相关论文: Artificial life properties of directed interaction…
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…
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…
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…
Biological processes underlying the basic functions of a cell involve complex interactions between genes. From a technical point of view, these interactions can be represented through a graph where genes and their connections are,…
The process of genetic recombination can be seen as a chemical reaction network with mass-action kinetics. We review the known results on existence, uniqueness, and global stability of an equilibrium in every compatibility class and for all…
We study the implications of the modeling choice to use a graph, instead of a hypergraph, to represent real-world interconnected systems whose constituent relationships are of higher order by nature. Such a modeling choice typically…
Machine learning models are poised to make a transformative impact on chemical sciences by dramatically accelerating computational algorithms and amplifying insights available from computational chemistry methods. However, achieving this…
Motivation: The design of enzymes is as challenging as it is consequential for making chemical synthesis in medical and industrial applications more efficient, cost-effective and environmentally friendly. While several aspects of this…
Although LLM-based agents are proven to master tool orchestration in scientific fields, particularly chemistry, their single-task performance remains limited by underlying tool constraints. To this end, we propose tool amplification, a…
Many biological and social systems are naturally represented as edge-weighted directed or undirected hypergraphs since they exhibit group interactions involving three or more system units as opposed to pairwise interactions that can be…
In this paper we explore mathematical tools that can be used to relate directed and undirected random graph models to each other. We identify probability spaces on which a directed and an undirected graph model are equivalent, and…
We investigate Relational Graph Attention Networks, a class of models that extends non-relational graph attention mechanisms to incorporate relational information, opening up these methods to a wider variety of problems. A thorough…
The Bond Graph approach and the Chemical Reaction Network approach to modelling biomolecular systems developed independently. This paper brings together the two approaches by providing a bond graph interpretation of the chemical reaction…
The method of analytical continuation from imaginary to real chemical potential is tested in 2-color QCD. In comparison to previous studies in the same theory, an exact updating algorithm is used and simulations are performed closer to the…
Normal molecular dynamics simulations are usually unable to simulate chemical reactions due to the low probability of forming the transition state. Therefore, enhanced sampling methods are implemented to accelerate the occurrence of…
This paper presents an experimental study to compare analysis tools with management systems for querying and analysing graphs. Our experiment compares classic graph navigational operations queries where analytics tools and management…
Drug-drug interactions are preventable causes of medical injuries and often result in doctor and emergency room visits. Computational techniques can be used to predict potential drug-drug interactions. We approach the drug-drug interaction…
The string splicing was introduced by Tom Head which stands as an abstract model for the DNA recombination under the influence of restriction enzymes. The complex chemical process of three dimensional molecules in three dimensional space…
Large Language Models (LLMs) have taken the field of AI by storm, but their adoption in the field of Artificial Life (ALife) has been, so far, relatively reserved. In this work we investigate the potential synergies between LLMs and ALife,…
Gene interaction graphs aim to capture various relationships between genes and represent decades of biology research. When trying to make predictions from genomic data, those graphs could be used to overcome the curse of dimensionality by…