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  • 1. Baek, Yongjoo
    et al.
    Lee, Sang Hoon
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Jeong, Hawoong
    Market behavior and performance of different strategy evaluation schemes2010In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics: Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, ISSN 1063-651X, E-ISSN 1095-3787, Vol. 82, no 026109Article in journal (Refereed)
    Abstract [en]

    Strategy evaluation schemes are a crucial factor in any agent-based market model, as they determine the agents’ strategy preferences and consequently their behavioral pattern. This study investigates how the strategy evaluation schemes adopted by agents affect their performance in conjunction with the market circumstances. We observe the performance of three strategy evaluation schemes, the history-dependent wealth game, the trend-opposing minority game, and the trend-following majority game, in a stock market where the price is exogenously determined. The price is either directly adopted from the real stock market indices or generated with a Markov chain of order ≤2. Each scheme’s success is quantified by average wealth accumulated by the traders equipped with the scheme. The wealth game, as it learns from the history, shows relatively good performance unless the market is highly unpredictable. The majority game is successful in a trendy market dominated by long periods of sustained price increase or decrease. On the other hand, the minority game is suitable for a market with persistent zigzag price patterns. We also discuss the consequence of implementing finite memory in the scoring processes of strategies. Our findings suggest under which market circumstances each evaluation scheme is appropriate for modeling the behavior of real market traders.

  • 2.
    Holme, Petter
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Huss, Mikael
    Science for Life Laboratory Stockholm.
    Lee, Sang Hoon
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Atmospheric Reaction Systems as Null-Models to Identify Structural Traces of Evolution in Metabolism2011In: PLoS ONE, ISSN 1932-6203, Vol. 6, no 5, p. e19759-Article in journal (Refereed)
    Abstract [en]

    The metabolism is the motor behind the biological complexity of an organism. One problem of characterizing its large-scale structure is that it is hard to know what to compare it to. All chemical reaction systems are shaped by the same physics that gives molecules their stability and affinity to react. These fundamental factors cannot be captured by standard null-models based on randomization. The unique property of organismal metabolism is that it is controlled, to some extent, by an enzymatic machinery that is subject to evolution. In this paper, we explore the possibility that reaction systems of planetary atmospheres can serve as a null-model against which we can define metabolic structure and trace the influence of evolution. We find that the two types of data can be distinguished by their respective degree distributions. This is especially clear when looking at the degree distribution of the reaction network (of reaction connected to each other if they involve the same molecular species). For the Earth's atmospheric network and the human metabolic network, we look into more detail for an underlying explanation of this deviation. However, we cannot pinpoint a single cause of the difference, rather there are several concurrent factors. By examining quantities relating to the modular-functional organization of the metabolism, we confirm that metabolic networks have a more complex modular organization than the atmospheric networks, but not much more. We interpret the more variegated modular arrangement of metabolism as a trace of evolved functionality. On the other hand, it is quite remarkable how similar the structures of these two types of networks are, which emphasizes that the constraints from the chemical properties of the molecules has a larger influence in shaping the reaction system than does natural selection.

  • 3.
    Lee, Sang Hoon
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Finite-size scaling in random K-satisfiability problems2010In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics: Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, ISSN 1063-651X, E-ISSN 1095-3787, Vol. 82, no 061109Article in journal (Refereed)
    Abstract [en]

    We provide a comprehensive view of various phase transitions in random K-satisfiability problems solved by stochastic-local-search algorithms. In particular, we focus on the finite-size scaling (FSS) exponent, which is mathematically important and practically useful in analyzing finite systems. Using the FSS theory of nonequilibrium absorbing phase transitions, we show that the density of unsatisfied clauses clearly indicates the transition from the solvable (absorbing) phase to the unsolvable (active) phase as varying the noise parameter and the density of constraints. Based on the solution clustering (percolation-type) argument, we conjecture two possible values of the FSS exponent, which are confirmed reasonably well in numerical simulations for 2≤K≤3.

  • 4.
    Lee, Sang Hoon
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Bernhardsson, Sebastian
    FOI, Swedish Defence Research Agency, Tumba SE-14725, Sweden.
    Holme, Petter
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Kim, Beom Jun
    Department of Physics, Sungkyunkwan University, Suwon 440-746, Korea.
    Minnhagen, Petter
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Neutral theory of chemical reaction networks2012In: New Journal of Physics, ISSN 1367-2630, E-ISSN 1367-2630, Vol. 14, p. 033032-Article in journal (Refereed)
    Abstract [en]

    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. Here we compare two classes of chemical networks: one that has been subjected to biological evolution (the chemical reaction network of metabolism in living cells) and one that has not (the atmospheric planetary chemical reaction networks). Their degree distributions are shown to share the very same neutral system-independent features. The shape of the broad distributions is to a large extent controlled by a single parameter, the network size. From this perspective, there is little difference between atmospheric and metabolic networks; they are just different sizes of the same random assembling network. In other words, the shape of the degree distribution is a neutral characteristic feature and has no functional or evolutionary implications in itself; it is not a matter of life and death.

