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Massimiliano Zanin

Publications and source records attributed to Massimiliano Zanin.

At least 37 records · Page 2Linked to original sources
arXiv2018

Evaluating Wikipedia as a source of information for disease understanding

The increasing availability of biological data is improving our understanding of diseases and providing new insight into their underlying relationships. Thanks to the improvements on both text mining techniques and computational capacity, the combination of biological data with semantic information obtained from medical publications has proven to be a very promising path. However, the limitations in the access to these data and their lack of structure pose challenges to this approach. In this document we propose the use of Wikipedia - the free online encyclopedia - as a source of accessible textual information for disease understanding research. To check its validity, we compare its performance in the determination of relationships between diseases with that of PubMed, one of the most consulted data sources of medical texts. The obtained results suggest that the information extracted from Wikipedia is as relevant as that obtained from PubMed abstracts (i.e. the free access portion of its articles), although further research is proposed to verify its reliability for medical studies.

cs.IR↗
arXiv2018

Understanding diseases as increased heterogeneity: a complex network computational framework

Due to the complexity of the human body, most diseases present a high inter-personal variability in the way they manifest, i.e. in their phenotype, which has important clinical repercussions - as for instance the difficulty in defining objective diagnostic rules. We here explore the hypothesis that signs and symptoms used to define a disease should be understood in terms of the dispersion (as opposed to the average) of physical observables. To that end, we propose a computational framework, based on complex networks theory, to map groups of subjects to a network structure, based on their pairwise phenotypical similarity. We demonstrate that the resulting structure can be used to improve the performance of classification algorithms, especially in the case of a limited number of instances, both with synthetic and real data sets. Beyond providing an alternative conceptual understanding of diseases, the proposed framework could be of special relevance in the growing field of personalised, or N-to-1, medicine.

physics.soc-ph↗
arXiv2018

Topological structures are consistently overestimated in functional complex networks

Functional complex networks have meant a pivotal change in the way we understand complex systems, being the most outstanding one the human brain. These networks have classically been reconstructed using a frequentist approach that, while simple, completely disregards the uncertainty that derives from data finiteness. We here provide an alternative solution based on Bayesian inference, with link weights treated as random variables described by probability distributions, from which ensembles of networks are sampled. By using both statistical and topological considerations, we prove that the role played by links' uncertainty is equivalent to the introduction of a random rewiring, whose omission leads to a consistent overestimation of topological structures. We further show that this bias is enhanced in short time series, suggesting the existence of a theoretical time resolution limit for obtaining reliable structures. We also propose a simple sampling process for correcting topological values obtained in frequentist networks. We finally validate these concepts through synthetic and real network examples, the latter representing the brain electrical activity of a group of people during a cognitive task.

physics.data-an↗
arXiv2018

From the difference of structures to the structure of the difference

When dealing with evolving or multi-dimensional complex systems, network theory provides with elegant ways of describing their constituting components, through respectively time-varying and multi-layer complex networks. Nevertheless, the analysis of how these components are related is still an open problem. We here propose a framework for analysing the evolution of a (complex) system, by describing the structure created by the difference between multiple networks by means of the Information Content metric. As opposed to other approaches, as for instance the use of global overlap or entropies, the proposed one allows to understand if the observed changes are due to random noise, or to structural (targeted) modifications. We validate the framework by means of sets of synthetic networks, as well as networks representing real technological, social and biological evolving systems. We further propose a way of reconstructing network correlograms, which allow to convert the system's evolution to the frequency domain.

physics.soc-ph↗
arXiv2017

Credit card fraud detection through parenclitic network analysis

The detection of frauds in credit card transactions is a major topic in financial research, of profound economic implications. While this has hitherto been tackled through data analysis techniques, the resemblances between this and other problems, like the design of recommendation systems and of diagnostic / prognostic medical tools, suggest that a complex network approach may yield important benefits. In this contribution we present a first hybrid data mining / complex network classification algorithm, able to detect illegal instances in a real card transaction data set. It is based on a recently proposed network reconstruction algorithm that allows creating representations of the deviation of one instance from a reference group. We show how the inclusion of features extracted from the network data representation improves the score obtained by a standard, neural network-based classification algorithm; and additionally how this combined approach can outperform a commercial fraud detection system in specific operation niches. Beyond these specific results, this contribution represents a new example on how complex networks and data mining can be integrated as complementary tools, with the former providing a view to data beyond the capabilities of the latter.

