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Marc-Thorsten Hütt

Publications and source records attributed to Marc-Thorsten Hütt.

At least 19 recordsLinked to original sources

Message interaction dynamics covary with brain volume across mammalian connectomes

Brain network communication models typically assume that signals propagate independently, despite the high network density and small diameter of mammalian connectomes, where interactions among simultaneously propagating messages are likely. We investigate these interactions using the copy-spread-annihilate (CSA) model, a synchronous Markovian message-passing process in which messages spread through the binarized network while undergoing collision-dependent deletion. Simulations on a large comparative dataset of mammalian connectomes show that CSA dynamics produce robust positively-skewed lognormal distributions of message survival across species. Despite using only binary network topology without spatial embedding, message survival accounts for over half of the variance in brain volume across mammal species and outperforms a broad range of established graph-theoretic measures and an alternative communication model with interacting messages. Degree-preserving switch randomization weakens this relationship, indicating that higher-order structural organization contributes to the observed scaling law. We describe a mechanistic explanation of model dynamics that suggests message creation differences among networks shapes message survival. Together, these findings suggest that interactions among propagating messages constitute an important and underexplored determinant of communication dynamics in mammalian brain networks.

q-bio.NC↗

Copy-Spread-Annihilate Dynamics in Degree-Assortative Networks

In many systems, communication proceeds by broadcasting rather than single source-target routing, but network structures that maximize signal lifetime are not well understood. Degree correlations are known to influence robustness and spreading, yet their effect on signal persistence has remained unclear. Here we introduce Copy-Spread-Annihilate dynamics, a minimal synchronous broadcasting model with annihilation. We show that signal lifetimes vary non-monotonically with assortativity and are maximized near neutral assortativity, where hub-driven amplification is strong but annihilation via short cycles is still limited. Applying this framework to the mouse connectome suggests assortativity as a structural control parameter for broadcast signal persistence in brain-like and other complex networks.

q-bio.NC↗

Nucleation transitions in polycontextural networks toward consensus

Recently, we proposed polycontextural networks as a model of evolving systems of interacting beliefs. Here, we present an analysis of the phase transition as well as the scaling properties. The model contains interacting agents that strive for consensus, each with only subjective perception. Depending on a parameter that governs how responsive the agents are to changing their belief systems the model exhibits a phase transition that mediates between an active phase where the agents constantly change their beliefs and a frozen phase, where almost no changes appear. We observe the build-up of convention-aligned clusters only in the intermediate regime of diverging susceptibility. Here, we analyze in detail the behavior of polycontextural networks close to this transition. We provide an analytical estimate of the critical point and show that the scaling properties and the space-time structure of these clusters show self-similar behavior. Our results not only contribute to a better understanding of the emergence of consensus in systems of distributed beliefs but also show that polycontextural networks are models, motivated by social systems, where susceptibility -- the sensitivity to change own beliefs -- drives the growth of consensus clusters.

cond-mat.stat-mech↗

Structural insulators and promotors in networks under generic problem-solving dynamics

The collective coordination of distributed tasks in a complex system can be represented as decision dynamics on a graph. This abstract representation allows studying the performance of local decision heuristics as a function of task complexity and network architecture. Here we identify hard-to-solve and easy-to-solve networks in a social differentiation task within the basic model of small-world graphs. We show that, depending on the details of the decision heuristic as well as the length of the added links, shortcuts can serve as structural promotors, which speed up convergence towards a solution, but also as structural insulators, which make the network more difficult to solve. Our findings have implications for situations where, in distributed decision systems, regional solutions emerge, which are globally incompatible as for example during the emergence of technological standards.

physics.soc-ph↗

Is a model equivalent to its computer implementation?

A recent trend in mathematical modeling is to publish the computer code together with the research findings. Here we explore the formal question, whether and in which sense a computer implementation is distinct from the mathematical model. We argue that, despite the convenience of implemented models, a set of implicit assumptions is perpetuated with the implementation to the extent that even in widely used models the causal link between the (formal) mathematical model and the set of results is no longer certain. Moreover, code publication is often seen as an important contributor to reproducible research, we suggest that in some cases the opposite may be true. A new perspective on this topic stems from the accelerating trend that in some branches of research only implemented models are used, e.g., in artificial intelligence (AI). With the advent of quantum computers we argue that completely novel challenges arise in the distinction between models and implementations.

cs.CY↗

Microbiome abundance patterns as attractors and the implications for the inference of microbial interaction networks