  • 5.
    Lee, Sang Hoon
    et al.
    Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea.
    Hawoong, Jeong
    Effects of substrate network topologies on competition dynamics2006In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics: Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, ISSN 1063-651X, E-ISSN 1095-3787, Vol. 74, no 026118Article in journal (Refereed)
    Abstract [en]

    We study a competition dynamics, based on the minority game, endowed with various substrate network structures. We observe the effects of the network topologies by investigating the volatility of the system and the structure of follower networks. The topology of substrate structures significantly influences the system efficiency represented by the volatility and such substrate networks are shown to amplify the herding effect and cause inefficiency in most cases. The follower networks emerging from the leadership structure show a power-law incoming degree distribution. This study shows the emergence of scale-free structures of leadership in the minority game and the effects of the interaction among players on the networked version of the game.

  • 6.
    Lee, Sang Hoon
    et al.
    Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea.
    Hawoong, Jeong
    Jae Dong, Noh
    Random field Ising model on networks with inhomogeneous connections2006In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics: Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, ISSN 1063-651X, E-ISSN 1095-3787, Vol. 74, no 031118Article in journal (Refereed)
    Abstract [en]

    We study a zero-temperature phase transition in the random field Ising model on scale-free networks with the degree exponent γ. Using an analytic mean-field theory, we find that the spins are always in the ordered phase for γ<3. On the other hand, the spins undergo a phase transition from an ordered phase to a disordered phase as the dispersion of the random fields increases for γ>3. The phase transition may be either continuous or discontinuous depending on the shape of the random field distribution. We derive the condition for the nature of the phase transition. Numerical simulations are performed to confirm the results.

  • 7.
    Lee, Sang Hoon
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Holme, Petter
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Exploring maps with greedy navigators2012In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 108, no 12, p. 8701-Article in journal (Refereed)
    Abstract [en]

    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. We present a simple greedy spatial navigation strategy as a probe to explore spatial networks. These greedy navigators use directional information in every move they take, without being trapped in a dead end based on their memory about previous routes. We suggest that the centralities measures have to be modified to incorporate the navigators’ behavior, and present the intriguing effect of navigators’ greediness where removing some edges may actually enhance the routing efficiency, which is reminiscent of Braess’s paradox. In addition, using samples of road structures in large cities around the world, it is shown that the navigability measure we define reflects unique structural properties, which are not easy to predict from other topological characteristics. In this respect, we believe that our routing scheme significantly moves the routing problem on networks one step closer to reality, incorporating the inevitable incompleteness of navigators’ information.

  • 8.
    Lee, Sang Hoon
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Holme, Petter
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Pathlength scaling in graphs with incomplete navigational information2011In: Physica A: Statistical Mechanics and its Applications, ISSN 0378-4371, E-ISSN 1873-2119, Vol. 390, no 21-22, p. 3996-4001Article in journal (Refereed)
    Abstract [en]

    The graph-navigability problem concerns how one can find as short paths as possible between a pair of vertices, given an incomplete picture of a graph. We study the navigability of graphs where the vertices are tagged by a number (between 1 and the total number of vertices) in a way to aid navigation. This information is too little to ensure errorfree navigation but enough, as we will show, for the agents to do significantly better than a random walk. In our setup, given a graph, we first assign information to the vertices that agents can utilize for their navigation. To evaluate the navigation, we calculate the average distance traveled over random pairs of source and target and different graph realizations. We show that this type of embedding can be made quite efficiently; the more information is embedded, the more efficient it gets. We also investigate the embedded navigational information in a standard graph layout algorithm and find that although this information does not make algorithms as efficient as the above-mentioned schemes, it is significantly helpful.

  • 9.
    Lee, Sang Hoon
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Kim, Pan-Jun
    Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, USA.
    Jeong, Hawoong
    Institute for the BioCentury and Department of Physics, Korea Advanced Institute of Science and Technology, Korea.
    Global organization of protein complexome in the yeast Saccharomyces cerevisiae2011In: BMC Systems Biology, ISSN 1752-0509, E-ISSN 1752-0509, Vol. 5, no 126, p. 15-Article in journal (Refereed)
    Abstract [en]

    Background: Proteins in organisms, rather than act alone, usually form protein complexes to perform cellular functions. We analyze the topological network structure of protein complexes and their component proteins in the budding yeast in terms of the bipartite network and its projections, where the complexes and proteins are its two distinct components. Compared to conventional protein-protein interaction networks, the networks from the protein complexes show more homogeneous structures than those of the binary protein interactions, implying the formation of complexes that cause a relatively more uniform number of interaction partners. In addition, we suggest a new optimization method to determine the abundance and function of protein complexes, based on the information of their global organization. Estimating abundance and biological functions is of great importance for many researches, by providing a quantitative description of cell behaviors, instead of just a "catalogues" of the lists of protein interactions.

