Dynamics of excitable neural networks with heterogeneous connectivity

A central issue of neuroscience is to understand how neural units integrates internal and external signals to create coherent states. Recently, it has been shown that the sensitivity and dynamic range of neural assemblies are optimal at a critical coupling among its elements. Complex architectures of connections seem to play a constructive role on the reliable coordination of neural units. Here we show that, the synchronizability and sensitivity of excitable neural networks can be tuned by diversity in the connections strengths. We illustrate our findings for weighted networks with regular, random and complex topologies. Additional comparisons of real brain networks support previous studies suggesting that heterogeneity in the connectivity may play a constructive role on information processing. These findings provide insights into the relationship between structure and function of neural circuits.     

Dynamic connections in neural networks

Massively parallel (neural-like) networks are receiving increasing attention as a mechanism for expressing information processing models. By exploiting powerful primitive units and stability-preserving construction rules, various workers have been able to construct and test quite complex models, particularly in vision research. But all of the detailed technical work was concerned with the structure and behavior offixed networks. The purpose of this paper is to extend the methodology to cover several aspects of change and memory.     

Organization of excitable dynamics in hierarchical biological networks

This study investigates the contributions of network topology features to the dynamic behavior of hierarchically organized excitable networks. Representatives of different types of hierarchical networks as well as two biological neural networks are explored with a three-state model of node activation for systematically varying levels of random background network stimulation. The results demonstrate that two principal topological aspects of hierarchical networks, node centrality and network modularity, correlate with the network activity patterns at different levels of spontaneous network activation. The approach also shows that the dynamic behavior of the cerebral cortical systems network in the cat is dominated by the network's modular organization, while the activation behavior of the cellular neuronal network of Caenorhabditis elegans is strongly influenced by hub nodes. These findings indicate the interaction of multiple topological features and dynamic states in the function of complex biological networks.     

Pattern separability in a random neural net with inhibitory connections

Some interesting properties on pattern separation have been shown through researches by neural models of cerebellar cortex. It seems to us that those results are a part of the properties of pattern separation. A two layer random nerve net with inhibitory connections is given as a model of the cerebellar cortex. The model is composed of threshold elements there. A more general theory of pattern separation than those studied earlier is given, and the pattern separability of the model is considered. It is revealed that the standard deviation of threshold values of threshold elements has a great effect on the pattern separability and the control of the firing rate. The present study is also intended to investigate the pattern separability in such a case that the firing rate of input patterns are not equal, and a pattern includes the other pattern. It is assumed there that the standard deviation is small. Some properties of the degree of pattern separation are cleaned up.     

Correlations in spiking neuronal networks with distance dependent connections

Can the topology of a recurrent spiking network be inferred from observed activity dynamics? Which statistical parameters of network connectivity can be extracted from firing rates, correlations and related measurable quantities? To approach these questions, we analyze distance dependent correlations of the activity in small-world networks of neurons with current-based synapses derived from a simple ring topology. We find that in particular the distribution of correlation coefficients of subthreshold activity can tell apart random networks from networks with distance dependent connectivity. Such distributions can be estimated by sampling from random pairs. We also demonstrate the crucial role of the weight distribution, most notably the compliance with Dales principle, for the activity dynamics in recurrent networks of different types.     

Connectivity in random networks

Applications of randomly connected networks are reviewed briefly. The connectivity of a random network has been defined in a variety of ways including output connectivity, total or network connectivity, connectance, expected path length and radius. One or more of these definitions may prove more convenient in a given experimental system. Interrelations among these definitions are derived and displayed and asymptotic results provided in the form of two theorems. Computer simulations were used to explore the range of application of these asymptotic approximations. The results were used to determine the output connectivity of the neurons of the brain.     

SIR dynamics in random networks with heterogeneous connectivity

Random networks with specified degree distributions have been proposed as realistic models of population structure, yet the problem of dynamically modeling SIR-type epidemics in random networks remains complex. I resolve this dilemma by showing how the SIR dynamics can be modeled with a system of three nonlinear ODE’s. The method makes use of the probability generating function (PGF) formalism for representing the degree distribution of a random network and makes use of network-centric quantities such as the number of edges in a well-defined category rather than node-centric quantities such as the number of infecteds or susceptibles. The PGF provides a simple means of translating between network and node-centric variables and determining the epidemic incidence at any time. The theory also provides a simple means of tracking the evolution of the degree distribution among susceptibles or infecteds. The equations are used to demonstrate the dramatic effects that the degree distribution plays on the final size of an epidemic as well as the speed with which it spreads through the population. Power law degree distributions are observed to generate an almost immediate expansion phase yet have a smaller final size compared to homogeneous degree distributions such as the Poisson. The equations are compared to stochastic simulations, which show good agreement with the theory. Finally, the dynamic equations provide an alternative way of determining the epidemic threshold where large-scale epidemics are expected to occur, and below which epidemic behavior is limited to finite-sized outbreaks.      

