Related papers: Striking a balance with Recon 2.1
With neural networks being used to control safety-critical systems, they increasingly have to be both accurate (in the sense of matching inputs to outputs) and robust. However, these two properties are often at odds with each other and a…
Metabolic pathways are fundamental maps in biochemistry that detail how molecules are transformed through various reactions. The complexity of metabolic network, where a single compound can play a part in multiple pathways, poses a…
In computational metabolic design, it is often necessary to modify the original constraint-based metabolic networks to lead to growth-coupled production, where cell growth forces target metabolite production. However, in genome-scale…
A new type of robust estimation problem is introduced where the goal is to recover a statistical model that has been corrupted after it has been estimated from data. Methods are proposed for "repairing" the model using only the design and…
Metabolism displays striking and robust regularities in the forms of modularity and hierarchy, whose composition may be compactly described. This renders metabolic architecture comprehensible as a system, and suggests the order in which…
This research is to search for alternatives to the resolution of complex medical diagnosis where human knowledge should be apprehended in a general fashion. Successful application examples show that human diagnostic capabilities are…
Reaction networks (RNs) comprise a set $X$ of species and a set $\mathscr{R}$ of reactions $Y\to Y'$, each converting a multiset of educts $Y\subseteq X$ into a multiset $Y'\subseteq X$ of products. RNs are equivalent to directed…
Binary neural networks (BNNs) have received ever-increasing popularity for their great capability of reducing storage burden as well as quickening inference time. However, there is a severe performance drop compared with real-valued…
Understanding design principles of complex cellular organization is one of the major challenges in biology. Recent analysis of the large-scale cellular organization has revealed the scale-free nature and robustness of metabolic and protein…
Efforts to catalogue the structure of metabolic networks have generated highly detailed, genome-scale atlases of biochemical reactions in the cell. Unfortunately, these atlases fall short of capturing the kinetic details of metabolic…
In this paper we study how to determine if a linear biochemical network satisfies the detailed balance condition, without knowing the details of all the reactions taking place in the network. To this end, we use the formalism of response…
The network structure (or topology) of a dynamical network is often unavailable or uncertain. Hence, we consider the problem of network reconstruction. Network reconstruction aims at inferring the topology of a dynamical network using…
Characterizing the in uence of network properties on the global emerging behavior of interacting elements constitutes a central question in many areas, from physical to social sciences. In this article we study a primary model of disordered…
Background: A metabolic genotype comprises all chemical reactions an organism can catalyze via enzymes encoded in its genome. A genotype is viable in a given environment if it is capable of producing all biomass components the organism…
Metabolism and evolution are closely connected: if a mutation incurs extra energetic costs for an organism, there is a baseline selective disadvantage that may or may not be compensated for by other adaptive effects. A long-standing, but to…
The sheer amounts of biological data that are generated in recent years have driven the development of network analysis tools to facilitate the interpretation and representation of these data. A fundamental challenge in this domain is the…
Chemical reaction networks underpin biological and physical phenomena across scales, from microbial interactions to planetary atmosphere dynamics. Bacterial communities exhibit complex competitive interactions for resources, human organs…
Background: Elucidating gene regulatory networks is crucial for understanding normal cell physiology and complex pathologic phenotypes. Existing computational methods for the genome-wide ``reverse engineering'' of such networks have been…
We investigate the stability properties of two different classes of metabolic cycles using a combination of analytical and computational methods. Using principles from structural kinetic modeling (SKM), we show that the stability of…
We present a systematic procedure for testing whether reaction networks exhibit non-expansivity or monotonicity. This procedure identifies explicit norms under which a network is non-expansive or cones for which the system is monotone-or…