arXiv subjects

Bernat Corominas-Murtra

Publications and source records attributed to Bernat Corominas-Murtra.

36 records · Page 2Linked to original sources

arXiv2015

Non-Equilibrium Thermodynamics of Self-Replicating Protocells

We provide a non-equilibrium thermodynamic description of the life-cycle of a droplet based, chemically feasible, system of protocells. By coupling the protocells metabolic kinetics with its thermodynamics, we demonstrate how the system can be driven out of equilibrium to ensure protocell growth and replication. This coupling allows us to derive the equations of evolution and to rigorously demonstrate how growth and replication life-cycle can be understood as a non-equilibrium thermodynamic cycle. The process does not appeal to genetic information or inheritance, and is based only on non-equilibrium physics considerations. Our non-equilibrium thermodynamic description of simple, yet realistic, processes of protocell growth and replication, represents an advance in our physical understanding of a central biological phenomenon both in connection to the origin of life and for modern biology.

cond-mat.soft↗

arXiv2014

Detection of the elite structure in a virtual multiplex social system by means of a generalized $K$-core

Elites are subgroups of individuals within a society that have the ability and means to influence, lead, govern, and shape societies. Members of elites are often well connected individuals, which enables them to impose their influence to many and to quickly gather, process, and spread information. Here we argue that elites are not only composed of highly connected individuals, but also of intermediaries connecting hubs to form a cohesive and structured elite-subgroup at the core of a social network. For this purpose we present a generalization of the $K$-core algorithm that allows to identify a social core that is composed of well-connected hubs together with their `connectors'. We show the validity of the idea in the framework of a virtual world defined by a massive multiplayer online game, on which we have complete information of various social networks. Exploiting this multiplex structure, we find that the hubs of the generalized $K$-core identify those individuals that are high social performers in terms of a series of indicators that are available in the game. In addition, using a combined strategy which involves the generalized $K$-core and the recently introduced $M$-core, the elites of the different 'nations' present in the game are perfectly identified as modules of the generalized $K$-core. Interesting sudden shifts in the composition of the elite cores are observed at deep levels. We show that elite detection with the traditional $K$-core is not possible in a reliable way. The proposed method might be useful in a series of more general applications, such as community detection.

physics.soc-ph↗

arXiv2014

The weak core and the structure of elites in social multiplex networks

Recent approaches on elite identification highlighted the important role of {\em intermediaries}, by means of a new definition of the core of a multiplex network, the {\em generalised} $K$-core. This newly introduced core subgraph crucially incorporates those individuals who, in spite of not being very connected, maintain the cohesiveness and plasticity of the core. Interestingly, it has been shown that the performance on elite identification of the generalised $K$-core is sensibly better that the standard $K$-core. Here we go further: Over a multiplex social system, we isolate the community structure of the generalised $K$-core and we identify the weakly connected regions acting as bridges between core communities, ensuring the cohesiveness and connectivity of the core region. This gluing region is the {\em Weak core} of the multiplex system. We test the suitability of our method on data from the society of 420.000 players of the Massive Multiplayer Online Game {\em Pardus}. Results show that the generalised $K$-core displays a clearly identifiable community structure and that the weak core gluing the core communities shows very low connectivity and clustering. Nonetheless, despite its low connectivity, the weak core forms a unique, cohesive structure. In addition, we find that members populating the weak core have the best scores on social performance, when compared to the other elements of the generalised $K$-core. The weak core provides a new angle on understanding the social structure of elites, highlighting those subgroups of individuals whose role is to glue different communities in the core.

physics.soc-ph↗

arXiv2013

On the origin of ambiguity in efficient communication

This article studies the emergence of ambiguity in communication through the concept of logical irreversibility and within the framework of Shannon's information theory. This leads us to a precise and general expression of the intuition behind Zipf's vocabulary balance in terms of a symmetry equation between the complexities of the coding and the decoding processes that imposes an unavoidable amount of logical uncertainty in natural communication. Accordingly, the emergence of irreversible computations is required if the complexities of the coding and the decoding processes are balanced in a symmetric scenario, which means that the emergence of ambiguous codes is a necessary condition for natural communication to succeed.