Unraveling spurious properties of interaction networks with tailored random networks

We investigate interaction networks that we derive from multivariate time series with methods frequently employed in diverse scientific fields such as biology, quantitative finance, physics, earth and climate sciences, and the neurosciences. Mimicking experimental situations, we generate time series with finite length and varying frequency content but from independent stochastic processes. Using the correlation coefficient and the maximum cross-correlation, we estimate interdependencies between these time series. With clustering coefficient and average shortest path length, we observe unweighted interaction networks, derived via thresholding the values of interdependence, to possess non-trivial topologies as compared to Erd?s-Rényi networks, which would indicate small-world characteristics. These topologies reflect the mostly unavoidable finiteness of the data, which limits the reliability of typically used estimators of signal interdependence. We propose random networks that are tailored to the way interaction networks are derived from empirical data. Through an exemplary investigation of multichannel electroencephalographic recordings of epileptic seizures--known for their complex spatial and temporal dynamics--we show that such random networks help to distinguish network properties of interdependence structures related to seizure dynamics from those spuriously induced by the applied methods of analysis.     

Wave speed in noncircular collapsible ducts

The wave speed in initially elliptical collapsible tubes was studied. The celerity c of pressure waves of small amplitude was calculated from the numerically defined area-pressure law of the buckled cross section. In addition to the fact that the wave speed variation with transmural pressure was strongly dependent upon the initial eccentricity of the cross section, the wave speed value was found to be discontinuous at the contact pressure pc and reached a minimum on the right-hand side of the discontinuity. These results were compared with experimental data obtained in an annular duct.     

Pattern separability and the effect of the number of connections in a random neural net with inhibitory connections

It has been claimed that pattern separation in cerebellar cortex plays an important role in controlling movements and balance for vertebrates. A number of the neural models for cerebellar cortex have been proposed and their pattern separability has been analyzed. These results, however, only explain a part of pattern separability in random neural nets. The present paper is intended to study an extended theory of pattern separability in a new model with inhibitory connections. In addition to this, the effect of the number of connections on pattern separability is cleared up. It is also shown that the signal from the inhibitory connections has crucial importance for pattern separability.1977–1978 Exchange Visitor, on leave from the Department of Information Processing Engineering, Technical College, Yamaguchi University, Yamaguchi University     

Optimal, efficient reconstruction of phylogenetic networks with constrained recombination

A phylogenetic network is a generalization of a phylogenetic tree, allowing structural properties that are not tree-like. In a seminal paper, Wang et al.(1) studied the problem of constructing a phylogenetic network, allowing recombination between sequences, with the constraint that the resulting cycles must be disjoint. We call such a phylogenetic network a "galled-tree". They gave a polynomial-time algorithm that was intended to determine whether or not a set of sequences could be generated on galled-tree. Unfortunately, the algorithm by Wang et al.(1) is incomplete and does not constitute a necessary test for the existence of a galled-tree for the data. In this paper, we completely solve the problem. Moreover, we prove that if there is a galled-tree, then the one produced by our algorithm minimizes the number of recombinations over all phylogenetic networks for the data, even allowing multiple-crossover recombinations. We also prove that when there is a galled-tree for the data, the galled-tree minimizing the number of recombinations is "essentially unique". We also note two additional results: first, any set of sequences that can be derived on a galled tree can be derived on a true tree (without recombination cycles), where at most one back mutation per site is allowed; second, the site compatibility problem (which is NP-hard in general) can be solved in polynomial time for any set of sequences that can be derived on a galled tree. Perhaps more important than the specific results about galled-trees, we introduce an approach that can be used to study recombination in general phylogenetic networks. This paper greatly extends the conference version that appears in an earlier work.(8) PowerPoint slides of the conference talk can be found at our website.(7).     

Further consideration on pattern separability in a random neural net with inhibitory connections

A two-layer random neural net with inhibitory connections composing of threshold elements has been regarded as a model of the cerebellar cortex. Many properties of pattern separation with the model have been disclosed through consideration on the degree of pattern separation. However, we have not shown yet that the degree of pattern separation is given by some different functions which are decided by the relation between the firing rates of input patterns. The present study is intended to reveal that the functions of the degree of pattern separation are synthesized with some different partial functions, and they are differently given on the relation between the firing rates of input patterns. Simultaneously, it is proved that the number of the functions also depend on the number of connections between two layers in the model. We also disclose the properties of the degree of pattern separation, and give some suggestions on the sizes of the firing rates of mossy fibers and granule cells under the knowledge about them.     

Exploring biological network structure with clustered random networks

Background  

Complex biological systems are often modeled as networks of interacting units. Networks of biochemical interactions among proteins, epidemiological contacts among hosts, and trophic interactions in ecosystems, to name a few, have provided useful insights into the dynamical processes that shape and traverse these systems. The degrees of nodes (numbers of interactions) and the extent of clustering (the tendency for a set of three nodes to be interconnected) are two of many well-studied network properties that can fundamentally shape a system. Disentangling the interdependent effects of the various network properties, however, can be difficult. Simple network models can help us quantify the structure of empirical networked systems and understand the impact of various topological properties on dynamics.     