Inferring microbial interaction networks from abundance patterns is an important approach to advance our understanding of microbial communities in general and the human microbiome in particular. Here we suggest discriminating two levels of information contained in microbial abundance data: (1) the quantitative abundance values and (2) the pattern of presences and absences of microbial organisms. The latter allows for a binary view on microbiome data and a novel interpretation of microbial data as attractors, or more precisely as fixed points, of a Boolean network. Starting from these attractors, our aim is to infer an interaction network between the species present in the microbiome samples. To accomplish this task, we introduce a novel inference method that combines the previously published ESABO (Entropy Shifts of Abundance vectors under Boolean Operations) method with an evolutionary algorithm. The key idea of our approach is that the inferred network should reproduce the original set of (observed) binary abundance patterns as attractors. We study the accuracy and runtime properties of this evolutionary method, as well as its behavior under incomplete knowledge of the attractor sets. Based on this theoretical understanding of the method we then show an application to empirical data.

q-bio.PE↗

Predicting attractors from spectral properties of stylized gene regulatory networks

How the architecture of gene regulatory networks ultimately shapes gene expression patterns is an open question, which has been approached from a multitude of angles. The dominant strategy has been to identify non-random features in these networks and then argue for the function of these features using mechanistic modelling. Here we establish the foundation of an alternative approach by studying the correlation of eigenvectors with synthetic gene expression data simulated with a basic and popular model of gene expression dynamics -- attractors of Boolean threshold dynamics in signed directed graphs. Eigenvectors of the graph Laplacian are known to explain collective dynamical states (stationary patterns) in Turing dynamics on graphs. In this study, we show that eigenvectors can also predict collective states (attractors) for a markedly different type of dynamics, Boolean threshold dynamics, and category of graphs, signed directed graphs. However, the overall predictive power depends on details of the network architecture, in a predictable fashion. Our results are a set of statistical observations, providing the first systematic step towards a further theoretical understanding of the role of eigenvectors in dynamics on graphs.

q-bio.MN↗

Network location and clustering of genetic mutations determine chronicity in a stylized model of genetic diseases

In a highly simplified view, a disease can be seen as the phenotype emerging from the interplay of genetic predisposition and fluctuating environmental stimuli. We formalize this situation in a minimal model, where a network (representing cellular regulation) serves as an interface between an input layer (representing environment) and an output layer (representing functional phenotype). Genetic predisposition for a disease is represented as a loss of function of some network nodes. Reduced, but non-zero, output indicates disease. The simplicity of this genetic disease model and its deep relationship to percolation theory allows us to understand the interplay between disease, network topology and the location and clusters of affected network nodes. We find that our model generates two different characteristics of diseases, which can be interpreted as chronic and acute diseases. In its stylized form, our model provides a new view on the relationship between genetic mutations and the type and severity of a disease.

q-bio.MN↗

Physics is organized around transformations connecting contextures in a polycontextural world

The rich body of physical theories defines the foundation of our understanding of the world. Its mathematical formulation is based on classical Aristotelian (binary) logic. In the philosophy of science the ambiguities, paradoxes, and the possibility of subjective interpretations of facts have challenged binary logic, leading, among other developments, to Gotthard Günther's theory of polycontexturality (often also termed 'transclassical logic'). Günther's theory explains how observers with subjective perception can become aware of their own subjectivity and provides means to describe contradicting or even paradox observations in a logically sound formalism. Here we summarize the formalism behind Günther's theory and apply it to two well-known examples from physics where different observers operate in distinct and only locally valid logical systems. Using polycontextural logic we show how the emerging awareness of these limitations of logical systems entails the design of mathematical transformations, which then become an integral part of the theory. In our view, this approach offers a novel perspective on the structure of physical theories and, at the same time, emphasizes the relevance of the theory of polycontexturality in modern sciences.

physics.hist-ph↗

Collective patterns and stable misunderstandings in networks striving for consensus without a common value system

Collective phenomena in systems of interacting agents have helped us understand diverse social, ecological and biological observations. The corresponding explanations are challenged by incorrect information processing. In particular, the models typically assume a shared understanding of signals or a common truth or value system, i.e., an agreement of whether the measurement or perception of information is `right' or `wrong'. It is an open question whether a collective consensus can emerge without these conditions. Here we introduce a model of interacting agents that strive for consensus, however, each with only a subjective perception of the world. Our communication model does not presuppose a definition of right or wrong and the actors can hence not distinguish between correct and incorrect observations. Depending on a single parameter that governs how responsive the agents are to changing their world-view we observe a transition between an unordered phase of individuals that are not able to communicate with each other and a phase of an emerging shared signalling framework. We find that there are two types of convention-aligned clusters: one, where all social actors in the cluster have the same set of conventions, and one, where neighbouring actors have different but compatible conventions (`stable misunderstandings').

