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The fundamental decomposition of a chemical reaction network (also called its "$\mathscr{F}$-decomposition") is the set of subnetworks generated by the partition of its set of reactions into the "fundamental classes" introduced by Ji and…

A decomposition of a chemical reaction network (CRN) is produced by partitioning its set of reactions. The partition induces networks, called subnetworks, that are "smaller" than the given CRN which, at this point, can be called parent…

The fundamental decomposition of a chemical reaction network (CRN) is induced by partitioning the reaction set into "fundamental classes". It was the basis of the Higher Deficiency Algorithm for mass action systems of Ji and Feinberg, and…

Chemical reaction networks (CRNs) are directed graphs with reactant or product complexes as vertices, and reactions as arcs. A CRN is weakly reversible if each of its connected components is strongly connected. Weakly reversible networks…

A chemical reaction network (CRN) is composed of reactions that can be seen as interactions among entities called species, which exist within the system. Endowed with kinetics, CRN has a corresponding set of ordinary differential equations…

The analysis of complex reaction networks is of great importance in several chemical and biochemical fields (interstellar chemistry, prebiotic chemistry, reaction mechanism, etc). In this article, we propose to simultaneously refine and…

In this work, we demonstrate that Linear Discriminant Analysis (LDA) applied to atomic positions in two different states of a biomolecule produces a good reaction coordinate between those two states. Atomic coordinates of a macromolecule…

This paper presents novel decomposition classes of chemical reaction networks (CRNs) derived from S-system kinetics. Based on the network decomposition theory initiated by Feinberg in 1987, we introduce the concept of incidence independent…

In the context of classification problems, Deep Learning (DL) approaches represent state of art. Many DL approaches are based on variations of standard multi-layer feed-forward neural networks. These are also referred to as deep networks.…

In many modern computer application problems, the classification of image data plays an important role. Among many different supervised machine learning models, convolutional neural networks (CNNs) and linear discriminant analysis (LDA) as…

Convolutional neural networks (CNNs) have been successful in representing the fully-connected inferencing ability perceived to be seen in the human brain: they take full advantage of the hierarchy-style patterns commonly seen in complex…

Functional decomposition of logic circuits has profound influence on all quality aspects of the cost-effective implementation of modern digital systems. In this paper, a relational approach to the decomposition of logic circuits is…

The heterogeneous structure implies that a very few nodes may play the critical role in maintaining structural and functional properties of a large-scale network. Identifying these vital nodes is one of the most important tasks in network…

In the first part of this paper, we propose new optimization-based methods for the computation of preferred (dense, sparse, reversible, detailed and complex balanced) linearly conjugate reaction network structures with mass action dynamics.…

Convolutional neural network (CNN) is a class of artificial neural networks widely used in computer vision tasks. Most CNNs achieve excellent performance by stacking certain types of basic units. In addition to increasing the depth and…

Accurate image segmentation remains challenging, particularly in generating sharp, confident boundaries. While modern architectures have advanced the field, many of them still rely on standard loss functions like Cross-Entropy and Dice,…

This paper studies chemical kinetic systems which decompose into weakly reversible complex factorizable (CF) systems. Among power law kinetic systems, CF systems (denoted as PL-RDK systems) are those where branching reactions of a reactant…

Attribute bias in federated learning (FL) typically leads local models to optimize inconsistently due to the learning of non-causal associations, resulting degraded performance. Existing methods either use data augmentation for increasing…

Being among the easiest ways to find meaningful structure from discrete data, Latent Dirichlet Allocation (LDA) and related component models have been applied widely. They are simple, computationally fast and scalable, interpretable, and…

We investigate the sensitivity of the LHC to flavour-changing neutral current interactions involving the top quark and a photon using a model-independent effective field theory framework, focusing on two complementary processes: single top…