Petter Holme | Umeå University (original) (raw)

Papers by Petter Holme

Abstract Complex chronic diseases are usually not caused by changes in a single causal gene but b... more Abstract Complex chronic diseases are usually not caused by changes in a single causal gene but by an unbalanced regulating network resulting from the dysfunctions of multiple genes or their products. Therefore, network based systems approach can be helpful for the identification of candidate genes related to complex diseases and their relationships.

Abstract: To understand the system-wide organization of metabolism, different lines of study have... more Abstract: To understand the system-wide organization of metabolism, different lines of study have devised different categorizations of metabolites. The relationship and difference between categories can provide new insights for a more detailed description of the organization of metabolism.

We consider methods for quantifying the similarity of vertices in networks. We propose a measure ... more We consider methods for quantifying the similarity of vertices in networks. We propose a measure of similarity based on the concept that two vertices are similar if their immediate neighbors in the network are themselves similar. This leads to a self-consistent matrix formulation of similarity that can be evaluated iteratively using only a knowledge of the adjacency matrix of the network.

Abstract Most severe disasters cause large population movements. These movements make it difficul... more Abstract Most severe disasters cause large population movements. These movements make it difficult for relief organizations to efficiently reach people in need. Understanding and predicting the locations of affected people during disasters is key to effective humanitarian relief operations and to long-term societal reconstruction.

The XY gauge glass model1 has attracted much interest in connection to the vortex glass phase of ... more The XY gauge glass model1 has attracted much interest in connection to the vortex glass phase of high-Tc superconductors. 2 In three dimensions 3D there is a general consensus that the XY gauge glass model exhibits a finitetemperature glass transition. 1, 3–5 However, in 2D there exist conflicting evidences: On the one hand, equilibrium studies of defect energy, 3, 5–7 Monte Carlo MC simulations of the root-mean-square current, 8 and resistance calculation9 have suggested that no finite-T ordering exists.

Abstract. Interaction between consumers and companies can create conflict. When a consensus is un... more Abstract. Interaction between consumers and companies can create conflict. When a consensus is unreachable there are legal authorities to resolve the case. This letter is a study of data from the Brazilian Department of Justice from which we build a bipartite network of categories of complaints linked to the companies receiving those complaints. We find the complaint categories organised in an hierarchical way where companies only get complaints of lower degree if they already got complaints of higher degree.

Abstract: The graph layouts used for complex network studies have been mainly been developed to i... more Abstract: The graph layouts used for complex network studies have been mainly been developed to improve visualization. If we interpret the layouts in metric spaces such as Euclidean ones, however, the embedded spatial information can be a valuable cue for various purposes. In this work, we focus on the navigational properties of spatial graphs. We use an recently user-centric navigation protocol to explore spatial layouts of complex networks that are optimal for navigation.

The XY model is one of the classical and most versatile spin models of statistical mechanics. It ... more The XY model is one of the classical and most versatile spin models of statistical mechanics. It has been used in many physical contexts, from superconductors 1 to lattice gauge theory of quantum chromodynamics 2, and furthermore applied to emergent phenomena in systems such as bird flocks 3 and parallel discrete-time simulations 4. In general, the XY model describes a system of N pairwise interacting units.

Abstract: Symmetry--invariance to certain operators--is a fundamental concept in many branches of... more Abstract: Symmetry--invariance to certain operators--is a fundamental concept in many branches of physics. We propose ways to measure symmetric properties of vertices, and their surroundings, in networks. To be stable to the randomness inherent in many complex networks, we consider measures that are continuous rather than dichotomous. The main operator we suggest is permutations of the paths of a certain length leading out from a vertex.

We study a model of opinion formation where the collective decision of a group is said to happen ... more We study a model of opinion formation where the collective decision of a group is said to happen if the fraction of agents having the most common opinion exceeds a threshold value, a critical mass. We find that there exists a unique nontrivial critical mass giving the most efficient convergence to consensus. In addition, we observe that for small critical masses, the characteristic time scale for the relaxation to consensus splits into two.