physics.soc-ph↗

Local topological features of robust supply networks

The design of robust supply and distribution systems is one of the fundamental challenges at the interface of network science and logistics. Given the multitude of performance criteria, real-world constraints, and external influences acting upon such a system, even formulating an appropriate research question to address this topic is non-trivial. Here we present an abstraction of a supply and distribution system leading to a minimal model, which only retains stylized facts of the systemic function and, in this way, allows us to investigate the generic properties of robust supply networks. On this level of abstraction, a supply and distribution system is the strategic use of transportation to eliminate mismatches between production patterns (i.e., the amounts of goods produced at each production site of a company) and demand patterns (i.e., the amount of goods consumed at each location). When creating networks based on this paradigm and furthermore requiring the robustness of the system with respect to the loss of transportation routes (edge of the network) we see that robust networks are built from specific sets of subgraphs, while vulnerable networks display a markedly different subgraph composition. Our findings confirm a long-standing hypothesis in the field of network science, namely, that network motifs -- statistically over-represented small subgraphs -- are informative about the robust functioning of a network. Also, our findings offer a blueprint for enhancing the robustness of real-world supply and distribution systems.

cs.SI↗

A network analysis of decision strategies of human experts in steel manufacturing

Steel production scheduling is typically accomplished by human expert planners. Hence, instead of fully automated scheduling systems steel manufacturers prefer auxiliary recommendation algorithms. Through the suggestion of suitable orders, these algorithms assist human expert planners who are tasked with the selection and scheduling of production orders. However, it is hard to estimate, what degree of complexity these algorithms should have as steel campaign planning lacks precise rule-based procedures; in fact, it requires extensive domain knowledge as well as intuition that can only be acquired by years of business experience. Here, instead of developing new algorithms or improving older ones, we introduce a shuffling-aided network method to assess the complexity of the selection patterns established by a human expert. This technique allows us to formalize and represent the tacit knowledge that enters the campaign planning. As a result of the network analysis, we have discovered that the choice of production orders is primarily determined by the orders' carbon content. Surprisingly, trace elements like manganese, silicon, and titanium have a lesser impact on the selection decision than assumed by the pertinent literature. Our approach can serve as an input to a range of decision-support systems, whenever a human expert needs to create groups of orders ('campaigns') that fulfill certain implicit selection criteria.

cs.AI↗

A stylised view on structural and functional connectivity in dynamical processes in networks

The relationship of network structure and dynamics is one of most extensively investigated problems in the theory of complex systems of the last years. Understanding this relationship is of relevance to a range of disciplines -- from Neuroscience to Geomorphology. A major strategy of investigating this relationship is the quantitative comparison of a representation of network architecture (structural connectivity) with a (network) representation of the dynamics (functional connectivity). Analysing such SC/FC relationships has over the past years contributed substantially to our understanding of the functional role of network properties, such as modularity, hierarchical organization, hubs and cycles. Here, we show that one can distinguish two classes of functional connectivity -- one based on simultaneous activity (co-activity) of nodes the other based on sequential activity of nodes. We delineate these two classes in different categories of dynamical processes -- excitations, regular and chaotic oscillators -- and provide examples for SC/FC correlations of both classes in each of these models. We expand the theoretical view of the SC/FC relationships, with conceptual instances of the SC and the two classes of FC for various application scenarios in Geomorphology, Freshwater Ecology, Systems Biology, Neuroscience and Social-Ecological Systems. Seeing the organization of a dynamical processes in a network either as governed by co-activity or by sequential activity allows us to bring some order in the myriad of observations relating structure and function of complex networks.

physics.soc-ph↗

A system-wide network reconstruction of gene regulation and metabolism in Escherichia coli