cs.SI↗
arXiv2016

Phase changes in delay propagation networks

The analysis of the dynamics of delays propagation is one of the major topics inside Air Transport Management research. Delays are generated by the elements of the system, but their propagation is a global process fostered by relationships inside the network. If the topology of such propagation process has been extensively studied in the literature, little attention has been devoted to the fact that such topology may have a dynamical nature. Here we differentiate between two phases of the system by applying two causality metrics, respectively describing the standard phase (i.e. propagation of normal delays) and a disrupted one (corresponding to abnormal and unexpected delays). We identify the critical point triggering the change of the topology of the system, in terms of delays magnitude, using a historical data set of flights crossing Europe in 2011. We anticipate that the proposed results will open new doors towards the understanding of the delay propagation dynamics and the mitigation of extreme events.

physics.soc-ph↗
arXiv2016

On causality of extreme events

Multiple metrics have been developed to detect causality relations between data describing the elements constituting complex systems, all of them considering their evolution through time. Here we propose a metric able to detect causality within static data sets, by analysing how extreme events in one element correspond to the appearance of extreme events in a second one. The metric is able to detect non- linear causalities; to analyse both cross-sectional and longitudinal data sets; and to discriminate between real causalities and correlations caused by confounding factors. We validate the metric through synthetic data, dynamical and chaotic systems, and data representing the human brain activity in a cognitive task. We further show how the proposed metric is able to outperform classical causality metrics, provided non-linear relationships are present and large enough data sets are available.

physics.data-an↗
arXiv2016

Beware of the Small-World neuroscientist!

The SW has undeniably been one of the most popular network descriptors in the neuroscience literature. Two main reasons for its lasting popularity are its apparent ease of computation and the intuitions it is thought to provide on how networked systems operate. Over the last few years, some pitfalls of the SW construct and, more generally, of network summary measures, have widely been acknowledged.

q-bio.NC↗
arXiv2016

The topology of card transaction money flows

Money flow models are essential tools to understand different economical phenomena, like saving propensities and wealth distributions. In spite of their importance, most of them are based on synthetic transaction networks with simple topologies, e.g. random or scale-free ones, as the characterisation of real networks is made difficult by the confidentiality and sensitivity of money transaction data. Here we present an analysis of the topology created by real credit card transactions from one of the biggest world banks, and show how different distributions, e.g. number of transactions per card or amount, have nontrivial characteristics. We further describe a stochastic model to create transactions data sets, feeding from the obtained distributions, which will allow researchers to create more realistic money flow models.

q-fin.GN↗
arXiv2015

Probabilistic Constraint Programming for Parameters Optimisation of Generative Models

Complex networks theory has commonly been used for modelling and understanding the interactions taking place between the elements composing complex systems. More recently, the use of generative models has gained momentum, as they allow identifying which forces and mechanisms are responsible for the appearance of given structural properties. In spite of this interest, several problems remain open, one of the most important being the design of robust mechanisms for finding the optimal parameters of a generative model, given a set of real networks. In this contribution, we address this problem by means of Probabilistic Constraint Programming. By using as an example the reconstruction of networks representing brain dynamics, we show how this approach is superior to other solutions, in that it allows a better characterisation of the parameters space, while requiring a significantly lower computational cost.

physics.soc-ph↗
arXiv2015

On alternative formulations of the small-world metric in complex networks

Small-world networks, i.e. networks displaying both a high clustering coefficient and a small characteristic path length, are obliquitous in nature. Since their identification, the "small-worldness" metric, as proposed by Humphries and Gurney, has frequently been used to detect such structural property in real-world complex networks, to a large extent in the study of brain dynamics. Here I discuss several of its drawbacks, including its lack of definition in disconnected networks and the impossibility of assessing a statistical significance; and present different alternative formulations to overcome these difficulties, validated through the phenospaces representing a set of 48 real networks.

physics.soc-ph↗
arXiv2015

Can we neglect the multi-layer structure of functional networks?

