PhD Candidate, Queen Mary University of London
I'm a PhD researcher focused on the analysis and modelling of real-world multi-dimensional networks
A mathematical framework can be used to describe many real systems. This assumption underpins my research, which can be placed in the network science field and is focused on complex systems. These systems are made up of a large number of elementary units which, as a whole, show properties that cannot be predicted by the mere knowledge of the individual parts. The standard approach to network description of complex systems consists of studying the mathematical object, also called graph, resulting from the aggregation of all the interactions (edges) observed between a certain set of elementary units (nodes). A social system, for instance, can be described as a set of individuals through an aggregation of friendships, communications, collaborations, and working relationships, just to mention some of them. However, considering all the interactions on an equal footing might in general discard important information about the structure and functioning of the original real system. Therefore, a better description of the system is given by the so-called ``multi-layer networks'', i.e., networks where each node appears in a set of different layers, and each layer describes all the edges of a given type (e.g. a different kind of social interaction). My PhD project aims to develop new measures, based on optimisation principles and information theory techniques, to extract relevant features from large-scale multi-layer networks, by filtering out noise and redundant information. In particular, the identification of key components, which should retain the maximum amount of information, will help to speed up the process of comparison among different multilayer networks and lay the foundation for the construction of a multilayer ''backbone''. These methods can be applied to several aspects of transportation networks, biological systems, and human behaviours, including mobility and social interactions. As an example, we are currently working on the human brain network reconstructed from the medical scans (fMRI and DTI) of several patients. The aim of this research is to extract features from the mathematical formulation, which can be used to distinguish between healthy and non-healthy patients (in our case, patients with Autism Spectrum Disorder).
Abstract: Author(s): Manlio De Domenico and Jacob BiamonteDisorder—known as entropy—is inherent to all systems, natural and manmade. A way of quantifying a complex network’s entropy is proposed.[Phys. Rev. X 6, 041062] Published Wed Dec 21, 2016Disorder—known as entropy—is inherent to all systems, natural and manmade. A way of quantifying a complex network’s entropy is proposed.
Pub.: 21 Dec '16, Pinned: 23 Jan '18
Abstract: Understanding how the human brain is structured, and how its architecture is related to the function, is of paramount importance for a variety of applications, including, but not limited to, new ways to prevent, deal with and cure brain diseases, such as Alzheimer's or Parkinson's, and psychiatric disorders, such as Schizophrenia. The recent advances in structural and functional neuroimaging, together with the increasing attitude to interdisciplinary approaches involving computer science, mathematics and physics, are fostering interesting results from computational neuroscience, that are quite often based on the analysis of complex network representation of human brain. In the last years, this representation experienced a theoretical and computational revolution that are breaching neuroscience, allowing to cope with the increasing complexity of human brain across multiple scales and in multiple dimensions, and to model structural and functional connectivity from new perspectives, often combined with each other. In this work, we will review the main achievements obtained from interdisciplinary research based on magnetic resonance imaging and establishing, de facto, the birth of multilayer network analysis and modeling of human brain.
Pub.: 23 Mar '17, Pinned: 23 Jan '18
Abstract: Many complex systems can be represented as networks consisting of distinct types of interactions, which can be categorized as links belonging to different layers. For example, a good description of the full protein-protein interactome requires, for some organisms, up to seven distinct network layers, accounting for different genetic and physical interactions, each containing thousands of protein-protein relationships. A fundamental open question is then how many layers are indeed necessary to accurately represent the structure of a multilayered complex system. Here we introduce a method based on quantum theory to reduce the number of layers to a minimum while maximizing the distinguishability between the multilayer network and the corresponding aggregated graph. We validate our approach on synthetic benchmarks and we show that the number of informative layers in some real multilayer networks of protein-genetic interactions, social, economical and transportation systems can be reduced by up to 75%.
Pub.: 24 Apr '15, Pinned: 23 Jan '18
Abstract: Despite substantial recent progress, our understanding of the principles and mechanisms underlying complex brain function and cognition remains incomplete. Network neuroscience proposes to tackle these enduring challenges. Approaching brain structure and function from an explicitly integrative perspective, network neuroscience pursues new ways to map, record, analyze and model the elements and interactions of neurobiological systems. Two parallel trends drive the approach: the availability of new empirical tools to create comprehensive maps and record dynamic patterns among molecules, neurons, brain areas and social systems; and the theoretical framework and computational tools of modern network science. The convergence of empirical and computational advances opens new frontiers of scientific inquiry, including network dynamics, manipulation and control of brain networks, and integration of network processes across spatiotemporal domains. We review emerging trends in network neuroscience and attempt to chart a path toward a better understanding of the brain as a multiscale networked system.
