1,720,981 research outputs found
Entropy of a network ensemble: definitions and applications to genomic data
No full textIn this paper we introduce the framework for the application of statistical mechanics to network theory, with a particular emphasis to the concept of entropy of network ensembles. This formalism provides novel observables and insights for the analysis of high-throughput transcriptomics data, integrated with apriori biological knowledge, embedded in-to available public databases of protein-protein interaction and cell signaling
Network measures for protein folding state discrimination
Full text linkProteins fold using a two-state or multi-state kinetic mechanisms, but up to now there is not a first-principle model to explain this different behavior. We exploit the network properties of protein structures by introducing novel observables to address the problem of classifying the different types of folding kinetics. These observables display a plain physical meaning, in terms of vibrational modes, possible configurations compatible with the native protein structure, and folding cooperativity. The relevance of these observables is supported by a classification performance up to 90%, even with simple classifiers such as discriminant analysis
Multiscale characterization of ageing and cancer progression by a novel network entropy measure
No full textWe characterize different cell states, related to cancer and ageing phenotypes, by a measure of entropy of network ensembles, integrating gene expression profiling values and protein interaction network topology. In our case studies, network entropy, that by definition estimates the number of possible network instances satisfying the given constraints, can be interpreted as a measure of the ‘‘parameter space’’ available to the cell. Network entropy was able to characterize specific pathological conditions: normal versus cancer cells, primary tumours that developed metastasis or relapsed, and extreme longevity samples. Moreover, this approach has been applied at different scales, from whole network to specific subnetworks (biological pathways defined on a priori biological knowledge) and single nodes (genes), allowing a deeper understanding of the cell processes involved
Two-Step Optimization of Envelope Design for the Reduction of Building Energy Demand
No full textThe path towards nearly-Zero Energy Buildings has enforced stricter constraints in construction design while promoting the investigation of new architectural solutions, in residential and producing sectors. Energy simulations, integrated with machine learning, helps academics and professionals to investigate novel strategies for energy saving. We present here a 2-step methodology based on genetic algorithms, aiming to reduce the energy consumption for indoor heating and cooling, while identifying the most suitable commercial solutions for external wall and roof constructions. We compare it with a 1-step optimization algorithm with the goal to determine pros and cons of both methodologies. Even if the two methodologies are comparable in terms of energy reduction, the 2-step algorithm is less computationally expensive and finds several plausible architectural solutions, with equivalent energy profile
Network Controllability Is Determined by the Density of Low In-Degree and Out-Degree Nodes
No full textThe problem of controllability of the dynamical state of a network is central in network theory and has wide applications ranging from network medicine to financial markets. The driver nodes of the network are the nodes that can bring the network to the desired dynamical state if an external signal is applied to them. Using the framework of structural controllability, here we show that the density of nodes with in-degree and out-degree equal to 0, 1 and 2 determines the number of driver nodes of random networks. Moreover we show that networks with minimum in-degree and out-degree greater than 2, are always fully controllable by an infinitesimal fraction of driver nodes, regardless on the other properties of the degree distribution. Finally, based on these results, we propose an algorithm to improve the controllability of networks
Simulations in agricultural buildings: a machine learning approach to forecast seasonal energy need
Full text linkA fast and reliable estimation of building energy need is essential in agricultural building design, nonetheless, a large number of simulations is required to obtain better energy saving solutions. The aim of this work is to understand if machine learning can substitute numerical simulations and speed up the building design process and assess the incidence of specific architectural elements. Supervised regression models has been trained and tested in a data-set of thousands simulations performed on a case-study agricultural building. Among the algorithms, the tree-based Extreme Gradient Boosting showed the best performance. A study on model explainability has been carried out using SHAP and features importance, which is fundamental to help academics and professionals devise better design strategies for both new constructions and retrofitting interventions
Entropy-Based Network Representation of the Individual Metabolic Phenotype
Full text link<p>We approach here the problem of defining and estimating the nature of the metabolite-metabolite association network underlying the human individual metabolic phenotype in healthy subjects. We retrieved significant associations using an entropy-based approach and a multiplex network formalism. We defined a significantly over-represented network formed by biologically interpretable metabolite modules. The entropy of the individual metabolic phenotype is also introduced and discussed.</p
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
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