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At the heart of many contemporary theories of life is the concept of biological self-organisation: organisms have to continuously produce and maintain the conditions of their own existence in order to stay alive. The way in which these…

Charged excitations are electronic transitions that involve a change in the total charge of a molecule or material. Understanding the properties and reactivity of charged species requires insights from theoretical calculations that can…

Rationale is defined as a subset of input features that best explains or supports the prediction by machine learning models. Rationale identification has improved the generalizability and interpretability of neural networks on vision and…

A theory about the implication structure in graph coloring is presented. Discovering hidden relations is a crucial activity in every scientific discipline. The development of mathematical models to study and discover such hidden relations…

Graph theory provides a language for studying the structure of relations, and it is often used to study interactions over time too. However, it poorly captures the both temporal and structural nature of interactions, that calls for a…

Model-Based Anomaly Detection has been a successful approach to identify deviations from the expected behavior of Cyber-Physical Production Systems. Since manual creation of these models is a time-consuming process, it is advantageous to…

Building biological models by inferring functional dependencies from experimental data is an im- portant issue in Molecular Biology. To relieve the biologist from this traditionally manual process, various approaches have been proposed to…

Biology has changed radically in the last two decades, transitioning from a descriptive science into a design science. Synthetic biology allows us to bioengineer cells to synthesize novel valuable molecules such as renewable biofuels or…

Chain graphs (CG) use undirected and directed edges to represent both structural and associative dependences. Like acyclic directed graphs (ADGs), the CG associated with a statistical Markov model may not be unique, so CGs fall into Markov…

Directed acyclic graphs are a fundamental class of networks that includes citation networks, food webs, and family trees, among others. Here we define a random graph model for directed acyclic graphs and give solutions for a number of the…

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…

In our understanding, a mind-map is an adaptive engine that basically works incrementally on the fundament of existing transactional streams. Generally, mind-maps consist of symbolic cells that are connected with each other and that become…

Graphical models can represent a multivariate distribution in a convenient and accessible form as a graph. Causal models can be viewed as a special class of graphical models that not only represent the distribution of the observed system…

Recent advances in generative AI have accelerated the discovery of novel chemicals and materials. However, scaling these discoveries to industrial production remains a major bottleneck due to the synthesis gap -- the need to develop…

Similarly to other connectionist models, Graph Neural Networks (GNNs) lack transparency in their decision-making. A number of sub-symbolic approaches have been developed to provide insights into the GNN decision making process. These are…

The biological immune system is a robust, complex, adaptive system that defends the body from foreign pathogens. It is able to categorize all cells (or molecules) within the body as self-cells or non-self cells. It does this with the help…

The modern thermodynamics of discrete systems is based on graph theory, which provides both algebraic methods to define observables and a geometric intuition of their meaning and role. However, because chemical reactions are usually…

Artifact systems are a novel paradigm for specifying and implementing business processes described in terms of interacting modules called artifacts. Artifacts consist of data and lifecycles, accounting respectively for the relational…

Most controlled natural languages (CNLs) are processed with the help of a pipeline architecture that relies on different software components. We investigate in this paper in an experimental way how well answer set programming (ASP) is…

Complex networks describe a wide range of systems in nature and society, much quoted examples including the cell, a network of chemicals linked by chemical reactions, or the Internet, a network of routers and computers connected by physical…