相关论文: On Dynamically Generating Relevant Elementary Flux…
Energy-Based Models (EBMs) present a flexible and appealing way to represent uncertainty. Despite recent advances, training EBMs on high-dimensional data remains a challenging problem as the state-of-the-art approaches are costly, unstable,…
Biological systems are governed by coupled interactions between intracellular metabolism and bioreactor operation that span multiple time scales. Constraint-based metabolic models are widely used to describe intracellular metabolism, but…
Cellular metabolism, the integrated interconversion of thousands of metabolic substrates through enzyme-catalyzed biochemical reactions, is the most investigated complex intercellular web of molecular interactions. While the topological…
Networks coming from protein-protein interactions, transcriptional regulation, signaling, or metabolism may appear to have "unusual" properties. To quantify this, it is appropriate to randomize the network and test the hypothesis that the…
Organisms have evolved a variety of mechanisms to cope with the unpredictability of environmental conditions, and yet mainstream models of metabolic regulation are typically based on strict optimality principles that do not account for…
The impressive growth of wireless data networks has recently led to increased attention to the issue of electromagnetic pollution and the fulfillment of electromagnetic field (EMF) exposure limits. This paper tackles the problem of power…
Modeling the dynamical flows on networks of biomolecular machines often entails computing node populations and edge fluxes with Master Equations and correlating machine performance with entropy production. But this alone is not sufficient…
Elastic MicroPhase Separation (EMPS) provides a simple route to create soft materials with homogeneous microstructures by leveraging the supersaturation of crosslinked polymer networks with liquids. At low supersaturation, network…
Accurately depicting multiphysics interactions in interfacial systems requires computational frameworks capable of reconciling geometric adaptability with strict conservation fidelity. However, traditional spatiotemporal discretisation…
While denoising diffusion and flow matching have driven major advances in generative modeling, their application to tabular data remains limited, despite its ubiquity in real-world applications. To this end, we develop TabbyFlow, a…
Multiresolution Matrix Factorization (MMF) is unusual amongst fast matrix factorization algorithms in that it does not make a low rank assumption. This makes MMF especially well suited to modeling certain types of graphs with complex…
This paper deals with temporal enzyme distribution in the activation of biochemical pathways. Pathway activation arises when production of a certain biomolecule is required due to changing environmental conditions. Under the premise that…
Energy-based models (EBMs) are a powerful class of probabilistic generative models due to their flexibility and interpretability. However, relationships between potential flows and explicit EBMs remain underexplored, while contrastive…
When the underlying physical network layer in optimal network flow problems is a large graph, the associated optimization problem has a large set of decision variables. In this paper, we discuss how the cycle basis from graph theory can be…
Metabolic cybergenetics is a promising concept that interfaces gene expression and cellular metabolism with computers for real-time dynamic metabolic control. The focus is on control at the transcriptional level, serving as a means to…
With more energy networks being interconnected to form integrated energy systems (IESs), the optimal energy flow (OEF) problem has drawn increasing attention. Extant studies on OEF models mostly utilize the finite difference method (FDM) to…
13C-Metabolic Flux Analysis (13C-MFA) and Flux Balance Analysis (FBA) are widely used to investigate the operation of biochemical networks in both biological and biotechnological research. Both of these methods use metabolic reaction…
The dramatic increase of network infrastructure comes at the cost of rapidly increasing energy consumption, which makes optimization of energy efficiency (EE) an important topic. Since EE is often modeled as the ratio of rate to power, we…
Sparse portfolio optimization is a fundamental yet challenging problem in quantitative finance, since traditional approaches heavily relying on historical return statistics and static objectives can hardly adapt to dynamic market regimes.…
Numerical simulations of flow and transport in porous media usually rely on hybrid-dimensional models, i.e., the fracture is considered as objects of a lower dimension compared to the embedding matrix. Such models are usually combined with…