cs.CL↗

arXiv2013

On the Origins of Hierarchy in Complex Networks

Hierarchy seems to pervade complexity in both living and artificial systems. Despite its relevance, no general theory that captures all features of hierarchy and its origins has been proposed yet. Here we present a formal approach resulting from the convergence of theoretical morphology and network theory that allows constructing a 3D morphospace of hierarchies and hence comparing the hierarchical organization of ecological, cellular, technological and social networks. Embedded within large voids in the morphospace of all possible hierarchies, four major groups are identified. Two of them match the expected from random networks with similar connectivity, thus suggesting that non-adaptive factors are at work. Ecological and gene networks define the other two, indicating that their topological order is the result of functional constraints. These results are consistent with an exploration of the morphospace using in silico evolved networks.

physics.soc-ph↗

arXiv2011

Measuring the Hierarchy of Feedforward Networks

In this paper we explore the concept of hierarchy as a quantifiable descriptor of ordered structures, departing from the definition of three conditions to be satisfied for a hierarchical structure: {\em order}, {\em predictability} and {\em pyramidal structure}. According to these principles we define a hierarchical index taking concepts from graph and information theory. This estimator allows to quantify the hierarchical character of any system susceptible to be abstracted in a feedforward causal graph, i.e., a directed acyclic graph defined in a single connected structure. Our hierarchical index is a balance between this predictability and pyramidal condition by the definition of two entropies: one attending the onward flow and other for the backward reversion. We show how this index allows to identify hierarchical, anti-hierarchical and non hierarchical structures. Our formalism reveals that departing from the defined conditions for a hierarchical structure, feedforward trees and the inverted tree graphs emerge as the only causal structures of maximal hierarchical and anti-hierarchical systems, respectively. Conversely, null values of the hierarchical index are attributed to a number of different configuration networks; from linear chains, due to their lack of pyramid structure, to full-connected feedforward graphs where the diversity of onward pathways is canceled by the uncertainty (lack of predictability) when going backwards. Some illustrative examples are provided for the distinction among these three types of hierarchical causal graphs.

physics.data-an↗

arXiv2011

Emergence of Zipf's Law in the Evolution of Communication

Zipf's law seems to be ubiquitous in human languages and appears to be a universal property of complex communicating systems. Following the early proposal made by Zipf concerning the presence of a tension between the efforts of speaker and hearer in a communication system, we introduce evolution by means of a variational approach to the problem based on Kullback's Minimum Discrimination of Information Principle. Therefore, using a formalism fully embedded in the framework of information theory, we demonstrate that Zipf's law is the only expected outcome of an evolving, communicative system under a rigorous definition of the communicative tension described by Zipf.

nlin.AO↗

arXiv2010

Universality in percolation of arbitrary Uncorrelated Nested Subgraphs

The study of percolation in so-called {\em nested subgraphs} implies a generalization of the concept of percolation since the results are not linked to specific graph process. Here the behavior of such graphs at criticallity is studied for the case where the nesting operation is performed in an uncorrelated way. Specifically, I provide an analyitic derivation for the percolation inequality showing that the cluster size distribution under a generalized process of uncorrelated nesting at criticality follows a power law with universal exponent $γ=3/2$. The relevance of the result comes from the wide variety of processes responsible for the emergence of the giant component that fall within the category of nesting operations, whose outcome is a family of nested subgraphs.

cond-mat.dis-nn↗

arXiv2010

Topological reversibility and causality in feed-forward networks

Systems whose organization displays causal asymmetry constraints, from evolutionary trees to river basins or transport networks, can be often described in terms of directed paths (causal flows) on a discrete state space. Such a set of paths defines a feed-forward, acyclic network. A key problem associated with these systems involves characterizing their intrinsic degree of path reversibility: given an end node in the graph, what is the uncertainty of recovering the process backwards until the origin? Here we propose a novel concept, \textit{topological reversibility}, which rigorously weigths such uncertainty in path dependency quantified as the minimum amount of information required to successfully revert a causal path. Within the proposed framework we also analytically characterize limit cases for both topologically reversible and maximally entropic structures. The relevance of these measures within the context of evolutionary dynamics is highlighted.

