Related papers: Higher-order port-graph rewriting
Biological and cellular systems are often modeled as graphs in which vertices represent objects of interest (genes, proteins, drugs) and edges represent relational ties among these objects (binds-to, interacts-with, regulates). This…
Ptychography is a computational imaging technique widely used for high-resolution materials characterization, but high-quality reconstructions often require the use of regularization functions that largely remain manually designed. We…
We develop a rewriting theory suitable for diagrammatic algebras and lay down the foundations of a systematic study of their higher structures. In this paper, we focus on the question of finding bases. As an application, we give the first…
In this paper we present a proof system that operates on graphs instead of formulas. Starting from the well-known relationship between formulas and cographs, we drop the cograph-conditions and look at arbitrary undirected) graphs. This…
With the advent of the big data, graph are processed in an iterative manner, which incrementally described in the form of graph in big data applications. Most currently, graph processing methods treat the underlying map data as black boxes.…
We introduce graph normalizing flows: a new, reversible graph neural network model for prediction and generation. On supervised tasks, graph normalizing flows perform similarly to message passing neural networks, but at a significantly…
The vertices of a finite state system are usually a subset of the natural numbers. Most algorithms relative to these systems only use this fact to select vertices. For infinite state systems, however, the situation is different: in…
Orthologous genes, which arise through speciation, play a key role in comparative genomics and functional inference. In particular, graph-based methods allow for the inference of orthology estimates without prior knowledge of the underlying…
The next step in the understanding of the genome organization, after the determination of complete sequences, involves proteomics. The proteome includes the whole set of protein-protein interactions, and two recent independent studies have…
Prompt learning has attracted increasing attention in the graph domain as a means to bridge the gap between pretext and downstream tasks. Existing studies on heterogeneous graph prompting typically use feature prompts to modify node…
Optimization, a key tool in machine learning and statistics, relies on regularization to reduce overfitting. Traditional regularization methods control a norm of the solution to ensure its smoothness. Recently, topological methods have…
Network topology matrices are algebraic representations of graphs that are widely used in modeling and analysis of various applications including electrical circuits, communication networks and transportation systems. In this paper, we…
Here we introduce simple structures for the analysis of complex hypergraphs, hypergraph animals. These structures are designed to describe the local node neighbourhoods of nodes in hypergraphs. We establish their relationships to lattice…
Deep neural networks excel at image classification, but their performance is far less robust to input perturbations than human perception. In this work we explore whether this shortcoming may be partly addressed by incorporating…
Hierarchical graph rewriting is a highly expressive computational formalism that manipulates graphs enhanced with box structures for representing hierarchies. It has provided the foundations of various graph-based modeling tools, but the…
The aim of this research is a practical method to draw cable plans of complex machines. Such plans consist of electronic components and cables connecting specific ports of the components. Since the machines are configured for each client…
We develop a theory of covering digraphs, similar to the theory of covering spaces. By applying this theory to Cayley digraphs, we build a "bridge" between GLMY-theory and group homology theory, which helps to reduce path homology…
Refactoring is an established technique from the OO-community to restructure code: it aims at improving software readability, maintainability and extensibility. Although refactoring is not tied to the OO-paradigm in particular, its ideas…
Complex systems are difficult to study not only because they are nonlinear, multiscale, and often nonstationary, but because their scientifically relevant organization is often invisible at the level of individual components, pairwise…
Robotic cell injection is used for automatically delivering substances into a cell and is an integral component of drug development, genetic engineering and many other areas of cell biology. Traditionally, the correctness of functionality…