathcal G$ in which every graph has components in a class $\mathcal{C}$ of connected graphs. We provide a framework for the asymptotic study of $\lvert\mathcal{G}_{n,N}\rvert$, the number of graphs in…
Using a quantum processor to embed and process classical data enables the generation of correlations between variables that are inefficient to represent through classical computation. A fundamental question is whether these correlations…
Chemical reaction networks (CRNs) model the behavior of chemical reactions in well-mixed solutions and they can be designed to perform computations. In this tutorial we give an overview of various computational models for CRNs. Moreover, we…
Recent advances and achievements of artificial intelligence (AI) as well as deep and graph learning models have established their usefulness in biomedical applications, especially in drug-drug interactions (DDIs). DDIs refer to a change in…
Chemical algorithms are statistical algorithms described and represented as chemical reaction networks. They are particularly attractive for traffic shaping and general control of network dynamics; they are analytically tractable, they…
Kaemika is an app available on the four major app stores. It provides deterministic and stochastic simulation, supporting natural chemical notation enhanced with recursive and conditional generation of chemical reaction networks. It has a…
Graph rewrite formalisms are a powerful approach to modeling complex molecular systems. They capture the intrinsic concurrency of molecular interactions, thereby enabling a formal notion of mechanism (a partially ordered set of events) that…
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…
An introduction to the Quantum Chemistry Package (QCP), implemented in the computer algebra system Maple, is presented. The QCP combines sophisticated electronic structure methods and Maple's easy-to-use graphical interface to enable…
Chemical reaction networks (CRNs) exhibit complex dynamics governed by their underlying network structure. In this paper, we propose a novel approach to study the dynamics of CRNs by representing them on species graphs (S-graphs). By…
We present a conceptually new approach to describe state-of-the-art photonic quantum experiments using Graph Theory. There, the quantum states are given by the coherent superpositions of perfect matchings. The crucial observation is that…
The goal of this paper is to gather and develop some necessary and sufficient criteria for injectivity and multistationarity in vector fields associated with a chemical reaction network under a variety of more or less general assumptions on…
We present an algorithm turning any term of a linear quantum $\lambda$-calculus into a quantum circuit. The essential ingredient behind the proposed algorithm is Girard's geometry of interaction, which, differently from its well-known uses…