During the last decade of network research focusing on structural and dynamical properties of net... more During the last decade of network research focusing on structural and dynamical properties of networks, the role of network users has been more or less underestimated from the bird's-eye view of global perspective. In this era of global positioning system equipped smartphones, however, a user's ability to access local geometric information and find efficient pathways on networks plays a crucial role, rather than the globally optimal pathways.

Abstract. To what extent do the characteristic features of a chemical reaction network reflect it... more Abstract. To what extent do the characteristic features of a chemical reaction network reflect its purpose and function? In general, one argues that correlations between specific features and specific functions are key to understanding a complex structure. However, specific features may sometimes be neutral and uncorrelated with any system-specific purpose, function or causal chain. Such neutral features are caused by chance and randomness.

Abstract: What are the dynamics behind youth subcultures such as punk, hippie, or hip-hop culture... more Abstract: What are the dynamics behind youth subcultures such as punk, hippie, or hip-hop cultures? How does the global dynamics of these subcultures relate to the individual's search for a personal identity? We propose a simple dynamical model to address these questions and find that only a few assumptions of the individual's behaviour are necessary to regenerate known features of youth culture.

Abstract One approach to study the system-wide organization of biochemistry is to use statistical... more Abstract One approach to study the system-wide organization of biochemistry is to use statistical graph theory. In such heavily simplified methods, which disregard most of the dynamic aspects of biochemistry, one is faced with fundamental questions. One such question is how the chemical reaction systems should be reduced to a graph retaining as much functional information as possible from the original reaction system.

Abstract The structure of the Internet at the autonomous system (AS) level has been studied by th... more Abstract The structure of the Internet at the autonomous system (AS) level has been studied by the physics, mathematics and computer science communities. We extend this work to include features of the core and the periphery, taking a radial perspective on AS network structure. New methods for plotting AS data are described, and they are used to analyse datasets that have been extended to contain edges missing from earlier collections.

Abstract Many recent large-scale studies of interaction networks have focused on networks of accu... more Abstract Many recent large-scale studies of interaction networks have focused on networks of accumulated contacts. In this letter we explore social networks of ongoing relationships with an emphasis on dynamical aspects. We find a distribution of response times (times between consecutive contacts of different direction between two actors) that has a power law shape over a large range.

We model a system of networking agents that seek to optimize their centrality in the network whil... more We model a system of networking agents that seek to optimize their centrality in the network while keeping their cost, the number of connections they are participating in, low. Unlike other game-theory based models for network evolution, the success of the agents is related only to their position in the network. The agents use strategies based on local information to improve their chance of success. Both the evolution of strategies and network structure are investigated.

Any system, natural or man-made, consisting of entities that interact pairwise can be described i... more Any system, natural or man-made, consisting of entities that interact pairwise can be described in terms of a network. Networks in the real life often contain some degree of randomness, and have also some structure arising from the strategies or laws the entities follow to make new contacts. Such networks—that can only be described as having both randomness and structure—are called complex networks and have lately received much attention in the physicist community 1, 2.

Abstract: The large-scale shape and function of metabolic networks are intriguing topics of syste... more Abstract: The large-scale shape and function of metabolic networks are intriguing topics of systems biology. Such networks are on one hand commonly regarded as modular (ie built by a number of relatively independent subsystems), but on the other hand they are robust in a way not expected of a purely modular system. To address this question we carefully discuss the partition of metabolic networks into subnetworks.

The central points of communication network flow have often been identified using graph theoretic... more The central points of communication network flow have often been identified using graph theoretical centrality measures. In real networks, the state of traffic density arises from an interplay between the dynamics of the flow and the underlying network structure. In this work we investigate the relationship between centrality measures and the density of traffic for some simple particle hopping models on networks with emerging scale-free degree distributions.