Genome-scale metabolic models have become a fundamental tool for examining metabolic principles. However, metabolism is not solely characterized by the underlying biochemical reactions and catalyzing enzymes, but also affected by regulatory events. Since the pioneering work of Covert and co-workers as well as Shlomi and co-workers it is debated, how regulation and metabolism synergistically characterize a coherent cellular state. The first approaches started from metabolic models which were extended by the regulation of the encoding genes of the catalyzing enzymes. By now, bioinformatics databases in principle allow addressing the challenge of integrating regulation and metabolism on a system-wide level. Collecting information from several databases we provide a network representation of the integrated gene regulatory and metabolic system for Escherichia coli, including major cellular processes, from metabolic processes via protein modification to a variety of regulatory events. Besides transcriptional regulation, we also take into account regulation of translation, enzyme activities and reactions. Our network model provides novel topological characterizations of system components based on their positions in the network. We show that network characteristics suggest a representation of the integrated system as three network domains (regulatory, metabolic and interface networks) instead of two. This new three-domain representation reveals the structural centrality of components with known high functional relevance. This integrated network can serve as a platform for understanding coherent cellular states as active subnetworks and to elucidate crossover effects between metabolism and gene regulation.

q-bio.MN↗

The interdependent network of gene regulation and metabolism is robust where it needs to be

The major biochemical networks of the living cell, the network of interacting genes and the network of biochemical reactions, are highly interdependent, however, they have been studied mostly as separate systems so far. In the last years an appropriate theoretical framework for studying interdependent networks has been developed in the context of statistical physics. Here we study the interdependent network of gene regulation and metabolism of the model organism Escherichia coli using the theoretical framework of interdependent networks. In particular we aim at understanding how the biological system can consolidate the conflicting tasks of reacting rapidly to (internal and external) perturbations, while being robust to minor environmental fluctuations, at the same time. For this purpose we study the network response to localized perturbations and find that the interdependent network is sensitive to gene regulatory and protein-level perturbations, yet robust against metabolic changes. This first quantitative application of the theory of interdependent networks to systems biology shows how studying network responses to localized perturbations can serve as a useful strategy for analyzing a wide range of other interdependent networks.

q-bio.MN↗

Network heterogeneity and node capacity lead to heterogeneous scaling of fluctuations in random walks on graphs

Random walks are one of the best investigated dynamical processes on graphs. A particularly fascinating phenomenon is the scaling relationship of fluctuations $σ$ with the average flux $\langle f \rangle $. Here we analyze how network topology and nodes with finite capacity lead to deviations from a simple scaling law $σ\sim \langle f \rangle ^α$. Sources of randomness are the random walk itself (internal noise) and the fluctuation of the number of walkers (external noise). We obtained exact results for the extreme case of a star network which are indicative of the behavior of large scale systems with a broad degree distribution.The latter are subsequently studied using Monte Carlo simulations. We find that the network heterogeneity amplifies the effects of external noise. By computing the `effective' scaling of each node we show that multiple scaling relationships can coexist in a graph with a heterogeneous degree distribution at an intermediate level of external noise. Finally, we analyze the effect of a finite capacity of nodes for random walkers and find that this also can lead to a heterogeneous scaling of fluctuations.

physics.soc-ph↗

Motif-based success scores in coauthorship networks are highly sensitive to author name disambiguation

Following the work of Krumov et al. [Eur. Phys. J. B 84, 535 (2011)] we revisit the question whether the usage of large citation datasets allows for the quantitative assessment of social (by means of coauthorship of publications) influence on the progression of science. Applying a more comprehensive and well-curated dataset containing the publications in the journals of the American Physical Society during the whole 20th century we find that the measure chosen in the original study, a score based on small induced subgraphs, has to be used with caution, since the obtained results are highly sensitive to the exact implementation of the author disambiguation task.

physics.soc-ph↗

Patterns of subnet usage reveal distinct scales of regulation in the transcriptional regulatory network of Escherichia coli

The set of regulatory interactions between genes, mediated by transcription factors, forms a species' transcriptional regulatory network (TRN). By comparing this network with measured gene expression data one can identify functional properties of the TRN and gain general insight into transcriptional control. We define the subnet of a node as the subgraph consisting of all nodes topologically downstream of the node, including itself. Using a large set of microarray expression data of the bacterium Escherichia coli, we find that the gene expression in different subnets exhibits a structured pattern in response to environmental changes and genotypic mutation. Subnets with less changes in their expression pattern have a higher fraction of feed-forward loop motifs and a lower fraction of small RNA targets within them. Our study implies that the TRN consists of several scales of regulatory organization: 1) subnets with more varying gene expression controlled by both transcription factors and post-transcriptional RNA regulation, and 2) subnets with less varying gene expression having more feed-forward loops and less post-transcriptional RNA regulation.

q-bio.MN↗