    Results: With our new optimization method, we present genome-wide assignments of abundance and biological functions for complexes, as well as previously unknown abundance and functions of proteins, which can provide significant information for further investigations in proteomics. It is strongly supported by a number of biologically relevant examples, such as the relationship between the cytoskeleton proteins and signal transduction and the metabolic enzyme Eno2's involvement in the cell division process.

    Conclusions: We believe that our methods and findings are applicable not only to the specific area of proteomics, but also to much broader areas of systems biology with the concept of optimization principle.

  • 10.
    Lee, Sang Hoon
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Lee, Sungmin
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Son, Seung-Woo
    Department of Applied Physics, Hanyang University, Korea.
    Holme, Petter
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Phase-shift inversion in oscillator systems with periodically switching couplings2012In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 85, no 2, p. 027202-Article in journal (Refereed)
    Abstract [en]

    A system's response to external periodic changes can provide crucial information about its dynamical properties. We investigate the synchronization transition, an archetypical example of a dynamic phase transition, in the framework of such a temporal response. The Kuramoto model under periodically switching interactions has the same type of phase transition as the original mean-field model. Furthermore, we see that the signature of the synchronization transition appears in the relative delay of the order parameter with respect to the phase of oscillating interactions as well. Specifically, the phase shift becomes significantly larger as the system gets closer to the phase transition, so that the order parameter at the minimum interaction density can even be larger than that at the maximum interaction density, counterintuitively. We argue that this phase-shift inversion is caused by the diverging relaxation time, in a similar way to the resonance near the critical point in the kinetic Ising model. Our result, based on exhaustive simulations on globally coupled systems as well as scale-free networks, shows that an oscillator system's phase transition can be manifested in the temporal response to the topological dynamics of the underlying connection structure.

  • 11.
    Lee, Sang Hoon
    et al.
    Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea.
    Meesoon, Ha
    Hawoong, Jeong
    Jae Dong, Noh
    Hyunggyu, Park
    Critical behavior of the Ising model in annealed scale-free networks2009In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics: Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, ISSN 1063-651X, E-ISSN 1095-3787, Vol. 80, no 051127Article in journal (Refereed)
    Abstract [en]

    We study the critical behavior of the Ising model in annealed scale-free (SF) networks of finite system size with forced upper cutoff in degree. By mapping the model onto the weighted fully connected Ising model, we derive analytic results for the finite-size scaling (FSS) near the phase transition, characterized by the cutoff-dependent two-parameter scaling with four distinct scaling regimes, in highly heterogeneous networks. These results are essentially the same as those found for the nonequilibrium contact process in annealed SF networks, except for an additional complication due to the trivial critical point shift in finite systems. The discrepancy of the FSS theories between annealed and quenched SF networks still remains in the equilibrium Ising model, like some other nonequilibrium models. All of our analytic results are confirmed reasonably well by numerical simulations.

  • 12.
    Lee, Sang Hoon
    et al.
    Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea.
    Pan-Jun, Kim
    Hawoong, Jeong
    Statistical properties of sampled networks2006In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics: Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, ISSN 1063-651X, E-ISSN 1095-3787, Vol. 73, no 016102Article in journal (Refereed)
    Abstract [en]

    We study the statistical properties of the sampled scale-free networks, deeply related to the proper identification of various real-world networks. We exploit three methods of sampling and investigate the topological properties such as degree and betweenness centrality distribution, average path length, assortativity, and clustering coefficient of sampled networks compared with those of original networks. It is found that the quantities related to those properties in sampled networks appear to be estimated quite differently for each sampling method. We explain why such a biased estimation of quantities would emerge from the sampling procedure and give appropriate criteria for each sampling method to prevent the quantities from being overestimated or underestimated.

  • 13.
    Lee, Sang Hoon
    et al.
    Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea.
    Pan-Jun, Kim
    Yong-Yeol, Ahn
    Hawoong, Jeong
    Googling social interactions: web search engine based social network construction2010In: PLoS ONE, ISSN 1932-6203, Vol. 5, no 7, p. e11233-Article in journal (Refereed)
    Abstract [en]

    Social network analysis has long been an untiring topic of sociology. However, until the era of information technology, the availability of data, mainly collected by the traditional method of personal survey, was highly limited and prevented large-scale analysis. Recently, the exploding amount of automatically generated data has completely changed the pattern of research. For instance, the enormous amount of data from so-called high-throughput biological experiments has introduced a systematic or network viewpoint to traditional biology. Then, is “high-throughput” sociological data generation possible? Google, which has become one of the most influential symbols of the new Internet paradigm within the last ten years, might provide torrents of data sources for such study in this (now and forthcoming) digital era. We investigate social networks between people by extracting information on the Web and introduce new tools of analysis of such networks in the context of statistical physics of complex systems or socio-physics. As a concrete and illustrative example, the members of the 109th United States Senate are analyzed and it is demonstrated that the methods of construction and analysis are applicable to various other weighted networks.

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