Functional networks, i.e. networks representing dynamic relationships between the components of a complex system, have been instrumental for our understanding of, among others, the human brain. Due to limited data availability, the multi-layer nature of numerous functional networks has hitherto been neglected, and nodes are endowed with a single type of links even when multiple relationships coexist at different physical levels. A relevant problem is the assessment of the benefits yielded by studying a multi-layer functional network, against the simplicity guaranteed by the reconstruction and use of the corresponding single layer projection. Here, I tackle this issue by using as a test case, the functional network representing the dynamics of delay propagation through European airports. Neglecting the multi-layer structure of a functional network has dramatic consequences on our understanding of the underlying system, a fact to be taken into account when a projection is the only available information.

physics.soc-ph↗
arXiv2014

Information content: assessing meso-scale structures in complex networks

We propose a novel measure to assess the presence of meso-scale structures in complex networks. This measure is based on the identification of regular patterns in the adjacency matrix of the network, and on the calculation of the quantity of information lost when pairs of nodes are iteratively merged. We show how this measure is able to quantify several meso-scale structures, like the presence of modularity, bipartite and core-periphery configurations, or motifs. Results corresponding to a large set of real networks are used to validate its ability to detect non-trivial topological patterns.

physics.soc-ph↗
arXiv2013

Parenclitic networks: a multilayer description of heterogeneous and static data-sets

Describing a complex system is in many ways a problem akin to identifying an object, in that it involves defining boundaries, constituent parts and their relationships by the use of grouping laws. Here we propose a novel method which extends the use of complex networks theory to a generalized class of non-Gestaltic systems, taking the form of collections of isolated, possibly heterogeneous, scalars, e.g. sets of biomedical tests. The ability of the method to unveil relevant information is illustrated for the case of gene expression in the response to osmotic stress of {\it Arabidopsis thaliana}. The most important genes turn out to be the nodes with highest centrality in appropriately reconstructed networks. The method allows predicting a set of 15 genes whose relationship with such stress was previously unknown in the literature. The validity of such predictions is demonstrated by means of a target experiment, in which the predicted genes are one by one artificially induced, and the growth of the corresponding phenotypes turns out to feature statistically significant differences when compared to that of the wild-type.

physics.soc-ph↗
arXiv2013

Emergence of network features from multiplexity

Many biological and man-made networked systems are characterized by the simultaneous presence of different sub-networks organized in separate layers, with links and nodes of qualitatively different types. While during the past few years theoretical studies have examined a variety of structural features of complex networks, the outstanding question is whether such features are characterizing all single layers, or rather emerge as a result of coarse-graining, i.e. when going from the multilayered to the aggregate network representation. Here we address this issue with the help of real data. We analyze the structural properties of an intrinsically multilayered real network, the European Air Transportation Multiplex Network in which each commercial airline defines a network layer. We examine how several structural measures evolve as layers are progressively merged together. In particular, we discuss how the topology of each layer affects the emergence of structural properties in the aggregate network.

physics.soc-ph↗
arXiv2013

Modelling the Air Transport with Complex Networks: a short review

Air transport is a key infrastructure of modern societies. In this paper we review some recent approaches to air transport, which make extensive use of theory of complex networks. We discuss possible networks that can be defined for the air transport and we focus our attention to networks of airports connected by flights. We review several papers investigating the topology of these networks and their dynamics for time scales ranging from years to intraday intervals, and consider also the resilience properties of air networks to extreme events. Finally we discuss the results of some recent papers investigating the dynamics on air transport network, with emphasis on passengers traveling in the network and epidemic spreading mediated by air transport.

physics.soc-ph↗
arXiv2012

Modeling the Multi-layer Nature of the European Air Transport Network: Resilience and Passengers Re-scheduling under random failures

We study the dynamics of the European Air Transport Network by using a multiplex network formalism. We will consider the set of flights of each airline as an interdependent network and we analyze the resilience of the system against random flight failures in the passenger's rescheduling problem. A comparison between the single-plex approach and the corresponding multiplex one is presented illustrating that the multiplexity strongly affects the robustness of the European Air Network.

physics.soc-ph↗