cond-mat.dis-nn↗

arXiv2010

Exploring the randomness of Directed Acyclic Networks

The feed-forward relationship naturally observed in time-dependent processes and in a diverse number of real systems -such as some food-webs and electronic and neural wiring- can be described in terms of so-called directed acyclic graphs (DAGs). An important ingredient of the analysis of such networks is a proper comparison of their observed architecture against an ensemble of randomized graphs, thereby quantifying the {\em randomness} of the real systems with respect to suitable null models. This approximation is particularly relevant when the finite size and/or large connectivity of real systems make inadequate a comparison with the predictions obtained from the so-called {\em configuration model}. In this paper we analyze four methods of DAG randomization as defined by the desired combination of topological invariants (directed and undirected degree sequence and component distributions) aimed to be preserved. A highly ordered DAG, called \textit{snake}-graph and a Erd\:os-Rényi DAG were used to validate the performance of the algorithms. Finally, three real case studies, namely, the \textit{C. elegans} cell lineage network, a PhD student-advisor network and the Milgram's citation network were analyzed using each randomization method. Results show how the interpretation of degree-degree relations in DAGs respect to their randomized ensembles depend on the topological invariants imposed. In general, real DAGs provide disordered values, lower than the expected by chance when the directedness of the links is not preserved in the randomization process. Conversely, if the direction of the links is conserved throughout the randomization process, disorder indicators are close to the obtained from the null-model ensemble, although some deviations are observed.

physics.soc-ph↗

arXiv2010

Diversity, competition, extinction: the ecophysics of language change

As early indicated by Charles Darwin, languages behave and change very much like living species. They display high diversity, differentiate in space and time, emerge and disappear. A large body of literature has explored the role of information exchanges and communicative constraints in groups of agents under selective scenarios. These models have been very helpful in providing a rationale on how complex forms of communication emerge under evolutionary pressures. However, other patterns of large-scale organization can be described using mathematical methods ignoring communicative traits. These approaches consider shorter time scales and have been developed by exploiting both theoretical ecology and statistical physics methods. The models are reviewed here and include extinction, invasion, origination, spatial organization, coexistence and diversity as key concepts and are very simple in their defining rules. Such simplicity is used in order to catch the most fundamental laws of organization and those universal ingredients responsible for qualitative traits. The similarities between observed and predicted patterns indicate that an ecological theory of language is emerging, supporting (on a quantitative basis) its ecological nature, although key differences are also present. Here we critically review some recent advances lying and outline their implications and limitations as well as open problems for future research.

q-bio.PE↗

arXiv2009

On the basic computational structure of gene regulatory networks

Gene regulatory networks constitute the first layer of the cellular computation for cell adaptation and surveillance. In these webs, a set of causal relations is built up from thousands of interactions between transcription factors and their target genes. The large size of these webs and their entangled nature make difficult to achieve a global view of their internal organisation. Here, this problem has been addressed through a comparative study for {\em Escherichia coli}, {\em Bacillus subtilis} and {\em Saccharomyces cerevisiae} gene regulatory networks. We extract the minimal core of causal relations, uncovering the hierarchical and modular organisation from a novel dynamical/causal perspective. Our results reveal a marked top-down hierarchy containing several small dynamical modules for \textit{E. coli} and \textit{B. subtilis}. Conversely, the yeast network displays a single but large dynamical module in the middle of a bow-tie structure. We found that these dynamical modules capture the relevant wiring among both common and organism-specific biological functions such as transcription initiation, metabolic control, signal transduction, response to stress, sporulation and cell cycle. Functional and topological results suggest that two fundamentally different forms of logic organisation may have evolved in bacteria and yeast.

q-bio.MN↗

arXiv2009

Switcher-random-walks: a cognitive-inspired mechanism for network exploration

Semantic memory is the subsystem of human memory that stores knowledge of concepts or meanings, as opposed to life specific experiences. The organization of concepts within semantic memory can be understood as a semantic network, where the concepts (nodes) are associated (linked) to others depending on perceptions, similarities, etc. Lexical access is the complementary part of this system and allows the retrieval of such organized knowledge. While conceptual information is stored under certain underlying organization (and thus gives rise to a specific topology), it is crucial to have an accurate access to any of the information units, e.g. the concepts, for efficiently retrieving semantic information for real-time needings. An example of an information retrieval process occurs in verbal fluency tasks, and it is known to involve two different mechanisms: -clustering-, or generating words within a subcategory, and, when a subcategory is exhausted, -switching- to a new subcategory. We extended this approach to random-walking on a network (clustering) in combination to jumping (switching) to any node with certain probability and derived its analytical expression based on Markov chains. Results show that this dual mechanism contributes to optimize the exploration of different network models in terms of the mean first passage time. Additionally, this cognitive inspired dual mechanism opens a new framework to better understand and evaluate exploration, propagation and transport phenomena in other complex systems where switching-like phenomena are feasible.

