arXiv subjects

Konstantin Klemm

Publications and source records attributed to Konstantin Klemm.

At least 37 records · Page 2Linked to original sources

arXiv2013

Searchability of central nodes in networks

Social networks are discrete systems with a large amount of heterogeneity among nodes (individuals). Measures of centrality aim at a quantification of nodes' importance for structure and function. Here we ask to which extent the most central nodes can be found by purely local search. We find that many networks have close-to-optimal searchability under eigenvector centrality, outperforming searches for degree and betweenness. Searchability of the strongest spreaders in epidemic dynamics tends to be substantially larger for supercritical than for subcritical spreading.

physics.soc-ph↗

arXiv2013

Prediction of lethal and synthetically lethal knock-outs in regulatory networks

The complex interactions involved in regulation of a cell's function are captured by its interaction graph. More often than not, detailed knowledge about enhancing or suppressive regulatory influences and cooperative effects is lacking and merely the presence or absence of directed interactions is known. Here we investigate to which extent such reduced information allows to forecast the effect of a knock-out or a combination of knock-outs. Specifically we ask in how far the lethality of eliminating nodes may be predicted by their network centrality, such as degree and betweenness, without knowing the function of the system. The function is taken as the ability to reproduce a fixed point under a discrete Boolean dynamics. We investigate two types of stochastically generated networks: fully random networks and structures grown with a mechanism of node duplication and subsequent divergence of interactions. On all networks we find that the out-degree is a good predictor of the lethality of a single node knock-out. For knock-outs of node pairs, the fraction of successors shared between the two knocked-out nodes (out-overlap) is a good predictor of synthetic lethality. Out-degree and out-overlap are locally defined and computationally simple centrality measures that provide a predictive power close to the optimal predictor.

q-bio.MN↗

arXiv2012

Impact of individual nodes in Boolean network dynamics

Boolean networks serve as discrete models of regulation and signaling in biological cells. Identifying the key controllers of such processes is important for understanding the dynamical systems and planning further analysis. Here we quantify the dynamical impact of a node as the probability of damage spreading after switching the node's state. We find that the leading eigenvector of the adjacency matrix is a good predictor of dynamical impact in the case of long-term spreading. This so-called eigenvector centrality is also a good proxy measure of the influence a node's initial state has on the attractor the system eventually arrives at. Quality of prediction is further improved when eigenvector centrality is based on the weighted matrix of activities rather than the unweighted adjacency matrix. Simulations are performed with ensembles of random Boolean networks and a Boolean model of signaling in fibroblasts. The findings are supported by analytic arguments from a linear approximation of damage spreading.

q-bio.MN↗

arXiv2012

Landscape encodings enhance optimization

Hard combinatorial optimization problems deal with the search for the minimum cost solutions (ground states) of discrete systems under strong constraints. A transformation of state variables may enhance computational tractability. It has been argued that these state encodings are to be chosen invertible to retain the original size of the state space. Here we show how redundant non-invertible encodings enhance optimization by enriching the density of low-energy states. In addition, smooth landscapes may be established on encoded state spaces to guide local search dynamics towards the ground state.

cond-mat.dis-nn↗

arXiv2012

A measure of individual role in collective dynamics

Identifying key players in collective dynamics remains a challenge in several research fields, from the efficient dissemination of ideas to drug target discovery in biomedical problems. The difficulty lies at several levels: how to single out the role of individual elements in such intermingled systems, or which is the best way to quantify their importance. Centrality measures describe a node's importance by its position in a network. The key issue obviated is that the contribution of a node to the collective behavior is not uniquely determined by the structure of the system but it is a result of the interplay between dynamics and network structure. We show that dynamical influence measures explicitly how strongly a node's dynamical state affects collective behavior. For critical spreading, dynamical influence targets nodes according to their spreading capabilities. For diffusive processes it quantifies how efficiently real systems may be controlled by manipulating a single node.

physics.soc-ph↗

arXiv2011

A model of macro-evolution as a branching process based on innovations

We introduce a model for the evolution of species triggered by generation of novel features and exhaustive combination with other available traits. Under the assumption that innovations are rare, we obtain a bursty branching process of speciations. Analysis of the trees representing the branching history reveals structures qualitatively different from those of random processes. For a tree with n leaves, the average distance of leaves from root scales as (log n)^2 to be compared to log n for random branching. The mean values and standard deviations for the tree shape indices depth (Sackin index) and imbalance (Colless index) of the model are compatible with those of real phylogenetic trees from databases. Earlier models, such as the Aldous' branching (AB) model, show a larger deviation from data with respect to the shape indices.