Pub.: 24 Feb '17, Pinned: 23 Jan '18
Abstract: The brain is expensive, incurring high material and metabolic costs for its size--relative to the size of the body--and many aspects of brain network organization can be mostly explained by a parsimonious drive to minimize these costs. However, brain networks or connectomes also have high topological efficiency, robustness, modularity and a 'rich club' of connector hubs. Many of these and other advantageous topological properties will probably entail a wiring-cost premium. We propose that brain organization is shaped by an economic trade-off between minimizing costs and allowing the emergence of adaptively valuable topological patterns of anatomical or functional connectivity between multiple neuronal populations. This process of negotiating, and re-negotiating, trade-offs between wiring cost and topological value continues over long (decades) and short (millisecond) timescales as brain networks evolve, grow and adapt to changing cognitive demands. An economical analysis of neuropsychiatric disorders highlights the vulnerability of the more costly elements of brain networks to pathological attack or abnormal development.
Pub.: 14 Apr '12, Pinned: 23 Jan '18
Abstract: In the last decade, network science has shed new light both on the structural (anatomical) and on the functional (correlations in the activity) connectivity among the different areas of the human brain. The analysis of brain networks has made possible to detect the central areas of a neural system and to identify its building blocks by looking at overabundant small subgraphs, known as motifs. However, network analysis of the brain has so far mainly focused on anatomical and functional networks as separate entities. The recently developed mathematical framework of multi-layer networks allows us to perform an analysis of the human brain where the structural and functional layers are considered together. In this work, we describe how to classify the subgraphs of a multiplex network, and we extend the motif analysis to networks with an arbitrary number of layers. We then extract multi-layer motifs in brain networks of healthy subjects by considering networks with two layers, anatomical and functional, respectively, obtained from diffusion and functional magnetic resonance imaging. Results indicate that subgraphs in which the presence of a physical connection between brain areas (links at the structural layer) coexists with a non-trivial positive correlation in their activities are statistically overabundant. Finally, we investigate the existence of a reinforcement mechanism between the two layers by looking at how the probability to find a link in one layer depends on the intensity of the connection in the other one. Showing that functional connectivity is non-trivially constrained by the underlying anatomical network, our work contributes to a better understanding of the interplay between the structure and function in the human brain.
Pub.: 01 May '17, Pinned: 23 Jan '18
Abstract: Network analysis provides a powerful tool to analyze complex influences of social and ecological structures on community and household dynamics. Most network studies of social–ecological systems use simple, undirected, unweighted networks. We analyze multiplex, directed, and weighted networks of subsistence food flows collected in three small indigenous communities in Arctic Alaska potentially facing substantial economic and ecological changes. Our analysis of plausible future scenarios suggests that changes to social relations and key households have greater effects on community robustness than changes to specific wild food resources.
Pub.: 16 Nov '16, Pinned: 23 Jan '18
Abstract: We explore how to study dynamical interactions between brain regions using functional multilayer networks whose layers represent the different frequency bands at which a brain operates. Specifically, we investigate the consequences of considering the brain as a multilayer network in which all brain regions can interact with each other at different frequency bands, instead of as a multiplex network, in which interactions between different frequency bands are only allowed within each brain region and not between them. We study the second smallest eigenvalue of the combinatorial supra-Laplacian matrix of the multilayer network in detail, and we thereby show that the heterogeneity of interlayer edges and, especially, the fraction of missing edges crucially modify the spectral properties of the multilayer network. We illustrate our results with both synthetic network models and real data sets obtained from resting state magnetoencephalography. Our work demonstrates an important issue in the construction of frequency-based multilayer brain networks.
Pub.: 17 Mar '17, Pinned: 23 Jan '18
Abstract: We formulate and propose an algorithm (MultiRank) for the ranking of nodes and layers in large multiplex networks. MultiRank takes into account the full multiplex network structure of the data and exploits the dual nature of the network in terms of nodes and layers. The proposed centrality of the layers (influences) and the centrality of the nodes are determined by a coupled set of equations. The basic idea consists in assigning more centrality to nodes that receive links from highly influential layers and from already central nodes. The layers are more influential if highly central nodes are active in them. The algorithm applies to directed/undirected as well as to weighted/unweighted multiplex networks. We discuss the application of MultiRank to three major examples of multiplex network datasets: the European Air Transportation Multiplex Network, the Pierre Auger Multiplex Collaboration Network and the FAO Multiplex Trade Network.