Abstract Complex chronic diseases are usually not caused by changes in a single causal gene but b... more Abstract Complex chronic diseases are usually not caused by changes in a single causal gene but by an unbalanced regulating network resulting from the dysfunctions of multiple genes or their products. Therefore, network based systems approach can be helpful for the identification of candidate genes related to complex diseases and their relationships.

Abstract: To understand the system-wide organization of metabolism, different lines of study have... more Abstract: To understand the system-wide organization of metabolism, different lines of study have devised different categorizations of metabolites. The relationship and difference between categories can provide new insights for a more detailed description of the organization of metabolism.

We consider methods for quantifying the similarity of vertices in networks. We propose a measure ... more We consider methods for quantifying the similarity of vertices in networks. We propose a measure of similarity based on the concept that two vertices are similar if their immediate neighbors in the network are themselves similar. This leads to a self-consistent matrix formulation of similarity that can be evaluated iteratively using only a knowledge of the adjacency matrix of the network.

Abstract Most severe disasters cause large population movements. These movements make it difficul... more Abstract Most severe disasters cause large population movements. These movements make it difficult for relief organizations to efficiently reach people in need. Understanding and predicting the locations of affected people during disasters is key to effective humanitarian relief operations and to long-term societal reconstruction.

The XY gauge glass model1 has attracted much interest in connection to the vortex glass phase of ... more The XY gauge glass model1 has attracted much interest in connection to the vortex glass phase of high-Tc superconductors. 2 In three dimensions 3D there is a general consensus that the XY gauge glass model exhibits a finitetemperature glass transition. 1, 3–5 However, in 2D there exist conflicting evidences: On the one hand, equilibrium studies of defect energy, 3, 5–7 Monte Carlo MC simulations of the root-mean-square current, 8 and resistance calculation9 have suggested that no finite-T ordering exists.

Abstract. Interaction between consumers and companies can create conflict. When a consensus is un... more Abstract. Interaction between consumers and companies can create conflict. When a consensus is unreachable there are legal authorities to resolve the case. This letter is a study of data from the Brazilian Department of Justice from which we build a bipartite network of categories of complaints linked to the companies receiving those complaints. We find the complaint categories organised in an hierarchical way where companies only get complaints of lower degree if they already got complaints of higher degree.

Abstract: The graph layouts used for complex network studies have been mainly been developed to i... more Abstract: The graph layouts used for complex network studies have been mainly been developed to improve visualization. If we interpret the layouts in metric spaces such as Euclidean ones, however, the embedded spatial information can be a valuable cue for various purposes. In this work, we focus on the navigational properties of spatial graphs. We use an recently user-centric navigation protocol to explore spatial layouts of complex networks that are optimal for navigation.

The XY model is one of the classical and most versatile spin models of statistical mechanics. It ... more The XY model is one of the classical and most versatile spin models of statistical mechanics. It has been used in many physical contexts, from superconductors 1 to lattice gauge theory of quantum chromodynamics 2, and furthermore applied to emergent phenomena in systems such as bird flocks 3 and parallel discrete-time simulations 4. In general, the XY model describes a system of N pairwise interacting units.

Abstract: Symmetry--invariance to certain operators--is a fundamental concept in many branches of... more Abstract: Symmetry--invariance to certain operators--is a fundamental concept in many branches of physics. We propose ways to measure symmetric properties of vertices, and their surroundings, in networks. To be stable to the randomness inherent in many complex networks, we consider measures that are continuous rather than dichotomous. The main operator we suggest is permutations of the paths of a certain length leading out from a vertex.

We study a model of opinion formation where the collective decision of a group is said to happen ... more We study a model of opinion formation where the collective decision of a group is said to happen if the fraction of agents having the most common opinion exceeds a threshold value, a critical mass. We find that there exists a unique nontrivial critical mass giving the most efficient convergence to consensus. In addition, we observe that for small critical masses, the characteristic time scale for the relaxation to consensus splits into two.

