Related papers: Weak Independence and Coupled Parallelism in Biolo…
In Petri net synthesis we ask whether a given transition system $A$ can be implemented by a Petri net $N$. Depending on the level of accuracy, there are three ways how $N$ can implement $A$: an embedding, the least accurate implementation,…
This paper examines how weak synaptic coupling can achieve rapid synchronization in heterogeneous networks. The assumptions aim at capturing the key mathematical properties that make this possible for biophysical networks. In particular,…
We introduce a mathematical model of symbiosis between different species by taking into account the influence of each species on the carrying capacities of the others. The modeled entities can pertain to biological and ecological societies…
We present a model, in which some nodes (called interconnecting nodes) in two networks merge and play the roles in both the networks. The model analytic and simulation discussions show a monotonically increasing dependence of…
The principle of similarity, or homophily, is often used to explain patterns observed in complex networks such as transitivity and the abundance of triangles (3-cycles). However, many phenomena from division of labor to protein-protein…
Synchronization, in which individual dynamical units keep in pace with each other in a decentralized fashion, depends both on the dynamical units and on the properties of the interaction network. Yet, the role played by the network has…
Protein-protein interactions (PPIs) are crucial in various biological processes and their study has significant implications for drug development and disease diagnosis. Existing deep learning methods suffer from significant performance…
We propose Weak and Entropy PINNs (WE-PINNs) for the approximation of entropy solutions to nonlinear hyperbolic conservation laws. Standard physics-informed neural networks enforce governing equations in strong differential form, an…
Analogous to biological sequence comparison, comparing cellular networks is an important problem that could provide insight into biological understanding and therapeutics. For technical reasons, comparing large networks is computationally…
This paper describes a stand-alone, no-frills tool supporting the analysis of (labelled) place/transition Petri nets and the synthesis of labelled transition systems into Petri nets. It is implemented as a collection of independent,…
Scientists are frequently faced with the important decision to start or terminate a creative partnership. This process can be influenced by strategic motivations, as early career researchers are pursuers, whereas senior researchers are…
Reversing Petri nets (RPNs) have recently been proposed as a net-basedapproach to model causal and out-of-causal order reversibility. They are based on the notion of individual tokens that can be connected together via bonds. In this paper…
Understanding the dependence and interplay between architecture and function in biological networks has great relevance to disease progression, biological fabrication and biological systems in general. We propose methods to assess the…
Deciphering the control principles of metabolism and its interaction with other cellular functions is central to biomedicine and biotechnology. Yet, understanding the efficient control of metabolic fluxes remains elusive for large-scale…
The execution of different cases of a process is often restricted by inter-case dependencies through e.g., queueing or shared resources. Various high-level Petri net formalisms have been proposed that are able to model and analyze…
State-of-the-art simulations of detailed neural models follow the Bulk Synchronous Parallel execution model. Execution is divided in equidistant communication intervals, equivalent to the shortest synaptic delay in the network. Neurons…
Technologies and their production systems are used by archaeologists and anthropologists to study complexity of sociotechnical systems. However, there are several issues that hamper agreement about what constitutes complexity and how we can…
The Click-though Rate (CTR) prediction task is a basic task in recommendation system. Most of the previous researches of CTR models built based on Wide \& deep structure and gradually evolved into parallel structures with different modules.…
Living systems operate in a critical dynamical regime -- between order and chaos -- where they are both resilient to perturbation, and flexible enough to evolve. To characterize such critical dynamics, the established 'structural theory' of…
Quantitative descriptions of network structure in big data can provide fundamental insights into the function of interconnected complex systems. Small-world structure, commonly diagnosed by high local clustering yet short average path…