Pub.: 16 Mar '17, Pinned: 23 Jan '18
Abstract: The architecture of many complex systems is well described by multiplex interaction networks, and their dynamics is often the result of several intertwined processes taking place at different levels. However only in a few cases can such multi-layered architecture be empirically observed, as one usually only has experimental access to such structure from an aggregated projection. A fundamental question is thus to determine whether the hidden underlying architecture of complex systems is better modelled as a single interaction layer or results from the aggregation and interplay of multiple layers. Here we show that, by only using local information provided by a random walker navigating the aggregated network, it is possible to decide in a robust way if the underlying structure is a multiplex and, in the latter case, to determine the most probable number of layers. The proposed methodology detects and estimates the optimal architecture capable of reproducing observable non- Markovian dynamics taking place on networks, with applications ranging from human or animal mobility to electronic transport or molecular motors. Furthermore, the mathematical theory extends above and beyond detection of physical layers in networked complex systems, as it provides a general solution for the optimal decomposition of complex dynamics in a Markov switching combination of simple (diffusive) dynamics.
Pub.: 12 May '17, Pinned: 23 Jan '18
Abstract: Network models of language have provided a way of linking cognitive processes to language structure. However, current approaches focus only on one linguistic relationship at a time, missing the complex multi-relational nature of language. In this work, we overcome this limitation by modelling the mental lexicon of English-speaking toddlers as a multiplex lexical network, i.e. a multi-layered network where N = 529 words/nodes are connected according to four relationship: (i) free association, (ii) feature sharing, (iii) co-occurrence, and (iv) phonological similarity. We investigate the topology of the resulting multiplex and then proceed to evaluate single layers and the full multiplex structure on their ability to predict empirically observed age of acquisition data of English speaking toddlers. We find that the multiplex topology is an important proxy of the cognitive processes of acquisition, capable of capturing emergent lexicon structure. In fact, we show that the multiplex structure is fundamentally more powerful than individual layers in predicting the ordering with which words are acquired. Furthermore, multiplex analysis allows for a quantification of distinct phases of lexical acquisition in early learners: while initially all the multiplex layers contribute to word learning, after about month 23 free associations take the lead in driving word acquisition.
Pub.: 25 Apr '17, Pinned: 23 Jan '18
Abstract: Optimal percolation is the problem of finding the minimal set of nodes whose removal from a network fragments the system into non-extensive disconnected clusters. The solution to this problem is important for strategies of immunization in disease spreading, and influence maximization in opinion dynamics. Optimal percolation has received considerable attention in the context of isolated networks. However, its generalization to multiplex networks has not yet been considered. Here we show that approximating the solution of the optimal percolation problem on a multiplex network with solutions valid for single-layer networks extracted from the multiplex may have serious consequences in the characterization of the true robustness of the system. We reach this conclusion by extending many of the methods for finding approximate solutions of the optimal percolation problem from single-layer to multiplex networks, and performing a systematic analysis on synthetic and real-world multiplex networks.
Pub.: 18 Nov '17, Pinned: 23 Jan '18
Abstract: The behavior of many complex systems is determined by a core of densely interconnected units. While many methods are available to identify the core of a network when connections between nodes are all of the same type, a principled approach to define the core when multiple types of connectivity are allowed is still lacking. Here we introduce a general framework to define and extract the core-periphery structure of multi-layer networks by explicitly taking into account the connectivity of the nodes at each layer. We show how our method works on synthetic networks with different size, density, and overlap between the cores at the different layers. We then apply the method to multiplex brain networks whose layers encode information both on the anatomical and the functional connectivity among regions of the human cortex. Results confirm the presence of the main known hubs, but also suggest the existence of novel brain core regions that have been discarded by previous analysis which focused exclusively on the structural layer. Our work is a step forward in the identification of the core of the human connectome, and contributes to shed light to a fundamental question in modern neuroscience.
Pub.: 23 Dec '17, Pinned: 23 Jan '18
Abstract: We model the formation of multi-layer transportation networks as a multi-objective optimization process, where service providers compete for passengers, and the creation of routes is determined by a multi-objective cost function encoding a trade-off between efficiency and competition. The resulting zero-parameter model reproduces the structural properties of the real six continental air transportation networks using only minimal information on the original systems. We find that the network of routes operated by each airline is indeed very close to the theoretical Pareto front in the efficiency-competition plane, suggesting that these systems are compatible with the proposed optimization model. Our results shed light on the fundamental role played by multiplexity and multi-objective optimization principles in shaping the structure of large-scale transportation systems, and provide novel insights about potential strategies for individual airlines to increase their revenues by a clever selection of new routes.
Pub.: 03 Oct '17, Pinned: 23 Jan '18
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