q-bio.PE↗

arXiv2011

Stability of Boolean and continuous dynamics

Regulatory dynamics in biology is often described by continuous rate equations for continuously varying chemical concentrations. Binary discretization of state space and time leads to Boolean dynamics. In the latter, the dynamics has been called unstable if flip perturbations lead to damage spreading. Here we find that this stability classification strongly differs from the stability properties of the original continuous dynamics under small perturbations of the state vector. In particular, random networks of nodes with large sensitivity yield stable dynamics under small perturbations.

physics.bio-ph↗

arXiv2011

Efficient exploration of discrete energy landscapes

Many physical and chemical processes, such as folding of biopolymers, are best described as dynamics on large combinatorial energy landscapes. A concise approximate description of dynamics is obtained by partitioning the micro-states of the landscape into macro-states. Since most landscapes of interest are not tractable analytically, the probabilities of transitions between macro-states need to be extracted numerically from the microscopic ones, typically by full enumeration of the state space. Here we propose to approximate transition probabilities by a Markov chain Monte-Carlo method. For landscapes of the number partitioning problem and an RNA switch molecule we show that the method allows for accurate probability estimates with significantly reduced computational cost.

q-bio.BM↗

arXiv2010

Finding attractors in asynchronous Boolean dynamics

We present a computational method for finding attractors (ergodic sets of states) of Boolean networks under asynchronous update. The approach is based on a systematic removal of state transitions to render the state transition graph acyclic. In this reduced state transition graph, all attractors are fixed points that can be enumerated with little effort in most instances. This attractor set is then extended to the attractor set of the original dynamics. Our numerical tests on standard Kauffman networks indicate that the method is efficient in the sense that the total number of state vectors visited grows moderately with the number of states contained in attractors.

cond-mat.dis-nn↗

arXiv2010

Knockouts, Robustness and Cell Cycles

The response to a knockout of a node is a characteristic feature of a networked dynamical system. Knockout resilience in the dynamics of the remaining nodes is a sign of robustness. Here we study the effect of knockouts for binary state sequences and their implementations in terms of Boolean threshold networks. Beside random sequences with biologically plausible constraints, we analyze the cell cycle sequence of the species Saccharomyces cerevisiae and the Boolean networks implementing it. Comparing with an appropriate null model we do not find evidence that the yeast wildtype network is optimized for high knockout resilience. Our notion of knockout resilience weakly correlates with the size of the basin of attraction, which has also been considered a measure of robustness.

q-bio.MN↗

arXiv2009

Regulatory networks and connected components of the neutral space

The functioning of a living cell is largely determined by the structure of its regulatory network, comprising non-linear interactions between regulatory genes. An important factor for the stability and evolvability of such regulatory systems is neutrality - typically a large number of alternative network structures give rise to the necessary dynamics. Here we study the discretized regulatory dynamics of the yeast cell cycle [Li et al., PNAS, 2004] and the set of networks capable of reproducing it, which we call functional. Among these, the empirical yeast wildtype network is close to optimal with respect to sparse wiring. Under point mutations, which establish or delete single interactions, the neutral space of functional networks is fragmented into 4.7 * 10^8 components. One of the smaller ones contains the wildtype network. On average, functional networks reachable from the wildtype by mutations are sparser, have higher noise resilience and fewer fixed point attractors as compared with networks outside of this wildtype component.

q-bio.MN↗

arXiv2009

Conservation laws for voter-like models on directed networks

We study the voter model, under node and link update, and the related invasion process on a single strongly connected component of a directed network. We implement an analytical treatment in the thermodynamic limit using the heterogeneous mean field assumption. From the dynamical rules at the microscopic level, we find the equations for the evolution of the relative densities of nodes in a given state on heterogeneous networks with arbitrary degree distribution and degree-degree correlations. We prove that conserved quantities as weighted linear superpositions of spin states exist for all three processes and, for uncorrelated directed networks, we derive their specific expressions. We also discuss the time evolution of the relative densities that decay exponentially to a homogeneous stationary value given by the conserved quantity. The conservation laws obtained in the thermodynamic limit for a system that does not order in that limit determine the probabilities of reaching the absorbing state for a finite system. The contribution of each degree class to the conserved quantity is determined by a local property. Depending on the dynamics, the highest contribution is associated to influential nodes reaching a large number of outgoing neighbors, not too influenceable ones with a low number of incoming connections, or both at the same time.

