Related papers: An Interoperable Syntax for Gas Scattering Reactio…
Chemical reaction networks can be automatically generated from graph grammar descriptions, where rewrite rules model reaction patterns. Because a molecule graph is connected and reactions in general involve multiple molecules, the rewriting…
Finding the main product of a chemical reaction is one of the important problems of organic chemistry. This paper describes a method of applying a neural machine translation model to the prediction of organic chemical reactions. In order to…
Reaction coordinates are widely used throughout chemical physics to model and understand complex chemical transformations. We introduce a definition of the natural reaction coordinate, suitable for condensed phase and biomolecular systems,…
We present the first steps of interaction spaces theory, a universal mathematical theory of complex systems which is able to embed cellular automata, agent based models, master equation based models, stochastic or deterministic, continuous…
It is believed that consistent notation helps the research community in many ways. First and foremost, it provides a consistent interface of communication. Subjective experiments described according to uniform rules are easier to understand…
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…
Stochasticity is a key characteristic of intracellular processes such as gene regulation and chemical signalling. Therefore, characterising stochastic effects in biochemical systems is essential to understand the complex dynamics of living…
Stochastic reaction-diffusion processes may be presented in terms of integrable quantum chains and can be used to describe various biological and chemical systems. Exploiting the integrability of the models one finds in some cases good…
Explainability is crucial for complex systems like pervasive smart environments, as they collect and analyze data from various sensors, follow multiple rules, and control different devices resulting in behavior that is not trivial and,…
To harness the power of large language models in safety-critical domains, we need to ensure the explainability of their predictions. However, despite the significant attention to model interpretability, there remains an unexplored domain in…
We provide a novel notion of what it means to be interpretable, looking past the usual association with human understanding. Our key insight is that interpretability is not an absolute concept and so we define it relative to a target model,…
The purpose of this paper is twofold. First, we present the extension of the Li\`ege Intranuclear Cascade model to reactions induced by light ions. Second, we describe the C++ version of the code, which it is physics-wise equivalent to the…
Language sciences rely less and less on formal syntax as their base. The reason is probably its lack of psychological reality, knowingly avoided. Philosophers of science call for a paradigm shift in which explanations are by mechanisms, as…
We present a unified formalism for describing chemical reaction rates of trapped, ultracold molecules. This formalism reduces the scattering to its essential features, namely, a propagation of the reactant molecules through a gauntlet of…
The main contribution of this paper, is to propose a novel semantic approach based on a Natural Language Processing technique in order to ensure a semantic unification of unstructured process patterns which are expressed not only in…
We present an extension of a simple automaton model to incorporate non-local interactions extending over a spatial range in lattice gases. {}From the viewpoint of Statistical Mechanics, the lattice gas with interaction range may serve as a…
This thesis explores the generation of local explanations for already deployed machine learning models, aiming to identify optimal conditions for producing meaningful explanations considering both data and user requirements. The primary…
The calculation of molecular excited states is critically important to decipher a plethora of molecular properties. In this manuscript, we develop an equation of motion formalism on top of a bi-exponentially parametrized ground state…
We develop a novel method to analyze the dynamics of stochastic rewriting systems evolving over finitary adhesive, extensive categories. Our formalism is based on the so-called rule algebra framework and exhibits an intimate relationship…
Without the assumption of complete, shared awareness, it is necessary to consider communication between agents who may entertain different representations of the world. A syntactic (language-based) approach provides powerful tools to…