cs.AI↗

arXiv2007

Nested Subgraphs of Complex Networks

We analytically explore the scaling properties of a general class of nested subgraphs in complex networks, which includes the $K$-core and the $K$-scaffold, among others. We name such class of subgraphs $K$-nested subgraphs due to the fact that they generate families of subgraphs such that $...S_{K+1}({\cal G})\subseteq S_K({\cal G})\subseteq S_{K-1}({\cal G})...$. Using the so-called {\em configuration model} it is shown that any family of nested subgraphs over a network with diverging second moment and finite first moment has infinite elements (i.e. lacking a percolation threshold). Moreover, for a scale-free network with the above properties, we show that any nested family of subgraphs is self-similar by looking at the degree distribution. Both numerical simulations and real data are analyzed and display good agreement with our theoretical predictions.

cond-mat.dis-nn↗

arXiv2007

Robustness of the European power grids under intentional attack

The power grid defines one of the most important technological networks of our times and sustains our complex society. It has evolved for more than a century into an extremely huge and seemingly robust and well understood system. But it becomes extremely fragile as well, when unexpected, usually minimal, failures turn into unknown dynamical behaviours leading, for example, to sudden and massive blackouts. Here we explore the fragility of the European power grid under the effect of selective node removal. A mean field analysis of fragility against attacks is presented together with the observed patterns. Deviations from the theoretical conditions for network percolation (and fragmentation) under attacks are analysed and correlated with non topological reliability measures.

physics.soc-ph↗

arXiv2007

Emergence of Scale-Free Syntax Networks

The evolution of human language allowed the efficient propagation of nongenetic information, thus creating a new form of evolutionary change. Language development in children offers the opportunity of exploring the emergence of such complex communication system and provides a window to understanding the transition from protolanguage to language. Here we present the first analysis of the emergence of syntax in terms of complex networks. A previously unreported, sharp transition is shown to occur around two years of age from a (pre-syntactic) tree-like structure to a scale-free, small world syntax network. The nature of such transition supports the presence of an innate component pervading the emergence of full syntax. This observation is difficult to interpret in terms of any simple model of network growth, thus suggesting that some internal, perhaps innate component was at work. We explore this problem by using a minimal model that is able to capture several statistical traits. Our results provide evidence for adaptive traits, but it also indicates that some key features of syntax might actually correspond to non-adaptive phenomena.

q-bio.NC↗

arXiv2007

K-Scaffold subgraphs of Complex networks

Complex networks with high numbers of nodes or links are often difficult to analyse. However, not all elements contribute equally to their structural patterns. A small number of elements (the hubs) seem to play a particularly relevant role in organizing the overall structure around them. But other parts of the architecture (such as hub-hub connecting elements) are also important. In this letter we present a new type of substructure, to be named the $K$-scaffold subgraph, able to capture all the essential network components. Their key features, including the so called critical scaffold graph, are analytically derived.

physics.soc-ph↗

arXiv2007

Network statistics on early English Syntax: Structural criteria

This paper includes a reflection on the role of networks in the study of English language acquisition, as well as a collection of practical criteria to annotate free-speech corpora from children utterances. At the theoretical level, the main claim of this paper is that syntactic networks should be interpreted as the outcome of the use of the syntactic machinery. Thus, the intrinsic features of such machinery are not accessible directly from (known) network properties. Rather, what one can see are the global patterns of its use and, thus, a global view of the power and organization of the underlying grammar. Taking a look into more practical issues, the paper examines how to build a net from the projection of syntactic relations. Recall that, as opposed to adult grammars, early-child language has not a well-defined concept of structure. To overcome such difficulty, we develop a set of systematic criteria assuming constituency hierarchy and a grammar based on lexico-thematic relations. At the end, what we obtain is a well defined corpora annotation that enables us i) to perform statistics on the size of structures and ii) to build a network from syntactic relations over which we can perform the standard measures of complexity. We also provide a detailed example.

cs.CL↗