相关论文: Artificial chemistry experiments with chemlambda, …
String diagrams are a powerful tool for reasoning about physical processes, logic circuits, tensor networks, and many other compositional structures. Dixon, Duncan and Kissinger introduced string graphs, which are a combinatoric…
We present a novel method for identifying a biochemical reaction network based on multiple sets of estimated reaction rates in the corresponding reaction rate equations arriving from various (possibly different) experiments. The current…
Knowledge graphs are often visualized using node-link diagrams that reveal relationships and structure. In many applications using graphs, it is desirable to allow users to edit graphs to ensure data accuracy or provides updates. Commonly…
Rapid discovery of new reactions and molecules in recent years has been facilitated by the advancements in high throughput screening, accessibility to a much more complex chemical design space, and the development of accurate molecular…
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…
Reactive programs combine traditional sequential programming constructs with primitives to allow communication with other concurrent agents. They are ubiquitous in modern applications, ranging from components systems and web services, to…
The study of quantum evolution on graphs for diversified topologies is beneficial to modeling various realistic systems. A systematic method, the dimerized decomposition, is proposed to analyze the dynamics on an arbitrary network. By…
Several graph visualization tools exist. However, they are not able to handle large graphs, and/or they do not allow interaction. We are interested on large graphs, with hundreds of thousands of nodes. Such graphs bring two challenges: the…
Girard's Geometry of Interaction (GoI), a semantics designed for linear logic proofs, has been also successfully applied to programming language semantics. One way is to use abstract machines that pass a token on a fixed graph along a path…
Motivated by recent progress on the interplay between graph theory, dynamics, and systems theory, we revisit the analysis of chemical reaction networks described by mass action kinetics. For reaction networks possessing a thermodynamic…
The goal of the paper is to automatize the selection of mechanisms which are able to describe a set of measurements. In order to do so first we construct a set of possible mechanism fulfilling chemically reasonable requirements with a given…
Quantum computing, an innovative computing system carrying prominent processing rate, is meant to be the solutions to problems in many fields. Among these realms, the most intuitive application is to help chemical researchers correctly…
Given a graph $G$, a vertex switch of $v \in V(G)$ results in a new graph where neighbors of $v$ become nonneighbors and vice versa. This operation gives rise to an equivalence relation over the set of labeled digraphs on $n$ vertices. The…
We explore different strategies to integrate prior domain knowledge into the design of a deep neural network (DNN). We focus on graph neural networks (GNN), with a use case of estimating the potential energy of chemical systems (molecules…
Molecular property calculations are the bedrock of chemical physics. High-fidelity \textit{ab initio} modeling techniques for computing the molecular properties can be prohibitively expensive, and motivate the development of…
We introduce a new distributed algorithm for aligning graphs or finding substructures within a given graph. It is based on the cavity method and is used to study the maximum-clique and the graph-alignment problems in random graphs. The…
The chemical production of graphene as well as its controlled wet- chemical modification is a challenge for synthetic chemists and the characterization of reaction products requires sophisticated analytic methods. In this review we first…
We describe a tool to create, edit, visualise and compute with interaction nets - a form of graph rewriting systems. The editor, called GraphPaper, allows users to create and edit graphs and their transformation rules using an intuitive…
An analogy between combinatorial chemistry and Monte Carlo computer simulation is pursued. Examples of how to design libraries for both materials discovery and protein molecular evolution are given. For materials discovery, the concept of…
In this paper, we present a hybrid graph-drawing algorithm (GDA) for layouting large, naturally-clustered, disconnected graphs. We called it a hybrid algorithm because it is an implementation of a series of already known graph-drawing and…