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Abnormal metabolism is an emerging hallmark of cancer. Cancer cells utilize both aerobic glycolysis and oxidative phosphorylation (OXPHOS) for energy production and biomass synthesis. Understanding the metabolic reprogramming in cancer can…
The metabolic network of a living cell involves several hundreds or thousands of interconnected biochemical reactions. Previous research has shown that under realistic conditions only a fraction of these reactions is concurrently active in…
Empirical complex systems can be characterized not only by pairwise interactions, but also by higher-order (group) interactions influencing collective phenomena, from metabolic reactions to epidemics. Nevertheless, higher-order networks'…
Underpinning the past decades of work on the design, initialization, and optimization of neural networks is a seemingly innocuous assumption: that the network is trained on a \textit{stationary} data distribution. In settings where this…
The quantification of controllability and observability has recently received new interest in the context of large, complex networks of dynamical systems. A fundamental but computationally difficult problem is the placement or selection of…
Topology and weights are closely related in weighted complex networks and this is reflected in their modular structure. We present a simple network model where the weights are generated dynamically and they shape the developing topology. By…
Resilience is a system's ability to maintain its function when perturbations and errors occur. Whilst we understand low-dimensional networked systems' behavior well, our understanding of systems consisting of a large number of components is…
Biological networks, such as cellular metabolic pathways or networks of corticocortical connections in the brain, are intricately organized, yet remarkably robust toward structural damage. Whereas many studies have investigated specific…
The methodology named LIFE (Linear-in-Flux-Expressions) was developed with the purpose of simulating and analyzing large metabolic systems. With LIFE, the number of model parameters is reduced by accounting for correlations among the…
Bond graphs can be used to build thermodynamically-compliant hierarchical models of biomolecular systems. As bond graphs have been widely used to model, analyse and synthesise engineering systems, this paper suggests that they can play the…
The rapid advancement of technology underscores the critical importance of robustness in complex network systems. This paper presents a framework for investigating the structural robustness of interconnected network models. This paper…
We present a systematic mathematical analysis of the qualitative steady-state response to rate perturbations in large classes of reaction networks. This includes multimolecular reactions and allows for catalysis, enzymatic reactions,…
Previous work has shown that the dynamical regime of Recurrent Neural Networks (RNNs) - ranging from oscillatory to chaotic and fixpoint behavior - can be controlled by the global distribution of weights in connection matrices with…
Complex systems are large collections of entities that organize themselves into non-trivial structures that can be represented by networks. A key emergent property of such systems is robustness against random failures or targeted attacks…
Many algorithms have been proposed to predict missing links in a variety of real networks. These studies focus on mainly both accuracy and efficiency of these algorithms. However, little attention is paid to their robustness against either…
A quantitative understanding of how cells interact with their extracellular matrix via molecular bonds is fundamental for many important processes in cell biology and engineering. In these interactions, the deformability of cells and matrix…
Multimodal learning seeks to utilize data from multiple sources to improve the overall performance of downstream tasks. It is desirable for redundancies in the data to make multimodal systems robust to missing or corrupted observations in…
This paper serves as a framework for designing advanced models for drug action on metabolism. Drug treatment may affect metabolism by either enhancing or inhibiting metabolic reactions comprising a metabolic network. We introduce the…
Many real-world complex networks exhibit a community structure, in which the modules correspond to actual functional units. Identifying these communities is a key challenge for scientists. A common approach is to search for the network…
Bone remodeling involves the coordinated removal of bone by osteoclasts and addition of bone by osteoblasts, a process that is modulated by the prevailing mechanical environment. In this paper a fully coupled model of bone remodeling is…