cond-mat.dis-nn↗

arXiv2009

Simple models for scaling in phylogenetic trees

Many processes and models --in biological, physical, social, and other contexts-- produce trees whose depth scales logarithmically with the number of leaves. Phylogenetic trees, describing the evolutionary relationships between biological species, are examples of trees for which such scaling is not observed. With this motivation, we analyze numerically two branching models leading to non-logarithmic scaling of the depth with the number of leaves. For Ford's alpha model, although a power-law scaling of the depth with tree size was established analytically, our numerical results illustrate that the asymptotic regime is approached only at very large tree sizes. We introduce here a new model, the activity model, showing analytically and numerically that it also displays a power-law scaling of the depth with tree size at a critical parameter value.

q-bio.QM↗

arXiv2008

Universal scaling in the branching of the Tree of Life

Understanding the patterns and processes of diversification of life in the planet is a key challenge of science. The Tree of Life represents such diversification processes through the evolutionary relationships among the different taxa, and can be extended down to intra-specific relationships. Here we examine the topological properties of a large set of interspecific and intraspecific phylogenies and show that the branching patterns follow allometric rules conserved across the different levels in the Tree of Life, all significantly departing from those expected from the standard null models. The finding of non-random universal patterns of phylogenetic differentiation suggests that similar evolutionary forces drive diversification across the broad range of scales, from macro-evolutionary to micro-evolutionary processes, shaping the diversity of life on the planet.

q-bio.PE↗

arXiv2007

Funnels in Energy Landscapes

Local minima and the saddle points separating them in the energy landscape are known to dominate the dynamics of biopolymer folding. Here we introduce a notion of a "folding funnel" that is concisely defined in terms of energy minima and saddle points, while at the same time conforming to a notion of a "folding funnel" as it is discussed in the protein folding literature.

q-bio.BM↗

arXiv2005

Binary and Multivariate Stochastic Models of Consensus Formation

A current paradigm in computer simulation studies of social sciences problems by physicists is the emergence of consensus. The question is to establish when the dynamics of a set of interacting agents that can choose among several options (political vote, opinion, cultural features, etc.) leads to a consensus in one of these options, or when a state with several coexisting social options prevail. We consider here stochastic dynamic models naturally studied by computer simulations. We will first review some basic results for the voter model. This is a binary option stochastic model, and probably the simplest model of collective behavior. Next we consider a model proposed by Axelrod for the dissemination of culture. This model can be considered as a multivariable elaboration of the voter model dynamics.

physics.soc-ph↗

arXiv2005

Statistics of cycles in large networks

We present a Markov Chain Monte Carlo method for sampling cycle length in large graphs. Cycles are treated as microstates of a system with many degrees of freedom. Cycle length corresponds to energy such that the length histogram is obtained as the density of states from Metropolis sampling. In many growing networks, mean cycle length increases algebraically with system size. The cycle exponent $α$ is characteristic of the local growth rules and not determined by the degree exponent $γ$. For example, $α=0.76(4)$ for the Internet at the Autonomous Systems level.

cond-mat.dis-nn↗

arXiv2005

Stable and unstable attractors in Boolean networks

Boolean networks at the critical point have been a matter of debate for many years as, e.g., scaling of number of attractor with system size. Recently it was found that this number scales superpolynomially with system size, contrary to a common earlier expectation of sublinear scaling. We here point to the fact that these results are obtained using deterministic parallel update, where a large fraction of attractors in fact are an artifact of the updating scheme. This limits the significance of these results for biological systems where noise is omnipresent. We here take a fresh look at attractors in Boolean networks with the original motivation of simplified models for biological systems in mind. We test stability of attractors w.r.t. infinitesimal deviations from synchronous update and find that most attractors found under parallel update are artifacts arising from the synchronous clocking mode. The remaining fraction of attractors are stable against fluctuating response delays. For this subset of stable attractors we observe sublinear scaling of the number of attractors with system size.

cond-mat.dis-nn↗