Altruism in networks: the effect of connections

Why are individuals altruistic to their friends? Theory suggests that individual, relationship and network factors will all influence the levels of altruism; but to date, the effects of social network structure have received relatively little attention. The present study uses a novel correlational design to test the prediction that an individual will be more altruistic to friends who are well-connected to the individual''s other friends. The result shows that, as predicted, even when controlling for a range of individual and relationship factors, the network factor (number of connections) makes a significant contribution to altruism, thus showing that individuals are more likely to be altruistic to better-connected members of their social networks. The implications of incorporating network structure into studies of altruism are discussed.     

Biased excitable networks: how cells direct motion in response to gradients

The actin cytoskeleton in motile cells has many of the hallmarks of an excitable medium, including the presence of propagating waves. This excitable behavior can account for the spontaneous migration of cells. A number of reports have suggested that the chemoattractant-mediated signaling can bias excitability, thus providing a means by which cell motility can be directed. In this review, we discuss some of these observations and theories proposed to explain them. We also suggest a mechanism for cell polarity that can be incorporated into the existing framework.     

Predicting genetic interactions with random walks on biological networks

Background  

Several studies have demonstrated that synthetic lethal genetic interactions between gene mutations provide an indication of functional redundancy between molecular complexes and pathways. These observations help explain the finding that organisms are able to tolerate single gene deletions for a large majority of genes. For example, system-wide gene knockout/knockdown studies in S. cerevisiae and C. elegans revealed non-viable phenotypes for a mere 18% and 10% of the genome, respectively. It has been postulated that the low percentage of essential genes reflects the extensive amount of genetic buffering that occurs within genomes. Consistent with this hypothesis, systematic double-knockout screens in S. cerevisiae and C. elegans show that, on average, 0.5% of tested gene pairs are synthetic sick or synthetic lethal. While knowledge of synthetic lethal interactions provides valuable insight into molecular functionality, testing all combinations of gene pairs represents a daunting task for molecular biologists, as the combinatorial nature of these relationships imposes a large experimental burden. Still, the task of mapping pairwise interactions between genes is essential to discovering functional relationships between molecular complexes and pathways, as they form the basis of genetic robustness. Towards the goal of alleviating the experimental workload, computational techniques that accurately predict genetic interactions can potentially aid in targeting the most likely candidate interactions. Building on previous studies that analyzed properties of network topology to predict genetic interactions, we apply random walks on biological networks to accurately predict pairwise genetic interactions. Furthermore, we incorporate all published non-interactions into our algorithm for measuring the topological relatedness between two genes. We apply our method to S. cerevisiae and C. elegans datasets and, using a decision tree classifier, integrate diverse biological networks and show that our method outperforms established methods.     

IMU-based ambulatory walking speed estimation in constrained treadmill and overground walking

This study evaluated the performance of a walking speed estimation system based on using an inertial measurement unit (IMU), a combination of accelerometers and gyroscopes. The walking speed estimation algorithm segments the walking sequence into individual stride cycles (two steps) based on the inverted pendulum-like behaviour of the stance leg during walking and it integrates the angular velocity and linear accelerations of the shank to determine the displacement of each stride. The evaluation was performed in both treadmill and overground walking experiments with various constraints on walking speed, step length and step frequency to provide a relatively comprehensive assessment of the system. Promising results were obtained in providing accurate and consistent walking speed/step length estimation in different walking conditions. An overall percentage root mean squared error (%RMSE) of 4.2 and 4.0% was achieved in treadmill and overground walking experiments, respectively. With an increasing interest in understanding human walking biomechanics, the IMU-based ambulatory system could provide a useful walking speed/step length measurement/control tool for constrained walking studies.     

IMU-based ambulatory walking speed estimation in constrained treadmill and overground walking

This study evaluated the performance of a walking speed estimation system based on using an inertial measurement unit (IMU), a combination of accelerometers and gyroscopes. The walking speed estimation algorithm segments the walking sequence into individual stride cycles (two steps) based on the inverted pendulum-like behaviour of the stance leg during walking and it integrates the angular velocity and linear accelerations of the shank to determine the displacement of each stride. The evaluation was performed in both treadmill and overground walking experiments with various constraints on walking speed, step length and step frequency to provide a relatively comprehensive assessment of the system. Promising results were obtained in providing accurate and consistent walking speed/step length estimation in different walking conditions. An overall percentage root mean squared error (%RMSE) of 4.2 and 4.0% was achieved in treadmill and overground walking experiments, respectively. With an increasing interest in understanding human walking biomechanics, the IMU-based ambulatory system could provide a useful walking speed/step length measurement/control tool for constrained walking studies.