During the last decade of network research focusing on structural and dynamical properties of net... more During the last decade of network research focusing on structural and dynamical properties of networks, the role of network users has been more or less underestimated from the bird's-eye view of global perspective. In this era of global positioning system equipped smartphones, however, a user's ability to access local geometric information and find efficient pathways on networks plays a crucial role, rather than the globally optimal pathways.

Abstract. To what extent do the characteristic features of a chemical reaction network reflect it... more Abstract. To what extent do the characteristic features of a chemical reaction network reflect its purpose and function? In general, one argues that correlations between specific features and specific functions are key to understanding a complex structure. However, specific features may sometimes be neutral and uncorrelated with any system-specific purpose, function or causal chain. Such neutral features are caused by chance and randomness.

Abstract: What are the dynamics behind youth subcultures such as punk, hippie, or hip-hop culture... more Abstract: What are the dynamics behind youth subcultures such as punk, hippie, or hip-hop cultures? How does the global dynamics of these subcultures relate to the individual's search for a personal identity? We propose a simple dynamical model to address these questions and find that only a few assumptions of the individual's behaviour are necessary to regenerate known features of youth culture.

Abstract One approach to study the system-wide organization of biochemistry is to use statistical... more Abstract One approach to study the system-wide organization of biochemistry is to use statistical graph theory. In such heavily simplified methods, which disregard most of the dynamic aspects of biochemistry, one is faced with fundamental questions. One such question is how the chemical reaction systems should be reduced to a graph retaining as much functional information as possible from the original reaction system.

Abstract The structure of the Internet at the autonomous system (AS) level has been studied by th... more Abstract The structure of the Internet at the autonomous system (AS) level has been studied by the physics, mathematics and computer science communities. We extend this work to include features of the core and the periphery, taking a radial perspective on AS network structure. New methods for plotting AS data are described, and they are used to analyse datasets that have been extended to contain edges missing from earlier collections.

Abstract Many recent large-scale studies of interaction networks have focused on networks of accu... more Abstract Many recent large-scale studies of interaction networks have focused on networks of accumulated contacts. In this letter we explore social networks of ongoing relationships with an emphasis on dynamical aspects. We find a distribution of response times (times between consecutive contacts of different direction between two actors) that has a power law shape over a large range.

We model a system of networking agents that seek to optimize their centrality in the network whil... more We model a system of networking agents that seek to optimize their centrality in the network while keeping their cost, the number of connections they are participating in, low. Unlike other game-theory based models for network evolution, the success of the agents is related only to their position in the network. The agents use strategies based on local information to improve their chance of success. Both the evolution of strategies and network structure are investigated.

Any system, natural or man-made, consisting of entities that interact pairwise can be described i... more Any system, natural or man-made, consisting of entities that interact pairwise can be described in terms of a network. Networks in the real life often contain some degree of randomness, and have also some structure arising from the strategies or laws the entities follow to make new contacts. Such networks—that can only be described as having both randomness and structure—are called complex networks and have lately received much attention in the physicist community 1, 2.

Abstract: The large-scale shape and function of metabolic networks are intriguing topics of syste... more Abstract: The large-scale shape and function of metabolic networks are intriguing topics of systems biology. Such networks are on one hand commonly regarded as modular (ie built by a number of relatively independent subsystems), but on the other hand they are robust in a way not expected of a purely modular system. To address this question we carefully discuss the partition of metabolic networks into subnetworks.

The central points of communication network flow have often been identified using graph theoretic... more The central points of communication network flow have often been identified using graph theoretical centrality measures. In real networks, the state of traffic density arises from an interplay between the dynamics of the flow and the underlying network structure. In this work we investigate the relationship between centrality measures and the density of traffic for some simple particle hopping models on networks with emerging scale-free degree distributions.